From aa56b67912d1e6b2969ef645c60f785c9116d907 Mon Sep 17 00:00:00 2001 From: Reena Date: Thu, 25 Jun 2026 11:11:49 -0400 Subject: [PATCH 1/3] Add eFP/ePlant gene ID validation, microarray probeset support, and master DB list Adds per-eFP-project regex validation (EFP_PROJECT_REGEXES, is_efp_gene_valid) covering both canonical gene IDs and microarray probeset IDs, with a database-to-project mapping (DATABASE_EFP_PROJECT) so gene_expression.py can validate against the right format per database. Adds the eFP+ePlant discovery/validation pipeline: - scrape_view_databases.py / scrape_species_view_info.py: live-discover every eFP and ePlant view across 55 sites, tagging eFP-only vs ePlant-only vs both - build_proj_id_view_mapping.py: resolves multi-paper databases (e.g. atgenexp_*) to per-view proj_id breakdowns - validate_db_regex_coverage.py: tests every database's real sample IDs against production validation, including legacy databases no longer linked from a live dropdown - build_master_db_list.py: rolls everything up by species, tagging source (efp/eplant/both/legacy) and platform (microarray/rna_seq) 193 databases validated, 0 unexplained failures. --- api/models/efp_schemas.py | 2 +- api/resources/gene_expression.py | 47 +- api/utils/bar_utils.py | 469 +- api/utils/efp_utils.py | 6 +- api/utils/gene_id_utils.py | 551 +- build_master_db_list.py | 127 + build_proj_id_view_mapping.py | 125 + config/databases/soybean_nssnp.sql | 3 +- config/databases/tomato_nssnp.sql | 3 +- config/init.sh | 92 +- data/efp_info/db_source_summary.json | 154 + .../efp_eplant_species_view_info.json | 35178 ++++++++++++++++ data/efp_info/master_db_list.json | 3811 ++ db_regex_coverage_report.csv | 194 + efp_regex_audit_prod.csv | 60 + proj_id_view_mapping.json | 1025 + scrape_species_view_info.py | 273 + scrape_view_databases.py | 420 + species_databases.json | 368 + tests/resources/test_eplant_arabidopsis.py | 88 + tests/resources/test_gene_expression.py | 261 + tests/utils/test_bar_utils.py | 116 +- validate_db_regex_coverage.py | 137 + 23 files changed, 42986 insertions(+), 524 deletions(-) create mode 100644 build_master_db_list.py create mode 100644 build_proj_id_view_mapping.py create mode 100644 data/efp_info/db_source_summary.json create mode 100644 data/efp_info/efp_eplant_species_view_info.json create mode 100644 data/efp_info/master_db_list.json create mode 100644 db_regex_coverage_report.csv create mode 100644 efp_regex_audit_prod.csv create mode 100644 proj_id_view_mapping.json create mode 100644 scrape_species_view_info.py create mode 100644 scrape_view_databases.py create mode 100644 species_databases.json create mode 100644 tests/resources/test_eplant_arabidopsis.py create mode 100644 tests/resources/test_gene_expression.py create mode 100644 validate_db_regex_coverage.py diff --git a/api/models/efp_schemas.py b/api/models/efp_schemas.py index 4bcbdd2b..4f12396f 100644 --- a/api/models/efp_schemas.py +++ b/api/models/efp_schemas.py @@ -181,7 +181,7 @@ def _schema(species: str, charset: str = "latin1") -> DatabaseSpec: ("root_Schaefer_lab", "root Schaefer lab"), ("rpatel", "rpatel"), ("seed_db", "seed db"), - ("seedcoat", "oat"), + ("seedcoat", "arabidopsis seedcoat"), ("selaginella", "selaginella"), ("shoot_apex", "arabidopsis"), ("silique", "arabidopsis"), diff --git a/api/resources/gene_expression.py b/api/resources/gene_expression.py index d777e3e5..9f95949c 100644 --- a/api/resources/gene_expression.py +++ b/api/resources/gene_expression.py @@ -1,26 +1,12 @@ -""" -Reena Obmina | BCB330 Project 2025-2026 | University of Toronto - -REST endpoint for gene expression queries across all eFP databases. - -Routes: GET /gene_expression/expression// - -All gene IDs are validated by species before reaching the query layer. -Probeset conversion is applied automatically for microarray databases. -""" from flask_restx import Namespace, Resource from markupsafe import escape from api.services.efp_data import query_efp_database_dynamic from api.utils.bar_utils import BARUtils from api.utils.gene_id_utils import ( - CROSS_SPECIES_DATABASES, DATABASE_SPECIES, - PROBESET_DATABASES, - convert_gene_to_probeset, - is_probeset_id, - normalize_gene_id, - validate_gene_id, + GeneIdUtils, + DATABASE_EFP_PROJECT, ) gene_expression = Namespace( @@ -46,38 +32,21 @@ ) class GeneExpression(Resource): def get(self, database, gene_id): - """Retrieve expression values for a gene from a given eFP database. - """ + """Retrieve expression values for a gene from a given eFP database.""" database = str(escape(database)) gene_id = str(escape(gene_id)) - # 1. Resolve database species and expected input species. - # Cross-species databases (e.g. phelipanche) accept an Arabidopsis AGI - # even though the database itself belongs to a different species. species = DATABASE_SPECIES.get(database) if species is None: return BARUtils.error_exit(f"Unknown database '{database}'"), 400 - input_species = CROSS_SPECIES_DATABASES.get(database, species) - # 2. If the caller already supplied a probeset ID, use it directly - if is_probeset_id(gene_id): + if GeneIdUtils.is_probeset_id(gene_id): query_id = gene_id else: - # 3. Validate gene ID format against the expected input species regex - if not validate_gene_id(gene_id, input_species): - return BARUtils.error_exit(f"Invalid {input_species} gene ID: '{gene_id}'"), 400 - - # 4. Normalise (e.g. strip maize transcript suffix _T##) - gene_id = normalize_gene_id(gene_id, species) - - # 5. Microarray / non-direct databases need gene ID -> probeset conversion - if database in PROBESET_DATABASES: - probeset, err = convert_gene_to_probeset(gene_id, species, database) - if err: - return BARUtils.error_exit(err), 404 - query_id = probeset - else: - query_id = gene_id + if not GeneIdUtils.validate_gene_for_database(gene_id, database): + label = DATABASE_EFP_PROJECT.get(database) or species or database + return BARUtils.error_exit(f"Invalid gene ID for {label}: '{gene_id}'"), 400 + query_id = GeneIdUtils.normalize_gene_id(gene_id, species) result = query_efp_database_dynamic(database, query_id) diff --git a/api/utils/bar_utils.py b/api/utils/bar_utils.py index fcf75af1..effc28d1 100644 --- a/api/utils/bar_utils.py +++ b/api/utils/bar_utils.py @@ -2,6 +2,188 @@ import redis import os +# fmt: off +# Per-eFP-project input validation regexes sourced from efpWeb.cgi. +# Each pattern covers canonical gene IDs AND (where applicable) microarray probeset IDs. +EFP_PROJECT_REGEXES: dict = { + "efp": ( + r"^([Aa][Tt][12345CM][Gg][0-9]{5})$" + r"|^([0-9]{6}(_[xsfi])?_at)$" + r"|^([0-9]{6,9})$" + # ATH1 Affymetrix bacterial/control spike-in probes, shared by all Affy platforms + r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$" + r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" + ), + "efp_arabidopsis": ( + r"^([Aa][Tt][12345CM][Gg][0-9]{5})$" + r"|^([0-9]{6}(_[xsfi])?_at)$" + r"|^([0-9]{6,9})$" + r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$" + r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" + ), + # Seedcoat uses CATMA probes (At\d{8}) and AROS probes (\D\d+_\d+) in addition to ATH1 + "efp_seedcoat": ( + r"^(At[12345CM]g[0-9]{5})$" + r"|^([0-9]{6}(_[xsfi])?_at)$" + r"|^([0-9]{6,9})$" + r"|^(\D\d+_\d+)$" + r"|^(At\d{8})$" + ), + "efp_barley": ( + r"^((HM|HV).*)$|^(HV.*_at)$" + r"|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4})_at)$" + r"|^([0-9]{4,5}\.AF[0-9]{5}(_|_x_)at)$" + r"|^(A[0-9]{5}\.[0-9]{1}(_|_x_|_s_)at)$" + r"|^(([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)(_|_x_|_s_|_CDS-[0-9]{1,2}_|_CDS-[0-9]{1,2}_s_)at)$" + r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$" + r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" + r"|^(ChlorContig[0-9]{1,2}(_|_x_|_s_)at)$" + r"|^(((MitoContig|Contig)[0-9]{1,6})(_|_x_|_s_)at)$" + r"|^(D[0-9]{5}_at)$" + r"|^(Dhn[0-9]{2}\(Morex\)(_|_s_)at)$" + r"|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2}(_|_s_|_x_)at)$" + r"|^(Franka(_|_b_)3pri[0-9]{1,2}(_|_s_|_x_)at)$" + r"|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$" + r"|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$" + r"|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru](_|_x_|_s_)at)$" + r"|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1}(_|_x_|_s_)at)$" + r"|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2}(_|_x_|_s_)at)$" + r"|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4}))$" + r"|^([0-9]{4,5}\.AF[0-9]{5})$" + r"|^(A[0-9]{5}\.[0-9]{1})$" + r"|^([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)$" + r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX))$" + r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre))$" + r"|^(ChlorContig[0-9]{1,2})$" + r"|^((MitoContig|Contig)[0-9]{1,6})$" + r"|^(D[0-9]{5})$" + r"|^(Dhn[0-9]{2}\(Morex\))$" + r"|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2})$" + r"|^(Franka(_|_b_)3pri[0-9]{1,2})$" + r"|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$" + r"|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$" + r"|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru])$" + r"|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1})$" + r"|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2})$" + r"|^(HO)$" + r"|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$" + r"|^(AK[0-9]{6}\.1)$" + r"|^(AJ[0-9]{6}\.1)$" + ), + "efp_rice": ( + r"^(LOC_Os[0-9]{2}g[0-9]{5})$" + r"|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$" + r"|^(AFFX-OS-(18SrRNA|25SrRNA|5\.8SrRNA)_(s_at|at))$" + r"|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$" + r"|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$" + r"|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$" + r"|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" + r"|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" + ), + "efp_medicago": ( + r"^(Medtr\d{1}g\d{6})$" + r"|^(Medtr\d{1}g\d{6}\.[0-9]{1})$" + # Medicago array probesets: Mtr/Msa/Sme prefix, any Affymetrix suffix variant + r"|^(Mtr\.\d{4,5}\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$" + r"|^(Msa\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$" + r"|^(Sme\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$" + r"|^(AFFX-(Bio|Cre|Dap|Lys|Phe|Thr|Trpn)(B|C|Dn|X)-(3|5|M)_at)$" + r"|^(AFFX-(Msa|Mtr)-(actin|gapc|gsta|ubq11|TrpnX)-(3|5|M)_(at|x_at|s_at))$" + r"|^(AFFX-r2-(Bs|Ec|P1)-(cre|dap|lys|phe|thr|bioB|bioC|bioD)-(3|5|M)_(at|s_at|x_at))$" + r"|^(AFFX-Mtr-ubq11-(3|5|M)_(at|s_at|x_at))$" + r"|^(AFFX-r2-Tag[A-Z]{1,2}_at)$" + r"|^(Medtr_v1_\d{6})$" + ), + "efp_poplar": ( + r"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$" + r"|^((eugene3)\.\d{6,12})$" + r"|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$" + r"|^((grail3\.)\d{8,12})$" + r"|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$" + r"|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$" + r"|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$" + # poplar_hormone's real sample IDs omit the transcript suffix entirely + r"|^(Potri\.[0-9]{3}G[0-9]{6}(\.[0-9]{1})?)$" + ), + "efp_soybean": ( + r"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$" + r"|^(Glyma\.\d{1,3}g\d{1,8}))$" + ), + "efp_maize": ( + r"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$" + r"|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$" + r"|^(GRMZM(2|5)G[0-9]{6})$" + r"|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$" + r"|^(Zm\d+d\d+)$" + r"|^(Zm\d{1,10}eb\d{1,10})$" + # Maize Affymetrix probeset IDs, e.g. Zm011368_at, Zm039842_s_at + r"|^(Zm\d{6}(_[xsa])?_at)$" + ), + # TaAffx.* probes occur alongside Ta.* — handle both prefixes + "efp_triticale": r"^((Ta|TaAffx)\.\d+\.\d+\.[A-Z]\d+_(at|s_at|x_at|a_at))$", + # Affymetrix human probeset IDs (1557575_at, 202019_s_at) plus a loose fallback + "efp_human": r"^(\d{6,7}(_[xsa])?_at)$|^(\D{0,12}\d{0,12})$|^(\d{1,12})$", + # Remaining eFP projects, sourced verbatim from Vincent's efp_regex_audit_prod.csv + "efp_Eutrema": r"^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$", + "efp_actinidia": r"^(Acc\d+\.\d{0,3})$", + "efp_apple": r"^(MfusH1_\d\dg\d{1,8})$", + # CSV pattern is lowercase-only; lipid species names use mixed case (e.g. "TG 54:5; ...") + "efp_arabidopsis_lipid": r"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$", + "efp_arachis": r"^(Adur\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Aipa_c\d+_g\d+_i\d+)$|^(Aipa\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Adur_c\d+_g\d+_i\d+)$", + "efp_brachypodium": r"^(Bradi\d+g\d+.\d)$|^(Bradi\d+s\d+.\d)$|^(Bradi\d+.g\d+)$", + "efp_brachypodium_metabolites": r"(?i)^[a-z\s\-]{1,60}$", + "efp_brassica_rapa": r"^(Bra.\d+g\d{0,10})$", + "efp_cacao_ccn": r"^(CCN-51_Chr\d{1,3}v\d{1,3}_\d{1,9})$", + "efp_cacao_sca": r"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$", + "efp_cacao_tc": r"^(Tc\d+v2_g\d+)$", + "efp_camelina": r"^(Csa\d{0,5}[gs]\d{0,6}.\d{0,3})$|^(At\d[cgm]\d{0,6})$", + "efp_cannabis": r"(^C\d+$)|(^scaffold\d+$)|(^AGQN\d+$)", + "efp_canola": r"^(Bna\D\d{1,3}g\d{1,8}\D)$|^(Bna\Dnng\d{1,8}\D)$", + "efp_durum_wheat": r"^(TrturSVE\d\D\d{1,3}G\d{1,12})$|^(TrturSVE\d\D\d{1,3}G\d{1,12}_ncBOCREA)$", + "efp_euphorbia": r"^(Ep_chr\d_g\d{1,8})$", + "efp_eutrema": r"^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$", + "efp_grape": r"^(VIT_\d{1,2}s\d{4}g\d{5})$|^CHRUN[a-z0-9_]{1,20}$|^CHR\d{1,2}[a-z0-9_]{1,2}$", + "efp_kalanchoe": r"^(Kaladp\d+s\d+)$", + "efp_little_millet": r"^(TRINITY_DN\d+_c\d+_g\d+_i\d+)$", + "efp_lupin": r"^(Luan_Oskar_.{1,12}_\d{1,12})$", + # is_efp_gene_valid matches without re.IGNORECASE, so these freeform-text + # patterns (enzyme/metabolite/category NAMES, not gene IDs) need an explicit + # (?i) -- real sample data is mixed-case ("GAPDH (NAD)", "Citric Acid"). + "efp_maize_enzyme": r"(?i)^[a-z0-9\s\-\(\)]{1,50}$", + "efp_maize_metabolite": r"(?i)^[a-z0-9\s,\.\-\(\)_'\+]{1,60}$", + # Lipid species names (TG_52_1, MGDG_38_6), same freeform style as efp_arabidopsis_lipid + "efp_maize_lipid_map": r"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$", + # tomato_trait stores root-architecture trait descriptions, not gene IDs + "efp_tomato_trait": r"^[A-Za-z][A-Za-z0-9\s\.,\-\(\)]{1,100}$", + "efp_maize_transcriptomics": r"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$", + "efp_mangosteen": r"^(DN\d{1,10})$", + "efp_marchantia": r"^(Mp.{1,3}g\d{1,7}\.?\d{1,3}?)$", + "efp_oat": r"(^N0\.HOG\d{1,10}$|^\D{1,10}\.*\d{1,10}.{1,10}\d{1,10}$)", + "efp_phelipanche": r"^(OrAeBC\d+_\d+\.\d{1,5})|(At\d[gcm]\d{1,6})$", + "efp_physcomitrella": r"^(Pp)\d+s\d+_\d+V\d\.\d$|^Phypa_\d+$", + "efp_potato": r"^(PGSC0003DMG4\d{8})$", + "efp_rice_metabolite": r"(?i)^[a-z0-9,\s\.\-]{1,40}$", + "efp_rice_transcriptomics": r"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$", + "efp_selaginella": r"^(Smo\d+)$", + "efp_sorghum": r"^(Sobic.\d{0,5}G\d{0,10}$|^Sobic.K\d{0,10}$|^ENSRNA\d{0,12}$|^SORBI_\d{1,6}G\d{1,10})$", + "efp_strawberry": r"^(FvH4_c?\d{1,3}g\d{1,7})$|^(gene\d{1,10})$", + "efp_striga": r"^(StHeBC3\_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$", + "efp_tomato": r"^(Solyc\d{2}g\d{6}\.?\d{0,3})$|^(TU\d{6})$", + "efp_triphysaria": r"^(TrVeBC\d+_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$", + "efp_tung_tree": r"^(Vf\d+G\d+)$", + "efp_wheat": r"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$", + "efpconfig": r".{0,16}", + "mouse_efp": r"^(XM_\d{0,8}\.\d{0,3})$|^(\d{1,10}\D\d{0,4}\D{0,4})$|^(\D{1,8}\d{0,8}\D{0,8})$|^(ENSMUSG\d{1,15})$|^(NM_\d{0,12}\d.\d{0,3})$", +} +# Aliases for alternate eFP project key spellings used by the BAR +EFP_PROJECT_REGEXES["efpbarley"] = EFP_PROJECT_REGEXES["efp_barley"] +EFP_PROJECT_REGEXES["efprice"] = EFP_PROJECT_REGEXES["efp_rice"] +EFP_PROJECT_REGEXES["efpmedicago"] = EFP_PROJECT_REGEXES["efp_medicago"] +EFP_PROJECT_REGEXES["efppop"] = EFP_PROJECT_REGEXES["efp_poplar"] +EFP_PROJECT_REGEXES["efpsoybean"] = EFP_PROJECT_REGEXES["efp_soybean"] +EFP_PROJECT_REGEXES["maizeefp"] = EFP_PROJECT_REGEXES["efp_maize"] +# fmt: on + class BARUtils: @staticmethod @@ -43,41 +225,138 @@ def normalize_arabidopsis_gene(gene): return "At" + lowered[2:] return gene + @staticmethod + def is_actinidia_gene_valid(gene): + """Validates kiwifruit (Actinidia) gene IDs: Acc23558.1""" + return bool(gene and re.search(r"^Acc\d{5}\.\d+$", gene, re.I)) + + @staticmethod + def is_apple_gene_valid(gene): + """Validates apple gene IDs: MfusH1_01g00343""" + return bool(gene and re.search(r"^MfusH1_\d{2}g\d{5}$", gene, re.I)) + + @staticmethod + def is_barley_gene_valid(gene): + """Validates barley gene IDs: HORVU0Hr1G000320, HORVU.MOREX.r3.1HG0003350.1, + or HORVU.MOREX.r3.UnG0797170.1 (Un = unplaced scaffold, no chromosome digit)""" + return bool( + gene and re.search(r"^HORVU(\d+Hr\d+G\d+|\.MOREX\.r\d+\.(\dH|Un)G\d+\.\d+)$", gene, re.I) + ) + + @staticmethod + def is_brachypodium_gene_valid(gene): + """Validates Brachypodium gene IDs: Bradi1g04930.1""" + return bool(gene and re.search(r"^Bradi\d+g\d+\.\d+$", gene, re.I)) + + @staticmethod + def is_cacao_gene_valid(gene): + """Validates cacao gene IDs: CCN-51_Chr1v1_08396, SCA-6_Chr1v1_00610, Tc01v2_g002690""" + return bool(gene and re.search(r"^((CCN-51|SCA-6)_Chr\d+v\d+_\d+|Tc\d+v\d+_g\d+)$", gene)) + + @staticmethod + def is_camelina_gene_valid(gene): + """Validates Camelina gene IDs: Csa01g012560.1, Csa00462s060.1""" + return bool(gene and re.search(r"^Csa\d+[gs]\d+\.\d+$", gene, re.I)) + + @staticmethod + def is_cassava_gene_valid(gene): + """Validates cassava gene IDs: Manes.01G040000.v8.1""" + return bool(gene and re.search(r"^Manes\.\d{2}G\d+\.v\d+\.\d+$", gene, re.I)) + + @staticmethod + def is_cuscuta_gene_valid(gene): + """Validates Cuscuta gene IDs: Cc000663.t1 or Cc000082""" + return bool(gene and re.search(r"^Cc\d+(\.t\d+)?$", gene, re.I)) + + @staticmethod + def is_eucalyptus_gene_valid(gene): + """Validates Eucalyptus gene IDs: Eucgr.A01716""" + return bool(gene and re.search(r"^Eucgr\.[A-Z]\d+$", gene, re.I)) + + @staticmethod + def is_euphorbia_gene_valid(gene): + """Validates Euphorbia gene IDs: Ep_chr1_g00698""" + return bool(gene and re.search(r"^Ep_chr\d+_g\d+$", gene, re.I)) + @staticmethod def is_grape_gene_valid(gene): - """This function verifies if grape gene is valid: VIT_00s0120g00060 - :param gene: - :return: - """ - if re.search(r"^VIT_\d{0,3}\D\d{0,5}g\d{0,6}$", gene, re.I): - return True - else: - return False + """Validates grape gene IDs: CHR11_JGVV37_114_T01, CHR2_GSVIVT00001265001_T01, + CHRUN_JGVV479_1_T01 (CHRUN = unplaced), or legacy VIT_00s0120g00060""" + return bool( + gene + and re.search( + r"^(CHR(\d+|UN)_[A-Z]+\d+(_\d+)?_T\d+|VIT_\d{0,3}\D\d{0,5}g\d{0,6})$", gene, re.I + ) + ) @staticmethod def is_poplar_gene_valid(gene): - """This function verifies if Poplar v3 gene is valid + """This function verifies if Poplar v3 gene (Potri.001G123456.1) or World Map + atlas probe (Potri.T174200) is valid :param gene: :return: True if valid """ - if re.search(r"^POTRI\.\d{3}g\d{6}.?\d{0,3}$", gene, re.I): + if re.search(r"^POTRI\.(\d{3}G\d{6}\.?\d{0,3}|T\d{6})$", gene, re.I): return True else: return False @staticmethod def is_rice_gene_valid(gene, isoform_id=False): - """This function verifies if rice gene is valid - :param gene: - :param isoform_id: True if you want to verifiy isoform ID - :return: True if valid - """ + """Validates rice gene IDs: LOC_Os01g01430, LOC_Os01g01430.1 (isoform), or Os01g0138100""" + if not gene: + return False if isoform_id and re.search(r"^LOC_Os\d{2}g\d{5}\.\d{1,2}$", gene, re.I): return True - elif isoform_id is False and re.search(r"^LOC_Os\d{2}g\d{5}$", gene, re.I): + if not isoform_id and re.search(r"^LOC_Os\d{2}g\d{5}$", gene, re.I): return True - else: - return False + if re.search(r"^Os\d{2}g\d+$", gene, re.I): + return True + return False + + @staticmethod + def is_spruce_gene_valid(gene): + """Validates spruce clone IDs from either of two cDNA libraries: + GQ0031_G08.1 or WS0321_C07.1 / WS03217_B11.1""" + return bool(gene and re.search(r"^(GQ|WS)\d{4,5}_[A-Z]\d{2}\.\d+$", gene)) + + @staticmethod + def is_sugarcane_gene_valid(gene): + """Validates sugarcane gene IDs: Sh01_g004010 or BAC-clone-based + Sh_209L02_contig-1_g000020 / Sh_135M16_g000010""" + return bool( + gene and re.search(r"^(Sh\d+_g\d+|Sh_[A-Z0-9]+(_contig-\d+)?_g\d+)$", gene, re.I) + ) + + @staticmethod + def is_sunflower_gene_valid(gene): + """Validates sunflower gene IDs: Ha10_00000854""" + return bool(gene and re.search(r"^Ha\d+_\d+$", gene, re.I)) + + @staticmethod + def is_tung_tree_gene_valid(gene): + """Validates tung tree gene IDs: Vf01G0116""" + return bool(gene and re.search(r"^Vf\d+G\d+$", gene, re.I)) + + @staticmethod + def is_wheat_gene_valid(gene): + """Validates wheat gene IDs: TraesCS1A01G268900LC, TraesCS1A02G311600LC.1, TrturSVE1A02G00066260""" + return bool( + gene + and re.search(r"^(TraesCS[0-9A-Z]+(\.\d+)?|TrturSVE[0-9A-Z]+G\d+)$", gene, re.I) + ) + + @staticmethod + def is_willow_gene_valid(gene): + """Validates willow Trinity gene IDs: comp170315_c0_seq1""" + return bool(gene and re.search(r"^comp\d+_c\d+_seq\d+$", gene, re.I)) + + @staticmethod + def is_thellungiella_gene_valid(gene): + """Validates native Thellungiella (Eutrema salsugineum) gene IDs. + Accepts Thhalv format (Thhalv10000089m.g) and novel locus IDs (nXLOC_003010). + """ + return bool(re.search(r"^Thhalv\d+m\.g$", gene) or re.search(r"^nXLOC_\d+$", gene)) @staticmethod def is_tomato_gene_valid(gene, isoform_id=False): @@ -88,7 +367,7 @@ def is_tomato_gene_valid(gene, isoform_id=False): """ if isoform_id and re.search(r"^Solyc\d\dg\d{6}\.\d\.\d$", gene, re.I): return True - elif isoform_id is False and re.search(r"^Solyc\d\dg\d{6}$", gene, re.I): + elif isoform_id is False and re.search(r"^Solyc\d\dg\d{6}(\.\d+)?$", gene, re.I): return True else: return False @@ -106,14 +385,18 @@ def is_cannabis_gene_valid(gene): @staticmethod def is_canola_gene_valid(gene): - """This function verifies if canola gene (BnaC07g42830D) is valid - :param gene: - :return: - """ - if re.search(r"^Bna[AC]\d{2}g\d{5}[A-D]?$", gene, re.I): - return True - else: - return False + """Validates canola gene IDs: BnaA01g34660D, BoC01g03100.09V4, BoBC_1096g00001.01V4, + legacy BrChr4g00368.01V4 / BrBA_1327g00001.01V4 (canola_original* dbs), or + legacy EST contig IDs (Contig18943)""" + return bool( + gene + and re.search( + r"^(Bna[AC]\d{2}g\d{5}[A-D]?|Bo[A-Z]+_?\d+g\d+\.\d+V\d+" + r"|Br(Chr\d{1,2}|BA_\d+)g\d{5}\.\d{2}V\d|Contig\d+)$", + gene, + re.I, + ) + ) @staticmethod def is_arachis_gene_valid(gene): @@ -128,14 +411,77 @@ def is_arachis_gene_valid(gene): @staticmethod def is_brassica_rapa_gene_valid(gene): - """This function verifies if Brassica rapa gene is valid: BraA01g000010 - :param gene: - :return: True if valid - """ - if gene and re.search(r"^BraA.{1,4}g\d{1,9}$", gene, re.I): - return True - else: - return False + """Validates Brassica rapa gene IDs: BraA01g000010 or A01g510040.1_BraROA""" + return bool( + gene + and re.search(r"^(BraA.{1,4}g\d{1,9}|[A-Z]\d{2}[gp]\d+\.\d+_BraROA)$", gene, re.I) + ) + + @staticmethod + def is_human_gene_valid(gene): + """Validates human NCBI Entrez gene IDs (10057), HGNC gene symbols (KRT79, + MIR1285-1), and Ensembl clone-based names (RP11-108K3.3, CTD-2162K18.3, + AC012360.2) used by RNA-seq atlases like human_body_map_2""" + return bool( + gene + and re.search( + r"^\d{1,10}$" + r"|^[A-Z][A-Z0-9]{1,9}(-\d{1,3})?$" + r"|^[A-Z]{2,4}\d{0,3}-\d{2,4}[A-Z]\d{1,3}\.\d{1,3}$" + r"|^A[CL]\d{6}\.\d{1,3}$", + gene, + re.I, + ) + ) + + @staticmethod + def is_little_millet_gene_valid(gene): + """Validates little millet Trinity gene IDs: TRINITY_DN101568_c0_g1_i1""" + return bool(gene and re.search(r"^TRINITY_DN\d+_c\d+_g\d+_i\d+$", gene, re.I)) + + @staticmethod + def is_lupin_gene_valid(gene): + """Validates lupin gene IDs: Luan_Oskar_PB12_103067 or Luan_Oskar_Trin_111463""" + return bool(gene and re.search(r"^Luan_Oskar_(PB\d+|Trin)_\d+$", gene, re.I)) + + @staticmethod + def is_mangosteen_gene_valid(gene): + """Validates mangosteen Trinity gene IDs: DN118788""" + return bool(gene and re.search(r"^DN\d+$", gene, re.I)) + + @staticmethod + def is_marchantia_gene_valid(gene): + """Validates Marchantia polymorpha gene IDs: Mp1g01370.1, or unplaced-scaffold + Mpzg00730.1""" + return bool(gene and re.search(r"^Mp\w{1,3}g\d+\.\d+$", gene, re.I)) + + @staticmethod + def is_medicago_gene_valid(gene): + """Validates Medicago gene IDs: Medtr1g018805, Medtr0010s0370, MtrunA17Chr1g0153991, Medtr_v1_003290""" + return bool( + gene + and re.search(r"^(Medtr(\d+[gs]\d+|_v1_\d+)|MtrunA17Chr\dg\d+)$", gene, re.I) + ) + + @staticmethod + def is_mouse_gene_valid(gene): + """Validates mouse RefSeq transcript IDs: XM_122892.1""" + return bool(gene and re.search(r"^XM_\d+\.\d+$", gene, re.I)) + + @staticmethod + def is_oat_gene_valid(gene): + """Validates oat gene IDs: AVESA.00001b.r1.2AG01080490""" + return bool(gene and re.search(r"^AV[A-Z]{3}\.\d{5}[a-z]\.r\d+\.\d[A-Z]{2}\d{8}$", gene)) + + @staticmethod + def is_potato_gene_valid(gene): + """Validates potato gene IDs: PGSC0003DMG400001801 or EPlSTUG00000003328""" + return bool(gene and re.search(r"^(PGSC0003DMG\d+|EPlSTUG\d+)$", gene, re.I)) + + @staticmethod + def is_quinoa_gene_valid(gene): + """Validates quinoa gene IDs: CquiG00000000055""" + return bool(gene and re.search(r"^CquiG\d+$", gene, re.I)) @staticmethod def is_soybean_gene_valid(gene): @@ -150,29 +496,25 @@ def is_soybean_gene_valid(gene): @staticmethod def is_maize_gene_valid(gene): - """This function verifies if maize gene is valid: Zm00001d046170 - :param gene: - :return: True if valid - """ - if gene and re.search( - r"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})|(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})|(GRMZM(2|5)G[0-9]{6})|(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})|(Zm\d+d\d+)$", - gene, - re.I, - ): - return True - else: - return False + """Validates maize gene IDs: Zm00001d046170, Zm00001eb006030, AC195946.3_FG003, GRMZM2G000116""" + return bool( + gene + and re.search( + r"^(AC[0-9]{6}\.[0-9]+_FGT?[0-9]{3}|GRMZM[25]G[0-9]{6}(_T[0-9]{2})?|Zm\d+(d|eb)\d+)$", + gene, + re.I, + ) + ) @staticmethod def is_sorghum_gene_valid(gene): - """This function verifies if Arabidopsis gene is valid - :param gene: - :return: - """ - if re.search(r"^(Sobic.\d{0,5}G\d{0,10}|Sobic.K\d{0,10})$", gene, re.I): - return True - else: - return False + """Validates sorghum gene IDs: Sobic.001G003400, Sobic.001G085800.1, SORBI_3001G060800, ENSRNA049471574""" + return bool( + gene + and re.search( + r"^(Sobic\.\d+G\d+(\.\d+)?|Sobic\.K\d+|SORBI_\d+G\d+|ENSRNA\d+)$", gene, re.I + ) + ) @staticmethod def is_kalanchoe_gene_valid(gene): @@ -281,6 +623,23 @@ def format_poplar(poplar_gene): """ return poplar_gene.translate(str.maketrans("pOTRIg", "PotriG")) + @staticmethod + def is_efp_gene_valid(gene: str, efp_project: str) -> bool: + """Validate a gene ID against the named eFP project's input regex. + + Accepts both canonical gene IDs (e.g. AT1G01010 for Arabidopsis) and + microarray probeset IDs (e.g. 267643_at, Contig7905_at) depending on the + project. Returns False if the eFP project name is unknown. + + :param gene: Gene identifier to validate + :param efp_project: eFP project key (e.g. 'efp_arabidopsis', 'efpbarley') + :return: True if the gene ID matches the project's accepted format + """ + pattern = EFP_PROJECT_REGEXES.get(efp_project) + if not pattern: + return False + return bool(re.search(pattern, gene)) + @staticmethod def connect_redis(): """This function connects to redis diff --git a/api/utils/efp_utils.py b/api/utils/efp_utils.py index 533016ab..74fb30e7 100644 --- a/api/utils/efp_utils.py +++ b/api/utils/efp_utils.py @@ -57,12 +57,12 @@ def is_efp_input_valid(efp, view, mode, gene_1, gene_2=None): # Maybe this part could be improved if efp == "efp_arabidopsis": - # Validate gene ids - if not BARUtils.is_arabidopsis_gene_valid(gene_1): + # Accept AGI format (AT1G01010) or microarray probeset IDs (267643_at) + if not BARUtils.is_efp_gene_valid(gene_1, "efp_arabidopsis"): return False, "Gene 1 is invalid." if mode == "Compare": - if not BARUtils.is_arabidopsis_gene_valid(gene_2): + if not BARUtils.is_efp_gene_valid(gene_2, "efp_arabidopsis"): return False, "Gene 2 is invalid." if efp == "efp_arachis": diff --git a/api/utils/gene_id_utils.py b/api/utils/gene_id_utils.py index e326c92d..64ee2949 100644 --- a/api/utils/gene_id_utils.py +++ b/api/utils/gene_id_utils.py @@ -1,50 +1,16 @@ -""" -Reena Obmina | BCB330 Project 2025-2026 | University of Toronto - -Gene identifier utilities: species detection, format validation, and probeset conversion. - -Probeset IDs (Affymetrix chips) end in '_at', e.g.: - 261585_at (Arabidopsis ATH1) - AB004882_at (Maize gdowns — GenBank accession probesets) - PtpAffx.224570.1.S1_at (Poplar) - TU000001 (Tomato Rose Lab Atlas — Tomato Unigene chip, no _at suffix) - -Note: not all non-_at IDs are gene IDs. Some databases (e.g. Tomato, Soybean) use gene-model -IDs as their primary key rather than Affymetrix probe IDs. - -Only Arabidopsis AGI-to-probeset conversion is fully implemented. -All other species with pending lookup tables return an actionable error message. -""" - from __future__ import annotations import re -from typing import Optional from api.utils.bar_utils import BARUtils -# --------------------------------------------------------------------------- -# Probeset detection -# --------------------------------------------------------------------------- - -# Most chips: ends in _at (e.g. 261585_at, PtpAffx.200227.1.S1_s_at) -# AROS chip: A######_## format (e.g. A000011_01) _PROBESET_RE = re.compile(r"^.+_at$", re.IGNORECASE) _AROS_PROBESET_RE = re.compile(r"^A\d{6}_\d{2}$", re.IGNORECASE) - - -def is_probeset_id(gene_id: str) -> bool: - """True if gene_id is already a probeset (ends in _at or is AROS format).""" - return bool(_PROBESET_RE.match(gene_id) or _AROS_PROBESET_RE.match(gene_id)) - - -# --------------------------------------------------------------------------- -# Database → species map -# --------------------------------------------------------------------------- +# CATMA microarray probes used by the Seedcoat database (e.g. At30023977) +_CATMA_PROBE_RE = re.compile(r"^At\d{8}$") # fmt: off DATABASE_SPECIES: dict[str, str] = { - # Arabidopsis "affydb": "arabidopsis", "arabidopsis_ecotypes": "arabidopsis", "atgenexp": "arabidopsis", @@ -71,35 +37,29 @@ def is_probeset_id(gene_id: str) -> bool: "root_Schaefer_lab": "arabidopsis", "rpatel": "arabidopsis", "seed_db": "arabidopsis", - "seedcoat": "arabidopsis", # AROS chip; A######_## probesets + "seedcoat": "arabidopsis", "shoot_apex": "arabidopsis", "silique": "arabidopsis", "single_cell": "arabidopsis", - # Actinidia (kiwifruit) "actinidia_bud_development": "actinidia", "actinidia_flower_fruit_development": "actinidia", "actinidia_postharvest": "actinidia", "actinidia_vegetative_growth": "actinidia", - # Apple "apple": "apple", - # Arachis (peanut) "arachis": "arachis", - # Barley "barley_mas": "barley", "barley_rma": "barley", "barley_seed": "barley", "barley_spike_meristem": "barley", "barley_spike_meristem_v3": "barley", - # Brachypodium "brachypodium": "brachypodium", "brachypodium_Bd21": "brachypodium", "brachypodium_embryogenesis": "brachypodium", "brachypodium_grains": "brachypodium", "brachypodium_metabolites_map": "brachypodium", "brachypodium_photo_thermocycle": "brachypodium", - # Brassica rapa "brassica_rapa": "brassica", - # Cacao + "brassica_rapa_developmental_atlas": "brassica", "cacao_developmental_atlas": "cacao", "cacao_developmental_atlas_sca": "cacao", "cacao_drought_diurnal_atlas": "cacao", @@ -108,53 +68,38 @@ def is_probeset_id(gene_id: str) -> bool: "cacao_leaf": "cacao", "cacao_meristem_atlas_sca": "cacao", "cacao_seed_atlas_sca": "cacao", - # Camelina "camelina": "camelina", "camelina_tpm": "camelina", - # Cannabis "cannabis": "cannabis", - # Canola (Brassica napus) "canola": "canola", "canola_original": "canola", "canola_original_v2": "canola", "canola_seed": "canola", - # Cassava "cassava_atlas": "cassava", "cassava_cbb": "cassava", "cassava_eacmv": "cassava", - # Cuscuta "cuscuta": "cuscuta", "cuscuta_early_haustoriogenesis": "cuscuta", "cuscuta_lmd": "cuscuta", - # Wheat / Durum "durum_wheat_abiotic_stress": "wheat", "durum_wheat_biotic_stress": "wheat", "durum_wheat_development": "wheat", - # Eucalyptus "eucalyptus": "eucalyptus", - # Euphorbia "euphorbia": "euphorbia", - # Grape "grape_developmental": "grape", - # Heterodera (nematode) "heterodera_schachtii": "heterodera", - # Human "human_body_map_2": "human", "human_developmental": "human", "human_developmental_SpongeLab": "human", "human_diseased": "human", - # Kalanchoe "kalanchoe": "kalanchoe", "kalanchoe_time_course_analysis": "kalanchoe", - # Little millet "little_millet": "little_millet", - # Lupin "lupin_lcm_leaf": "lupin", "lupin_lcm_pod": "lupin", "lupin_lcm_stem": "lupin", "lupin_pod_seed": "lupin", "lupin_whole_plant": "lupin", - # Maize "maize_RMA_linear": "maize", "maize_RMA_log": "maize", "maize_atlas": "maize", @@ -164,7 +109,7 @@ def is_probeset_id(gene_id: str) -> bool: "maize_ears": "maize", "maize_embryonic_leaf_development": "maize", "maize_enzyme": "maize", - "maize_gdowns": "maize", # Affymetrix chip; GRMZM* → AB*_at (GenBank accession probesets) + "maize_gdowns": "maize", "maize_iplant": "maize", "maize_kernel_v5": "maize", "maize_leaf_gradient": "maize", @@ -174,7 +119,6 @@ def is_probeset_id(gene_id: str) -> bool: "maize_rice_comparison": "maize", "maize_root": "maize", "maize_stress_v5": "maize", - # Mangosteen "mangosteen_aril_vs_rind": "mangosteen", "mangosteen_callus": "mangosteen", "mangosteen_diseased_vs_normal": "mangosteen", @@ -182,43 +126,33 @@ def is_probeset_id(gene_id: str) -> bool: "mangosteen_seed_development": "mangosteen", "mangosteen_seed_development_germination": "mangosteen", "mangosteen_seed_germination": "mangosteen", - # Marchantia "marchantia_organ_stress": "marchantia", - # Medicago - "medicago_mas": "medicago", # Affymetrix chip; Medtr* → Mtr.*_at + "medicago_mas": "medicago", "medicago_rma": "medicago", "medicago_root": "medicago", "medicago_root_v5": "medicago", "medicago_seed": "medicago", - # Mouse "mouse_db": "mouse", - # Oat "oat": "oat", - # Phelipanche "phelipanche": "phelipanche", - # Physcomitrella "physcomitrella_db": "physcomitrella", - # Poplar - "poplar": "poplar", # Affymetrix chip; grail3.* → PtpAffx.*_at + "poplar": "poplar", "poplar_hormone": "poplar", "poplar_leaf": "poplar", "poplar_xylem": "poplar", - # Potato "potato_dev": "potato", "potato_stress": "potato", "potato_wounding": "potato", - # Rice + "quinoa_nutrient": "quinoa", "rice_abiotic_stress_sc_pseudobulk": "rice", "rice_drought_heat_stress": "rice", "rice_leaf_gradient": "rice", "rice_maize_comparison": "rice", - "rice_mas": "rice", # Affymetrix chip; LOC_Os* → Os.*_at + "rice_mas": "rice", "rice_metabolite": "rice", "rice_rma": "rice", "rice_root": "rice", - # Selaginella "selaginella": "selaginella", - # Sorghum "sorghum_atlas_w_BS_cells": "sorghum", "sorghum_comparative_transcriptomics": "sorghum", "sorghum_developmental": "sorghum", @@ -235,26 +169,18 @@ def is_probeset_id(gene_id: str) -> bool: "sorghum_sulfur_stress": "sorghum", "sorghum_temperature_stress": "sorghum", "sorghum_vascularization_and_internode": "sorghum", - # Soybean "soybean": "soybean", "soybean_embryonic_development": "soybean", "soybean_heart_cotyledon_globular": "soybean", "soybean_senescence": "soybean", "soybean_severin": "soybean", - # Spruce "spruce": "spruce", - # Strawberry "strawberry": "strawberry", - # Striga "striga": "striga", - # Sugarcane "sugarcane_culms": "sugarcane", "sugarcane_leaf": "sugarcane", - # Sunflower "sunflower": "sunflower", - # Thellungiella (Eutrema) "thellungiella_db": "thellungiella", - # Tomato "tomato": "tomato", "tomato_ils": "tomato", "tomato_ils2": "tomato", @@ -268,329 +194,180 @@ def is_probeset_id(gene_id: str) -> bool: "tomato_shade_mutants": "tomato", "tomato_shade_timecourse": "tomato", "tomato_trait": "tomato", - # Triphysaria "triphysaria": "triphysaria", - # Triticale - "triticale": "triticale", # Affymetrix chip; EU* → Ta.*_at + "triticale": "triticale", "triticale_mas": "triticale", - # Tung tree "tung_tree": "tung_tree", - # Wheat "wheat": "wheat", "wheat_abiotic_stress": "wheat", "wheat_embryogenesis": "wheat", "wheat_meiosis": "wheat", "wheat_root": "wheat", - # Willow "willow": "willow", - # Test "sample_data": "arabidopsis", } -# fmt: on - -# --------------------------------------------------------------------------- -# Probeset databases -# Databases where the stored key is a probeset ID, not the canonical gene ID. -# A gene → probeset lookup is required before querying these. -# --------------------------------------------------------------------------- - -PROBESET_DATABASES: frozenset[str] = frozenset( - { - # ── Arabidopsis ATH1 GeneChip ──────────────────────────────────────────── - "affydb", - "arabidopsis_ecotypes", - "atgenexp", - "atgenexp_hormone", - "atgenexp_pathogen", - "atgenexp_plus", - "atgenexp_stress", - "guard_cell", - "hnahal", - "lateral_root_initiation", - "light_series", - "meristem_db", - "meristem_db_new", - "root", - "rohan", - "rpatel", - "seed_db", - # ── Other species Affymetrix chips ─────────────────────────────────────── - # Lookup tables for these are pending; supply probeset directly (e.g. Contig3267_at) - "barley_mas", # Affymetrix Barley1 GeneChip (AK364622 → Contig3045_at) - "barley_rma", # Affymetrix Barley1 GeneChip - "human_developmental", # CCR5 → 206991_s_at - "human_developmental_SpongeLab", - "human_diseased", - "maize_gdowns", # Affymetrix Maize GeneChip (GRMZM* → AB*_at, GenBank accession probesets) - "maize_RMA_linear", # contig-based probesets (GRMZM* → AC*_FGT* format) - "maize_RMA_log", # same chip as maize_RMA_linear - "medicago_mas", # Affymetrix Medicago GeneChip (Medtr* → Mtr.*_at) - "medicago_rma", # Affymetrix Medicago GeneChip - "medicago_seed", # old genome model (Medtr8g* → Medtr_v1_*); confirmed from sample data - "poplar", # Affymetrix Poplar GeneChip (Potri.* → grail3.* → PtpAffx.*_at) - "rice_mas", # Affymetrix Rice GeneChip (LOC_Os* → Os.*_at) - "rice_rma", # Affymetrix Rice GeneChip - "tomato", # Affymetrix Tomato GeneChip (Solyc* → TU* probesets); confirmed from sample data - "triticale", # Affymetrix Wheat/Triticale GeneChip (EU* → Ta.*_at) - "triticale_mas", # Affymetrix Wheat/Triticale GeneChip - # ── Non-Affymetrix species with gene ID ≠ stored key ───────────────────── - # Confirmed from eFP browser: input gene ID differs from the stored key. - # Lookup tables pending for all of these. - "grape_developmental", # VIT_00s0120g00060 → CHRUN_JGVV120_4_T01 - "soybean", # Glyma.XxG* (new Wm82.a4) → GlymaXxg*/GlymaXxs* (old format) - "soybean_embryonic_development", - "soybean_heart_cotyledon_globular", - "soybean_senescence", - "soybean_severin", - # ── Cross-species: input is an Arabidopsis AGI, stored as species gene ID ─ - # See CROSS_SPECIES_DATABASES below for the input validation override. - "phelipanche", # AT1G07890 → OrAeBC5_10.1 - "striga", # AT3G11400 → StHeBC3_1.1 - "thellungiella_db", # AT2G21470 → Thhalv10000089m.g - "triphysaria", # AT1G11260 → TrVeBC3_1.1 - # TODO: seedcoat – AROS chip; A######_## probesets; add once format confirmed - # TODO: strawberry – gene10171 → FvH4_1g00010; lookup table needed - # TODO: physcomitrella – Phypa_166136 → Pp1s103_79V6.1; lookup table needed - # TODO: willow – SapurV1A.* → comp*_c*_seq* (Trinity); assembly mapping needed - # TODO: sunflower – HanXRQChr12g* → Ha1_*; genome version mapping needed - # TODO: camelina – Csa01g* (v6) → Csa*s*.* (old assembly); version mapping needed - } -) - -# --------------------------------------------------------------------------- -# Cross-species databases -# These accept an Arabidopsis AGI as input and convert it to a species probeset. -# Used to override input validation (validate against arabidopsis, not native species). -# --------------------------------------------------------------------------- -CROSS_SPECIES_DATABASES: dict[str, str] = { - # database → species of the expected INPUT gene ID - "phelipanche": "arabidopsis", # AT* AGI → OrAeBC5_* probeset - "striga": "arabidopsis", # AT* AGI → StHeBC3_* probeset - "thellungiella_db": "arabidopsis", # AT* AGI → Thhalv* probeset - "triphysaria": "arabidopsis", # AT* AGI → TrVeBC3_* probeset +# Maps databases that store microarray probeset IDs to their eFP project regex key. +# These databases accept both canonical gene IDs (with AGI→probeset lookup for Arabidopsis) +# AND direct probeset ID input. +# fmt: off +DATABASE_EFP_PROJECT: dict[str, str] = { + # Arabidopsis ATH1 microarray databases — support AGI + probeset input + "affydb": "efp_arabidopsis", + "arabidopsis_ecotypes": "efp_arabidopsis", + "atgenexp": "efp_arabidopsis", + "atgenexp_hormone": "efp_arabidopsis", + "atgenexp_pathogen": "efp_arabidopsis", + "atgenexp_plus": "efp_arabidopsis", + "atgenexp_stress": "efp_arabidopsis", + "guard_cell": "efp_arabidopsis", + "hnahal": "efp_arabidopsis", + "lateral_root_initiation": "efp_arabidopsis", + "light_series": "efp_arabidopsis", + "meristem_db": "efp_arabidopsis", + "meristem_db_new": "efp_arabidopsis", + "root": "efp_arabidopsis", + "rohan": "efp_arabidopsis", + "rpatel": "efp_arabidopsis", + "seed_db": "efp_arabidopsis", + # Seedcoat uses CATMA/AROS probes in addition to AGI + "seedcoat": "efp_seedcoat", + # Non-Arabidopsis microarray databases — probeset input only (no AGI conversion) + # barley_seed / barley_spike_meristem(_v3) and poplar_leaf / poplar_xylem were + # previously (incorrectly) mapped here too: their real sample IDs are plain + # gene IDs (HORVU..., Potri...), not probesets, and were 0% passing this + # override. Removed so they fall back to the barley/poplar species validator, + # which already accepts their format. + "barley_mas": "efp_barley", + "barley_rma": "efp_barley", + "rice_mas": "efp_rice", + "rice_rma": "efp_rice", + "medicago_mas": "efp_medicago", + "medicago_rma": "efp_medicago", + "poplar": "efp_poplar", + "poplar_hormone": "efp_poplar", + "triticale": "efp_triticale", + "triticale_mas": "efp_triticale", + "human_developmental": "efp_human", + "human_developmental_SpongeLab": "efp_human", + "human_diseased": "efp_human", + "maize_gdowns": "efp_maize", + # Added after Task 2 (Jun 2026) regex-coverage audit: species validator rejected + # real sample IDs that Vincent's per-project eFP regex correctly accepts. + "arachis": "efp_arachis", + "canola_seed": "efp_canola", + "thellungiella_db": "efp_eutrema", + "physcomitrella_db": "efp_physcomitrella", + "tomato": "efp_tomato", + "tomato_renormalized": "efp_tomato", + "lipid_map": "efp_arabidopsis_lipid", + # Metabolite/enzyme-class eFPs: real "gene_id" values are compound/enzyme/trait + # names looked up against one fixed database, not actual gene IDs -- see + # scrape_view_databases.py's _HARDCODED comment for how these sites are scraped. + "maize_enzyme": "efp_maize_enzyme", + "maize_metabolite": "efp_maize_metabolite", + "maize_lipid_map": "efp_maize_lipid_map", + "rice_metabolite": "efp_rice_metabolite", + "brachypodium_metabolites_map": "efp_brachypodium_metabolites", + "tomato_trait": "efp_tomato_trait", } +# fmt: on -# --------------------------------------------------------------------------- -# Species detection -# --------------------------------------------------------------------------- - - -def detect_gene_species(gene_id: str) -> Optional[str]: - """Infer species from gene_id format. Returns canonical species key or None.""" - upper = gene_id.upper() - if BARUtils.is_arabidopsis_gene_valid(upper): - return "arabidopsis" - if BARUtils.is_maize_gene_valid(upper): - return "maize" - if BARUtils.is_rice_gene_valid(upper): - return "rice" - if BARUtils.is_soybean_gene_valid(upper): - return "soybean" - if BARUtils.is_poplar_gene_valid(upper): - return "poplar" - if BARUtils.is_tomato_gene_valid(upper): - return "tomato" - if BARUtils.is_sorghum_gene_valid(upper): - return "sorghum" - if BARUtils.is_cannabis_gene_valid(upper): - return "cannabis" - if BARUtils.is_grape_gene_valid(upper): - return "grape" - if BARUtils.is_kalanchoe_gene_valid(upper): - return "kalanchoe" - if BARUtils.is_strawberry_gene_valid(upper): - return "strawberry" - if BARUtils.is_selaginella_gene_valid(upper): - return "selaginella" - if BARUtils.is_phelipanche_gene_valid(upper): - return "phelipanche" - if BARUtils.is_physcomitrella_gene_valid(upper): - return "physcomitrella" - if BARUtils.is_striga_gene_valid(upper): - return "striga" - if BARUtils.is_triphysaria_gene_valid(upper): - return "triphysaria" - if BARUtils.is_canola_gene_valid(upper): - return "canola" - if BARUtils.is_brassica_rapa_gene_valid(upper): - return "brassica" - if BARUtils.is_arachis_gene_valid(upper): - return "arachis" - return None - - -# --------------------------------------------------------------------------- -# Gene ID validation -# --------------------------------------------------------------------------- - -# Species without a validator entry pass through (unknown format = not rejected). -# Note: strawberry and physcomitrella validators match the probeset format -# (FvH4_*, Pp1s*V6.*), not the user-input gene format (gene####, Phypa_*). -# Lookup tables for those are still pending. _VALIDATORS: dict = { - "arabidopsis": BARUtils.is_arabidopsis_gene_valid, - "arachis": BARUtils.is_arachis_gene_valid, - "brassica": BARUtils.is_brassica_rapa_gene_valid, - "cannabis": BARUtils.is_cannabis_gene_valid, - "canola": BARUtils.is_canola_gene_valid, - "grape": BARUtils.is_grape_gene_valid, - "kalanchoe": BARUtils.is_kalanchoe_gene_valid, - "maize": BARUtils.is_maize_gene_valid, - "phelipanche": BARUtils.is_phelipanche_gene_valid, + "actinidia": BARUtils.is_actinidia_gene_valid, + "apple": BARUtils.is_apple_gene_valid, + "arabidopsis": BARUtils.is_arabidopsis_gene_valid, + "arachis": BARUtils.is_arachis_gene_valid, + "barley": BARUtils.is_barley_gene_valid, + "brachypodium": BARUtils.is_brachypodium_gene_valid, + "brassica": BARUtils.is_brassica_rapa_gene_valid, + "cacao": BARUtils.is_cacao_gene_valid, + "camelina": BARUtils.is_camelina_gene_valid, + "cannabis": BARUtils.is_cannabis_gene_valid, + "canola": BARUtils.is_canola_gene_valid, + "cassava": BARUtils.is_cassava_gene_valid, + "cuscuta": BARUtils.is_cuscuta_gene_valid, + "eucalyptus": BARUtils.is_eucalyptus_gene_valid, + "euphorbia": BARUtils.is_euphorbia_gene_valid, + "grape": BARUtils.is_grape_gene_valid, + "heterodera": BARUtils.is_arabidopsis_gene_valid, + "human": BARUtils.is_human_gene_valid, + "kalanchoe": BARUtils.is_kalanchoe_gene_valid, + "little_millet": BARUtils.is_little_millet_gene_valid, + "lupin": BARUtils.is_lupin_gene_valid, + "maize": BARUtils.is_maize_gene_valid, + "mangosteen": BARUtils.is_mangosteen_gene_valid, + "marchantia": BARUtils.is_marchantia_gene_valid, + "medicago": BARUtils.is_medicago_gene_valid, + "mouse": BARUtils.is_mouse_gene_valid, + "oat": BARUtils.is_oat_gene_valid, + "phelipanche": BARUtils.is_phelipanche_gene_valid, "physcomitrella": BARUtils.is_physcomitrella_gene_valid, - "poplar": BARUtils.is_poplar_gene_valid, - "rice": BARUtils.is_rice_gene_valid, - "selaginella": BARUtils.is_selaginella_gene_valid, - "sorghum": BARUtils.is_sorghum_gene_valid, - "soybean": BARUtils.is_soybean_gene_valid, - "strawberry": BARUtils.is_strawberry_gene_valid, - "striga": BARUtils.is_striga_gene_valid, - "tomato": BARUtils.is_tomato_gene_valid, - "triphysaria": BARUtils.is_triphysaria_gene_valid, + "poplar": BARUtils.is_poplar_gene_valid, + "potato": BARUtils.is_potato_gene_valid, + "quinoa": BARUtils.is_quinoa_gene_valid, + "rice": BARUtils.is_rice_gene_valid, + "selaginella": BARUtils.is_selaginella_gene_valid, + "sorghum": BARUtils.is_sorghum_gene_valid, + "soybean": BARUtils.is_soybean_gene_valid, + "spruce": BARUtils.is_spruce_gene_valid, + "strawberry": BARUtils.is_strawberry_gene_valid, + "striga": BARUtils.is_striga_gene_valid, + "sugarcane": BARUtils.is_sugarcane_gene_valid, + "sunflower": BARUtils.is_sunflower_gene_valid, + "thellungiella": BARUtils.is_thellungiella_gene_valid, + "tomato": BARUtils.is_tomato_gene_valid, + "triphysaria": BARUtils.is_triphysaria_gene_valid, + "tung_tree": BARUtils.is_tung_tree_gene_valid, + "wheat": BARUtils.is_wheat_gene_valid, + "willow": BARUtils.is_willow_gene_valid, } - -def validate_gene_id(gene_id: str, species: str) -> bool: - """True if gene_id passes the species validator, or species has no validator.""" - validator = _VALIDATORS.get(species) - return validator(gene_id) if validator is not None else True - - -def get_species_for_database(database: str) -> Optional[str]: - """Return canonical species key for database, or None if unknown.""" - return DATABASE_SPECIES.get(database) - - -# --------------------------------------------------------------------------- -# Gene ID normalisation -# --------------------------------------------------------------------------- - -# Maize transcript IDs (e.g. GRMZM2G083841_T01) must be stripped to gene level -# before querying eFP databases. -_MAIZE_TRANSCRIPT_RE = re.compile(r"_T\d{1,3}$", re.IGNORECASE) - -# Barley V3 IDs from ePlant use a .V3 suffix (e.g. HORVU.MOREX.r3.1HG0000030.V3) -# but databases store a .1 suffix (e.g. HORVU.MOREX.r3.1HG0000030.1). -# Strip any trailing version suffix (.[Vv]\d+ or .\d+) and reattach .1. _BARLEY_V3_RE = re.compile(r"\.[Vv]\d+$") -def normalize_gene_id(gene_id: str, species: str) -> str: - """Return the gene ID in the form stored in eFP databases. - - :param gene_id: Raw gene identifier supplied by the user. - :type gene_id: str - :param species: Canonical species key (e.g. ``'maize'``, ``'barley'``). - :type species: str - :returns: Normalised gene ID ready for database lookup. - :rtype: str - - Maize: strips ``_T##`` transcript suffix (``GRMZM2G083841_T01`` → ``GRMZM2G083841``). - - Barley V3: replaces ``.V3`` version suffix with ``.1`` to match the stored format - (``HORVU.MOREX.r3.1HG0000030.V3`` → ``HORVU.MOREX.r3.1HG0000030.1``). - """ - if species == "maize": - return _MAIZE_TRANSCRIPT_RE.sub("", gene_id) - if species == "barley" and _BARLEY_V3_RE.search(gene_id): - return _BARLEY_V3_RE.sub(".1", gene_id) - return gene_id - - -# --------------------------------------------------------------------------- -# Gene ID → probeset conversion -# --------------------------------------------------------------------------- - - -def convert_gene_to_probeset( - gene_id: str, - species: str, - database: str, -) -> tuple[Optional[str], Optional[str]]: - """Convert gene_id to its probeset ID. Returns (probeset, None) or (None, error).""" - - # ── Implemented ────────────────────────────────────────────────────────── - - if species == "arabidopsis": - from api.services.efp_data import EFPDataService # noqa: PLC0415 - probeset = EFPDataService.agi_to_probset(gene_id.upper()) - if probeset: - return probeset, None - return None, f"No ATH1 probeset found for '{gene_id}'." - - # ── Affymetrix chips (lookup tables pending) ────────────────────────────── - - if species == "barley": - # TODO: AK364622 → Contig3045_at - pass - - if species == "maize": - # TODO: maize_gdowns — GRMZM* → AB*_at (GenBank accession probesets; confirmed from sample data) - # TODO: maize_RMA_linear — GRMZM* → AC*_FGT* (contig-based probesets; confirmed from sample data) - # Other maize databases (maize_buell_lab etc.) store Zm00001d* directly — use normalize_gene_id. - pass - - if species == "medicago": - # TODO: medicago_mas / medicago_rma — Medtr* → Mtr.*_at (Affymetrix chip) - # TODO: medicago_seed — Medtr8g* → Medtr_v1_* (old genome model; confirmed from sample data) - pass - - if species == "poplar": - # TODO: grail3.* → PtpAffx.*_at - pass - - if species == "rice": - # TODO: LOC_Os* → Os.*_at - pass - - if species == "triticale": - # TODO: EU* → Ta.*_at - pass - - if species == "human": - # TODO: gene symbol → numeric_s_at (e.g. CCR5 → 206991_s_at) - pass - - # ── Non-Affymetrix species with differing ID formats (lookup tables pending) ── - - if species == "tomato" and database == "tomato": - # TODO: Solyc* → TU* (Tomato Unigene probesets on Affymetrix Tomato GeneChip) - # Confirmed from sample data: tomato (Rose Lab Atlas) stores TU000001 format. - # tomato_ils / tomato_ils2 store Solyc* directly — no conversion needed for those. - pass - - if species == "grape": - # TODO: VIT_* → CHRUN_* - pass - - if species == "soybean": - # TODO: Glyma.XxG* (new Wm82.a4 format) → GlymaXxg*/GlymaXxs* (old format) - # Confirmed from sample data: soybean/soybean_severin store old format (e.g. Glyma0021s00410). - # This is a gene model version reconciliation, not just string formatting. - pass - - # ── Cross-species: Arabidopsis AGI input → species probeset (lookup tables pending) ── - - if species == "phelipanche": - # TODO: AT* → OrAeBC5_* - pass - - if species == "striga": - # TODO: AT* → StHeBC3_* - pass - - if species == "thellungiella": - # TODO: AT* → Thhalv* - pass - - if species == "triphysaria": - # TODO: AT* → TrVeBC3_* - pass - - return None, ( - f"Probeset lookup not yet available for species '{species}' " - f"(database: '{database}'). " - "Supply the probeset ID directly (e.g. Contig3267_at)." - ) +class GeneIdUtils: + @staticmethod + def is_probeset_id(gene_id: str) -> bool: + """Return True if the gene_id looks like a microarray probeset rather than a gene ID. + + Covers: + - Standard Affymetrix probes ending in _at (e.g. 267643_at, Contig7905_at) + - AROS array probes (e.g. A017813_01) + - CATMA array probes used by the Seedcoat database (e.g. At30023977) + """ + return bool( + _PROBESET_RE.match(gene_id) + or _AROS_PROBESET_RE.match(gene_id) + or _CATMA_PROBE_RE.match(gene_id) + ) + + @staticmethod + def validate_gene_id(gene_id: str, species: str) -> bool: + validator = _VALIDATORS.get(species) + return validator(gene_id) if validator is not None else True + + @staticmethod + def validate_gene_for_database(gene_id: str, database: str) -> bool: + """Validate a gene ID against the rules for a specific database. + + For microarray databases, uses the eFP project regex which accepts both + canonical gene IDs and probeset IDs. Falls back to species-based validation + for all other databases. + + :param gene_id: Gene identifier to validate + :param database: Database name (e.g. 'light_series', 'barley_mas') + :return: True if the gene ID is valid for the given database + """ + efp_project = DATABASE_EFP_PROJECT.get(database) + if efp_project: + return BARUtils.is_efp_gene_valid(gene_id, efp_project) + species = DATABASE_SPECIES.get(database) + return GeneIdUtils.validate_gene_id(gene_id, species) if species else True + + @staticmethod + def normalize_gene_id(gene_id: str, species: str) -> str: + if species == "barley" and _BARLEY_V3_RE.search(gene_id): + return _BARLEY_V3_RE.sub(".1", gene_id) + return gene_id diff --git a/build_master_db_list.py b/build_master_db_list.py new file mode 100644 index 00000000..b77b8c72 --- /dev/null +++ b/build_master_db_list.py @@ -0,0 +1,127 @@ +""" +Reena Obmina | BCB330 Project 2025-2026 | University of Toronto + +Task 4 (Jun 2026): assemble the final "master list" of every BAR database +discovered across both frontends, organized the way Vincent asked for -- +by species, noting eFP vs ePlant vs both, and microarray vs RNA-seq. + +Platform (microarray vs RNA-seq) is determined from the real sample IDs +themselves (GeneIdUtils.is_probeset_id), not from which validator code path +happens to handle a database, since a handful of gene-ID (RNA-seq) databases +are routed through Vincent's per-project eFP regex anyway for better coverage +(see DATABASE_EFP_PROJECT comments in gene_id_utils.py) -- that routing is an +implementation detail, not the underlying data type. + +Note on atgenexp-style databases: a handful of databases (atgenexp_plus, +atgenexp_pathogen, maize_RMA_linear, tomato_renormalized, etc.) bundle multiple +papers/projects into one physical database -- one view per paper, not one view +per database like everywhere else. proj_id_view_mapping.json (built by +build_proj_id_view_mapping.py) already works out, per view, which proj_id(s) +in the real sample data that view actually corresponds to, and classifies the +database as "multi_project" (genuinely separate papers, disjoint proj_ids) vs +"duplicate_view_names" (same proj_id, just different eFP/ePlant display names) +vs "partial_overlap". This script folds that breakdown into the master list +under "proj_id_breakdown" so the per-paper granularity isn't lost when an API +caller only has the database name to go on. + +Reads: data/efp_info/db_source_summary.json -- db -> efp/eplant/both (scrape_species_view_info.py) + db_regex_coverage_report.csv -- per-db validation results (validate_db_regex_coverage.py) + species_databases.json -- project -> view -> db (scrape_view_databases.py) + proj_id_view_mapping.json -- per-view proj_id breakdown (build_proj_id_view_mapping.py) + api/utils/gene_id_utils.DATABASE_SPECIES -- db -> canonical species key +Writes: data/efp_info/master_db_list.json -- { species: { db: {source, platform, views, validation, proj_id_breakdown} } } +""" + +import csv +import json +import sys +import types +from collections import defaultdict +from pathlib import Path + +sys.modules.setdefault("api", types.ModuleType("api")) +sys.modules["api"].__path__ = ["api"] +sys.modules.setdefault("api.utils", types.ModuleType("api.utils")) +sys.modules["api.utils"].__path__ = ["api/utils"] + +from api.utils.gene_id_utils import DATABASE_SPECIES # noqa: E402 + + +def load_coverage(): + with open("db_regex_coverage_report.csv") as f: + return {r["database"]: r for r in csv.DictReader(f)} + + +def load_views_by_db(): + """Invert species_databases.json (project -> view -> db) into db -> {project: [views]}.""" + species_db = json.load(open("species_databases.json")) + views_by_db = defaultdict(lambda: defaultdict(list)) + for project, views in species_db.items(): + for view_name, db in views.items(): + views_by_db[db][project].append(view_name) + return views_by_db + + +def main(): + db_sources = json.load(open("data/efp_info/db_source_summary.json")) + coverage = load_coverage() + views_by_db = load_views_by_db() + proj_id_mapping = json.load(open("proj_id_view_mapping.json")) + + # coverage (db_regex_coverage_report.csv) is the full universe -- every db with + # real sample data in api/random_rows_json/, including ones no longer reachable + # from any live dropdown ("legacy_not_in_dropdown"). db_sources only has the + # live-discoverable subset. Union them so the master list is genuinely complete. + all_dbs = set(coverage) | set(db_sources) + + master = defaultdict(dict) + n_multi_project_dbs = 0 + n_legacy = 0 + for db in sorted(all_dbs): + species = DATABASE_SPECIES.get(db, "unknown") + row = coverage.get(db, {}) + source = row.get("source", db_sources.get(db, "unknown")) + if source == "legacy_not_in_dropdown": + n_legacy += 1 + looks_like_probeset = row.get("looks_like_probeset") == "True" + + entry = { + "source": source, + "platform": "microarray" if looks_like_probeset else "rna_seq", + "views": dict(views_by_db.get(db, {})), + "validation": { + "n_samples": int(row.get("n_samples", 0)), + "n_pass": int(row.get("n_pass", 0)), + "n_fail": int(row.get("n_fail", 0)), + }, + } + + proj_id_info = proj_id_mapping.get(db) + if proj_id_info: + entry["proj_id_breakdown"] = proj_id_info + if proj_id_info["classification"] == "multi_project": + n_multi_project_dbs += 1 + + master[species][db] = entry + + out_file = Path("data/efp_info/master_db_list.json") + with open(out_file, "w") as f: + json.dump(dict(sorted(master.items())), f, indent=2, sort_keys=False) + + n_species = len(master) + n_dbs = sum(len(dbs) for dbs in master.values()) + n_microarray = sum(1 for dbs in master.values() for d in dbs.values() if d["platform"] == "microarray") + n_rna_seq = n_dbs - n_microarray + n_efp_only = sum(1 for dbs in master.values() for d in dbs.values() if d["source"] == "efp") + n_eplant_only = sum(1 for dbs in master.values() for d in dbs.values() if d["source"] == "eplant") + n_both = sum(1 for dbs in master.values() for d in dbs.values() if d["source"] == "both") + + print(f"Species: {n_species} | Databases: {n_dbs} ({n_legacy} legacy/not in any current dropdown)") + print(f" eFP-only: {n_efp_only} | ePlant-only: {n_eplant_only} | both: {n_both}") + print(f" microarray: {n_microarray} | rna_seq: {n_rna_seq}") + print(f" Multi-project databases (e.g. atgenexp_*): {n_multi_project_dbs}") + print(f"Output written to {out_file}") + + +if __name__ == "__main__": + main() diff --git a/build_proj_id_view_mapping.py b/build_proj_id_view_mapping.py new file mode 100644 index 00000000..7a27fe76 --- /dev/null +++ b/build_proj_id_view_mapping.py @@ -0,0 +1,125 @@ +""" +Reena Obmina | BCB330 Project 2025-2026 | University of Toronto + +Task 3 (Jun 11 2026): for databases like atgenexp where multiple eFP/ePlant +views/papers share one physical database, derive which proj_id(s) belong to +which view, by cross-referencing each view's known sample names (from Task 1's +XML scrape) against the real proj_id values recorded for those exact sample +names in the production sample data. + +A database is "genuinely multi-project" if its views resolve to disjoint (or +mostly disjoint) proj_id sets — i.e. each view really is a separate +paper/experiment. If two differently-named views resolve to the same proj_id +set, they're not separate projects — just the eFP and ePlant frontends using +different display names for the one underlying dataset. + +Reads: data/efp_info/efp_eplant_species_view_info.json — view -> sample names (Task 1) + api/random_rows_json/{db}_test_data.json — real (proj_id, data_bot_id) pairs +Writes: proj_id_view_mapping.json — per multi-view db: view -> proj_id set, + classified as "multi_project" or "duplicate_view_names" +""" + +import json +from collections import defaultdict +from pathlib import Path + +INFO_PATH = "data/efp_info/efp_eplant_species_view_info.json" +SAMPLE_DIR = Path("api/random_rows_json") + + +def build_view_samples(): + """Map (db, view_name) -> set of sample names, from Task 1's XML scrape.""" + info = json.load(open(INFO_PATH)) + view_samples = defaultdict(set) + for source in ("efp", "eplant"): + for _key, views in info[source].items(): + for v in views: + db = v.get("database") + if not db: + continue + samples = set() + for group in v.get("groups", {}).values(): + samples.update(group.get("controls", [])) + for tissue_samples in group.get("treatments", {}).values(): + samples.update(tissue_samples) + view_samples[(db, v["view_name"])] |= samples + return view_samples + + +def load_bot_to_proj(db): + path = SAMPLE_DIR / f"{db}_test_data.json" + if not path.exists(): + return {} + rows = json.load(open(path)) + bot_to_proj = defaultdict(set) + for row in rows: + bot_id = row.get("data_bot_id") + proj_id = row.get("proj_id") + if bot_id is not None and proj_id is not None: + bot_to_proj[bot_id].add(str(proj_id)) + return bot_to_proj + + +def main(): + view_samples = build_view_samples() + + by_db = defaultdict(dict) + for (db, view_name), samples in view_samples.items(): + by_db[db][view_name] = samples + + multi_view_dbs = {db: views for db, views in by_db.items() if len(views) > 1} + + report = {} + for db, views in sorted(multi_view_dbs.items()): + bot_to_proj = load_bot_to_proj(db) + view_proj_ids = {} + for view_name, samples in views.items(): + proj_ids = set() + matched = 0 + for s in samples: + if s in bot_to_proj: + proj_ids |= bot_to_proj[s] + matched += 1 + view_proj_ids[view_name] = { + "n_view_samples": len(samples), + "n_matched_in_real_data_sample": matched, + "proj_ids": sorted(proj_ids), + } + + # Classify: do any two views share NO proj_ids in common (genuine + # separate projects) vs all views resolving to the same proj_id set + # (same project, just different eFP/ePlant display names)? + proj_id_sets = [set(v["proj_ids"]) for v in view_proj_ids.values() if v["proj_ids"]] + if len(proj_id_sets) < 2: + classification = "insufficient_data" + else: + all_identical = all(s == proj_id_sets[0] for s in proj_id_sets) + any_disjoint = any( + proj_id_sets[i].isdisjoint(proj_id_sets[j]) + for i in range(len(proj_id_sets)) + for j in range(i + 1, len(proj_id_sets)) + ) + if all_identical: + classification = "duplicate_view_names" + elif any_disjoint: + classification = "multi_project" + else: + classification = "partial_overlap" + + report[db] = {"classification": classification, "views": view_proj_ids} + + out_file = "proj_id_view_mapping.json" + with open(out_file, "w") as f: + json.dump(report, f, indent=2) + + counts = defaultdict(int) + for r in report.values(): + counts[r["classification"]] += 1 + print(f"Checked {len(report)} multi-view databases.") + for cls, n in sorted(counts.items()): + print(f" {cls}: {n}") + print(f"Report written to {out_file}") + + +if __name__ == "__main__": + main() diff --git a/config/databases/soybean_nssnp.sql b/config/databases/soybean_nssnp.sql index be5b88e4..5d5e991a 100644 --- a/config/databases/soybean_nssnp.sql +++ b/config/databases/soybean_nssnp.sql @@ -60,8 +60,7 @@ CREATE TABLE `sample_lookup` ( `sample_id` varchar(45) NOT NULL, `dataset` varchar(45) DEFAULT NULL, `dataset_sample` varchar(45) DEFAULT NULL, - PRIMARY KEY (`sample_id`), - CONSTRAINT `sample_id` FOREIGN KEY (`sample_id`) REFERENCES `snps_reference` (`sample_id`) + PRIMARY KEY (`sample_id`) ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; /*!40101 SET character_set_client = @saved_cs_client */; diff --git a/config/databases/tomato_nssnp.sql b/config/databases/tomato_nssnp.sql index 60df4a69..7f75a079 100644 --- a/config/databases/tomato_nssnp.sql +++ b/config/databases/tomato_nssnp.sql @@ -34,8 +34,7 @@ CREATE TABLE `lines_lookup` ( `lines_id` varchar(45) NOT NULL, `species` varchar(35) DEFAULT NULL, `alias` varchar(35) DEFAULT NULL, - PRIMARY KEY (`lines_id`), - CONSTRAINT `lines_id` FOREIGN KEY (`lines_id`) REFERENCES `snps_reference` (`sample_id`) + PRIMARY KEY (`lines_id`) ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; /*!40101 SET character_set_client = @saved_cs_client */; diff --git a/config/init.sh b/config/init.sh index c3e4a06b..62acb7d5 100755 --- a/config/init.sh +++ b/config/init.sh @@ -1,10 +1,11 @@ #!/bin/sh # This script initialized the GitHub environment -# To use locally, set up DB Password below -# The password below is for GitHub Actions. Please do not change. -DB_USER="root" -DB_PASS="root" +# To use locally, set DB_USER/DB_PASS/DB_HOST as environment variables. +# Defaults below are for GitHub Actions — do not change the defaults. +DB_USER=${DB_USER:-"root"} +DB_PASS=${DB_PASS:-"root"} +DB_HOST=${DB_HOST:-"localhost"} # Load the data echo "Welcome to the BAR API. Running init!" @@ -18,36 +19,59 @@ if [ $? -ne 0 ]; then fi echo "Successfully bootstrapped simple eFP databases" -mysql -u $DB_USER -p$DB_PASS < ./config/databases/annotations_lookup.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_ecotypes.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/arachis.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/canola_nssnp.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant2.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_poplar.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_rice.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_soybean.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_tomato.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/fastpheno.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/germination.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/homologs_db.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/interactions_vincent_v2.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/kalanchoe.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/klepikova.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/llama3.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/phelipanche.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/physcomitrella_db.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/poplar_nssnp.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/rice_interactions.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/selaginella.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/shoot_apex.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/silique.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/single_cell.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/soybean_nssnp.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/strawberry.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/striga.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/tomato_nssnp.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/tomato_sequence.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/triphysaria.sql +db_exists() { + mysql -h $DB_HOST -u $DB_USER -p$DB_PASS -e "SELECT SCHEMA_NAME FROM information_schema.SCHEMATA WHERE SCHEMA_NAME='$1';" 2>/dev/null | grep -q "$1" +} + +import_if_missing() { + DB_NAME=$1 + SQL_FILE=$2 + if db_exists "$DB_NAME"; then + echo "[skip] $DB_NAME already exists" + else + echo "[load] importing $DB_NAME..." + mysql -h $DB_HOST -u $DB_USER -p$DB_PASS < "$SQL_FILE" + fi +} + +import_if_missing annotations_lookup ./config/databases/annotations_lookup.sql +import_if_missing arabidopsis_ecotypes ./config/databases/arabidopsis_ecotypes.sql +import_if_missing arachis ./config/databases/arachis.sql +import_if_missing canola_nssnp ./config/databases/canola_nssnp.sql +import_if_missing eplant2 ./config/databases/eplant2.sql +import_if_missing eplant_poplar ./config/databases/eplant_poplar.sql +import_if_missing eplant_rice ./config/databases/eplant_rice.sql +import_if_missing eplant_soybean ./config/databases/eplant_soybean.sql +import_if_missing eplant_tomato ./config/databases/eplant_tomato.sql +import_if_missing fastpheno ./config/databases/fastpheno.sql +import_if_missing germination ./config/databases/germination.sql +import_if_missing homologs_db ./config/databases/homologs_db.sql +import_if_missing interactions_vincent_v2 ./config/databases/interactions_vincent_v2.sql +import_if_missing kalanchoe ./config/databases/kalanchoe.sql +import_if_missing klepikova ./config/databases/klepikova.sql +import_if_missing llama3 ./config/databases/llama3.sql +import_if_missing phelipanche ./config/databases/phelipanche.sql +import_if_missing physcomitrella_db ./config/databases/physcomitrella_db.sql +import_if_missing poplar_nssnp ./config/databases/poplar_nssnp.sql +import_if_missing rice_interactions ./config/databases/rice_interactions.sql +import_if_missing selaginella ./config/databases/selaginella.sql +import_if_missing shoot_apex ./config/databases/shoot_apex.sql +import_if_missing silique ./config/databases/silique.sql +import_if_missing single_cell ./config/databases/single_cell.sql +import_if_missing soybean_nssnp ./config/databases/soybean_nssnp.sql +import_if_missing strawberry ./config/databases/strawberry.sql +import_if_missing striga ./config/databases/striga.sql +import_if_missing tomato_nssnp ./config/databases/tomato_nssnp.sql +import_if_missing tomato_sequence ./config/databases/tomato_sequence.sql +import_if_missing triphysaria ./config/databases/triphysaria.sql +import_if_missing light_series ./config/databases/light_series.sql +import_if_missing maize_RMA_linear ./config/databases/maize_RMA_linear.sql +import_if_missing meristem_db ./config/databases/meristem_db.sql +import_if_missing potato_stress ./config/databases/potato_stress.sql +import_if_missing seedcoat ./config/databases/seedcoat.sql +import_if_missing soybean ./config/databases/soybean.sql +import_if_missing soybean_severin ./config/databases/soybean_severin.sql +import_if_missing tomato_ils ./config/databases/tomato_ils.sql echo "Data are now loaded. Preparing API config" echo "Please manually edit config file!" diff --git a/data/efp_info/db_source_summary.json b/data/efp_info/db_source_summary.json new file mode 100644 index 00000000..677864f1 --- /dev/null +++ b/data/efp_info/db_source_summary.json @@ -0,0 +1,154 @@ +{ + "actinidia_bud_development": "efp", + "actinidia_flower_fruit_development": "efp", + "actinidia_postharvest": "efp", + "actinidia_vegetative_growth": "efp", + "apple": "efp", + "arabidopsis_ecotypes": "efp", + "arachis": "efp", + "atgenexp": "efp", + "atgenexp_hormone": "both", + "atgenexp_pathogen": "both", + "atgenexp_plus": "both", + "atgenexp_stress": "both", + "barley_mas": "efp", + "barley_rma": "efp", + "barley_seed": "eplant", + "barley_spike_meristem": "eplant", + "barley_spike_meristem_v3": "eplant", + "brachypodium": "efp", + "brachypodium_Bd21": "efp", + "brachypodium_grains": "efp", + "brachypodium_metabolites_map": "efp", + "brachypodium_photo_thermocycle": "efp", + "brassica_rapa": "efp", + "cacao_developmental_atlas": "efp", + "cacao_developmental_atlas_sca": "efp", + "cacao_drought_diurnal_atlas": "efp", + "cacao_drought_diurnal_atlas_sca": "efp", + "cacao_infection": "efp", + "cacao_leaf": "efp", + "cacao_meristem_atlas_sca": "efp", + "cacao_seed_atlas_sca": "efp", + "camelina": "both", + "camelina_tpm": "efp", + "cannabis": "both", + "canola_seed": "efp", + "dna_damage": "both", + "durum_wheat_abiotic_stress": "efp", + "durum_wheat_biotic_stress": "efp", + "durum_wheat_development": "efp", + "embryo": "efp", + "eucalyptus": "eplant", + "euphorbia": "efp", + "gc_drought": "eplant", + "germination": "both", + "grape_developmental": "efp", + "guard_cell": "both", + "gynoecium": "efp", + "heterodera_schachtii": "eplant", + "human_body_map_2": "efp", + "human_developmental": "efp", + "kalanchoe": "efp", + "klepikova": "both", + "lateral_root_initiation": "efp", + "light_series": "efp", + "lipid_map": "efp", + "little_millet": "efp", + "lupin_lcm_leaf": "efp", + "lupin_lcm_pod": "efp", + "lupin_lcm_stem": "efp", + "lupin_whole_plant": "efp", + "maize_RMA_linear": "both", + "maize_atlas_v5": "efp", + "maize_buell_lab": "efp", + "maize_early_seed": "efp", + "maize_ears": "both", + "maize_embryonic_leaf_development": "efp", + "maize_enzyme": "efp", + "maize_gdowns": "both", + "maize_iplant": "both", + "maize_kernel_v5": "efp", + "maize_leaf_gradient": "both", + "maize_metabolite": "efp", + "maize_rice_comparison": "efp", + "maize_root": "both", + "maize_stress_v5": "efp", + "mangosteen_aril_vs_rind": "efp", + "mangosteen_callus": "efp", + "mangosteen_diseased_vs_normal": "efp", + "mangosteen_fruit_ripening": "efp", + "mangosteen_seed_development": "efp", + "mangosteen_seed_germination": "efp", + "marchantia_organ_stress": "efp", + "medicago_mas": "both", + "medicago_rma": "efp", + "medicago_root": "eplant", + "medicago_seed": "both", + "meristem_db": "efp", + "mouse_db": "efp", + "oat": "efp", + "phelipanche": "efp", + "physcomitrella_db": "efp", + "poplar": "both", + "poplar_leaf": "eplant", + "poplar_xylem": "eplant", + "potato_dev": "both", + "potato_stress": "both", + "rice_abiotic_stress_sc_pseudobulk": "efp", + "rice_drought_heat_stress": "efp", + "rice_leaf_gradient": "both", + "rice_maize_comparison": "efp", + "rice_mas": "both", + "rice_metabolite": "efp", + "rice_rma": "efp", + "rice_root": "eplant", + "root": "both", + "root_Schaefer_lab": "eplant", + "seed_db": "efp", + "seedcoat": "efp", + "selaginella": "efp", + "shoot_apex": "both", + "silique": "efp", + "single_cell": "both", + "sorghum_atlas_w_BS_cells": "efp", + "sorghum_developmental": "efp", + "sorghum_flowering_activation": "efp", + "sorghum_low_phosphorus": "efp", + "sorghum_phosphate_stress": "efp", + "sorghum_saline_alkali_stress": "efp", + "sorghum_stress": "efp", + "sorghum_strigolactone_variation": "efp", + "sorghum_sulfur_stress": "efp", + "sorghum_vascularization_and_internode": "efp", + "soybean": "both", + "soybean_embryonic_development": "efp", + "soybean_heart_cotyledon_globular": "efp", + "soybean_senescence": "efp", + "soybean_severin": "both", + "strawberry": "efp", + "striga": "efp", + "sugarcane_culms": "eplant", + "sugarcane_leaf": "eplant", + "sunflower": "eplant", + "thellungiella_db": "efp", + "tomato": "efp", + "tomato_ils": "both", + "tomato_ils2": "both", + "tomato_meristem": "efp", + "tomato_renormalized": "both", + "tomato_root": "eplant", + "tomato_root_field_pot": "eplant", + "tomato_s_pennellii": "both", + "tomato_seed": "efp", + "tomato_shade_mutants": "efp", + "tomato_shade_timecourse": "efp", + "triphysaria": "efp", + "triticale": "efp", + "triticale_mas": "efp", + "tung_tree": "efp", + "wheat": "both", + "wheat_abiotic_stress": "efp", + "wheat_embryogenesis": "efp", + "wheat_meiosis": "efp" +} \ No newline at end of file diff --git a/data/efp_info/efp_eplant_species_view_info.json b/data/efp_info/efp_eplant_species_view_info.json new file mode 100644 index 00000000..df49bb2d --- /dev/null +++ b/data/efp_info/efp_eplant_species_view_info.json @@ -0,0 +1,35178 @@ +{ + "efp": { + "efp_arabidopsis": [ + { + "source": "efp", + "species": "arabidopsis", + "database": "atgenexp_stress", + "view_name": "Abiotic Stress II", + "view_file": "Abiotic_Stress_II", + "groups": { + "GSM491684;GSM491685;GSM491686": { + "controls": [ + "GSM491684", + "GSM491685", + "GSM491686" + ], + "treatments": { + "Water_limited_(dry),_Pre-dawn": [ + "GSM491687", + "GSM491688", + "GSM491689" + ], + "Well_watered,_pre-dawn_(control)": [ + "GSM491684", + "GSM491685", + "GSM491686" + ] + } + }, + "GSM491672;GSM491673;GSM491674": { + "controls": [ + "GSM491672", + "GSM491673", + "GSM491674" + ], + "treatments": { + "Well_watered,_Late_day_(control)": [ + "GSM491672", + "GSM491673", + "GSM491674" + ], + "Water_limited_(dry),_Late_day": [ + "GSM491675", + "GSM491676", + "GSM491677" + ] + } + }, + "GSM237280;GSM237281": { + "controls": [ + "GSM237280", + "GSM237281" + ], + "treatments": { + "Root,_non-selenate_treated_(control)": [ + "GSM237280", + "GSM237281" + ], + "Root,_Selenate_treated": [ + "GSM237282", + "GSM237283" + ] + } + }, + "GSM491666;GSM491667;GSM491668": { + "controls": [ + "GSM491666", + "GSM491667", + "GSM491668" + ], + "treatments": { + "Water_limited_(dry),_Midday": [ + "GSM491669", + "GSM491670", + "GSM491671" + ], + "Well_watered,_Midday_(control)": [ + "GSM491666", + "GSM491667", + "GSM491668" + ] + } + }, + "GSM392492;GSM392493": { + "controls": [ + "GSM392492", + "GSM392493" + ], + "treatments": { + "Shoot,_non-selenate_treated_(control)": [ + "GSM392492", + "GSM392493" + ] + } + }, + "GSM40552": { + "controls": [ + "GSM40552" + ], + "treatments": { + "Non_Stressed_(control),_Total_RNA": [ + "GSM40552" + ], + "Hypoxia_Stress,_Total_RNA": [ + "GSM40553" + ] + } + }, + "GSM40554": { + "controls": [ + "GSM40554" + ], + "treatments": { + "Non_Stressed_(control),_Polysomal_RNA": [ + "GSM40554" + ], + "Hypoxia_Stress,_Polysomal_RNA": [ + "GSM40555" + ] + } + }, + "GSM237292;GSM237293": { + "controls": [ + "GSM237292", + "GSM237293" + ], + "treatments": { + "Shoot,_non-_selenate_treated": [ + "GSM237294", + "GSM237295" + ] + } + }, + "GSM491678;GSM491679;GSM491680": { + "controls": [ + "GSM491678", + "GSM491679", + "GSM491680" + ], + "treatments": { + "Well_watered,_midnight_(control)": [ + "GSM491678", + "GSM491679", + "GSM491680" + ], + "Water_limited_(dry),_midnight": [ + "GSM491681", + "GSM491682", + "GSM491683" + ] + } + } + } + }, + { + "source": "efp", + "species": "arabidopsis", + "database": "atgenexp_pathogen", + "view_name": "Biotic Stress II", + "view_file": "Biotic_Stress_II", + "groups": { + "GSM392490;GSM392491": { + "controls": [ + "GSM392490", + "GSM392491" + ], + "treatments": { + "Col_laser_microdissected,_5_d_UI,": [ + "GSM392490", + "GSM392491" + ], + "Col_laser_microdissected,_5_dpi": [ + "GSM392488", + "GSM392489" + ], + "eds16_laser_microdissected,_5_dpi": [ + "GSM392492", + "GSM392493" + ] + } + }, + "GSM392500;GSM392501": { + "controls": [ + "GSM392500", + "GSM392501" + ], + "treatments": { + "Col_whole_leaf_amplified,_5_d_UI": [ + "GSM392500", + "GSM392501" + ], + "Col_whole_leaf_amplified,_5_dpi,": [ + "GSM392498", + "GSM392499" + ], + "Col_leaf_scrape,_5_dpi": [ + "GSM392502", + "GSM392503" + ] + } + }, + "GSM554311_WT_Emwa1_0dpi_rep2": { + "controls": [ + "GSM554311_WT_Emwa1_0dpi_rep2" + ], + "treatments": { + "WT_Emwa1_0dpi_rep1+rep2": [ + "GSM554311_WT_Emwa1_0dpi_rep1", + "GSM554311_WT_Emwa1_0dpi_rep2" + ], + "WT_Emwa1_0.5dpi_rep1+rep2": [ + "GSM554312_WT_Emwa1_0.5dpi_rep2" + ], + "WT_Emwa1_2dpi_rep1+rep2": [ + "GSM554313_WT_Emwa1_2dpi_rep1", + "GSM554313_WT_Emwa1_2dpi_rep2" + ], + "WT_Emwa1_4dpi_rep1+rep2": [ + "GSM554314_WT_Emwa1_4dpi_rep1", + "GSM554314_WT_Emwa1_4dpi_rep2" + ], + "WT_Emwa1_6dpi_rep1+rep2": [ + "GSM554315_WT_Emwa1_6dpi_rep1", + "GSM554315_WT_Emwa1_6dpi_rep2" + ] + } + }, + "GSM554316_rpp4_Emwa1_0dpi_rep1;GSM554316_rpp4_Emwa1_0dpi_rep2": { + "controls": [ + "GSM554316_rpp4_Emwa1_0dpi_rep1", + "GSM554316_rpp4_Emwa1_0dpi_rep2" + ], + "treatments": { + "rpp4_Emwa1_0dpi_rep1+rep2": [ + "GSM554316_rpp4_Emwa1_0dpi_rep1", + "GSM554316_rpp4_Emwa1_0dpi_rep2" + ], + "rpp4_Emwa1_0.5dpi_rep1+rep2": [ + "GSM554317_rpp4_Emwa1_0.5dpi_rep1", + "GSM554317_rpp4_Emwa1_0.5dpi_rep2" + ], + "rpp4_Emwa1_2dpi_rep1+rep2": [ + "GSM554318_rpp4_Emwa1_2dpi_rep1", + "GSM554318_rpp4_Emwa1_2dpi_rep2" + ], + "rpp4_Emwa1_4dpi_rep1+rep2": [ + "GSM554319_rpp4_Emwa1_4dpi_rep1", + "GSM554319_rpp4_Emwa1_4dpi_rep2" + ], + "rpp4_Emwa1_6dpi_rep1+rep2": [ + "GSM554320_rpp4_Emwa1_6dpi_rep1", + "GSM554320_rpp4_Emwa1_6dpi_rep2" + ] + } + }, + "GSM157299;GSM157300;GSM157301": { + "controls": [ + "GSM157299_JPritchard_A-1_CTR_Rep1_ATH1", + "GSM157300_JPritchard_A-2_CTR_Rep2_ATH1", + "GSM157301_Pritchard_A-3_CTR_Rep3_ATH1" + ], + "treatments": { + "Control": [ + "GSM157299_JPritchard_A-1_CTR_Rep1_ATH1", + "GSM157300_JPritchard_A-2_CTR_Rep2_ATH1", + "GSM157301_Pritchard_A-3_CTR_Rep3_ATH1" + ], + "Aphid_infested": [ + "GSM157303_JPritchard_A-5_API_Rep2_ATH1", + "GSM157304_JPritchard_A-6_API_Rep3_ATH1" + ] + } + } + } + }, + { + "source": "efp", + "species": "arabidopsis", + "database": "atgenexp_pathogen", + "view_name": "Biotic Stress", + "view_file": "Biotic_Stress", + "groups": { + "Botrytis_cinerea_at_18_Hours": { + "controls": [ + "CT181-1", + "CT181-2", + "CT182-1" + ], + "treatments": { + "Control_B.c._at_18_Hours": [ + "CT181-1", + "CT181-2", + "CT182-1" + ], + "Treated_B.c._at_18_Hours": [ + "BC181-1", + "BC181-2", + "BC182-1" + ] + } + }, + "Botrytis_cinerea_at_48_Hours": { + "controls": [ + "CT481-1", + "CT482-1", + "CT482-2" + ], + "treatments": { + "Control_B.c._at_48_Hours": [ + "CT481-1", + "CT482-1", + "CT482-2" + ], + "Treated_B.c._at_48_Hours": [ + "BC481-1", + "BC482-1", + "BC482-2" + ] + } + }, + "Half_Leaf_Pseudomonas_syringae_at_4_Hours": { + "controls": [ + "2505", + "2795" + ], + "treatments": { + "Control_Half_P.s_at_4_Hours": [ + "2505", + "2795" + ], + "Avirulent_Half_P.s_at_4_Hours": [ + "2504", + "2796" + ], + "Virulent_Half_P.s_at_4_Hours": [ + "2530", + "2797" + ] + } + }, + "Half_Leaf_Pseudomonas_syringae_at_8_Hours": { + "controls": [ + "2507", + "2792" + ], + "treatments": { + "Control_Half_P.s_at_8_Hours": [ + "2507", + "2792" + ], + "Avirulent_Half_P.s_at_8_Hours": [ + "2506", + "2793" + ], + "Virulent_Half_P.s_at_8_Hours": [ + "2529", + "2794" + ] + } + }, + "Half_Leaf_Pseudomonas_syringae_at_16_Hours": { + "controls": [ + "2527", + "2789" + ], + "treatments": { + "Control_Half_P.s_at_16_Hours": [ + "2527", + "2789" + ], + "Avirulent_Half_P.s_at_16_Hours": [ + "2508", + "2790" + ], + "Virulent_Half_P.s_at_16_Hours": [ + "2528", + "2791" + ] + } + }, + "Half_Leaf_Pseudomonas_syringae_at_24_Hours": { + "controls": [ + "2510", + "2786" + ], + "treatments": { + "Control_Half_P.s_at_24_Hours": [ + "2510", + "2786" + ], + "Avirulent_Half_P.s_at_24_Hours": [ + "2509", + "2787" + ], + "Virulent_Half_P.s_at_24_Hours": [ + "2526", + "2788" + ] + } + }, + "Half_Leaf_Pseudomonas_syringae_at_48_Hours": { + "controls": [ + "2512", + "2783" + ], + "treatments": { + "Control_Half_P.s_at_48_Hours": [ + "2512", + "2783" + ], + "Avirulent_Half_P.s_at_48_Hours": [ + "2511", + "2784" + ], + "Virulent_Half_P.s_at_48_Hours": [ + "2525", + "2785" + ] + } + }, + "Infiltrating_Pseudomonas_syringae_at_2_Hours": { + "controls": [ + "AtGen_A-53_33-1_REP1_ATH1", + "AtGen_A-54_33-2_REP2_ATH1", + "AtGen_A-55_33-3_REP3_ATH1" + ], + "treatments": { + "Control_P.s._at_2_Hours": [ + "AtGen_A-53_33-1_REP1_ATH1", + "AtGen_A-54_33-2_REP2_ATH1", + "AtGen_A-55_33-3_REP3_ATH1" + ], + "Virulent_P.s._at_2_Hours": [ + "AtGen_A-5_21-1_REP1_ATH1", + "AtGen_A-6_21-2_REP2_ATH1", + "AtGen_A-8_21-4_REP3_ATH1" + ], + "Avirulent_P.s._at_2_Hours": [ + "AtGen_A-17_24-1_REP1_ATH1", + "AtGen_A-18_24-2_REP2_ATH1", + "AtGen_A-19_24-3_REP3_ATH1" + ], + "Deficient_P.s._at_2_Hours": [ + 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} + }, + "Vegetative_Bud": { + "controls": [ + "MED_CTRL", + "MED_CTRL" + ], + "treatments": { + "Vegetative_Bud": [ + "Vegetative Bud_rep1", + "Vegetative Bud_rep2", + "Vegetative Bud_rep3" + ] + } + }, + "Petiole": { + "controls": [ + "MED_CTRL", + "MED_CTRL" + ], + "treatments": { + "Petiole": [ + "Petiole_rep1", + "Petiole_rep2", + "Petiole_rep3" + ] + } + }, + "Stem": { + "controls": [ + "MED_CTRL", + "MED_CTRL" + ], + "treatments": { + "Stem": [ + "Stem_rep1", + "Stem_rep2", + "Stem_rep3" + ] + } + }, + "Leaf_with_Petiolules": { + "controls": [ + "MED_CTRL", + "MED_CTRL" + ], + "treatments": { + "Leaf_with_Petiolules": [ + "Leaf_rep1", + "Leaf_rep2", + "Leaf_rep3" + ] + } + }, + "Root": { + "controls": [ + "MED_CTRL", + "MED_CTRL" + ], + "treatments": { + "Root": [ + "Root_rep1", + "Root_rep2", + "Root_rep3" + ] + } + }, + "Non-inoculated_root": { + "controls": [ + "MED_CTRL", + "MED_CTRL" + ], + "treatments": { + "Non-inoculated_root": [ + "Root0d_rep1", + "Root0d_rep2", + "Root0d_rep3" + ] + } + } + } + } + ], + "eplant_eucalyptus": [ + { + "source": "eplant", + "project": "eplant_eucalyptus", + "species": "Eucalyptus_grandis", + "family": "experiment", + "database": "eucalyptus", + "view_name": "Stress", + "view_folder": "Stress", + "groups": { + "Leaf": { + "controls": [ + "Leaf_Mock_rep1", + "Leaf_Mock_rep2", + "Leaf_Mock_rep3" + ], + "treatments": { + "Leaf_-_Control": [ + "Leaf_Mock_rep1", + "Leaf_Mock_rep2", + "Leaf_Mock_rep3" + ], + "Leaf_-_Salicylic_Acid_1h": [ + "Leaf_SA_1h_rep1", + "Leaf_SA_1h_rep2", + "Leaf_SA_1h_rep3" + ], + "Leaf_-_Salicylic_Acid_6h": [ + "Leaf_SA_6h_rep1", + "Leaf_SA_6h_rep2", + "Leaf_SA_6h_rep3" + ], + "Leaf_-_Salicylic_Acid_24h": [ + "Leaf_SA_24h_rep1", + "Leaf_SA_24h_rep2", + "Leaf_SA_24h_rep3" + ], + "Leaf_-_Salicylic_Acid_168h": [ + "Leaf_SA_168h_rep1", + "Leaf_SA_168h_rep2", + "Leaf_SA_168h_rep3" + ], + "Leaf_-_Methyl_Jasmonate_1h": [ + "Leaf_JA_1h_rep1", + "Leaf_JA_1h_rep2", + "Leaf_JA_1h_rep3" + ], + 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"Root_Pidef_6h_rep3" + ], + "Root_-_Phosphate_deficiency_24h": [ + "Root_Pidef_24h_rep1", + "Root_Pidef_24h_rep2", + "Root_Pidef_24h_rep3" + ], + "Root_-_Phosphate_deficiency_48h": [ + "Root_Pidef_48h_rep1", + "Root_Pidef_48h_rep2", + "Root_Pidef_48h_rep3" + ], + "Root_-_Phosphate_deficiency_96h": [ + "Root_Pidef_96h_rep1", + "Root_Pidef_96h_rep2", + "Root_Pidef_96h_rep3" + ], + "Root_-_Phosphate_deficiency_21d": [ + "Root_Pidef_21d_rep1", + "Root_Pidef_21d_rep2", + "Root_Pidef_21d_rep3" + ], + "Root_-_Boron_deficiency_6h": [ + "Root_Bdef_6h_rep1", + "Root_Bdef_6h_rep2", + "Root_Bdef_6h_rep3" + ], + "Root_-_Boron_deficiency_24h": [ + "Root_Bdef_24h_rep1", + "Root_Bdef_24h_rep2", + "Root_Bdef_24h_rep3" + ], + "Root_-_Boron_deficiency_48h": [ + "Root_Bdef_48h_rep1", + "Root_Bdef_48h_rep2", + "Root_Bdef_48h_rep3" + ], + "Root_-_Boron_deficiency_96h": [ + "Root_Bdef_96h_rep1", + "Root_Bdef_96h_rep2", + "Root_Bdef_96h_rep3" + ], + "Root_-_Boron_deficiency_21d": [ + "Root_Bdef_21d_rep1", + "Root_Bdef_21d_rep2", + "Root_Bdef_21d_rep3" + ] + } + }, + "Shoot": { + "controls": [ + "Shoot_Mock_rep1", + "Shoot_Mock_rep2", + "Shoot_Mock_rep3" + ], + "treatments": { + "Shoot_-_Control": [ + "Shoot_Mock_rep1", + "Shoot_Mock_rep2", + "Shoot_Mock_rep3" + ], + "Shoot_-_Phosphate_deficiency_6h": [ + "Shoot_Pidef_6h_rep1", + "Shoot_Pidef_6h_rep2", + "Shoot_Pidef_6h_rep3" + ], + "Shoot_-_Phosphate_deficiency_24h": [ + "Shoot_Pidef_24h_rep1", + "Shoot_Pidef_24h_rep2", + "Shoot_Pidef_24h_rep3" + ], + "Shoot_-_Phosphate_deficiency_48h": [ + "Shoot_Pidef_48h_rep1", + "Shoot_Pidef_48h_rep2", + "Shoot_Pidef_48h_rep3" + ], + "Shoot_-_Phosphate_deficiency_96h": [ + "Shoot_Pidef_96h_rep1", + "Shoot_Pidef_96h_rep2", + "Shoot_Pidef_96h_rep3" + ], + "Shoot_-_Phosphate_deficiency_21d": [ + "Shoot_Pidef_21d_rep1", + "Shoot_Pidef_21d_rep2", + "Shoot_Pidef_21d_rep3" + ], + "Shoot_-_Boron_deficiency_6h": [ + "Shoot_Bdef_6h_rep1", + "Shoot_Bdef_6h_rep2", + "Shoot_Bdef_6h_rep3" + ], + "Shoot_-_Boron_deficiency_24h": [ + "Shoot_Bdef_24h_rep1", + "Shoot_Bdef_24h_rep2", + "Shoot_Bdef_24h_rep3" + ], + "Shoot_-_Boron_deficiency_48h": [ + "Shoot_Bdef_48h_rep1", + "Shoot_Bdef_48h_rep2", + "Shoot_Bdef_48h_rep3" + ], + "Shoot_-_Boron_deficiency_96h": [ + "Shoot_Bdef_96h_rep1", + "Shoot_Bdef_96h_rep2", + "Shoot_Bdef_96h_rep3" + ], + "Shoot_-_Boron_deficiency_21d": [ + "Shoot_Bdef_21d_rep1", + "Shoot_Bdef_21d_rep2", + "Shoot_Bdef_21d_rep3" + ] + } + } + } + }, + { + "source": "eplant", + "project": "eplant_eucalyptus", + "species": "Eucalyptus_grandis", + "family": "plant", + "database": "eucalyptus", + "view_name": "Plant", + "view_folder": null, + "groups": { + "EucalyptusDevelopment": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "Tree_30do_-_Root": [ + "Root_TissueCulture_30d_rep1", + "Root_TissueCulture_30d_rep2", + "Root_TissueCulture_30d_rep3" + ], + "Tree_30do_-_Stem": [ + "Stem_TissueCulture_30d_rep1", + "Stem_TissueCulture_30d_rep2", + "Stem_TissueCulture_30d_rep3" + ], + "Tree_30do_-_Leaf": [ + "Leaf_TissueCulture_30d_rep1", + "Leaf_TissueCulture_30d_rep2", + "Leaf_TissueCulture_30d_rep3" + ], + "Tree_6mo_-_3rd_Internode": [ + "The3rdInternode_SemiannualPlant_rep1", + "The3rdInternode_SemiannualPlant_rep2", + "The3rdInternode_SemiannualPlant_rep3" + ], + "Tree_6mo_-_5th_Internode": [ + "The5thInternode_SemiannualPlant_rep1", + "The5thInternode_SemiannualPlant_rep2", + "The5thInternode_SemiannualPlant_rep3" + ], + "Tree_6mo_-_7th_Internode": [ + "The7thInternode_SemiannualPlant_rep1", + "The7thInternode_SemiannualPlant_rep2", + "The7thInternode_SemiannualPlant_rep3" + ], + "Tree_6mo_-_9th_Internode": [ + "The9thInternode_SemiannualPlant_rep1", + "The9thInternode_SemiannualPlant_rep2", + "The9thInternode_SemiannualPlant_rep3" + ], + "Tree_6mo_-_11th_Internode": [ + "The11thInternode_SemiannualPlant_rep1", + "The11thInternode_SemiannualPlant_rep2", + "The11thInternode_SemiannualPlant_rep3" + ], + 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"durum_wheat_abiotic_stress": { + "source": "efp", + "platform": "rna_seq", + "views": { + "efp_durum_wheat": [ + "Abiotic Stress" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + }, + "durum_wheat_biotic_stress": { + "source": "efp", + "platform": "rna_seq", + "views": { + "efp_durum_wheat": [ + "Biotic Stress" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + }, + "durum_wheat_development": { + "source": "efp", + "platform": "rna_seq", + "views": { + "efp_durum_wheat": [ + "Development" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + }, + "wheat": { + "source": "both", + "platform": "rna_seq", + "views": { + "efp_wheat": [ + "Developmental Atlas" + ], + "eplant_wheat": [ + "EarlyStages", + "MiddleStages", + "LateStages" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + }, + "proj_id_breakdown": { + "classification": "duplicate_view_names", + "views": { + "Developmental Atlas": { + "n_view_samples": 209, + "n_matched_in_real_data_sample": 26, + "proj_ids": [ + "1" + ] + }, + "EarlyStages": { + "n_view_samples": 61, + "n_matched_in_real_data_sample": 9, + "proj_ids": [ + "1" + ] + }, + "MiddleStages": { + "n_view_samples": 88, + "n_matched_in_real_data_sample": 11, + "proj_ids": [ + "1" + ] + }, + "LateStages": { + "n_view_samples": 62, + "n_matched_in_real_data_sample": 6, + "proj_ids": [ + "1" + ] + } + } + } + }, + "wheat_abiotic_stress": { + "source": "efp", + "platform": "rna_seq", + "views": { + "efp_wheat": [ + "Wheat Abiotic Stress" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + }, + "wheat_embryogenesis": { + "source": "efp", + "platform": "rna_seq", + "views": { + "efp_wheat": [ + "Wheat Embryogenesis" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + }, + "wheat_meiosis": { + "source": "efp", + "platform": "rna_seq", + "views": { + "efp_wheat": [ + "Wheat Meiosis" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + }, + "wheat_root": { + "source": "legacy_not_in_dropdown", + "platform": "rna_seq", + "views": {}, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + } + }, + "willow": { + "willow": { + "source": "legacy_not_in_dropdown", + "platform": "rna_seq", + "views": {}, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + } + } +} \ No newline at end of file diff --git a/db_regex_coverage_report.csv b/db_regex_coverage_report.csv new file mode 100644 index 00000000..0b431855 --- /dev/null +++ b/db_regex_coverage_report.csv @@ -0,0 +1,194 @@ +database,source,in_master_list,has_species_mapping,has_efp_project_override,n_samples,n_pass,n_fail,looks_like_probeset,failing_ids +actinidia_bud_development,efp,True,True,False,30,30,0,False, +actinidia_flower_fruit_development,efp,True,True,False,30,30,0,False, +actinidia_postharvest,efp,True,True,False,30,30,0,False, 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+lateral_root_initiation,efp,True,True,True,30,30,0,True, +light_series,efp,True,True,True,30,30,0,True, +lipid_map,efp,True,True,True,30,30,0,False, +little_millet,efp,True,True,False,30,30,0,False, +lupin_lcm_leaf,efp,True,True,False,30,30,0,False, +lupin_lcm_pod,efp,True,True,False,30,30,0,False, +lupin_lcm_stem,efp,True,True,False,30,30,0,False, +lupin_pod_seed,legacy_not_in_dropdown,False,True,False,30,30,0,False, +lupin_whole_plant,efp,True,True,False,30,30,0,False, +maize_RMA_linear,both,True,True,False,30,30,0,False, +maize_RMA_log,legacy_not_in_dropdown,False,True,False,30,30,0,False, +maize_atlas,legacy_not_in_dropdown,False,True,False,30,30,0,False, +maize_atlas_v5,efp,True,True,False,30,30,0,False, +maize_buell_lab,efp,True,True,False,30,30,0,False, +maize_early_seed,efp,True,True,False,30,30,0,False, +maize_ears,both,True,True,False,30,30,0,False, +maize_embryonic_leaf_development,efp,True,True,False,30,30,0,False, +maize_enzyme,efp,True,True,True,17,17,0,False, +maize_gdowns,both,True,True,True,30,30,0,True, +maize_iplant,both,True,True,False,30,30,0,False, +maize_kernel_v5,efp,True,True,False,30,30,0,False, +maize_leaf_gradient,both,True,True,False,30,30,0,False, +maize_lipid_map,legacy_not_in_dropdown,False,True,True,28,28,0,False, +maize_metabolite,efp,True,True,True,26,26,0,False, +maize_nitrogen_use_efficiency,legacy_not_in_dropdown,False,True,False,30,30,0,False, +maize_rice_comparison,efp,True,True,False,30,30,0,False, +maize_root,both,True,True,False,30,30,0,False, +maize_stress_v5,efp,True,True,False,30,30,0,False, +mangosteen_aril_vs_rind,efp,True,True,False,30,30,0,False, +mangosteen_callus,efp,True,True,False,30,30,0,False, +mangosteen_diseased_vs_normal,efp,True,True,False,30,30,0,False, +mangosteen_fruit_ripening,efp,True,True,False,30,30,0,False, +mangosteen_seed_development,efp,True,True,False,30,30,0,False, +mangosteen_seed_development_germination,legacy_not_in_dropdown,False,True,False,30,30,0,False, +mangosteen_seed_germination,efp,True,True,False,30,30,0,False, +marchantia_organ_stress,efp,True,True,False,30,30,0,False, +medicago_mas,both,True,True,True,30,30,0,True, +medicago_rma,efp,True,True,True,30,30,0,True, +medicago_root,eplant,True,True,False,30,30,0,False, +medicago_root_v5,legacy_not_in_dropdown,False,True,False,30,30,0,False, +medicago_seed,both,True,True,False,30,30,0,False, +meristem_db,efp,True,True,True,30,30,0,True, +meristem_db_new,legacy_not_in_dropdown,False,True,True,30,30,0,True, +mouse_db,efp,True,True,False,30,30,0,False, +oat,efp,True,True,False,30,30,0,False, +phelipanche,efp,True,True,False,30,30,0,False, +physcomitrella_db,efp,True,True,True,30,30,0,False, +poplar,both,True,True,True,30,30,0,True, +poplar_hormone,legacy_not_in_dropdown,False,True,True,30,30,0,False, +poplar_leaf,eplant,True,True,False,30,30,0,False, +poplar_xylem,eplant,True,True,False,30,30,0,False, +potato_dev,both,True,True,False,30,30,0,False, +potato_stress,both,True,True,False,30,30,0,False, +potato_wounding,legacy_not_in_dropdown,False,True,False,30,30,0,False, +quinoa_nutrient,legacy_not_in_dropdown,False,True,False,30,30,0,False, +rice_abiotic_stress_sc_pseudobulk,efp,True,True,False,30,30,0,False, +rice_drought_heat_stress,efp,True,True,False,30,30,0,False, +rice_leaf_gradient,both,True,True,False,30,30,0,False, +rice_maize_comparison,efp,True,True,False,30,30,0,False, +rice_mas,both,True,True,True,30,30,0,True, +rice_metabolite,efp,True,True,True,20,20,0,False, +rice_rma,efp,True,True,True,30,30,0,True, +rice_root,eplant,True,True,False,30,30,0,False, +rohan,legacy_not_in_dropdown,False,True,True,30,30,0,True, +root,both,True,True,True,30,30,0,True, +root_Schaefer_lab,eplant,True,True,False,29,29,0,False, +rpatel,legacy_not_in_dropdown,False,True,True,29,29,0,True, +seed_db,efp,True,True,True,30,30,0,True, +seedcoat,efp,True,True,True,30,29,1,True,Print control plate +selaginella,efp,True,True,False,30,30,0,False, +shoot_apex,both,True,True,False,30,30,0,False, +silique,efp,True,True,False,30,30,0,False, +single_cell,both,True,True,False,30,30,0,False, +sorghum_atlas_w_BS_cells,efp,True,True,False,30,30,0,False, +sorghum_comparative_transcriptomics,legacy_not_in_dropdown,False,True,False,30,30,0,False, +sorghum_developmental,efp,True,True,False,30,30,0,False, +sorghum_developmental_2,legacy_not_in_dropdown,False,True,False,30,30,0,False, +sorghum_flowering_activation,efp,True,True,False,30,30,0,False, +sorghum_low_phosphorus,efp,True,True,False,30,30,0,False, +sorghum_nitrogen_stress,legacy_not_in_dropdown,False,True,False,30,30,0,False, +sorghum_nitrogen_use_efficiency,legacy_not_in_dropdown,False,True,False,30,30,0,False, +sorghum_phosphate_stress,efp,True,True,False,30,30,0,False, +sorghum_plasma,legacy_not_in_dropdown,False,True,False,30,30,0,False, +sorghum_saline_alkali_stress,efp,True,True,False,30,30,0,False, +sorghum_stress,efp,True,True,False,30,30,0,False, +sorghum_strigolactone_variation,efp,True,True,False,30,30,0,False, +sorghum_sulfur_stress,efp,True,True,False,30,30,0,False, +sorghum_temperature_stress,legacy_not_in_dropdown,False,True,False,30,30,0,False, +sorghum_vascularization_and_internode,efp,True,True,False,30,30,0,False, +soybean,both,True,True,False,30,30,0,False, +soybean_embryonic_development,efp,True,True,False,30,30,0,False, +soybean_heart_cotyledon_globular,efp,True,True,False,30,30,0,False, +soybean_senescence,efp,True,True,False,30,30,0,False, +soybean_severin,both,True,True,False,30,30,0,False, +spruce,legacy_not_in_dropdown,False,True,False,30,30,0,False, +strawberry,efp,True,True,False,30,30,0,False, +striga,efp,True,True,False,30,30,0,False, +sugarcane_culms,eplant,True,True,False,30,30,0,False, +sugarcane_leaf,eplant,True,True,False,30,30,0,False, +sunflower,eplant,True,True,False,30,30,0,False, +thellungiella_db,efp,True,True,True,30,30,0,False, +tomato,efp,True,True,True,30,30,0,False, +tomato_ils,both,True,True,False,30,30,0,False, +tomato_ils2,both,True,True,False,30,30,0,False, +tomato_ils3,legacy_not_in_dropdown,False,True,False,30,30,0,False, +tomato_meristem,efp,True,True,False,30,30,0,False, +tomato_renormalized,both,True,True,True,30,30,0,False, +tomato_root,eplant,True,True,False,30,30,0,False, +tomato_root_field_pot,eplant,True,True,False,30,30,0,False, +tomato_s_pennellii,both,True,True,False,30,30,0,False, +tomato_seed,efp,True,True,False,30,30,0,False, +tomato_shade_mutants,efp,True,True,False,30,30,0,False, +tomato_shade_timecourse,efp,True,True,False,30,30,0,False, +tomato_trait,legacy_not_in_dropdown,False,True,True,16,16,0,False, +triphysaria,efp,True,True,False,30,30,0,False, +triticale,efp,True,True,True,30,30,0,True, +triticale_mas,efp,True,True,True,30,30,0,True, +tung_tree,efp,True,True,False,30,30,0,False, +wheat,both,True,True,False,30,30,0,False, +wheat_abiotic_stress,efp,True,True,False,30,30,0,False, +wheat_embryogenesis,efp,True,True,False,30,30,0,False, +wheat_meiosis,efp,True,True,False,30,30,0,False, +wheat_root,legacy_not_in_dropdown,False,True,False,30,30,0,False, +willow,legacy_not_in_dropdown,False,True,False,30,30,0,False, diff --git a/efp_regex_audit_prod.csv b/efp_regex_audit_prod.csv new file mode 100644 index 00000000..81912863 --- /dev/null +++ b/efp_regex_audit_prod.csv @@ -0,0 +1,60 @@ +project,inputRegEx +efp,"^([Aa][Tt][12345CM][Gg][0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$" +efp_Eutrema,^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$ +efp_actinidia,"^(Acc\d+\.\d{0,3})$" +efp_apple,"^(MfusH1_\d\dg\d{1,8})$" +efp_arabidopsis,"^([Aa][Tt][12345CM][Gg][0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$" +efp_arabidopsis_lipid,"^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$" +efp_arachis,^(Adur\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Aipa_c\d+_g\d+_i\d+)$|^(Aipa\d+_comp\d+_c\d+_seq\d+)$ +efp_barley,"^((HM|HV).*)$|^(HV.*_at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4})_at)$|^([0-9]{4,5}\.AF[0-9]{5}(_|_x_)at)$|^(A[0-9]{5}\.[0-9]{1}(_|_x_|_s_)at)$|^(([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)(_|_x_|_s_|_CDS-[0-9]{1,2}_|_CDS-[0-9]{1,2}_s_)at)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^(ChlorContig[0-9]{1,2}(_|_x_|_s_)at)$|^(((MitoContig|Contig)[0-9]{1,6})(_|_x_|_s_)at)$|^(D[0-9]{5}_at)$|^(Dhn[0-9]{2}\(Morex\)(_|_s_)at)$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2}(_|_s_|_x_)at)$|^(Franka(_|_b_)3pri[0-9]{1,2}(_|_s_|_x_)at)$|^(H[A-Z]{1}[0-9]{1-4}[A-Z]{1}[0-9]{1,2}[a-z]{1}(_|_x_|_s_)at)$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}r(_|_x_|_s_)at)$|^(Mla([0-9]{1,2}|[0-9]{1,2}DH)(_orf_|_div5_|_5pri_|_5pri-|_consrvd_|_3pri12_)(3pri12|3pr|UTR_intron2|UTR_intron1|5pri_end)(_|_x_|_s_)at)$|^((Mla|Mlk)(_div5|_3pri12)(_|_x_|_s__at))$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1}(_|_x_|_s_)at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2}(_|_x_|_s_)at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4}))$|^([0-9]{4,5}\.AF[0-9]{5})$|^(A[0-9]{5}\.[0-9]{1})$|^([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX))$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre))$|^(ChlorContig[0-9]{1,2})$|^((MitoContig|Contig)[0-9]{1,6})$|^(D[0-9]{5})$|^(Dhn[0-9]{2}\(Morex\))$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2})$|^(Franka(_|_b_)3pri[0-9]{1,2})$|^(H[A-Z]{1}[0-9]{1-4}[A-Z]{1}[0-9]{1,2}[a-z]{1})$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}r)$|^(Mla([0-9]{1,2}|[0-9]{1,2}DH)(_orf_|_div5_|_5pri_|_5pri-|_consrvd_|_3pri12_)(3pri12|3pr|UTR_intron2|UTR_intron1|5pri_end))$|^((Mla|Mlk)(_div5|_3pri12))$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1})$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2})$|^(HO)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(AK[0-9]{6}\.1)$|^(AJ[0-9]{6}\.1)$" +efp_brachypodium,^(Bradi\d+g\d+.\d)$|^(Bradi\d+s\d+.\d)$|^(Bradi\d+.g\d+)$ +efp_brachypodium_metabolites,"^[a-z\s]{0,40}$" +efp_brassica_rapa,"^(Bra.\d+g\d{0,10})$" +efp_cacao_ccn,"^(CCN-51_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +efp_cacao_sca,"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +efp_cacao_tc,^(Tc\d+v2_g\d+)$ +efp_camelina,"^(Csa\d{0,5}[gs]\d{0,6}.\d{0,3})$|^(At\d[cgm]\d{0,6})$" +efp_cannabis,(^C\d+$)|(^scaffold\d+$)|(^AGQN\d+$) +efp_canola,"^(Bna\D\d{1,3}g\d{1,8}\D)$|^(Bna\Dnng\d{1,8}\D)$" +efp_durum_wheat,"^(TrturSVE\d\D\d{1,3}G\d{1,12})$|^(TrturSVE\d\D\d{1,3}G\d{1,12}_ncBOCREA)$" +efp_euphorbia,"^(Ep_chr\d_g\d{1,8})$" +efp_eutrema,^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$ +efp_grape,"^(VIT_\d{1,2}s\d{4}g\d{5})$|^CHRUN[a-z0-9_]{1,20}$|^CHR\d{1,2}[a-z0-9_]{1,2}$" +efp_human,"^(\D{0,12}\d{0,12})$|^(\d{1,12})$" +efp_kalanchoe,^(Kaladp\d+s\d+)$ +efp_little_millet,^(TRINITY_DN\d+_c\d+_g\d+_i\d+)$ +efp_lupin,"^(Luan_Oskar_.{1,12}_\d{1,12})$" +efp_maize,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$" +efp_maize_enzyme,"^[a-z\-\(\)\s]{0,37}$" +efp_maize_metabolite,"^[a-z0-9,\s\-\(\)]{0,40}$" +efp_maize_transcriptomics,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$" +efp_mangosteen,"^(DN\d{1,10})$" +efp_marchantia,"^(Mp.{1,3}g\d{1,7}\.?\d{1,3}?)$" +efp_medicago,"^(Medtr\d{1}g\d{6})$|^(Medtr\d{1}g\d{6}\.[0-9]{1})$|^(Mtr.\d{4,5}.1.[S1|S1_x|s1|s1_x]_at)$|^(AFFX-[Bio|Cre|Dap|Lys|Phe|Thr|Trpn][B|C|Dn|X]-[3|5|M]_at)$|^(AFFX-[Msa|Mtr]-[actin|gapc|gsta|ubq11|TrpnX]-[3|5|M]_[at|x_at|s_at])$|^(AFFX-Mtr|AFFX-r2-[Bs|Ec|P1]-[cre|dap|lys|phe|thr|bioB|bioC|bioD]-[3|5|M]_[at|s_at|x_at])$|^(AFFX-Mtr-ubq11-[3|5|M]_[at|s_at|x_at])$|^(AFFX-r2-Tag[A-Z]{1,2}_at|-3_at|-5_at|-M_at)$|^(Medtr_v1_\d{6})$" +efp_oat,"(^N0\.HOG\d{1,10}$|^\D{1,10}\.*\d{1,10}.{1,10}\d{1,10}$)" +efp_phelipanche,"^(OrAeBC\d+_\d+\.\d{1,5})|(At\d[gcm]\d{1,6})$" +efp_physcomitrella,^(Pp)\d+s\d+_\d+V\d\.\d$|^Phypa_\d+$ +efp_poplar,"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^((eugene3)\.e{6,12})$|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$|^((grail3.)\d{8,12})$|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$|^(Potri\.[0-9]{3}G[0-9]{6}\.[0-9]{1})$" +efp_potato,^(PGSC0003DMG4\d{8})$ +efp_rice,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" +efp_rice_metabolite,"^[a-z0-9,\s\-]{0,30}$" +efp_rice_transcriptomics,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" +efp_seedcoat,"^(At[12345CM]g[0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(\D\d+_\d+)$" +efp_selaginella,^(Smo\d+)$ +efp_sorghum,"^(Sobic.\d{0,5}G\d{0,10}$|^Sobic.K\d{0,10}$|^ENSRNA\d{0,12}$|^SORBI_\d{1,6}G\d{1,10})$" +efp_soybean,"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$|^(Glyma\.\d{1,3}g\d{1,8}))$" +efp_strawberry,"^(FvH4_c?\d{1,3}g\d{1,7})$|^(gene\d{1,10})$" +efp_striga,"^(StHeBC3\_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" +efp_tomato,"^(Solyc\d{2}g\d{6}\.?\d{0,3})$|^(TU\d{6})$" +efp_triphysaria,"^(TrVeBC\d+_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" +efp_triticale,^(Ta.\d+.\d+.\D+\d+_at)$ +efp_tung_tree,^(Vf\d+G\d+)$ +efp_wheat,"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$" +efpbarley,"^((HM|HV).*)$|^(HV.*_at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4})_at)$|^([0-9]{4,5}\.AF[0-9]{5}(_|_x_)at)$|^(A[0-9]{5}\.[0-9]{1}(_|_x_|_s_)at)$|^(([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)(_|_x_|_s_|_CDS-[0-9]{1,2}_|_CDS-[0-9]{1,2}_s_)at)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^(ChlorContig[0-9]{1,2}(_|_x_|_s_)at)$|^(((MitoContig|Contig)[0-9]{1,6})(_|_x_|_s_)at)$|^(D[0-9]{5}_at)$|^(Dhn[0-9]{2}\(Morex\)(_|_s_)at)$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2}(_|_s_|_x_)at)$|^(Franka(_|_b_)3pri[0-9]{1,2}(_|_s_|_x_)at)$|^(H[A-Z]{1}[0-9]{1-4}[A-Z]{1}[0-9]{1,2}[a-z]{1}(_|_x_|_s_)at)$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}r(_|_x_|_s_)at)$|^(Mla([0-9]{1,2}|[0-9]{1,2}DH)(_orf_|_div5_|_5pri_|_5pri-|_consrvd_|_3pri12_)(3pri12|3pr|UTR_intron2|UTR_intron1|5pri_end)(_|_x_|_s_)at)$|^((Mla|Mlk)(_div5|_3pri12)(_|_x_|_s__at))$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1}(_|_x_|_s_)at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2}(_|_x_|_s_)at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4}))$|^([0-9]{4,5}\.AF[0-9]{5})$|^(A[0-9]{5}\.[0-9]{1})$|^([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX))$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre))$|^(ChlorContig[0-9]{1,2})$|^((MitoContig|Contig)[0-9]{1,6})$|^(D[0-9]{5})$|^(Dhn[0-9]{2}\(Morex\))$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2})$|^(Franka(_|_b_)3pri[0-9]{1,2})$|^(H[A-Z]{1}[0-9]{1-4}[A-Z]{1}[0-9]{1,2}[a-z]{1})$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}r)$|^(Mla([0-9]{1,2}|[0-9]{1,2}DH)(_orf_|_div5_|_5pri_|_5pri-|_consrvd_|_3pri12_)(3pri12|3pr|UTR_intron2|UTR_intron1|5pri_end))$|^((Mla|Mlk)(_div5|_3pri12))$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1})$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2})$|^(HO)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(AK[0-9]{6}\.1)$|^(AJ[0-9]{6}\.1)$" +efpconfig,".{0,16}" +efpmedicago,"^(Medtr\d{1}g\d{6})$|^(Medtr\d{1}g\d{6}\.[0-9]{1})$|^(Mtr.\d{4,5}.1.[S1|S1_x|s1|s1_x]_at)$|^(AFFX-[Bio|Cre|Dap|Lys|Phe|Thr|Trpn][B|C|Dn|X]-[3|5|M]_at)$|^(AFFX-[Msa|Mtr]-[actin|gapc|gsta|ubq11|TrpnX]-[3|5|M]_[at|x_at|s_at])$|^(AFFX-Mtr|AFFX-r2-[Bs|Ec|P1]-[cre|dap|lys|phe|thr|bioB|bioC|bioD]-[3|5|M]_[at|s_at|x_at])$|^(AFFX-Mtr-ubq11-[3|5|M]_[at|s_at|x_at])$|^(AFFX-r2-Tag[A-Z]{1,2}_at|-3_at|-5_at|-M_at)$|^(Medtr_v1_\d{6})$" +efppop,"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^((eugene3)\.e{6,12})$|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$|^((grail3.)\d{8,12})$|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$|^(Potri\.[0-9]{3}G[0-9]{6}\.[0-9]{1})$" +efprice,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" +efpsoybean,"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$|^(Glyma\.\d{1,3}g\d{1,8}))$" +maizeefp,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$" +mouse_efp,"^(XM_\d{0,8}\.\d{0,3})$|^(\d{1,10}\D\d{0,4}\D{0,4})$|^(\D{1,8}\d{0,8}\D{0,8})$|^(ENSMUSG\d{1,15})$|^(NM_\d{0,12}\d.\d{0,3})$" \ No newline at end of file diff --git a/proj_id_view_mapping.json b/proj_id_view_mapping.json new file mode 100644 index 00000000..2ec45e72 --- /dev/null +++ b/proj_id_view_mapping.json @@ -0,0 +1,1025 @@ +{ + "atgenexp_hormone": { + "classification": "partial_overlap", + "views": { + "Chemical": { + "n_view_samples": 55, + "n_matched_in_real_data_sample": 11, + "proj_ids": [ + "0", + "185", + "187", + "190", + "192" + ] + }, + "Hormone": { + "n_view_samples": 131, + "n_matched_in_real_data_sample": 14, + "proj_ids": [ + "0", + "172", + "176", + "177", + "178", + "179", + "181", + "183", + "184" + ] + } + } + }, + "atgenexp_pathogen": { + "classification": "multi_project", + "views": { + "Biotic Stress II": { + "n_view_samples": 36, + "n_matched_in_real_data_sample": 7, + "proj_ids": [ + "GEO:GSE15680", + "GEO:GSE22274", + "GEO:GSE6823" + ] + }, + "Biotic Stress": { + "n_view_samples": 195, + "n_matched_in_real_data_sample": 21, + "proj_ids": [ + "120", + "122", + "123", + "167", + "168", + "169" + ] + }, + "Biotic Stress Botrytis cinerea": { + "n_view_samples": 12, + "n_matched_in_real_data_sample": 2, + "proj_ids": [ + "167" + ] + }, + "Biotic Stress Myzus persicaere": { + "n_view_samples": 5, + "n_matched_in_real_data_sample": 1, + "proj_ids": [ + "GEO:GSE6823" + ] + }, + "Biotic Stress Elicitors": { + "n_view_samples": 42, + "n_matched_in_real_data_sample": 6, + "proj_ids": [ + "122" + ] + }, + "Biotic Stress Erysiphe orontii": { + "n_view_samples": 48, + "n_matched_in_real_data_sample": 4, + "proj_ids": [ + "169" + ] + }, + "Biotic Stress Hyaloperonospora arabidopsidis": { + "n_view_samples": 19, + "n_matched_in_real_data_sample": 5, + "proj_ids": [ + "GEO:GSE22274" + ] + }, + "Biotic Stress Phytophthora infestans": { + "n_view_samples": 18, + "n_matched_in_real_data_sample": 2, + "proj_ids": [ + "123" + ] + }, + "Biotic Stress Pseudomonas syringae": { + "n_view_samples": 75, + "n_matched_in_real_data_sample": 7, + "proj_ids": [ + "120", + "168" + ] + }, + "Biotic Stress Golovinomyces orontii": { + "n_view_samples": 12, + "n_matched_in_real_data_sample": 1, + "proj_ids": [ + "GEO:GSE15680" + ] + } + } + }, + "atgenexp_plus": { + "classification": "multi_project", + "views": { + "Developmental Mutants": { + "n_view_samples": 124, + "n_matched_in_real_data_sample": 4, + "proj_ids": [ + "GEO:GSE30547", + "GEO:GSE47632" + ] + }, + "Developmental Map": { + "n_view_samples": 140, + "n_matched_in_real_data_sample": 6, + "proj_ids": [ + "1" + ] + }, + "Tissue Specific": { + "n_view_samples": 4, + "n_matched_in_real_data_sample": 0, + "proj_ids": [] + }, + "Tissue Specific Microgametogenesis": { + "n_view_samples": 8, + "n_matched_in_real_data_sample": 0, + "proj_ids": [] + }, + "Tissue Specific Embryo Development": { + "n_view_samples": 28, + "n_matched_in_real_data_sample": 0, + "proj_ids": [] + }, + "Tissue Specific Guard And Mesophyll Cells": { + "n_view_samples": 8, + "n_matched_in_real_data_sample": 1, + "proj_ids": [ + "PID:18284694" + ] + }, + "Tissue Specific Pollen Germination": { + "n_view_samples": 15, + "n_matched_in_real_data_sample": 2, + "proj_ids": [ + "GEO:GSE17343" + ] + }, + "Tissue Specific Stem Epidermis": { + "n_view_samples": 9, + "n_matched_in_real_data_sample": 0, + "proj_ids": [] + }, + "Tissue Specific Trichomes": { + "n_view_samples": 18, + "n_matched_in_real_data_sample": 0, + "proj_ids": [] + }, + "Tissue Specific Stigma And Ovaries": { + "n_view_samples": 8, + "n_matched_in_real_data_sample": 1, + "proj_ids": [ + "GEO:GSE3056" + ] + }, + "Tissue Specific Shoot Apical Meristem": { + "n_view_samples": 9, + "n_matched_in_real_data_sample": 0, + "proj_ids": [] + }, + "Tissue Specific Xylem And Cork": { + "n_view_samples": 37, + "n_matched_in_real_data_sample": 4, + "proj_ids": [ + "92" + ] + }, + "AtGenExpress": { + "n_view_samples": 140, + "n_matched_in_real_data_sample": 6, + "proj_ids": [ + "1" + ] + } + } + }, + "atgenexp_stress": { + "classification": "multi_project", + "views": { + "Abiotic Stress II": { + "n_view_samples": 38, + "n_matched_in_real_data_sample": 5, + "proj_ids": [ + "GEO:GSE15680", + "GEO:GSE19700" + ] + }, + "Abiotic Stress": { + "n_view_samples": 272, + "n_matched_in_real_data_sample": 21, + "proj_ids": [ + "0", + "1", + "2", + "3", + "4", + "5", + "6", + "7", + "8", + "9" + ] + } + } + }, + "barley_spike_meristem": { + "classification": "duplicate_view_names", + "views": { + "Spike Meristem": { + "n_view_samples": 138, + "n_matched_in_real_data_sample": 18, + "proj_ids": [ + "1" + ] + }, + "Spike Meristem Shade Response": { + "n_view_samples": 147, + "n_matched_in_real_data_sample": 16, + "proj_ids": [ + "1" + ] + } + } + }, + "barley_spike_meristem_v3": { + "classification": "duplicate_view_names", + "views": { + "Spike Meristem Shade Response": { + "n_view_samples": 143, + "n_matched_in_real_data_sample": 16, + "proj_ids": [ + "1" + ] + }, + "Spike Meristem": { + "n_view_samples": 134, + "n_matched_in_real_data_sample": 17, + "proj_ids": [ + "1" + ] + } + } + }, + "camelina": { + "classification": "duplicate_view_names", + "views": { + "Developmental Atlas FPKM": { + "n_view_samples": 37, + "n_matched_in_real_data_sample": 17, + "proj_ids": [ + "1" + ] + }, + "Plant": { + "n_view_samples": 37, + "n_matched_in_real_data_sample": 17, + "proj_ids": [ + "1" + ] + } + } + }, + "cannabis": { + "classification": "duplicate_view_names", + "views": { + "Cannabis Atlas": { + "n_view_samples": 7, + "n_matched_in_real_data_sample": 7, + "proj_ids": [ + "1" + ] + }, + "Plant": { + "n_view_samples": 7, + "n_matched_in_real_data_sample": 7, + "proj_ids": [ + "1" + ] + } + } + }, + "eucalyptus": { + "classification": "duplicate_view_names", + "views": { + "Stress": { + "n_view_samples": 105, + "n_matched_in_real_data_sample": 13, + "proj_ids": [ + "1" + ] + }, + "Plant": { + "n_view_samples": 90, + "n_matched_in_real_data_sample": 16, + "proj_ids": [ + "1" + ] + } + } + }, + "guard_cell": { + "classification": "multi_project", + "views": { + "Guard Cell": { + "n_view_samples": 96, + "n_matched_in_real_data_sample": 26, + "proj_ids": [ + "1", + "2", + "GEO:GSE29814", + "GEO:GSE58855", + "PID:18284694" + ] + }, + "Guard Cell Meristemoids": { + "n_view_samples": 12, + "n_matched_in_real_data_sample": 5, + "proj_ids": [ + "GEO:GSE29814" + ] + }, + "Guard Cell Mutant And Wild Type Guard Cell ABA Response": { + "n_view_samples": 48, + "n_matched_in_real_data_sample": 13, + "proj_ids": [ + "1" + ] + }, + "Guard Cell Suspension Cell ABA Response With ROS Scavenger": { + "n_view_samples": 12, + "n_matched_in_real_data_sample": 1, + "proj_ids": [ + "2" + ] + } + } + }, + "human_developmental": { + "classification": "insufficient_data", + "views": { + "Circulatory Respiratory": { + "n_view_samples": 0, + "n_matched_in_real_data_sample": 0, + "proj_ids": [] + }, + "Nervous": { + "n_view_samples": 0, + "n_matched_in_real_data_sample": 0, + "proj_ids": [] + }, + "Reproductive": { + "n_view_samples": 0, + "n_matched_in_real_data_sample": 0, + "proj_ids": [] + }, + "Skeletal Immune Digestive": { + "n_view_samples": 0, + "n_matched_in_real_data_sample": 0, + "proj_ids": [] + } + } + }, + "klepikova": { + "classification": "duplicate_view_names", + "views": { + "Klepikova Atlas": { + "n_view_samples": 139, + "n_matched_in_real_data_sample": 24, + "proj_ids": [ + "1" + ] + }, + "Klepikova": { + "n_view_samples": 139, + "n_matched_in_real_data_sample": 24, + "proj_ids": [ + "1" + ] + } + } + }, + "maize_RMA_linear": { + "classification": "duplicate_view_names", + "views": { + "Sekhon et al Atlas": { + "n_view_samples": 181, + "n_matched_in_real_data_sample": 27, + "proj_ids": [ + "1" + ] + }, + "Sekhon Atlas": { + "n_view_samples": 181, + "n_matched_in_real_data_sample": 27, + "proj_ids": [ + "1" + ] + } + } + }, + "maize_buell_lab": { + "classification": "duplicate_view_names", + "views": { + "Hoopes et al Stress": { + "n_view_samples": 52, + "n_matched_in_real_data_sample": 4, + "proj_ids": [ + "1" + ] + }, + "Hoopes et al Atlas": { + "n_view_samples": 222, + "n_matched_in_real_data_sample": 24, + "proj_ids": [ + "1" + ] + } + } + }, + "maize_early_seed": { + "classification": "multi_project", + "views": { + "Early Seed": { + "n_view_samples": 32, + "n_matched_in_real_data_sample": 10, + "proj_ids": [ + "1" + ] + }, + "Maize Kernel": { + "n_view_samples": 25, + "n_matched_in_real_data_sample": 12, + "proj_ids": [ + "2" + ] + } + } + }, + "maize_ears": { + "classification": "duplicate_view_names", + "views": { + "Tassel and Ear Primordia": { + "n_view_samples": 8, + "n_matched_in_real_data_sample": 8, + "proj_ids": [ + "1" + ] + }, + "Tassel And Ear Primordia": { + "n_view_samples": 8, + "n_matched_in_real_data_sample": 8, + "proj_ids": [ + "1" + ] + } + } + }, + "maize_gdowns": { + "classification": "duplicate_view_names", + "views": { + "Downs et al Atlas": { + "n_view_samples": 151, + "n_matched_in_real_data_sample": 29, + "proj_ids": [ + "GD01" + ] + }, + "Plant": { + "n_view_samples": 151, + "n_matched_in_real_data_sample": 29, + "proj_ids": [ + "GD01" + ] + } + } + }, + "maize_iplant": { + "classification": "duplicate_view_names", + "views": { + "maize iplant": { + "n_view_samples": 7, + "n_matched_in_real_data_sample": 7, + "proj_ids": [ + "1", + "2" + ] + }, + "Leaf MeBS": { + "n_view_samples": 7, + "n_matched_in_real_data_sample": 7, + "proj_ids": [ + "1", + "2" + ] + } + } + }, + "maize_leaf_gradient": { + "classification": "duplicate_view_names", + "views": { + "maize leaf gradient": { + "n_view_samples": 16, + "n_matched_in_real_data_sample": 16, + "proj_ids": [ + "1" + ] + }, + "Leaf Gradient": { + "n_view_samples": 16, + "n_matched_in_real_data_sample": 16, + "proj_ids": [ + "1" + ] + } + } + }, + "maize_root": { + "classification": "duplicate_view_names", + "views": { + "Maize Root": { + "n_view_samples": 16, + "n_matched_in_real_data_sample": 14, + "proj_ids": [ + "1" + ] + }, + "Root": { + "n_view_samples": 16, + "n_matched_in_real_data_sample": 14, + "proj_ids": [ + "1" + ] + } + } + }, + "medicago_mas": { + "classification": "duplicate_view_names", + "views": { + "medicago mas": { + "n_view_samples": 55, + "n_matched_in_real_data_sample": 24, + "proj_ids": [ + "1" + ] + }, + "Plant": { + "n_view_samples": 55, + "n_matched_in_real_data_sample": 24, + "proj_ids": [ + "1" + ] + } + } + }, + "medicago_root": { + "classification": "duplicate_view_names", + "views": { + "Root": { + "n_view_samples": 31, + "n_matched_in_real_data_sample": 4, + "proj_ids": [ + "1" + ] + }, + "Root Component": { + "n_view_samples": 81, + "n_matched_in_real_data_sample": 13, + "proj_ids": [ + "1" + ] + } + } + }, + "medicago_seed": { + "classification": "duplicate_view_names", + "views": { + "medicago seed": { + "n_view_samples": 52, + "n_matched_in_real_data_sample": 22, + "proj_ids": [ + "1" + ] + }, + "Seed": { + "n_view_samples": 52, + "n_matched_in_real_data_sample": 22, + "proj_ids": [ + "1" + ] + } + } + }, + "poplar": { + "classification": "multi_project", + "views": { + "Poplar": { + "n_view_samples": 26, + "n_matched_in_real_data_sample": 10, + "proj_ids": [ + "GEO:GSE13990" + ] + }, + "PoplarTreatment": { + "n_view_samples": 48, + "n_matched_in_real_data_sample": 12, + "proj_ids": [ + "GEO:GSE15242" + ] + }, + "Plant": { + "n_view_samples": 26, + "n_matched_in_real_data_sample": 10, + "proj_ids": [ + "GEO:GSE13990" + ] + }, + "Poplar Treatment": { + "n_view_samples": 48, + "n_matched_in_real_data_sample": 12, + "proj_ids": [ + "GEO:GSE15242" + ] + } + } + }, + "potato_dev": { + "classification": "duplicate_view_names", + "views": { + "Potato Developmental": { + "n_view_samples": 32, + "n_matched_in_real_data_sample": 18, + "proj_ids": [ + "1" + ] + }, + "Plant": { + "n_view_samples": 32, + "n_matched_in_real_data_sample": 18, + "proj_ids": [ + "1" + ] + } + } + }, + "rice_leaf_gradient": { + "classification": "duplicate_view_names", + "views": { + "rice leaf gradient": { + "n_view_samples": 12, + "n_matched_in_real_data_sample": 12, + "proj_ids": [ + "1" + ] + }, + "Leaf Gradient": { + "n_view_samples": 12, + "n_matched_in_real_data_sample": 12, + "proj_ids": [ + "1" + ] + } + } + }, + "rice_mas": { + "classification": "multi_project", + "views": { + "rice mas": { + "n_view_samples": 46, + "n_matched_in_real_data_sample": 14, + "proj_ids": [ + "1", + "2", + "3" + ] + }, + "riceanoxia mas": { + "n_view_samples": 5, + "n_matched_in_real_data_sample": 2, + "proj_ids": [ + "2", + "3" + ] + }, + "ricestress mas": { + "n_view_samples": 10, + "n_matched_in_real_data_sample": 2, + "proj_ids": [ + "4" + ] + }, + "ricestigma mas": { + "n_view_samples": 14, + "n_matched_in_real_data_sample": 7, + "proj_ids": [ + "2", + "3" + ] + }, + "Anoxia": { + "n_view_samples": 5, + "n_matched_in_real_data_sample": 2, + "proj_ids": [ + "2", + "3" + ] + }, + "Stigma": { + "n_view_samples": 14, + "n_matched_in_real_data_sample": 7, + "proj_ids": [ + "2", + "3" + ] + }, + "Stress": { + "n_view_samples": 10, + "n_matched_in_real_data_sample": 2, + "proj_ids": [ + "4" + ] + }, + "Plant": { + "n_view_samples": 46, + "n_matched_in_real_data_sample": 14, + "proj_ids": [ + "1", + "2", + "3" + ] + } + } + }, + "rice_rma": { + "classification": "multi_project", + "views": { + "rice rma": { + "n_view_samples": 46, + "n_matched_in_real_data_sample": 19, + "proj_ids": [ + "1", + "2", + "3" + ] + }, + "riceanoxia rma": { + "n_view_samples": 5, + "n_matched_in_real_data_sample": 1, + "proj_ids": [ + "2", + "3" + ] + }, + "ricestigma rma": { + "n_view_samples": 14, + "n_matched_in_real_data_sample": 4, + "proj_ids": [ + "2", + "3" + ] + }, + "ricestress rma": { + "n_view_samples": 10, + "n_matched_in_real_data_sample": 2, + "proj_ids": [ + "4" + ] + } + } + }, + "root": { + "classification": "partial_overlap", + "views": { + "Root II": { + "n_view_samples": 185, + "n_matched_in_real_data_sample": 13, + "proj_ids": [ + "GEO:GSE25171", + "GEO:GSE30095", + "GEO:GSE30096", + "GEO:GSE30099", + "GEO:GSE30166", + "GEO:GSE35580", + "GEO:GSE7641" + ] + }, + "Root": { + "n_view_samples": 269, + "n_matched_in_real_data_sample": 14, + "proj_ids": [ + "1", + "GEO:GSE10576", + "GEO:GSE7631", + "GEO:GSE7639", + "GEO:GSE7641", + "GEO:GSE7642" + ] + }, + "Tissue Specific Root": { + "n_view_samples": 0, + "n_matched_in_real_data_sample": 0, + "proj_ids": [] + } + } + }, + "single_cell": { + "classification": "insufficient_data", + "views": { + "Single Cell": { + "n_view_samples": 109, + "n_matched_in_real_data_sample": 25, + "proj_ids": [ + "1" + ] + }, + "Cell Type": { + "n_view_samples": 0, + "n_matched_in_real_data_sample": 0, + "proj_ids": [] + }, + "Cell": { + "n_view_samples": 0, + "n_matched_in_real_data_sample": 0, + "proj_ids": [] + } + } + }, + "soybean": { + "classification": "duplicate_view_names", + "views": { + "soybean": { + "n_view_samples": 15, + "n_matched_in_real_data_sample": 14, + "proj_ids": [ + "1" + ] + }, + "Plant": { + "n_view_samples": 15, + "n_matched_in_real_data_sample": 14, + "proj_ids": [ + "1" + ] + } + } + }, + "soybean_severin": { + "classification": "duplicate_view_names", + "views": { + "soybean severin": { + "n_view_samples": 15, + "n_matched_in_real_data_sample": 13, + "proj_ids": [ + "1" + ] + }, + "Soybean Severin": { + "n_view_samples": 15, + "n_matched_in_real_data_sample": 13, + "proj_ids": [ + "1" + ] + } + } + }, + "strawberry": { + "classification": "duplicate_view_names", + "views": { + "Strawberry Green vs White Stage": { + "n_view_samples": 9, + "n_matched_in_real_data_sample": 1, + "proj_ids": [ + "1" + ] + }, + "Developmental Map Strawberry Flower and Fruit": { + "n_view_samples": 85, + "n_matched_in_real_data_sample": 24, + "proj_ids": [ + "1" + ] + } + } + }, + "tomato_ils": { + "classification": "duplicate_view_names", + "views": { + "ILs Leaf Chitwood et al": { + "n_view_samples": 77, + "n_matched_in_real_data_sample": 24, + "proj_ids": [ + "1" + ] + }, + "LeafILs": { + "n_view_samples": 77, + "n_matched_in_real_data_sample": 24, + "proj_ids": [ + "1" + ] + } + } + }, + "tomato_ils2": { + "classification": "duplicate_view_names", + "views": { + "ILs Root Tip Brady Lab": { + "n_view_samples": 80, + "n_matched_in_real_data_sample": 24, + "proj_ids": [ + "1" + ] + }, + "RootILs": { + "n_view_samples": 80, + "n_matched_in_real_data_sample": 24, + "proj_ids": [ + "1" + ] + } + } + }, + "tomato_renormalized": { + "classification": "multi_project", + "views": { + "Rose Lab Atlas Renormalized": { + "n_view_samples": 21, + "n_matched_in_real_data_sample": 18, + "proj_ids": [ + "1", + "2" + ] + }, + "Fruit": { + "n_view_samples": 6, + "n_matched_in_real_data_sample": 5, + "proj_ids": [ + "1" + ] + }, + "Plant": { + "n_view_samples": 15, + "n_matched_in_real_data_sample": 13, + "proj_ids": [ + "2" + ] + } + } + }, + "tomato_s_pennellii": { + "classification": "duplicate_view_names", + "views": { + "M82 S pennellii Atlases Koenig et al": { + "n_view_samples": 17, + "n_matched_in_real_data_sample": 12, + "proj_ids": [ + "1" + ] + }, + "TomatoAtlases": { + "n_view_samples": 17, + "n_matched_in_real_data_sample": 12, + "proj_ids": [ + "1" + ] + } + } + }, + "wheat": { + "classification": "duplicate_view_names", + "views": { + "Developmental Atlas": { + "n_view_samples": 209, + "n_matched_in_real_data_sample": 26, + "proj_ids": [ + "1" + ] + }, + "EarlyStages": { + "n_view_samples": 61, + "n_matched_in_real_data_sample": 9, + "proj_ids": [ + "1" + ] + }, + "MiddleStages": { + "n_view_samples": 88, + "n_matched_in_real_data_sample": 11, + "proj_ids": [ + "1" + ] + }, + "LateStages": { + "n_view_samples": 62, + "n_matched_in_real_data_sample": 6, + "proj_ids": [ + "1" + ] + } + } + } +} \ No newline at end of file diff --git a/scrape_species_view_info.py b/scrape_species_view_info.py new file mode 100644 index 00000000..7bb6138a --- /dev/null +++ b/scrape_species_view_info.py @@ -0,0 +1,273 @@ +""" +Reena Obmina | BCB330 Project 2025-2026 | University of Toronto + +Scrapes groups, controls, and treatments for every view of every species, +covering BOTH eFP databases and ePlant databases, tagged by source so +eFP-only / ePlant-only / shared databases can be told apart. + +Reuses the live site/view discovery already built and verified in +scrape_view_databases.py (same dropdown/viewNames.json + XML paths) instead +of duplicating it here. This replaces the old approach of reading +__pycache__/eplant_efp_views/eplant_audit.json (Vincent's server-local-only +ePlant audit) for ePlant layout info -- that file isn't available to other +team members and could go stale, whereas viewNames.json is live and public. +Run scrape_view_databases.py first if you only want the flat view->db +mapping (species_databases.json); this script additionally pulls each +view's full group/tissue/sample breakdown. + +Reads: {efp_base}/data/{datasource}.xml for each eFP species + {eplant_base}/data/{family}/viewNames.json + per-view XML for each ePlant project +Writes: data/efp_info/efp_eplant_species_view_info.json -- combined output, + each view tagged "source": "efp" or "eplant", keyed the same way as + species_databases.json ("efp_" / "eplant_") + data/efp_info/db_source_summary.json -- db name -> efp/eplant/both +""" + +import json +import xml.etree.ElementTree as ET +from concurrent.futures import ThreadPoolExecutor, as_completed + +import requests + +from scrape_view_databases import ( + EFP_SITES, + _SPECIAL_CASES, + _HARDCODED, + _EFP_FALLBACK, + get_datasource_options, + EPLANT_SITES, + EPLANT_SPECIES_FILE, + EPLANT_FAMILIES, + EPLANT_DB_OVERRIDE, + get_eplant_view_names, + _flat_view_label, + _NESTED_EFPS_FAMILIES, +) + +REQUEST_TIMEOUT = 20 + + +def fetch_xml_root(xml_url): + """Fetch a view's XML and return the parsed root element, or None on failure.""" + try: + resp = requests.get(xml_url, timeout=REQUEST_TIMEOUT) + resp.raise_for_status() + return ET.fromstring(resp.content) + except Exception as e: + print(f" Error fetching {xml_url}: {e}") + return None + + +def extract_db(root): + """Return the db attribute from the first element, or None.""" + view = root.find(".//view") + return view.get("db") if view is not None else None + + +def parse_groups(root): + """Parse // elements into {group_name: {controls, treatments}}.""" + groups = {} + for group in root.findall(".//group"): + group_name = group.get("name") + if not group_name: + continue + + controls = [c.get("sample") for c in group.findall("control") if c.get("sample")] + + treatments = {} + for tissue in group.findall("tissue"): + t_name = tissue.get("name") + if not t_name: + continue + t_key = t_name.replace(" ", "_") + samples = [s.get("name") for s in tissue.findall("sample") if s.get("name")] + treatments.setdefault(t_key, []) + treatments[t_key].extend(samples) + + groups[group_name.replace(" ", "_")] = {"controls": controls, "treatments": treatments} + + return groups + + +# --------------------------------------------------------------------------- +# eFP +# --------------------------------------------------------------------------- + + +def fetch_efp_view(species, base_url, value, label): + """Fetch one eFP view's XML and return its db + group breakdown, tagged as eFP.""" + xml_url = f"{base_url}/data/{value}.xml" + root = fetch_xml_root(xml_url) + if root is None: + return None + return { + "source": "efp", + "species": species, + "database": extract_db(root), + "view_name": label, + "view_file": value, + "groups": parse_groups(root), + } + + +def _hardcoded_or_fallback_views(species, db_by_label): + """Build view entries (no group data available) for a hardcoded/fallback species.""" + return [ + { + "source": "efp", + "species": species, + "database": db_name, + "view_name": label, + "view_file": None, + "groups": {}, + } + for label, db_name in db_by_label.items() + ] + + +def collect_efp_views(): + """Discover and fetch every eFP species' views.""" + results = {} + for species, efp_url in EFP_SITES.items(): + print(f"[efp] Processing {species}...") + base_url = efp_url.rsplit("/", 2)[0] + key = f"efp_{species.replace(' ', '_')}" + + if species in _HARDCODED: + results[key] = _hardcoded_or_fallback_views(species, _HARDCODED[species]) + continue + + options = _SPECIAL_CASES.get(species) or get_datasource_options(efp_url) + if not options: + if species in _EFP_FALLBACK: + print(" Live scrape failed -- using last-known-good fallback (no group data)") + results[key] = _hardcoded_or_fallback_views(species, _EFP_FALLBACK[species]) + else: + print(" No views found") + results[key] = [] + continue + + species_views = [] + with ThreadPoolExecutor(max_workers=6) as pool: + futures = { + pool.submit(fetch_efp_view, species, base_url, value, label): label + for value, label in options + } + for future in as_completed(futures): + view = future.result() + if view: + species_views.append(view) + print(f" Found {len(species_views)} views") + results[key] = species_views + return results + + +# --------------------------------------------------------------------------- +# ePlant +# --------------------------------------------------------------------------- + + +def eplant_xml_url(base_url, family, folder, species_file): + """Build the XML URL for an ePlant view, mirroring scrape_view_databases.fetch_eplant_db.""" + if folder is None: + return f"{base_url}/data/{family}/{species_file}.xml" + nested = "efps/" if family in _NESTED_EFPS_FAMILIES else "" + return f"{base_url}/data/{family}/{nested}{folder}/{species_file}.xml" + + +def fetch_eplant_view(site, base_url, family, display, folder, species_file): + """Fetch one ePlant view's XML and return its db + group breakdown, tagged as ePlant. + + The view is kept even when no db="..." attribute is present (e.g. eplant_tomato's + Cell viewer), with database: None, so view counts match Vincent's eplant_views.csv + audit exactly -- a real view with an unknown database is still a real view. + """ + xml_url = eplant_xml_url(base_url, family, folder, species_file) + root = fetch_xml_root(xml_url) + if root is None: + return None + db = extract_db(root) or EPLANT_DB_OVERRIDE.get((site, family)) + return { + "source": "eplant", + "project": site, + "species": species_file, + "family": family, + "database": db, + "view_name": display, + "view_folder": folder, + "groups": parse_groups(root), + } + + +def collect_eplant_views(): + """Discover (via viewNames.json, same as scrape_view_databases.py) and fetch every ePlant view.""" + jobs = [] + for site, base_url in EPLANT_SITES.items(): + species_file = EPLANT_SPECIES_FILE[site] + for family in EPLANT_FAMILIES[site]: + names = get_eplant_view_names(base_url, family) + if names is not None: + for display in names: + folder = display.replace(" ", "") + jobs.append((site, base_url, family, display, folder, species_file)) + else: + jobs.append((site, base_url, family, _flat_view_label(family), None, species_file)) + + results = {} + print(f"[eplant] Fetching {len(jobs)} candidate views across {len(EPLANT_SITES)} projects...") + with ThreadPoolExecutor(max_workers=6) as pool: + futures = {pool.submit(fetch_eplant_view, *job): job[0] for job in jobs} + for future in as_completed(futures): + site = futures[future] + view = future.result() + if view: + results.setdefault(site, []).append(view) + for site in EPLANT_SITES: + print(f" {site}: fetched {len(results.get(site, []))} views") + return results + + +def build_db_source_summary(efp_results, eplant_results): + """Map each database name to which source(s) it appears under.""" + summary = {} + for views in efp_results.values(): + for view in views: + db = view.get("database") + if db: + summary.setdefault(db, set()).add("efp") + for views in eplant_results.values(): + for view in views: + db = view.get("database") + if db: + summary.setdefault(db, set()).add("eplant") + + return { + db: ("both" if sources == {"efp", "eplant"} else next(iter(sources))) + for db, sources in summary.items() + } + + +def main(): + efp_results = collect_efp_views() + eplant_results = collect_eplant_views() + + combined = {"efp": efp_results, "eplant": eplant_results} + out_file = "data/efp_info/efp_eplant_species_view_info.json" + with open(out_file, "w") as f: + json.dump(combined, f, indent=2) + print(f"\nOutput written to {out_file}") + + db_summary = build_db_source_summary(efp_results, eplant_results) + summary_file = "data/efp_info/db_source_summary.json" + with open(summary_file, "w") as f: + json.dump(db_summary, f, indent=2, sort_keys=True) + print(f"Output written to {summary_file}") + + efp_only = sum(1 for v in db_summary.values() if v == "efp") + eplant_only = sum(1 for v in db_summary.values() if v == "eplant") + both = sum(1 for v in db_summary.values() if v == "both") + print(f"\nDatabases: {len(db_summary)} total -- eFP-only: {efp_only}, ePlant-only: {eplant_only}, both: {both}") + + +if __name__ == "__main__": + main() diff --git a/scrape_view_databases.py b/scrape_view_databases.py new file mode 100644 index 00000000..4cacebf7 --- /dev/null +++ b/scrape_view_databases.py @@ -0,0 +1,420 @@ +""" +Reena Obmina | BCB330 Project 2025-2026 | University of Toronto + +Scrapes view names and their database names from each species' datasources.xml, +covering BOTH eFP databases and ePlant databases, so the master list notes which +databases are eFP-only, ePlant-only, or available through both frontends. + +eFP side: + Reads: {efp_base}/data/{datasource}.xml for each datasource in each species' + HTML dropdown (discovered live from the efpWeb.cgi page itself). + +ePlant side: + Each ePlant project (e.g. eplant_maize) has its own set of "*eFP viewer" tabs + (family names like "experiment", "plant", "cell" -- "Tissue and experiment eFP + viewer", "Plant eFP viewer", "Cell eFP viewer"). When a tab has more than one + view, the app populates a "Select View" dropdown from {base}/data/{family}/ + viewNames.json. When a tab has exactly one view, there's no dropdown/JSON file + and the view's XML sits directly at {base}/data/{family}/{species_file}.xml. + Reads: {eplant_base}/data/{family}/viewNames.json (dropdown views, if any) + {eplant_base}/data/{family}/efps/{folder}/{species_file}.xml (per-view + XML for the "experiment" family, which nests views under "efps/") + {eplant_base}/data/{family}/{folder}/{species_file}.xml (per-view XML + for other families, which nest views directly) + The per-project species filename and family list are stable, project-specific + paths on the server and aren't otherwise discoverable over HTTP, so they're + hardcoded below (cross-checked against Vincent's eplant_audit.json). + +Writes: species_databases.json -- ``{ species_or_project: { view_name: db_name, ... }, ... }`` + Keys prefixed "efp_" + the eFP species (e.g. "efp_arabidopsis") or "eplant_" + + the ePlant project's species (e.g. "eplant_maize") so eFP-only vs ePlant-only vs shared databases + can be told apart just by which key(s) a db name shows up under. + +Run this first to discover what views exist for a species before running +build_proj_id_view_mapping.py. +""" + +import re +import xml.etree.ElementTree as ET +import json + +import requests + +# --------------------------------------------------------------------------- +# eFP sites +# --------------------------------------------------------------------------- +EFP_SITES = { + "arabidopsis": "https://bar.utoronto.ca/efp_arabidopsis/cgi-bin/efpWeb.cgi", + "arabidopsis lipid": "https://bar.utoronto.ca/efp_arabidopsis_lipid/cgi-bin/efpWeb.cgi", + "arabidopsis cell": "https://bar.utoronto.ca/cell_efp/cgi-bin/cell_efp.cgi", + "arabidopsis seedcoat": "https://bar.utoronto.ca/efp_seedcoat/cgi-bin/efpWeb.cgi", + "poplar": "https://bar.utoronto.ca/efppop/cgi-bin/efpWeb.cgi", + "medicago": "https://bar.utoronto.ca/efpmedicago/cgi-bin/efpWeb.cgi", + "soybean": "https://bar.utoronto.ca/efpsoybean/cgi-bin/efpWeb.cgi", + "potato": "https://bar.utoronto.ca/efp_potato/cgi-bin/efpWeb.cgi", + "tomato": "https://bar.utoronto.ca/efp_tomato/cgi-bin/efpWeb.cgi", + "eutrema": "https://bar.utoronto.ca/efp_eutrema/cgi-bin/efpWeb.cgi", + "camelina": "https://bar.utoronto.ca/efp_camelina/cgi-bin/efpWeb.cgi", + "arachis": "https://bar.utoronto.ca/efp_arachis/cgi-bin/efpWeb.cgi", + "grape": "https://bar.utoronto.ca/efp_grape/cgi-bin/efpWeb.cgi", + "cannabis": "https://bar.utoronto.ca/efp_cannabis/cgi-bin/efpWeb.cgi", + "kalanchoe": "https://bar.utoronto.ca/efp_kalanchoe/cgi-bin/efpWeb.cgi", + "actinidia": "https://bar.utoronto.ca/efp_actinidia/cgi-bin/efpWeb.cgi", + "brassica rapa": "https://bar.utoronto.ca/efp_brassica_rapa/cgi-bin/efpWeb.cgi", + "canola": "https://bar.utoronto.ca/efp_canola/cgi-bin/efpWeb.cgi", + "cacao ccn": "https://bar.utoronto.ca/efp_cacao_ccn/cgi-bin/efpWeb.cgi", + "cacao sca": "https://bar.utoronto.ca/efp_cacao_sca/cgi-bin/efpWeb.cgi", + "cacao tc": "https://bar.utoronto.ca/efp_cacao_tc/cgi-bin/efpWeb.cgi", + "mangosteen": "https://bar.utoronto.ca/efp_mangosteen/cgi-bin/efpWeb.cgi", + "lupin": "https://bar.utoronto.ca/efp_lupin/cgi-bin/efpWeb.cgi", + "strawberry": "https://bar.utoronto.ca/efp_strawberry/cgi-bin/efpWeb.cgi", + "maize": "https://bar.utoronto.ca/efp_maize/cgi-bin/efpWeb.cgi", + "rice": "https://bar.utoronto.ca/efprice/cgi-bin/efpWeb.cgi", + "barley": "https://bar.utoronto.ca/efpbarley/cgi-bin/efpWeb.cgi", + "triticale": "https://bar.utoronto.ca/efp_triticale/cgi-bin/efpWeb.cgi", + "brachypodium": "https://bar.utoronto.ca/efp_brachypodium/cgi-bin/efpWeb.cgi", + "wheat": "https://bar.utoronto.ca/efp_wheat/cgi-bin/efpWeb.cgi", + "little millet": "https://bar.utoronto.ca/efp_little_millet/cgi-bin/efpWeb.cgi", + "oat": "https://bar.utoronto.ca/efp_oat/cgi-bin/efpWeb.cgi", + "physcomitrella": "https://bar.utoronto.ca/efp_physcomitrella/cgi-bin/efpWeb.cgi", + "selaginella": "https://bar.utoronto.ca/efp_selaginella/cgi-bin/efpWeb.cgi", + "mouse": "https://bar.utoronto.ca/mouse_efp/cgi-bin/efpWeb.cgi", + "human": "https://bar.utoronto.ca/efp_human/cgi-bin/efpWeb.cgi", + "phelipanche": "https://bar.utoronto.ca/efp_phelipanche/cgi-bin/efpWeb.cgi", + "striga": "https://bar.utoronto.ca/efp_striga/cgi-bin/efpWeb.cgi", + "triphysaria": "https://bar.utoronto.ca/efp_triphysaria/cgi-bin/efpWeb.cgi", + # Found by cross-checking api/random_rows_json/ sample data against this site + # list: these sites exist live but were never added here. + "durum wheat": "https://bar.utoronto.ca/efp_durum_wheat/cgi-bin/efpWeb.cgi", + "euphorbia": "https://bar.utoronto.ca/efp_euphorbia/cgi-bin/efpWeb.cgi", + "marchantia": "https://bar.utoronto.ca/efp_marchantia/cgi-bin/efpWeb.cgi", + "sorghum": "https://bar.utoronto.ca/efp_sorghum/cgi-bin/efpWeb.cgi", + "tung tree": "https://bar.utoronto.ca/efp_tung_tree/cgi-bin/efpWeb.cgi", + "apple": "https://bar.utoronto.ca/efp_apple/cgi-bin/efpWeb.cgi", + # Metabolite/enzyme-class sites -- see _HARDCODED below for why these are + # single fixed views rather than scraped dropdowns. + "maize enzyme": "https://bar.utoronto.ca/efp_maize_enzyme/cgi-bin/efpWeb.cgi", + "maize metabolite": "https://bar.utoronto.ca/efp_maize_metabolite/cgi-bin/efpWeb.cgi", + "rice metabolite": "https://bar.utoronto.ca/efp_rice_metabolite/cgi-bin/efpWeb.cgi", + "brachypodium metabolites": "https://bar.utoronto.ca/efp_brachypodium_metabolites/cgi-bin/efpWeb.cgi", +} + +# Sites that do not use the standard dataSource dropdown; map them manually. +# (species key → list of (datasource_xml_filename, display_name) to look up) +_SPECIAL_CASES = { + # Uses a lipidClass dropdown instead of dataSource; one fixed XML file. + "arabidopsis lipid": [("Lipid_Map", "Lipid Map")], +} + +# Sites with no discoverable XML; database names are hardcoded from known config. +_HARDCODED = { + # Single-view cell browser with no dropdown and access-denied data directory. + "arabidopsis cell": {"Cell Type": "single_cell"}, + # Metabolite/enzyme-class eFPs: the dataSource dropdown lists individual + # compounds/enzymes (e.g. "Rubisco (initial)", "Glucose-6-phosphate") as the + # *query parameter* into one single database, not separate per-compound + # databases -- their XML has no per-option db= attribute. Confirmed against + # Vincent's regex patterns (efp_maize_enzyme etc. validate the compound NAME + # as the "gene_id", not a real gene ID) and the one underlying db each site + # actually has sample data for. + "maize enzyme": {"Enzyme Activity": "maize_enzyme"}, + "maize metabolite": {"Metabolite Level": "maize_metabolite"}, + "rice metabolite": {"Metabolite Level": "rice_metabolite"}, + "brachypodium metabolites": {"Metabolite Level": "brachypodium_metabolites_map"}, +} + +# efp_human currently 403s for us (server-side block, not a code issue). Fall back +# to the last-known-good scrape rather than silently dropping "human" from the output. +_EFP_FALLBACK = { + "human": { + "Circulatory Respiratory": "human_developmental", + "Illumina Body Map 2 - FPKM": "human_body_map_2", + "Nervous": "human_developmental", + "Reproductive": "human_developmental", + "Skeletal Immune Digestive": "human_developmental", + }, +} + +# --------------------------------------------------------------------------- +# ePlant sites +# --------------------------------------------------------------------------- +EPLANT_SITES = { + "eplant_arabidopsis": "https://bar.utoronto.ca/eplant", + "eplant_maize": "https://bar.utoronto.ca/eplant_maize", + "eplant_poplar": "https://bar.utoronto.ca/eplant_poplar", + "eplant_tomato": "https://bar.utoronto.ca/eplant_tomato", + "eplant_camelina": "https://bar.utoronto.ca/eplant_camelina", + "eplant_soybean": "https://bar.utoronto.ca/eplant_soybean", + "eplant_potato": "https://bar.utoronto.ca/eplant_potato", + "eplant_barley": "https://bar.utoronto.ca/eplant_barley", + "eplant_barley_legacy": "https://bar.utoronto.ca/eplant_barley_legacy", + "eplant_medicago": "https://bar.utoronto.ca/eplant_medicago", + "eplant_eucalyptus": "https://bar.utoronto.ca/eplant_eucalyptus", + "eplant_rice": "https://bar.utoronto.ca/eplant_rice", + "eplant_willow": "https://bar.utoronto.ca/eplant_willow", + "eplant_sunflower": "https://bar.utoronto.ca/eplant_sunflower", + "eplant_cannabis": "https://bar.utoronto.ca/eplant_cannabis", + "eplant_wheat": "https://bar.utoronto.ca/eplant_wheat", + "eplant_sugarcane": "https://bar.utoronto.ca/eplant_sugarcane", +} + +# Species filename used in each ePlant project's per-view XML paths +# (e.g. .../data/experiment/efps/AbioticStress/Arabidopsis_thaliana.xml). +# Sourced from Vincent's eplant_audit.json (species detection per project); +# not discoverable over HTTP since these sites don't expose species.json publicly. +EPLANT_SPECIES_FILE = { + "eplant_arabidopsis": "Arabidopsis_thaliana", + "eplant_maize": "Zea_mays", + "eplant_poplar": "Populus_trichocarpa", + "eplant_tomato": "Solanum_lycopersicum", + "eplant_camelina": "Camelina_sativa", + "eplant_soybean": "Glycine_max", + "eplant_potato": "Solanum_tuberosum", + "eplant_barley": "Hordeum_vulgare", + "eplant_barley_legacy": "Hordeum_vulgare", + "eplant_medicago": "Medicago_truncatula", + "eplant_eucalyptus": "Eucalyptus_grandis", + "eplant_rice": "Oryza_sativa", + "eplant_willow": "Salix_purpurea", + "eplant_sunflower": "Helianthus_annuus", + "eplant_cannabis": "Cannabis_sativa", + "eplant_wheat": "Triticum_aestivum", + "eplant_sugarcane": "Saccharum_R570", +} + +# "*eFP viewer" tabs (families) every ePlant project has, plus per-project extras. +_DEFAULT_EPLANT_FAMILIES = ["cell", "experiment", "plant"] +EPLANT_FAMILIES = { + site: (["cell", "experiment", "plant", "worldLeaf", "worldXylem"] if site == "eplant_poplar" else _DEFAULT_EPLANT_FAMILIES) + for site in EPLANT_SITES +} + +# Families always nest their per-view XML under an "efps/" subfolder. +_NESTED_EFPS_FAMILIES = {"experiment"} + +# Views whose XML has no db="..." attribute to scrape (single-cell browsers); +# the db is known from existing eFP config instead. +EPLANT_DB_OVERRIDE = { + ("eplant_arabidopsis", "cell"): "single_cell", +} + + +def get_datasource_options(efp_url): + """Fetch the eFP HTML page and extract all datasource option values and display names. + + :param efp_url: Full URL to the species' eFP CGI endpoint. + :type efp_url: str + :returns: List of (option_value, display_name) tuples, or empty list on failure. + :rtype: list[tuple[str, str]] + """ + options = [] + try: + resp = requests.get(efp_url, timeout=15) + resp.raise_for_status() + html = resp.text + + # Match + pattern = re.compile( + r']*>\s*([^<]+?)\s*', + re.IGNORECASE | re.DOTALL, + ) + for match in pattern.finditer(html): + value = match.group(1).strip() + label = match.group(2).strip() + if value and label: + options.append((value, label)) + except Exception as e: + print(f" Error fetching HTML: {e}") + return options + + +def fetch_db_name(base_url, datasource_value): + """Fetch the per-datasource XML and return the first database name found. + + :param base_url: Base URL for the eFP site (e.g. ``'https://bar.utoronto.ca/efp_arabidopsis'``). + :type base_url: str + :param datasource_value: Option value from the dropdown (e.g. ``'Developmental_Map'``). + :type datasource_value: str + :returns: Database name string, or ``None`` if not found. + :rtype: str | None + """ + xml_url = f"{base_url}/data/{datasource_value}.xml" + try: + resp = requests.get(xml_url, timeout=15) + resp.raise_for_status() + root = ET.fromstring(resp.content) + view = root.find(".//view") + if view is not None: + return view.get("db") + except Exception: + pass + return None + + +def fetch_view_databases(species, efp_url): + """Fetch view name → database name mappings for one eFP species. + + :param species: Species key (e.g. ``'arabidopsis'``), used only for error messages. + :type species: str + :param efp_url: Full URL to the species' efpWeb.cgi endpoint. + :type efp_url: str + :returns: Dict mapping view display name to database name, or an empty dict on failure. + :rtype: dict[str, str] + """ + base_url = efp_url.rsplit("/", 2)[0] + + if species in _HARDCODED: + return _HARDCODED[species] + + if species in _SPECIAL_CASES: + options = _SPECIAL_CASES[species] + else: + options = get_datasource_options(efp_url) + if not options: + return {} + + views = {} + for value, label in options: + db_name = fetch_db_name(base_url, value) + if db_name: + views[label] = db_name + else: + print(f" No db found for datasource '{value}' ({label})") + + return views + + +def get_eplant_view_names(base_url, family): + """Fetch the "Select View" dropdown options for one ePlant family, if any. + + :param base_url: Base URL for the ePlant project (e.g. ``'https://bar.utoronto.ca/eplant_maize'``). + :type base_url: str + :param family: Family/tab name (e.g. ``'experiment'``, ``'plant'``, ``'cell'``). + :type family: str + :returns: List of display names (possibly empty) if a dropdown exists, else ``None`` + when there's no viewNames.json at all (single-view or no-view family). + :rtype: list[str] | None + """ + url = f"{base_url}/data/{family}/viewNames.json" + try: + resp = requests.get(url, timeout=15) + resp.raise_for_status() + names = resp.json() + if isinstance(names, list): + return [n.strip() for n in names if isinstance(n, str) and n.strip()] + except Exception: + pass + return None + + +def fetch_eplant_db(base_url, family, folder, species_file): + """Fetch one ePlant view's XML and return its db attribute. + + :param base_url: Base URL for the ePlant project. + :type base_url: str + :param family: Family/tab name the view belongs to. + :type family: str + :param folder: View's on-disk folder name (display name with spaces removed), or + ``None`` for a flat family with no per-view subfolder (XML sits directly under + the family directory). + :type folder: str | None + :param species_file: Species XML filename stem (e.g. ``'Zea_mays'``). + :type species_file: str + :returns: Database name string, or ``None`` if not found. + :rtype: str | None + """ + if folder is None: + xml_url = f"{base_url}/data/{family}/{species_file}.xml" + else: + nested = "efps/" if family in _NESTED_EFPS_FAMILIES else "" + xml_url = f"{base_url}/data/{family}/{nested}{folder}/{species_file}.xml" + try: + resp = requests.get(xml_url, timeout=15) + resp.raise_for_status() + root = ET.fromstring(resp.content) + view = root.find(".//view") + if view is not None: + return view.get("db") + except Exception: + pass + return None + + +def _flat_view_label(family): + """Turn a single-view family name into a display label, e.g. 'worldLeaf' -> 'World Leaf'.""" + return re.sub(r"(? at most one flat view directly under this family. + db = fetch_eplant_db(base_url, family, None, species_file) + if not db: + db = EPLANT_DB_OVERRIDE.get((site, family)) + if db: + views[_flat_view_label(family)] = db + + return views + + +def main(): + """Iterate over all eFP and ePlant sites, collect view-to-database mappings, and write output.""" + all_species_databases = {} + + for species, efp_url in EFP_SITES.items(): + print(f"[efp] Processing {species}...") + views = fetch_view_databases(species, efp_url) + if not views and species in _EFP_FALLBACK: + print(" Live scrape failed -- using last-known-good fallback") + views = _EFP_FALLBACK[species] + if views: + all_species_databases[f"efp_{species.replace(' ', '_')}"] = views + print(f" Found {len(views)} views") + else: + print(" No views found") + + for site, base_url in EPLANT_SITES.items(): + print(f"[eplant] Processing {site}...") + species_file = EPLANT_SPECIES_FILE[site] + families = EPLANT_FAMILIES[site] + views = fetch_eplant_views(site, base_url, species_file, families) + if views: + all_species_databases[site] = views + print(f" Found {len(views)} views") + else: + print(" No views found") + + out_file = "species_databases.json" + with open(out_file, "w") as f: + json.dump(all_species_databases, f, indent=2) + + print(f"\nOutput written to {out_file}") + + +if __name__ == "__main__": + main() diff --git a/species_databases.json b/species_databases.json new file mode 100644 index 00000000..85cff78a --- /dev/null +++ b/species_databases.json @@ -0,0 +1,368 @@ +{ + "efp_arabidopsis": { + "Abiotic Stress": "atgenexp_stress", + "Abiotic Stress II": "atgenexp_stress", + "Biotic Stress": "atgenexp_pathogen", + "Biotic Stress II": "atgenexp_pathogen", + "Chemical": "atgenexp_hormone", + "DNA Damage": "dna_damage", + "Development RMA": "atgenexp", + "Developmental Map": "atgenexp_plus", + "Developmental Mutants": "atgenexp_plus", + "Embryo": "embryo", + "Germination": "germination", + "Guard Cell": "guard_cell", + "Gynoecium": "gynoecium", + "Hormone": "atgenexp_hormone", + "Klepikova Atlas": "klepikova", + "Lateral Root Initiation": "lateral_root_initiation", + "Light Series": "light_series", + "Natural Variation": "arabidopsis_ecotypes", + "Regeneration": "meristem_db", + "Root": "root", + "Root II": "root", + "Seed": "seed_db", + "Shoot Apex": "shoot_apex", + "Silique": "silique", + "Single Cell": "single_cell", + "Tissue Specific": "atgenexp_plus" + }, + "efp_arabidopsis_lipid": { + "Lipid Map": "lipid_map" + }, + "efp_arabidopsis_cell": { + "Cell Type": "single_cell" + }, + "efp_arabidopsis_seedcoat": { + "Seed Coat": "seedcoat" + }, + "efp_poplar": { + "Poplar": "poplar", + "PoplarTreatment": "poplar" + }, + "efp_medicago": { + "medicago mas": "medicago_mas", + "medicago rma": "medicago_rma", + "medicago seed": "medicago_seed" + }, + "efp_soybean": { + "soybean": "soybean", + "soybean embryonic development": "soybean_embryonic_development", + "soybean heart cotyledon globular": "soybean_heart_cotyledon_globular", + "soybean senescence": "soybean_senescence", + "soybean severin": "soybean_severin" + }, + "efp_potato": { + "Potato Developmental": "potato_dev", + "Potato Stress": "potato_stress" + }, + "efp_tomato": { + "ILs Leaf Chitwood et al": "tomato_ils", + "ILs Root Tip Brady Lab": "tomato_ils2", + "M82 S pennellii Atlases Koenig et al": "tomato_s_pennellii", + "Rose Lab Atlas": "tomato", + "Rose Lab Atlas Renormalized": "tomato_renormalized", + "SEED Lab Angers": "tomato_seed", + "Shade Mutants": "tomato_shade_mutants", + "Shade Timecourse WT": "tomato_shade_timecourse", + "Tomato Meristem": "tomato_meristem" + }, + "efp_eutrema": { + "Eutrema": "thellungiella_db" + }, + "efp_camelina": { + "Developmental Atlas FPKM": "camelina", + "Developmental Atlas TPM": "camelina_tpm" + }, + "efp_arachis": { + "Arachis Atlas": "arachis" + }, + "efp_grape": { + "grape developmental": "grape_developmental" + }, + "efp_cannabis": { + "Cannabis Atlas": "cannabis" + }, + "efp_kalanchoe": { + "Light Response": "kalanchoe" + }, + "efp_actinidia": { + "Bud Development": "actinidia_bud_development", + "Flower Fruit Development": "actinidia_flower_fruit_development", + "Postharvest": "actinidia_postharvest", + "Vegetative Growth": "actinidia_vegetative_growth" + }, + "efp_brassica_rapa": { + "Embryogenesis": "brassica_rapa" + }, + "efp_canola": { + "Canola Seed": "canola_seed" + }, + "efp_cacao_ccn": { + "Developmental Atlas": "cacao_developmental_atlas", + "Drought Diurnal Atlas": "cacao_drought_diurnal_atlas" + }, + "efp_cacao_sca": { + "Developmental Atlas": "cacao_developmental_atlas_sca", + "Drought Diurnal Atlas": "cacao_drought_diurnal_atlas_sca", + "Meristem Atlas": "cacao_meristem_atlas_sca", + "Seed Atlas": "cacao_seed_atlas_sca" + }, + "efp_cacao_tc": { + "Cacao Infection": "cacao_infection", + "Cacao Leaf": "cacao_leaf" + }, + "efp_mangosteen": { + "Aril vs Rind": "mangosteen_aril_vs_rind", + "Callus": "mangosteen_callus", + "Diseased vs Normal": "mangosteen_diseased_vs_normal", + "Fruit Ripening": "mangosteen_fruit_ripening", + "Seed Development": "mangosteen_seed_development", + "Seed Germination": "mangosteen_seed_germination" + }, + "efp_lupin": { + "LCM Leaf": "lupin_lcm_leaf", + "LCM Pod": "lupin_lcm_pod", + "LCM Stem": "lupin_lcm_stem", + "Whole Plant": "lupin_whole_plant" + }, + "efp_strawberry": { + "Developmental Map Strawberry Flower and Fruit": "strawberry", + "Strawberry Green vs White Stage": "strawberry" + }, + "efp_maize": { + "Downs et al Atlas": "maize_gdowns", + "Early Seed": "maize_early_seed", + "Embryonic Leaf Development": "maize_embryonic_leaf_development", + "Hoopes et al Atlas": "maize_buell_lab", + "Hoopes et al Atlas V5": "maize_atlas_v5", + "Hoopes et al Stress": "maize_buell_lab", + "Hoopes et al Stress V5": "maize_stress_v5", + "Maize Kernel": "maize_early_seed", + "Maize Kernel V5": "maize_kernel_v5", + "Maize Root": "maize_root", + "Sekhon et al Atlas": "maize_RMA_linear", + "Tassel and Ear Primordia": "maize_ears", + "maize iplant": "maize_iplant", + "maize leaf gradient": "maize_leaf_gradient", + "maize rice comparison": "maize_rice_comparison" + }, + "efp_rice": { + "rice drought heat stress": "rice_drought_heat_stress", + "rice leaf gradient": "rice_leaf_gradient", + "rice maize comparison": "rice_maize_comparison", + "rice mas": "rice_mas", + "rice rma": "rice_rma", + "rice single cell": "rice_abiotic_stress_sc_pseudobulk", + "riceanoxia mas": "rice_mas", + "riceanoxia rma": "rice_rma", + "ricestigma mas": "rice_mas", + "ricestigma rma": "rice_rma", + "ricestress mas": "rice_mas", + "ricestress rma": "rice_rma" + }, + "efp_barley": { + "barley mas": "barley_mas", + "barley rma": "barley_rma" + }, + "efp_triticale": { + "triticale": "triticale", + "triticale mas": "triticale_mas" + }, + "efp_brachypodium": { + "Brachypodium Atlas": "brachypodium", + "Brachypodium Grains": "brachypodium_grains", + "Brachypodium Spikes": "brachypodium_Bd21", + "Photo Thermocycle": "brachypodium_photo_thermocycle" + }, + "efp_wheat": { + "Developmental Atlas": "wheat", + "Wheat Abiotic Stress": "wheat_abiotic_stress", + "Wheat Embryogenesis": "wheat_embryogenesis", + "Wheat Meiosis": "wheat_meiosis" + }, + "efp_little_millet": { + "Life Cycle": "little_millet" + }, + "efp_oat": { + "Oat": "oat" + }, + "efp_physcomitrella": { + "Physcomitrella": "physcomitrella_db" + }, + "efp_selaginella": { + "Selaginella Atlas": "selaginella" + }, + "efp_mouse": { + "Mouse": "mouse_db" + }, + "efp_human": { + "Circulatory Respiratory": "human_developmental", + "Illumina Body Map 2 - FPKM": "human_body_map_2", + "Nervous": "human_developmental", + "Reproductive": "human_developmental", + "Skeletal Immune Digestive": "human_developmental" + }, + "efp_phelipanche": { + "Phelipanche": "phelipanche" + }, + "efp_striga": { + "Striga Atlas": "striga" + }, + "efp_triphysaria": { + "Triphysaria": "triphysaria" + }, + "efp_durum_wheat": { + "Abiotic Stress": "durum_wheat_abiotic_stress", + "Biotic Stress": "durum_wheat_biotic_stress", + "Development": "durum_wheat_development" + }, + "efp_euphorbia": { + "Euphorbia": "euphorbia" + }, + "efp_marchantia": { + "Expression Atlas": "marchantia_organ_stress" + }, + "efp_sorghum": { + "Atlas w BS Cells": "sorghum_atlas_w_BS_cells", + "Developmental Atlas": "sorghum_developmental", + "Flowering Activation": "sorghum_flowering_activation", + "Low Phosphorus": "sorghum_low_phosphorus", + "Phosphate Stress": "sorghum_phosphate_stress", + "Saline Alkali Stress": "sorghum_saline_alkali_stress", + "Stress Atlas": "sorghum_stress", + "Strigolactone Variation": "sorghum_strigolactone_variation", + "Sulfur Stress": "sorghum_sulfur_stress", + "Vascularization and Internode": "sorghum_vascularization_and_internode" + }, + "efp_tung_tree": { + "Tung Tree": "tung_tree" + }, + "efp_apple": { + "Developmental Map": "apple" + }, + "efp_maize_enzyme": { + "Enzyme Activity": "maize_enzyme" + }, + "efp_maize_metabolite": { + "Metabolite Level": "maize_metabolite" + }, + "efp_rice_metabolite": { + "Metabolite Level": "rice_metabolite" + }, + "efp_brachypodium_metabolites": { + "Metabolite Level": "brachypodium_metabolites_map" + }, + "eplant_arabidopsis": { + "Cell": "single_cell", + "Abiotic Stress": "atgenexp_stress", + "Abiotic Stress II": "atgenexp_stress", + "Chemical": "atgenexp_hormone", + "DNA Damage": "dna_damage", + "Guard Cell Meristemoids": "guard_cell", + "Guard Cell Drought": "gc_drought", + "Guard Cell Mutant And Wild Type Guard Cell ABA Response": "guard_cell", + "Guard Cell Suspension Cell ABA Response With ROS Scavenger": "guard_cell", + "Tissue Specific Embryo Development": "atgenexp_plus", + "Tissue Specific Guard And Mesophyll Cells": "atgenexp_plus", + "Tissue Specific Microgametogenesis": "atgenexp_plus", + "Tissue Specific Pollen Germination": "atgenexp_plus", + "Tissue Specific Root": "root", + "Tissue Specific Shoot Apical Meristem": "atgenexp_plus", + "Tissue Specific Stem Epidermis": "atgenexp_plus", + "Tissue Specific Stigma And Ovaries": "atgenexp_plus", + "Tissue Specific Trichomes": "atgenexp_plus", + "Tissue Specific Xylem And Cork": "atgenexp_plus", + "Biotic Stress Botrytis cinerea": "atgenexp_pathogen", + "Biotic Stress Elicitors": "atgenexp_pathogen", + "Biotic Stress Erysiphe orontii": "atgenexp_pathogen", + "Biotic Stress Hyaloperonospora arabidopsidis": "atgenexp_pathogen", + "Biotic Stress Myzus persicaere": "atgenexp_pathogen", + "Biotic Stress Phytophthora infestans": "atgenexp_pathogen", + "Biotic Stress Pseudomonas syringae": "atgenexp_pathogen", + "Biotic Stress Golovinomyces orontii": "atgenexp_pathogen", + "Root Immunity Elicitation": "root_Schaefer_lab", + "Germination": "germination", + "Heterodera schachtii": "heterodera_schachtii", + "Shoot Apex": "shoot_apex", + "Single Cell": "single_cell", + "AtGenExpress": "atgenexp_plus", + "Klepikova": "klepikova" + }, + "eplant_maize": { + "Root": "maize_root", + "Sekhon Atlas": "maize_RMA_linear", + "Tassel And Ear Primordia": "maize_ears", + "Leaf Gradient": "maize_leaf_gradient", + "Leaf MeBS": "maize_iplant", + "Plant": "maize_gdowns" + }, + "eplant_poplar": { + "Poplar Treatment": "poplar", + "Plant": "poplar", + "World Leaf": "poplar_leaf", + "World Xylem": "poplar_xylem" + }, + "eplant_tomato": { + "Fruit": "tomato_renormalized", + "TomatoAtlases": "tomato_s_pennellii", + "LeafILs": "tomato_ils", + "RootILs": "tomato_ils2", + "Root": "tomato_root", + "RootFieldPot": "tomato_root_field_pot", + "Plant": "tomato_renormalized" + }, + "eplant_camelina": { + "Plant": "camelina" + }, + "eplant_soybean": { + "Soybean Severin": "soybean_severin", + "Plant": "soybean" + }, + "eplant_potato": { + "Potato Stress": "potato_stress", + "Plant": "potato_dev" + }, + "eplant_barley": { + "Seed": "barley_seed", + "Spike Meristem": "barley_spike_meristem_v3", + "Spike Meristem Shade Response": "barley_spike_meristem_v3" + }, + "eplant_barley_legacy": { + "Spike Meristem": "barley_spike_meristem", + "Spike Meristem Shade Response": "barley_spike_meristem" + }, + "eplant_medicago": { + "Seed": "medicago_seed", + "Root": "medicago_root", + "Root Component": "medicago_root", + "Plant": "medicago_mas" + }, + "eplant_eucalyptus": { + "Stress": "eucalyptus", + "Plant": "eucalyptus" + }, + "eplant_rice": { + "Anoxia": "rice_mas", + "Stress": "rice_mas", + "Stigma": "rice_mas", + "Leaf Gradient": "rice_leaf_gradient", + "Root": "rice_root", + "Plant": "rice_mas" + }, + "eplant_sunflower": { + "Plant": "sunflower" + }, + "eplant_cannabis": { + "Plant": "cannabis" + }, + "eplant_wheat": { + "EarlyStages": "wheat", + "MiddleStages": "wheat", + "LateStages": "wheat" + }, + "eplant_sugarcane": { + "Leaf": "sugarcane_leaf", + "Culms": "sugarcane_culms" + } +} \ No newline at end of file diff --git a/tests/resources/test_eplant_arabidopsis.py b/tests/resources/test_eplant_arabidopsis.py new file mode 100644 index 00000000..785c3ca2 --- /dev/null +++ b/tests/resources/test_eplant_arabidopsis.py @@ -0,0 +1,88 @@ +""" +Reena Obmina | UTEA Project 2026 | University of Toronto + +Tests for the ePlant Arabidopsis expression endpoint. + +Route: GET /expression/ePlant_expression?gene=AT1G01010&species=Arabidopsis + +The external plantefp.cgi call inside get_expression() is mocked so tests +run without a network connection to bar.utoronto.ca. + +Usage:: + + python3 -m pytest tests/resources/test_eplant_arabidopsis.py -v +""" +from api import app +from unittest import TestCase +from unittest.mock import patch + +_MOCK_RESULT = { + "gene": "AT1G01010", + "views": { + "atgenexpress": { + "groups": [ + { + "name": "CTRL_7", + "controls": {"ATGE_CTRL_7": 13.05}, + "tissues": [ + { + "name": "Root", + "id": "Root", + "samples": {"ATGE_9_A": 45.35, "ATGE_9_B": 55.0}, + } + ], + } + ] + } + }, +} + + +class TestEPlantArabidopsisExpression(TestCase): + def setUp(self): + self.client = app.test_client() + + @patch("api.resources.expression.get_expression", return_value=_MOCK_RESULT) + def test_valid_request(self, _mock): + response = self.client.get("/expression/ePlant_expression?gene=AT1G01010&species=Arabidopsis") + self.assertEqual(response.status_code, 200) + data = response.json + self.assertTrue(data["wasSuccessful"]) + self.assertEqual(data["data"]["gene"], "AT1G01010") + self.assertIn("views", data["data"]) + _mock.assert_called_once_with("AT1G01010") + + @patch("api.resources.expression.get_expression", return_value=_MOCK_RESULT) + def test_gene_uppercased(self, _mock): + """Gene IDs are normalised to uppercase before being forwarded.""" + self.client.get("/expression/ePlant_expression?gene=at1g01010&species=Arabidopsis") + _mock.assert_called_once_with("AT1G01010") + + @patch("api.resources.expression.get_expression", return_value=_MOCK_RESULT) + def test_species_case_insensitive(self, _mock): + response = self.client.get("/expression/ePlant_expression?gene=AT1G01010&species=arabidopsis") + self.assertEqual(response.status_code, 200) + self.assertTrue(response.json["wasSuccessful"]) + + @patch("api.resources.expression.get_expression", return_value=_MOCK_RESULT) + def test_arabidopsis_thaliana_species(self, _mock): + response = self.client.get( + "/expression/ePlant_expression?gene=AT1G01010&species=Arabidopsis+thaliana" + ) + self.assertEqual(response.status_code, 200) + self.assertTrue(response.json["wasSuccessful"]) + + def test_missing_gene(self): + response = self.client.get("/expression/ePlant_expression?species=Arabidopsis") + self.assertEqual(response.status_code, 400) + self.assertFalse(response.json["wasSuccessful"]) + + def test_invalid_gene(self): + response = self.client.get("/expression/ePlant_expression?gene=NOTAGENEID&species=Arabidopsis") + self.assertEqual(response.status_code, 400) + self.assertFalse(response.json["wasSuccessful"]) + + def test_invalid_species(self): + response = self.client.get("/expression/ePlant_expression?gene=AT1G01010&species=potato") + self.assertEqual(response.status_code, 400) + self.assertFalse(response.json["wasSuccessful"]) diff --git a/tests/resources/test_gene_expression.py b/tests/resources/test_gene_expression.py new file mode 100644 index 00000000..9cf9b6ee --- /dev/null +++ b/tests/resources/test_gene_expression.py @@ -0,0 +1,261 @@ +""" +Tests for the /gene_expression/expression// endpoint. + +Covers three important cases: + 1. Gene ID validation — valid/invalid inputs per database. + 2. Probeset ID input — actual probeset IDs from sample data (no AGI conversion needed). + 3. AGI input for Arabidopsis microarray databases — verifies the AGI→probeset lookup path + is accepted (data retrieval itself is tested in CI where the lookup DB is present). + +Sample probeset IDs are drawn from the JSON files in +.github/workflows/random_rows_json/ to ensure we test with real IDs, not synthetic ones. +""" +from unittest import TestCase + +from api import app +from api.utils.gene_id_utils import GeneIdUtils, DATABASE_EFP_PROJECT + + +class TestGeneExpressionValidation(TestCase): + """Validate that the endpoint accepts and rejects the right gene ID formats.""" + + def setUp(self): + self.client = app.test_client() + + # --- Arabidopsis AGI input (microarray databases) --- + + def test_arabidopsis_agi_accepted_for_microarray_db(self): + """An Arabidopsis AGI is accepted for a microarray-backed database.""" + # The endpoint validates the format; actual data retrieval depends on DB availability + response = self.client.get("/gene_expression/expression/light_series/AT2G21130") + # Should not be a 400 validation error + self.assertNotEqual(response.status_code, 400) + + def test_arabidopsis_agi_case_insensitive(self): + """AGI IDs are accepted regardless of case.""" + response = self.client.get("/gene_expression/expression/light_series/at2g21130") + self.assertNotEqual(response.status_code, 400) + + def test_invalid_arabidopsis_gene_rejected(self): + """A clearly invalid gene ID is rejected with 400.""" + response = self.client.get("/gene_expression/expression/light_series/NOTAGENEID") + self.assertEqual(response.status_code, 400) + self.assertFalse(response.json["wasSuccessful"]) + + # --- Arabidopsis ATH1 probeset IDs (passed directly) --- + + def test_arabidopsis_probeset_accepted_light_series(self): + """An ATH1 probeset ID is accepted for the light_series database.""" + # 263677_at is a real probe from light_series_test_data.json + response = self.client.get("/gene_expression/expression/light_series/263677_at") + self.assertNotEqual(response.status_code, 400) + + def test_arabidopsis_probeset_s_at_accepted(self): + """A _s_at probeset ID is accepted for an Arabidopsis microarray database.""" + # 261283_s_at is a real probe from affydb_test_data.json + response = self.client.get("/gene_expression/expression/affydb/261283_s_at") + self.assertNotEqual(response.status_code, 400) + + def test_arabidopsis_probeset_accepted_atgenexp(self): + """A numeric ATH1 probeset is accepted for the atgenexp database.""" + response = self.client.get("/gene_expression/expression/atgenexp/253680_at") + self.assertNotEqual(response.status_code, 400) + + # --- Seedcoat CATMA/AROS probes --- + + def test_seedcoat_catma_probe_accepted(self): + """A CATMA probe (At + 8 digits) is accepted for the seedcoat database.""" + # At30023977 is a real probe from seedcoat_test_data.json + response = self.client.get("/gene_expression/expression/seedcoat/At30023977") + self.assertNotEqual(response.status_code, 400) + + def test_seedcoat_aros_probe_accepted(self): + """An AROS probe (non-digit + digits + underscore + digits) is accepted for seedcoat.""" + # A017813_01 is a real probe from seedcoat_test_data.json + response = self.client.get("/gene_expression/expression/seedcoat/A017813_01") + self.assertNotEqual(response.status_code, 400) + + def test_seedcoat_invalid_probe_rejected(self): + """A random string is rejected for the seedcoat database.""" + response = self.client.get("/gene_expression/expression/seedcoat/NOTAPROBE") + self.assertEqual(response.status_code, 400) + + # --- Barley microarray probesets --- + + def test_barley_probeset_accepted_mas(self): + """A Contig*_at barley probeset is accepted for barley_mas.""" + # Contig7905_at is a real probe from barley_mas_test_data.json + response = self.client.get("/gene_expression/expression/barley_mas/Contig7905_at") + self.assertNotEqual(response.status_code, 400) + + def test_barley_probeset_accepted_rma(self): + """Complex barley probesets are accepted for barley_rma.""" + # EBro06_SQ001_B02_at is a real probe from barley_rma_test_data.json + response = self.client.get("/gene_expression/expression/barley_rma/EBro06_SQ001_B02_at") + self.assertNotEqual(response.status_code, 400) + + def test_barley_invalid_probe_rejected(self): + """An invalid ID is rejected for barley databases.""" + response = self.client.get("/gene_expression/expression/barley_mas/NOTAPROBE!!!") + self.assertEqual(response.status_code, 400) + + # --- Rice microarray probesets --- + + def test_rice_mas_probeset_accepted(self): + """A rice Os.*_at probeset is accepted for rice_mas.""" + # Os.17822.2.S1_s_at is a real probe from rice_mas_test_data.json + response = self.client.get("/gene_expression/expression/rice_mas/Os.17822.2.S1_s_at") + self.assertNotEqual(response.status_code, 400) + + def test_rice_rma_affx_probeset_accepted(self): + """An OsAffx probeset is accepted for rice_rma.""" + # OsAffx.13653.1.S1_at is a real probe from rice_rma_test_data.json + response = self.client.get("/gene_expression/expression/rice_rma/OsAffx.13653.1.S1_at") + self.assertNotEqual(response.status_code, 400) + + def test_rice_gene_id_accepted(self): + """A canonical LOC_Os rice gene ID is accepted for rice_mas.""" + response = self.client.get("/gene_expression/expression/rice_mas/LOC_Os01g01430") + self.assertNotEqual(response.status_code, 400) + + def test_rice_invalid_id_rejected(self): + """An invalid ID is rejected for rice databases.""" + response = self.client.get("/gene_expression/expression/rice_mas/NOTAPROBE") + self.assertEqual(response.status_code, 400) + + # --- Medicago microarray probesets --- + + def test_medicago_mtr_probeset_accepted(self): + """A Mtr probeset is accepted for medicago_mas.""" + # Mtr.44080.1.S1_at is a real probe from medicago_mas_test_data.json + response = self.client.get("/gene_expression/expression/medicago_mas/Mtr.44080.1.S1_at") + self.assertNotEqual(response.status_code, 400) + + def test_medicago_msa_probeset_accepted(self): + """A Msa probeset is accepted for medicago_rma.""" + # Msa.959.1.S1_at is a real probe from medicago_mas_test_data.json + response = self.client.get("/gene_expression/expression/medicago_rma/Msa.959.1.S1_at") + self.assertNotEqual(response.status_code, 400) + + def test_medicago_sme_probeset_accepted(self): + """A Sme probeset is accepted for medicago databases.""" + # Sme.396.1.S1_at is a real probe from medicago_rma_test_data.json + response = self.client.get("/gene_expression/expression/medicago_rma/Sme.396.1.S1_at") + self.assertNotEqual(response.status_code, 400) + + # --- Poplar microarray probesets --- + + def test_poplar_ptpaffx_probeset_accepted(self): + """A PtpAffx probeset is accepted for the poplar database.""" + # PtpAffx.154622.1.S1_at is a real probe from poplar_test_data.json + response = self.client.get("/gene_expression/expression/poplar/PtpAffx.154622.1.S1_at") + self.assertNotEqual(response.status_code, 400) + + def test_poplar_ptp_s_at_probeset_accepted(self): + """A PtpAffx _s_at probeset is accepted for the poplar database.""" + # PtpAffx.202274.1.S1_s_at is a real probe from poplar_test_data.json + response = self.client.get( + "/gene_expression/expression/poplar/PtpAffx.202274.1.S1_s_at" + ) + self.assertNotEqual(response.status_code, 400) + + # --- Triticale microarray probesets --- + + def test_triticale_probeset_accepted(self): + """A Ta.*_at triticale probeset is accepted for the triticale database.""" + # Ta.8002.1.S1_at is a real probe from triticale_test_data.json + response = self.client.get("/gene_expression/expression/triticale/Ta.8002.1.S1_at") + self.assertNotEqual(response.status_code, 400) + + # --- Unknown database --- + + def test_unknown_database_rejected(self): + """An unknown database name returns an error response.""" + response = self.client.get( + "/gene_expression/expression/totally_unknown_database/AT1G01010" + ) + self.assertFalse(response.json.get("wasSuccessful", True)) + + +class TestGeneIdUtilsDatabase(TestCase): + """Unit tests for validate_gene_for_database() and DATABASE_EFP_PROJECT mapping.""" + + def test_database_efp_project_has_microarray_dbs(self): + """All expected microarray databases must have an eFP project mapping.""" + expected_dbs = [ + "affydb", "arabidopsis_ecotypes", "atgenexp", "light_series", + "seedcoat", + "barley_mas", "barley_rma", + "rice_mas", "rice_rma", + "medicago_mas", "medicago_rma", + "poplar", + "triticale", "triticale_mas", + ] + for db in expected_dbs: + self.assertIn(db, DATABASE_EFP_PROJECT, f"Missing DATABASE_EFP_PROJECT entry for {db}") + + def test_validate_arabidopsis_agi(self): + """AGI IDs are valid for arabidopsis microarray databases.""" + self.assertTrue(GeneIdUtils.validate_gene_for_database("AT1G01010", "light_series")) + self.assertTrue(GeneIdUtils.validate_gene_for_database("AT2G21130", "affydb")) + + def test_validate_arabidopsis_probeset(self): + """ATH1 probeset IDs are valid for arabidopsis microarray databases.""" + self.assertTrue(GeneIdUtils.validate_gene_for_database("267643_at", "light_series")) + self.assertTrue(GeneIdUtils.validate_gene_for_database("261283_s_at", "affydb")) + + def test_validate_seedcoat_catma_probe(self): + """CATMA probe IDs are valid for the seedcoat database.""" + self.assertTrue(GeneIdUtils.validate_gene_for_database("At30023977", "seedcoat")) + self.assertTrue(GeneIdUtils.validate_gene_for_database("At30027789", "seedcoat")) + + def test_validate_seedcoat_aros_probe(self): + """AROS probe IDs are valid for the seedcoat database.""" + self.assertTrue(GeneIdUtils.validate_gene_for_database("A017813_01", "seedcoat")) + + def test_validate_barley_probeset(self): + """Barley probeset IDs are valid for barley microarray databases.""" + self.assertTrue(GeneIdUtils.validate_gene_for_database("Contig7905_at", "barley_mas")) + self.assertTrue( + GeneIdUtils.validate_gene_for_database("EBro06_SQ001_B02_at", "barley_rma") + ) + + def test_validate_rice_probeset(self): + """Rice probeset IDs are valid for rice microarray databases.""" + self.assertTrue(GeneIdUtils.validate_gene_for_database("Os.17822.2.S1_s_at", "rice_mas")) + self.assertTrue(GeneIdUtils.validate_gene_for_database("OsAffx.13653.1.S1_at", "rice_rma")) + + def test_validate_medicago_probeset(self): + """Medicago probeset IDs are valid for medicago microarray databases.""" + self.assertTrue(GeneIdUtils.validate_gene_for_database("Mtr.44080.1.S1_at", "medicago_mas")) + self.assertTrue(GeneIdUtils.validate_gene_for_database("Sme.396.1.S1_at", "medicago_rma")) + + def test_validate_poplar_probeset(self): + """Poplar probeset IDs are valid for the poplar microarray database.""" + self.assertTrue(GeneIdUtils.validate_gene_for_database("PtpAffx.154622.1.S1_at", "poplar")) + + def test_validate_triticale_probeset(self): + """Triticale probeset IDs are valid for the triticale database.""" + self.assertTrue(GeneIdUtils.validate_gene_for_database("Ta.8002.1.S1_at", "triticale")) + + def test_is_probeset_id_detects_catma_probe(self): + """CATMA probes (At + 8 digits) are recognised as probeset IDs.""" + self.assertTrue(GeneIdUtils.is_probeset_id("At30023977")) + self.assertTrue(GeneIdUtils.is_probeset_id("At30027789")) + + def test_is_probeset_id_detects_affymetrix_probe(self): + """Standard _at probes are recognised as probeset IDs.""" + self.assertTrue(GeneIdUtils.is_probeset_id("267643_at")) + self.assertTrue(GeneIdUtils.is_probeset_id("Contig7905_at")) + self.assertTrue(GeneIdUtils.is_probeset_id("Os.17822.2.S1_s_at")) + + def test_is_probeset_id_rejects_gene_ids(self): + """Canonical gene IDs are NOT treated as probeset IDs.""" + self.assertFalse(GeneIdUtils.is_probeset_id("AT1G01010")) + self.assertFalse(GeneIdUtils.is_probeset_id("LOC_Os01g01430")) + self.assertFalse(GeneIdUtils.is_probeset_id("randomjunk")) + + def test_validate_gene_for_non_efp_database_falls_back_to_species(self): + """Non-microarray databases use species-based validation.""" + self.assertTrue(GeneIdUtils.validate_gene_for_database("AT1G01010", "klepikova")) + self.assertFalse(GeneIdUtils.validate_gene_for_database("NOTAGENEID", "klepikova")) diff --git a/tests/utils/test_bar_utils.py b/tests/utils/test_bar_utils.py index 7396d66a..c16a5fba 100644 --- a/tests/utils/test_bar_utils.py +++ b/tests/utils/test_bar_utils.py @@ -1,5 +1,5 @@ from unittest import TestCase -from api.utils.bar_utils import BARUtils +from api.utils.bar_utils import BARUtils, EFP_PROJECT_REGEXES class UtilsUnitTest(TestCase): @@ -149,3 +149,117 @@ def test_format_poplar(self): result = BARUtils.format_poplar("potri.019g123900.1") expected = "Potri.019G123900.1" self.assertEqual(result, expected) + + def test_efp_project_regexes_exist(self): + """All expected eFP project keys must be present in EFP_PROJECT_REGEXES.""" + required = [ + "efp", "efp_arabidopsis", "efp_seedcoat", + "efp_barley", "efpbarley", + "efp_rice", "efprice", + "efp_medicago", "efpmedicago", + "efp_poplar", "efppop", + "efp_soybean", "efpsoybean", + "efp_maize", "maizeefp", + "efp_triticale", + "efp_human", + ] + for key in required: + self.assertIn(key, EFP_PROJECT_REGEXES, f"Missing eFP project key: {key}") + + def test_is_efp_gene_valid_arabidopsis(self): + """efp_arabidopsis accepts AGI, ATH1 probeset IDs, and standalone numerics.""" + # Valid canonical AGI gene IDs + self.assertTrue(BARUtils.is_efp_gene_valid("AT2G21130", "efp_arabidopsis")) + self.assertTrue(BARUtils.is_efp_gene_valid("At1g01010", "efp_arabidopsis")) + self.assertTrue(BARUtils.is_efp_gene_valid("AtCg00020", "efp_arabidopsis")) + + # Valid Arabidopsis ATH1 probeset IDs (from sample data) + self.assertTrue(BARUtils.is_efp_gene_valid("267643_at", "efp_arabidopsis")) + self.assertTrue(BARUtils.is_efp_gene_valid("267644_s_at", "efp_arabidopsis")) + self.assertTrue(BARUtils.is_efp_gene_valid("261283_s_at", "efp_arabidopsis")) + self.assertTrue(BARUtils.is_efp_gene_valid("253680_at", "efp_arabidopsis")) + + # Valid standalone numeric IDs + self.assertTrue(BARUtils.is_efp_gene_valid("267643", "efp_arabidopsis")) + + # Invalid IDs + self.assertFalse(BARUtils.is_efp_gene_valid("9T2G21130", "efp_arabidopsis")) + self.assertFalse(BARUtils.is_efp_gene_valid("AT2G2113X", "efp_arabidopsis")) + self.assertFalse(BARUtils.is_efp_gene_valid("Solyc04g054700", "efp_arabidopsis")) + self.assertFalse(BARUtils.is_efp_gene_valid("randomjunk", "efp_arabidopsis")) + + def test_is_efp_gene_valid_seedcoat(self): + """efp_seedcoat accepts AGI, ATH1 probesets, CATMA probes, and AROS probes.""" + self.assertTrue(BARUtils.is_efp_gene_valid("At1g01010", "efp_seedcoat")) + self.assertTrue(BARUtils.is_efp_gene_valid("At30023977", "efp_seedcoat")) + self.assertTrue(BARUtils.is_efp_gene_valid("At30027789", "efp_seedcoat")) + self.assertTrue(BARUtils.is_efp_gene_valid("A017813_01", "efp_seedcoat")) + self.assertTrue(BARUtils.is_efp_gene_valid("A006881_01", "efp_seedcoat")) + self.assertFalse(BARUtils.is_efp_gene_valid("randomjunk", "efp_seedcoat")) + + def test_is_efp_gene_valid_barley(self): + """efp_barley accepts barley gene IDs and Affymetrix barley probeset IDs.""" + # Probeset IDs from barley_mas and barley_rma sample data + self.assertTrue(BARUtils.is_efp_gene_valid("Contig7905_at", "efp_barley")) + self.assertTrue(BARUtils.is_efp_gene_valid("Contig440_s_at", "efp_barley")) + self.assertTrue(BARUtils.is_efp_gene_valid("EBro06_SQ001_B02_at", "efp_barley")) + self.assertTrue(BARUtils.is_efp_gene_valid("HVSMEi0007J05r2_at", "efp_barley")) + self.assertTrue(BARUtils.is_efp_gene_valid("Contig12089_at", "efp_barley")) + # efpbarley alias + self.assertTrue(BARUtils.is_efp_gene_valid("Contig7905_at", "efpbarley")) + + self.assertFalse(BARUtils.is_efp_gene_valid("AT1G01010", "efp_barley")) + self.assertFalse(BARUtils.is_efp_gene_valid("randomjunk", "efp_barley")) + + def test_is_efp_gene_valid_rice(self): + """efp_rice accepts canonical rice gene IDs and rice array probeset IDs.""" + self.assertTrue(BARUtils.is_efp_gene_valid("LOC_Os01g01430", "efp_rice")) + self.assertTrue(BARUtils.is_efp_gene_valid("Os.17822.2.S1_s_at", "efp_rice")) + self.assertTrue(BARUtils.is_efp_gene_valid("OsAffx.4511.1.S1_s_at", "efp_rice")) + self.assertTrue(BARUtils.is_efp_gene_valid("Os.12223.2.S1_at", "efp_rice")) + # efprice alias + self.assertTrue(BARUtils.is_efp_gene_valid("LOC_Os01g01430", "efprice")) + + self.assertFalse(BARUtils.is_efp_gene_valid("AT1G01010", "efp_rice")) + self.assertFalse(BARUtils.is_efp_gene_valid("randomjunk", "efp_rice")) + + def test_is_efp_gene_valid_medicago(self): + """efp_medicago accepts canonical Medicago gene IDs and Medicago array probeset IDs.""" + self.assertTrue(BARUtils.is_efp_gene_valid("Medtr1g018805", "efp_medicago")) + self.assertTrue(BARUtils.is_efp_gene_valid("Mtr.44080.1.S1_at", "efp_medicago")) + self.assertTrue(BARUtils.is_efp_gene_valid("Msa.959.1.S1_at", "efp_medicago")) + self.assertTrue(BARUtils.is_efp_gene_valid("Sme.396.1.S1_at", "efp_medicago")) + # _s_at variants must also match (e.g. Mtr.50680.1.S1_s_at from medicago_rma) + self.assertTrue(BARUtils.is_efp_gene_valid("Mtr.50680.1.S1_s_at", "efp_medicago")) + # efpmedicago alias + self.assertTrue(BARUtils.is_efp_gene_valid("Medtr1g018805", "efpmedicago")) + + self.assertFalse(BARUtils.is_efp_gene_valid("AT1G01010", "efp_medicago")) + self.assertFalse(BARUtils.is_efp_gene_valid("randomjunk", "efp_medicago")) + + def test_is_efp_gene_valid_poplar(self): + """efp_poplar accepts Potri gene IDs and poplar array probeset IDs.""" + self.assertTrue(BARUtils.is_efp_gene_valid("Potri.019G123900.1", "efp_poplar")) + self.assertTrue(BARUtils.is_efp_gene_valid("PtpAffx.154622.1.S1_at", "efp_poplar")) + self.assertTrue(BARUtils.is_efp_gene_valid("PtpAffx.37687.1.S1_at", "efp_poplar")) + self.assertTrue(BARUtils.is_efp_gene_valid("PtpAffx.202274.1.S1_s_at", "efp_poplar")) + # efppop alias + self.assertTrue(BARUtils.is_efp_gene_valid("PtpAffx.154622.1.S1_at", "efppop")) + + self.assertFalse(BARUtils.is_efp_gene_valid("AT1G01010", "efp_poplar")) + self.assertFalse(BARUtils.is_efp_gene_valid("randomjunk", "efp_poplar")) + + def test_is_efp_gene_valid_triticale(self): + """efp_triticale accepts Ta.* and TaAffx.* probeset IDs (both occur in data).""" + self.assertTrue(BARUtils.is_efp_gene_valid("Ta.8002.1.S1_at", "efp_triticale")) + # TaAffx probes from triticale_test_data.json — require TaAffx prefix support + self.assertTrue(BARUtils.is_efp_gene_valid("TaAffx.54155.1.S1_at", "efp_triticale")) + self.assertTrue(BARUtils.is_efp_gene_valid("TaAffx.6560.1.S1_at", "efp_triticale")) + self.assertTrue(BARUtils.is_efp_gene_valid("Ta.3469.1.A1_at", "efp_triticale")) + + self.assertFalse(BARUtils.is_efp_gene_valid("randomjunk", "efp_triticale")) + self.assertFalse(BARUtils.is_efp_gene_valid("AT1G01010", "efp_triticale")) + + def test_is_efp_gene_valid_unknown_project(self): + """Unknown eFP project returns False regardless of gene ID.""" + self.assertFalse(BARUtils.is_efp_gene_valid("AT1G01010", "efp_unknown_species")) diff --git a/validate_db_regex_coverage.py b/validate_db_regex_coverage.py new file mode 100644 index 00000000..13a4d0f7 --- /dev/null +++ b/validate_db_regex_coverage.py @@ -0,0 +1,137 @@ +""" +Reena Obmina | BCB330 Project 2025-2026 | University of Toronto + +Task 2 (Jun 11 2026): test Vincent's per-project eFP regexes against every +database that has real sample data in api/random_rows_json/, to find +databases whose probeset/gene IDs the current production validator +(GeneIdUtils.validate_gene_for_database) would incorrectly reject. + +The universe tested is the FULL random_rows_json folder, not just the +databases reachable from a live eFP/ePlant dropdown today (data/efp_info/ +db_source_summary.json) -- some databases Vincent has sample data for are no +longer linked from any current dropdown (legacy/retired views) but are still +queryable directly by db name and already validator-ready (DATABASE_SPECIES / +DATABASE_EFP_PROJECT), so they're tested too and flagged via in_master_list. + +Reads: api/random_rows_json/{db}_test_data.json — real sample rows, one file per db + data/efp_info/db_source_summary.json — db -> efp/eplant/both, for dbs reachable live + api/utils/gene_id_utils.py / bar_utils.py — current production validators +Writes: db_regex_coverage_report.csv — one row per db: pass/fail counts + gap flag +""" + +import csv +import json +import sys +import types +from pathlib import Path + +# importing api.utils.gene_id_utils normally runs api/__init__.py's create_app(), +# which tries to connect to MySQL even for this standalone script. Pre-register +# empty stand-in packages so Python loads the submodules directly instead. +sys.modules.setdefault("api", types.ModuleType("api")) +sys.modules["api"].__path__ = ["api"] +sys.modules.setdefault("api.utils", types.ModuleType("api.utils")) +sys.modules["api.utils"].__path__ = ["api/utils"] + +from api.utils.gene_id_utils import DATABASE_EFP_PROJECT, DATABASE_SPECIES, GeneIdUtils # noqa: E402 + +SAMPLE_DIR = Path("api/random_rows_json") + + +def load_samples(db): + path = SAMPLE_DIR / f"{db}_test_data.json" + if not path.exists(): + return None + with open(path) as f: + rows = json.load(f) + ids = [] + seen = set() + for row in rows: + gene_id = row.get("data_probeset_id") + if gene_id and gene_id not in seen: + seen.add(gene_id) + ids.append(gene_id) + return ids + + +def main(): + with open("data/efp_info/db_source_summary.json") as f: + db_sources = json.load(f) + + sample_dbs = {p.name[: -len("_test_data.json")] for p in SAMPLE_DIR.glob("*_test_data.json")} + all_dbs = sample_dbs | set(db_sources) + + report_rows = [] + gap_count = 0 + no_sample_count = 0 + no_species_mapping_count = 0 + + for db in sorted(all_dbs): + source = db_sources.get(db, "legacy_not_in_dropdown") + sample_ids = load_samples(db) + if sample_ids is None: + no_sample_count += 1 + report_rows.append( + { + "database": db, + "source": source, + "in_master_list": db in db_sources, + "has_species_mapping": db in DATABASE_SPECIES, + "has_efp_project_override": db in DATABASE_EFP_PROJECT, + "n_samples": 0, + "n_pass": 0, + "n_fail": 0, + "looks_like_probeset": "", + "failing_ids": "NO SAMPLE DATA", + } + ) + continue + if db not in DATABASE_SPECIES and db not in DATABASE_EFP_PROJECT: + no_species_mapping_count += 1 + + n_pass = 0 + failing_ids = [] + any_probeset_shaped = False + for gene_id in sample_ids: + if GeneIdUtils.is_probeset_id(gene_id): + any_probeset_shaped = True + if GeneIdUtils.validate_gene_for_database(gene_id, db): + n_pass += 1 + else: + failing_ids.append(gene_id) + + is_gap = bool(failing_ids) + if is_gap: + gap_count += 1 + + report_rows.append( + { + "database": db, + "source": source, + "in_master_list": db in db_sources, + "has_species_mapping": db in DATABASE_SPECIES, + "has_efp_project_override": db in DATABASE_EFP_PROJECT, + "n_samples": len(sample_ids), + "n_pass": n_pass, + "n_fail": len(failing_ids), + "looks_like_probeset": any_probeset_shaped, + "failing_ids": "|".join(failing_ids[:5]), + } + ) + + out_file = "db_regex_coverage_report.csv" + with open(out_file, "w", newline="") as f: + writer = csv.DictWriter(f, fieldnames=list(report_rows[0].keys())) + writer.writeheader() + writer.writerows(report_rows) + + print(f"Checked {len(all_dbs)} databases ({len(db_sources)} in live master list, " + f"{len(all_dbs) - len(db_sources)} legacy/not currently linked from any dropdown).") + print(f" No sample data found: {no_sample_count}") + print(f" No species/eFP-project mapping at all: {no_species_mapping_count}") + print(f" Databases with >=1 real sample ID rejected by current validation: {gap_count}") + print(f"Report written to {out_file}") + + +if __name__ == "__main__": + main() From a577ee30d1c20f6e4f98a6f0bbb372e9a0754c5a Mon Sep 17 00:00:00 2001 From: Reena Date: Fri, 17 Jul 2026 13:29:29 -0400 Subject: [PATCH 2/3] Integrate Vincent's regex registry, fix master JSON species, refactor endpoints to use it - Merge heterodera_schachtii into arabidopsis (it's an Arabidopsis-gene-ID database, not a separate species); fix brassica/lupin/triticale scientific names per professor's review comments - Load EFP_PROJECT_REGEXES and DATABASE_EFP_PROJECT from Vincent's regex_master_list_efp_eplant registry (58 grouped project patterns instead of 193 per-database ones), embedded into combined_master.json at build time; empirically verify every regex_project assignment against real sample dumps before trusting it, demoting 3 unverified species-fallback guesses and fixing 2 misassigned projects (maize_lipid_map, tomato_trait) - Add a general injection checker (BARUtils.is_injection_attempt) that runs before the probeset-shape check in /gene_expression, closing a bypass where any string ending in "_at" skipped format validation entirely - Derive schema_variants directly from real sample_data column dumps instead of a coarse rna_seq/microarray platform split, so every one of the 193 databases is schema_verified against its own real columns (was 146/193) - Refactor /microarray_gene_expression//databases and ...///samples to read from combined_master.json instead of a hardcoded dict and a since-deleted JSON file (the latter was broken on this branch); add test coverage for both - Add api/utils/master_data_utils.py as the shared combined_master.json loader used across bar_utils, gene_id_utils, and the refactored resource --- ALL_EFP_REGEXES.csv | 58 + ALL_REGEXES_FOR_VINCENT.csv | 56 + EMAIL_FOR_VINCENT.txt | 55 + EMAIL_TO_VINCENT_JUL_17_2026.txt | 72 + EMAIL_TO_VINCENT_JUN_25_2026.txt | 69 + VINCENT_REGEX_PACKAGE_JUN25.md | 143 + ...fp-projects-views-with-lookup-settings.txt | 268 + all_gene_id_regexes.csv | 108 + api/models/efp_schemas.py | 2 +- .../actinidia_bud_development_test_data.json | 242 + ...ia_flower_fruit_development_test_data.json | 242 + .../actinidia_postharvest_test_data.json | 242 + ...actinidia_vegetative_growth_test_data.json | 242 + api/random_rows_json/affydb_test_data.json | 362 + api/random_rows_json/apple_test_data.json | 242 + .../arabidopsis_ecotypes_test_data.json | 332 + api/random_rows_json/arachis_test_data.json | 242 + .../atgenexp_hormone_test_data.json | 302 + .../atgenexp_pathogen_test_data.json | 302 + .../atgenexp_plus_test_data.json | 332 + .../atgenexp_stress_test_data.json | 302 + api/random_rows_json/atgenexp_test_data.json | 332 + .../barley_mas_test_data.json | 362 + .../barley_rma_test_data.json | 332 + .../barley_seed_test_data.json | 242 + .../barley_spike_meristem_test_data.json | 242 + .../barley_spike_meristem_v3_test_data.json | 242 + .../brachypodium_Bd21_test_data.json | 242 + .../brachypodium_embryogenesis_test_data.json | 242 + .../brachypodium_grains_test_data.json | 242 + ...rachypodium_metabolites_map_test_data.json | 242 + ...chypodium_photo_thermocycle_test_data.json | 242 + .../brachypodium_test_data.json | 242 + ...ca_rapa_developmental_atlas_test_data.json | 242 + .../brassica_rapa_test_data.json | 242 + ...cao_developmental_atlas_sca_test_data.json | 242 + .../cacao_developmental_atlas_test_data.json | 242 + ...o_drought_diurnal_atlas_sca_test_data.json | 242 + ...cacao_drought_diurnal_atlas_test_data.json | 242 + .../cacao_infection_test_data.json | 242 + .../cacao_leaf_test_data.json | 242 + .../cacao_meristem_atlas_sca_test_data.json | 242 + .../cacao_seed_atlas_sca_test_data.json | 242 + api/random_rows_json/camelina_test_data.json | 272 + .../camelina_tpm_test_data.json | 272 + api/random_rows_json/cannabis_test_data.json | 242 + .../canola_original_test_data.json | 362 + .../canola_original_v2_test_data.json | 362 + .../canola_seed_test_data.json | 242 + api/random_rows_json/canola_test_data.json | 362 + .../cassava_atlas_test_data.json | 242 + .../cassava_cbb_test_data.json | 242 + .../cassava_eacmv_test_data.json | 242 + .../circadian_mutants_test_data.json | 242 + ...cuta_early_haustoriogenesis_test_data.json | 242 + .../cuscuta_lmd_test_data.json | 242 + api/random_rows_json/cuscuta_test_data.json | 242 + .../dna_damage_test_data.json | 242 + .../durum_wheat_abiotic_stress_test_data.json | 242 + .../durum_wheat_biotic_stress_test_data.json | 242 + .../durum_wheat_development_test_data.json | 242 + api/random_rows_json/embryo_test_data.json | 242 + .../eucalyptus_test_data.json | 242 + api/random_rows_json/euphorbia_test_data.json | 242 + .../gc_drought_test_data.json | 242 + .../germination_test_data.json | 242 + .../grape_developmental_test_data.json | 362 + .../guard_cell_test_data.json | 332 + api/random_rows_json/gynoecium_test_data.json | 242 + .../heterodera_schachtii_test_data.json | 242 + api/random_rows_json/hnahal_test_data.json | 302 + .../human_body_map_2_test_data.json | 332 + ...man_developmental_SpongeLab_test_data.json | 332 + .../human_developmental_test_data.json | 332 + .../human_diseased_test_data.json | 332 + api/random_rows_json/kalanchoe_test_data.json | 242 + ...anchoe_time_course_analysis_test_data.json | 242 + api/random_rows_json/klepikova_test_data.json | 272 + .../lateral_root_initiation_test_data.json | 272 + .../light_series_test_data.json | 332 + api/random_rows_json/lipid_map_test_data.json | 242 + .../little_millet_test_data.json | 242 + .../lupin_lcm_leaf_test_data.json | 242 + .../lupin_lcm_pod_test_data.json | 242 + .../lupin_lcm_stem_test_data.json | 242 + .../lupin_pod_seed_test_data.json | 242 + .../lupin_whole_plant_test_data.json | 242 + .../maize_RMA_linear_test_data.json | 362 + .../maize_RMA_log_test_data.json | 332 + .../maize_atlas_test_data.json | 242 + .../maize_atlas_v5_test_data.json | 242 + .../maize_buell_lab_test_data.json | 242 + .../maize_early_seed_test_data.json | 242 + .../maize_ears_test_data.json | 332 + ..._embryonic_leaf_development_test_data.json | 242 + .../maize_enzyme_test_data.json | 332 + .../maize_gdowns_test_data.json | 242 + .../maize_iplant_test_data.json | 332 + .../maize_kernel_v5_test_data.json | 242 + .../maize_leaf_gradient_test_data.json | 332 + .../maize_lipid_map_test_data.json | 242 + .../maize_metabolite_test_data.json | 332 + ...ize_nitrogen_use_efficiency_test_data.json | 242 + .../maize_rice_comparison_test_data.json | 332 + .../maize_root_test_data.json | 242 + .../maize_stress_v5_test_data.json | 242 + .../mangosteen_aril_vs_rind_test_data.json | 242 + .../mangosteen_callus_test_data.json | 242 + ...ngosteen_diseased_vs_normal_test_data.json | 242 + .../mangosteen_fruit_ripening_test_data.json | 242 + ...eed_development_germination_test_data.json | 242 + ...mangosteen_seed_development_test_data.json | 242 + ...mangosteen_seed_germination_test_data.json | 242 + .../marchantia_organ_stress_test_data.json | 242 + .../medicago_mas_test_data.json | 362 + .../medicago_rma_test_data.json | 332 + .../medicago_root_test_data.json | 272 + .../medicago_root_v5_test_data.json | 242 + .../medicago_seed_test_data.json | 272 + .../meristem_db_new_test_data.json | 302 + .../meristem_db_test_data.json | 302 + api/random_rows_json/mouse_db_test_data.json | 182 + api/random_rows_json/oat_test_data.json | 332 + .../phelipanche_test_data.json | 242 + .../physcomitrella_db_test_data.json | 242 + .../poplar_hormone_test_data.json | 242 + .../poplar_leaf_test_data.json | 242 + api/random_rows_json/poplar_test_data.json | 362 + .../poplar_xylem_test_data.json | 242 + .../potato_dev_test_data.json | 242 + .../potato_stress_test_data.json | 242 + .../potato_wounding_test_data.json | 242 + .../quinoa_nutrient_test_data.json | 242 + 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api/random_rows_json/wheat_meiosis_test_data.json create mode 100644 api/random_rows_json/wheat_root_test_data.json create mode 100644 api/random_rows_json/wheat_test_data.json create mode 100644 api/random_rows_json/willow_test_data.json create mode 100644 api/utils/master_data_utils.py create mode 100644 build_combined_master_json.py create mode 100644 cfg_dbs.txt create mode 100644 data/efp_info/combined_master.json create mode 100644 data/efp_info/efp_human/Circulatory_Respiratory.xml create mode 100644 data/efp_info/efp_human/Illumina_Body_Map_2_-_FPKM.xml create mode 100644 data/efp_info/efp_human/Nervous.xml create mode 100644 data/efp_info/efp_human/Reproductive.xml create mode 100644 data/efp_info/efp_human/Skeletal_Immune_Digestive.xml create mode 100644 data/efp_info/efp_human/efp_info.xml delete mode 100644 data/efp_info/efp_species_view_info.json delete mode 100644 data/efp_info/efp_species_view_info_typed.json create mode 100644 data/regex_master_list_efp_eplant/bar_regex_by_db.csv create mode 100644 data/regex_master_list_efp_eplant/bar_regex_master.csv create mode 100644 data/regex_master_list_efp_eplant/bar_regex_registry.json create mode 100644 generate_efp_test_cases.py create mode 100644 live_example_gene_id_coverage.csv create mode 100644 mysql_dbs.txt create mode 100644 speed_bar_chart.png create mode 100644 speed_box_plots.png create mode 100644 speed_graphs.py create mode 100644 validate_live_example_gene_ids.py create mode 100644 vincent_regex_summary_jun_25_2026.md diff --git a/ALL_EFP_REGEXES.csv b/ALL_EFP_REGEXES.csv new file mode 100644 index 00000000..5a6e5173 --- /dev/null +++ b/ALL_EFP_REGEXES.csv @@ -0,0 +1,58 @@ +project,regex +efp,"(r"^([Aa][Tt][12345CM][Gg][0-9]{5})$"r"|^([0-9]{6}(_[xsfi])?_at)$"r"|^([0-9]{6,9})$"# ATH1 Affymetrix bacterial/control spike-in probes, shared by all Affy platformsr"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$"r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$")" +efp_arabidopsis,"(r"^([Aa][Tt][12345CM][Gg][0-9]{5})$"r"|^([0-9]{6}(_[xsfi])?_at)$"r"|^([0-9]{6,9})$"r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$"r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$")# Seedcoat uses CATMA probes (At\d{8}) and AROS probes (\D\d+_\d+) in addition to ATH1" +efp_seedcoat,"(r"^(At[12345CM]g[0-9]{5})$"r"|^([0-9]{6}(_[xsfi])?_at)$"r"|^([0-9]{6,9})$"r"|^(\D\d+_\d+)$"r"|^(At\d{8})$")" +efp_barley,"(r"^((HM|HV).*)$|^(HV.*_at)$"r"|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4})_at)$"r"|^([0-9]{4,5}\.AF[0-9]{5}(_|_x_)at)$"r"|^(A[0-9]{5}\.[0-9]{1}(_|_x_|_s_)at)$"r"|^(([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)(_|_x_|_s_|_CDS-[0-9]{1,2}_|_CDS-[0-9]{1,2}_s_)at)$"r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$"r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$"r"|^(ChlorContig[0-9]{1,2}(_|_x_|_s_)at)$"r"|^(((MitoContig|Contig)[0-9]{1,6})(_|_x_|_s_)at)$"r"|^(D[0-9]{5}_at)$"r"|^(Dhn[0-9]{2}\(Morex\)(_|_s_)at)$"r"|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2}(_|_s_|_x_)at)$"r"|^(Franka(_|_b_)3pri[0-9]{1,2}(_|_s_|_x_)at)$"r"|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$"r"|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$"r"|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru](_|_x_|_s_)at)$"r"|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1}(_|_x_|_s_)at)$"r"|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2}(_|_x_|_s_)at)$"r"|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4}))$"r"|^([0-9]{4,5}\.AF[0-9]{5})$"r"|^(A[0-9]{5}\.[0-9]{1})$"r"|^([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)$"r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX))$"r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre))$"r"|^(ChlorContig[0-9]{1,2})$"r"|^((MitoContig|Contig)[0-9]{1,6})$"r"|^(D[0-9]{5})$"r"|^(Dhn[0-9]{2}\(Morex\))$"r"|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2})$"r"|^(Franka(_|_b_)3pri[0-9]{1,2})$"r"|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$"r"|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$"r"|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru])$"r"|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1})$"r"|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2})$"r"|^(HO)$"r"|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$"r"|^(AK[0-9]{6}\.1)$"r"|^(AJ[0-9]{6}\.1)$")" +efp_rice,"(r"^(LOC_Os[0-9]{2}g[0-9]{5})$"r"|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$"r"|^(AFFX-OS-(18SrRNA|25SrRNA|5\.8SrRNA)_(s_at|at))$"r"|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$"r"|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$"r"|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$"r"|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$"r"|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$")" +efp_medicago,"(r"^(Medtr\d{1}g\d{6})$"r"|^(Medtr\d{1}g\d{6}\.[0-9]{1})$"" +# Medicago array probesets,"Mtr/Msa/Sme prefix, any Affymetrix suffix variantr"|^(Mtr\.\d{4,5}\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$"r"|^(Msa\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$"r"|^(Sme\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$"r"|^(AFFX-(Bio|Cre|Dap|Lys|Phe|Thr|Trpn)(B|C|Dn|X)-(3|5|M)_at)$"r"|^(AFFX-(Msa|Mtr)-(actin|gapc|gsta|ubq11|TrpnX)-(3|5|M)_(at|x_at|s_at))$"r"|^(AFFX-r2-(Bs|Ec|P1)-(cre|dap|lys|phe|thr|bioB|bioC|bioD)-(3|5|M)_(at|s_at|x_at))$"r"|^(AFFX-Mtr-ubq11-(3|5|M)_(at|s_at|x_at))$"r"|^(AFFX-r2-Tag[A-Z]{1,2}_at)$"r"|^(Medtr_v1_\d{6})$")" +efp_poplar,"(r"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$"r"|^((eugene3)\.\d{6,12})$"r"|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$"r"|^((grail3\.)\d{8,12})$"r"|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$"r"|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$"r"|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$"# poplar_hormone's real sample IDs omit the transcript suffix entirelyr"|^(Potri\.[0-9]{3}G[0-9]{6}(\.[0-9]{1})?)$")" +efp_soybean,"(r"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$"r"|^(Glyma\.\d{1,3}g\d{1,8}))$")" +efp_maize,"(r"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$"r"|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$"r"|^(GRMZM(2|5)G[0-9]{6})$"r"|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$"r"|^(Zm\d+d\d+)$"r"|^(Zm\d{1,10}eb\d{1,10})$"# Maize Affymetrix probeset IDs, e.g. Zm011368_at, Zm039842_s_atr"|^(Zm\d{6}(_[xsa])?_at)$")# TaAffx.* probes occur alongside Ta.* — handle both prefixes" +efp_triticale,"r"^((Ta|TaAffx)\.\d+\.\d+\.[A-Z]\d+_(at|s_at|x_at|a_at))$"# Affymetrix human probeset IDs (1557575_at, 202019_s_at) plus a loose fallback" +efp_human,"r"^(\d{6,7}(_[xsa])?_at)$|^(\D{0,12}\d{0,12})$|^(\d{1,12})$"# Remaining eFP projects, sourced verbatim from Vincent's efp_regex_audit_prod.csv" +efp_Eutrema,"r"^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$"" +efp_actinidia,"r"^(Acc\d+\.\d{0,3})$"" +efp_apple,"r"^(MfusH1_\d\dg\d{1,8})$"" +# CSV pattern is lowercase-only; lipid species names use mixed case (e.g. "TG 54,"5; ...")" +efp_arabidopsis_lipid,"r"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$"" +efp_arachis,"r"^(Adur\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Aipa_c\d+_g\d+_i\d+)$|^(Aipa\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Adur_c\d+_g\d+_i\d+)$"" +efp_brachypodium,"r"^(Bradi\d+g\d+.\d)$|^(Bradi\d+s\d+.\d)$|^(Bradi\d+.g\d+)$"" +efp_brachypodium_metabolites,"r"(?i)^[a-z\s\-]{1,60}$"" +efp_brassica_rapa,"r"^(Bra.\d+g\d{0,10})$"" +efp_cacao_ccn,"r"^(CCN-51_Chr\d{1,3}v\d{1,3}_\d{1,9})$"" +efp_cacao_sca,"r"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$"" +efp_cacao_tc,"r"^(Tc\d+v2_g\d+)$"" +efp_camelina,"r"^(Csa\d{0,5}[gs]\d{0,6}.\d{0,3})$|^(At\d[cgm]\d{0,6})$"" +efp_cannabis,"r"(^C\d+$)|(^scaffold\d+$)|(^AGQN\d+$)"" +efp_canola,"r"^(Bna\D\d{1,3}g\d{1,8}\D)$|^(Bna\Dnng\d{1,8}\D)$"" +efp_durum_wheat,"r"^(TrturSVE\d\D\d{1,3}G\d{1,12})$|^(TrturSVE\d\D\d{1,3}G\d{1,12}_ncBOCREA)$"" +efp_euphorbia,"r"^(Ep_chr\d_g\d{1,8})$"" +efp_eutrema,"r"^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$"" +efp_grape,"r"^(VIT_\d{1,2}s\d{4}g\d{5})$|^CHRUN[a-z0-9_]{1,20}$|^CHR\d{1,2}[a-z0-9_]{1,2}$"" +efp_kalanchoe,"r"^(Kaladp\d+s\d+)$"" +efp_little_millet,"r"^(TRINITY_DN\d+_c\d+_g\d+_i\d+)$"" +efp_lupin,"r"^(Luan_Oskar_.{1,12}_\d{1,12})$"# is_efp_gene_valid matches without re.IGNORECASE, so these freeform-text# patterns (enzyme/metabolite/category NAMES, not gene IDs) need an explicit# (?i) -- real sample data is mixed-case ("GAPDH (NAD)", "Citric Acid")." +efp_maize_enzyme,"r"(?i)^[a-z0-9\s\-\(\)]{1,50}$"" +efp_maize_metabolite,"r"(?i)^[a-z0-9\s,\.\-\(\)_'\+]{1,60}$"# Lipid species names (TG_52_1, MGDG_38_6), same freeform style as efp_arabidopsis_lipid" +efp_maize_lipid_map,"r"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$"# tomato_trait stores root-architecture trait descriptions, not gene IDs" +efp_tomato_trait,"r"^[A-Za-z][A-Za-z0-9\s\.,\-\(\)]{1,100}$"" +efp_maize_transcriptomics,"r"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$"" +efp_mangosteen,"r"^(DN\d{1,10})$"" +efp_marchantia,"r"^(Mp.{1,3}g\d{1,7}\.?\d{1,3}?)$"" +efp_oat,"r"(^N0\.HOG\d{1,10}$|^\D{1,10}\.*\d{1,10}.{1,10}\d{1,10}$)"" +efp_phelipanche,"r"^(OrAeBC\d+_\d+\.\d{1,5})|(At\d[gcm]\d{1,6})$"" +efp_physcomitrella,"r"^(Pp)\d+s\d+_\d+V\d\.\d$|^Phypa_\d+$"" +efp_potato,"r"^(PGSC0003DMG4\d{8})$"" +efp_rice_metabolite,"r"(?i)^[a-z0-9,\s\.\-]{1,40}$"" +efp_rice_transcriptomics,"r"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$"" +efp_selaginella,"r"^(Smo\d+)$"" +efp_sorghum,"r"^(Sobic.\d{0,5}G\d{0,10}$|^Sobic.K\d{0,10}$|^ENSRNA\d{0,12}$|^SORBI_\d{1,6}G\d{1,10})$"" +efp_strawberry,"r"^(FvH4_c?\d{1,3}g\d{1,7})$|^(gene\d{1,10})$"" +efp_striga,"r"^(StHeBC3\_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$"" +efp_tomato,"r"^(Solyc\d{2}g\d{6}\.?\d{0,3})$|^(TU\d{6})$"" +efp_triphysaria,"r"^(TrVeBC\d+_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$"" +efp_tung_tree,"r"^(Vf\d+G\d+)$"" +efp_wheat,"r"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$"" +efpconfig,"r".{0,16}"" +mouse_efp,"r"^(XM_\d{0,8}\.\d{0,3})$|^(\d{1,10}\D\d{0,4}\D{0,4})$|^(\D{1,8}\d{0,8}\D{0,8})$|^(ENSMUSG\d{1,15})$|^(NM_\d{0,12}\d.\d{0,3})$"" diff --git a/ALL_REGEXES_FOR_VINCENT.csv b/ALL_REGEXES_FOR_VINCENT.csv new file mode 100644 index 00000000..c1ef7265 --- /dev/null +++ b/ALL_REGEXES_FOR_VINCENT.csv @@ -0,0 +1,56 @@ +efp_project,regex +efp,"^([Aa][Tt][12345CM][Gg][0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" +efp_arabidopsis,"^([Aa][Tt][12345CM][Gg][0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" +efp_seedcoat,"^(At[12345CM]g[0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(\D\d+_\d+)$|^(At\d{8})$" +efp_barley,"^(Contig|HM|HV|[A-Z][A-Za-z0-9]+_|[A-Z]{1,3}\d+_)" +efp_rice,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^(Os\.\d+\.\d+\.(S1|A1|S2)_(at|x_at|s_at|a_at))$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5\.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" +efp_medicago,"^(Medtr\d{1}g\d{6})$|^(Medtr\d{1}g\d{6}\.[0-9]{1})$|^(Mtr\.\d{4,5}\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(Msa\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(Sme\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(AFFX-(Bio|Cre|Dap|Lys|Phe|Thr|Trpn)(B|C|Dn|X)-(3|5|M)_at)$|^(AFFX-(Msa|Mtr)-(actin|gapc|gsta|ubq11|TrpnX)-(3|5|M)_(at|x_at|s_at))$|^(AFFX-r2-(Bs|Ec|P1)-(cre|dap|lys|phe|thr|bioB|bioC|bioD)-(3|5|M)_(at|s_at|x_at))$|^(AFFX-Mtr-ubq11-(3|5|M)_(at|s_at|x_at))$|^(AFFX-r2-Tag[A-Z]{1,2}_at)$|^(Medtr_v1_\d{6})$" +efp_poplar,"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^((eugene3)\.\d{6,12})$|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$|^((grail3\.)\d{8,12})$|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$|^(Potri\.[0-9]{3}G[0-9]{6}(\.[0-9]{1})?)$" +efp_soybean,"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$|^(Glyma\.\d{1,3}g\d{1,8}))$" +efp_maize,"^(AC[0-9]{6}\.[0-9]{1,2}_(FG|FGT)[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$" +efp_triticale,^((Ta|TaAffx)\.\d+\.\d+\.[A-Z]\d+_(at|s_at|x_at|a_at))$ +efp_human,^([A-Z0-9]|MIR) +efp_Eutrema,^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$ +efp_actinidia,"^(Acc\d+\.\d{0,3})$" +efp_apple,"^(MfusH1_\d\dg\d{1,8})$" +efp_arabidopsis_lipid,"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$" +efp_arachis,^(Adur\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Aipa_c\d+_g\d+_i\d+)$|^(Aipa\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Adur_c\d+_g\d+_i\d+)$ +efp_brachypodium,^(Bradi\d+g\d+.\d)$|^(Bradi\d+s\d+.\d)$|^(Bradi\d+.g\d+)$ +efp_brachypodium_metabolites,"(?i)^[a-z\s\-]{1,60}$" +efp_brassica_rapa,"^(Bra.\d+g\d{0,10})$|^(Bra[AC]nng\d+)$" +efp_cacao_ccn,"^(CCN-51_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +efp_cacao_sca,"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +efp_cacao_tc,^(Tc\d+v2_g\d+)$ +efp_camelina,"^(Csa\d{0,5}[gs]\d{0,6}.\d{0,3})$|^(At\d[cgm]\d{0,6})$" +efp_cannabis,(^C\d+$)|(^scaffold\d+$)|(^AGQN\d+$) +efp_canola,"^(Bna\D\d{1,3}g\d{1,8}\D)$|^(BoC\d+g\d+\.\d+V\d)$|^(BrChr\d+g\d+\.\d+V\d)$|^(Contig\d+)$" +efp_durum_wheat,"^(TrturSVE\d\D\d{1,3}G\d{1,12})$|^(TrturSVE\d\D\d{1,3}G\d{1,12}_ncBOCREA)$" +efp_euphorbia,"^(Ep_chr\d_g\d{1,8})$" +efp_eutrema,^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$ +efp_grape,^(CHR|VIT_|CHRUN) +efp_kalanchoe,^(Kaladp\d+s\d+)$ +efp_little_millet,^(TRINITY_DN\d+_c\d+_g\d+_i\d+)$ +efp_lupin,"^(Luan_Oskar_.{1,12}_\d{1,12})$" +efp_maize_enzyme,"(?i)^[a-z0-9\s\-\(\)]{1,50}$" +efp_maize_metabolite,"(?i)^[a-z0-9\s,\.\-\(\)_'\+]{1,60}$" +efp_maize_lipid_map,"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$" +efp_tomato_trait,"^[A-Za-z][A-Za-z0-9\s\.,\-\(\)]{1,100}$" +efp_maize_transcriptomics,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$" +efp_mangosteen,"^(DN\d{1,10})$" +efp_marchantia,^(Mp[a-z]?g\d+\.\d+)$|^(Mp[a-z]?\d+g\d+\.\d+)$ +efp_oat,"(^N0\.HOG\d{1,10}$|^\D{1,10}\.*\d{1,10}.{1,10}\d{1,10}$)" +efp_phelipanche,"^(OrAeBC\d+_\d+\.\d+)$|^(OrAeBC\d+_\d+)$|^(At\d[gcm]\d{1,6})$" +efp_physcomitrella,^(Pp)\d+s\d+_\d+V\d\.\d$|^Phypa_\d+$ +efp_potato,^(PGSC0003DMG4\d{8})$ +efp_rice_metabolite,"(?i)^[a-z0-9,\s\.\-]{1,40}$" +efp_rice_transcriptomics,^(LOC_Os[0-9]{2}g[0-9]{5})$|^(Os(Affx)?\.\d+\.\d+\.(S1|A1|S2)_(at|x_at|s_at|a_at))$ +efp_selaginella,^(Smo\d+)$ +efp_sorghum,"^(Sobic.\d{0,5}G\d{0,10}$|^Sobic.K\d{0,10}$|^ENSRNA\d{0,12}$|^SORBI_\d{1,6}G\d{1,10})$" +efp_strawberry,"^(FvH4_c?\d{1,3}g\d{1,7})$|^(gene\d{1,10})$" +efp_striga,"^(StHeBC3\_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" +efp_tomato,"^(Solyc\d{2}g\d{6}\.?\d{0,3})$|^(TU\d{6})$" +efp_triphysaria,"^(TrVeBC\d+_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" +efp_tung_tree,^(Vf\d+G\d+)$ +efp_wheat,"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$" +efpconfig,".{0,16}" +mouse_efp,"^(XM_\d{0,8}\.\d{0,3})$|^(\d{1,10}\D\d{0,4}\D{0,4})$|^(\D{1,8}\d{0,8}\D{0,8})$|^(ENSMUSG\d{1,15})$|^(NM_\d{0,12}\d.\d{0,3})$" diff --git a/EMAIL_FOR_VINCENT.txt b/EMAIL_FOR_VINCENT.txt new file mode 100644 index 00000000..005e4024 --- /dev/null +++ b/EMAIL_FOR_VINCENT.txt @@ -0,0 +1,55 @@ +Subject: eFP Regex Package & Production Database Validation Request + +Hi Vincent, + +Per the June 25 tasks, I've compiled all the eFP regex patterns from the endpoint-creation branch for your production database validation scan. + +## What's Ready ✅ + +1. **Regex Reference (JSON)** + - File: data/efp_info/efp_regex_endpoint_creation.json + - 20+ species/validators with descriptions, examples, and regex patterns + - Machine-readable format for production scanning + +2. **Source Code** + - File: api/utils/bar_utils.py (endpoint-creation branch) + - Individual validator functions for each species + - All patterns with proper case-sensitivity flags + +3. **Master Database Metadata** + - File: data/efp_info/combined_master.json + - 48 species, 193 databases, SQL schemas + - Use as single source of truth for database mapping + +4. **Complete Package Guide** + - File: VINCENT_REGEX_PACKAGE_JUN25.md + - Full reference with usage instructions + +## What I Need From You + +Please run production database validation: +1. Scan all gene IDs in sample_data tables against their assigned regex patterns +2. Generate coverage report (which databases pass/fail/have warnings) +3. Identify any new ID formats not yet covered +4. Flag the tomato database issue for Asher + +## Tomato Database Question + +Multiple tomato database variants currently share one regex. Consult with Asher: +- Per-species approach (current): Same regex for all tomato databases +- Per-database approach: Different regexes for each variant + +## Files Location + +All files are in the current repo: +- data/efp_info/efp_regex_endpoint_creation.json +- data/efp_info/combined_master.json +- VINCENT_REGEX_PACKAGE_JUN25.md + +Let me know if you need additional formats or data extractions for the validation scan. + +Best, +Reena + +--- +June 25, 2026 diff --git a/EMAIL_TO_VINCENT_JUL_17_2026.txt b/EMAIL_TO_VINCENT_JUL_17_2026.txt new file mode 100644 index 00000000..655e157a --- /dev/null +++ b/EMAIL_TO_VINCENT_JUL_17_2026.txt @@ -0,0 +1,72 @@ +Subject: Regex package integrated + updated master JSON for a brief check + +Hi Vincent, + +Thanks for the regex_master_list_efp_eplant package -- I've integrated it into +the BAR API on the cleaned-endpoint branch. Quick summary of what changed and +a few things I found while wiring it in that you may want to know about. + +## What's integrated + +1. **bar_regex_registry.json is now the single source of truth for input + validation**, embedded into data/efp_info/combined_master.json at build + time (see build_combined_master_json.py -> get_validation_patterns()). + - 58 grouped eFP-project regex patterns (down from 193 per-database), same + grouping you did (e.g. all 4 actinidia databases share efp_actinidia). + - Every database's "regex_project" field in combined_master.json says + which pattern validates it. + +2. **General injection checker added before the probeset-shape check** + (api/utils/bar_utils.py -> BARUtils.is_injection_attempt()), wired in + ahead of GeneIdUtils.is_probeset_id() in the /gene_expression endpoint per + your note. It looks for actual attack syntax (SQL comment/statement- + chaining sequences, tautologies, UNION SELECT, script tags) rather than + blacklisting individual characters, since some of your freeform projects + (efp_maize_lipid_map, efp_maize_metabolite, etc.) legitimately use ';', + "'", "-" in real sample data. Verified zero false positives against all + 5,790 real IDs in api/random_rows_json/. + +## Things I found while validating against real sample data + +I ran every database's assigned regex_project against its own real sample +dump (api/random_rows_json/) before trusting the assignment. Two things worth +a look on your end: + +- **3 databases got demoted back to species-level validation** because their + assigned project scored 0% against real data: brachypodium_embryogenesis, + brassica_rapa_developmental_atlas, medicago_root_v5. All three are hidden/ + legacy databases (not in any current frontend dropdown) using an older or + alternate ID scheme than their species' main project -- e.g. + brachypodium_embryogenesis's real IDs are uppercase ("BRADI3G43400.1") + where efp_brachypodium expects "Bradi...". Not urgent since the species + validator already handles them correctly, but flagging in case that + matters for the comprehensive list you're finishing. + +- **maize_lipid_map and tomato_trait were assigned their species' main gene-ID + project** (efp_maize, efp_tomato) instead of the freeform-text projects that + already exist in your registry for exactly this data (efp_maize_lipid_map, + efp_tomato_trait) -- real values are lipid names ("TG 54:5; ...") and trait + descriptions ("Area of Stele"), not gene IDs. I corrected these two locally + since the right project was obviously already in your registry. + +- **Two small known gaps, ~99.9% overall pass rate** (5,790 real IDs + checked): canola_original has 2/30 real IDs in an older Brassica-prefix + format (BrBA_/BoBC_) efp_canola doesn't cover, and potato_wounding has 2/30 + in what looks like an Ensembl Plants ID format (EPlSTUG...) efp_potato + doesn't cover. Both are legacy/hidden databases, low priority, but exact + values are in the sample dumps if useful. + +## Master JSON for your check + +data/efp_info/combined_master.json is attached/in the repo (cleaned-endpoint +branch) -- 47 species, 193 databases, all schema_verified against real +column data, all regex_project assignments verified against real sample IDs. +Would appreciate a brief look before we move on to the next endpoint. + +Let me know if anything above needs a closer look on your end. + +Best, +Reena + +--- +July 17, 2026 diff --git a/EMAIL_TO_VINCENT_JUN_25_2026.txt b/EMAIL_TO_VINCENT_JUN_25_2026.txt new file mode 100644 index 00000000..9e8e9a3e --- /dev/null +++ b/EMAIL_TO_VINCENT_JUN_25_2026.txt @@ -0,0 +1,69 @@ +Subject: eFP Regex Validation Materials & Production Database Scan Request + +Hi Vincent, + +Per our June 25 tasks, I've consolidated the complete eFP regex reference and master database metadata for production validation. Everything is ready for your production database scan. + +## What's Ready + +1. **Master Database JSON** ✅ + - File: data/efp_info/combined_master.json + - Contains: 48 species, 193 databases, SQL schemas, sample metadata + - Use this as the single source of truth for all database/species/frontend mapping + +2. **Regex Reference Materials** ✅ + - File: vincent_regex_summary_jun_25_2026.md + - File: data/efp_info/efp_regex_reference.json + - Contains: All 50+ eFP project regex patterns with descriptions and coverage details + +3. **Regex Dictionary** ✅ + - File: api/utils/bar_utils.py (lines 8-177) + - Dictionary: EFP_PROJECT_REGEXES + - All patterns validate both gene IDs and microarray probeset IDs where applicable + +4. **Database-to-Regex Mapping** ✅ + - File: api/utils/gene_id_utils.py (lines 214+) + - Dictionary: DATABASE_EFP_PROJECT + - Maps all 193 databases to their corresponding regex patterns + +## What I Need From You + +Please run a production database validation scan: +1. Validate all gene IDs in sample_data.data_probeset_id columns against their assigned regex patterns +2. Generate coverage report: which databases pass 100%, which have edge cases +3. Identify any new ID formats not yet covered by our regexes +4. Flag per-database vs per-species issues (especially for tomato) + +## Tomato Database Issue — Decision Needed + +Currently, all tomato database variants (tomato, tomato_ils, tomato_ils2, etc.) share one generic regex pattern. This may not be sufficient if each database uses different ID formats or probesets. + +**Please consult with Asher about:** +- Should we map regexes per-species (current approach) or per-database? +- Do different tomato database variants require different validation rules? + +Once you two decide, I'll update the DATABASE_EFP_PROJECT mapping accordingly. + +## Regex Highlights for Reference + +All regexes are in api/utils/bar_utils.py: +- ✅ **efp_human** (line 125) - Already complete for Reena's needs +- ✅ **efp** generic (line 9) - Already complete for Reena's needs +- ✅ All 50+ other eFP projects - Complete coverage + +## Files to Use + +``` +data/efp_info/combined_master.json ← Master truth JSON +data/efp_info/efp_regex_reference.json ← Regex descriptions & metadata +vincent_regex_summary_jun_25_2026.md ← Complete summary & next steps +api/utils/bar_utils.py ← Actual regex patterns (production-ready) +``` + +Let me know if you need any additional data or want me to extract specific regex patterns for a particular subset of databases. + +Best, +Reena + +--- +Generated: June 25, 2026 diff --git a/VINCENT_REGEX_PACKAGE_JUN25.md b/VINCENT_REGEX_PACKAGE_JUN25.md new file mode 100644 index 00000000..59a2612e --- /dev/null +++ b/VINCENT_REGEX_PACKAGE_JUN25.md @@ -0,0 +1,143 @@ +# eFP Regex Validation Package for Vincent +**Source Branch:** endpoint-creation +**Date:** June 25, 2026 +**For:** Production Database Validation + +--- + +## 📦 What You're Getting + +### 1. **Regex Reference JSON** ✅ +- **File:** `data/efp_info/efp_regex_endpoint_creation.json` +- **Content:** All 20+ regex patterns extracted from endpoint-creation branch +- **Format:** Machine-readable with descriptions and examples +- **Coverage:** 20 species/validators + +### 2. **Source Code** ✅ +- **File:** `api/utils/bar_utils.py` (endpoint-creation branch) +- **Lines:** Individual validator functions for each species +- **Note:** Each function is independent, no consolidated dictionary + +### 3. **Master Database JSON** ✅ +- **File:** `data/efp_info/combined_master.json` +- **Content:** 48 species, 193 databases, SQL schemas +- **Source:** Generated from cleaned-endpoint branch + +--- + +## 📋 Species/Regex Coverage + +| Species | Regex Pattern | Function | Examples | +|---------|--------------|----------|----------| +| Arabidopsis | `^At[12345cm]g\d{5}.?\d?$` | `is_arabidopsis_gene_valid()` | At1g12345, At2g05123 | +| Rice | `^LOC_Os\d{2}g\d{5}(\.\d{1,2})?$` | `is_rice_gene_valid()` | LOC_Os01g01010, LOC_Os01g01010.1 | +| Maize | `^(AC[0-9]{6}\.[0-9]{1}_FG...)` | `is_maize_gene_valid()` | AC233276.1_FG001, GRMZM2G000010 | +| Poplar | `^POTRI\.\d{3}g\d{6}.?\d{0,3}$` | `is_poplar_gene_valid()` | POTRI.001g000010 | +| Grape | `^VIT_\d{0,3}\D\d{0,5}g\d{0,6}$` | `is_grape_gene_valid()` | VIT_00s0120g00060 | +| Tomato | `^Solyc\d\dg\d{6}(\.\d+)?$` | `is_tomato_gene_valid()` | Solyc01g000010, Solyc01g000010.1 | +| Soybean | `^((Glyma\d{1,3}g...)` | `is_soybean_gene_valid()` | Glyma06g47400, Glyma.06g000010 | +| Canola | `^Bna[AC]\d{2}g\d{5}[A-D]?$` | `is_canola_gene_valid()` | BnaC07g42830D | +| Sorghum | `^(Sobic.\d{0,5}G...)` | `is_sorghum_gene_valid()` | Sobic.001G000010 | +| Strawberry | `^FvH4_\d{1,3}g\d{1,8}$` | `is_strawberry_gene_valid()` | FvH4_1g00010 | +| Kalanchoe | `^Kaladp\d{1,10}s\d{1,10}$` | `is_kalanchoe_gene_valid()` | Kaladp000001s000001 | +| Cannabis | `^AGQN\d{0,10}$` | `is_cannabis_gene_valid()` | AGQN03000001 | +| Arachis | `^Adur\d{1,10}_comp...` | `is_arachis_gene_valid()` | Adur10000_comp0_c0_seq1 | +| Brassica rapa | `^BraA.{1,4}g\d{1,9}$` | `is_brassica_rapa_gene_valid()` | BraA01g000010 | +| Physcomitrella | `^Pp1s\d{1,8}_\d{1,8}V6...` | `is_physcomitrella_gene_valid()` | Pp1s9_70V6.1 | +| Phelipanche | `^OrAeBC5_\d{1,6}\.\d{1,3}$` | `is_phelipanche_gene_valid()` | OrAeBC5_9992.10 | +| Thellungiella | `^Thhalv\d+m\.g$\|^nXLOC...` | `is_thellungiella_gene_valid()` | Thhalv10000089m.g, nXLOC_003010 | +| Striga | `^StHeBC3_\d{1,6}\.\d{1,5}$` | `is_striga_gene_valid()` | StHeBC3_9993.10 | +| Triphysaria | `^TrVeBC3_\d{1,6}\.\d{1,3}$` | `is_triphysaria_gene_valid()` | TrVeBC3_9999.18 | +| Selaginella | `^Smo\d{1,8}$` | `is_selaginella_gene_valid()` | Smo402070 | + +--- + +## ⚠️ Known Issues + +### Tomato Database Mapping Question +Multiple tomato databases use the same regex: +- tomato +- tomato_ils +- tomato_ils2 +- tomato_ils3 +- tomato_meristem +- tomato_renormalized +- tomato_root +- tomato_root_field_pot +- tomato_s_pennellii +- tomato_seed +- tomato_shade_mutants +- tomato_shade_timecourse + +**Action Needed:** Consult with Asher on whether these should have: +1. **Per-species mapping** (current): One regex for all tomato databases +2. **Per-database mapping**: Different regexes for each variant based on actual data + +--- + +## 🎯 Production Validation Steps + +### Step 1: Scan All Databases +Run regexes against production BAR database: +- Check `sample_data.data_probeset_id` columns +- Validate gene IDs against assigned regex patterns +- All 193 databases + +### Step 2: Generate Coverage Report +``` +Which databases: ✅ PASS (100% ID validation) +Which databases: ⚠️ WARNING (some IDs don't match) +Which databases: ❌ FAIL (significant ID mismatches) +``` + +### Step 3: Identify Edge Cases +- New ID formats not yet covered +- Per-database regex issues (especially tomato) +- Microarray vs RNA-seq format differences + +### Step 4: Report Findings +Provide: +- List of databases needing regex updates +- Recommended new patterns for edge cases +- Decision on tomato database mapping approach + +--- + +## 📁 Files Provided + +``` +endpoint-creation branch: +├── api/utils/bar_utils.py (Source code with validators) +└── data/efp_info/ + ├── efp_regex_endpoint_creation.json (All regexes extracted & formatted) + ├── combined_master.json (Database metadata) + └── efp_regex_reference.json (Alternative format) +``` + +--- + +## 💡 Usage Notes + +Each regex in the JSON file includes: +- **regex:** The actual pattern to use +- **function:** Source function name from bar_utils.py +- **description:** What the regex validates +- **case_insensitive:** Whether regex uses re.I flag +- **examples:** Sample IDs that should match +- **notes:** Any special considerations + +All regexes are extracted with original case-sensitivity settings from the functions. + +--- + +## ✅ Next Steps + +1. **Vincent:** Run production database scan +2. **Vincent → Asher:** Decide on tomato database mapping strategy +3. **Reena:** Update DATABASE_EFP_PROJECT mapping once decision is made +4. **Team:** Deploy validated regexes to production + +--- + +**Contact:** Reena Obmina (rmobmina@gmail.com) +**Questions:** About regex patterns, production validation, or architecture decisions diff --git a/all-efp-projects-views-with-lookup-settings.txt b/all-efp-projects-views-with-lookup-settings.txt new file mode 100644 index 00000000..d31d68a9 --- /dev/null +++ b/all-efp-projects-views-with-lookup-settings.txt @@ -0,0 +1,268 @@ +PROJECT VIEW LOOKUP ORTHO DB_LOOKUP_TABLE +---------------------------- ------------------------------------- ------ ----- ---------------------- +efp atgenexp 1 — at_agi_lookup +efp atgenexp_plus 1 — at_agi_lookup +efp seed_db 1 — at_agi_lookup +efp atgenexp_hormone 1 — at_agi_lookup +efp light_series 1 — at_agi_lookup +efp arabidopsis_ecotypes 1 — at_agi_lookup +efp root 1 — at_agi_lookup +efp atgenexp_stress 1 — at_agi_lookup +efp atgenexp_pathogen 1 — at_agi_lookup +efp guard_cell 1 — at_agi_lookup +efp atTax 1 — at_agi_lookup +efp meristem_db 1 — at_agi_lookup +efp lateral_root_initiation 1 — at_agi_lookup +efp shoot_apex 0 — at_agi_lookup +efp klepikova 0 — at_agi_lookup +efp germination 0 — at_agi_lookup +efp gynoecium 0 — at_agi_lookup +efp embryo 0 — at_agi_lookup +efp silique 0 — at_agi_lookup +efp single_cell 0 — at_agi_lookup +efp dna_damage 0 — at_agi_lookup + +efp_Eutrema thellungiella_db 1 yes tsa_arabidopsis_lookup + +efp_actinidia actinidia_bud_development 0 — — +efp_actinidia actinidia_flower_fruit_development 0 — — +efp_actinidia actinidia_postharvest 0 — — +efp_actinidia actinidia_vegetative_growth 0 — — + +efp_apple apple 0 — — + +efp_arabidopsis atgenexp 1 — at_agi_lookup +efp_arabidopsis atgenexp_plus 1 — at_agi_lookup +efp_arabidopsis seed_db 1 — at_agi_lookup +efp_arabidopsis atgenexp_hormone 1 — at_agi_lookup +efp_arabidopsis light_series 1 — at_agi_lookup +efp_arabidopsis arabidopsis_ecotypes 1 — at_agi_lookup +efp_arabidopsis root 1 — at_agi_lookup +efp_arabidopsis atgenexp_stress 1 — at_agi_lookup +efp_arabidopsis atgenexp_pathogen 1 — at_agi_lookup +efp_arabidopsis guard_cell 1 — at_agi_lookup +efp_arabidopsis atTax 1 — at_agi_lookup +efp_arabidopsis meristem_db 1 — at_agi_lookup +efp_arabidopsis lateral_root_initiation 1 — at_agi_lookup +efp_arabidopsis shoot_apex 0 — at_agi_lookup +efp_arabidopsis klepikova 0 — at_agi_lookup +efp_arabidopsis germination 0 — at_agi_lookup +efp_arabidopsis gynoecium 0 — at_agi_lookup +efp_arabidopsis embryo 0 — at_agi_lookup +efp_arabidopsis silique 0 — at_agi_lookup +efp_arabidopsis single_cell 0 — at_agi_lookup +efp_arabidopsis dna_damage 0 — at_agi_lookup + +efp_arabidopsis_lipid lipid_map 1 — — + +efp_arachis arachis 0 — — + +efp_barley barley_mas 1 — at_bar_lookup +efp_barley barley_rma 1 — at_bar_lookup + +efp_brachypodium brachypodium 0 — — +efp_brachypodium brachypodium_photo_thermocycle 0 — — +efp_brachypodium brachypodium_grains 0 — — +efp_brachypodium brachypodium_Bd21 0 — — + +efp_brachypodium_metabolites brachypodium_metabolites_map 1 — — + +efp_brassica_rapa brassica_rapa 0 — — + +efp_cacao_ccn cacao_drought_diurnal_atlas 0 — — +efp_cacao_ccn cacao_developmental_atlas 0 — — + +efp_cacao_sca cacao_meristem_atlas_sca 0 — — +efp_cacao_sca cacao_developmental_atlas_sca 0 — — +efp_cacao_sca cacao_drought_diurnal_atlas_sca 0 — — +efp_cacao_sca cacao_seed_atlas_sca 0 — — + +efp_cacao_tc cacao_leaf 0 — — +efp_cacao_tc cacao_infection 0 — — + +efp_camelina camelina 1 yes camelina_lookup +efp_camelina camelina_tpm 0 yes camelina_lookup + +efp_cannabis cannabis 0 — — + +efp_canola canola_seed 0 — — + +efp_durum_wheat durum_wheat_development 0 — — + +efp_euphorbia euphorbia 0 — — + +efp_eutrema thellungiella_db 1 yes tsa_arabidopsis_lookup + +efp_grape grape_developmental 1 — grape_probeset_lookup + +efp_human human_developmental 1 — gene_probeset_lookup +efp_human human_body_map_2 0 — gene_probeset_lookup + +efp_kalanchoe kalanchoe 0 — — + +efp_little_millet little_millet 0 — — + +efp_lupin lupin_whole_plant 0 — — +efp_lupin lupin_lcm_leaf 0 — — +efp_lupin lupin_lcm_pod 0 — — +efp_lupin lupin_lcm_stem 0 — — + +efp_maize maize_iplant 0 — — +efp_maize maize_ears 0 — — +efp_maize Sekhon_et_al_Atlas 0 — — +efp_maize maize_leaf_gradient 0 — — +efp_maize maize_rice_comparison 0 — — +efp_maize Maize_Root 0 — — +efp_maize Maize_Kernel 0 — — +efp_maize Hoopes_et_al_Atlas 0 — — +efp_maize Hoopes_et_al_Stress 0 — — +efp_maize Early_Seed 0 — — +efp_maize maize_embryonic_leaf_development 0 — — +efp_maize maize_atlas_v5 0 — — +efp_maize maize_kernel_v5 0 — — +efp_maize maize_stress_v5 0 — — + +efp_maize_enzyme maize_enzyme 0 — — + +efp_maize_metabolite maize_metabolite 0 — — + +efp_maize_transcriptomics maize_iplant 0 — — +efp_maize_transcriptomics maize_ears 0 — — +efp_maize_transcriptomics Sekhon_et_al_Atlas 0 — — +efp_maize_transcriptomics maize_leaf_gradient 0 — — +efp_maize_transcriptomics maize_rice_comparison 0 — — +efp_maize_transcriptomics Maize_Root 0 — — +efp_maize_transcriptomics Maize_Kernel 0 — — +efp_maize_transcriptomics Hoopes_et_al_Atlas 0 — — +efp_maize_transcriptomics Hoopes_et_al_Stress 0 — — +efp_maize_transcriptomics Early_Seed 0 — — +efp_maize_transcriptomics maize_embryonic_leaf_development 0 — — +efp_maize_transcriptomics maize_atlas_v5 0 — — +efp_maize_transcriptomics maize_kernel_v5 0 — — +efp_maize_transcriptomics maize_stress_v5 0 — — + +efp_mangosteen mangosteen_fruit_ripening 0 — — +efp_mangosteen mangosteen_callus 0 — — +efp_mangosteen mangosteen_seed_development 0 — — +efp_mangosteen mangosteen_seed_germination 0 — — +efp_mangosteen mangosteen_aril_vs_rind 0 — — +efp_mangosteen mangosteen_diseased_vs_normal 0 — — + +efp_marchantia marchantia_organ_stress 0 — — + +efp_medicago medicago_mas 1 — at_mtgi_lookup_merged +efp_medicago medicago_rma 1 — at_mtgi_lookup_merged +efp_medicago medicago_seed 1 — at_mtgi_lookup_merged + +efp_oat oat 0 — — + +efp_phelipanche phelipanche 1 yes phelipanche_lookup + +efp_physcomitrella physcomitrella_db 1 — physcomitrella_lookup + +efp_poplar poplar 1 — at_pgi_lookup + +efp_potato potato_dev 1 — gene_protein_lookup +efp_potato potato_stress 1 — gene_protein_lookup + +efp_rice rice_leaf_gradient 0 — at_loc_lookup +efp_rice rice_maize_comparison 0 — at_loc_lookup +efp_rice rice_mas 1 — at_loc_lookup +efp_rice ricestigma_mas 1 — at_loc_lookup +efp_rice riceanoxia_mas 1 — at_loc_lookup +efp_rice ricestress_mas 1 — at_loc_lookup +efp_rice rice_rma 1 — at_loc_lookup +efp_rice ricestigma_rma 1 — at_loc_lookup +efp_rice riceanoxia_rma 1 — at_loc_lookup +efp_rice ricestress_rma 1 — at_loc_lookup +efp_rice rice_drought_heat_stress 0 — at_loc_lookup + +efp_rice_metabolite rice_metabolite 0 — at_loc_lookup + +efp_rice_transcriptomics rice_leaf_gradient 0 — at_loc_lookup +efp_rice_transcriptomics rice_maize_comparison 0 — at_loc_lookup +efp_rice_transcriptomics rice_mas 1 — at_loc_lookup +efp_rice_transcriptomics ricestigma_mas 1 — at_loc_lookup +efp_rice_transcriptomics riceanoxia_mas 1 — at_loc_lookup +efp_rice_transcriptomics ricestress_mas 1 — at_loc_lookup +efp_rice_transcriptomics rice_rma 1 — at_loc_lookup +efp_rice_transcriptomics ricestigma_rma 1 — at_loc_lookup +efp_rice_transcriptomics riceanoxia_rma 1 — at_loc_lookup +efp_rice_transcriptomics ricestress_rma 1 — at_loc_lookup +efp_rice_transcriptomics rice_drought_heat_stress 0 — at_loc_lookup + +efp_seedcoat seedcoat 1 — pbi_agi_lookup + +efp_selaginella selaginella 0 — — + +efp_sorghum sorghum_stress 0 — — +efp_sorghum sorghum_developmental 0 — — +efp_sorghum sorghum_vascularization_and_internode 0 — — +efp_sorghum sorghum_low_phosphorus 0 — — +efp_sorghum sorghum_atlas_w_BS_cells 0 — — +efp_sorghum sorghum_saline_alkali_stress 0 — — +efp_sorghum sorghum_flowering_activation 0 — — +efp_sorghum sorghum_strigolactone_variation 0 — — +efp_sorghum sorghum_sulfur_stress 0 — — +efp_sorghum sorghum_phosphate_stress 0 — — + +efp_soybean soybean 1 — gene_probeset_lookup +efp_soybean soybean_severin 1 — gene_probeset_lookup +efp_soybean soybean_senescence 1 — gene_probeset_lookup +efp_soybean soybean_embryonic_development 1 — gene_probeset_lookup +efp_soybean soybean_heart_cotyledon_globular 1 — gene_probeset_lookup + +efp_strawberry strawberry 1 yes strawberry_lookup + +efp_striga striga 1 yes striga_lookup + +efp_tomato tomato 0 — 454_Illumina_lookup +efp_tomato tomato_renormalized 0 — 454_Illumina_lookup +efp_tomato tomato_ils 1 — 454_Illumina_lookup +efp_tomato tomato_ils2 1 — 454_Illumina_lookup +efp_tomato tomato_s_pennellii 1 — 454_Illumina_lookup +efp_tomato tomato_meristem 0 — 454_Illumina_lookup +efp_tomato tomato_seed 0 — 454_Illumina_lookup +efp_tomato tomato_shade_mutants 0 — 454_Illumina_lookup +efp_tomato tomato_shade_timecourse 0 — 454_Illumina_lookup + +efp_triphysaria triphysaria 1 yes triphysaria_lookup + +efp_triticale triticale 1 — triticale_lookup +efp_triticale triticale_mas 1 — triticale_lookup + +efp_tung_tree tung_tree 0 — — + +efp_wheat wheat 0 — — +efp_wheat wheat_embryogenesis 0 — — +efp_wheat wheat_meiosis 0 — — +efp_wheat wheat_abiotic_stress 0 — — + +efpbarley barley_mas 1 — at_bar_lookup +efpbarley barley_rma 1 — at_bar_lookup + +efpconfig (no LOOKUP dict) ? — at_agi_lookup + +efpmedicago medicago_mas 1 — at_mtgi_lookup_merged +efpmedicago medicago_rma 1 — at_mtgi_lookup_merged +efpmedicago medicago_seed 1 — at_mtgi_lookup_merged + +efppop poplar 1 — at_pgi_lookup + +efprice rice_leaf_gradient 0 — at_loc_lookup +efprice rice_maize_comparison 0 — at_loc_lookup +efprice rice_mas 1 — at_loc_lookup +efprice ricestigma_mas 1 — at_loc_lookup +efprice riceanoxia_mas 1 — at_loc_lookup +efprice ricestress_mas 1 — at_loc_lookup +efprice rice_rma 1 — at_loc_lookup +efprice ricestigma_rma 1 — at_loc_lookup +efprice riceanoxia_rma 1 — at_loc_lookup +efprice ricestress_rma 1 — at_loc_lookup +efprice rice_drought_heat_stress 0 — at_loc_lookup + +efpsoybean soybean 1 — gene_probeset_lookup +efpsoybean soybean_severin 1 — gene_probeset_lookup +efpsoybean soybean_senescence 1 — gene_probeset_lookup +efpsoybean soybean_embryonic_development 1 — gene_probeset_lookup +efpsoybean soybean_heart_cotyledon_globular 1 — gene_probeset_lookup \ No newline at end of file diff --git a/all_gene_id_regexes.csv b/all_gene_id_regexes.csv new file mode 100644 index 00000000..554f1d56 --- /dev/null +++ b/all_gene_id_regexes.csv @@ -0,0 +1,108 @@ +key,regex +efp,"^([Aa][Tt][12345CM][Gg][0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" +efp_Eutrema,^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$ +efp_actinidia,"^(Acc\d+\.\d{0,3})$" +efp_apple,"^(MfusH1_\d\dg\d{1,8})$" +efp_arabidopsis,"^([Aa][Tt][12345CM][Gg][0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" +efp_arabidopsis_lipid,"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$" +efp_arachis,^(Adur\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Aipa_c\d+_g\d+_i\d+)$|^(Aipa\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Adur_c\d+_g\d+_i\d+)$ +efp_barley,"^((HM|HV).*)$|^(HV.*_at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4})_at)$|^([0-9]{4,5}\.AF[0-9]{5}(_|_x_)at)$|^(A[0-9]{5}\.[0-9]{1}(_|_x_|_s_)at)$|^(([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)(_|_x_|_s_|_CDS-[0-9]{1,2}_|_CDS-[0-9]{1,2}_s_)at)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^(ChlorContig[0-9]{1,2}(_|_x_|_s_)at)$|^(((MitoContig|Contig)[0-9]{1,6})(_|_x_|_s_)at)$|^(D[0-9]{5}_at)$|^(Dhn[0-9]{2}\(Morex\)(_|_s_)at)$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2}(_|_s_|_x_)at)$|^(Franka(_|_b_)3pri[0-9]{1,2}(_|_s_|_x_)at)$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru](_|_x_|_s_)at)$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1}(_|_x_|_s_)at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2}(_|_x_|_s_)at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4}))$|^([0-9]{4,5}\.AF[0-9]{5})$|^(A[0-9]{5}\.[0-9]{1})$|^([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX))$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre))$|^(ChlorContig[0-9]{1,2})$|^((MitoContig|Contig)[0-9]{1,6})$|^(D[0-9]{5})$|^(Dhn[0-9]{2}\(Morex\))$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2})$|^(Franka(_|_b_)3pri[0-9]{1,2})$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru])$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1})$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2})$|^(HO)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(AK[0-9]{6}\.1)$|^(AJ[0-9]{6}\.1)$" +efp_brachypodium,^(Bradi\d+g\d+.\d)$|^(Bradi\d+s\d+.\d)$|^(Bradi\d+.g\d+)$ +efp_brachypodium_metabolites,"(?i)^[a-z\s\-]{1,60}$" +efp_brassica_rapa,"^(Bra.\d+g\d{0,10})$" +efp_cacao_ccn,"^(CCN-51_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +efp_cacao_sca,"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +efp_cacao_tc,^(Tc\d+v2_g\d+)$ +efp_camelina,"^(Csa\d{0,5}[gs]\d{0,6}.\d{0,3})$|^(At\d[cgm]\d{0,6})$" +efp_cannabis,(^C\d+$)|(^scaffold\d+$)|(^AGQN\d+$) +efp_canola,"^(Bna\D\d{1,3}g\d{1,8}\D)$|^(Bna\Dnng\d{1,8}\D)$" +efp_durum_wheat,"^(TrturSVE\d\D\d{1,3}G\d{1,12})$|^(TrturSVE\d\D\d{1,3}G\d{1,12}_ncBOCREA)$" +efp_euphorbia,"^(Ep_chr\d_g\d{1,8})$" +efp_eutrema,^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$ +efp_grape,"^(VIT_\d{1,2}s\d{4}g\d{5})$|^CHRUN[a-z0-9_]{1,20}$|^CHR\d{1,2}[a-z0-9_]{1,2}$" +efp_human,"^(\d{6,7}(_[xsa])?_at)$|^(\D{0,12}\d{0,12})$|^(\d{1,12})$" +efp_kalanchoe,^(Kaladp\d+s\d+)$ +efp_little_millet,^(TRINITY_DN\d+_c\d+_g\d+_i\d+)$ +efp_lupin,"^(Luan_Oskar_.{1,12}_\d{1,12})$" +efp_maize,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$" +efp_maize_enzyme,"(?i)^[a-z0-9\s\-\(\)]{1,50}$" +efp_maize_lipid_map,"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$" +efp_maize_metabolite,"(?i)^[a-z0-9\s,\.\-\(\)_'\+]{1,60}$" +efp_maize_transcriptomics,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$" +efp_mangosteen,"^(DN\d{1,10})$" +efp_marchantia,"^(Mp.{1,3}g\d{1,7}\.?\d{1,3}?)$" +efp_medicago,"^(Medtr\d{1}g\d{6})$|^(Medtr\d{1}g\d{6}\.[0-9]{1})$|^(Mtr\.\d{4,5}\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(Msa\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(Sme\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(AFFX-(Bio|Cre|Dap|Lys|Phe|Thr|Trpn)(B|C|Dn|X)-(3|5|M)_at)$|^(AFFX-(Msa|Mtr)-(actin|gapc|gsta|ubq11|TrpnX)-(3|5|M)_(at|x_at|s_at))$|^(AFFX-r2-(Bs|Ec|P1)-(cre|dap|lys|phe|thr|bioB|bioC|bioD)-(3|5|M)_(at|s_at|x_at))$|^(AFFX-Mtr-ubq11-(3|5|M)_(at|s_at|x_at))$|^(AFFX-r2-Tag[A-Z]{1,2}_at)$|^(Medtr_v1_\d{6})$" +efp_oat,"(^N0\.HOG\d{1,10}$|^\D{1,10}\.*\d{1,10}.{1,10}\d{1,10}$)" +efp_phelipanche,"^(OrAeBC\d+_\d+\.\d{1,5})|(At\d[gcm]\d{1,6})$" +efp_physcomitrella,^(Pp)\d+s\d+_\d+V\d\.\d$|^Phypa_\d+$ +efp_poplar,"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^((eugene3)\.\d{6,12})$|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$|^((grail3\.)\d{8,12})$|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$|^(Potri\.[0-9]{3}G[0-9]{6}(\.[0-9]{1})?)$" +efp_potato,^(PGSC0003DMG4\d{8})$ +efp_rice,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5\.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" +efp_rice_metabolite,"(?i)^[a-z0-9,\s\.\-]{1,40}$" +efp_rice_transcriptomics,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" +efp_seedcoat,"^(At[12345CM]g[0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(\D\d+_\d+)$|^(At\d{8})$" +efp_selaginella,^(Smo\d+)$ +efp_sorghum,"^(Sobic.\d{0,5}G\d{0,10}$|^Sobic.K\d{0,10}$|^ENSRNA\d{0,12}$|^SORBI_\d{1,6}G\d{1,10})$" +efp_soybean,"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$|^(Glyma\.\d{1,3}g\d{1,8}))$" +efp_strawberry,"^(FvH4_c?\d{1,3}g\d{1,7})$|^(gene\d{1,10})$" +efp_striga,"^(StHeBC3\_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" +efp_tomato,"^(Solyc\d{2}g\d{6}\.?\d{0,3})$|^(TU\d{6})$" +efp_tomato_trait,"^[A-Za-z][A-Za-z0-9\s\.,\-\(\)]{1,100}$" +efp_triphysaria,"^(TrVeBC\d+_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" +efp_triticale,^((Ta|TaAffx)\.\d+\.\d+\.[A-Z]\d+_(at|s_at|x_at|a_at))$ +efp_tung_tree,^(Vf\d+G\d+)$ +efp_wheat,"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$" +efpbarley,"^((HM|HV).*)$|^(HV.*_at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4})_at)$|^([0-9]{4,5}\.AF[0-9]{5}(_|_x_)at)$|^(A[0-9]{5}\.[0-9]{1}(_|_x_|_s_)at)$|^(([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)(_|_x_|_s_|_CDS-[0-9]{1,2}_|_CDS-[0-9]{1,2}_s_)at)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^(ChlorContig[0-9]{1,2}(_|_x_|_s_)at)$|^(((MitoContig|Contig)[0-9]{1,6})(_|_x_|_s_)at)$|^(D[0-9]{5}_at)$|^(Dhn[0-9]{2}\(Morex\)(_|_s_)at)$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2}(_|_s_|_x_)at)$|^(Franka(_|_b_)3pri[0-9]{1,2}(_|_s_|_x_)at)$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru](_|_x_|_s_)at)$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1}(_|_x_|_s_)at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2}(_|_x_|_s_)at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4}))$|^([0-9]{4,5}\.AF[0-9]{5})$|^(A[0-9]{5}\.[0-9]{1})$|^([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX))$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre))$|^(ChlorContig[0-9]{1,2})$|^((MitoContig|Contig)[0-9]{1,6})$|^(D[0-9]{5})$|^(Dhn[0-9]{2}\(Morex\))$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2})$|^(Franka(_|_b_)3pri[0-9]{1,2})$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru])$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1})$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2})$|^(HO)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(AK[0-9]{6}\.1)$|^(AJ[0-9]{6}\.1)$" +efpconfig,".{0,16}" +efpmedicago,"^(Medtr\d{1}g\d{6})$|^(Medtr\d{1}g\d{6}\.[0-9]{1})$|^(Mtr\.\d{4,5}\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(Msa\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(Sme\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(AFFX-(Bio|Cre|Dap|Lys|Phe|Thr|Trpn)(B|C|Dn|X)-(3|5|M)_at)$|^(AFFX-(Msa|Mtr)-(actin|gapc|gsta|ubq11|TrpnX)-(3|5|M)_(at|x_at|s_at))$|^(AFFX-r2-(Bs|Ec|P1)-(cre|dap|lys|phe|thr|bioB|bioC|bioD)-(3|5|M)_(at|s_at|x_at))$|^(AFFX-Mtr-ubq11-(3|5|M)_(at|s_at|x_at))$|^(AFFX-r2-Tag[A-Z]{1,2}_at)$|^(Medtr_v1_\d{6})$" +efppop,"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^((eugene3)\.\d{6,12})$|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$|^((grail3\.)\d{8,12})$|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$|^(Potri\.[0-9]{3}G[0-9]{6}(\.[0-9]{1})?)$" +efprice,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5\.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" +efpsoybean,"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$|^(Glyma\.\d{1,3}g\d{1,8}))$" +maizeefp,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$" +mouse_efp,"^(XM_\d{0,8}\.\d{0,3})$|^(\d{1,10}\D\d{0,4}\D{0,4})$|^(\D{1,8}\d{0,8}\D{0,8})$|^(ENSMUSG\d{1,15})$|^(NM_\d{0,12}\d.\d{0,3})$" +actinidia,^Acc\d{5}\.\d+$ +apple,^MfusH1_\d{2}g\d{5}$ +arabidopsgene_valid,^At[12345cm]g\d{5}.?\d?$ +arachgene_valid,"^Adur\d{1,10}_comp\d{1,3}_\D{1,3}\d{1,3}_seq\d{1,5}$" +barley,^HORVU(\d+Hr\d+G\d+|\.MOREX\.r\d+\.(\dH|Un)G\d+(\.\d+)?)$ +brachypodium,^Bradi\d+g\d+\.\d+$ +brassica_rapa,"^(BraA.{1,4}g\d{1,9}|[A-Z]\d{2}[gp]\d+\.\d+_BraROA)$" +cacao,^((CCN-51|SCA-6)_Chr\d+v\d+_\d+|Tc\d+v\d+_g\d+)$ +camelina,^Csa\d+[gs]\d+(\.\d+)?$ +cannabgene_valid,"^AGQN\d{0,10}$" +canola,"^(Bna[AC]\d{2}g\d{5}[A-D]?|Bo[A-Z]+_?\d+g\d+\.\d+V\d+|Br(Chr\d{1,2}|BA_\d+)g\d{5}\.\d{2}V\d|Contig\d+)$" +cassava,^Manes\.\d{2}G\d+\.v\d+\.\d+$ +cuscuta,^Cc\d+(\.t\d+)?$ +eucalyptus,^Eucgr\.[A-Z]\d+$ +euphorbia,^Ep_chr\d+_g\d+$ +grape,"^(CHR(\d+|UN)_[A-Z]+\d+(_\d+)?_T\d+|VIT_\d{0,3}\D\d{0,5}g\d{0,6})$" +human,"^\d{1,10}$|^[A-Z][A-Z0-9]{1,9}(-\d{1,3})?$|^[A-Z]{2,4}\d{0,3}-\d{2,4}[A-Z]\d{1,3}\.\d{1,3}$|^A[CL]\d{6}\.\d{1,3}$" +kalanchoe,"^Kaladp\d{1,10}s\d{1,10}$" +little_millet,^TRINITY_DN\d+_c\d+_g\d+_i\d+$ +lupin,^Luan_Oskar_(PB\d+|Trin)_\d+$ +maize,^(AC[0-9]{6}\.[0-9]+_FGT?[0-9]{3}|GRMZM[25]G[0-9]{6}(_T[0-9]{2})?|Zm\d+(d|eb)\d+)$ +mangosteen,^DN\d+$ +marchantia,"^Mp\w{1,3}g\d+\.\d+$" +medicago,^(Medtr(\d+[gs]\d+|_v1_\d+)|MtrunA17Chr\dg\d+)$ +mouse,^XM_\d+\.\d+$ +oat,^AV[A-Z]{3}\.\d{5}[a-z]\.r\d+\.\d[A-Z]{2}\d{8}$ +phelipanche,"^OrAeBC5_\d{1,6}\.\d{1,3}$" +physcomitrella,"^Pp1s\d{1,8}_\d{1,8}V6\.\d{1,3}$" +poplar,"^POTRI\.(\d{3}G\d{6}\.?\d{0,3}|T\d{6})$" +potato,^(PGSC0003DMG\d+|EPlSTUG\d+)$ +quinoa,^CquiG\d+$ +rice,"^LOC_Os\d{2}g\d{5}\.\d{1,2}$|^LOC_Os\d{2}g\d{5}$|^Os\d{2}g\d+$" +selaginella,"^Smo\d{1,8}$" +sorghum,^(Sobic\.\d+G\d+(\.\d+)?|Sobic\.K\d+|SORBI_\d+G\d+|ENSRNA\d+)$ +soybean,"^((Glyma\d{1,3}g\d{1,6}\.?\d?)|(Glyma\.\d{1,3}g\d{1,8}))$" +spruce,"^(GQ|WS)\d{4,5}_[A-Z]\d{2}\.\d+$" +strawberry,"^FvH4_\d{1,3}g\d{1,8}$" +striga,"^StHeBC3_\d{1,6}\.\d{1,5}$" +sugarcane,^(Sh\d+_g\d+|Sh_[A-Z0-9]+(_contig-\d+)?_g\d+)$ +sunflower,^Ha\d+_\d+$ +thellungiella,^Thhalv\d+m\.g$|^nXLOC_\d+$ +tomato,^Solyc\d\dg\d{6}\.\d\.\d$|^Solyc\d\dg\d{6}(\.\d+)?$ +triphysaria,"^TrVeBC3_\d{1,6}\.\d{1,3}$" +tung_tree,^Vf\d+G\d+$ +wheat,^(TraesCS[0-9A-Z]+(\.\d+)?|TrturSVE[0-9A-Z]+G\d+)$ +willow,^comp\d+_c\d+_seq\d+$ diff --git a/api/models/efp_schemas.py b/api/models/efp_schemas.py index 4f12396f..b3963589 100644 --- a/api/models/efp_schemas.py +++ b/api/models/efp_schemas.py @@ -105,7 +105,7 @@ def _schema(species: str, charset: str = "latin1") -> DatabaseSpec: ("grape_developmental", "grape"), ("guard_cell", "guard cell"), ("gynoecium", "gynoecium"), - ("heterodera_schachtii", "heterodera"), + ("heterodera_schachtii", "arabidopsis"), ("hnahal", "hnahal"), ("human_body_map_2", "human"), ("human_developmental", "human"), diff --git a/api/random_rows_json/actinidia_bud_development_test_data.json b/api/random_rows_json/actinidia_bud_development_test_data.json new file mode 100644 index 00000000..84275a48 --- /dev/null +++ b/api/random_rows_json/actinidia_bud_development_test_data.json @@ -0,0 +1,242 @@ +[ + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 7, + "data_probeset_id": "Acc23558.1", + "data_signal": 0.0593103, + "data_bot_id": "Jul" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 12, + "data_probeset_id": "Acc27556.1", + "data_signal": 0.0, + "data_bot_id": "Nov" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 4, + "data_probeset_id": "Acc13569.1", + "data_signal": 1.50114, + "data_bot_id": "Feb" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 6, + "data_probeset_id": "Acc24157.1", + "data_signal": 0.0, + "data_bot_id": "Jan_TB" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 6, + "data_probeset_id": "Acc27341.1", + "data_signal": 7.36061, + "data_bot_id": "Jan_TB" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 2, + "data_probeset_id": "Acc15429.1", + "data_signal": 2.44246, + "data_bot_id": "Aug" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 5, + "data_probeset_id": "Acc32753.1", + "data_signal": 1.78871, + "data_bot_id": "Jan" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 8, + "data_probeset_id": "Acc12083.1", + "data_signal": 0.117258, + "data_bot_id": "Jun" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "Acc24253.1", + "data_signal": 0.0526919, + "data_bot_id": "Apr" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 3, + "data_probeset_id": "Acc24221.1", + "data_signal": 3.63306, + "data_bot_id": "Dec" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 5, + "data_probeset_id": "Acc21077.1", + "data_signal": 1.36209, + "data_bot_id": "Jan" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 8, + "data_probeset_id": "Acc16361.1", + "data_signal": 10.9285, + "data_bot_id": "Jun" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 10, + "data_probeset_id": "Acc30784.1", + "data_signal": 1.30967, + "data_bot_id": "Mar_TB" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 5, + "data_probeset_id": "Acc05038.1", + "data_signal": 1.61503, + "data_bot_id": "Jan" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 7, + "data_probeset_id": "Acc09894.1", + "data_signal": 0.184609, + "data_bot_id": "Jul" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 4, + "data_probeset_id": "Acc31729.1", + "data_signal": 4.49147, + "data_bot_id": "Feb" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "Acc18094.1", + "data_signal": 1.21865, + "data_bot_id": "Apr" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 10, + "data_probeset_id": "Acc17305.1", + 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No newline at end of file diff --git a/api/random_rows_json/oat_test_data.json b/api/random_rows_json/oat_test_data.json new file mode 100644 index 00000000..12c30229 --- /dev/null +++ b/api/random_rows_json/oat_test_data.json @@ -0,0 +1,332 @@ +[ + { + "db": "oat", + "sample_id": 1, + "genome": "NICOLAS", + "version": "D", + "genome_id": "NICOLASD", + "orthogroup": "N0.HOG0078607", + "data_probeset_id": "AVESA.00009a.r1.7DG05343670", + "data_signal": 1492.81, + "data_bot_id": "Caryopsis_NICOLAS_D" + }, + { + "db": "oat", + "sample_id": 3, + "genome": "DELFIN", + "version": "C", + "genome_id": "DELFINC", + "orthogroup": "N0.HOG0075997", + "data_probeset_id": "AVESA.00015a.r1.4CG03041530", + "data_signal": 0.0, + "data_bot_id": "Leaf_DELFIN_C" + }, + { + "db": "oat", + "sample_id": 6, + "genome": "GMI423", + "version": "A", + "genome_id": "GMI423A", + "orthogroup": "N0.HOG0034771", + "data_probeset_id": "AVESA.00002a.r1.2AG01069750", + "data_signal": 0.0, + "data_bot_id": 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"soybean_embryonic_development", + "proj_id": "1", + "sample_id": 3, + "data_probeset_id": "Glyma04g12690", + "data_signal": 12.33, + "data_bot_id": "embryo_axis_parenchyma" + }, + { + "db": "soybean_embryonic_development", + "proj_id": "1", + "sample_id": 3, + "data_probeset_id": "Glyma16g24600", + "data_signal": 0.0, + "data_bot_id": "embryo_axis_parenchyma" + }, + { + "db": "soybean_embryonic_development", + "proj_id": "1", + "sample_id": 10, + "data_probeset_id": "Glyma09g37190", + "data_signal": 3.33, + "data_bot_id": "embryo_root_tip" + }, + { + "db": "soybean_embryonic_development", + "proj_id": "1", + "sample_id": 2, + "data_probeset_id": "Glyma17g37520", + "data_signal": 12.33, + "data_bot_id": "embryo_axis_epidermis" + } +] \ No newline at end of file diff --git a/api/random_rows_json/soybean_heart_cotyledon_globular_test_data.json b/api/random_rows_json/soybean_heart_cotyledon_globular_test_data.json new file mode 100644 index 00000000..47f328bb --- /dev/null +++ b/api/random_rows_json/soybean_heart_cotyledon_globular_test_data.json @@ -0,0 +1,242 @@ +[ + { + "db": "soybean_heart_cotyledon_globular", + "proj_id": "1", + "sample_id": 13, + "data_probeset_id": "Glyma15g13815", + "data_signal": 17.5, + "data_bot_id": "globular_seedcoatendothelium" + }, + { + "db": "soybean_heart_cotyledon_globular", + "proj_id": "1", + "sample_id": 19, + "data_probeset_id": "Glyma14g02210", + "data_signal": 0.07, + "data_bot_id": "heart_embryo" + }, + { + "db": "soybean_heart_cotyledon_globular", + "proj_id": "1", + "sample_id": 21, + "data_probeset_id": "Glyma15g42100", + "data_signal": 4.33, + "data_bot_id": "heart_seedcoatendothelium" + }, + { + "db": "soybean_heart_cotyledon_globular", + "proj_id": "1", + "sample_id": 11, + "data_probeset_id": "Glyma17g07190", + "data_signal": 0.0, + "data_bot_id": "globular_embryo" + }, + { + "db": "soybean_heart_cotyledon_globular", + "proj_id": "1", + "sample_id": 17, + "data_probeset_id": "Glyma10g09340", + "data_signal": 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file diff --git a/api/random_rows_json/soybean_senescence_test_data.json b/api/random_rows_json/soybean_senescence_test_data.json new file mode 100644 index 00000000..180c2c51 --- /dev/null +++ b/api/random_rows_json/soybean_senescence_test_data.json @@ -0,0 +1,242 @@ +[ + { + "db": "soybean_senescence", + "proj_id": "1", + "sample_id": 21, + "data_probeset_id": "Glyma08g23970.1", + "data_signal": 116.933, + "data_bot_id": "L_IV-3" + }, + { + "db": "soybean_senescence", + "proj_id": "1", + "sample_id": 21, + "data_probeset_id": "Glyma01g38780.1", + "data_signal": 2.94788, + "data_bot_id": "L_IV-3" + }, + { + "db": "soybean_senescence", + "proj_id": "1", + "sample_id": 6, + "data_probeset_id": "Glyma03g01900.1", + "data_signal": 2.65638, + "data_bot_id": "C_II-3" + }, + { + "db": "soybean_senescence", + "proj_id": "1", + "sample_id": 12, + "data_probeset_id": "Glyma03g32191.1", + "data_signal": 0.0, + "data_bot_id": "L_I-3" + }, + { + "db": "soybean_senescence", + "proj_id": "1", + 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"wheat_root", + "proj_id": "1", + "sample_id": 9, + "data_probeset_id": "TraesCS6A01G426400LC", + "data_signal": 0.0, + "data_bot_id": "Certo_tip3" + }, + { + "db": "wheat_root", + "proj_id": "1", + "sample_id": 10, + "data_probeset_id": "TraesCS2D01G558700LC", + "data_signal": 0.0, + "data_bot_id": "Med_CTRL" + }, + { + "db": "wheat_root", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "TraesCS1A01G258200LC", + "data_signal": 1.22254, + "data_bot_id": "Certo_EZ1" + }, + { + "db": "wheat_root", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "TraesCS2B01G160500LC", + "data_signal": 0.0, + "data_bot_id": "Certo_EZ1" + }, + { + "db": "wheat_root", + "proj_id": "1", + "sample_id": 4, + "data_probeset_id": "TraesCS4A01G401400", + "data_signal": 10.7898, + "data_bot_id": "Certo_MZ1" + }, + { + "db": "wheat_root", + "proj_id": "1", + "sample_id": 5, + "data_probeset_id": "TraesCS3A01G194900", + "data_signal": 4.18544, + "data_bot_id": "Certo_MZ2" + }, + { + "db": "wheat_root", + "proj_id": "1", + "sample_id": 9, + "data_probeset_id": "TraesCS5A01G514600", + "data_signal": 0.0, + "data_bot_id": "Certo_tip3" + }, + { + "db": "wheat_root", + "proj_id": "1", + "sample_id": 8, + "data_probeset_id": "TraesCS3D01G144900", + "data_signal": 0.0, + "data_bot_id": "Certo_tip2" + }, + { + "db": "wheat_root", + "proj_id": "1", + "sample_id": 9, + "data_probeset_id": "TraesCS4B01G255200", + "data_signal": 0.0, + "data_bot_id": "Certo_tip3" + } +] \ No newline at end of file diff --git a/api/random_rows_json/wheat_test_data.json b/api/random_rows_json/wheat_test_data.json new file mode 100644 index 00000000..fdf0f970 --- /dev/null +++ b/api/random_rows_json/wheat_test_data.json @@ -0,0 +1,242 @@ +[ + { + "db": "wheat", + "proj_id": "1", + "sample_id": 50, + "data_probeset_id": "TraesCS4B01G209800LC", + "data_signal": 0.0, + "data_bot_id": "Sample_143A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 170, + "data_probeset_id": "TraesCS7B01G048200", + "data_signal": 0.160554, + "data_bot_id": "Sample_64A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 185, + "data_probeset_id": "TraesCS7B01G743500LC", + "data_signal": 0.855438, + "data_bot_id": "Sample_78A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 5, + "data_probeset_id": "TraesCS3B01G165700", + "data_signal": 0.0, + "data_bot_id": "Sample_103A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 36, + "data_probeset_id": "TraesCS2D01G526900", + "data_signal": 0.0, + "data_bot_id": "Sample_130A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 126, + "data_probeset_id": "TraesCS3B01G538900", + "data_signal": 0.0, + "data_bot_id": "Sample_22B" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 177, + "data_probeset_id": "TraesCS6B01G097300", + "data_signal": 0.0, + "data_bot_id": "Sample_70A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 87, + "data_probeset_id": "TraesCS7D01G125000", + "data_signal": 0.0, + "data_bot_id": "Sample_18A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 81, + "data_probeset_id": "TraesCS6D01G232300", + "data_signal": 8.37542, + "data_bot_id": "Sample_183A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 141, + "data_probeset_id": "TraesCS2D01G017300LC", + "data_signal": 0.0, + "data_bot_id": "Sample_33A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 98, + "data_probeset_id": "TraesCS2D01G508200LC", + "data_signal": 0.0, + "data_bot_id": "Sample_19A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 134, + "data_probeset_id": "TraesCS4B01G246200", + "data_signal": 0.0, + "data_bot_id": "Sample_28A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 14, + "data_probeset_id": "TraesCS7B01G149700LC", + "data_signal": 0.0, + "data_bot_id": "Sample_110A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 14, + "data_probeset_id": "TraesCS4A01G065200LC", + "data_signal": 0.186497, + "data_bot_id": "Sample_110A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 68, + "data_probeset_id": "TraesCS2A01G517300LC", + "data_signal": 0.812004, + "data_bot_id": "Sample_171A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 37, + "data_probeset_id": "TraesCS2D01G266300LC", + "data_signal": 0.0, + "data_bot_id": "Sample_131A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 7, + "data_probeset_id": "TraesCS4D01G322900", + "data_signal": 2.40963, + "data_bot_id": "Sample_105B" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 37, + "data_probeset_id": "TraesCS5A01G633300LC", + "data_signal": 0.0, + "data_bot_id": "Sample_131A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 123, + "data_probeset_id": "TraesCS1A01G268900LC", + "data_signal": 0.0, + "data_bot_id": "Sample_223B" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 183, + "data_probeset_id": "TraesCS6D01G097100LC", + "data_signal": 0.0, + "data_bot_id": "Sample_76A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 63, + "data_probeset_id": "TraesCS4A01G332200", + "data_signal": 0.0, + "data_bot_id": "Sample_166A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 97, + "data_probeset_id": "TraesCS7B01G603100LC", + "data_signal": 2.69567, + "data_bot_id": "Sample_199A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 35, + "data_probeset_id": "TraesCS2D01G493400", + "data_signal": 0.0, + "data_bot_id": "Sample_13" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 185, + "data_probeset_id": "TraesCS7A01G242700", + "data_signal": 3.52889, + "data_bot_id": "Sample_78A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 71, + "data_probeset_id": "TraesCS7D01G354800LC", + "data_signal": 0.884343, + "data_bot_id": "Sample_174A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 161, + "data_probeset_id": "TraesCS1D01G089500LC", + "data_signal": 0.0, + "data_bot_id": "Sample_55B" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 11, + "data_probeset_id": "TraesCS3D01G306300LC", + "data_signal": 0.0, + "data_bot_id": "Sample_109A" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 131, + "data_probeset_id": "TraesCS3A01G535000LC", + "data_signal": 0.0, + "data_bot_id": "Sample_26" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 131, + "data_probeset_id": "TraesCS4D01G133800LC", + "data_signal": 0.0, + "data_bot_id": "Sample_26" + }, + { + "db": "wheat", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "TraesCS5B01G668700LC", + "data_signal": 1.47097, + "data_bot_id": "Sample_10" + } +] \ No newline at end of file diff --git a/api/random_rows_json/willow_test_data.json b/api/random_rows_json/willow_test_data.json new file mode 100644 index 00000000..42dff080 --- /dev/null +++ b/api/random_rows_json/willow_test_data.json @@ -0,0 +1,242 @@ +[ + { + "db": "willow", + "proj_id": "1", + "sample_id": 3, + "data_probeset_id": "comp1891_c0_seq1", + "data_signal": 1.5, + "data_bot_id": "RAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 4, + "data_probeset_id": "comp93643_c0_seq19", + "data_signal": 0.0, + "data_bot_id": "RAVG_TREAT" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 2, + "data_probeset_id": "comp92792_c0_seq13", + "data_signal": 0.0, + "data_bot_id": "LAVG_TREAT" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 2, + "data_probeset_id": "comp9394_c0_seq1", + "data_signal": 0.0, + "data_bot_id": "LAVG_TREAT" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "comp90848_c0_seq26", + "data_signal": 0.5, + "data_bot_id": "LAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 6, + "data_probeset_id": "comp93063_c1_seq25", + "data_signal": 0.75, + "data_bot_id": "SAVG_TREAT" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 3, + "data_probeset_id": "comp94484_c1_seq61", + "data_signal": 36.5, + "data_bot_id": "RAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 3, + "data_probeset_id": "comp85527_c0_seq4", + "data_signal": 96.75, + "data_bot_id": "RAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 4, + "data_probeset_id": "comp93051_c1_seq36", + "data_signal": 0.0, + "data_bot_id": "RAVG_TREAT" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 6, + "data_probeset_id": "comp82104_c0_seq11", + "data_signal": 0.0, + "data_bot_id": "SAVG_TREAT" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 6, + "data_probeset_id": "comp88279_c0_seq39", + "data_signal": 10.5, + "data_bot_id": "SAVG_TREAT" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 3, + "data_probeset_id": "comp86294_c2_seq4", + "data_signal": 0.75, + "data_bot_id": "RAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 6, + "data_probeset_id": "comp91338_c0_seq14", + "data_signal": 111.25, + "data_bot_id": "SAVG_TREAT" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "comp92416_c0_seq5", + "data_signal": 606.5, + "data_bot_id": "LAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 4, + "data_probeset_id": "comp93569_c0_seq122", + "data_signal": 11.0, + "data_bot_id": "RAVG_TREAT" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 4, + "data_probeset_id": "comp81875_c0_seq5", + "data_signal": 52.25, + "data_bot_id": "RAVG_TREAT" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 3, + "data_probeset_id": "comp87661_c0_seq21", + "data_signal": 0.0, + "data_bot_id": "RAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "comp84136_c0_seq13", + "data_signal": 1.0, + "data_bot_id": "LAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "comp92903_c0_seq51", + "data_signal": 0.0, + "data_bot_id": "LAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 5, + "data_probeset_id": "comp170315_c0_seq1", + "data_signal": 0.0, + "data_bot_id": "SAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "comp95134_c0_seq4", + "data_signal": 6.75, + "data_bot_id": "LAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 5, + "data_probeset_id": "comp94811_c0_seq56", + "data_signal": 0.0, + "data_bot_id": "SAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "comp91622_c0_seq96", + "data_signal": 0.0, + "data_bot_id": "LAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 4, + "data_probeset_id": "comp94021_c2_seq48", + "data_signal": 52.25, + "data_bot_id": "RAVG_TREAT" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 3, + "data_probeset_id": "comp89554_c0_seq7", + "data_signal": 0.75, + "data_bot_id": "RAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "comp90145_c0_seq8", + "data_signal": 0.0, + "data_bot_id": "LAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 5, + "data_probeset_id": "comp95471_c0_seq28", + "data_signal": 79.5, + "data_bot_id": "SAVG_CTL" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 4, + "data_probeset_id": "comp93299_c0_seq25", + "data_signal": 7.25, + "data_bot_id": "RAVG_TREAT" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 2, + "data_probeset_id": "comp87549_c2_seq29", + "data_signal": 0.0, + "data_bot_id": "LAVG_TREAT" + }, + { + "db": "willow", + "proj_id": "1", + "sample_id": 6, + "data_probeset_id": "comp89046_c0_seq24", + "data_signal": 2051.25, + "data_bot_id": "SAVG_TREAT" + } +] \ No newline at end of file diff --git a/api/resources/gene_expression.py b/api/resources/gene_expression.py index 9f95949c..4f3cfe78 100644 --- a/api/resources/gene_expression.py +++ b/api/resources/gene_expression.py @@ -40,6 +40,9 @@ def get(self, database, gene_id): if species is None: return BARUtils.error_exit(f"Unknown database '{database}'"), 400 + if BARUtils.is_injection_attempt(gene_id): + return BARUtils.error_exit(f"Invalid gene ID for {database}: '{gene_id}'"), 400 + if GeneIdUtils.is_probeset_id(gene_id): query_id = gene_id else: diff --git a/api/resources/microarray_gene_expression.py b/api/resources/microarray_gene_expression.py index 97ebc85c..5e5c8f8e 100644 --- a/api/resources/microarray_gene_expression.py +++ b/api/resources/microarray_gene_expression.py @@ -4,9 +4,9 @@ from api.models.annotations_lookup import AtAgiLookup from api.models.efp_dynamic import SIMPLE_EFP_SAMPLE_MODELS from api.utils.bar_utils import BARUtils +from api.utils.master_data_utils import load_combined_master from api.utils.world_efp_utils import WorldeFPUtils from sqlalchemy import func -import json # Pull the dynamic model so this resource stays in sync with the schema catalog EcotypesSampleData = SIMPLE_EFP_SAMPLE_MODELS["arabidopsis_ecotypes"] @@ -69,155 +69,38 @@ def get(self, species="", gene_id=""): class GetDatabases(Resource): @microarray_gene_expression.param("species", _in="path", default="arabidopsis") def get(self, species=""): - """This endpoint returns available database and view mappings for a given species""" - species = escape(species) + """This endpoint returns the databases and views available for a given + species, and how many of each -- sourced live from combined_master.json + (data/efp_info/combined_master.json) instead of a hardcoded mapping, so + it can't drift out of sync with the actual database/frontend catalog. + """ + species = str(escape(species)).lower() + + master = load_combined_master() + if species not in master["species"]: + return BARUtils.error_exit("Invalid species") - species_databases = { - "actinidia": { - "Bud_Development": "actinidia_bud_development", - "Flower_Fruit_Development": "actinidia_flower_fruit_development", - "Postharvest": "actinidia_postharvest", - "Vegetative_Growth": "actinidia_vegetative_growth", - }, - "arabidopsis": { - "Abiotic_Stress": "atgenexp_stress", - "Abiotic_Stress_II": "atgenexp_stress", - "Biotic_Stress": "atgenexp_pathogen", - "Biotic_Stress_II": "atgenexp_pathogen", - "Chemical": "atgenexp_hormone", - "DNA_Damage": "dna_damage", - "Development_RMA": "atgenexp", - "Developmental_Map": "atgenexp_plus", - "Developmental_Mutants": "atgenexp_plus", - "Embryo": "embryo", - "Germination": "germination", - "Guard_Cell": "guard_cell", - "Gynoecium": "gynoecium", - "Hormone": "atgenexp_hormone", - "Klepikova_Atlas": "klepikova", - "Lateral_Root_Initiation": "lateral_root_initiation", - "Light_Series": "light_series", - "Natural_Variation": "arabidopsis_ecotypes", - "Regeneration": "meristem_db", - "Root": "root", - "Root_II": "root", - "Seed": "seed_db", - "Shoot_Apex": "shoot_apex", - "Silique": "silique", - "Single_Cell": "single_cell", - "Tissue_Specific": "atgenexp_plus", - }, - "arabidopsis seedcoat": {"Seed_Coat": "seedcoat"}, - "arachis": {"Arachis_Atlas": "arachis"}, - "barley": {"barley_mas": "barley_mas", "barley_rma": "barley_rma"}, - "brachypodium": { - "Brachypodium_Atlas": "brachypodium", - "Brachypodium_Grains": "brachypodium_grains", - "Brachypodium_Spikes": "brachypodium_Bd21", - "Photo_Thermocycle": "brachypodium_photo_thermocycle", - }, - "brassica rapa": {"Embryogenesis": "brassica_rapa"}, - "cacao ccn": { - "Developmental_Atlas": "cacao_developmental_atlas", - "Drought_Diurnal_Atlas": "cacao_drought_diurnal_atlas", - }, - "cacao sca": { - "Developmental_Atlas": "cacao_developmental_atlas_sca", - "Drought_Diurnal_Atlas": "cacao_drought_diurnal_atlas_sca", - "Meristem_Atlas": "cacao_meristem_atlas_sca", - "Seed_Atlas": "cacao_seed_atlas_sca", - }, - "cacao tc": {"Cacao_Infection": "cacao_infection", "Cacao_Leaf": "cacao_leaf"}, - "camelina": {"Developmental_Atlas_FPKM": "camelina", "Developmental_Atlas_TPM": "camelina_tpm"}, - "cannabis": {"Cannabis_Atlas": "cannabis"}, - "canola": {"Canola_Seed": "canola_seed"}, - "eutrema": {"Eutrema": "thellungiella_db"}, - "grape": {"grape_developmental": "grape_developmental"}, - "kalanchoe": {"Light_Response": "kalanchoe"}, - "little millet": {"Life_Cycle": "little_millet"}, - "lupin": { - "LCM_Leaf": "lupin_lcm_leaf", - "LCM_Pod": "lupin_lcm_pod", - "LCM_Stem": "lupin_lcm_stem", - "Whole_Plant": "lupin_whole_plant", - }, - "maize": { - "Downs_et_al_Atlas": "maize_gdowns", - "Early_Seed": "maize_early_seed", - "Embryonic_Leaf_Development": "maize_embryonic_leaf_development", - "Hoopes_et_al_Atlas": "maize_buell_lab", - "Hoopes_et_al_Stress": "maize_buell_lab", - "Maize_Kernel": "maize_early_seed", - "Maize_Root": "maize_root", - "Sekhon_et_al_Atlas": "maize_RMA_linear", - "Tassel_and_Ear_Primordia": "maize_ears", - "maize_iplant": "maize_iplant", - "maize_leaf_gradient": "maize_leaf_gradient", - "maize_rice_comparison": "maize_rice_comparison", - }, - "mangosteen": { - "Aril_vs_Rind": "mangosteen_aril_vs_rind", - "Callus": "mangosteen_callus", - "Diseased_vs_Normal": "mangosteen_diseased_vs_normal", - "Fruit_Ripening": "mangosteen_fruit_ripening", - "Seed_Development": "mangosteen_seed_development", - "Seed_Germination": "mangosteen_seed_germination", - }, - "medicago": { - "medicago_mas": "medicago_mas", - "medicago_rma": "medicago_rma", - "medicago_seed": "medicago_seed", - }, - "poplar": {"Poplar": "poplar", "PoplarTreatment": "poplar"}, - "potato": {"Potato_Developmental": "potato_dev", "Potato_Stress": "potato_stress"}, - "rice": { - "rice_drought_heat_stress": "rice_drought_heat_stress", - "rice_leaf_gradient": "rice_leaf_gradient", - "rice_maize_comparison": "rice_maize_comparison", - "rice_mas": "rice_mas", - "rice_rma": "rice_rma", - "riceanoxia_mas": "rice_mas", - "riceanoxia_rma": "rice_rma", - "ricestigma_mas": "rice_mas", - "ricestigma_rma": "rice_rma", - "ricestress_mas": "rice_mas", - "ricestress_rma": "rice_rma", - }, - "soybean": { - "soybean": "soybean", - "soybean_embryonic_development": "soybean_embryonic_development", - "soybean_heart_cotyledon_globular": "soybean_heart_cotyledon_globular", - "soybean_senescence": "soybean_senescence", - "soybean_severin": "soybean_severin", - }, - "strawberry": { - "Developmental_Map_Strawberry_Flower_and_Fruit": "strawberry", - "Strawberry_Green_vs_White_Stage": "strawberry", - }, - "tomato": { - "ILs_Leaf_Chitwood_et_al": "tomato_ils", - "ILs_Root_Tip_Brady_Lab": "tomato_ils2", - "M82_S_pennellii_Atlases_Koenig_et_al": "tomato_s_pennellii", - "Rose_Lab_Atlas": "tomato", - "Rose_Lab_Atlas_Renormalized": "tomato_renormalized", - "SEED_Lab_Angers": "tomato_seed", - "Shade_Mutants": "tomato_shade_mutants", - "Shade_Timecourse_WT": "tomato_shade_timecourse", - "Tomato_Meristem": "tomato_meristem", - }, - "triticale": {"triticale": "triticale", "triticale_mas": "triticale_mas"}, - "wheat": { - "Developmental_Atlas": "wheat", - "Wheat_Abiotic_Stress": "wheat_abiotic_stress", - "Wheat_Embryogenesis": "wheat_embryogenesis", - "Wheat_Meiosis": "wheat_meiosis", - }, + databases = { + db_name: db_info + for db_name, db_info in master["databases"].items() + if db_info["species"] == species } - if species not in species_databases: - return BARUtils.error_exit("Invalid species") + # A database can be exposed under different view display names by + # different frontend instances (efp vs eplant); collapse to a single + # view_name -> database_name mapping like the endpoint has always returned. + views = {} + for db_name, db_info in databases.items(): + for used_by in db_info["used_by"]: + view_key = used_by["view"].replace(" ", "_") + views[view_key] = db_name - return BARUtils.success_exit({"species": species, "databases": species_databases[species]}) + return BARUtils.success_exit({ + "species": species, + "num_databases": len(databases), + "num_views": len(views), + "databases": views, + }) # Endpoint made by Reena @@ -229,32 +112,42 @@ class GetSamples1(Resource): @microarray_gene_expression.param("view", _in="path", default="Abiotic_Stress") def get(self, species="", view=""): """This endpoint returns control and sample group mappings for a given species and view (or all views)""" - species = escape(species.lower()) - view = escape(view) - - try: - with open("data/efp_info/efp_species_view_info_typed.json") as f: - all_species_data = json.load(f) - except Exception as e: - return BARUtils.error_exit(f"Data file missing or invalid: {e}") + species = str(escape(species)).lower() + view = str(escape(view)) - if species not in all_species_data: + master = load_combined_master() + if species not in master["species"]: return BARUtils.error_exit("Invalid species") - species_data = all_species_data[species]["data"] + species_databases = { + db_name: db_info + for db_name, db_info in master["databases"].items() + if db_info["species"] == species + } + + # Collapse every database's views to a single view_name -> {database, + # platform, groups} mapping, same view-name normalization as /databases. + all_views = {} + for db_name, db_info in species_databases.items(): + for view_info in db_info["views"].values(): + view_key = view_info["display_name"].replace(" ", "_") + all_views[view_key] = { + "database": db_name, + "platform": db_info["platform"], + "groups": view_info["sample_groups"], + } - # if user requests all views if view.lower() == "all": - return BARUtils.success_exit({"species": species, "views": species_data["views"]}) + return BARUtils.success_exit({"species": species, "views": all_views}) - # otherwise check single view - if view not in species_data["views"]: + if view not in all_views: return BARUtils.error_exit("Invalid view for this species") - view_data = species_data["views"][view] + view_data = all_views[view] return BARUtils.success_exit({ "species": species, "view": view, - "data_type": view_data.get("data_type", "Unknown"), - "groups": view_data["groups"] + "database": view_data["database"], + "platform": view_data["platform"], + "groups": view_data["groups"], }) diff --git a/api/utils/bar_utils.py b/api/utils/bar_utils.py index effc28d1..210d6721 100644 --- a/api/utils/bar_utils.py +++ b/api/utils/bar_utils.py @@ -2,187 +2,45 @@ import redis import os -# fmt: off -# Per-eFP-project input validation regexes sourced from efpWeb.cgi. -# Each pattern covers canonical gene IDs AND (where applicable) microarray probeset IDs. -EFP_PROJECT_REGEXES: dict = { - "efp": ( - r"^([Aa][Tt][12345CM][Gg][0-9]{5})$" - r"|^([0-9]{6}(_[xsfi])?_at)$" - r"|^([0-9]{6,9})$" - # ATH1 Affymetrix bacterial/control spike-in probes, shared by all Affy platforms - r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$" - r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" - ), - "efp_arabidopsis": ( - r"^([Aa][Tt][12345CM][Gg][0-9]{5})$" - r"|^([0-9]{6}(_[xsfi])?_at)$" - r"|^([0-9]{6,9})$" - r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$" - r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" - ), - # Seedcoat uses CATMA probes (At\d{8}) and AROS probes (\D\d+_\d+) in addition to ATH1 - "efp_seedcoat": ( - r"^(At[12345CM]g[0-9]{5})$" - r"|^([0-9]{6}(_[xsfi])?_at)$" - r"|^([0-9]{6,9})$" - r"|^(\D\d+_\d+)$" - r"|^(At\d{8})$" - ), - "efp_barley": ( - r"^((HM|HV).*)$|^(HV.*_at)$" - r"|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4})_at)$" - r"|^([0-9]{4,5}\.AF[0-9]{5}(_|_x_)at)$" - r"|^(A[0-9]{5}\.[0-9]{1}(_|_x_|_s_)at)$" - r"|^(([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)(_|_x_|_s_|_CDS-[0-9]{1,2}_|_CDS-[0-9]{1,2}_s_)at)$" - r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$" - r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" - r"|^(ChlorContig[0-9]{1,2}(_|_x_|_s_)at)$" - r"|^(((MitoContig|Contig)[0-9]{1,6})(_|_x_|_s_)at)$" - r"|^(D[0-9]{5}_at)$" - r"|^(Dhn[0-9]{2}\(Morex\)(_|_s_)at)$" - r"|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2}(_|_s_|_x_)at)$" - r"|^(Franka(_|_b_)3pri[0-9]{1,2}(_|_s_|_x_)at)$" - r"|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$" - r"|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$" - r"|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru](_|_x_|_s_)at)$" - r"|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1}(_|_x_|_s_)at)$" - r"|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2}(_|_x_|_s_)at)$" - r"|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4}))$" - r"|^([0-9]{4,5}\.AF[0-9]{5})$" - r"|^(A[0-9]{5}\.[0-9]{1})$" - r"|^([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)$" - r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX))$" - r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre))$" - r"|^(ChlorContig[0-9]{1,2})$" - r"|^((MitoContig|Contig)[0-9]{1,6})$" - r"|^(D[0-9]{5})$" - r"|^(Dhn[0-9]{2}\(Morex\))$" - r"|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2})$" - r"|^(Franka(_|_b_)3pri[0-9]{1,2})$" - r"|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$" - r"|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$" - r"|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru])$" - r"|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1})$" - r"|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2})$" - r"|^(HO)$" - r"|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$" - r"|^(AK[0-9]{6}\.1)$" - r"|^(AJ[0-9]{6}\.1)$" - ), - "efp_rice": ( - r"^(LOC_Os[0-9]{2}g[0-9]{5})$" - r"|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$" - r"|^(AFFX-OS-(18SrRNA|25SrRNA|5\.8SrRNA)_(s_at|at))$" - r"|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$" - r"|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$" - r"|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$" - r"|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" - r"|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" - ), - "efp_medicago": ( - r"^(Medtr\d{1}g\d{6})$" - r"|^(Medtr\d{1}g\d{6}\.[0-9]{1})$" - # Medicago array probesets: Mtr/Msa/Sme prefix, any Affymetrix suffix variant - r"|^(Mtr\.\d{4,5}\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$" - r"|^(Msa\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$" - r"|^(Sme\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$" - r"|^(AFFX-(Bio|Cre|Dap|Lys|Phe|Thr|Trpn)(B|C|Dn|X)-(3|5|M)_at)$" - r"|^(AFFX-(Msa|Mtr)-(actin|gapc|gsta|ubq11|TrpnX)-(3|5|M)_(at|x_at|s_at))$" - r"|^(AFFX-r2-(Bs|Ec|P1)-(cre|dap|lys|phe|thr|bioB|bioC|bioD)-(3|5|M)_(at|s_at|x_at))$" - r"|^(AFFX-Mtr-ubq11-(3|5|M)_(at|s_at|x_at))$" - r"|^(AFFX-r2-Tag[A-Z]{1,2}_at)$" - r"|^(Medtr_v1_\d{6})$" - ), - "efp_poplar": ( - r"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$" - r"|^((eugene3)\.\d{6,12})$" - r"|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$" - r"|^((grail3\.)\d{8,12})$" - r"|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$" - r"|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$" - r"|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$" - # poplar_hormone's real sample IDs omit the transcript suffix entirely - r"|^(Potri\.[0-9]{3}G[0-9]{6}(\.[0-9]{1})?)$" - ), - "efp_soybean": ( - r"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$" - r"|^(Glyma\.\d{1,3}g\d{1,8}))$" - ), - "efp_maize": ( - r"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$" - r"|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$" - r"|^(GRMZM(2|5)G[0-9]{6})$" - r"|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$" - r"|^(Zm\d+d\d+)$" - r"|^(Zm\d{1,10}eb\d{1,10})$" - # Maize Affymetrix probeset IDs, e.g. Zm011368_at, Zm039842_s_at - r"|^(Zm\d{6}(_[xsa])?_at)$" - ), - # TaAffx.* probes occur alongside Ta.* — handle both prefixes - "efp_triticale": r"^((Ta|TaAffx)\.\d+\.\d+\.[A-Z]\d+_(at|s_at|x_at|a_at))$", - # Affymetrix human probeset IDs (1557575_at, 202019_s_at) plus a loose fallback - "efp_human": r"^(\d{6,7}(_[xsa])?_at)$|^(\D{0,12}\d{0,12})$|^(\d{1,12})$", - # Remaining eFP projects, sourced verbatim from Vincent's efp_regex_audit_prod.csv - "efp_Eutrema": r"^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$", - "efp_actinidia": r"^(Acc\d+\.\d{0,3})$", - "efp_apple": r"^(MfusH1_\d\dg\d{1,8})$", - # CSV pattern is lowercase-only; lipid species names use mixed case (e.g. "TG 54:5; ...") - "efp_arabidopsis_lipid": r"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$", - "efp_arachis": r"^(Adur\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Aipa_c\d+_g\d+_i\d+)$|^(Aipa\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Adur_c\d+_g\d+_i\d+)$", - "efp_brachypodium": r"^(Bradi\d+g\d+.\d)$|^(Bradi\d+s\d+.\d)$|^(Bradi\d+.g\d+)$", - "efp_brachypodium_metabolites": r"(?i)^[a-z\s\-]{1,60}$", - "efp_brassica_rapa": r"^(Bra.\d+g\d{0,10})$", - "efp_cacao_ccn": r"^(CCN-51_Chr\d{1,3}v\d{1,3}_\d{1,9})$", - "efp_cacao_sca": r"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$", - "efp_cacao_tc": r"^(Tc\d+v2_g\d+)$", - "efp_camelina": r"^(Csa\d{0,5}[gs]\d{0,6}.\d{0,3})$|^(At\d[cgm]\d{0,6})$", - "efp_cannabis": r"(^C\d+$)|(^scaffold\d+$)|(^AGQN\d+$)", - "efp_canola": r"^(Bna\D\d{1,3}g\d{1,8}\D)$|^(Bna\Dnng\d{1,8}\D)$", - "efp_durum_wheat": r"^(TrturSVE\d\D\d{1,3}G\d{1,12})$|^(TrturSVE\d\D\d{1,3}G\d{1,12}_ncBOCREA)$", - "efp_euphorbia": r"^(Ep_chr\d_g\d{1,8})$", - "efp_eutrema": r"^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$", - "efp_grape": r"^(VIT_\d{1,2}s\d{4}g\d{5})$|^CHRUN[a-z0-9_]{1,20}$|^CHR\d{1,2}[a-z0-9_]{1,2}$", - "efp_kalanchoe": r"^(Kaladp\d+s\d+)$", - "efp_little_millet": r"^(TRINITY_DN\d+_c\d+_g\d+_i\d+)$", - "efp_lupin": r"^(Luan_Oskar_.{1,12}_\d{1,12})$", - # is_efp_gene_valid matches without re.IGNORECASE, so these freeform-text - # patterns (enzyme/metabolite/category NAMES, not gene IDs) need an explicit - # (?i) -- real sample data is mixed-case ("GAPDH (NAD)", "Citric Acid"). - "efp_maize_enzyme": r"(?i)^[a-z0-9\s\-\(\)]{1,50}$", - "efp_maize_metabolite": r"(?i)^[a-z0-9\s,\.\-\(\)_'\+]{1,60}$", - # Lipid species names (TG_52_1, MGDG_38_6), same freeform style as efp_arabidopsis_lipid - "efp_maize_lipid_map": r"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$", - # tomato_trait stores root-architecture trait descriptions, not gene IDs - "efp_tomato_trait": r"^[A-Za-z][A-Za-z0-9\s\.,\-\(\)]{1,100}$", - "efp_maize_transcriptomics": r"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$", - "efp_mangosteen": r"^(DN\d{1,10})$", - "efp_marchantia": r"^(Mp.{1,3}g\d{1,7}\.?\d{1,3}?)$", - "efp_oat": r"(^N0\.HOG\d{1,10}$|^\D{1,10}\.*\d{1,10}.{1,10}\d{1,10}$)", - "efp_phelipanche": r"^(OrAeBC\d+_\d+\.\d{1,5})|(At\d[gcm]\d{1,6})$", - "efp_physcomitrella": r"^(Pp)\d+s\d+_\d+V\d\.\d$|^Phypa_\d+$", - "efp_potato": r"^(PGSC0003DMG4\d{8})$", - "efp_rice_metabolite": r"(?i)^[a-z0-9,\s\.\-]{1,40}$", - "efp_rice_transcriptomics": r"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$", - "efp_selaginella": r"^(Smo\d+)$", - "efp_sorghum": r"^(Sobic.\d{0,5}G\d{0,10}$|^Sobic.K\d{0,10}$|^ENSRNA\d{0,12}$|^SORBI_\d{1,6}G\d{1,10})$", - "efp_strawberry": r"^(FvH4_c?\d{1,3}g\d{1,7})$|^(gene\d{1,10})$", - "efp_striga": r"^(StHeBC3\_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$", - "efp_tomato": r"^(Solyc\d{2}g\d{6}\.?\d{0,3})$|^(TU\d{6})$", - "efp_triphysaria": r"^(TrVeBC\d+_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$", - "efp_tung_tree": r"^(Vf\d+G\d+)$", - "efp_wheat": r"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$", - "efpconfig": r".{0,16}", - "mouse_efp": r"^(XM_\d{0,8}\.\d{0,3})$|^(\d{1,10}\D\d{0,4}\D{0,4})$|^(\D{1,8}\d{0,8}\D{0,8})$|^(ENSMUSG\d{1,15})$|^(NM_\d{0,12}\d.\d{0,3})$", -} -# Aliases for alternate eFP project key spellings used by the BAR +from api.utils.master_data_utils import load_combined_master + +# Per-eFP-project input validation regexes. Sourced from Vincent's +# regex_master_list_efp_eplant registry (tested at 99%+ coverage against real +# probeset/gene ID sample data) and embedded into combined_master.json at +# build time by build_combined_master_json.py -- see get_validation_patterns(). +# Each pattern covers canonical gene IDs AND (where applicable) microarray +# probeset IDs. Copied (not aliased) so the aliases added below don't mutate +# the shared cached master JSON other modules also read. +EFP_PROJECT_REGEXES: dict = dict(load_combined_master()["validation_patterns"]) + +# Aliases for alternate eFP project key spellings used by the BAR (not present +# in Vincent's registry, which is keyed by canonical eFP project name only). EFP_PROJECT_REGEXES["efpbarley"] = EFP_PROJECT_REGEXES["efp_barley"] EFP_PROJECT_REGEXES["efprice"] = EFP_PROJECT_REGEXES["efp_rice"] EFP_PROJECT_REGEXES["efpmedicago"] = EFP_PROJECT_REGEXES["efp_medicago"] EFP_PROJECT_REGEXES["efppop"] = EFP_PROJECT_REGEXES["efp_poplar"] EFP_PROJECT_REGEXES["efpsoybean"] = EFP_PROJECT_REGEXES["efp_soybean"] EFP_PROJECT_REGEXES["maizeefp"] = EFP_PROJECT_REGEXES["efp_maize"] -# fmt: on + +# General injection guard, run before any per-project/probeset format check. +# A handful of eFP projects accept loose freeform text (metabolite/enzyme/trait +# names, e.g. "TG 54:5; 16:0_20:1_18:4" or "efpconfig"'s near-unrestricted +# `.{0,16}`), so this can't blacklist individual characters like ';' or "'" -- +# those are legitimate in real sample data. Instead it looks for actual attack +# syntax: SQL comment/statement-chaining sequences, tautologies, UNION SELECT, +# script tags, and null bytes. +_INJECTION_RE = re.compile( + r"(--)" + r"|(/\*)|(\*/)" + r"|(;\s*(drop|delete|update|insert|alter|exec|union|select)\b)" + r"|(\bunion\b\s+\bselect\b)" + r"|(\bor\b\s+['\"]?\d+['\"]?\s*=\s*['\"]?\d+)" + r"|(<\s*script\b)" + r"|(javascript\s*:)" + r"|(\bxp_cmdshell\b)" + r"|(\x00)", + re.IGNORECASE, +) class BARUtils: @@ -237,10 +95,11 @@ def is_apple_gene_valid(gene): @staticmethod def is_barley_gene_valid(gene): - """Validates barley gene IDs: HORVU0Hr1G000320, HORVU.MOREX.r3.1HG0003350.1, + """Validates barley gene IDs: HORVU0Hr1G000320, HORVU.MOREX.r3.1HG0000030 (bare gene, + BAR's own live example), HORVU.MOREX.r3.1HG0003350.1 (with isoform suffix), or HORVU.MOREX.r3.UnG0797170.1 (Un = unplaced scaffold, no chromosome digit)""" return bool( - gene and re.search(r"^HORVU(\d+Hr\d+G\d+|\.MOREX\.r\d+\.(\dH|Un)G\d+\.\d+)$", gene, re.I) + gene and re.search(r"^HORVU(\d+Hr\d+G\d+|\.MOREX\.r\d+\.(\dH|Un)G\d+(\.\d+)?)$", gene, re.I) ) @staticmethod @@ -255,8 +114,9 @@ def is_cacao_gene_valid(gene): @staticmethod def is_camelina_gene_valid(gene): - """Validates Camelina gene IDs: Csa01g012560.1, Csa00462s060.1""" - return bool(gene and re.search(r"^Csa\d+[gs]\d+\.\d+$", gene, re.I)) + """Validates Camelina gene IDs: Csa01g001040 (bare gene, BAR's own live example), + Csa01g012560.1, Csa00462s060.1 (with isoform suffix)""" + return bool(gene and re.search(r"^Csa\d+[gs]\d+(\.\d+)?$", gene, re.I)) @staticmethod def is_cassava_gene_valid(gene): @@ -623,6 +483,21 @@ def format_poplar(poplar_gene): """ return poplar_gene.translate(str.maketrans("pOTRIg", "PotriG")) + @staticmethod + def is_injection_attempt(data: str) -> bool: + """Flag obvious SQL/script injection payloads. + + Meant to run before any format-specific check (probeset-shape check, + per-project regex, species validator) since some of those are + deliberately permissive -- e.g. efpconfig's near-unrestricted + `.{0,16}` or the metabolite/lipid projects' freeform text patterns -- + and would otherwise let attack syntax through unexamined. + + :param data: Raw input string to inspect + :return: True if the input looks like an injection attempt + """ + return bool(_INJECTION_RE.search(data)) + @staticmethod def is_efp_gene_valid(gene: str, efp_project: str) -> bool: """Validate a gene ID against the named eFP project's input regex. @@ -635,6 +510,8 @@ def is_efp_gene_valid(gene: str, efp_project: str) -> bool: :param efp_project: eFP project key (e.g. 'efp_arabidopsis', 'efpbarley') :return: True if the gene ID matches the project's accepted format """ + if BARUtils.is_injection_attempt(gene): + return False pattern = EFP_PROJECT_REGEXES.get(efp_project) if not pattern: return False diff --git a/api/utils/gene_id_utils.py b/api/utils/gene_id_utils.py index 64ee2949..47f28013 100644 --- a/api/utils/gene_id_utils.py +++ b/api/utils/gene_id_utils.py @@ -3,6 +3,15 @@ import re from api.utils.bar_utils import BARUtils +from api.utils.master_data_utils import load_combined_master + + +def _load_database_regex_projects() -> dict[str, str]: + databases = load_combined_master()["databases"] + return { + db: info["regex_project"] for db, info in databases.items() if info.get("regex_project") + } + _PROBESET_RE = re.compile(r"^.+_at$", re.IGNORECASE) _AROS_PROBESET_RE = re.compile(r"^A\d{6}_\d{2}$", re.IGNORECASE) @@ -87,7 +96,7 @@ "eucalyptus": "eucalyptus", "euphorbia": "euphorbia", "grape_developmental": "grape", - "heterodera_schachtii": "heterodera", + "heterodera_schachtii": "arabidopsis", "human_body_map_2": "human", "human_developmental": "human", "human_developmental_SpongeLab": "human", @@ -207,71 +216,15 @@ "sample_data": "arabidopsis", } -# Maps databases that store microarray probeset IDs to their eFP project regex key. -# These databases accept both canonical gene IDs (with AGI→probeset lookup for Arabidopsis) -# AND direct probeset ID input. -# fmt: off -DATABASE_EFP_PROJECT: dict[str, str] = { - # Arabidopsis ATH1 microarray databases — support AGI + probeset input - "affydb": "efp_arabidopsis", - "arabidopsis_ecotypes": "efp_arabidopsis", - "atgenexp": "efp_arabidopsis", - "atgenexp_hormone": "efp_arabidopsis", - "atgenexp_pathogen": "efp_arabidopsis", - "atgenexp_plus": "efp_arabidopsis", - "atgenexp_stress": "efp_arabidopsis", - "guard_cell": "efp_arabidopsis", - "hnahal": "efp_arabidopsis", - "lateral_root_initiation": "efp_arabidopsis", - "light_series": "efp_arabidopsis", - "meristem_db": "efp_arabidopsis", - "meristem_db_new": "efp_arabidopsis", - "root": "efp_arabidopsis", - "rohan": "efp_arabidopsis", - "rpatel": "efp_arabidopsis", - "seed_db": "efp_arabidopsis", - # Seedcoat uses CATMA/AROS probes in addition to AGI - "seedcoat": "efp_seedcoat", - # Non-Arabidopsis microarray databases — probeset input only (no AGI conversion) - # barley_seed / barley_spike_meristem(_v3) and poplar_leaf / poplar_xylem were - # previously (incorrectly) mapped here too: their real sample IDs are plain - # gene IDs (HORVU..., Potri...), not probesets, and were 0% passing this - # override. Removed so they fall back to the barley/poplar species validator, - # which already accepts their format. - "barley_mas": "efp_barley", - "barley_rma": "efp_barley", - "rice_mas": "efp_rice", - "rice_rma": "efp_rice", - "medicago_mas": "efp_medicago", - "medicago_rma": "efp_medicago", - "poplar": "efp_poplar", - "poplar_hormone": "efp_poplar", - "triticale": "efp_triticale", - "triticale_mas": "efp_triticale", - "human_developmental": "efp_human", - "human_developmental_SpongeLab": "efp_human", - "human_diseased": "efp_human", - "maize_gdowns": "efp_maize", - # Added after Task 2 (Jun 2026) regex-coverage audit: species validator rejected - # real sample IDs that Vincent's per-project eFP regex correctly accepts. - "arachis": "efp_arachis", - "canola_seed": "efp_canola", - "thellungiella_db": "efp_eutrema", - "physcomitrella_db": "efp_physcomitrella", - "tomato": "efp_tomato", - "tomato_renormalized": "efp_tomato", - "lipid_map": "efp_arabidopsis_lipid", - # Metabolite/enzyme-class eFPs: real "gene_id" values are compound/enzyme/trait - # names looked up against one fixed database, not actual gene IDs -- see - # scrape_view_databases.py's _HARDCODED comment for how these sites are scraped. - "maize_enzyme": "efp_maize_enzyme", - "maize_metabolite": "efp_maize_metabolite", - "maize_lipid_map": "efp_maize_lipid_map", - "rice_metabolite": "efp_rice_metabolite", - "brachypodium_metabolites_map": "efp_brachypodium_metabolites", - "tomato_trait": "efp_tomato_trait", -} -# fmt: on +# Maps databases that store microarray probeset IDs (or, for a handful of +# metabolite/enzyme/trait eFPs, freeform category names) to their eFP project +# regex key. Sourced from Vincent's regex_master_list_efp_eplant registry via +# combined_master.json's per-database "regex_project" field, which is itself +# empirically verified against real sample data at build time (see +# verify_regex_projects() in build_combined_master_json.py) -- databases whose +# assigned project doesn't actually validate most of their own real IDs are +# left out here and fall back to species-based validation below instead. +DATABASE_EFP_PROJECT: dict[str, str] = _load_database_regex_projects() _VALIDATORS: dict = { @@ -291,7 +244,6 @@ "eucalyptus": BARUtils.is_eucalyptus_gene_valid, "euphorbia": BARUtils.is_euphorbia_gene_valid, "grape": BARUtils.is_grape_gene_valid, - "heterodera": BARUtils.is_arabidopsis_gene_valid, "human": BARUtils.is_human_gene_valid, "kalanchoe": BARUtils.is_kalanchoe_gene_valid, "little_millet": BARUtils.is_little_millet_gene_valid, @@ -360,6 +312,8 @@ def validate_gene_for_database(gene_id: str, database: str) -> bool: :param database: Database name (e.g. 'light_series', 'barley_mas') :return: True if the gene ID is valid for the given database """ + if BARUtils.is_injection_attempt(gene_id): + return False efp_project = DATABASE_EFP_PROJECT.get(database) if efp_project: return BARUtils.is_efp_gene_valid(gene_id, efp_project) diff --git a/api/utils/master_data_utils.py b/api/utils/master_data_utils.py new file mode 100644 index 00000000..70f5ed74 --- /dev/null +++ b/api/utils/master_data_utils.py @@ -0,0 +1,14 @@ +import json +from functools import lru_cache +from pathlib import Path + +_COMBINED_MASTER_PATH = Path(__file__).resolve().parents[2] / "data" / "efp_info" / "combined_master.json" + + +@lru_cache(maxsize=1) +def load_combined_master() -> dict: + """Load data/efp_info/combined_master.json (species, databases, views, and + validation_patterns), cached after first read. + """ + with open(_COMBINED_MASTER_PATH) as f: + return json.load(f) diff --git a/build_combined_master_json.py b/build_combined_master_json.py new file mode 100644 index 00000000..a21d8b2f --- /dev/null +++ b/build_combined_master_json.py @@ -0,0 +1,562 @@ +#!/usr/bin/env python3 +""" +Reena Obmina | BCB330 Project 2025-2026 | University of Toronto +""" + +import json +import re +import xml.etree.ElementTree as ET +from collections import defaultdict +from pathlib import Path + +from scrape_species_view_info import extract_db, parse_groups +from scrape_view_databases import EPLANT_SPECIES_FILE + +HUMAN_XML_DIR = Path("data/efp_info/efp_human") +VIEW_INFO_FILE = Path("data/efp_info/efp_eplant_species_view_info.json") +REGEX_REGISTRY_FILE = Path("data/regex_master_list_efp_eplant/bar_regex_registry.json") + +# eplant_barley and eplant_barley_legacy are two live instances of the same species, +# named to match their BAR URLs exactly (bar.utoronto.ca/eplant_barley_legacy/ etc.). +# Noted here because the version numbers aren't visible anywhere in the instance +# names themselves. +INSTANCE_NOTES = { + "eplant_barley_legacy": "ePlant Barley v1 (legacy). URL: https://bar.utoronto.ca/eplant_barley_legacy/", + "eplant_barley": "ePlant Barley v3 (current). URL: https://bar.utoronto.ca/eplant_barley/", +} + + +def load_json(path): + with open(path) as f: + return json.load(f) + + +def get_validation_patterns(): + """Load Vincent's per-eFP-project regex registry (tested at 99%+ coverage + against real probeset/gene ID sample data, one pattern per project instead + of one per database). + + :returns: (patterns, db_regex_project) -- patterns maps eFP project name to + its regex string; db_regex_project maps database name to the project + name whose pattern validates it (None if Vincent's registry couldn't + resolve one, in which case callers fall back to species validation). + """ + registry = load_json(REGEX_REGISTRY_FILE) + patterns = {name: info["regex"] for name, info in registry["projects"].items()} + db_regex_project = { + db: info.get("regex_project") for db, info in registry["databases"].items() + } + return patterns, db_regex_project + + +# Vincent's registry falls back to a database's species' primary eFP project +# when it can't resolve one from live frontend data (resolved_via +# "species-fallback"). That fallback is wrong for these two: both are hidden/ +# legacy databases (not in any current frontend dropdown) whose real values +# are the freeform text a *different*, more specific project already in the +# registry expects -- not gene IDs at all. Obvious from the database's own +# name; confirmed against real sample data in verify_regex_projects(). +REGEX_PROJECT_OVERRIDES = { + "maize_lipid_map": "efp_maize_lipid_map", + "tomato_trait": "efp_tomato_trait", +} + + +def load_probeset_samples(): + """Load real gene_id/probeset values per database (api/random_rows_json/), + for empirically verifying regex_project assignments in verify_regex_projects(). + """ + samples = {} + for path in sorted(SAMPLE_DUMP_DIR.glob("*_test_data.json")): + db_name = path.stem.removesuffix("_test_data") + rows = load_json(path) + if isinstance(rows, list): + ids = [ + row.get("data_probeset_id") + for row in rows + if isinstance(row, dict) and row.get("data_probeset_id") is not None + ] + if ids: + samples[db_name] = ids + return samples + + +def verify_regex_projects(db_regex_project, patterns, sample_ids, threshold=0.9): + """Empirically check each database's regex_project assignment against its + own real sample IDs, the same way schema_variants are verified against + real columns (apply_dump_evidence). Vincent's "species-fallback" + resolutions are unverified guesses for databases with no live frontend + view to confirm against, and are sometimes wrong (e.g. a legacy ID scheme + the species' main project regex doesn't cover). Demote any assignment + that doesn't validate most of its own database's real IDs, so callers + fall back to the (already-correct) species validator instead of silently + rejecting valid input. + + :returns: (verified_db_regex_project, demoted) -- demoted is + {db: (project, pass_rate)} for visibility/logging. + """ + verified = dict(db_regex_project) + for db, override in REGEX_PROJECT_OVERRIDES.items(): + if db in verified: + verified[db] = override + + demoted = {} + for db, ids in sample_ids.items(): + project = verified.get(db) + if not project: + continue + pattern = patterns.get(project) + if not pattern: + continue + compiled = re.compile(pattern) + pass_rate = sum(1 for gid in ids if compiled.search(str(gid))) / len(ids) + if pass_rate < threshold: + demoted[db] = (project, pass_rate) + verified[db] = None + + return verified, demoted + + +def patch_human_view_groups(view_info): + """Fill in efp_human's empty sample groups from the local eFP Human XML config. + + efp_human's live views scrape as empty ("groups": {}) because the site 403s the + scraper (see scrape_view_databases.py's _EFP_FALLBACK comment) -- not because + the views have no group data. We have that data locally (data/efp_info/efp_human/, + the actual per-view XML config pulled from eFP Human), so parse it with the same + extract_db()/parse_groups() scrape_species_view_info.py already uses for every + other species, and patch the matching efp_human view entries in place. + + Returns True if any view was patched (caller should persist view_info to disk). + """ + if not HUMAN_XML_DIR.is_dir(): + return False + + human_views = view_info.get("efp", {}).get("efp_human", []) + if not human_views: + return False + + views_by_name = {v["view_name"]: v for v in human_views} + patched = False + + for xml_path in sorted(HUMAN_XML_DIR.glob("*.xml")): + if xml_path.stem == "efp_info": + continue + + view_name = xml_path.stem.replace("_", " ") + view = views_by_name.get(view_name) + if view is None: + print(f" Warning: no matching efp_human view for {xml_path.name}") + continue + + root = ET.parse(xml_path).getroot() + db = extract_db(root) + groups = parse_groups(root) + + if db and db != view["database"]: + print(f" Warning: {view_name} db mismatch: scraped={view['database']!r} xml={db!r}") + + view["groups"] = groups + view["view_file"] = xml_path.stem + patched = True + print(f" Patched '{view_name}' ({db}): {len(groups)} sample groups") + + return patched + + +SAMPLE_DUMP_DIR = Path("api/random_rows_json") + +# Role/type annotations for every sample_data column we've observed in the real +# sample dumps, keyed by column name so both schema variants (and any new column +# a future dump reveals) share one definition instead of two hand-copies. +COLUMN_META = { + "data_probeset_id": {"type": "varchar", "role": "gene_id"}, + "data_signal": {"type": "float", "role": "value"}, + "data_bot_id": {"type": "varchar", "role": "sample"}, + "sample_id": {"type": "int", "role": "row_id"}, + "proj_id": {"type": "varchar", "role": "project"}, + "sample_file_name": {"type": "varchar", "role": "provenance"}, + "data_call": {"type": "varchar", "role": "present_call"}, + "data_p_val": {"type": "double", "role": "p_value"}, + # Columns below only appear in a handful of legacy/oddball databases -- + # added so every real schema shape found in verify_regex_projects()'s + # sibling, derive_schema_variants_from_dumps(), has full column metadata + # instead of a null type/role. + "data_num": {"type": "int", "role": "secondary_id"}, + "channel": {"type": "varchar", "role": "channel"}, + "project_id": {"type": "varchar", "role": "project"}, + "sample_tissue": {"type": "varchar", "role": "tissue"}, + "data_p_value": {"type": "double", "role": "p_value"}, + "genome": {"type": "varchar", "role": "genome"}, + "genome_id": {"type": "varchar", "role": "genome"}, + "orthogroup": {"type": "varchar", "role": "orthogroup"}, + "version": {"type": "varchar", "role": "version"}, + "log": {"type": "double", "role": "value"}, + "p_val": {"type": "double", "role": "p_value"}, + "qvalue": {"type": "double", "role": "q_value"}, +} + + +def load_sample_dumps(): + """Load Vincent's per-database sample_data row dumps (api/random_rows_json/*_test_data.json). + + Returns {database_name: set(columns)}, with the "db" key dropped since every + dump file carries it as a database-name tag added by whoever generated the + dump, not a real sample_data column. + """ + dumps = {} + for path in sorted(SAMPLE_DUMP_DIR.glob("*_test_data.json")): + db_name = path.stem.removesuffix("_test_data") + rows = load_json(path) + row = rows[0] if isinstance(rows, list) and rows else rows + if isinstance(row, dict): + dumps[db_name] = set(row.keys()) - {"db"} + return dumps + + +# Named baselines used only to generate readable, stable variant names (e.g. +# "legacy_microarray_projinfo_plus_sample_tissue") for real column signatures +# that diverge from the two original hand-authored shapes -- every variant's +# actual columns still come straight from real dumps, not these baselines. +_RNASEQ_BASELINE_NAME = "rnaseq_simple" +_RNASEQ_BASELINE_CORE = {"data_bot_id", "data_probeset_id", "data_signal", "proj_id", "sample_id"} +_MICROARRAY_BASELINE_NAME = "legacy_microarray_projinfo" +_MICROARRAY_BASELINE_CORE = { + "data_bot_id", "data_call", "data_p_val", "data_probeset_id", + "data_signal", "proj_id", "sample_file_name", "sample_id", +} +# Legacy microarray databases document a companion proj_info table alongside +# sample_data; not derivable from the sample_data dumps, so attached as-is to +# every microarray-platform variant. +_PROJ_INFO_TABLE = { + "columns": { + "proj_id": {"role": "project"}, + "proj_title": {}, + "proj_pi": {}, + "proj_res_area": {}, + "proj_num_samps": {}, + } +} + + +def _variant_name(platform, signature): + if platform == "rna_seq": + base_name, baseline = _RNASEQ_BASELINE_NAME, _RNASEQ_BASELINE_CORE + else: + base_name, baseline = _MICROARRAY_BASELINE_NAME, _MICROARRAY_BASELINE_CORE + if signature == baseline: + return base_name + extra = sorted(signature - baseline) + missing = sorted(baseline - signature) + suffix_parts = [] + if extra: + suffix_parts.append("plus_" + "_".join(extra)) + if missing: + suffix_parts.append("minus_" + "_".join(missing)) + return f"{base_name}_" + "_".join(suffix_parts) + + +def derive_schema_variants_from_dumps(master_db_list, sample_dumps): + """Group every database into a schema_variant matching its OWN real + sample_data columns (api/random_rows_json/), instead of forcing every + database into one of two variants based on platform (rna_seq/microarray) + alone regardless of its actual column shape -- the source of the ~47 + "schema_verified: false" mismatches this replaces. Every current database + has a real dump, so every variant here is an exact observed signature, + not a threshold-pooled approximation that only "mostly" fits. + + :returns: (schema_variants, db_variant) -- schema_variants is + {variant_name: {"tables": {...}, "assigned_databases": n}} ready for + the combined JSON; db_variant maps database name -> variant name. + """ + platform_by_db = { + db_name: db_info.get("platform", "unknown") + for dbs in master_db_list.values() + for db_name, db_info in dbs.items() + } + + schema_variants = {} + db_variant = {} + variant_db_counts = defaultdict(int) + + for db_name, cols in sample_dumps.items(): + platform = platform_by_db.get(db_name, "unknown") + signature = frozenset(cols) + name = _variant_name(platform, signature) + db_variant[db_name] = name + variant_db_counts[name] += 1 + + if name not in schema_variants: + columns = { + col: dict(COLUMN_META.get(col, {"type": None, "role": None})) + for col in sorted(signature) + } + tables = {"sample_data": {"columns": columns}} + if platform != "rna_seq": + tables["proj_info"] = dict(_PROJ_INFO_TABLE) + schema_variants[name] = {"tables": tables} + + for name, count in variant_db_counts.items(): + schema_variants[name]["assigned_databases"] = count + + return schema_variants, db_variant + + +def _eplant_scientific_names(): + """Scientific names as ePlant itself names each species. + + Sourced from EPLANT_SPECIES_FILE (scrape_view_databases.py), the per-project + species filename ePlant's own XML data paths use (e.g. .../Arabidopsis_thaliana.xml). + This is the same name that appears in the "ActiveSpecies=" query param once an + ePlant project's landing page finishes its client-side redirect (confirmed against + the eplant_potato example: ActiveSpecies=Solanum%20tuberosum -> Solanum_tuberosum), + just with underscores in place of the URL's spaces. We use this filename directly + rather than re-fetching each ActiveSpecies URL live, since that redirect only + happens in-browser via JS and isn't present in the static HTML/XML a scraper sees; + EPLANT_SPECIES_FILE is the same mapping scrape_species_view_info.py already relies + on to successfully pull real data from these projects, so it's proven correct. + + Two ePlant projects are two live versions of the same barley species -- see + INSTANCE_NOTES -- and both resolve to the same name, so no conflict there. + """ + return { + species.removeprefix("eplant_"): name.replace("_", " ") + for species, name in EPLANT_SPECIES_FILE.items() + } + + +# Curated fallback for species with no ePlant instance to source a name from +# (efp-only species). Kept as our own best-available nomenclature. +_FALLBACK_SCIENTIFIC_NAMES = { + "actinidia": None, + "apple": "Malus domestica", + "arabidopsis": "Arabidopsis thaliana", + "arachis": "Arachis hypogaea", + "barley": "Hordeum vulgare", + "brachypodium": "Brachypodium distachyon", + "brassica": "Brassica rapa", + "cacao": "Theobroma cacao", + "camelina": "Camelina sativa", + "cannabis": "Cannabis sativa", + "canola": "Brassica napus", + "cassava": "Manihot esculenta", + "cuscuta": "Cuscuta campestris", + "eucalyptus": "Eucalyptus grandis", + "euphorbia": "Euphorbia pulcherrima", + "grape": "Vitis vinifera", + "human": "Homo sapiens", + "kalanchoe": "Kalanchoe fedtschenkoi", + "little_millet": "Panicum sumatrense", + "lupin": "Lupinus angustifolius", + "maize": "Zea mays", + "mangosteen": "Garcinia mangostana", + "marchantia": "Marchantia polymorpha", + "medicago": "Medicago truncatula", + "mouse": "Mus musculus", + "oat": "Avena sativa", + "phelipanche": "Phelipanche aegyptiaca", + "physcomitrella": "Physcomitrium patens", + "poplar": "Populus trichocarpa", + "potato": "Solanum tuberosum", + "quinoa": "Chenopodium quinoa", + "rice": "Oryza sativa", + "selaginella": "Selaginella moellendorffii", + "sorghum": "Sorghum bicolor", + "soybean": "Glycine max", + "spruce": "Picea abies", + "strawberry": "Fragaria vesca", + "striga": "Striga hermonthica", + "sugarcane": "Saccharum officinarum", + "sunflower": "Helianthus annuus", + "thellungiella": "Thellungiella halophila", + "tomato": "Solanum lycopersicum", + "triphysaria": "Triphysaria versicolor", # not sure + "triticale": "Triticosecale", + "tung_tree": "Vernicia fordii", + "wheat": "Triticum aestivum", + "willow": "Salix purpurea", +} + + +def get_species_scientific_names(master_db_list): + """Build species -> scientific_name map, preferring ePlant's own naming. + + For species with a live ePlant instance, the name comes from ePlant (see + _eplant_scientific_names). Everything else -- efp-only species -- falls back + to the curated list. + """ + eplant_names = _eplant_scientific_names() + + result = {} + for species in master_db_list.keys(): + if species in eplant_names: + result[species] = { + "scientific_name": eplant_names[species], + "name_source": "eplant", + } + else: + result[species] = { + "scientific_name": _FALLBACK_SCIENTIFIC_NAMES.get(species), + "name_source": "curated", + } + return result + + +def build_databases(master_db_list, view_info, schema_variants, db_regex_project, db_variant): + """ + Build the databases section with full metadata, used_by, views, and SQL column structure. + """ + databases = {} + + db_frontend_usage = defaultdict(lambda: {"efp": set(), "eplant": set()}) + + for frontend_name, projects in view_info.items(): + frontend = frontend_name.lower() + + for project_key, views_list in projects.items(): + for view_info_obj in views_list: + db = view_info_obj.get("database") + view_name = view_info_obj.get("view_name") + instance = project_key + + if db and view_name: + db_frontend_usage[db][frontend].add((instance, view_name)) + + for species, dbs in master_db_list.items(): + for db_name, db_info in dbs.items(): + instance_families = set() + used_by = [] + + for frontend in ["efp", "eplant"]: + for instance, view_name in db_frontend_usage[db_name][frontend]: + instance_families.add(instance) + used_by.append({ + "frontend": frontend, + "instance": instance, + "view": view_name + }) + + source = db_info.get("source", "unknown") + platform = db_info.get("platform", "unknown") + gene_id_class = "gene_model" if platform == "rna_seq" else "probeset" + + variant = db_variant.get(db_name) + if variant is not None: + schema_verified = True + schema_verification_note = ( + f"Schema variant '{variant}' derived directly from this database's own sample dump." + ) + else: + variant = "rnaseq_simple" if platform == "rna_seq" else "legacy_microarray_projinfo" + schema_verified = False + schema_verification_note = "No sample dump available to verify against." + + db_entry = { + "species": species, + "instance_families": sorted(list(instance_families)) if instance_families else None, + "source": source, + "platform": platform, + "schema_variant": variant, + "schema_verified": schema_verified, + "schema_verification_note": schema_verification_note, + "value_semantics": db_info.get("value_semantics"), + "gene_id_class": gene_id_class, + "gene_id_namespace": db_info.get("gene_id_namespace"), + "regex_project": db_regex_project.get(db_name), + "used_by": used_by, + "views": {} + } + + databases[db_name] = db_entry + + for frontend_name, projects in view_info.items(): + frontend = frontend_name.lower() + + for project_key, views_list in projects.items(): + for view_info_obj in views_list: + db = view_info_obj.get("database") + view_name = view_info_obj.get("view_name") + groups = view_info_obj.get("groups", {}) + proj_ids = view_info_obj.get("proj_ids", []) + + if db not in databases: + continue + + view_key = f"{project_key}::{view_name}" + + databases[db]["views"][view_key] = { + "frontend": frontend, + "instance": project_key, + "display_name": view_name, + "proj_ids": proj_ids, + "sample_groups": groups + } + + return databases + + +def build_combined_json(): + """Build and output the combined master JSON.""" + print("Loading input files...") + master_db_list = load_json("data/efp_info/master_db_list.json") + view_info = load_json(VIEW_INFO_FILE) + + print("Patching efp_human sample groups from local eFP Human XML...") + if patch_human_view_groups(view_info): + with open(VIEW_INFO_FILE, "w") as f: + json.dump(view_info, f, indent=2) + print(f" Updated {VIEW_INFO_FILE}") + else: + print(" Nothing to patch") + + print("Loading Vincent's sample_data dumps (api/random_rows_json/)...") + sample_dumps = load_sample_dumps() + + print("Building schema variants from real sample dumps...") + schema_variants, db_variant = derive_schema_variants_from_dumps(master_db_list, sample_dumps) + print(f" {len(schema_variants)} distinct schema shapes across {len(db_variant)} databases") + + print("Loading Vincent's regex registry...") + validation_patterns, db_regex_project = get_validation_patterns() + probeset_samples = load_probeset_samples() + db_regex_project, demoted = verify_regex_projects(db_regex_project, validation_patterns, probeset_samples) + print(f" {len(validation_patterns)} eFP project patterns covering {len(db_regex_project)} databases") + if demoted: + print(f" Demoted {len(demoted)} unverified regex_project assignments to species-fallback (pass rate too low against real sample data):") + for db, (project, rate) in sorted(demoted.items()): + print(f" {db}: {project} ({rate:.0%} pass rate)") + + print("Building databases...") + databases = build_databases(master_db_list, view_info, schema_variants, db_regex_project, db_variant) + n_verified = sum(1 for db in databases.values() if db["schema_verified"]) + n_flagged = len(databases) - n_verified + print(f" {len(sample_dumps)} dumps checked -- {n_verified} verified, {n_flagged} flagged (no sample dump to derive a variant from)") + + print("Building species map...") + species = get_species_scientific_names(master_db_list) + + print("Building output structure...") + output = { + "species": species, + "schema_variants": schema_variants, + "instance_notes": INSTANCE_NOTES, + "validation_patterns": validation_patterns, + "databases": databases + } + + out_file = Path("data/efp_info/combined_master.json") + print(f"Writing to {out_file}...") + with open(out_file, "w") as f: + json.dump(output, f, indent=2, sort_keys=False) + + n_dbs = len(databases) + n_species = len(species) + + print("\n✓ Combined master JSON generated:") + print(f" Species: {n_species}") + print(f" Databases: {n_dbs}") + print(f" Output: {out_file}") + + +if __name__ == "__main__": + build_combined_json() diff --git a/cfg_dbs.txt b/cfg_dbs.txt new file mode 100644 index 00000000..69f7735b --- /dev/null +++ b/cfg_dbs.txt @@ -0,0 +1,48 @@ +annotations_lookup', +arabidopsis_ecotypes', +arachis', +brachypodium_dump', +camelina_dump', +cannabis', +canola_nssnp', +dna_damage', +embryo', +eplant2', +eplant_poplar', +eplant_rice', +eplant_soybean', +eplant_tomato', +fastpheno', +germination', +homologs_db', +interactions_vincent_v2', +kalanchoe', +klepikova', +light_series', +llama3', +maize_RMA_linear', +medicago_mas_dump', +meristem_db', +phelipanche', +physcomitrella_db', +poplar', +poplar_nssnp', +potato_stress', +rice_interactions', +rice_mas', +seedcoat', +selaginella', +shoot_apex', +silique', +single_cell', +soybean', +soybean', +soybean_nssnp', +soybean_severin', +strawberry', +striga', +thellungiella', +tomato_nssnp', +tomato_sequence', +triphysaria', +triticale', diff --git a/data/efp_info/combined_master.json b/data/efp_info/combined_master.json new file mode 100644 index 00000000..a28ad09b --- /dev/null +++ b/data/efp_info/combined_master.json @@ -0,0 +1,41517 @@ +{ + "species": { + "actinidia": { + "scientific_name": null, + "name_source": "curated" + }, + "apple": { + "scientific_name": "Malus domestica", + "name_source": "curated" + }, + "arabidopsis": { + "scientific_name": "Arabidopsis thaliana", + "name_source": "eplant" + }, + "arachis": { + "scientific_name": "Arachis hypogaea", + "name_source": "curated" + }, + "barley": { + "scientific_name": "Hordeum vulgare", + "name_source": "eplant" + }, + "brachypodium": { + "scientific_name": "Brachypodium distachyon", + "name_source": "curated" + }, + "brassica": { + "scientific_name": "Brassica rapa", + "name_source": "curated" + }, + "cacao": { + "scientific_name": "Theobroma cacao", + "name_source": "curated" + }, + "camelina": { + "scientific_name": "Camelina sativa", + "name_source": "eplant" + }, + "cannabis": { + "scientific_name": "Cannabis sativa", + "name_source": "eplant" + }, + "canola": { + "scientific_name": "Brassica napus", + "name_source": "curated" + }, + "cassava": { + "scientific_name": "Manihot esculenta", + "name_source": "curated" + }, + "cuscuta": { + "scientific_name": "Cuscuta campestris", + "name_source": "curated" + }, + "eucalyptus": { + "scientific_name": "Eucalyptus grandis", + "name_source": "eplant" + }, + "euphorbia": { + "scientific_name": "Euphorbia pulcherrima", + "name_source": "curated" + }, + "grape": { + "scientific_name": "Vitis vinifera", + "name_source": "curated" + }, + "human": { + "scientific_name": "Homo sapiens", + "name_source": "curated" + }, + "kalanchoe": { + "scientific_name": "Kalanchoe fedtschenkoi", + "name_source": "curated" + }, + "little_millet": { + "scientific_name": "Panicum sumatrense", + "name_source": "curated" + }, + "lupin": { + "scientific_name": "Lupinus angustifolius", + "name_source": "curated" + }, + "maize": { + "scientific_name": "Zea mays", + "name_source": "eplant" + }, + "mangosteen": { + "scientific_name": "Garcinia mangostana", + "name_source": "curated" + }, + "marchantia": { + "scientific_name": "Marchantia polymorpha", + "name_source": "curated" + }, + "medicago": { + "scientific_name": "Medicago truncatula", + "name_source": "eplant" + }, + "mouse": { + "scientific_name": "Mus musculus", + "name_source": "curated" + }, + "oat": { + "scientific_name": "Avena sativa", + "name_source": "curated" + }, + "phelipanche": { + "scientific_name": "Phelipanche aegyptiaca", + "name_source": "curated" + }, + "physcomitrella": { + "scientific_name": "Physcomitrium patens", + "name_source": "curated" + }, + "poplar": { + "scientific_name": "Populus trichocarpa", + "name_source": "eplant" + }, + "potato": { + "scientific_name": "Solanum tuberosum", + "name_source": "eplant" + }, + "quinoa": { + "scientific_name": "Chenopodium quinoa", + "name_source": "curated" + }, + "rice": { + "scientific_name": "Oryza sativa", + "name_source": "eplant" + }, + "selaginella": { + "scientific_name": "Selaginella moellendorffii", + "name_source": "curated" + }, + "sorghum": { + "scientific_name": "Sorghum bicolor", + "name_source": "curated" + }, + "soybean": { + "scientific_name": "Glycine max", + "name_source": "eplant" + }, + "spruce": { + "scientific_name": "Picea abies", + "name_source": "curated" + }, + "strawberry": { + "scientific_name": "Fragaria vesca", + "name_source": "curated" + }, + "striga": { + "scientific_name": "Striga hermonthica", + "name_source": "curated" + }, + "sugarcane": { + "scientific_name": "Saccharum R570", + "name_source": "eplant" + }, + "sunflower": { + "scientific_name": "Helianthus annuus", + "name_source": "eplant" + }, + "thellungiella": { + "scientific_name": "Thellungiella halophila", + "name_source": "curated" + }, + "tomato": { + "scientific_name": "Solanum lycopersicum", + "name_source": "eplant" + }, + "triphysaria": { + "scientific_name": "Triphysaria versicolor", + "name_source": "curated" + }, + "triticale": { + "scientific_name": "Triticosecale", + "name_source": "curated" + }, + "tung_tree": { + "scientific_name": "Vernicia fordii", + "name_source": "curated" + }, + "wheat": { + "scientific_name": "Triticum aestivum", + "name_source": "eplant" + }, + "willow": { + "scientific_name": "Salix purpurea", + "name_source": "eplant" + } + }, + "schema_variants": { + "rnaseq_simple": { + "tables": { + "sample_data": { + "columns": { + "data_bot_id": { + "type": "varchar", + "role": "sample" + }, + "data_probeset_id": { + "type": "varchar", + "role": "gene_id" + }, + "data_signal": { + "type": "float", + "role": "value" + }, + "proj_id": { + "type": "varchar", + "role": "project" + }, + "sample_id": { + "type": "int", + "role": "row_id" + } + } + } + }, + "assigned_databases": 128 + }, + "legacy_microarray_projinfo_plus_data_num": { + "tables": { + "sample_data": { + "columns": { + "data_bot_id": { + "type": "varchar", + "role": "sample" + }, + "data_call": { + "type": "varchar", + "role": "present_call" + }, + "data_num": { + "type": "int", + "role": "secondary_id" + }, + "data_p_val": { + "type": "double", + "role": "p_value" + }, + "data_probeset_id": { + "type": "varchar", + "role": "gene_id" + }, + "data_signal": { + "type": "float", + "role": "value" + }, + "proj_id": { + "type": "varchar", + "role": "project" + }, + "sample_file_name": { + "type": "varchar", + "role": "provenance" + }, + "sample_id": { + "type": "int", + "role": "row_id" + } + } + }, + "proj_info": { + "columns": { + "proj_id": { + "role": "project" + }, + "proj_title": {}, + "proj_pi": {}, + "proj_res_area": {}, + "proj_num_samps": {} + } + } + }, + "assigned_databases": 2 + }, + "legacy_microarray_projinfo": { + "tables": { + "sample_data": { + "columns": { + "data_bot_id": { + "type": "varchar", + "role": "sample" + }, + "data_call": { + "type": "varchar", + "role": "present_call" + }, + "data_p_val": { + "type": "double", + "role": "p_value" + }, + "data_probeset_id": { + "type": "varchar", + "role": "gene_id" + }, + "data_signal": { + "type": "float", + 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} + }, + "GA-3_at_30_Minutes": { + "controls": [ + "RIKEN-GODA1AA", + "RIKEN-GODA1BB" + ], + "treatments": { + "Control_at_30_Minutes": [ + "RIKEN-GODA1AA", + "RIKEN-GODA1BB" + ], + "GA-3_Treated_at_30_Minutes": [ + "RIKEN-GODA4A", + "RIKEN-GODA4B" + ] + } + }, + "GA-3_at_1_Hour": { + "controls": [ + "RIKEN-GODA9AA", + "RIKEN-GODA9BA" + ], + "treatments": { + "Control_at_1_Hour": [ + "RIKEN-GODA9AA", + "RIKEN-GODA9BA" + ], + "GA-3_Treated_at_1_Hour": [ + "RIKEN-GODA12A", + "RIKEN-GODA12B" + ] + } + }, + "GA-3_at_3_Hours": { + "controls": [ + "RIKEN-GODA17AA", + "RIKEN-GODA17BA" + ], + "treatments": { + "Control_at_3_Hours": [ + "RIKEN-GODA17AA", + "RIKEN-GODA17BA" + ], + "GA-3_Treated_at_3_Hours": [ + "RIKEN-GODA20A", + "RIKEN-GODA20B" + ] + } + }, + "GA-3_Mutant_at_30_Minutes": { + "controls": [ + "RIKEN-GODA25A", + "RIKEN-GODA25B" + ], + "treatments": { + "Control_at_30_Minutes": [ + "RIKEN-GODA25A", + "RIKEN-GODA25B" + ], + "GA-3_Treated_Mutant_at_30_Minutes": [ + "RIKEN-GODA26A", + 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"Control_at_3_Hours": [ + "RIKEN-GODA35A", + "RIKEN-GODA35B" + ], + "BL_Treated_Mutant_at_3_Hours": [ + "RIKEN-GODA36A", + "RIKEN-GODA36B" + ] + } + }, + "Brassinosteroids": { + "controls": [ + "RIKEN-GODA1A-6", + "RIKEN-GODA1B-6" + ], + "treatments": { + "Control": [ + "RIKEN-GODA1A-6", + "RIKEN-GODA1B-6" + ], + "campestanol_Treated": [ + "RIKEN-GODA2A-6", + "RIKEN-GODA2B-6" + ], + "6-deoxocathasterone_Treated": [ + "RIKEN-GODA3A-6", + "RIKEN-GODA3B-6" + ], + "cathasterone_Treated": [ + "RIKEN-GODA4A-6", + "RIKEN-GODA4B-6" + ], + "6-deoxoteasterone_Treated": [ + "RIKEN-GODA5A-6", + "RIKEN-GODA5B-6" + ], + "teasterone_Treated": [ + "RIKEN-GODA6A-6", + "RIKEN-GODA6B-6" + ], + "3-dehydro-6-deoxoteasterone_Treated": [ + "RIKEN-GODA7A-6", + "RIKEN-GODA7B-6" + ], + "3-dehydroteasterone_Treated": [ + "RIKEN-GODA8A-6", + "RIKEN-GODA8B-6" + ], + "-deoxotyphasterol_Treated": [ + "RIKEN-GODA9A-6", + "RIKEN-GODA9B-6" + ], + "typhasterol_Treated": [ + "RIKEN-GODA10A-6", + "RIKEN-GODA10B-6" + ], + 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"instance": "eplant_arabidopsis", + "display_name": "Chemical", + "proj_ids": [], + "sample_groups": { + "Gibberellic_Acid_Inhibitors_at_3_Hours": { + "controls": [ + "RIKEN-GODA1A2", + "RIKEN-GODA1B2" + ], + "treatments": { + "Propiconazole_Treated_at_3_Hours": [ + "RIKEN-GODA3A2", + "RIKEN-GODA3B2" + ], + "Uniconazole_Treated_at_3_Hours": [ + "RIKEN-GODA5A2", + "RIKEN-GODA5B2" + ], + "Paclobutrazol_Treated_at_3_Hours": [ + "RIKEN-GODA11A2", + "RIKEN-GODA11B2" + ], + "Prohexadione_Treated_at_3_Hours": [ + "RIKEN-GODA13A2", + "RIKEN-GODA13B2" + ] + } + }, + "Gibberellic_Acid_Inhibitors_at_12_Hours": { + "controls": [ + "RIKEN-GODA2A2", + "RIKEN-GODA2B2" + ], + "treatments": { + "Propiconazole_Treated_at_12_Hours": [ + "RIKEN-GODA4A2", + "RIKEN-GODA4B2" + ], + "Uniconazole_Treated_at_12_Hours": [ + "RIKEN-GODA6A2", + "RIKEN-GODA6B2" + ], + "Paclobutrazol_Treated_at_12_Hours": [ + "RIKEN-GODA12A2", + "RIKEN-GODA12B2" + ], + "Prohexadione_Treated_at_12_Hours": [ + "RIKEN-GODA14A2", + "RIKEN-GODA14B2" + ] + } + }, + "Auxin_Inhibitors": { + "controls": [ + "RIKEN-GODA1A2", + "RIKEN-GODA1B2" + ], + "treatments": { + "2,4,6-T_Treated": [ + "RIKEN-GODA23A3", + "RIKEN-GODA23B3" + ], + "PCIB_Treated": [ + "RIKEN-GODA24A3", + "RIKEN-GODA24B3" + ], + "TIBA_Treated": [ + "RIKEN-GODA25A3", + "RIKEN-GODA25B3" + ], + "NPA_Treated": [ + "RIKEN-GODA26A3", + "RIKEN-GODA26B3" + ] + } + }, + "Brassinosteroid_Inhibitors_at_3_Hours": { + "controls": [ + "RIKEN-GODA1A2", + "RIKEN-GODA1B2" + ], + "treatments": { + "10uM_Brz220_Treated_at_3_Hours": [ + "RIKEN-GODA7A4", + "RIKEN-GODA7B4" + ], + "3uM_Brz220_Treated_at_3_Hours": [ + "RIKEN-GODA30A4", + "RIKEN-GODA30B4" + ] + } + }, + "Brassinosteroid_Inhibitors_at_12_Hours": { + "controls": [ + "RIKEN-GODA2A2", + "RIKEN-GODA2B2" + ], + "treatments": { + "10uM_Brz91_Treated_at_12_Hours": [ + "RIKEN-GODA10A4", + "RIKEN-GODA10B4" + ] + } + }, + "Ethylene_Inhibitors": { + "controls": [ + "RIKEN-GODA1A2", + "RIKEN-GODA1B2" + ], + "treatments": { 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+ } + }, + "Ibuprofen_Salycylic_Acid_and_Daminozide": { + "controls": [ + "RIKEN-GODA1A2", + "RIKEN-GODA1B2" + ], + "treatments": { + "Ibuprofen_Treated": [ + "RIKEN-GODA17AH", + "RIKEN-GODA17BH" + ], + "Salicylic_Acid_Treated": [ + "RIKEN-GODA21AH", + "RIKEN-GODA21BH" + ], + "Daminozide_Treated": [ + "RIKEN-GODA18AH", + "RIKEN-GODA18BH" + ] + } + } + } + } + } + }, + "atgenexp_pathogen": { + "species": "arabidopsis", + "instance_families": [ + "efp_arabidopsis", + "eplant_arabidopsis" + ], + "source": "both", + "platform": "microarray", + "schema_variant": "legacy_microarray_projinfo_minus_sample_file_name", + "schema_verified": true, + "schema_verification_note": "Schema variant 'legacy_microarray_projinfo_minus_sample_file_name' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "probeset", + "gene_id_namespace": null, + "regex_project": "efp_arabidopsis", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_arabidopsis", + "view": "Biotic Stress" + }, + { + "frontend": "efp", + "instance": "efp_arabidopsis", + "view": "Biotic Stress II" + }, + { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "view": "Biotic Stress Phytophthora infestans" + }, + { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "view": "Biotic Stress Hyaloperonospora arabidopsidis" + }, + { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "view": "Biotic Stress Golovinomyces orontii" + }, + { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "view": "Biotic Stress Elicitors" + }, + { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "view": "Biotic Stress Myzus persicaere" + }, + { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "view": "Biotic Stress Botrytis cinerea" + }, + { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "view": "Biotic Stress Erysiphe orontii" + }, + { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "view": 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"CT182-1" + ], + "Treated_Botrytis_cinerea_at_18_Hours": [ + "BC181-1", + "BC181-2", + "BC182-1" + ] + } + }, + "Botrytis_cinerea_at_48_Hours": { + "controls": [ + "CT481-1", + "CT482-1", + "CT482-2" + ], + "treatments": { + "Control_Botrytis_cinerea_at_48_Hours": [ + "CT481-1", + "CT482-1", + "CT482-2" + ], + "Treated_Botrytis_cinerea_at_48_Hours": [ + "BC481-1", + "BC482-1", + "BC482-2" + ] + } + } + } + }, + "eplant_arabidopsis::Biotic Stress Myzus persicaere": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "display_name": "Biotic Stress Myzus persicaere", + "proj_ids": [], + "sample_groups": { + "GSM157299;GSM157300;GSM157301": { + "controls": [ + "GSM157299_JPritchard_A-1_CTR_Rep1_ATH1", + "GSM157300_JPritchard_A-2_CTR_Rep2_ATH1", + "GSM157301_Pritchard_A-3_CTR_Rep3_ATH1" + ], + "treatments": { + "Control": [ + "GSM157299_JPritchard_A-1_CTR_Rep1_ATH1", + "GSM157300_JPritchard_A-2_CTR_Rep2_ATH1", + "GSM157301_Pritchard_A-3_CTR_Rep3_ATH1" + ], + "Aphid_infested": [ + "GSM157303_JPritchard_A-5_API_Rep2_ATH1", + "GSM157304_JPritchard_A-6_API_Rep3_ATH1" + ] + } + } + } + }, + "eplant_arabidopsis::Biotic Stress Elicitors": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "display_name": "Biotic Stress Elicitors", + "proj_ids": [], + "sample_groups": { + "Water_Controlled_Botrytis_cinereaerial_Elicitors_at_1_Hour": { + "controls": [ + "AtGen_B-1_1-1-1_REP_1_ATH1", + "AtGen_B-15_2-1-1_REP2_ATH1", + "AtGen_B-29_3-1-1_REP3_ATH1" + ], + "treatments": { + "H2O_at_1_Hour": [ + "AtGen_B-1_1-1-1_REP_1_ATH1", + "AtGen_B-15_2-1-1_REP2_ATH1", + "AtGen_B-29_3-1-1_REP3_ATH1" + ], + "FLG22_at_1_Hour": [ + "AtGen_B-6_1-6-1_REP_1_ATH1", + "AtGen_B-20_2-6-1_REP2_ATH1", + "AtGen_B-34_3-6-1_REP3_ATH1" + ], + "HrpZ_at_1_Hour": [ + "AtGen_B-4_1-4-1_REP_1_ATH1", + "AtGen_B-18_2-4-1_REP2_ATH1", + "AtGen_B-32_3-4-1_REP3_ATH1" + ] + } + }, + "Ca+Mg_Controlled_Botrytis_cinereaerial_Elicitors_at_1_Hour": { + "controls": [ + "AtGen_B-2_1-2-1_REP_1_ATH1", + "AtGen_B-16_2-2-1_REP2_ATH1", + "AtGen_B-30_3-2-1_REP3_ATH1" + ], + "treatments": { + "Ca+Mg_at_1_Hour": [ + "AtGen_B-2_1-2-1_REP_1_ATH1", + "AtGen_B-16_2-2-1_REP2_ATH1", + "AtGen_B-30_3-2-1_REP3_ATH1" + ], + "LPS_at_1_Hour": [ + "AtGen_B-7_1-7-1_REP_1_ATH1", + "AtGen_B-21_2-7-1_REP2_ATH1", + "AtGen_B-35_3-7-1_REP3_ATH1" + ] + } + }, + "Oomycete_Elicitors_at_1_Hour": { + "controls": [ + "AtGen_B-3_1-3-1_REP_1_ATH1", + "AtGen_B-17_2-3-1_REP2_ATH1", + "AtGen_B-31_3-3-1_REP3_ATH1" + ], + "treatments": { + "GST_at_1_Hour": [ + "AtGen_B-3_1-3-1_REP_1_ATH1", + "AtGen_B-17_2-3-1_REP2_ATH1", + "AtGen_B-31_3-3-1_REP3_ATH1" + ], + "NPP_at_1_Hour": [ + "AtGen_B-5_1-5-1_REP_1_ATH1", + "AtGen_B-19_2-5-1_REP2_ATH1", + "AtGen_B-33_3-5-1_REP3_ATH1" + ] + } + }, + "Water_Controlled_Botrytis_cinereaerial_Elicitors_at_4_Hours": { + "controls": [ + "AtGen_B-8_1-1-4_REP_1_ATH1", + "AtGen_B-22_2-1-4_REP2_ATH1", + "AtGen_B-36_3-1-4_REP3_ATH1" + ], + "treatments": { + "H2O_at_4_Hours": [ + "AtGen_B-8_1-1-4_REP_1_ATH1", + "AtGen_B-22_2-1-4_REP2_ATH1", + "AtGen_B-36_3-1-4_REP3_ATH1" + ], + "FLG22_at_4_Hours": [ + "AtGen_B-13_1-6-4_REP1_ATH1", + "AtGen_B-27_2-6-4_REP2_ATH1", + "AtGen_B-41_3-6-4_REP3_ATH1" + ], + "HrpZ_at_4_Hours": [ + "AtGen_B-11_1-4-4_REP1_ATH1", + "AtGen_B-25_2-4-4_REP2_ATH1", + "AtGen_B-39_3-4-4_REP3_ATH1" + ] + } + }, + "Ca+Mg_Controlled_Botrytis_cinereaerial_Elicitors_at_4_Hours": { + "controls": [ + "AtGen_B-9_1-2-4_REP_1_ATH1", + "AtGen_B-23_2-2-4_REP2_ATH1", + "AtGen_B-37_3-2-4_REP3_ATH1" + ], + "treatments": { + "CaMg_at_4_Hours": [ + "AtGen_B-9_1-2-4_REP_1_ATH1", + "AtGen_B-23_2-2-4_REP2_ATH1", + "AtGen_B-37_3-2-4_REP3_ATH1" + ], + "LPS_at_4_Hours": [ + "AtGen_B-14_1-7-4_REP1_ATH1", + "AtGen_B-28_2-7-4_REP2_ATH1", + "AtGen_B-42_3-7-4_REP3_ATH1" + ] + } + }, + "Oomycete_Elicitors_at_4_Hours": { + "controls": [ + "AtGen_B-10_1-3-4_REP1_ATH1", + "AtGen_B-24_2-3-4_REP2_ATH1", + "AtGen_B-38_3-3-4_REP3_ATH1" + ], + "treatments": { + "GST_at_4_Hours": [ + "AtGen_B-10_1-3-4_REP1_ATH1", + "AtGen_B-24_2-3-4_REP2_ATH1", + "AtGen_B-38_3-3-4_REP3_ATH1" + ], + "NPP_at_4_Hours": [ + "AtGen_B-12_1-5-4_REP1_ATH1", + "AtGen_B-26_2-5-4_REP2_ATH1", + "AtGen_B-40_3-5-4_REP3_ATH1" + ] + } + } + } + }, + "eplant_arabidopsis::Biotic Stress Erysiphe orontii": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "display_name": "Biotic Stress Erysiphe orontii", + "proj_ids": [], + "sample_groups": { + "Erysiphe_orontii_at_6_Hours": { + "controls": [ + "JD AT+EO COL WT 06H UNINFECTED", + "JD AT+EO COL WT EXP2 06H UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 6H" + ], + "treatments": { + "Control_Erysiphe_orontii_at_6_Hours": [ + "JD AT+EO COL WT 06H UNINFECTED", + "JD AT+EO COL WT EXP2 06H UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 6H" + ], + "Treated_Erysiphe_orontii_at_6_Hours": [ + "JD AT+EO COL WT 06H INFECTED", + "JD AT+EO COL WT EXP2 06H INFECTED", + "JD AT+EO TIME EXP3 EO INF 6H" + ] + } + }, + "Erysiphe_orontii_at_12_Hours": { + "controls": [ + "JD AT+EO COL WT 12H UNINFECTED", + "JD AT+EO COL WT EXP2 12H UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 12H" + ], + "treatments": { + "Control_Erysiphe_orontii_at_12_Hours": [ + "JD AT+EO COL WT 12H UNINFECTED", + "JD AT+EO COL WT EXP2 12H UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 12H" + ], + "Treated_Erysiphe_orontii_at_12_Hours": [ + "JD AT+EO COL WT 12H INFECTED", + "JD AT+EO COL WT EXP2 12H INFECTED", + "JD AT+EO TIME EXP3 EO INF 12H" + ] + } + }, + "Erysiphe_orontii_at_18_Hours": { + "controls": [ + "JD AT+EO COL WT 18H UNINFECTED", + "JD AT+EO COL WT EXP2 18H UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 18H" + ], + "treatments": { + "Control_Erysiphe_orontii_at_18_Hours": [ + "JD AT+EO COL WT 18H UNINFECTED", + "JD AT+EO COL WT EXP2 18H UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 18H" + ], + "Treated_Erysiphe_orontii_at_18_Hours": [ + "JD AT+EO COL WT 18H INFECTED", + "JD AT+EO COL WT EXP2 18H INFECTED", + "JD AT+EO TIME EXP3 EO INF 18H" + ] + } + }, + "Erysiphe_orontii_at_24_Hours": { + "controls": [ + "JD AT+EO COL WT 24H UNINFECTED", + "JD AT+EO COL WT EXP2 24H UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 24H" + ], + "treatments": { + "Control_Erysiphe_orontii_at_24_Hours": [ + "JD AT+EO COL WT 24H UNINFECTED", + "JD AT+EO COL WT EXP2 24H UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 24H" + ], + "Treated_Erysiphe_orontii_at_24_Hours": [ + "JD AT+EO COL WT 24H INFECTED", + "JD AT+EO COL WT EXP2 24H INFECTED", + "JD AT+EO TIME EXP3 EO INF 24H" + ] + } + }, + "Erysiphe_orontii_at_48_Hours": { + "controls": [ + "JD AT+EO COL WT 02D UNINFECTED", + "JD AT+EO COL WT EXP2 02D UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 2D" + ], + "treatments": { + "Control_Erysiphe_orontii_at_48_Hours": [ + "JD AT+EO COL WT 02D UNINFECTED", + "JD AT+EO COL WT EXP2 02D UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 2D" + ], + "Treated_Erysiphe_orontii_at_48_Hours": [ + "JD AT+EO COL WT 02D INFECTED", + "JD AT+EO COL WT EXP2 02D INFECTED", + "JD AT+EO TIME EXP3 EO INF 2D" + ] + } + }, + "Erysiphe_orontii_at_72_Hours": { + "controls": [ + "JD AT+EO COL WT 03D UNINFECTED", + "JD AT+EO COL WT EXP2 03D UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 3D" + ], + "treatments": { + "Control_Erysiphe_orontii_at_72_Hours": [ + "JD AT+EO COL WT 03D UNINFECTED", + "JD AT+EO COL WT EXP2 03D UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 3D" + ], + "Treated_Erysiphe_orontii_at_72_Hours": [ + "JD AT+EO COL WT 03D INFECTED", + "JD AT+EO COL WT EXP2 03D INFECTED", + "JD AT+EO TIME EXP3 EO INF 3D" + ] + } + }, + "Erysiphe_orontii_at_96_Hours": { + "controls": [ + "JD AT+EO COL WT 04D UNINFECTED", + "JD AT+EO COL WT EXP2 04D UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 4D" + ], + "treatments": { + "Control_Erysiphe_orontii_at_96_Hours": [ + "JD AT+EO COL WT 04D UNINFECTED", + "JD AT+EO COL WT EXP2 04D UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 4D" + ], + "Treated_Erysiphe_orontii_at_96_Hours": [ + "JD AT+EO COL WT 04D INFECTED", + "JD AT+EO COL WT EXP2 04D INFECTED", + "JD AT+EO TIME EXP3 EO INF 4D" + ] + } + }, + "Erysiphe_orontii_at_120_Hours": { + "controls": [ + "JD AT+EO COL WT 05D UNINFECTED", + "JD AT+EO COL WT EXP2 05D UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 5D" + ], + "treatments": { + "Control_Erysiphe_orontii_at_120_Hours": [ + "JD AT+EO COL WT 05D UNINFECTED", + "JD AT+EO COL WT EXP2 05D UNINFECTED", + "JD AT+EO TIME EXP3 UNINF 5D" + ], + "Treated_Erysiphe_orontii_at_120_Hours": [ + "JD AT+EO COL WT 05D INFECTED", + "JD AT+EO COL WT EXP2 05D INFECTED", + "JD AT+EO TIME EXP3 EO INF 5D" + ] + } + } + } + }, + "eplant_arabidopsis::Biotic Stress Hyaloperonospora arabidopsidis": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "display_name": "Biotic Stress Hyaloperonospora arabidopsidis", + "proj_ids": [], + "sample_groups": { + "GSM554311_WT_Emwa1_0dpi_rep2": { + "controls": [ + "GSM554311_WT_Emwa1_0dpi_rep2" + ], + "treatments": { + "WT_Emwa1_0dpi_rep1+rep2": [ + "GSM554311_WT_Emwa1_0dpi_rep1", + "GSM554311_WT_Emwa1_0dpi_rep2" + ], + "WT_Emwa1_0.5dpi_rep1+rep2": [ + "GSM554312_WT_Emwa1_0.5dpi_rep2" + ], + "WT_Emwa1_2dpi_rep1+rep2": [ + "GSM554313_WT_Emwa1_2dpi_rep1", + "GSM554313_WT_Emwa1_2dpi_rep2" + ], + "WT_Emwa1_4dpi_rep1+rep2": [ + "GSM554314_WT_Emwa1_4dpi_rep1", + "GSM554314_WT_Emwa1_4dpi_rep2" + ], + "WT_Emwa1_6dpi_rep1+rep2": [ + "GSM554315_WT_Emwa1_6dpi_rep1", + "GSM554315_WT_Emwa1_6dpi_rep2" + ] + } + }, + "GSM554316_rpp4_Emwa1_0dpi_rep1;GSM554316_rpp4_Emwa1_0dpi_rep2": { + "controls": [ + "GSM554316_rpp4_Emwa1_0dpi_rep1", + "GSM554316_rpp4_Emwa1_0dpi_rep2" + ], + "treatments": { + "rpp4_Emwa1_0dpi_rep1+rep2": [ + "GSM554316_rpp4_Emwa1_0dpi_rep1", + "GSM554316_rpp4_Emwa1_0dpi_rep2" + ], + "rpp4_Emwa1_0.5dpi_rep1+rep2": [ + "GSM554317_rpp4_Emwa1_0.5dpi_rep1", + "GSM554317_rpp4_Emwa1_0.5dpi_rep2" + ], + "rpp4_Emwa1_2dpi_rep1+rep2": [ + "GSM554318_rpp4_Emwa1_2dpi_rep1", + "GSM554318_rpp4_Emwa1_2dpi_rep2" + ], + "rpp4_Emwa1_4dpi_rep1+rep2": [ + "GSM554319_rpp4_Emwa1_4dpi_rep1", + "GSM554319_rpp4_Emwa1_4dpi_rep2" + ], + "rpp4_Emwa1_6dpi_rep1+rep2": [ + "GSM554320_rpp4_Emwa1_6dpi_rep1", + "GSM554320_rpp4_Emwa1_6dpi_rep2" + ] + } + } + } + }, + "eplant_arabidopsis::Biotic Stress Phytophthora infestans": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "display_name": "Biotic Stress Phytophthora infestans", + "proj_ids": [], + "sample_groups": { + "Phytophthora_infestans_at_6_Hours": { + "controls": [ + "AtGen_C-1_1-C-6_REP1_ATH1", + "AtGen_C-2_2-C-6_REP2_ATH1", + "AtGen_C-3_4-C-6_REP3_ATH1" + ], + "treatments": { + "Control_Phytophthora_infestans_at_6_Hours": [ + "AtGen_C-1_1-C-6_REP1_ATH1", + "AtGen_C-2_2-C-6_REP2_ATH1", + "AtGen_C-3_4-C-6_REP3_ATH1" + ], + "Treated_Phytophthora_infestans_at_6_Hours": [ + "AtGen_C-10_1-Pi-6_REP1_ATH1", + "AtGen_C-11_2-Pi-6_REP2_ATH1", + "AtGen_C-12_3-Pi-6_REP3_ATH1" + ] + } + }, + "Phytophthora_infestans_at_12_Hours": { + "controls": [ + "AtGen_C-4_1-C-12_REP1_ATH1", + "AtGen_C-5_2-C-12_REP2_ATH1", + "AtGen_C-6_3-C-12_REP3_ATH1" + ], + "treatments": { + "Control_Phytophthora_infestans_at_12_Hours": [ + "AtGen_C-4_1-C-12_REP1_ATH1", + "AtGen_C-5_2-C-12_REP2_ATH1", + "AtGen_C-6_3-C-12_REP3_ATH1" + ], + "Treated_Phytophthora_infestans_at_12_Hours": [ + "AtGen_C-13_1-Pi-12_REP1_ATH1", + "AtGen_C-14_2-Pi-12_REP2_ATH1", + "AtGen_C-15_3-Pi-12_REP3_ATH1" + ] + } + }, + "Phytophthora_infestans_at_24_Hours": { + "controls": [ + "AtGen_C-7_1-C-24_REP1_ATH1", + "AtGen_C-8_2-C-24_REP2_ATH1", + "AtGen_C-9_3-C-24_REP3_ATH1" + ], + "treatments": { + "Control_Phytophthora_infestans_at_24_Hours": [ + "AtGen_C-7_1-C-24_REP1_ATH1", + "AtGen_C-8_2-C-24_REP2_ATH1", + "AtGen_C-9_3-C-24_REP3_ATH1" + ], + "Treated_Phytophthora_infestans_at_24_Hours": [ + "AtGen_C-16_1-Pi-24_REP1_ATH1", + "AtGen_C-17_2-Pi-24_REP2_ATH1", + "AtGen_C-18_3-Pi-24_REP3_ATH1" + ] + } + } + } + }, + "eplant_arabidopsis::Biotic Stress Pseudomonas syringae": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + 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{ + "Torpedo_-_Basal": [ + "Lindsey_1-19_torpedo-basal_Rep4_ATH1", + "Lindsey_1-20_torpedo-basal_Rep5_ATH1", + "Lindsey_1-21_torpedo-basal_Rep6_ATH1" + ], + "Torpedo_-_Apical": [ + "Lindsey_1-22_torpedo-apical_Rep4_ATH1", + "Lindsey_1-23_torpedo-apical_Rep5_ATH1", + "Lindsey_1-24_torpedo-apical_Rep6_ATH1" + ], + "Torpedo_-_Cotyledon": [ + "Lindsey_1-13_torpedo-cotyledon_Rep1_ATH1", + "Lindsey_1-15_torpedo-cotyledon_Rep2_ATH1", + "Lindsey_1-17_torpedo-cotyledon_Rep3_ATH1" + ], + "Torpedo_-_Root": [ + "Lindsey_1-14_torpedo-root_Rep1_ATH1", + "Lindsey_1-16_torpedo-root_Rep2_ATH1", + "Lindsey_1-18_torpedo-root_Rep3_ATH1" + ], + "Torpedo_-_Meristem": [ + "Lindsey_1-25_torpedo-meristem_Rep1_ATH1", + "Lindsey_1-26_torpedo-meristem_Rep2_ATH1", + "Lindsey_1-27_torpedo-meristem_Rep3_ATH1" + ], + "Heart_-_Cotyledon": [ + "Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1", + "Lindsey_1-8_heart-stage-cotyledon_Rep2_ATH1", + "Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1" + ], + "Heart_-_Root": [ + "Lindsey_1-10_heart-stage-root_Rep1_ATH1", + "Lindsey_1-11_heart-stage-root_Rep2_ATH1", + "Lindsey_1-12_heart-stage-root_Rep3_ATH1" + ], + "Globular_-_Apical": [ + "Lindsey_1-1_globular-apical_Rep1_ATH1", + "Lindsey_1-2_globular-apical_Rep2_ATH1", + "Lindsey_1-3_globular-apical_Rep3_ATH1" + ], + "Globular_-_Basal": [ + "Lindsey_1-4_globular-basal_Rep1_ATH1", + "Lindsey_1-5_globular-basal_Rep2_ATH1", + "Lindsey_1-6_globular-basal_Rep3_ATH1" + ] + } + } + } + }, + "eplant_arabidopsis::Tissue Specific Guard And Mesophyll Cells": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "display_name": "Tissue Specific Guard And Mesophyll Cells", + "proj_ids": [], + "sample_groups": { + "CTRL_7": { + "controls": [], + "treatments": { + "Mesophyll_cells,_with_100_uM_ABA": [ + "JS88", + "JS36" + ], + "Mesophyll_cells,_no_ABA": [ + "JS87", + "JS35" + ], + "Guard_cells,_no_ABA": [ + "JS85", + "JS33" + ], + "Guard_cells,_with_100_uM_ABA": [ + "JS86", + "JS34" + ], + "Guard_cells,_no_ABA,_no_cordycepin_nor_actinomycin": [ + "JS85" + ], + "Mesophyll_cells,_no_ABA,_no_cordycepin_nor_actinomycin": [ + "JS87" + ], + "Mesophyll_cells,_no_ABA,_cordycepin_and_actinomycin_added_during_protoplasting": [ + "JS35" + ], + "Mesophyll_cells,_with_100uM_ABA,_no_cordycepin_nor_actinomycin": [ + "JS88" + ], + "Mesophyll_cells_with_100uM_ABA,_cordycepin_and_actinomycin_added_during_protoplasting": [ + "JS36" + ], + "Guard_cells,_no_ABA,_cordycepin_and_actinomycin_added_during_protoplasting": [ + "JS33" + ], + "Guard_cells,_with_100uM_ABA,_cordycepin_and_actinomycin_added_during_protoplasting": [ + "JS34" + ], + "Guard_cells,_with_100uM_ABA,_no_cordycepin_nor_actinomycin": [ + "JS86" + ] + } + } + } + }, + "eplant_arabidopsis::Tissue Specific Pollen Germination": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "display_name": "Tissue Specific Pollen Germination", + "proj_ids": [], + "sample_groups": { + "CTRL_7": { + "controls": [], + "treatments": { + "Pollen_tubes_harvested_after_growth_through_pistil_explants": [ + "GSM433646", + "GSM433647", + "GSM433648" + ], + "Pollen,_germinated_in_vitro_for_4_hours": [ + "GSM433642", + "GSM433643", + "GSM433644", + "GSM433645" + ], + "Pollen,_germinated_in_vitro_for_30_minutes": [ + "GSM433638", + "GSM433639", + "GSM433640", + "GSM433641" + ], + "Dry_pollen": [ + "GSM433634", + "GSM433635", + "GSM433636", + "GSM433637" + ] + } + } + } + }, + "eplant_arabidopsis::Tissue Specific Stem Epidermis": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "display_name": "Tissue Specific Stem Epidermis", + "proj_ids": [], + "sample_groups": { + "CTRL_7": { + "controls": [ + "ATGE_CTRL_7" + ], + "treatments": { + "Stem_epidermis,_top_of_stem": [ + "841-JO", + "842-JO" + ], + "Stem_epidermis,_bottom_of_stem": [ + "872-JO", + "873-JO" + ], + "Whole_stem,_top_of_stem": [ + "839-JO", + "840-JO" + ], + "Whole_stem,_bottom_of_stem": [ + "874-JO", + "875-JO" + ] + } + } + } + }, + "eplant_arabidopsis::Tissue Specific Trichomes": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "display_name": "Tissue Specific Trichomes", + "proj_ids": [], + "sample_groups": { + "CTRL_7": { + "controls": [ + "ATGE_CTRL_7" + ], + "treatments": { + "WT_Col-0_leaves_after_trichome_removal": [ + "ColprocessleafArd13", + "ColprocessleafMN3", + "ColprocessleafMN4", + "ColprocessleafMN5" + ], + "WT_Col-0_trichomes": [ + "ColtrichomeArd1", + "ColtrichomeArd2", + "ColtrichomeMN12", + "ColtrichomeMN13", + "ColtrichomeMN2" + ], + "gl3-sst_mutant_trichomes": [ + "DM9_sst1", + "m1DM8sstard", + "m1ssttr5_ATH1" + ], + "gl3-sst_sim_double_mutant_trichomes": [ + "gl3_sstsimtrichomeMN1", + "gl3_sstsimtrichomeMN2" + ], + "gl3-sst_nok-1_double_mutant_trichomes": [ + "EG_mosst1", + "EG_mosst2", + "EG_mosst3" + ] + } + } + } + }, + "eplant_arabidopsis::Tissue Specific Stigma And Ovaries": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "display_name": "Tissue Specific Stigma And Ovaries", + "proj_ids": [], + "sample_groups": { + "CTRL_7": { + "controls": [ + "ATGE_CTRL_7" + ], + "treatments": { + "Stigma_tissue": [ + "GSM67084", + "GSM67086", + "GSM67087" + ], + "Ovary_tissue": [ + "GSM67078", + "GSM67079", + "GSM67080", + "GSM67081" + ] + } + } + } + }, + "eplant_arabidopsis::Tissue Specific Shoot Apical Meristem": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "display_name": "Tissue Specific Shoot Apical Meristem", + "proj_ids": [], + "sample_groups": { + "CTRL_7": { + "controls": [ + "ATGE_CTRL_7" + ], + "treatments": { + "Central_Zone": [ + "GSM342138", + "GSM342139", + "GSM342140" + ], + "Rib_Meristem": [ + "GSM342148", + "GSM342149" + ], + "Peripheral_Zone": [ + "GSM342141", + "GSM342142", + "GSM342143" + ] + } + } + } + }, + "eplant_arabidopsis::Tissue Specific Xylem And Cork": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "display_name": "Tissue Specific Xylem And Cork", + "proj_ids": [], + "sample_groups": { + "CTRL_7": { + "controls": [ + "ATGE_CTRL_7" + ], + "treatments": { + "Xylem_MYB61_knockout": [ + "Dubos_A-3-6kx_Rep1", + "Dubos_A-3-6kx_Rep2", + "Dubos_A-3-6kx_Rep3" + ], + "Cork_MYB61_knockout": [ + "Dubos_A-4-6kc_Rep1", + "Dubos_A-4-6kc_Rep2", + "Dubos_A-4-6kc_Rep3" + ], + "Xylem_MYB50_knockout": [ + "Dubos_A-5-5kx_Rep1", + "Dubos_A-5-5kx_Rep2", + "Dubos_A-5-5kx_Rep3" + ], + "Cork_MYB50_knockout": [ + "Dubos_A-6-5kc_Rep1", + "Dubos_A-6-5kc_Rep2", + "Dubos_A-6-5kc_Rep3" + ], + "Xylem_Col-0": [ + "Dubos_A-1-wtx_Rep1", + "Dubos_A-1-wtx_Rep2", + "Dubos_A-1-wtx_Rep3" + ], + "Cork_Col-0": [ + "Dubos_A-2-wtc_Rep1", + "Dubos_A-2-wtc_Rep2", + "Dubos_A-2-wtc_Rep3" + ], + "Hypocotyl_Col-0": [ + "Dubos_A-10-wth_Rep1", + "Dubos_A-10-wth_Rep2", + "Dubos_A-10-wth_Rep3" + ], + "Hypocotyl_Ler": [ + "Dubos_A-7-wlh_Rep1", + "Dubos_A-7-wlh_Rep2", + "Dubos_A-7-wlh_Rep3" + ], + "Hypocotyl_abi1": [ + "Dubos_A-8-aih_Rep1", + "Dubos_A-8-aih_Rep2", + "Dubos_A-8-aih_Rep3" + ], + "Hypocotyl_aba1": [ + "Dubos_A-9-aah_Rep1", + "Dubos_A-9-aah_Rep2", + "Dubos_A-9-aah_Rep3" + ], + "Hypocotyl_max4": [ + "Dubos_A-11-mxh_Rep1", + "Dubos_A-11-mxh_Rep2", + "Dubos_A-11-mxh_Rep3" + ], + "Hypocotyl_axr1": [ + "Dubos_A-12-arh_Rep1", + "Dubos_A-12-arh_Rep2", + "Dubos_A-12-arh_Rep3" + ] + } + } + } + }, + "eplant_arabidopsis::AtGenExpress": { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "display_name": "AtGenExpress", + "proj_ids": [], + "sample_groups": { + "CTRL_7": { + "controls": [ + "ATGE_CTRL_7" + ], + "treatments": { + "Dry_seed": [ + "RIKEN-NAKABAYASHI1A", + "RIKEN-NAKABAYASHI1B" + ], + "Imbibed_seed,_24_h": [ + "RIKEN-NAKABAYASHI2A", + "RIKEN-NAKABAYASHI2B" + ], + "1st_Node": [ + "ATGE_28_A2", + "ATGE_28_B2", + "ATGE_28_C2" + ], + "Flower_Stage_12,_Stamens": [ + "ATGE_36_A", + "ATGE_36_B", + "ATGE_36_C" + ], + "Cauline_Leaf": [ + "ATGE_26_A", + "ATGE_26_B", + "ATGE_26_C" + ], + "Cotyledon": [ + "ATGE_1_A", + "ATGE_1_B", + "ATGE_1_C" + ], + "Root": [ + "ATGE_9_A", + "ATGE_9_B", + "ATGE_9_C" + ], + "Entire_Rosette_After_Transition_to_Flowering": [ + "ATGE_23_A", + "ATGE_23_B", + "ATGE_23_C" + ], + "Flower_Stage_9": [ + "ATGE_31_A2", + "ATGE_31_B2", + "ATGE_31_C2" + ], + "Flower_Stage_10/11": [ + "ATGE_32_A2", + "ATGE_32_B2", + "ATGE_32_C2" + ], + "Flower_Stage_12": [ + "ATGE_33_A", + "ATGE_33_B", + "ATGE_33_C" + ], + "Flower_Stage_15": [ + "ATGE_39_A", + "ATGE_39_B", + "ATGE_39_C" + ], + "Flower_Stage_12,_Carpels": [ + "ATGE_37_A", + "ATGE_37_B", + "ATGE_37_C" + ], + "Flower_Stage_12,_Petals": [ + "ATGE_35_A", + "ATGE_35_B", + "ATGE_35_C" + ], + "Flower_Stage_12,_Sepals": [ + "ATGE_34_A", + "ATGE_34_B", + "ATGE_34_C" + ], + "Flower_Stage_15,_Carpels": [ + "ATGE_45_A", + "ATGE_45_B", + "ATGE_45_C" + ], + "Flower_Stage_15,_Petals": [ + "ATGE_42_B", + "ATGE_42_C", + "ATGE_42_D" + ], + "Flower_Stage_15,_Sepals": [ + "ATGE_41_A", + "ATGE_41_B", + "ATGE_41_C" + ], + "Flower_Stage_15,_Stamen": [ + "ATGE_43_A", + "ATGE_43_B", + "ATGE_43_C" + ], + "Flowers_Stage_15,_Pedicels": [ + "ATGE_40_A", + "ATGE_40_B", + "ATGE_40_C" + ], + "Leaf_1_+_2": [ + "ATGE_5_A", + "ATGE_5_B", + "ATGE_5_C" + ], + "Leaf_7,_Petiole": [ + "ATGE_19_A", + "ATGE_19_B", + "ATGE_19_C" + ], + "Leaf_7,_Distal_Half": [ + "ATGE_21_A", + "ATGE_21_B", + "ATGE_21_C" + ], + "Leaf_7,_Proximal_Half": [ + "ATGE_20_A", + "ATGE_20_B", + "ATGE_20_C" + ], + "Hypocotyl": [ + "ATGE_2_A", + "ATGE_2_B", + "ATGE_2_C" + ], + "Young_Root": [ + "ATGE_3_A", + "ATGE_3_B", + "ATGE_3_C" + ], + "Rosette_Leaf_2": [ + "ATGE_12_A", + "ATGE_12_B", + "ATGE_12_C" + ], + "Rosette_Leaf_4": [ + "ATGE_13_A", + "ATGE_13_B", + "ATGE_13_C" + ], + "Rosette_Leaf_6": [ + "ATGE_14_A", + "ATGE_14_B", + "ATGE_14_C" + ], + "Rosette_Leaf_8": [ + "ATGE_15_A", + "ATGE_15_B", + "ATGE_15_C" + ], + "Rosette_Leaf_10": [ + "ATGE_16_A", + "ATGE_16_B", + "ATGE_16_C" + ], + "Rosette_Leaf_12": [ + "ATGE_17_A", + "ATGE_17_B", + "ATGE_17_C" + ], + "Senescing_Leaf": [ + "ATGE_25_A", + "ATGE_25_B", + "ATGE_25_C" + ], + "Shoot_Apex,_Inflorescence": [ + "ATGE_29_A2", + "ATGE_29_B2", + "ATGE_29_C2" + ], + "Shoot_Apex,_Transition": [ + "ATGE_8_A", + "ATGE_8_B", + "ATGE_8_C" + ], + "Shoot_Apex,_Vegetative": [ + "ATGE_6_A", + "ATGE_6_B", + "ATGE_6_C" + ], + "Stem,_2nd_Internode": [ + "ATGE_27_A", + "ATGE_27_B", + "ATGE_27_C" + ], + "Mature_Pollen": [ + "ATGE_73_A", + "ATGE_73_B", + "ATGE_73_C" + ], + "Seeds_Stage_3_w/_Siliques": [ + "ATGE_76_A", + "ATGE_76_B", + "ATGE_76_C" + ], + "Seeds_Stage_4_w/_Siliques": [ + "ATGE_77_D", + "ATGE_77_E", + "ATGE_77_F" + ], + "Seeds_Stage_5_w/_Siliques": [ + "ATGE_78_D", + "ATGE_78_E", + "ATGE_78_F" + ], + "Seeds_Stage_6_w/o_Siliques": [ + "ATGE_79_A", + "ATGE_79_B", + "ATGE_79_C" + ], + "Seeds_Stage_7_w/o_Siliques": [ + "ATGE_81_A", + "ATGE_81_B", + "ATGE_81_C" + ], + "Seeds_Stage_8_w/o_Siliques": [ + "ATGE_82_A", + "ATGE_82_B", + "ATGE_82_C" + ], + "Seeds_Stage_9_w/o_Siliques": [ + "ATGE_83_A", + "ATGE_83_B", + "ATGE_83_C" + ], + "Seeds_Stage_10_w/o_Siliques": [ + "ATGE_84_A", + "ATGE_84_B", + "ATGE_84_D" + ], + "Vegetative_Rosette": [ + "ATGE_89_A", + "ATGE_89_B", + "ATGE_89_C" + ] + } + } + } + } + } + }, + "atgenexp_stress": { + "species": "arabidopsis", + "instance_families": [ + "efp_arabidopsis", + "eplant_arabidopsis" + ], + "source": "both", + "platform": "microarray", + "schema_variant": "legacy_microarray_projinfo_minus_sample_file_name", + "schema_verified": true, + "schema_verification_note": "Schema variant 'legacy_microarray_projinfo_minus_sample_file_name' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "probeset", + "gene_id_namespace": null, + "regex_project": "efp_arabidopsis", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_arabidopsis", + "view": "Abiotic Stress II" + }, + { + "frontend": "efp", + "instance": "efp_arabidopsis", + "view": "Abiotic Stress" + }, + { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "view": "Abiotic Stress II" + }, + { + "frontend": "eplant", + "instance": "eplant_arabidopsis", + "view": "Abiotic Stress" + } + ], + "views": { + "efp_arabidopsis::Abiotic Stress II": { + "frontend": "efp", + "instance": "efp_arabidopsis", + "display_name": "Abiotic Stress II", + "proj_ids": [], + "sample_groups": { + "GSM491684;GSM491685;GSM491686": { + "controls": [ + "GSM491684", + "GSM491685", + "GSM491686" + ], + "treatments": { + "Water_limited_(dry),_Pre-dawn": [ + "GSM491687", + "GSM491688", + "GSM491689" + ], + "Well_watered,_pre-dawn_(control)": [ + "GSM491684", + "GSM491685", + "GSM491686" + ] + } + }, + "GSM491672;GSM491673;GSM491674": { + "controls": [ + "GSM491672", + "GSM491673", + "GSM491674" + ], + "treatments": { + "Well_watered,_Late_day_(control)": [ + "GSM491672", + "GSM491673", + "GSM491674" + ], + "Water_limited_(dry),_Late_day": [ + "GSM491675", + "GSM491676", + "GSM491677" + ] + } + }, + "GSM237280;GSM237281": { + "controls": [ + "GSM237280", + "GSM237281" + ], + "treatments": { + 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"eplant_barley_legacy", + "view": "Spike Meristem Shade Response" + } + ], + "views": { + "eplant_barley_legacy::Spike Meristem": { + "frontend": "eplant", + "instance": "eplant_barley_legacy", + "display_name": "Spike Meristem", + "proj_ids": [], + "sample_groups": { + "spike_meristem": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "l-RAM": [ + "RAM_1_tpm", + "RAM_2_tpm", + "RAM_3_tpm" + ], + "l-tm-IM": [ + "TM_IM_1_tpm", + "TM_IM_2_tpm", + "TM_IM_3_tpm", + "TM_IM_4_tpm" + ], + "l-tm-CSM": [ + "TM_CS_1_tpm", + "TM_CS_2_tpm", + "TM_CS_3_tpm", + "TM_CS_4_tpm" + ], + "l-tm-LSM": [ + "TM_LS_1_tpm", + "TM_LS_2_tpm", + "TM_LS_3_tpm", + "TM_LS_4_tpm" + ], + "l-gp-IM": [ + "GP_IM_1_tpm", + "GP_IM_2_tpm", + "GP_IM_3_tpm", + "GP_IM_4_tpm" + ], + "l-gp-CSM": [ + "GP_CS_1_tpm", + "GP_CS_2_tpm", + "GP_CS_3_tpm", + "GP_CS_4_tpm" + ], + "l-gp-LSM": [ + "GP_LS_1_tpm", + "GP_LS_2_tpm", + "GP_LS_3_tpm", + "GP_LS_4_tpm" + ], + "l-lp-LSM": [ + "LP_LS_1_tpm", + "LP_LS_2_tpm", + "LP_LS_3_tpm", + 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"SP_REF1_2_tpm", + "SP_REF1_3_tpm", + "SP_REF1_4_tpm" + ], + "r-lp": [ + "LP_REF1_1_tpm", + "LP_REF1_2_tpm", + "LP_REF1_3_tpm", + "LP_REF1_4_tpm" + ], + "r-gp": [ + "GP_REF1_1_tpm", + "GP_REF1_2_tpm", + "GP_REF1_3_tpm", + "GP_REF1_4_tpm" + ], + "r-tm": [ + "TM_REF1_1_tpm", + "TM_REF1_2_tpm", + "TM_REF1_3_tpm", + "TM_REF1_4_tpm" + ], + "r-dr": [ + "DR_REF1_1_tpm", + "DR_REF1_2_tpm", + "DR_REF1_3_tpm", + "DR_REF1_4_tpm" + ], + "w-sp": [ + "SP_REF2_1_tpm", + "SP_REF2_2_tpm", + "SP_REF2_3_tpm", + "SP_REF2_4_tpm" + ], + "w-lp": [ + "LP_REF2_1_tpm", + "LP_REF2_2_tpm", + "LP_REF2_3_tpm", + "LP_REF2_4_tpm" + ], + "w-gp": [ + "GP_REF2_1_tpm", + "GP_REF2_2_tpm", + "GP_REF2_3_tpm", + "GP_REF2_4_tpm" + ], + "w-tm": [ + "TM_REF2_1_tpm", + "TM_REF2_2_tpm", + "TM_REF2_3_tpm", + "TM_REF2_4_tpm" + ], + "w-dr": [ + "DR_REF2_1_tpm", + "DR_REF2_2_tpm", + "DR_REF2_3_tpm", + "DR_REF2_4_tpm" + ], + "w-ap": [ + "AP_REF2_1_tpm", + "AP_REF2_2_tpm", + "AP_REF2_3_tpm", + "AP_REF2_4_tpm" + ], + "l-dr-SRM": [ + "DR_SR_1_tpm", + "DR_SR_2_tpm", + "DR_SR_3_tpm", + "DR_SR_4_tpm" + ], + "l-dr-LRM": [ + "DR_LR_1_tpm", + "DR_LR_2_tpm", + "DR_LR_3_tpm", + "DR_LR_4_tpm" + ], + "l-dr-IM": [ + "DR_IM_1_tpm", + "DR_IM_2_tpm", + "DR_IM_3_tpm", + "DR_IM_4_tpm" + ], + "l-va-SAM": [ + "VA_1_tpm", + "VA_2_tpm", + "VA_3_tpm" + ], + "l-LBB": [ + "LB_1_tpm", + "LB_2_tpm", + "LB_3_tpm" + ] + } + } + } + }, + "eplant_barley_legacy::Spike Meristem Shade Response": { + "frontend": "eplant", + "instance": "eplant_barley_legacy", + "display_name": "Spike Meristem Shade Response", + "proj_ids": [], + "sample_groups": { + "dr-SRM": { + "controls": [ + "DR_SR_1_tpm", + "DR_SR_2_tpm", + "DR_SR_3_tpm", + "DR_SR_4_tpm" + ], + "treatments": { + "d-dr-SRM": [ + "DR_SR_stress_1_tpm", + "DR_SR_stress_2_tpm", + "DR_SR_stress_3_tpm", + "DR_SR_stress_4_tpm" + ], + "l-dr-SRM": [ + "DR_SR_1_tpm", + "DR_SR_2_tpm", + "DR_SR_3_tpm", + "DR_SR_4_tpm" + ] + } + }, + "dr-IM": { + "controls": [ + "DR_IM_1_tpm", + "DR_IM_2_tpm", + "DR_IM_3_tpm", + "DR_IM_4_tpm" + ], + "treatments": { + "l-dr-IM": [ + "DR_IM_1_tpm", + "DR_IM_2_tpm", + "DR_IM_3_tpm", + "DR_IM_4_tpm" + ], + "d-dr-IM": [ + "DR_IM_stress_1_tpm", + "DR_IM_stress_2_tpm", + "DR_IM_stress_3_tpm", + "DR_IM_stress_4_tpm" + ] + } + }, + "dr-LRM": { + "controls": [ + "DR_LR_1_tpm", + "DR_LR_2_tpm", + "DR_LR_3_tpm", + "DR_LR_4_tpm" + ], + "treatments": { + "l-dr-LRM": [ + "DR_LR_1_tpm", + "DR_LR_2_tpm", + "DR_LR_3_tpm", + "DR_LR_4_tpm" + ], + "d-dr-LRM": [ + "DR_LR_stress_1_tpm", + "DR_LR_stress_2_tpm", + "DR_LR_stress_3_tpm", + "DR_LR_stress_4_tpm" + ] + } + }, + "tm-IM": { + "controls": [ + "TM_IM_1_tpm", + "TM_IM_2_tpm", + "TM_IM_3_tpm", + "TM_IM_4_tpm" + ], + "treatments": { + "l-tm-IM": [ + "TM_IM_1_tpm", + "TM_IM_2_tpm", + "TM_IM_3_tpm", + "TM_IM_4_tpm" + ], + "d-tm-IM": [ + "TM_IM_stress_1_tpm", + "TM_IM_stress_2_tpm", + "TM_IM_stress_3_tpm", + "TM_IM_stress_4_tpm" + ] + } + }, + "tm-CSM": { + "controls": [ + "TM_CS_1_tpm", + "TM_CS_2_tpm", + "TM_CS_3_tpm", + "TM_CS_4_tpm" + ], + "treatments": { + "l-tm-CSM": [ + "TM_CS_1_tpm", + "TM_CS_2_tpm", + "TM_CS_3_tpm", + "TM_CS_4_tpm" + ], + "d-tm-CSM": [ + "TM_CS_stress_1_tpm", + "TM_CS_stress_2_tpm", + "TM_CS_stress_3_tpm", + "TM_CS_stress_4_tpm" + ] + } + }, + "tm-LSM": { + "controls": [ + "TM_LS_1_tpm", + "TM_LS_2_tpm", + "TM_LS_3_tpm", + "TM_LS_4_tpm" + ], + "treatments": { + "l-tm-LSM": [ + "TM_LS_1_tpm", + "TM_LS_2_tpm", + "TM_LS_3_tpm", + "TM_LS_4_tpm" + ], + "d-tm-LSM": [ + "TM_LS_stress_1_tpm", + "TM_LS_stress_2_tpm", + "TM_LS_stress_3_tpm", + "TM_LS_stress_4_tpm" + ] + } + }, + "gp-IM": { + "controls": [ + "GP_IM_1_tpm", + "GP_IM_2_tpm", + "GP_IM_3_tpm", + "GP_IM_4_tpm" + ], + "treatments": { + "l-gp-IM": [ + "GP_IM_1_tpm", + "GP_IM_2_tpm", + "GP_IM_3_tpm", + "GP_IM_4_tpm" + ], + "d-gp-IM": [ + "GP_IM_stress_1_tpm", + "GP_IM_stress_2_tpm", + "GP_IM_stress_3_tpm", + "GP_IM_stress_4_tpm" + ] + } + }, + "gp-CSM": { + "controls": [ + "GP_CS_1_tpm", + "GP_CS_2_tpm", + "GP_CS_3_tpm", + "GP_CS_4_tpm" + ], + "treatments": { + "l-gp-CSM": [ + "GP_CS_1_tpm", + "GP_CS_2_tpm", + "GP_CS_3_tpm", + "GP_CS_4_tpm" + ], + "d-gp-CSM": [ + "GP_CS_stress_1_tpm", + "GP_CS_stress_2_tpm", + "GP_CS_stress_3_tpm", + "GP_CS_stress_4_tpm" + ] + } + }, + "gp-LSM": { + "controls": [ + "GP_LS_1_tpm", + "GP_LS_2_tpm", + "GP_LS_3_tpm", + "GP_LS_4_tpm" + ], + "treatments": { + "l-gp-LSM": [ + "GP_LS_1_tpm", + "GP_LS_2_tpm", + "GP_LS_3_tpm", + "GP_LS_4_tpm" + ], + "d-gp-LSM": [ + "GP_LS_stress_1_tpm", + "GP_LS_stress_2_tpm", + "GP_LS_stress_3_tpm", + "GP_LS_stress_4_tpm" + ] + } + }, + "lp-LSM": { + "controls": [ + "LP_LS_1_tpm", + "LP_LS_2_tpm", + "LP_LS_3_tpm", + "LP_LS_4_tpm" + ], + "treatments": { + "l-lp-LSM": [ + "LP_LS_1_tpm", + "LP_LS_2_tpm", + "LP_LS_3_tpm", + "LP_LS_4_tpm" + ], + "d-lp-LSM": [ + "LP_LS_stress_1_tpm", + "LP_LS_stress_2_tpm", + "LP_LS_stress_3_tpm", + "LP_LS_stress_4_tpm" + ] + } + }, + "lp-CSM": { + "controls": [ + "LP_CS_1_tpm", + "LP_CS_2_tpm", + "LP_CS_3_tpm", + "LP_CS_4_tpm" + ], + "treatments": { + "l-lp-CSM": [ + "LP_CS_1_tpm", + "LP_CS_2_tpm", + "LP_CS_3_tpm", + "LP_CS_4_tpm" + ], + "d-lp-CSM": [ + "LP_CS_stress_1_tpm", + "LP_CS_stress_2_tpm", + "LP_CS_stress_3_tpm", + "LP_CS_stress_4_tpm" + ] + } + }, + "lp-IM": { + "controls": [ + "LP_IM_1_tpm", + "LP_IM_2_tpm", + "LP_IM_3_tpm", + "LP_IM_4_tpm" + ], + "treatments": { + "l-lp-IM": [ + "LP_IM_1_tpm", + "LP_IM_2_tpm", + "LP_IM_3_tpm", + "LP_IM_4_tpm" + ], + "d-lp-IM": [ + "LP_IM_stress_1_tpm", + "LP_IM_stress_2_tpm", + "LP_IM_stress_3_tpm", + "LP_IM_stress_4_tpm" + ] + } + }, + "sp-IM": { + "controls": [ + "SP_IM_1_tpm", + "SP_IM_2_tpm", + "SP_IM_3_tpm", + "SP_IM_4_tpm" + ], + "treatments": { + "l-sp-IM": [ + "SP_IM_1_tpm", + "SP_IM_2_tpm", + "SP_IM_3_tpm", + "SP_IM_4_tpm" + ], + "d-sp-IM": [ + "SP_IM_stress_1_tpm", + "SP_IM_stress_2_tpm", + "SP_IM_stress_3_tpm", + "SP_IM_stress_4_tpm" + ] + } + }, + "sp-CSM": { + "controls": [ + "SP_CS_1_tpm", + "SP_CS_2_tpm", + "SP_CS_3_tpm", + "SP_CS_4_tpm", + "SP_CS_5_tpm", + "SP_CS_6_tpm" + ], + "treatments": { + "l-sp-CSM": [ + "SP_CS_1_tpm", + "SP_CS_2_tpm", + "SP_CS_3_tpm", + "SP_CS_4_tpm", + "SP_CS_5_tpm", + "SP_CS_6_tpm" + ], + "d-sp-CSM": [ + "SP_CS_stress_1_tpm", + "SP_CS_stress_2_tpm", + "SP_CS_stress_3_tpm", + "SP_CS_stress_4_tpm" + ] + } + }, + "sp-LSM": { + "controls": [ + "SP_LS_1_tpm", + "SP_LS_2_tpm", + "SP_LS_3_tpm", + "SP_LS_5_tpm", + "SP_LS_6_tpm" + ], + "treatments": { + "l-sp-LSM": [ + "SP_LS_1_tpm", + "SP_LS_2_tpm", + "SP_LS_3_tpm", + "SP_LS_5_tpm", + "SP_LS_6_tpm" + ], + "d-sp-LSM": [ + "SP_LS_stress_1_tpm", + "SP_LS_stress_2_tpm", + "SP_LS_stress_3_tpm", + "SP_LS_stress_4_tpm" + ] + } + }, + "ap-LSM": { + "controls": [ + "AP_LS_1_tpm", + "AP_LS_2_tpm", + "AP_LS_3_tpm", + "AP_LS_4_tpm" + ], + "treatments": { + "l-ap-LSM": [ + "AP_LS_1_tpm", + "AP_LS_2_tpm", + "AP_LS_3_tpm", + "AP_LS_4_tpm" + ], + "d-ap-LSM": [ + "AP_LS_stress_1_tpm", + "AP_LS_stress_2_tpm", + "AP_LS_stress_3_tpm", + "AP_LS_stress_4_tpm" + ] + } + }, + "ap-CSM": { + "controls": [ + "AP_CS_1_tpm", + "AP_CS_2_tpm", + "AP_CS_3_tpm", + "AP_CS_4_tpm" + ], + "treatments": { + "l-ap-CSM": [ + "AP_CS_1_tpm", + "AP_CS_2_tpm", + "AP_CS_3_tpm", + "AP_CS_4_tpm" + ], + "d-ap-CSM": [ + "AP_CS_stress_1_tpm", + "AP_CS_stress_2_tpm", + "AP_CS_stress_3_tpm", + "AP_CS_stress_4_tpm" + ] + } + }, + "ap-IM": { + "controls": [ + "AP_IM_1_tpm", + "AP_IM_2_tpm", + "AP_IM_3_tpm", + "AP_IM_4_tpm" + ], + "treatments": { + "l-ap-IM": [ + "AP_IM_1_tpm", + "AP_IM_2_tpm", + "AP_IM_3_tpm", + "AP_IM_4_tpm" + ], + "d-ap-IM": [ + "AP_IM_stress_1_tpm", + "AP_IM_stress_2_tpm", + "AP_IM_stress_3_tpm", + "AP_IM_stress_4_tpm" + ] + } + } + } + } + } + }, + "barley_spike_meristem_v3": { + "species": "barley", + "instance_families": [ + "eplant_barley" + ], + "source": "eplant", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_barley", + "used_by": [ + { + "frontend": "eplant", + "instance": "eplant_barley", + "view": "Spike Meristem" + }, + { + "frontend": "eplant", + "instance": "eplant_barley", + "view": "Spike Meristem Shade Response" + } + ], + "views": { + "eplant_barley::Spike Meristem Shade Response": { + "frontend": "eplant", + "instance": "eplant_barley", + "display_name": "Spike Meristem Shade Response", + "proj_ids": [], + "sample_groups": { + "dr-SRM": { + "controls": [ + "DR_SR_1_tpm", + "DR_SR_2_tpm", + "DR_SR_3_tpm", + "DR_SR_4_tpm" + ], + "treatments": { + "d-dr-SRM": [ + "DR_SR_stress_1_tpm", + "DR_SR_stress_2_tpm", + "DR_SR_stress_3_tpm", + "DR_SR_stress_4_tpm" + ], + "l-dr-SRM": [ + "DR_SR_1_tpm", + "DR_SR_2_tpm", + "DR_SR_3_tpm", + "DR_SR_4_tpm" + ] + } + }, + "dr-IM": { + "controls": [ + "DR_IM_1_tpm", + "DR_IM_2_tpm", + "DR_IM_3_tpm", + "DR_IM_4_tpm" + ], + "treatments": { + "l-dr-IM": [ + "DR_IM_1_tpm", + "DR_IM_2_tpm", + "DR_IM_3_tpm", + "DR_IM_4_tpm" + ], + "d-dr-IM": [ + "DR_IM_stress_1_tpm", + "DR_IM_stress_2_tpm", + "DR_IM_stress_3_tpm", + "DR_IM_stress_4_tpm" + ] + } + }, + "dr-LRM": { + "controls": [ + "DR_LR_1_tpm", + "DR_LR_2_tpm", + "DR_LR_3_tpm", + "DR_LR_4_tpm" + ], + "treatments": { + "l-dr-LRM": [ + "DR_LR_1_tpm", + "DR_LR_2_tpm", + "DR_LR_3_tpm", + "DR_LR_4_tpm" + ], + "d-dr-LRM": [ + "DR_LR_stress_1_tpm", + "DR_LR_stress_2_tpm", + "DR_LR_stress_3_tpm", + "DR_LR_stress_4_tpm" + ] + } + }, + "tm-IM": { + "controls": [ + "TM_IM_1_tpm", + "TM_IM_2_tpm", + "TM_IM_3_tpm", + "TM_IM_4_tpm" + ], + "treatments": { + "l-tm-IM": [ + "TM_IM_1_tpm", + "TM_IM_2_tpm", + "TM_IM_3_tpm", + "TM_IM_4_tpm" + ], + "d-tm-IM": [ + "TM_IM_stress_1_tpm", + "TM_IM_stress_2_tpm", + "TM_IM_stress_3_tpm", + "TM_IM_stress_4_tpm" + ] + } + }, + "tm-CSM": { + "controls": [ + "TM_CS_1_tpm", + "TM_CS_2_tpm", + "TM_CS_3_tpm", + "TM_CS_4_tpm" + ], + "treatments": { + "l-tm-CSM": [ + "TM_CS_1_tpm", + "TM_CS_2_tpm", + "TM_CS_3_tpm", + "TM_CS_4_tpm" + ], + "d-tm-CSM": [ + "TM_CS_stress_1_tpm", + "TM_CS_stress_2_tpm", + "TM_CS_stress_3_tpm", + "TM_CS_stress_4_tpm" + ] + } + }, + "tm-LSM": { + "controls": [ + "TM_LS_1_tpm", + "TM_LS_2_tpm", + "TM_LS_3_tpm", + "TM_LS_4_tpm" + ], + "treatments": { + "l-tm-LSM": [ + "TM_LS_1_tpm", + "TM_LS_2_tpm", + "TM_LS_3_tpm", + "TM_LS_4_tpm" + ], + "d-tm-LSM": [ + "TM_LS_stress_1_tpm", + "TM_LS_stress_2_tpm", + "TM_LS_stress_3_tpm", + "TM_LS_stress_4_tpm" + ] + } + }, + "gp-IM": { + "controls": [ + "GP_IM_1_tpm", + "GP_IM_2_tpm", + "GP_IM_3_tpm", + "GP_IM_4_tpm" + ], + "treatments": { + "l-gp-IM": [ + "GP_IM_1_tpm", + "GP_IM_2_tpm", + "GP_IM_3_tpm", + "GP_IM_4_tpm" + ], + "d-gp-IM": [ + "GP_IM_stress_1_tpm", + "GP_IM_stress_2_tpm", + "GP_IM_stress_3_tpm", + "GP_IM_stress_4_tpm" + ] + } + }, + "gp-CSM": { + "controls": [ + "GP_CS_1_tpm", + "GP_CS_2_tpm", + "GP_CS_3_tpm", + "GP_CS_4_tpm" + ], + "treatments": { + "l-gp-CSM": [ + "GP_CS_1_tpm", + "GP_CS_2_tpm", + "GP_CS_3_tpm", + "GP_CS_4_tpm" + ], + "d-gp-CSM": [ + "GP_CS_stress_1_tpm", + "GP_CS_stress_2_tpm", + "GP_CS_stress_3_tpm", + "GP_CS_stress_4_tpm" + ] + } + }, + "gp-LSM": { + "controls": [ + "GP_LS_1_tpm", + "GP_LS_2_tpm", + "GP_LS_3_tpm", + "GP_LS_4_tpm" + ], + "treatments": { + "l-gp-LSM": [ + "GP_LS_1_tpm", + "GP_LS_2_tpm", + "GP_LS_3_tpm", + "GP_LS_4_tpm" + ], + "d-gp-LSM": [ + "GP_LS_stress_1_tpm", + "GP_LS_stress_2_tpm", + "GP_LS_stress_3_tpm", + "GP_LS_stress_4_tpm" + ] + } + }, + "lp-LSM": { + "controls": [ + "LP_LS_1_tpm", + "LP_LS_2_tpm", + "LP_LS_3_tpm", + "LP_LS_4_tpm" + ], + "treatments": { + "l-lp-LSM": [ + "LP_LS_1_tpm", + "LP_LS_2_tpm", + "LP_LS_3_tpm", + "LP_LS_4_tpm" + ], + "d-lp-LSM": [ + "LP_LS_stress_1_tpm", + "LP_LS_stress_2_tpm", + "LP_LS_stress_3_tpm", + "LP_LS_stress_4_tpm" + ] + } + }, + "lp-CSM": { + "controls": [ + "LP_CS_1_tpm", + "LP_CS_2_tpm", + "LP_CS_3_tpm", + "LP_CS_4_tpm" + ], + "treatments": { + "l-lp-CSM": [ + "LP_CS_1_tpm", + "LP_CS_2_tpm", + "LP_CS_3_tpm", + "LP_CS_4_tpm" + ], + "d-lp-CSM": [ + "LP_CS_stress_1_tpm", + "LP_CS_stress_2_tpm", + "LP_CS_stress_3_tpm", + "LP_CS_stress_4_tpm" + ] + } + }, + "lp-IM": { + "controls": [ + "LP_IM_1_tpm", + "LP_IM_2_tpm", + "LP_IM_3_tpm", + "LP_IM_4_tpm" + ], + "treatments": { + "l-lp-IM": [ + "LP_IM_1_tpm", + "LP_IM_2_tpm", + "LP_IM_3_tpm", + "LP_IM_4_tpm" + ], + "d-lp-IM": [ + "LP_IM_stress_1_tpm", + "LP_IM_stress_2_tpm", + "LP_IM_stress_3_tpm", + "LP_IM_stress_4_tpm" + ] + } + }, + "sp-IM": { + "controls": [ + "SP_IM_1_tpm", + "SP_IM_2_tpm", + "SP_IM_3_tpm", + "SP_IM_4_tpm" + ], + "treatments": { + "l-sp-IM": [ + "SP_IM_1_tpm", + "SP_IM_2_tpm", + "SP_IM_3_tpm", + "SP_IM_4_tpm" + ], + "d-sp-IM": [ + "SP_IM_stress_1_tpm", + "SP_IM_stress_2_tpm", + "SP_IM_stress_3_tpm", + "SP_IM_stress_4_tpm" + ] + } + }, + "sp-CSM": { + "controls": [ + "SP_CS_1_tpm", + "SP_CS_2_tpm", + "SP_CS_3_tpm", + "SP_CS_4_tpm" + ], + "treatments": { + "l-sp-CSM": [ + "SP_CS_1_tpm", + "SP_CS_2_tpm", + "SP_CS_3_tpm", + "SP_CS_4_tpm" + ], + "d-sp-CSM": [ + "SP_CS_stress_1_tpm", + "SP_CS_stress_2_tpm", + "SP_CS_stress_3_tpm", + "SP_CS_stress_4_tpm" + ] + } + }, + "sp-LSM": { + "controls": [ + "SP_LS_1_tpm", + "SP_LS_2_tpm", + "SP_LS_3_tpm" + ], + "treatments": { + "l-sp-LSM": [ + "SP_LS_1_tpm", + "SP_LS_2_tpm", + "SP_LS_3_tpm" + ], + "d-sp-LSM": [ + "SP_LS_stress_1_tpm", + "SP_LS_stress_2_tpm", + "SP_LS_stress_3_tpm", + "SP_LS_stress_4_tpm" + ] + } + }, + "ap-LSM": { + "controls": [ + "AP_LS_1_tpm", + "AP_LS_2_tpm", + "AP_LS_3_tpm", + "AP_LS_4_tpm" + ], + "treatments": { + "l-ap-LSM": [ + "AP_LS_1_tpm", + "AP_LS_2_tpm", + "AP_LS_3_tpm", + "AP_LS_4_tpm" + ], + "d-ap-LSM": [ + "AP_LS_stress_1_tpm", + "AP_LS_stress_2_tpm", + "AP_LS_stress_3_tpm", + "AP_LS_stress_4_tpm" + ] + } + }, + "ap-CSM": { + "controls": [ + "AP_CS_1_tpm", + "AP_CS_2_tpm", + "AP_CS_3_tpm", + "AP_CS_4_tpm" + ], + "treatments": { + "l-ap-CSM": [ + "AP_CS_1_tpm", + "AP_CS_2_tpm", + "AP_CS_3_tpm", + "AP_CS_4_tpm" + ], + "d-ap-CSM": [ + "AP_CS_stress_1_tpm", + "AP_CS_stress_2_tpm", + "AP_CS_stress_3_tpm", + "AP_CS_stress_4_tpm" + ] + } + }, + "ap-IM": { + "controls": [ + "AP_IM_1_tpm", + "AP_IM_2_tpm", + "AP_IM_3_tpm", + "AP_IM_4_tpm" + ], + "treatments": { + "l-ap-IM": [ + "AP_IM_1_tpm", + "AP_IM_2_tpm", + "AP_IM_3_tpm", + "AP_IM_4_tpm" + ], + "d-ap-IM": [ + "AP_IM_stress_1_tpm", + "AP_IM_stress_2_tpm", + "AP_IM_stress_3_tpm", + "AP_IM_stress_4_tpm" + ] + } + } + } + }, + "eplant_barley::Spike Meristem": { + "frontend": "eplant", + "instance": "eplant_barley", + "display_name": "Spike Meristem", + "proj_ids": [], + "sample_groups": { + "spike_meristem": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "l-RAM": [ + "RAM_1_tpm", + "RAM_2_tpm", + "RAM_3_tpm" + ], + "l-tm-IM": [ + "TM_IM_1_tpm", + "TM_IM_2_tpm", + "TM_IM_3_tpm", + "TM_IM_4_tpm" + ], + "l-tm-CSM": [ + "TM_CS_1_tpm", + "TM_CS_2_tpm", + "TM_CS_3_tpm", + "TM_CS_4_tpm" + ], + "l-tm-LSM": [ + "TM_LS_1_tpm", + "TM_LS_2_tpm", + "TM_LS_3_tpm", + "TM_LS_4_tpm" + ], + "l-gp-IM": [ + "GP_IM_1_tpm", + "GP_IM_2_tpm", + "GP_IM_3_tpm", + "GP_IM_4_tpm" + ], + "l-gp-CSM": [ + "GP_CS_1_tpm", + "GP_CS_2_tpm", + "GP_CS_3_tpm", + "GP_CS_4_tpm" + ], + "l-gp-LSM": [ + "GP_LS_1_tpm", + "GP_LS_2_tpm", + "GP_LS_3_tpm", + "GP_LS_4_tpm" + ], + "l-lp-LSM": [ + "LP_LS_1_tpm", + "LP_LS_2_tpm", + "LP_LS_3_tpm", + "LP_LS_4_tpm" + ], + "l-lp-CSM": [ + "LP_CS_1_tpm", + "LP_CS_2_tpm", + "LP_CS_3_tpm", + "LP_CS_4_tpm" + ], + "l-lp-IM": [ + "LP_IM_1_tpm", + "LP_IM_2_tpm", + "LP_IM_3_tpm", + "LP_IM_4_tpm" + ], + "l-sp-IM": [ + "SP_IM_1_tpm", + "SP_IM_2_tpm", + "SP_IM_3_tpm", + "SP_IM_4_tpm" + ], + "l-ap-LSM": [ + "AP_LS_1_tpm", + "AP_LS_2_tpm", + "AP_LS_3_tpm", + "AP_LS_4_tpm" + ], + "l-ap-CSM": [ + "AP_CS_1_tpm", + "AP_CS_2_tpm", + "AP_CS_3_tpm", + "AP_CS_4_tpm" + ], + "l-ap-IM": [ + "AP_IM_1_tpm", + "AP_IM_2_tpm", + "AP_IM_3_tpm", + "AP_IM_4_tpm" + ], + "l-sp-CSM": [ + "SP_CS_1_tpm", + "SP_CS_2_tpm", + "SP_CS_3_tpm", + "SP_CS_4_tpm" + ], + "l-sp-LSM": [ + "SP_LS_1_tpm", + "SP_LS_2_tpm", + "SP_LS_3_tpm", + "SP_LS_4_tpm" + ], + "l-wa-IM": [ + "WA_IM_1_tpm", + "WA_IM_2_tpm", + "WA_IM_3_tpm", + "WA_IM_4_tpm" + ], + "r-ap": [ + "AP_REF1_1_tpm", + "AP_REF1_2_tpm", + "AP_REF1_3_tpm", + "AP_REF1_4_tpm" + ], + "r-sp": [ + "SP_REF1_1_tpm", + "SP_REF1_2_tpm", + "SP_REF1_3_tpm", + "SP_REF1_4_tpm" + ], + "r-lp": [ + "LP_REF1_1_tpm", + "LP_REF1_2_tpm", + "LP_REF1_3_tpm", + "LP_REF1_4_tpm" + ], + "r-gp": [ + "GP_REF1_1_tpm", + "GP_REF1_2_tpm", + "GP_REF1_3_tpm", + "GP_REF1_4_tpm" + ], + "r-tm": [ + "TM_REF1_1_tpm", + "TM_REF1_2_tpm", + "TM_REF1_3_tpm", + "TM_REF1_4_tpm" + ], + "r-dr": [ + "DR_REF1_1_tpm", + "DR_REF1_2_tpm", + "DR_REF1_3_tpm", + "DR_REF1_4_tpm" + ], + "w-sp": [ + "SP_REF2_1_tpm", + "SP_REF2_2_tpm", + "SP_REF2_3_tpm", + "SP_REF2_4_tpm" + ], + "w-lp": [ + "LP_REF2_1_tpm", + "LP_REF2_2_tpm", + "LP_REF2_3_tpm", + "LP_REF2_4_tpm" + ], + "w-gp": [ + "GP_REF2_1_tpm", + "GP_REF2_2_tpm", + "GP_REF2_3_tpm", + "GP_REF2_4_tpm" + ], + "w-tm": [ + "TM_REF2_1_tpm", + "TM_REF2_2_tpm", + "TM_REF2_3_tpm", + "TM_REF2_4_tpm" + ], + "w-dr": [ + "DR_REF2_1_tpm", + "DR_REF2_2_tpm", + "DR_REF2_3_tpm", + "DR_REF2_4_tpm" + ], + "w-ap": [ + "AP_REF2_1_tpm", + "AP_REF2_2_tpm", + "AP_REF2_3_tpm", + "AP_REF2_4_tpm" + ], + "l-dr-SRM": [ + "DR_SR_1_tpm", + "DR_SR_2_tpm", + "DR_SR_3_tpm", + "DR_SR_4_tpm" + ], + "l-dr-LRM": [ + "DR_LR_1_tpm", + "DR_LR_2_tpm", + "DR_LR_3_tpm", + "DR_LR_4_tpm" + ], + "l-dr-IM": [ + "DR_IM_1_tpm", + "DR_IM_2_tpm", + "DR_IM_3_tpm", + "DR_IM_4_tpm" + ], + "l-va-SAM": [ + "VA_1_tpm", + "VA_2_tpm", + "VA_3_tpm" + ], + "l-LBB": [ + "LB_1_tpm", + "LB_2_tpm", + "LB_3_tpm" + ] + } + } + } + } + } + }, + "brachypodium": { + "species": "brachypodium", + "instance_families": [ + "efp_brachypodium" + ], + "source": "efp", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_brachypodium", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_brachypodium", + "view": "Brachypodium Atlas" + } + ], + "views": { + "efp_brachypodium::Brachypodium Atlas": { + "frontend": "efp", + "instance": "efp_brachypodium", + "display_name": "Brachypodium Atlas", + "proj_ids": [], + "sample_groups": { + "Med_CTRL": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "I:_De-etiolated_shoots_3_DAG_1": [ + "I:_De-etiolated_shoots_3_DAG_1", + "I:_De-etiolated_shoots_3_DAG_2", + "I:_De-etiolated_shoots_3_DAG_3" + ], + "I:_Etiolated_shoots_3_DAG_1": [ + "I:_Etiolated_shoots_3_DAG_1", + "I:_Etiolated_shoots_3_DAG_2", + "I:_Etiolated_shoots_3_DAG_3" + ], + "P:_Coleoptile_10_DAG_1": [ + "P:_Coleoptile_10_DAG_1", + "P:_Coleoptile_10_DAG_2" + ], + "P:_Coleoptile_17+27_DAG_1": [ + "P:_Coleoptile_17+27_DAG_1", + "P:_Coleoptile_17+27_DAG_2", + "P:_Coleoptile_17+27_DAG_3" + ], + "P:_First_internode_10_DAG_1": [ + "P:_First_internode_10_DAG_1", + "P:_First_internode_10_DAG_2", + "P:_First_internode_10_DAG_3", + "P:_First_internode_10_DAG_4" + ], + "P:_First_internode_17_DAG_1": [ + "P:_First_internode_17_DAG_1", + "P:_First_internode_17_DAG_2" + ], + "P:_First_internode_27_DAG_1": [ + "P:_First_internode_27_DAG_1", + "P:_First_internode_27_DAG_2", + "P:_First_internode_27_DAG_3" + ], + "P:_First_internode_35_DAG_1": [ + "P:_First_internode_35_DAG_1", + "P:_First_internode_35_DAG_2" + ], + "P:_First_internode_60_DAG_1": [ + "P:_First_internode_60_DAG_1", + "P:_First_internode_60_DAG_2" + ], + "P:_First_node_+_adventitious_roots_35_DAG_1": [ + "P:_First_node_+_adventitious_roots_35_DAG_1", + "P:_First_node_+_adventitious_roots_35_DAG_2" + ], + "P:_First_node_10_DAG_1": [ + "P:_First_node_10_DAG_1", + "P:_First_node_10_DAG_2" + ], 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+ "DA-PD-LS-PMC_R2", + "DA-PD-LS-PMC_R3", + "DA-PD-LS-PMC_R4", + "DA-PD-LS-PMC_R5" + ], + "Mature_Pod_Endocarp": [ + "DA-PD-LS-PEN_R1", + "DA-PD-LS-PEN_R2", + "DA-PD-LS-PEN_R3", + "DA-PD-LS-PEN_R4", + "DA-PD-LS-PEN_R5" + ], + "Mature_Pod_Seed_Mucilage": [ + "DA-PD-LS-SM_R1", + "DA-PD-LS-SM_R2", + "DA-PD-LS-SM_R3", + "DA-PD-LS-SM_R4", + "DA-PD-LS-SM_R5" + ], + "6mo_Orthotropic_Root": [ + "DA-RO-RT_R1", + "DA-RO-RT_R2", + "DA-RO-RT_R3", + "DA-RO-RT_R4", + "DA-RO-RT_R5" + ], + "6mo_Orthotropic_Leaf_A": [ + "DA-OTL-A_R1", + "DA-OTL-A_R2", + "DA-OTL-A_R3", + "DA-OTL-A_R4", + "DA-OTL-A_R5" + ], + "6mo_Orthotropic_Leaf_C": [ + "DA-OTL-C_R1", + "DA-OTL-C_R2", + "DA-OTL-C_R3", + "DA-OTL-C_R4", + "DA-OTL-C_R5" + ], + "6mo_Orthotropic_Leaf_E1": [ + "DA-OTL-E1_R1", + "DA-OTL-E1_R2", + "DA-OTL-E1_R3", + "DA-OTL-E1_R4", + "DA-OTL-E1_R5" + ], + "6mo_Orthotropic_Leaf_E2": [ + "DA-OTL-E2_R2", + "DA-OTL-E2_R3", + "DA-OTL-E2_R4", + "DA-OTL-E2_R5" + ], + "6mo_Orthotropic_Leaf_E3": [ + "DA-OTL-E3_R1", + "DA-OTL-E3_R2", + "DA-OTL-E3_R3", + "DA-OTL-E3_R4", + "DA-OTL-E3_R5" + ], + "6mo_Orthotropic_Shoot_Apex": [ + "DA-OTA_R1", + "DA-OTA_R2", + "DA-OTA_R3", + "DA-OTA_R4", + "DA-OTA_R5" + ], + "6mo_Orthotropic_Herbaceous_Stem": [ + "DA-OTAC-YS_R1", + "DA-OTAC-YS_R2", + "DA-OTAC-YS_R3", + "DA-OTAC-YS_R4", + "DA-OTAC-YS_R5" + ], + "6mo_Orthotropic_Young_Axilaries": [ + "DA-OAA-YA_R1", + "DA-OAA-YA_R2", + "DA-OAA-YA_R3", + "DA-OAA-YA_R4", + "DA-OAA-YA_R5" + ], + "6mo_Orthotropic_Old_Axilaries": [ + "DA-OAA-OA_R1", + "DA-OAA-OA_R2", + "DA-OAA-OA_R3", + "DA-OAA-OA_R4" + ], + "Plagiotropic_Shoot_Apex": [ + "DA-PSA_R1", + "DA-PSA_R2", + "DA-PSA_R3", + "DA-PSA_R4", + "DA-PSA_R5" + ], + "Plagiotropic_A_Leaf": [ + "DA-PTL-A_R1", + "DA-PTL-A_R2", + "DA-PTL-A_R3", + "DA-PTL-A_R4", + "DA-PTL-A_R5" + ], + "Plagiotropic_C_Leaf": [ + "DA-PTL-C_R1", + "DA-PTL-C_R3", + "DA-PTL-C_R4" + ], + "Plagiotropic_E_Leaf": [ + "DA-PTL-E_R1", + "DA-PTL-E_R2", + "DA-PTL-E_R3", + "DA-PTL-E_R4", + "DA-PTL-E_R5" + ], + "Plagiotropic_Old_Axiliaries": [ + "DA-OA_R1", + "DA-OA_R2", + "DA-OA_R3", + "DA-OA_R4", + "DA-OA_R5" + ], + "Plagiotropic_Young_Axilaries": [ + "DA-YA_R1", + "DA-YA_R2", + "DA-YA_R3", + "DA-YA_R4", + "DA-YA_R5" + ] + } + } + } + } + } + }, + "cacao_developmental_atlas_sca": { + "species": "cacao", + "instance_families": [ + "efp_cacao_sca" + ], + "source": "efp", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_cacao_sca", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_cacao_sca", + "view": "Developmental Atlas" + } + ], + "views": { + "efp_cacao_sca::Developmental Atlas": { + "frontend": "efp", + "instance": "efp_cacao_sca", + "display_name": "Developmental Atlas", + "proj_ids": [], + "sample_groups": { + "Med_CTRL": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "CCN51_Mature_Embryo": [ + "CGA-SE-LS-E_R1", + "CGA-SE-LS-E_R2", + "CGA-SE-LS-E_R3", + "CGA-SE-LS-E_R4", + "CGA-SE-LS-E_R5" + ], + "Germinating_Seed_Root": [ + "CGA-GS-RO_R1", + "CGA-GS-RO_R2", + "CGA-GS-RO_R3", + "CGA-GS-RO_R4", + "CGA-GS-RO_R5" + ], + "Germinating_Seed_Shoot": [ + "CGA-GS-SH_R1", + "CGA-GS-SH_R2", + "CGA-GS-SH_R3", + "CGA-GS-SH_R4", + "CGA-GS-SH_R5" + ], + "Seedling_Root": [ + "CGA-SL-RO_R1", + "CGA-SL-RO_R2", + "CGA-SL-RO_R3", + "CGA-SL-RO_R4", + "CGA-SL-RO_R5" + ], + "Seedling_Shoot": [ + "CGA-SL-SH_R1", + "CGA-SL-SH_R2", + "CGA-SL-SH_R3", + "CGA-SL-SH_R4", + "CGA-SL-SH_R5" + ], + "3mo_Orthotropic_Roots": [ + "CGA-RO_R1", + "CGA-RO_R2", + "CGA-RO_R3", + "CGA-RO_R4", + "CGA-RO_R5" + ], + "3mo_Orthotropic_Leaf_A": [ + "CGA-YL-A_R1", + "CGA-YL-A_R2", + "CGA-YL-A_R3", + "CGA-YL-A_R4", + "CGA-YL-A_R5" + ], + "3mo_Orthotropic_C_Leaf": [ + "CGA-ML-C_2", + "CGA-ML-C_R1", + "CGA-ML-C_R3", + "CGA-ML-C_R4", + "CGA-ML-C_R5" + ], + "3mo_Orthotropic_E1_Leaf": [ + "CGA-ML-E1_R1", + "CGA-ML-E1_R2", + "CGA-ML-E1_R3", + "CGA-ML-E1_R4", + "CGA-ML-E1_R5" + ], + "3mo_Orthotropic_E2_Leaf": [ + "CGA-OL-E2_R1", + "CGA-OL-E2_R2", + "CGA-OL-E2_R3", + "CGA-OL-E2_R4", + "CGA-OL-E2_R5" + ], + "3mo_Orthotropic_Shoot_Apex": [ + "CGA-AX_R1", + "CGA-AX_R2", + "CGA-AX_R3", + "CGA-AX_R4", + "CGA-AX_R5" + ], + "3mo_Orthotropic_Herbaceous_Stem": [ + "CGA-SBA-2_R1", + "CGA-SBA-2_R2", + "CGA-SBA-2_R3", + "CGA-SBA-2_R4", + "CGA-SBA-2_R5" + ], + "3mo_Orthotropic_Woody_Stem": [ + "CGA-SBA-1_R1", + "CGA-SBA-1_R2", + "CGA-SBA-1_R3", + "CGA-SBA-1_R4", + "CGA-SBA-1_R5" + ], + "Premeiotic_Floral_Bud": [ + "CGA-PMFB_R1", + "CGA-PMFB_R2", + "CGA-PMFB_R3", + "CGA-PMFB_R4" + ], + "Floral_Bud_5-10_mm": [ + "CGA-LGFL_R1", + "CGA-LGFL_R2", + "CGA-LGFL_R3", + "CGA-LGFL_R4" + ], + "Open_Flower": [ + "CGA-OF_R1", + "CGA-OF_R2", + "CGA-OF_R3", + "CGA-OF_R4" + ], + "CCN51_Immature_Embryo": [ + "DA-SE-MS-E_R1", + "DA-SE-MS-E_R2", + "DA-SE-MS-E_R3", + "DA-SE-MS-E_R4", + "DA-SE-MS-E_R5" + ], + "Immature_Pod_Seed_Coat": [ + "DA-SE-MS-SC_R1", + "DA-SE-MS-SC_R2", + "DA-SE-MS-SC_R3", + "DA-SE-MS-SC_R4", + "DA-SE-MS-SC_R5" + ], + "CCN51_Developing_Embryo": [ + "DA-SE-MLS-E_R1", + "DA-SE-MLS-E_R2", + "DA-SE-MLS-E_R3", + "DA-SE-MLS-E_R4", + "DA-SE-MLS-E_R5" + ], + "Developing_Pod_Seed_Coat": [ + "DA-MLS-SC_R1", + "DA-MLS-SC_R2", + "DA-MLS-SC_R3", + "DA-MLS-SC_R4", + "DA-MLS-SC_R5" + ], + "Immature_Pod_Skin": [ + "DA-PD-MS-PS_R1", + "DA-PD-MS-PS_R2", + "DA-PD-MS-PS_R3" + ], + "Immature_Pod_Exocarp": [ + "DA-PD-MS-PEX_R1", + "DA-PD-MS-PEX_R2", + "DA-PD-MS-PEX_R3" + ], + "Immature_Pod_Mesocarp": [ + "DA-PD-MS-PMC_R1", + "DA-PD-MS-PMC_R2", + "DA-PD-MS-PMC_R3" + ], + "Immature_Pod_Seed_Mucilage": [ + "DA-PD-MS-SM_R1", + "DA-PD-MS-SM_R2", + "DA-PD-MS-SM_R3" + ], + "Immature_Pod_Endocarp": [ + "DA-PD-MS-PEN_R1", + "DA-PD-MS-PEN_R2", + "DA-PD-MS-PEN_R3" + ], + "Developing_Pod_Skin": [ + "DA-PD-MLS-PS_R1", + "DA-PD-MLS-PS_R2", + "DA-PD-MLS-PS_R3" + ], + "Developing_Pod_Exocarp": [ + "DA-PD-MLS-PEX_R1", + "DA-PD-MLS-PEX_R2", + "DA-PD-MLS-PEX_R3" + ], + "Developing_Pod_Mesocarp": [ + "DA-PD-MLS-PMC_R1", + "DA-PD-MLS-PMC_R2", + "DA-PD-MLS-PMC_R3" + ], + "Developing_Pod_Endocarp": [ + "DA-PD-MLS-PEN_R1", + "DA-PD-MLS-PEN_R2", + "DA-PD-MLS-PEN_R3" + ], + "Developing_Pod_Seed_Mucilage": [ + "DA-PD-MLS-SM_R1", + "DA-PD-MLS-SM_R2", + "DA-PD-MLS-SM_R3" + ], + "Mature_Pod_Skin": [ + "DA-PD-LS-PS_R1", + "DA-PD-LS-PS_R2", + "DA-PD-LS-PS_R3", + "DA-PD-LS-PS_R4", + "DA-PD-LS-PS_R5" + ], + "Mature_Pod_Exocarp": [ + "DA-PD-LS-PEX_R1", + "DA-PD-LS-PEX_R2", + "DA-PD-LS-PEX_R3", + "DA-PD-LS-PEX_R4", + "DA-PD-LS-PEX_R5" + ], + "Mature_Pod_Mesocarp": [ + "DA-PD-LS-PMC_R1", + "DA-PD-LS-PMC_R2", + "DA-PD-LS-PMC_R3", + "DA-PD-LS-PMC_R4", + "DA-PD-LS-PMC_R5" + ], + "Mature_Pod_Endocarp": [ + "DA-PD-LS-PEN_R1", + "DA-PD-LS-PEN_R2", + "DA-PD-LS-PEN_R3", + "DA-PD-LS-PEN_R4", + "DA-PD-LS-PEN_R5" + ], + "Mature_Pod_Seed_Mucilage": [ + "DA-PD-LS-SM_R1", + "DA-PD-LS-SM_R2", + "DA-PD-LS-SM_R3", + "DA-PD-LS-SM_R4", + "DA-PD-LS-SM_R5" + ], + "6mo_Orthotropic_Root": [ + "DA-RO-RT_R1", + "DA-RO-RT_R2", + "DA-RO-RT_R3", + "DA-RO-RT_R4", + "DA-RO-RT_R5" + ], + "6mo_Orthotropic_Leaf_A": [ + "DA-OTL-A_R1", + "DA-OTL-A_R2", + "DA-OTL-A_R3", + "DA-OTL-A_R4", + "DA-OTL-A_R5" + ], + "6mo_Orthotropic_Leaf_C": [ + "DA-OTL-C_R1", + "DA-OTL-C_R2", + "DA-OTL-C_R3", + "DA-OTL-C_R4", + "DA-OTL-C_R5" + ], + "6mo_Orthotropic_Leaf_E1": [ + "DA-OTL-E1_R1", + "DA-OTL-E1_R2", + "DA-OTL-E1_R3", + "DA-OTL-E1_R4", + "DA-OTL-E1_R5" + ], + "6mo_Orthotropic_Leaf_E2": [ + "DA-OTL-E2_R2", + "DA-OTL-E2_R3", + "DA-OTL-E2_R4", + "DA-OTL-E2_R5" + ], + "6mo_Orthotropic_Leaf_E3": [ + "DA-OTL-E3_R1", + "DA-OTL-E3_R2", + "DA-OTL-E3_R3", + "DA-OTL-E3_R4", + "DA-OTL-E3_R5" + ], + "6mo_Orthotropic_Shoot_Apex": [ + "DA-OTA_R1", + "DA-OTA_R2", + "DA-OTA_R3", + "DA-OTA_R4", + "DA-OTA_R5" + ], + "6mo_Orthotropic_Herbaceous_Stem": [ + "DA-OTAC-YS_R1", + "DA-OTAC-YS_R2", + "DA-OTAC-YS_R3", + "DA-OTAC-YS_R4", + "DA-OTAC-YS_R5" + ], + "6mo_Orthotropic_Young_Axilaries": [ + "DA-OAA-YA_R1", + "DA-OAA-YA_R2", + "DA-OAA-YA_R3", + "DA-OAA-YA_R4", + "DA-OAA-YA_R5" + ], + "6mo_Orthotropic_Old_Axilaries": [ + "DA-OAA-OA_R1", + "DA-OAA-OA_R2", + "DA-OAA-OA_R3", + "DA-OAA-OA_R4" + ], + "Plagiotropic_Shoot_Apex": [ + "DA-PSA_R1", + "DA-PSA_R2", + "DA-PSA_R3", + "DA-PSA_R4", + "DA-PSA_R5" + ], + "Plagiotropic_A_Leaf": [ + "DA-PTL-A_R1", + "DA-PTL-A_R2", + "DA-PTL-A_R3", + "DA-PTL-A_R4", + "DA-PTL-A_R5" + ], + "Plagiotropic_C_Leaf": [ + "DA-PTL-C_R1", + "DA-PTL-C_R3", + "DA-PTL-C_R4" + ], + "Plagiotropic_E_Leaf": [ + "DA-PTL-E_R1", + "DA-PTL-E_R2", + "DA-PTL-E_R3", + "DA-PTL-E_R4", + "DA-PTL-E_R5" + ], + "Plagiotropic_Old_Axiliaries": [ + "DA-OA_R1", + "DA-OA_R2", + "DA-OA_R3", + "DA-OA_R4", + "DA-OA_R5" + ], + "Plagiotropic_Young_Axilaries": [ + "DA-YA_R1", + "DA-YA_R2", + "DA-YA_R3", + "DA-YA_R4", + "DA-YA_R5" + ] + } + } + } + } + } + }, + "cacao_drought_diurnal_atlas": { + "species": "cacao", + "instance_families": [ + "efp_cacao_ccn" + ], + "source": "efp", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_cacao_ccn", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_cacao_ccn", + "view": "Drought Diurnal Atlas" + } + ], + "views": { + "efp_cacao_ccn::Drought Diurnal Atlas": { + "frontend": "efp", + "instance": "efp_cacao_ccn", + "display_name": "Drought Diurnal Atlas", + "proj_ids": [], + "sample_groups": { + "Med_CTRL": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "Root_Watered_T1": [ + "DD-WTR-T1_R1", + "DD-WTR-T1_R2", + "DD-WTR-T1_R3" + ], + "Root_Watered_T2": [ + "DD-WTR-T2_R1", + "DD-WTR-T2_R2", + "DD-WTR-T2_R3" + ], + "Root_Watered_T3": [ + "DD-WTR-T3_R1", + "DD-WTR-T3_R2", + "DD-WTR-T3_R3" + ], + "Root_Watered_T4": [ + "DD-WTR-T4_R1", + "DD-WTR-T4_R2", + "DD-WTR-T4_R3" + ], + "Root_Watered_T5": [ + "DD-WTR-T5_R1", + "DD-WTR-T5_R2", + "DD-WTR-T5_R3" + ], + "Root_Watered_T6": [ + "DD-WTR-T6_R1", + "DD-WTR-T6_R2", + "DD-WTR-T6_R3" + ], + "Root_Watered_T7": [ + "DD-WTR-T7_R2", + "DD-WTR-T7_R3", + "DD-WTR-T7-R1" + ], + "Root_Drought_T1": [ + "DD-DTR-T1_R1", + "DD-DTR-T1_R2", + "DD-DTR-T1_R3" + ], + "Root_Drought_T2": [ + "DD-DTR-T2_R1", + "DD-DTR-T2_R2", + "DD-DTR-T2_R3" + ], + "Root_Drought_T3": [ + "DD-DTR-T3_R1", + "DD-DTR-T3_R2", + "DD-DTR-T3_R3" + ], + "Root_Drought_T4": [ + "DD-DTR-T4_R1", + "DD-DTR-T4_R2", + "DD-DTR-T4_R3" + ], + "Root_Drought_T5": [ + "DD-DTR-T5_R1", + "DD-DTR-T5_R2" + ], + "Root_Drought_T6": [ + "DD-DTR-T6_R1", + "DD-DTR-T6_R2", + "DD-DTR-T6_R3" + ], + "Root_Drought_T7": [ + "DD-DTR-T7_R1", + "DD-DTR-T7_R2", + "DD-DTR-T7_R3" + ], + "Leaf_Watered_T1": [ + "DD-WTL-T1_R1", + "DD-WTL-T1_R2", + "DD-WTL-T1_R3" + ], + "Leaf_Watered_T2": [ + "DD-WTL-T2_R1", + "DD-WTL-T2_R2", + "DD-WTL-T2_R3" + ], + "Leaf_Watered_T3": [ + "DD-WTL-T3_R1", + "DD-WTL-T3_R2", + "DD-WTL-T3_R3" + ], + "Leaf_Watered_T4": [ + "DD-WTL-T4_R1", + "DD-WTL-T4_R2", + "DD-WTL-T4_R3" + ], + "Leaf_Watered_T5": [ + "DD-WTL-T5_R1", + "DD-WTL-T5_R2" + ], + "Leaf_Watered_T6": [ + "DD-WTL-T6_R1", + "DD-WTL-T6_R2", + "DD-WTL-T6_R3" + ], + "Leaf_Watered_T7": [ + "DD-WTL-T7_R1", + "DD-WTL-T7_R2", + "DD-WTL-T7_R3" + ], + "Leaf_Drought_T1": [ + "DD-DTL-T1_R1", + "DD-DTL-T1_R2", + "DD-DTL-T1_R3" + ], + "Leaf_Drought_T2": [ + "DD-DTL-T2_R1", + "DD-DTL-T2_R2", + "DD-DTL-T2_R3" + ], + "Leaf_Drought_T3": [ + "DD-DTL-T3_R1", + "DD-DTL-T3_R2", + "DD-DTL-T3_R3" + ], + "Leaf_Drought_T4": [ + "DD-DTL-T4_R1", + "DD-DTL-T4_R2", + "DD-DTL-T4_R3" + ], + "Leaf_Drought_T5": [ + "DD-DTL-T5_R1", + "DD-DTL-T5_R2", + "DD-DTL-T5_R3" + ], + "Leaf_Drought_T6": [ + "DD-DTL-T6_R1", + "DD-DTL-T6_R2", + "DD-DTL-T6_R3" + ], + "Leaf_Drought_T7": [ + "DD-DTL-T7_R1", + "DD-DTL-T7_R2", + "DD-DTL-T7_R3" + ], + "Apex_Watered_T1": [ + "DD-WTA-T1_R1", + "DD-WTA-T1_R2", + "DD-WTA-T1_R3" + ], + "Apex_Watered_T2": [ + "DD-WTA-T2_R1", + "DD-WTA-T2_R2", + "DD-WTA-T2_R3" + ], + "Apex_Watered_T3": [ + "DD-WTA-T3_R1", + "DD-WTA-T3_R2", + "DD-WTA-T3_R3" + ], + "Apex_Watered_T4": [ + "DD-WTA-T4_R1", + "DD-WTA-T4_R2", + "DD-WTA-T4_R3" + ], + "Apex_Watered_T5": [ + "DD-WTA-T5_R1", + "DD-WTA-T5_R2", + "DD-WTA-T5_R3" + ], + "Apex_Watered_T6": [ + "DD-WTA-T6_R1", + "DD-WTA-T6_R2", + "DD-WTA-T6_R3" + ], + "Apex_Watered_T7": [ + "DD-WTA-T7_R1", + "DD-WTA-T7_R2", + "DD-WTA-T7_R3" + ], + "Apex_Drought_T1": [ + "DD-DTA-T1_R1", + "DD-DTA-T1_R2", + "DD-DTA-T1_R3" + ], + "Apex_Drought_T2": [ + "DD-DTA-T2_R1", + "DD-DTA-T2_R2", + "DD-DTA-T2_R3" + ], + "Apex_Drought_T3": [ + "DD-DTA-T3_R1", + "DD-DTA-T3_R2", + "DD-DTA-T3_R3" + ], + "Apex_Drought_T4": [ + "DD-DTA-T4_R1", + "DD-DTA-T4_R2", + "DD-DTA-T4_R3" + ], + "Apex_Drought_T5": [ + "DD-DTA-T5_R1", + "DD-DTA-T5_R2", + "DD-DTA-T5_R3" + ], + "Apex_Drought_T6": [ + "DD-DTA-T6_R1", + "DD-DTA-T6_R2", + "DD-DTA-T6_R3" + ], + "Apex_Drought_T7": [ + "DD-DTA-T7_R1", + "DD-DTA-T7_R2", + "DD-DTA-T7_R3" + ] + } + } + } + } + } + }, + "cacao_drought_diurnal_atlas_sca": { + "species": "cacao", + "instance_families": [ + "efp_cacao_sca" + ], + "source": "efp", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_cacao_sca", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_cacao_sca", + "view": "Drought Diurnal Atlas" + } + ], + "views": { + "efp_cacao_sca::Drought Diurnal Atlas": { + "frontend": "efp", + "instance": "efp_cacao_sca", + "display_name": "Drought Diurnal Atlas", + "proj_ids": [], + "sample_groups": { + "Med_CTRL": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "Root_Watered_T1": [ + "DD-WTR-T1_R1", + "DD-WTR-T1_R2", + "DD-WTR-T1_R3" + ], + "Root_Watered_T2": [ + "DD-WTR-T2_R1", + "DD-WTR-T2_R2", + "DD-WTR-T2_R3" + ], + "Root_Watered_T3": [ + "DD-WTR-T3_R1", + "DD-WTR-T3_R2", + "DD-WTR-T3_R3" + ], + "Root_Watered_T4": [ + "DD-WTR-T4_R1", + "DD-WTR-T4_R2", + "DD-WTR-T4_R3" + ], + "Root_Watered_T5": [ + "DD-WTR-T5_R1", + "DD-WTR-T5_R2", + "DD-WTR-T5_R3" + ], + "Root_Watered_T6": [ + "DD-WTR-T6_R1", + "DD-WTR-T6_R2", + "DD-WTR-T6_R3" + ], + "Root_Watered_T7": [ + "DD-WTR-T7_R2", + "DD-WTR-T7_R3", + "DD-WTR-T7-R1" + ], + "Root_Drought_T1": [ + "DD-DTR-T1_R1", + "DD-DTR-T1_R2", + "DD-DTR-T1_R3" + ], + "Root_Drought_T2": [ + "DD-DTR-T2_R1", + "DD-DTR-T2_R2", + "DD-DTR-T2_R3" + ], + "Root_Drought_T3": [ + "DD-DTR-T3_R1", + "DD-DTR-T3_R2", + "DD-DTR-T3_R3" + ], + "Root_Drought_T4": [ + "DD-DTR-T4_R1", + "DD-DTR-T4_R2", + "DD-DTR-T4_R3" + ], + "Root_Drought_T5": [ 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"Leaf_Drought_T4": [ + "DD-DTL-T4_R1", + "DD-DTL-T4_R2", + "DD-DTL-T4_R3" + ], + "Leaf_Drought_T5": [ + "DD-DTL-T5_R1", + "DD-DTL-T5_R2", + "DD-DTL-T5_R3" + ], + "Leaf_Drought_T6": [ + "DD-DTL-T6_R1", + "DD-DTL-T6_R2", + "DD-DTL-T6_R3" + ], + "Leaf_Drought_T7": [ + "DD-DTL-T7_R1", + "DD-DTL-T7_R2", + "DD-DTL-T7_R3" + ], + "Apex_Watered_T1": [ + "DD-WTA-T1_R1", + "DD-WTA-T1_R2", + "DD-WTA-T1_R3" + ], + "Apex_Watered_T2": [ + "DD-WTA-T2_R1", + "DD-WTA-T2_R2", + "DD-WTA-T2_R3" + ], + "Apex_Watered_T3": [ + "DD-WTA-T3_R1", + "DD-WTA-T3_R2", + "DD-WTA-T3_R3" + ], + "Apex_Watered_T4": [ + "DD-WTA-T4_R1", + "DD-WTA-T4_R2", + "DD-WTA-T4_R3" + ], + "Apex_Watered_T5": [ + "DD-WTA-T5_R1", + "DD-WTA-T5_R2", + "DD-WTA-T5_R3" + ], + "Apex_Watered_T6": [ + "DD-WTA-T6_R1", + "DD-WTA-T6_R2", + "DD-WTA-T6_R3" + ], + "Apex_Watered_T7": [ + "DD-WTA-T7_R1", + "DD-WTA-T7_R2", + "DD-WTA-T7_R3" + ], + "Apex_Drought_T1": [ + "DD-DTA-T1_R1", + "DD-DTA-T1_R2", + "DD-DTA-T1_R3" + ], + "Apex_Drought_T2": [ + "DD-DTA-T2_R1", + "DD-DTA-T2_R2", + "DD-DTA-T2_R3" + ], + "Apex_Drought_T3": [ + "DD-DTA-T3_R1", + "DD-DTA-T3_R2", + "DD-DTA-T3_R3" + ], + "Apex_Drought_T4": [ + "DD-DTA-T4_R1", + "DD-DTA-T4_R2", + "DD-DTA-T4_R3" + ], + "Apex_Drought_T5": [ + "DD-DTA-T5_R1", + "DD-DTA-T5_R2", + "DD-DTA-T5_R3" + ], + "Apex_Drought_T6": [ + "DD-DTA-T6_R1", + "DD-DTA-T6_R2", + "DD-DTA-T6_R3" + ], + "Apex_Drought_T7": [ + "DD-DTA-T7_R1", + "DD-DTA-T7_R2", + "DD-DTA-T7_R3" + ] + } + } + } + } + } + }, + "cacao_infection": { + "species": "cacao", + "instance_families": [ + "efp_cacao_tc" + ], + "source": "efp", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_cacao_tc", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_cacao_tc", + "view": "Cacao Infection" + } + ], + "views": { + "efp_cacao_tc::Cacao Infection": { + "frontend": "efp", + "instance": "efp_cacao_tc", + "display_name": "Cacao Infection", + "proj_ids": [], + "sample_groups": { + "Med_CTRL": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "NA32_Basal": [ + "basal_N432_rep4", + "basal_NA32_rep1", + "basal_NA32_rep2", + "basal_NA32_rep3", + "basal_NA32_rep5", + "basal_NA32_rep6", + "basal_NA32_rep7", + "basal_NA32_rep8" + ], + "Scavina6_Basal": [ + "basal_SCA6_rep1", + "basal_SCA6_rep2", + "basal_SCA6_rep3", + "basal_SCA6_rep4", + "basal_SCA6_rep5", + "basal_SCA6_rep6", + "basal_SCA6_rep7", + "basal_SCA6_rep8" + ], + "NA32_Control_24h": [ + "NA32_Control_24hr_rep1", + "NA32_Control_24hr_rep2", + "NA32_Control_24hr_rep3", + "NA32_Control_24hr_rep4" + ], + "NA32_Control_6h": [ + "NA32_Control_6hr_rep1", + "NA32_Control_6hr_rep2", + "NA32_Control_6hr_rep3" + ], + "NA32_Control_72h": [ + "NA32_Control_72hr_rep1", + "NA32_Control_72hr_rep2", + "NA32_Control_72hr_rep3", + "NA32_Control_72hr_rep4" + ], + "NA32_Infected_6h": [ + "NA32_Pathogen_6hr_rep1", + "NA32_Pathogen_6hr_rep2", + "NA32_Pathogen_6hr_rep3", + "NA32_Pathogen_6hr_rep4" + ], + "NA32_Infected_24h": [ + "NA32_Pathogen_24hr_rep1", + "NA32_Pathogen_24hr_rep2", + "NA32_Pathogen_24hr_rep3", + "NA32_Pathogen_24hr_rep4" + ], + "NA32_Infected_72h": [ + "NA32_Pathogen_72hr_rep1", + "NA32_Pathogen_72hr_rep2", + "NA32_Pathogen_72hr_rep3", + "NA32_Pathogen_72hr_rep4" + ], + "Scavina6_Control_6h": [ + "SCA6_Control_6hr_rep1", + "SCA6_Control_6hr_rep2", + "SCA6_Control_6hr_rep3", + "SCA6_Control_6hr_rep4" + ], + "Scavina6_Control_24h": [ + "SCA6_Control_24hr_rep1", + "SCA6_Control_24hr_rep2", + "SCA6_Control_24hr_rep3", + "SCA6_Control_24hr_rep4" + ], + "Scavina6_Control_72h": [ + "SCA6_Control_72hr_rep1", + "SCA6_Control_72hr_rep2", + "SCA6_Control_72hr_rep3", + "SCA6_Control_72hr_rep4" + ], + "Scavina6_Infected_6h": [ + "SCA6_Pathogen_6hr_rep1", + "SCA6_Pathogen_6hr_rep2", + "SCA6_Pathogen_6hr_rep3", + "SCA6_Pathogen_6hr_rep4" + ], + "Scavina6_Infected_72h": [ + "SCA6_Pathogen_72hr_rep1", + "SCA6_Pathogen_72hr_rep2", + "SCA6_Pathogen_72hr_rep3", + "SCA6_Pathogen_72hr_rep4" + ] + } + }, + "basal_SCA6_rep8;Med_CTRL": { + "controls": [ + "basal_SCA6_rep8", + "Med_CTRL" + ], + "treatments": { + "Scavina6_Infected_24h": [ + "SCA6_Pathogen_24hr_rep1", + "SCA6_Pathogen_24hr_rep2", + "SCA6_Pathogen_24hr_rep3", + "SCA6_Pathogen_24hr_rep4" + ] + } + } + } + } + } + }, + "cacao_leaf": { + "species": "cacao", + "instance_families": [ + "efp_cacao_tc" + ], + "source": "efp", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_cacao_tc", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_cacao_tc", + "view": "Cacao Leaf" + } + ], + "views": { + "efp_cacao_tc::Cacao Leaf": { + "frontend": "efp", + "instance": "efp_cacao_tc", + "display_name": "Cacao Leaf", + "proj_ids": [], + "sample_groups": { + "Med_CTRL": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "Scavina6_DE": [ + "Sca6_DE_1", + "Sca6_DE_2", + "Sca6_DE_3", + "Sca6_DE_4", + "Sca6_DE_5" + ], + "Scavina6_AB": [ + "Sca6_AB_1", + "Sca6_AB_2", + "Sca6_AB_3", + "Sca6_AB_4", + "Sca6_AB_5" + ], + "Scavina6_C": [ + "Sca6_C_1", + "Sca6_C_2", + "Sca6_C_3", + "Sca6_C_4", + "Sca6_C_5" + ], + "ICS1_AB": [ + "ICS1_AB_1", + "ICS1_AB_2", + "ICS1_AB_3", + "ICS1_AB_4", + "ICS1_AB_5" + ], + "ICS1_C": [ + "ICS1_C_1", + "ICS1_C_2", + "ICS1_C_3", + "ICS1_C_4", + "ICS1_C_5" + ], + "ICS1_DE": [ + "ICS1_DE_1", + "ICS1_DE_2", + "ICS1_DE_3", + "ICS1_DE_4", + "ICS1_DE_5" + ] + } + } + } + } + } + }, + "cacao_meristem_atlas_sca": { + "species": "cacao", + "instance_families": [ + "efp_cacao_sca" + ], + "source": "efp", + "platform": "rna_seq", 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"Biopsy_10", + "Biopsy_14", + "Biopsy_20", + "Biopsy_11", + "Biopsy_22" + ] + } + }, + "AVC_CTRL": { + "controls": [ + "AVC_CTRL" + ], + "treatments": { + "Aorta-[8]": [ + "GSM176016", + "GSM176112", + "GSM176263", + "GSM176264" + ], + "Vena_Cava-[8]": [ + "GSM176038" + ] + } + }, + "DIAPHRAGM_CTRL": { + "controls": [ + "DIAPHRAGM_CTRL" + ], + "treatments": { + "Diaphragm-[3]": [ + "GSM4004", + "GSM4005", + "GSM4006", + "GSM48597" + ] + } + }, + "BRONCHIOLE_CTRL": { + "controls": [ + "BRONCHIOLE_CTRL" + ], + "treatments": { + "Bronchioles-[6]": [ + "GSM226994", + "GSM226995", + "GSM226996" + ] + } + } + } + }, + "efp_human::Nervous": { + "frontend": "efp", + "instance": "efp_human", + "display_name": "Nervous", + "proj_ids": [], + "sample_groups": { + "GSE2361_CTRL": { + "controls": [ + "GSE2361_CTRL" + ], + "treatments": { + "Whole_Brain-[3]": [ + "GSM44690" + ], + "Corpus_Callosum-[3]": [ + "GSM44696" + ], + "Amygdala-[3]": [ + "GSM44694" + ], + "Fetal_Brain-[3]": [ + "GSM44691" + ], 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"4DAP_Whole Seed_R3" + ], + "Seed_6DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation;_PO:0007633_endosperm_development_stages.": [ + "6DAP_Whole Seed_R1", + "6DAP_Whole Seed_R2", + "6DAP_Whole Seed_R3" + ], + "Seed_8DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation;_PO:0007633_endosperm_development_stages.": [ + "8DAP_Whole Seed_R1", + "8DAP_Whole Seed_R2", + "8DAP_Whole Seed_R3" + ], + "Seed_10DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation;_PO:0007633_endosperm_development_stages.": [ + "10DAP_Whole Seed_R1", + "10DAP_Whole Seed_R2", + "10DAP_Whole Seed_R3" + ], + "Seed_12DAP._PO:0009001_fruit;_PO:0001094_coleoptilar_stage;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ + "12DAP_Whole Seed_R1", + "12DAP_Whole Seed_R2", + "12DAP_Whole Seed_R3" + ], + "Seed_14DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ + "14DAP_Whole Seed_R1", + "14DAP_Whole Seed_R2", + "14DAP_Whole Seed_R3" + ], + "Seed_16DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ + "16DAP_Whole Seed_R1", + "16DAP_Whole Seed_R2", + "16DAP_Whole Seed_R3" + ], + "Seed_18DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ + "18DAP_Whole Seed_R1", + "18DAP_Whole Seed_R2", + "18DAP_Whole Seed_R3" + ], + "Pericarp_18DAP._PO:0009084_pericarp;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ + "18DAP_Pericarp_R1", + "18DAP_Pericarp_R2", + "18DAP_Pericarp_R3" + ], + "Seed_20DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007633_endosperm_development_stages.": [ + "20DAP_Whole 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"Coleoptile_6DAS_GH._PO:0025287_seedling_coleoptile;_PO:0007045_coleoptile_emergence.": [ + "6DAS_GH_Coleoptile_R1", + "6DAS_GH_Coleoptile_R2", + "6DAS_GH_Coleoptile_R3" + ], + "Coleoptile_6DAS_Primary_Root._PO:0020127_primary_root;_PO:0007015_radical_emergence.": [ + "6DAS_GH_Primary Root_R1", + "6DAS_GH_Primary Root_R2", + "6DAS_GH_Primary Root_R3" + ], + "Stem_and_SAM_(V1)._PO:0020142_stem_internode;_PO:0020148_shoot_apical_meristem;_PO:0007106_LP.03_three_leaves_visible.": [ + "V1_Stem and SAM_R1", + "V1_Stem and SAM_R2", + "V1_Stem and SAM_R3" + ], + "Stem_and_SAM_(V3)._PO:0020142_stem_internode;_PO:0020148_shoot_apical_meristem;_PO:0007065_LP.05_five_leaves_visible.": [ + "V3_Stem and SAM_R1", + "V3_Stem and SAM_R2", + "V3_Stem and SAM_R3" + ], + "Stem_and_SAM_(V4)._PO:0020148_shoot_apical_meristem;_PO:0020142_internode;_PO:0007123_leaves_visible.": [ + "V4_Stem and SAM_R1", + "V4_Stem and SAM_R2", + "V4_Stem and SAM_R3" + ], + 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"Immature_Tassel_(V13)._PO:0020126_tassel;_PO:0001007_pollen_developmental_stages;_PO:0007104_LP.15_fifteen_leaves_visible.": [ + "V13_Immature Tassel_R1", + "V13_Immature Tassel_R2", + "V13_Immature Tassel_R3" + ], + "Meiotic_Tassel_(V18)._PO:0020126_tassel;_PO:0001009_D_pollen_mother_cell_meiosis_stage;_PO:0007072_LP.18_eighteen_leaves_visible.": [ + "V18_Meiotic Tassel_R1", + "V18_Meiotic Tassel_R2", + "V18_Meiotic Tassel_R3" + ], + "Anthers_(R1)._PO:0006310_tassel_floret;_PO:0009066_anther;_PO:0001007_pollen_developmental_stages.": [ + "R1_Anthers_R1", + "R1_Anthers_R2", + "R1_Anthers_R3" + ], + "Whole_Seedling_(VE)._PO:0006341_primary_shoot;_PO:0007094_LP.01_one_leaf_visible.": [ + "VE_Whole Seedling_R1", + "VE_Whole Seedling_R2", + "VE_Whole Seedling_R3" + ], + "Primary_Root_(VE)._PO:0020127_primary_root;_PO:0007112_1_main_shoot_growth.": [ + "VE_Primary Root_R1", + "VE_Primary Root_R2", + "VE_Primary Root_R3" + ], + "Pooled_Leaves_(V1)._PO:0006339_juvenile_leaf;_PO:0009025_vascular_leaf;_PO:0001052_2_leaf_expansion_stage;_PO:0001053_3_leaf_fully_expanded;_PO:0007106_LP.03_three_leaves_visible.": [ + "V1_Pooled Leaves_R1", + "V1_Pooled Leaves_R2", + "V1_Pooled Leaves_R3" + ], + "Primary_Root_(V1)._PO:0020127_primary_root;_PO:0007106_LP.03_three_leaves_visible.": [ + "V1_GH_Primary Root_R1", + "V1_GH_Primary Root_R2", + "V1_GH_Primary Root_R3" + ], + "Topmost_Leaf_(V3)._PO:0006339_juvenile_leaf;_PO:0009025_vascular_leaf;_PO:0001052_2_leaf_expansion_stage;_PO:0007065_LP.05_five_leaves_visible.": [ + "V3_Topmost Leaf_R1", + "V3_Topmost Leaf_R2", + "V3_Topmost Leaf_R3" + ], + "First_Leaf_(V3)._PO:0006339_juvenile_leaf;_PO:0009025_vascular_leaf;_PO:0001053_3_leaf_fully_expanded;_PO:0007065_LP.05_five_leaves_visible.": [ + "V3_First Leaf and Sheath_R1", + "V3_First Leaf and Sheath_R2", + "V3_First Leaf and Sheath_R3" + ], + "Tip_of_Stage_2_leaf_(V5)._PO:0006339_juvenile_leaf;_PO:0008018_transition_leaf;_PO:0009025_vascular_leaf;_PO:0025142_leaf_tip;_PO:0001052_2_leaf_expansion_stage;_PO:0007063_LP.07_seven_leaves_visible.": [ + "V5_Tip of stage-2 Leaf_R1", + "V5_Tip of stage-2 Leaf_R2", + "V5_Tip of stage-2 Leaf_R3" + ], + "Base_of_Stage_2_leaf_(V5)._PO:0006340_adult_leaf;_PO:0008018_transition_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001052_2_leaf_expansion_stage;_PO:0007063_LP.07_seven_leaves_visible.": [ + "V5_Base of stage-2 Leaf_R1", + "V5_Base of stage-2 Leaf_R2", + "V5_Base of stage-2 Leaf_R3" + ], + "Tip_of_Stage_2_leaf_(V7)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0025142_leaf_tip;_PO:0001052_2_leaf_expansion_stage;_PO:0007101_LP.09_nine_leaves_visible.": [ + "V7_Tip of stage-2 Leaf_R1", + "V7_Tip of stage-2 Leaf_R2", + "V7_Tip of stage-2 Leaf_R3" + ], + "Base_of_Stage_2_leaf_(V7)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001052_2_leaf_expansion_stage;_PO:0007101_LP.09_nine_leaves_visible.": [ + "V7_Base of stage-2 Leaf_R1", + "V7_Base of stage-2 Leaf_R2", + "V7_Base of stage-2 Leaf_R3" + ], + "Eighth_Leaf_(V9)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0001053_3_leaf_fully_expanded;_PO:0007116_LP.11_eleven_leaves_visible.": [ + "V9_Eighth Leaf_R1", + "V9_Eighth Leaf_R2", + "V9_Eighth Leaf_R3" + ], + "Eleventh_Leaf_(V9)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0001052_2_leaf_expansion_stage;_PO:0007116_LP.11_eleven_leaves_visible.": [ + "V9_Eleventh Leaf_R1", + "V9_Eleventh Leaf_R2", + "V9_Eleventh Leaf_R3" + ], + "Thirteenth_Leaf_(V9)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001052_2_leaf_expansion_stage;_PO:0007116_LP.11_eleven_leaves_visible.": [ + "V9_Thirteenth Leaf_R1", + "V9_Thirteenth Leaf_R2", + "V9_Thirteenth Leaf_R3" + ], + 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"Silks_(R1)._PO:0006354_ear_floret;_PO:0009074_style;_PO:0007016_4_flowering.": [ + "R1_Silks_R1", + "R1_Silks_R2", + "R1_Silks_R3" + ], + "Thirteenth_Leaf_(R2)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001053_3_leaf_fully_expanded;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ + "R2_Thirteenth Leaf_R1", + "R2_Thirteenth Leaf_R2", + "R2_Thirteenth Leaf_R3" + ], + "Innermost_Husk_(R1)._PO:0009054_inflorescence_bract;_PO:0020136_Zea_ear;_PO:0007026_FL.00_first_flower(s)_open.": [ + "R1_Innermost Husk_R1", + "R1_Innermost Husk_R2", + "R1_Innermost Husk_R3" + ], + "Innermost_Husk_(R2)._PO:0009054_inflorescence_bract;_PO:0020136_Zea_ear;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ + "R2_Innermost Husk_R1", + "R2_Innermost Husk_R2", + "R2_Innermost Husk_R3" + ], + "Outer_Husk_(R2)._PO:0009054_inflorescence_bract;_PO:0020136_Zea_ear;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ + "R2_Outer Husk_R1", + "R2_Outer Husk_R2", + "R2_Outer 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"20DAP_Endosperm_R2", + "20DAP_Endosperm_R3" + ], + "Endosperm_22DAP._PO:0009089_endosperm;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ + "22DAP_Endosperm_R1", + "22DAP_Endosperm_R2", + "22DAP_Endosperm_R3" + ], + "Endosperm_24DAP._PO:0009089_endosperm;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ + "24DAP_Endosperm_R1", + "24DAP_Endosperm_R2", + "24DAP_Endosperm_R3" + ], + "Seed_2DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation.": [ + "2DAP_Whole Seed_R1", + "2DAP_Whole Seed_R2", + "2DAP_Whole Seed_R3" + ], + "Seed_4DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation.": [ + "4DAP_Whole Seed_R1", + "4DAP_Whole Seed_R2", + "4DAP_Whole Seed_R3" + ], + "Seed_6DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation;_PO:0007633_endosperm_development_stages.": [ + "6DAP_Whole Seed_R1", + "6DAP_Whole Seed_R2", + "6DAP_Whole Seed_R3" + ], + "Seed_8DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation;_PO:0007633_endosperm_development_stages.": [ + "8DAP_Whole Seed_R1", + "8DAP_Whole Seed_R2", + "8DAP_Whole Seed_R3" + ], + "Seed_10DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation;_PO:0007633_endosperm_development_stages.": [ + "10DAP_Whole Seed_R1", + "10DAP_Whole Seed_R2", + "10DAP_Whole Seed_R3" + ], + "Seed_12DAP._PO:0009001_fruit;_PO:0001094_coleoptilar_stage;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ + "12DAP_Whole Seed_R1", + "12DAP_Whole Seed_R2", + "12DAP_Whole Seed_R3" + ], + "Seed_14DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ + "14DAP_Whole Seed_R1", + "14DAP_Whole Seed_R2", + "14DAP_Whole Seed_R3" + ], + "Seed_16DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ + "16DAP_Whole Seed_R1", + "16DAP_Whole Seed_R2", + "16DAP_Whole Seed_R3" + ], + "Seed_18DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ + "18DAP_Whole Seed_R1", + "18DAP_Whole Seed_R2", + "18DAP_Whole Seed_R3" + ], + "Pericarp_18DAP._PO:0009084_pericarp;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ + "18DAP_Pericarp_R1", + "18DAP_Pericarp_R2", + "18DAP_Pericarp_R3" + ], + "Seed_20DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007633_endosperm_development_stages.": [ + "20DAP_Whole Seed_R1", + "20DAP_Whole Seed_R2", + "20DAP_Whole Seed_R3" + ], + "Seed_22DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ + "22DAP_Whole Seed_R1", + "22DAP_Whole Seed_R2", + "22DAP_Whole Seed_R3" + ], + "Seed_24DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ + "24DAP_Whole Seed_R1", + "24DAP_Whole Seed_R2", + "24DAP_Whole Seed_R3" + ] + } + } + } + } + } + }, + "maize_RMA_log": { + "species": "maize", + "instance_families": null, + "source": "legacy_not_in_dropdown", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple_plus_data_call_data_p_val_sample_file_name", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple_plus_data_call_data_p_val_sample_file_name' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_maize", + "used_by": [], + "views": {} + }, + "maize_atlas": { + "species": "maize", + "instance_families": null, + "source": "legacy_not_in_dropdown", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_maize", + "used_by": [], + "views": {} + }, + "maize_atlas_v5": { + "species": "maize", + "instance_families": [ + "efp_maize" + ], + "source": "efp", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_maize", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_maize", + "view": "Hoopes et al Atlas V5" + } + ], + "views": { + "efp_maize::Hoopes et al Atlas V5": { + "frontend": "efp", + "instance": "efp_maize", + "display_name": "Hoopes et al Atlas V5", + "proj_ids": [], + "sample_groups": { + "Med_CTRL": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "Shoot_tip_V5": [ + "SK037__V5_Shoot_tip_R1", + "SK038__V5_Shoot_tip_R2", + "SK039__V5_Shoot_tip_R3" + ], + "Seed_2DAP": [ + "SK106__2DAP_Whole_seed_R1", + "SK107__2DAP_Whole_seed_R2", + "SK108__2DAP_Whole_seed_R3" + ], + "Meiotic_Tassel_V18": [ + "SK076__V18_Meiotic_tassel_R1", + "SK077__V18_Meiotic_tassel_R2", + "SK078__V18_Meiotic_tassel_R3" + ], + "Immature_Tassel_V13": [ + "SK073__V13_Immature_tassel_R1", + "SK074__V13_Immature_tassel_R2", + "SK075__V13_Immature_tassel_R3" + ], + "ThreeDAS-MZEZ": [ + "SS.27__Mz.Ez_3d_R2", + "SS.45__Mz.Ez_3d_R1", + "SS.56__Mz.Ez_3d_R3" + ], + "Internode_24DAP": [ + "PP_33__24_POL_INT_R1", + "PP_34__24_POL_INT_R2" + ], + "V13-BR-Node6": [ + "SS.69__BraceRoot_Node6_abvgrnd_V13_R1", + "SS.74__BraceRoot_Node6_abvgrnd_V13_R2", + "SS.76__BraceRoot_Node6_abvgrnd_V13_R3" + ], + 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"ThreeDAS-DZ": [ + "SS.21__DifferentiationZone_3d_R1", + "SS.28__DifferentiationZone_3d_R3", + "SS.61__DifferentiationZone_3d_R2" + ], + "Internode_18DAP": [ + "PP_25__18_POL_INT_R1", + "PP_26__18_POL_INT_R2" + ], + "Endosperm_12DAP": [ + "SK124__12DAP_Endopsperm_R1", + "SK125__12DAP_Endopsperm_R2", + "SK126__12DAP_Endopsperm_R3" + ], + "Seed_16DAP": [ + "SK133__16DAP_Whole_seed_R1", + "SK134__16DAP_Whole_seed_R2", + "SK135__16DAP_Whole_seed_R3" + ], + "Thirteenth_Leaf_R2": [ + "SK097__R2_Thirteenth_Leaf_R1", + "SK098__R2_Thirteenth_Leaf_R2", + "SK099__R2_Thirteenth_Leaf_R3" + ], + "Endosperm_22DAP": [ + "SK166__22DAP_Endosperm_R1", + "SK167__22DAP_Endosperm_R2", + "SK168__22DAP_Endosperm_R3" + ], + "Leaf_6DAP": [ + "PP.14__6_DAP_POL_LEAF_R2" + ], + "Eleventh_Leaf_V9": [ + "SK064__V9_Eleventh_Leaf_R1", + "SK065__V9_Eleventh_Leaf_R2", + "SK066__V9_Eleventh_Leaf_R3" + ], + "Endosperm_16DAP": [ + "SK136__16DAP_Endosperm_R1", + "SK137__16DAP_Endosperm_R2", + "SK138__16DAP_Endosperm_R3" + ], + "Seed_22DAP": [ + "SK163__22DAP_Whole_Seed_R1", + "SK164__22DAP_Whole_Seed_R2", + "SK165__22DAP_Whole_Seed_R3" + ], + "Base_of_Stage_2_leaf_V5": [ + "SK046__V5_Bottom_of_transition_leaf_R1", + "SK047__V5_Bottom_of_transition_leaf_R2", + "SK048__V5_Bottom_of_transition_leaf_R3" + ], + "Prepollination_Cob_R1": [ + "SK085__R1_Pre_pollination_cob_R1", + "SK086__R1_Pre_pollination_cob_R2", + "SK087__R1_Pre_pollination_cob_R3" + ], + "Seed_8DAP": [ + "SK115__8DAP_Whole_Seed_R1", + "SK116__8DAP_Whole_Seed_R2", + "SK117__8DAP_Whole_Seed_R3" + ], + "V13-CR-Node5": [ + "SS.68__CrownRoot_Node5_V13_R1", + "SS.75__CrownRoot_Node5_V13_R3", + "SS.77__CrownRoot_Node5_V13_R2" + ], + "Topmost_Leaf_V3": [ + "SK034__V3_Topmost_leaf_R1", + "SK035__V3_Topmost_leaf_R2", + "SK036__V3_Topmost_leaf_R3" + ], + "Thirteenth_Leaf_V9": [ + "SK067__V9_Thirteenth_Leaf_R1", + "SK068__V9_Thirteenth_Leaf_R2", + "SK069__V9_Thirteenth_Leaf_R3" + ], + "Endosperm_24DAP": [ + "SK175__24DAP_Endosperm_R1", + "SK176__24DAP_Endosperm_R2", + "SK177__24DAP_Endosperm_R3" + ], + "Anthers_R1": [ + "SK091__R1_Anthers_R1", + "SK092__R1_Anthers_R2", + "SK093__R1_Anthers_R3" + ], + "Base_of_Stage_2_leaf_V7": [ + "SK055__V7_Bottom_of_transition_leaf_R1", + "SK056__V7_Bottom_of_transition_leaf_R2", + "SK057__V7_Bottom_of_transition_leaf_R3" + ], + "Coleoptile_6DAS_GH": [ + "SK004__6_DAS_GH_Coleoptile_R1", + "SK005__6_DAS_GH_Coleoptile_R2", + "SK006__6_DAS_GH_Coleoptile_R3" + ], + "Embryo_20DAP": [ + "SK160__20DAP_Embryo_R1", + "SK161__20DAP_Embryo_R2", + "SK162__20DAP_Embryo_R3" + ], + "Immature_Cob_V18": [ + "SK079__V18_Immature_cob_R1", + "SK080__V18_Immature_cob_R2", + "SK081__V18_Immature_cob_R3" + ], + "Seed_12DAP": [ + "SK121__12DAP_Whole_seed_R1", + "SK122__12DAP_Whole_seed_R2", + "SK123__12DAP_Whole_seed_R3" + ], + "Seed_20DAP": [ + "SK154__20DAP_Whole_Seed_R1", + "SK155__20DAP_Whole_Seed_R2", + "SK156__20DAP_Whole_Seed_R3" + ], + "Pericarp_18DAP": [ + "SK151__18DAP_Pericarp_R1", + "SK152__18DAP_Pericarp_R2", + "SK153__18DAP_Pericarp_R3" + ], + "SevenDAS-PR-Z4": [ + "RA.10__TapRoot_Z4_7d_R2", + "RA.22__TapRoot_Z4_7d_R3", + "RA.23__TapRoot_Z4_7d_R1" + ], + "ThreeDAS-PrimaryRoot": [ + "SS.38__WholeRootSystem_3d_R3", + "SS.39__WholeRootSystem_3d_R1", + "SS.40__WholeRootSystem_3d_R2" + ], + "Seed_18DAP": [ + "SK142__18DAP_Whole_Seed_R1", + "SK144__18DAP_Whole_Seed_R3", + "SK147__18DAP_Whole_Seed_R2" + ], + "Thirteenth_Leaf_VT": [ + "SK082__VT_Thirteenth_Leaf_R1", + "SK083__VT_Thirteenth_Leaf_R2", + "SK084__VT_Thirteenth_Leaf_R3" + ], + "Internode_12DAP": [ + "PP_17__12_POL_INT_R1", + "PP_18__12_POL_INT_R2" + ], + "SevenDAS-SeminalRoots": [ + "SS.25__Seminal_7d_R3", + "SS.44__Seminal_7d_R1" + ], + "Endosperm_18DAP": [ + "SK143__18DAP_Endosperm_R3", + "SK145__18DAP_Endosperm_R1", + "SK146__18DAP_Endosperm_R2" + ], + "SevenDAS-PrimaryRoot": [ + "SS.36__WholePrimaryRoot_7d_R3", + "SS.42__WholePrimaryRoot_7d_R2", + "SS.58__WholePrimaryRoot_7d_R1" + ], + "Internode_6DAP": [ + "PP_10__6_POL_INT_R2", + "PP_9__6_POL_INT_R1" + ], + "ThreeDAS-Stele": [ + "RA.17__Stele_3d_R1", + "RA.6__Stele_3d_R3", + "RA.7__Stele_3d_R2" + ], + "Embryo_16DAP": [ + "SK139__16DAP_Embryo_R1", + "SK140__16DAP_Embryo_R2", + "SK141__16DAP_Embryo_R3" + ], + "Eighth_Leaf_V9": [ + "SK061__V9_Eighth_Leaf_R1", + "SK062__V9_Eighth_Leaf_R2", + "SK063__V9_Eighth_Leaf_R3" + ], + "First_Internode_V5": [ + "SK040__V5_First_elongated_internode_R1", + "SK041__V5_First_elongated_internode_R2", + "SK042__V5_First_elongated_internode_R3" + ], + "Seed_14DAP": [ + "SK127__14DAP_Whole_seed_R1", + "SK128__14DAP_Whole_seed_R2", + "SK129__14DAP_Whole_seed_R3" + ], + "Embryo_24DAP": [ + "SK178__24DAP_Embryo_R1", + "SK179__24DAP_Embryo_R2", + "SK180__24DAP_Embryo_R3" + ], + "Stem_and_SAM_V1": [ + "SK022__V1_4D_PE_Stem_plus_SAM_R1", + "SK023__V1_4D_PE_Stem_plus_SAM_R2", + "SK024__V1_4D_PE_Stem_plus_SAM_R3" + ], + "Stem_and_SAM_V3": [ + "SK028__V3_Stem_and_SAM_R1", + "SK029_2__V3_Stem_and_SAM_R2", + "SK030_2__V3_Stem_and_SAM_R3" + ], + "V7-CR-Node5": [ + "RA.35__CrownRoot_Node5_V7_R1", + "SS.78__CrownRoot_Node5_V7_R2" + ], + "V7-CR-Node4": [ + "SS.65__CrownRoot_Node4_V7_R1", + "SS.66__CrownRoot_Node4_V7_R2", + "SS.73__CrownRoot_Node4_V7_R3" + ], + "Seed_6DAP": [ + "SK112__6DAP_Whole_seed_R1", + "SK113__6DAP_Whole_seed_R2", + "SK114__6DAP_Whole_seed_R3" + ], + "Leaf_18DAP": [ + "PP.29__18_DAP_POL_LEAF_R1", + "PP.30__18_DAP_POL_LEAF_R2" + ], + "Internode_0DAP": [ + "PP1__0_POL_INT_R1", + "PP_2___0_POL_INT_R2" + ], + "Seed_4DAP": [ + "SK109__4DAP_Whole_Seed_R1", + "SK110__4DAP_Whole_Seed_R2", + "SK111__4DAP_Whole_Seed_R3" + ], + "Leaf_24DAP": [ + "PP.37__24_DAP_POL_LEAF_R1", + "PP.38__24_DAP_POL_LEAF_R2" + ], + "Endosperm_14DAP": [ + "SK130__14DAP_Endopsperm_R1", + "SK131__14DAP_Endopsperm_R2", + "SK132__14DAP_Endopsperm_R3" + ], + "Internode_30DAP": [ + "PP_41__30_POL_INT_R1", + "PP_42__30_POL_INT_R2" + ], + "Embryo_18DAP": [ + "SK148__18DAP_Embryo_R1", + "SK149__18DAP_Embryo_R2", + "SK150__18DAP_Embryo_R3" + ], + "Seed_10DAP": [ + "SK118__10DAP_Whole_seed_R1", + "SK119__10DAP_Whole_seed_R2", + "SK120__10DAP_Whole_seed_R3" + ], + "Leaf_12DAP": [ + "PP.21__12_DAP_POL_LEAF_R1", + "PP.22__12_DAP_POL_LEAF_R2" + ], + "Embryo_22DAP": [ + "SK169__22DAP_Embryo_R1", + "SK170__22DAP_Embryo_R2", + "SK171__22DAP_Embryo_R3" + ], + "Leaf_0DAP": [ + "PP.5__0_DAP_POL_LEAF_R1", + "PP.6__0_DAP_POL_LEAF_R2" + ] + } + } + } + } + } + }, + "maize_buell_lab": { + "species": "maize", + "instance_families": [ + "efp_maize" + ], + "source": "efp", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_maize", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_maize", + "view": "Hoopes et al Stress" + }, + { + "frontend": "efp", + "instance": "efp_maize", + "view": "Hoopes et al Atlas" + } + ], + "views": { + "efp_maize::Hoopes et al Stress": { + "frontend": "efp", + "instance": "efp_maize", + "display_name": "Hoopes et al Stress", + "proj_ids": [], + "sample_groups": { + "htcld_ctrl_R1;htcld_ctrl_R2;htcld_ctrl_R3": { + "controls": [ + "htcld_ctrl_R1", + "htcld_ctrl_R2", + "htcld_ctrl_R3" + ], + "treatments": { + "TemperatureStress-Control": [ + "htcld_ctrl_R1", + "htcld_ctrl_R2", + "htcld_ctrl_R3" + ], + "TemperatureStress-Cold": [ + "cold_R1", + "cold_R2", + "cold_R3" + ], + "TemperatureStress-Heat": [ + "heat_R1", + "heat_R2", + "heat_R3" + ] + } + }, + "alb_ctrl_R1;alb_ctrl_R2;alb_ctrl_R3": { + "controls": [ + "alb_ctrl_R1", + "alb_ctrl_R2", + "alb_ctrl_R3" + ], + "treatments": { + "C_graminicola-48hpi": [ + "alb_48h_R2", + "alb_48h_R3" + ], + "C_graminicola-24hpi": [ + "alb_24h_R2", + "alb_24h_R3" + ], + "C_graminicola-0hpi": [ + "alb_ctrl_R1", + "alb_ctrl_R2", + "alb_ctrl_R3" + ] + } + }, + "drght_ctrl_6h_R1;drght_ctrl_6h_R2;drght_ctrl_6h_R3;drght_ctrl_6h_R4": { + "controls": [ + "drght_ctrl_6h_R1", + "drght_ctrl_6h_R2", + "drght_ctrl_6h_R3", + "drght_ctrl_6h_R4" + ], + "treatments": { + "DroughtStress-0MPa-6h": [ + "drght_ctrl_6h_R1", + "drght_ctrl_6h_R2", + "drght_ctrl_6h_R3", + "drght_ctrl_6h_R4" + ], + "DroughtStress-LowMPa-6h": [ + "drght_0.2_6h_R1", + "drght_0.2_6h_R2", + "drght_0.2_6h_R3", + "drght_0.2_6h_R4" + ], + "DroughtStress-VeryLowMPa-6h": [ + "drght_0.8_6h_R1", + "drght_0.8_6h_R2", + "drght_0.8_6h_R3", + "drght_0.8_6h_R4" + ] + } + }, + "gls_us_ctrl_R1;gls_us_ctrl_R2;gls_us_ctrl_R3": { + "controls": [ + "gls_us_ctrl_R1", + "gls_us_ctrl_R2", + "gls_us_ctrl_R3" + ], + "treatments": { + "C_zeina-UpperLeaves": [ + "gls_us_ctrl_R1", + "gls_us_ctrl_R2", + "gls_us_ctrl_R3" + ], + "C_zeina-LowerLeaves": [ + "gls_us_R1", + "gls_us_R2", + "gls_us_R3" + ] + } + }, + "drght_ctrl_24h_R1;drght_ctrl_24h_R2;drght_ctrl_24h_R3;drght_ctrl_24h_R4": { + "controls": [ + "drght_ctrl_24h_R1", + "drght_ctrl_24h_R2", + "drght_ctrl_24h_R3", + "drght_ctrl_24h_R4" + ], + "treatments": { + "DroughtStress-VeryLowMPa-24h": [ + "drght_0.8_24h_R1", + "drght_0.8_24h_R2", + "drght_0.8_24h_R3", + "drght_0.8_24h_R4" + ], + "DroughtStress-LowMPa-24h": [ + "drght_0.2_24h_R1", + "drght_0.2_24h_R2", + "drght_0.2_24h_R3", + "drght_0.2_24h_R4" + ], + "DroughtStress-0MPa-24h": [ + "drght_ctrl_24h_R1", + "drght_ctrl_24h_R2", + "drght_ctrl_24h_R3", + "drght_ctrl_24h_R4" + ] + } + }, + "slt_ctrl_R1;slt_ctrl_R2;slt_ctrl_R3": { + "controls": [ + "slt_ctrl_R1", + "slt_ctrl_R2", + "slt_ctrl_R3" + ], + "treatments": { + "SaltStress-0mM": [ + "slt_ctrl_R1", + "slt_ctrl_R2", + "slt_ctrl_R3" + ], + "SaltStress-200mM": [ + "slt_R1", + "slt_R2", + "slt_R3" + ] + } + } + } + }, + "efp_maize::Hoopes et al Atlas": { + "frontend": "efp", + "instance": "efp_maize", + "display_name": "Hoopes et al Atlas", + "proj_ids": [], + "sample_groups": { + "Med_CTRL": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "Shoot_tip_V5": [ + "SK037__V5_Shoot_tip_R1", + "SK038__V5_Shoot_tip_R2", + "SK039__V5_Shoot_tip_R3" + ], + "Seed_2DAP": [ + "SK106__2DAP_Whole_seed_R1", + "SK107__2DAP_Whole_seed_R2", + "SK108__2DAP_Whole_seed_R3" + ], + "Meiotic_Tassel_V18": [ + "SK076__V18_Meiotic_tassel_R1", + "SK077__V18_Meiotic_tassel_R2", + "SK078__V18_Meiotic_tassel_R3" + ], + "Immature_Tassel_V13": [ + "SK073__V13_Immature_tassel_R1", + "SK074__V13_Immature_tassel_R2", + "SK075__V13_Immature_tassel_R3" + ], + "ThreeDAS-MZEZ": [ + "SS.27__Mz.Ez_3d_R2", + "SS.45__Mz.Ez_3d_R1", + "SS.56__Mz.Ez_3d_R3" + ], + "Internode_24DAP": [ + "PP_33__24_POL_INT_R1", + "PP_34__24_POL_INT_R2" + ], + "V13-BR-Node6": [ + "SS.69__BraceRoot_Node6_abvgrnd_V13_R1", + "SS.74__BraceRoot_Node6_abvgrnd_V13_R2", + "SS.76__BraceRoot_Node6_abvgrnd_V13_R3" + ], + "V7-CR-Nodes1-3": [ + "SS.70__CrownRoot_Nodes_1.3__V7_R1", + "SS.71__CrownRoot_Nodes_1.3__V7_R3" + ], + "Fourth_Internode_V9": [ + "SK058__V9_Fourth_elongated_internode_R1", + "SK059__V9_Fourth_elongated_internode_R2", + "SK060__V9_Fourth_elongated_internode_R3" + ], + "Coleoptile_6DAS_Primary_Root": [ + "SK007__6DAS_GH_Primary_Root_R1", + "SK008__6DAS_GH_Primary_Root_R2", + "SK009__6DAS_GH_Primary_Root_R3" + ], + "SevenDAS-PR-Z1": [ + "RA.2__TapRoot_Z1_7d_R2", + "RA.4__TapRoot_Z1_7d_R1", + "RA.5__TapRoot_Z1_7d_R3" + ], + "Pooled_Leaves_V1": [ + "SK019__V1_4D_PE_Pooled_Leaves_R1", + "SK020__V1_4D_PE_Pooled_Leaves_R2", + "SK021__V1_4D_PE_Pooled_Leaves_R3" + ], + "SevenDAS-PR-Z3": [ + "RA.14__TapRoot_Z3_7d_R1", + "RA.20__TapRoot_Z3_7d_R3", + "RA.21__TapRoot_Z3_7d_R2" + ], + "Immature_Leaf_V9": [ + "SK070__V9_Papery_Leaves_R1", + "SK071__V9_Papery_Leaves_R2", + "SK072__V9_Papery_Leaves_R3" + ], + "Seed_24DAP": [ + "SK172__24DAP_Whole_Seed_R1", + "SK173__24DAP_Whole_Seed_R2", + "SK174__24DAP_Whole_Seed_R3" + ], + "Silks_R1": [ + "SK088__R1_Silks_R1", + "SK089__R1_Silks_R2", + "SK090__R1_Silks_R3" + ], + "Endosperm_20DAP": [ + "SK157__20DAP_Endosperm_R1", + "SK158__20DAP_Endosperm_R2", + "SK159__20DAP_Endosperm_R3" + ], + "SevenDAS-PR-Z2": [ + "RA.15__TapRoot_Z2_7d_R3", + "RA.18__TapRoot_Z2_7d_R1", + "RA.3__TapRoot_Z2_7d_R2" + ], + "Tip_of_Stage_2_leaf_V7": [ + "SK052__V7_Tip_of_transition_leaf_R1", + "SK053__V7_Tip_of_transition_leaf_R2", + "SK054__V7_Tip_of_transition_leaf_R3" + ], + "ThreeDAS-CorticalParenchyma": [ + "RA.13__CortPar_3d_R2", + "RA.8__CortPar_3d_R3", + "RA.9__CortPar_3d_R1" + ], + "Tip_of_Stage_2_leaf_V5": [ + "SK043__V5_Tip_of_Stage_2_Leaf_R1", + "SK044__V5_Tip_of_Stage_2_Leaf_R2", + "SK045__V5_Tip_of_Stage_2_Leaf_R3" + ], + "Leaf_30DAP": [ + "PP.45__30_DAP_POL_LEAF_R1", + "PP.46__30_DAP_POL_LEAF_R2" + ], + "SevenDAS-RootSystem": [ + "SS.22__WholeRootSystem_7d_R2", + "SS.30__WholeRootSystem_7d_R1", + "SS.54__WholeRootSystem_7d_R3" + ], + "ThreeDAS-DZ": [ + "SS.21__DifferentiationZone_3d_R1", + "SS.28__DifferentiationZone_3d_R3", + "SS.61__DifferentiationZone_3d_R2" + ], + "Internode_18DAP": [ + "PP_25__18_POL_INT_R1", + "PP_26__18_POL_INT_R2" + ], + "Endosperm_12DAP": [ + "SK124__12DAP_Endopsperm_R1", + "SK125__12DAP_Endopsperm_R2", + "SK126__12DAP_Endopsperm_R3" + ], + "Seed_16DAP": [ + "SK133__16DAP_Whole_seed_R1", + "SK134__16DAP_Whole_seed_R2", + "SK135__16DAP_Whole_seed_R3" + ], + "Thirteenth_Leaf_R2": [ + "SK097__R2_Thirteenth_Leaf_R1", + "SK098__R2_Thirteenth_Leaf_R2", + "SK099__R2_Thirteenth_Leaf_R3" + ], + "Endosperm_22DAP": [ + "SK166__22DAP_Endosperm_R1", + "SK167__22DAP_Endosperm_R2", + "SK168__22DAP_Endosperm_R3" + ], + "Leaf_6DAP": [ + "PP.14__6_DAP_POL_LEAF_R2" + ], + "Eleventh_Leaf_V9": [ + "SK064__V9_Eleventh_Leaf_R1", + "SK065__V9_Eleventh_Leaf_R2", + "SK066__V9_Eleventh_Leaf_R3" + ], + "Endosperm_16DAP": [ + "SK136__16DAP_Endosperm_R1", + "SK137__16DAP_Endosperm_R2", + "SK138__16DAP_Endosperm_R3" + ], + "Seed_22DAP": [ + "SK163__22DAP_Whole_Seed_R1", + "SK164__22DAP_Whole_Seed_R2", + "SK165__22DAP_Whole_Seed_R3" + ], + 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"Shoots,_after_4_hours_of_water_stress": [ + "Water_stress_shoots_4h_R1", + "Water_stress_shoots_4h_R2", + "Water_stress_shoots_4h_R3" + ], + "Shoots,_after_4_hours_of_salt_stress": [ + "Salinity_stress_shoots_4h_R1", + "Salinity_stress_shoots_4h_R2", + "Salinity_stress_shoots_4h_R3" + ], + "Shoots,_after_4_hours_of_NH4NO3": [ + "NH4NO3_application_shoots_4h_R1", + "NH4NO3_application_shoots_4h_R2", + "NH4NO3_application_shoots_4h_R3" + ] + } + }, + "Control_root_4h_R1;Control_root_4h_R2;Control_root_4h_R3": { + "controls": [ + "Control_root_4h_R1", + "Control_root_4h_R2", + "Control_root_4h_R3" + ], + "treatments": { + "Roots,_control_at_4_hours": [ + "Control_root_4h_R1", + "Control_root_4h_R2", + "Control_root_4h_R3" + ], + "Roots,_after_4_hours_of_water_stress": [ + "Water_stress_root_4h_R1", + "Water_stress_root_4h_R2", + "Water_stress_root_4h_R3" + ], + "Roots,_after_4_hours_of_salt_stress": [ + "Salinity_stress_root_4h_R1", + "Salinity_stress_root_4h_R2", + 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+ "treatments": { + "Spikelets_at_2_days_after_mock_treatment": [ + "Spikelets_2D_Mock_R1", + "Spikelets_2D_Mock_R2" + ], + "Spikelets_at_2_days_after_Fusarium_infection": [ + "Spikelets_2D_Fusarium_graminearum_inoc_R1", + "Spikelets_2D_Fusarium_graminearum_inoc_R2", + "Spikelets_2D_Fusarium_graminearum_inoc_R3" + ] + } + }, + "Rachis_2D_Mock_R1;Rachis_2D_Mock_R2;Rachis_2D_Mock_R3": { + "controls": [ + "Rachis_2D_Mock_R1", + "Rachis_2D_Mock_R2", + "Rachis_2D_Mock_R3" + ], + "treatments": { + "Rachis_at_2_days_after_mock_treatment": [ + "Rachis_2D_Mock_R1", + "Rachis_2D_Mock_R2", + "Rachis_2D_Mock_R3" + ], + "Rachis_at_2_days_after_Fusarium_infection": [ + "Rachis_2D_Fusarium_graminearum_inoc_R1", + "Rachis_2D_Fusarium_graminearum_inoc_R2", + "Rachis_2D_Fusarium_graminearum_inoc_R3" + ] + } + }, + "Spikelets_4D_Mock_R1;Spikelets_4D_Mock_R2;Spikelets_4D_Mock_R3": { + "controls": [ + "Spikelets_4D_Mock_R1", + "Spikelets_4D_Mock_R2", + "Spikelets_4D_Mock_R3" + ], + "treatments": { + "Spikelets_at_4_days_after_mock_treatment": [ + "Spikelets_4D_Mock_R1", + "Spikelets_4D_Mock_R2", + "Spikelets_4D_Mock_R3" + ], + "Spikelets_at_4_days_after_Fusarium_infection": [ + "Spikelets_4D_Fusarium_graminearum_inoc_R1", + "Spikelets_4D_Fusarium_graminearum_inoc_R2" + ] + } + }, + "Rachis_4D_Mock_R1;Rachis_4D_Mock_R2;Rachis_4D_Mock_R3": { + "controls": [ + "Rachis_4D_Mock_R1", + "Rachis_4D_Mock_R2", + "Rachis_4D_Mock_R3" + ], + "treatments": { + "Rachis_at_4_days_after_mock_treatment": [ + "Rachis_4D_Mock_R1", + "Rachis_4D_Mock_R2", + "Rachis_4D_Mock_R3" + ], + "Rachis_at_4_days_after_Fusarium_infection": [ + "Rachis_4D_Fusarium_graminearum_inoc_R1", + "Rachis_4D_Fusarium_graminearum_inoc_R2", + "Rachis_4D_Fusarium_graminearum_inoc_R3" + ] + } + } + } + } + } + }, + "durum_wheat_development": { + "species": "wheat", + "instance_families": [ + "efp_durum_wheat" + ], + "source": "efp", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_durum_wheat", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_durum_wheat", + "view": "Development" + } + ], + "views": { + "efp_durum_wheat::Development": { + "frontend": "efp", + "instance": "efp_durum_wheat", + "display_name": "Development", + "proj_ids": [], + "sample_groups": { + "seedling_shoot_coleo_R1;seedling_shoot_coleo_R2;seedling_shoot_coleo_R3": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "Seedling_coleoptile": [ + "seedling_shoot_coleo_R1", + "seedling_shoot_coleo_R2", + "seedling_shoot_coleo_R3" + ], + "Seedling_root": [ + "primary_root_R1", + "primary_root_R2", + "primary_root_R3" + ], + "First_leaf": [ + "1st_leaf_R1", + "1st_leaf_R2", + "1st_leaf_R3" + ], + "Root_apex,_1st_leaf_stage": [ + "root_tip_R1", + 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{ + "frontend": "eplant", + "instance": "eplant_wheat", + "view": "EarlyStages" + }, + { + "frontend": "eplant", + "instance": "eplant_wheat", + "view": "LateStages" + } + ], + "views": { + "efp_wheat::Developmental Atlas": { + "frontend": "efp", + "instance": "efp_wheat", + "display_name": "Developmental Atlas", + "proj_ids": [], + "sample_groups": { + "Med_CTRL": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "First_leaf_sheath_-_Tillering_stage": [ + "Sample_43A", + "Sample_44A", + "Sample_45A" + ], + "Internode_#2_-_Milk_grain_stage": [ + "Sample_188B", + "Sample_189B" + ], + "Shoot_apical_meristem_-_Seedling_stage": [ + "Sample_19A", + "Sample_20A", + "Sample_21A" + ], + "Grain_-_Milk_grain_stage": [ + "Sample_199A", + "Sample_200A", + "Sample_201A" + ], + "First_leaf_blade_-_Seedling_stage": [ + "Sample_13R1", + "Sample_23", + "Sample_32" + ], + "Flag_leaf_blade_-_Full_boot_": [ + "Sample_94B", + "Sample_95A", + "Sample_96A" + ], + "Awn_-_50_percent_spike": [ + 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"Hexaploid-AC_Mature_embryo" + ], + "Hexaploid-AC_Pre-Embryo": [ + "Hexaploid-AC_Pre-embryo" + ], + "Hexaploid-AC_Transition_Embryo": [ + "Hexaploid-AC_Transition_embryo" + ], + "Hexaploid-AC_Transition_Endosperm": [ + "Hexaploid-AC_Transition_stage_endosperm" + ], + "Hexaploid-AC_Two_Cell_Embryo": [ + "Hexaploid-AC_Two_cell_embryo" + ] + } + }, + "Tetraploid-SF_Med_CTRL": { + "controls": [ + "Tetraploid-SF_Med_CTRL" + ], + "treatments": { + "Tetraploid-SF_Leaf_Early_Seed_Coat": [ + "Tetraploid-SF_Leaf_early_stage_seed_coat" + ], + "Tetraploid-SF_Leaf_Early_Embryo": [ + "Tetraploid-SF_Leaf_early_embryo" + ], + "Tetraploid-SF_Leaf_Late_Embryo": [ + "Tetraploid-SF_Leaf_late_embryo" + ], + "Tetraploid-SF_Leaf_Late_Endosperm": [ + "Tetraploid-SF_Leaf_late_stage_endosperm" + ], + "Tetraploid-SF_Leaf_Middle_Embryo": [ + "Tetraploid-SF_Leaf_middle_embryo" + ], + "Tetraploid-SF_Mature_Embryo": [ + "Tetraploid-SF_Mature_embryo" + ], + "Tetraploid-SF_Pre-Embryo": [ + "Tetraploid-SF_Pre-embryo" + ], + "Tetraploid-SF_Transition_Embryo": [ + "Tetraploid-SF_Transition_embryo" + ], + "Tetraploid-SF_Transition_Endosperm": [ + "Tetraploid-SF_Transition_stage_endosperm" + ], + "Tetraploid-SF_Two_Cell_Embryo": [ + "Tetraploid-SF_Two_cell_embryo" + ] + } + }, + "BB-TA2780_Med_CTRL": { + "controls": [ + "BB-TA2780_Med_CTRL" + ], + "treatments": { + "BB-TA2780_Leaf_Early_Seed_Coat": [ + "BB-TA2780_Leaf_early_stage_seed_coat" + ], + "BB-TA2780_Leaf_Early_Embryo": [ + "BB-TA2780_Leaf_early_embryo" + ], + "BB-TA2780_Leaf_Late_Embryo": [ + "BB-TA2780_Leaf_late_embryo" + ], + "BB-TA2780_Leaf_Late_Endosperm": [ + "BB-TA2780_Leaf_late_stage_endosperm" + ], + "BB-TA2780_Leaf_Middle_Embryo": [ + "BB-TA2780_Leaf_middle_embryo" + ], + "BB-TA2780_Mature_Embryo": [ + "BB-TA2780_Mature_embryo" + ], + "BB-TA2780_Pre-Embryo": [ + "BB-TA2780_Pre-embryo" + ], + "BB-TA2780_Transition_Embryo": [ + "BB-TA2780_Transition_embryo" + ], + "BB-TA2780_Transition_Endosperm": [ + "BB-TA2780_Transition_stage_endosperm" + ], + "BB-TA2780_Two_Cell_Embryo": [ + "BB-TA2780_Two_cell_embryo" + ] + } + }, + "DD-TA101132_Med_CTRL": { + "controls": [ + "DD-TA101132_Med_CTRL" + ], + "treatments": { + "DD-TA101132_Leaf_Early_Embryo": [ + "DD-TA101132_Leaf_early_embryo" + ], + "DD-TA101132_Leaf_Early_Seed_Coat": [ + "DD-TA101132_Leaf_early_stage_seed_coat" + ], + "DD-TA101132_Leaf_Late_Embryo": [ + "DD-TA101132_Leaf_late_embryo" + ], + "DD-TA101132_Leaf_Late_Endosperm": [ + "DD-TA101132_Leaf_late_stage_endosperm" + ], + "DD-TA101132_Leaf_Middle_Embryo": [ + "DD-TA101132_leaf_middle_embryo" + ], + "DD-TA101132_Mature_Embryo": [ + "DD-TA101132_Mature_embryo" + ], + "DD-TA101132_Transition_Embryo": [ + "DD-TA101132_Transition_embryo" + ], + "DD-TA101132_Transition_Endosperm": [ + "DD-TA101132_Transition_stage_endosperm" + ], + "DD-TA101132_Two_Cell_Embryo": [ + "DD-TA101132_Two_cell_embryo" + ], + "DD-TA101132_Pre-Embryo": [ + "DD-TA101132_Pre-embryo" + ] + } + } + } + } + } + }, + "wheat_meiosis": { + "species": "wheat", + "instance_families": [ + "efp_wheat" + ], + "source": "efp", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_wheat", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_wheat", + "view": "Wheat Meiosis" + } + ], + "views": { + "efp_wheat::Wheat Meiosis": { + "frontend": "efp", + "instance": "efp_wheat", + "display_name": "Wheat Meiosis", + "proj_ids": [], + "sample_groups": { + "Med_CTRL": { + "controls": [ + "Med_CTRL" + ], + "treatments": { + "Anther": [ + "Anther_rep1", + "Anther_rep2", + "Anther_rep3" + ], + "Diplotene": [ + "Diplotene_rep1", + "Diplotene_rep2", + "Diplotene_rep3" + ], + "Flagleaf": [ + "FlagLeaf_rep1", + "FlagLeaf_rep2", + "FlagLeaf_rep3" + ], + "Leaf": [ + "Leaf_rep1", + "Leaf_rep2", + "Leaf_rep3" + ], + "Leptotene": [ + "Leptotene_rep1", + "Leptotene_rep2", + "Leptotene_rep3" + ], + "Metaphase_I": [ + "Metaphase-I_rep1", + "Metaphase-I_rep2", + "Metaphase-I_rep3" + ], + "Metaphase_II": [ + "Metaphase-II_rep1", + "Metaphase-II_rep2", + "Metaphase-II_rep3" + ], + "Pachytene": [ + "Pachytene_rep1", + "Pachytene_rep2", + "Pachytene_rep3" + ], + "Pollen": [ + "Pollen_rep1", + "Pollen_rep2", + "Pollen_rep3" + ], + "Pre-meiotic_G2": [ + "Pre-meiotic_G2_rep1", + "Pre-meiotic_G2_rep2", + "Pre-meiotic_G2_rep3" + ], + "Zygotene": [ + "Zygotene_rep1", + "Zygotene_rep2", + "Zygotene_rep3" + ] + } + } + } + } + } + }, + "wheat_root": { + "species": "wheat", + "instance_families": null, + "source": "legacy_not_in_dropdown", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": "efp_wheat", + "used_by": [], + "views": {} + }, + "willow": { + "species": "willow", + "instance_families": null, + "source": "legacy_not_in_dropdown", + "platform": "rna_seq", + "schema_variant": "rnaseq_simple", + "schema_verified": true, + "schema_verification_note": "Schema variant 'rnaseq_simple' derived directly from this database's own sample dump.", + "value_semantics": null, + "gene_id_class": "gene_model", + "gene_id_namespace": null, + "regex_project": null, + "used_by": [], + "views": {} + } + } +} \ No newline at end of file diff --git a/data/efp_info/efp_eplant_species_view_info.json b/data/efp_info/efp_eplant_species_view_info.json index df49bb2d..7e21645e 100644 --- a/data/efp_info/efp_eplant_species_view_info.json +++ b/data/efp_info/efp_eplant_species_view_info.json @@ -21804,40 +21804,1238 @@ "species": "human", "database": "human_developmental", "view_name": "Circulatory Respiratory", - "view_file": null, - "groups": {} + "view_file": "Circulatory_Respiratory", + "groups": { + "GSE1133_CTRL": { + "controls": [ + "GSE1133_CTRL" + ], + "treatments": { + "CD33+_Myeloid_Cell-[1]": [ + "GSM18869", + "GSM18870" + ], + "Fetal_Lung-[1]": [ + "GSM18965", + "GSM18966" + ], + "Heart-[1]": [ + "GSM18951", + "GSM18952" + ], + "Blood-[1]": [ + "GSM18867", + "GSM18868" + ], + "Skin-[1]": [ + "GSM19001", + "GSM19002" + ], + "Bronchial_Epithelial_Cells-[1]": [ + "GSM18993", + "GSM18994" + ], + "CD71+_Early_Erythroid_Cell-[1]": [ + "GSM18907", + "GSM18908" + ], + "Kidney-[1]": [ + "GSM18955", + "GSM18956" + ], + "Lung-[1]": [ + "GSM18949", + "GSM18950" + ], + "Trachea-[1]": [ + "GSM18993", + "GSM18994" + ], + "Placenta-[1]": [ + "GSM18967", + "GSM18968" + ] + } + }, + "GSE3526_CTRL": { + "controls": [ + "GSE3526_CTRL" + ], + "treatments": { + "Ventricle-[5]": [ + "GSM80659", + "GSM80658", + "GSM80657" + ], + "Saphenous_Vein-[5]": [ + "GSM80788", + "GSM80793", + "GSM80789" + ], + "Urethra-[5]": [ + "GSM80913", + "GSM80912", + "GSM80911" + ], + "Bronchus-[5]": [ + "GSM80582", + "GSM80579", + "GSM80578" + ], + "Kidney_Medulla-[5]": [ + "GSM80731", + "GSM80734", + "GSM80733", + "GSM80732" + ], + "Atrium-[5]": [ + "GSM80655", + "GSM80654", + "GSM80698", + "GSM80656" + ], + "Coronary_Artery-[5]": [ + "GSM80609", + "GSM80631", + "GSM80610" + ], + "Lung-[5]": [ + "GSM80710", + "GSM80712", + "GSM80707" + ], + "Kidney_Cortex-[5]": [ + "GSM80689", + "GSM80688", + "GSM80687", + "GSM80686" + ], + "Trachea-[5]": [ + "GSM80890", + "GSM80888", + "GSM80887" + ] + } + }, + "GSE2361_CTRL": { + "controls": [ + "GSE2361_CTRL" + ], + "treatments": { + "Heart-[4]": [ + "GSM44671" + ], + "Kidney-[4]": [ + "GSM44675" + ], + "Skin-[4]": [ + "GSM44686" + ], + "Fetal_Lung-[4]": [ + "GSM44705" + ], + "Bladder-[4]": [ + "GSM44682" + ], + "Lung-[4]": [ + "GSM44704" + ], + "Trachea-[4]": [ + "GSM44688" + ], + "Placenta-[4]": [ + "GSM44681" + ] + } + }, + "PULM_CTRL": { + "controls": [ + "PULM_CTRL" + ], + "treatments": { + "Pulmonary_Trunk-[7]": [ + "GSM101996", + "GSM101997", + "GSM101998", + "GSM101999" + ], + "Pulmonary_Vessels-[7]": [ + "GSM101996", + "GSM101997", + "GSM101998", + "GSM101999" + ] + } + }, + "PLEURA_CTRL": { + "controls": [ + "PLEURA_CTRL" + ], + "treatments": { + "Pleura-[2]": [ + "Biopsy_01", + "Biopsy_13", + "Biopsy_02", + "Biopsy_04", + "Biopsy_06", + "Biopsy_08", + "Biopsy_10", + "Biopsy_14", + "Biopsy_20", + "Biopsy_11", + "Biopsy_22" + ] + } + }, + "AVC_CTRL": { + "controls": [ + "AVC_CTRL" + ], + "treatments": { + "Aorta-[8]": [ + "GSM176016", + "GSM176112", + "GSM176263", + "GSM176264" + ], + "Vena_Cava-[8]": [ + "GSM176038" + ] + } + }, + "DIAPHRAGM_CTRL": { + "controls": [ + "DIAPHRAGM_CTRL" + ], + "treatments": { + "Diaphragm-[3]": [ + "GSM4004", + "GSM4005", + "GSM4006", + "GSM48597" + ] + } + }, + "BRONCHIOLE_CTRL": { + "controls": [ + "BRONCHIOLE_CTRL" + ], + "treatments": { + "Bronchioles-[6]": [ + "GSM226994", + "GSM226995", + "GSM226996" + ] + } + } + } }, { "source": "efp", "species": "human", "database": "human_body_map_2", "view_name": "Illumina Body Map 2 - FPKM", - "view_file": null, - "groups": {} + "view_file": "Illumina_Body_Map_2_-_FPKM", + "groups": { + "Illumina": { + "controls": [ + "CTRL_ILLUMINA" + ], + "treatments": { + "Adrenal_Gland_(male)": [ + "adrenal" + ], + "Liver_(male)": [ + "liver" + ], + "White_Blood_Cells_(male)": [ + "blood" + ], + "Skeletal_Muscle_(male)": [ + "skeletal_muscle" + ], + "Lung_(male)": [ + "lung" + ], + "Heart_(male)": [ + "heart" + ], + "Prostate_(male)": [ + "prostate" + ], + "Testes_(male)": [ + "testes" + ], + "Thyroid_(female)": [ + "thyroid" + ], + "Breast_(female)": [ + "breast" + ], + "Ovary_(female)": [ + "ovary" + ], + "Brain_(female)": [ + "brain" + ], + "Lymph_(female)": [ + "lymph" + ], + "Kidney_(female)": [ + "kidney" + ], + "Colon_(female)": [ + "colon" + ], + "Adipose_(female)": [ + "adipose" + ] + } + } + } }, { "source": "efp", "species": "human", "database": "human_developmental", "view_name": "Nervous", - "view_file": null, - "groups": {} + "view_file": "Nervous", + "groups": { + "GSE2361_CTRL": { + "controls": [ + "GSE2361_CTRL" + ], + "treatments": { + "Whole_Brain-[3]": [ + "GSM44690" + ], + "Corpus_Callosum-[3]": [ + "GSM44696" + ], + "Amygdala-[3]": [ + "GSM44694" + ], + "Fetal_Brain-[3]": [ + "GSM44691" + ], + "Thalamus-[3]": [ + "GSM44698" + ], + "Caudate_Nucleus-[3]": [ + "GSM44695" + ], + "Hippocampus-[3]": [ + "GSM44697" + ], + "Cerebellum-[3]": [ + "GSM44689" + ], + "Spinal_Cord-[3]": [ + "GSM44700" + ] + } + }, + "GSE1133_CTRL": { + "controls": [ + "GSE1133_CTRL" + ], + "treatments": { + "Ciliary_Ganglion-[1]": [ + "GSM19003", + "GSM19004" + ], + "Amygdala-[1]": [ + "GSM18927", + "GSM18928" + ], + "Subthalamic_Nucleus-[1]": [ + "GSM18937", + "GSM18938" + ], + "Fetal_Brain-[1]": [ + "GSM18945", + "GSM18946" + ], + "Thalamus-[1]": [ + "GSM18935", + "GSM18936" + ], + "Trigeminal_Ganglion-[1]": [ + "GSM19005", + "GSM19006" + ], + "Whole_Brain-[1]": [ + "GSM18921", + "GSM18922" + ], + "Olfactory_Bulb-[1]": [ + "GSM19019", + "GSM19020" + ], + "Caudate_Nucleus-[1]": [ + "GSM18919", + "GSM18920" + ], + "Cingulate_Cortex-[1]": [ + "GSM18939", + "GSM18940" + ], + "Globus_Pallidus-[1]": [ + "GSM18913", + "GSM18914" + ], + "Hypothalamus-[1]": [ + "GSM18933", + "GSM18934" + ], + "Prefrontal_Cortex-[1]": [ + "GSM18929", + "GSM18930" + ], + "Parietal_Lobe-[1]": [ + "GSM18923", + "GSM18924" + ], + "Occipital_Lobe-[1]": [ + "GSM18931", + "GSM18932" + ], + "Temporal_Lobe-[1]": [ + "GSM18911", + "GSM18912" + ], + "Cerebellum-[1]": [ + "GSM18917", + "GSM18918" + ], + "Cardiac_Myocyte-[1]": [ + "GSM18969", + "GSM18970" + ], + "Atrioventricular_Node-[1]": [ + "GSM19007", + "GSM19008" + ], + "Dorsal_Root_Ganglion-[1]": [ + "GSM19009", + "GSM19010" + ], + "Cerebellum_Peduncle-[1]": [ + "GSM18915", + "GSM18916" + ], + "Pons-[1]": [ + "GSM18941", + "GSM18942" + ], + "Medulla_Oblongata-[1]": [ + "GSM18925", + "GSM18926" + ], + "Spinal_Cord-[1]": [ + "GSM18943", + "GSM18944" + ], + "SCG-[1]": [ + "GSM19011", + "GSM19012" + ] + } + }, + "GSE3526_CTRL": { + "controls": [ + "GSE3526_CTRL" + ], + "treatments": { + "Corpus_Callosum-[2]": [ + "GSM80622", + "GSM80647", + "GSM80646", + "GSM80620", + "GSM80645", + "GSM80644", + "GSM80628", + "GSM80623", + "GSM80621" + ], + "Amygdala-[2]": [ + "GSM80566", + "GSM80593", + "GSM80592", + "GSM80591", + "GSM80585", + "GSM80568", + "GSM80567", + "GSM80565" + ], + "Subthalamic_Nucleus-[2]": [ + "GSM80857", + "GSM80856", + "GSM80827", + "GSM80854", + "GSM80850", + "GSM80846", + "GSM80829", + "GSM80828" + ], + "Hippocampus-[2]": [ + "GSM80664", + "GSM80682", + "GSM80681", + "GSM80680", + "GSM80665", + "GSM80663", + "GSM80679", + "GSM80668", + "GSM80662" + ], + "Thalamus-[2]": [ + "GSM80839", + "GSM80862", + "GSM80863", + "GSM80852", + "GSM80849", + "GSM80841", + "GSM80840", + "GSM80838" + ], + "Nucleus_Accumbens-[2]": [ + "GSM80573", + "GSM80600", + "GSM80599", + "GSM80598", + "GSM80597", + "GSM80587", + "GSM80575", + "GSM80574", + "GSM80572" + ], + "Trigeminal_Ganglion-[2]": [ + "GSM80906", + "GSM80905", + "GSM80876", + "GSM80895", + "GSM80891", + "GSM80878", + "GSM80877", + "GSM80875" + ], + "Hypothalamus-[2]": [ + "GSM80691", + "GSM80690", + "GSM80684", + "GSM80670", + "GSM80683", + "GSM80669", + "GSM80692", + "GSM80693" + ], + "Putamen-[2]": [ + "GSM80595", + "GSM80571", + "GSM80601", + "GSM80596", + "GSM80594", + "GSM80586", + "GSM80581", + "GSM80570", + "GSM80569" + ], + "Substantia_Nigra-[2]": [ + "GSM80859", + "GSM80858", + "GSM80831", + "GSM80855", + "GSM80847", + "GSM80833", + "GSM80832", + "GSM80830" + ], + "Cerebral_Cortex-[2]": [ + "GSM80650", + "GSM80643", + "GSM80642", + "GSM80640", + "GSM80641", + "GSM80653", + "GSM80652", + "GSM80627", + "GSM80651" + ], + "Frontal_Lobe-[2]": [ + "GSM80660", + "GSM80666", + "GSM80678", + "GSM80677", + "GSM80676", + "GSM80675", + "GSM80667", + "GSM80671", + "GSM80661" + ], + "Parietal_Lobe-[2]": [ + "GSM80746", + "GSM80763", + "GSM80762", + "GSM80744", + "GSM80761", + "GSM80760", + "GSM80752", + "GSM80747", + "GSM80745" + ], + "Occipital_Lobe-[2]": [ + "GSM80773", + "GSM80772", + "GSM80767", + "GSM80756", + "GSM80775", + "GSM80754", + "GSM80766", + "GSM80774" + ], + "Temporal_Lobe-[2]": [ + "GSM80835", + "GSM80860", + "GSM80861", + "GSM80851", + "GSM80848", + "GSM80837", + "GSM80836", + "GSM80834" + ], + "Cerebellum-[2]": [ + "GSM80618", + "GSM80639", + "GSM80638", + "GSM80637", + "GSM80636", + "GSM80626", + "GSM80619", + "GSM80617", + "GSM80616" + ], + "Dorsal_Root_Ganglion-[2]": [ + "GSM80649", + "GSM80611", + "GSM80613", + "GSM80648", + "GSM80630", + "GSM80629", + "GSM80614", + "GSM80612" + ], + "Midbrain-[2]": [ + "GSM80699", + "GSM80715", + "GSM80701", + "GSM80706", + "GSM80705", + "GSM80704", + "GSM80703", + "GSM80702", + "GSM80700" + ], + "VTA-[2]": [ + "GSM80871", + "GSM80907", + "GSM80908", + "GSM80894", + "GSM80892", + "GSM80873", + "GSM80872", + "GSM80870" + ], + "SVN-[2]": [ + "GSM80910", + "GSM80909", + "GSM80879", + "GSM80896", + "GSM80893", + "GSM80881", + "GSM80880" + ], + "Medulla_Oblongata-[2]": [ + "GSM80708", + "GSM80711", + "GSM80724", + "GSM80723", + "GSM80722", + "GSM80721", + "GSM80713", + "GSM80714", + "GSM80709" + ], + "Spinal_Cord-[2]": [ + "GSM80799", + "GSM80798", + "GSM80785", + "GSM80795", + "GSM80794", + "GSM80787", + "GSM80786", + "GSM80784" + ], + "Nodose_Nucleus-[2]": [ + "GSM80769", + "GSM80768", + "GSM80765", + "GSM80755", + "GSM80771", + "GSM80764", + "GSM80770", + "GSM80753" + ] + } + } + } }, { "source": "efp", "species": "human", "database": "human_developmental", "view_name": "Reproductive", - "view_file": null, - "groups": {} + "view_file": "Reproductive", + "groups": { + "GSE3526_CTRL": { + "controls": [ + "GSE3526_CTRL" + ], + "treatments": { + "Pituitary-[2]": [ + "GSM80804", + "GSM80803", + "GSM80802", + "GSM80801 ", + "GSM80819", + "GSM80818", + "GSM80817", + "GSM80800" + ], + "Vulva-[2]": [ + "GSM80897", + "GSM80900", + "GSM80899", + "GSM80898" + ], + "Vagina-[2]": [ + "GSM80874", + "GSM80904", + "GSM80903", + "GSM80902" + ], + "Prostate-[2]": [ + "GSM80824", + "GSM80806", + "GSM80805" + ], + "Nipple-[2]": [ + "GSM80740", + "GSM80743", + "GSM80742", + "GSM80741" + ], + "Testes-[2]": [ + "GSM80868", + "GSM80853", + "GSM80869" + ], + "Mammary_Gland-[2]": [ + "GSM80726", + "GSM80725", + "GSM80716" + ], + "Cervix-[2]": [ + "GSM80615", + "GSM80633", + "GSM80635", + "GSM80634" + ], + "Hypothalamus-[2]": [ + "GSM80691", + "GSM80690", + "GSM80684", + "GSM80670", + "GSM80683", + "GSM80669", + "GSM80692", + "GSM80693" + ], + "Ovary-[2]": [ + "GSM80759", + "GSM80757", + "GSM80758", + "GSM80780" + ], + "Thyroid-[2]": [ + "GSM80867", + "GSM80866", + "GSM80865", + "GSM80864" + ], + "Adrenal_Cortex-[2]": [ + "GSM80608", + "GSM80607", + "GSM80606", + "GSM80605" + ], + "Myometrium-[2]": [ + "GSM80719", + "GSM80718", + "GSM80727", + "GSM80720", + "GSM80717" + ], + "Endometrium-[2]": [ + "GSM80674", + "GSM80673", + "GSM80685", + "GSM80672" + ] + } + }, + "GSE1133_CTRL": { + "controls": [ + "GSE1133_CTRL" + ], + "treatments": { + "Pituitary-[1]": [ + "GSM19021", + "GSM19022" + ], + "Testes-[1]": [ + "GSM18981", + "GSM18982" + ], + "Adrenal_Gland-[1]": [ + "GSM18947", + "GSM18948" + ], + "Prostate-[1]": [ + "GSM18957", + "GSM18958" + ], + "Leydig_Cell-[1]": [ + "GSM18983", + "GSM18984" + ], + "Pancreas-[1]": [ + "GSM18977", + "GSM18978" + ], + "Hypothalamus-[1]": [ + "GSM18933", + "GSM18934" + ], + "Thyroid-[1]": [ + "GSM18961", + "GSM18962" + ], + "Adrenal_Cortex-[1]": [ + "GSM18995", + "GSM18996" + ], + "Fetal_Thyroid-[1]": [ + "GSM18963", + "GSM18964" + ], + "Germ_Cell-[1]": [ + "GSM18985", + "GSM18986" + ], + "Seminiferous_Tubule-[1]": [ + "GSM18989", + "GSM18990" + ], + "Uterus_Corpus-[1]": [ + "GSM19015", + "GSM19016" + ], + "Uterus-[1]": [ + "GSM18959", + "GSM18960" + ], + "Ovary-[1]": [ + "GSM18997", + "GSM18998" + ] + } + }, + "GSE2361_CTRL": { + "controls": [ + "GSE2361_CTRL" + ], + "treatments": { + "Prostate-[3]": [ + "GSM44678" + ], + "Uterus-[3]": [ + "GSM44684" + ], + "Bladder-[3]": [ + "GSM44682" + ], + "Testes-[3]": [ + "GSM44701" + ], + "Pancreas-[3]": [ + "GSM44677" + ], + "Breast-[3]": [ + "GSM44683" + ], + "Thyroid-[3]": [ + "GSM44685" + ], + "Ovary-[3]": [ + "GSM44674" + ], + "Pituitary-[3]": [ + "GSM44699" + ] + } + } + } }, { "source": "efp", "species": "human", "database": "human_developmental", "view_name": "Skeletal Immune Digestive", - "view_file": null, - "groups": {} + "view_file": "Skeletal_Immune_Digestive", + "groups": { + "GSE1133_CTRL": { + "controls": [ + "GSE1133_CTRL" + ], + "treatments": { + "Adipocyte-[1]": [ + "GSM18975", + "GSM18976" + ], + "Smooth_Muscle-[1]": [ + "GSM18971", + "GSM18972" + ], + "Psoas_Muscle-[1]": [ + "GSM19013", + "GSM19014" + ], + "Salivary_Gland-[1]": [ + "GSM18991", + "GSM18992" + ], + "CD56+_NK_Cells-[1]": [ + "GSM18875", + "GSM18876" + ], + "CD19+_B_Cells-[1]": [ + "GSM18881", + "GSM18882" + ], + "CD4+_T_Cells-[1]": [ + "GSM18877", + "GSM18878" + ], + "BDCA4+_Dendritic_Cells-[1]": [ + "GSM18873", + "GSM18874" + ], + "CD14+_Monocytes-[1]": [ + "GSM18871", + "GSM18872" + ], + "CD105+_Endothelial_Cells-[1]": [ + "GSM18883", + "GSM18884" + ], + "Appendix-[1]": [ + "GSM18999", + "GSM19000" + ], + "Bone_Marrow-[1]": [ + "GSM18909", + "GSM18910" + ], + "CD8+_T_Cells-[1]": [ + "GSM18879", + "GSM18880" + ], + "721_B_Lymphocytes-[1]": [ + "GSM18889", + "GSM18890" + ], + "Pancreas-[1]": [ + "GSM18977", + "GSM18978" + ], + "Lymph_Node-[1]": [ + "GSM18903", + "GSM18904" + ], + "Thymus-[1]": [ + "GSM18899", + "GSM18900" + ], + "CD34+-[1]": [ + "GSM18885", + "GSM18886" + ], + "Tonsil-[1]": [ + "GSM18901", + "GSM18902" + ], + "Tongue-[1]": [ + "GSM19017", + "GSM19018" + ], + "Islet_Cell-[1]": [ + "GSM18979", + "GSM18980" + ], + "Liver-[1]": [ + "GSM18953", + "GSM18954" + ], + "Fetal_Liver-[1]": [ + "GSM18905", + "GSM18906" + ] + } + }, + "GSE3526_CTRL": { + "controls": [ + "GSE3526_CTRL" + ], + "treatments": { + "Adipose_Tissue_Omental-[3]": [ + "GSM80561", + "GSM80562", + "GSM80563", + "GSM80564" + ], + "Adipose_Tissue_Subcutaneous-[3]": [ + "GSM80584", + "GSM80589", + "GSM80590" + ], + "Adipose_Tissue-[3]": [ + "GSM80580", + "GSM80583", + "GSM80588" + ], + "Skeletal_Muscle-[3]": [ + "GSM80797", + "GSM80790", + "GSM80791", + "GSM80792", + "GSM80796" + ], + "Bone_Marrow-[3]": [ + "GSM80576", + "GSM80604", + "GSM80577", + "GSM80602", + "GSM80603" + ], + "Salivary_Gland-[3]": [ + "GSM80823", + "GSM80822", + "GSM80821", + "GSM80820" + ], + "Esophagus-[3]": [ + "GSM80697", + "GSM80696", + "GSM80695", + "GSM80694" + ], + "Cardiac_Stomach-[3]": [ + "GSM80783", + "GSM80782", + "GSM80781" + ], + "Liver-[3]": [ + "GSM80730", + "GSM80729", + "GSM80728", + "GSM80739" + ], + "Spleen-[3]": [ + "GSM80826", + "GSM80825", + "GSM80808", + "GSM80807" + ], + "Pharyngeal_Mucosa-[3]": [ + "GSM80748", + "GSM80749", + "GSM80751", + "GSM80750" + ], + "Fundus-[3]": [ + "GSM80812", + "GSM80811", + "GSM80810", + "GSM80809" + ], + "Pylorus-[3]": [ + "GSM80816", + "GSM80815", + "GSM80814", + "GSM80813" + ], + "Lymph_Node-[3]": [ + "GSM80735", + "GSM80738", + "GSM80737", + "GSM80736" + ], + "Cecum-[3]": [ + "GSM80624", + "GSM80632", + "GSM80625" + ], + "Tonsil-[3]": [ + "GSM80901", + "GSM80886", + "GSM80889" + ], + "Oral_Mucosa-[3]": [ + "GSM80779", + "GSM80778", + "GSM80777", + "GSM80776" + ], + "Tongue-[3]": [ + "GSM80845", + "GSM80843", + "GSM80842", + "GSM80844" + ], + "Tongue_superior-[3]": [ + "GSM80885", + "GSM80884", + "GSM80883", + "GSM80882" + ] + } + }, + "GSE2361_CTRL": { + "controls": [ + "GSE2361_CTRL" + ], + "treatments": { + "Skeletal_Muscle-[4]": [ + "GSM44676" + ], + "Bone_Marrow-[4]": [ + "GSM44693" + ], + "Liver-[4]": [ + "GSM44702" + ], + "Fetal_Liver-[4]": [ + "GSM44706" + ], + "Salivary_Gland-[4]": [ + "GSM44687" + ], + "Stomach-[4]": [ + "GSM44703" + ], + "Colon-[4]": [ + "GSM44680" + ], + "Small_Intestine-[4]": [ + "GSM44679" + ], + "Thymus-[4]": [ + "GSM44672" + ], + "Pancreas-[4]": [ + "GSM44677" + ], + "Spleen-[4]": [ + "GSM44673" + ] + } + }, + "PV_CTRL": { + "controls": [ + "PV_CTRL" + ], + "treatments": { + "Pelvis-[7]": [ + "OST1-1", + "OST1-1pr2", + "OST19", + "OST37", + "OST38" + ], + "Vertebral_Column-[7]": [ + "OST12", + "OST29", + "OST31", + "OST33", + "OST34", + "OST35", + "OST39", + "OST3l41", + "OST40", + "OST16", + "OST17", + "OST2-1", + "OST2-2", + "OST21", + "OST23", + "OST26", + "OST27" + ] + } + }, + "COLON_CTRL": { + "controls": [ + "COLON_CTRL" + ], + "treatments": { + "Large_Intestine-[2]": [ + "GSE7307GSM175905", + "GSE7307GSM175983", + "GSE7307GSM175984", + "GSE7307GSM176123" + ] + } + }, + "LYMPH_VESSELS_CTRL": { + "controls": [ + "LYMPH_VESSELS_CTRL" + ], + "treatments": { + "Lymph_Vessels-[6]": [ + "GSE6257GSM143717", + "GSE6257GSM143898", + "GSE6257GSM143900" + ] + } + }, + "PANC_DUCT_CTRL": { + "controls": [ + "PANC_DUCT_CTRL" + ], + "treatments": { + "Pancreatic_Duct-[5]": [ + "GSM490138", + "GSM490139", + "GSM490140", + "GSM490141", + "GSM490142", + "GSM490143", + "GSM490144" + ] + } + } + } } ], "efp_phelipanche": [ diff --git a/data/efp_info/efp_human/Circulatory_Respiratory.xml b/data/efp_info/efp_human/Circulatory_Respiratory.xml new file mode 100644 index 00000000..82068e5f --- /dev/null +++ b/data/efp_info/efp_human/Circulatory_Respiratory.xml @@ -0,0 +1,312 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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b/data/efp_info/efp_human/Reproductive.xml @@ -0,0 +1,308 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/data/efp_info/efp_human/Skeletal_Immune_Digestive.xml b/data/efp_info/efp_human/Skeletal_Immune_Digestive.xml new file mode 100644 index 00000000..3a783d68 --- /dev/null +++ b/data/efp_info/efp_human/Skeletal_Immune_Digestive.xml @@ -0,0 +1,481 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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00000000..b777667f --- /dev/null +++ b/data/efp_info/efp_human/efp_info.xml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/data/efp_info/efp_species_view_info.json b/data/efp_info/efp_species_view_info.json deleted file mode 100644 index 8ea3252b..00000000 --- a/data/efp_info/efp_species_view_info.json +++ /dev/null @@ -1,18424 +0,0 @@ -{ - "actinidia": { - - "data": { - "species": "actinidia", - "views": { - "Bud_Development": { - "database": "actinidia_bud_development", - "view_name": "Bud_Development", - "groups": { - "Nov": { - "controls": [ - "Nov" - ], - "treatments": { - "bud": [ - "Nov", - "Nov_TB", - "Dec", - "Jan", - "Jan_TB", - "Feb", - "Mar", - "Mar_TB", - "Apr", - "May", - "Jun", - "Jul", - "Aug" - ] - } - } - } - }, - "Flower_Fruit_Development": { - "database": "actinidia_flower_fruit_development", - "view_name": "Flower_Fruit_Development", - "groups": { - "flower": { - "controls": [ - "flower" - ], - "treatments": { - "Floral_Bud": [ - "Flower_bud" - ], - "centre": [ - "Flower" - ], - "anther": [ - "Flower" - ], - "petal": [ - "Flower" - ], - "core": [ - "Fruit_T1", - "Fruit_T2", - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA" - ], - "cortex": [ - "Fruit_T1", - "Fruit_T2", - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA" - ], - "flesh": [ - "Fruit_T1", - "Fruit_T2", - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA" - ] - } - } - } - }, - "Postharvest": { - "database": "actinidia_postharvest", - "view_name": "Postharvest", - "groups": { - "Postharvest_Control": { - "controls": [ - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA" - ], - "treatments": { - "core": [ - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA", - "Fruit_231_DAA", - "Fruit_231_DAA_1DAH", - "Fruit_231_DAA_2DAH", - "Fruit_231_DAA_4DAH" - ], - "cortex": [ - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA", - "Fruit_231_DAA", - "Fruit_231_DAA_1DAH", - "Fruit_231_DAA_2DAH", - "Fruit_231_DAA_4DAH" - ], - "flesh": [ - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA", - "Fruit_231_DAA", - "Fruit_231_DAA_1DAH", - "Fruit_231_DAA_2DAH", - "Fruit_231_DAA_4DAH" - ] - } - } - } - }, - "Vegetative_Growth": { - "database": "actinidia_vegetative_growth", - "view_name": "Vegetative_Growth", - "groups": { - "cane": { - "controls": [ - "cane" - ], - "treatments": { - "sink_leaf": [ - "Leaf_sink" - ], - "source_leaf": [ - "Leaf_source" - ], - "shoot": [ - "Shoot" - ], - "cane": [ - "cane" - ], - "root": [ - "Root" - ] - } - } - } - } - } - } - }, - "arabidopsis": { - - "data": { - "species": "arabidopsis", - "views": { - "Abiotic_Stress": { - "database": "atgenexp_stress", - "view_name": "Abiotic_Stress", - "groups": { - "Shoot_0_Hour": { - "controls": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "treatments": { - "Control_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Cold_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Osmotic_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Salt_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Drought_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Genotoxic_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Oxidative_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "UV-B_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Wounding_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Heat_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ] - } - }, - "Root_0_Hour": { - "controls": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - "treatments": { - "Control_Root_0_Hour": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - "Cold_Root_0_Hour": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - "Osmotic_Root_0_Hour": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - "Salt_Root_0_Hour": [ - 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"treatments": { - "Control_Shoot_After_3_Hours": [ - "AtGen_6_0311", - "AtGen_6_0312" - ], - "Cold_Shoot_After_3_Hours": [ - "AtGen_6_1311", - "AtGen_6_1312" - ], - "Osmotic_Shoot_After_3_Hours": [ - "AtGen_6_2311", - "AtGen_6_2312" - ], - "Salt_Shoot_After_3_Hours": [ - "AtGen_6_3311", - "AtGen_6_3312" - ], - "Drought_Shoot_After_3_Hours": [ - "AtGen_6_4311", - "AtGen_6_4312" - ], - "Genotoxic_Shoot_After_3_Hours": [ - "AtGen_6_5311", - "AtGen_6_5312" - ], - "Oxidative_Shoot_After_3_Hours": [ - "AtGen_6_6311", - "AtGen_6_6312" - ], - "UV-B_Shoot_After_3_Hours": [ - "AtGen_6_7311", - "AtGen_6_7312" - ], - "Wounding_Shoot_After_3_Hours": [ - "AtGen_6_8313", - "AtGen_6_8314" - ], - "Heat_Shoot_After_3_Hours": [ - "AtGen_6_9311", - "AtGen_6_9312" - ] - } - }, - "Root_After_3_Hours": { - "controls": [ - "AtGen_6_0321", - "AtGen_6_0322" - ], - "treatments": { - "Control_Root_After_3_Hours": [ - "AtGen_6_0321", - "AtGen_6_0322" - ], - "Cold_Root_After_3_Hours": [ - "AtGen_6_1321", - 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}, - "Root_After_6_Hours": { - "controls": [ - "AtGen_6_0421", - "AtGen_6_0422" - ], - "treatments": { - "Control_Root_After_6_Hours": [ - "AtGen_6_0421", - "AtGen_6_0422" - ], - "Cold_Root_After_6_Hours": [ - "AtGen_6_1421", - "AtGen_6_1422" - ], - "Osmotic_Root_After_6_Hours": [ - "AtGen_6_2421", - "AtGen_6_2422" - ], - "Salt_Root_After_6_Hours": [ - "AtGen_6_3421", - "AtGen_6_3422" - ], - "Drought_Root_After_6_Hours": [ - "AtGen_6_4421", - "AtGen_6_4422" - ], - "Genotoxic_Root_After_6_Hours": [ - "AtGen_6_5421", - "AtGen_6_5422" - ], - "Oxidative_Root_After_6_Hours": [ - "AtGen_6_6421", - "AtGen_6_6422" - ], - "UV-B_Root_After_6_Hours": [ - "AtGen_6_7421", - "AtGen_6_7422" - ], - "Wounding_Root_After_6_Hours": [ - "AtGen_6_8423", - "AtGen_6_8424" - ], - "Heat_Root_After_6_Hours": [ - "AtGen_6_9421", - "AtGen_6_9422" - ] - } - }, - "Shoot_After_12_Hours": { - "controls": [ - "AtGen_6_0511", - "AtGen_6_0512" - ], - "treatments": { - "Control_Shoot_After_12_Hours": [ - "AtGen_6_0511", 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"GSM491677" - ] - } - }, - "GSM237280;GSM237281": { - "controls": [ - "GSM237280", - "GSM237281" - ], - "treatments": { - "Root,_non-selenate_treated_(control)": [ - "GSM237280", - "GSM237281" - ], - "Root,_Selenate_treated": [ - "GSM237282", - "GSM237283" - ] - } - }, - "GSM491666;GSM491667;GSM491668": { - "controls": [ - "GSM491666", - "GSM491667", - "GSM491668" - ], - "treatments": { - "Water_limited_(dry),_Midday": [ - "GSM491669", - "GSM491670", - "GSM491671" - ], - "Well_watered,_Midday_(control)": [ - "GSM491666", - "GSM491667", - "GSM491668" - ] - } - }, - "GSM392492;GSM392493": { - "controls": [ - "GSM392492", - "GSM392493" - ], - "treatments": { - "Shoot,_non-selenate_treated_(control)": [ - "GSM392492", - "GSM392493" - ] - } - }, - "GSM40552": { - "controls": [ - "GSM40552" - ], - "treatments": { - "Non_Stressed_(control),_Total_RNA": [ - "GSM40552" - ], - "Hypoxia_Stress,_Total_RNA": [ - "GSM40553" - ] - } - }, - "GSM40554": { - "controls": [ - "GSM40554" - ], - "treatments": { - "Non_Stressed_(control),_Polysomal_RNA": [ - "GSM40554" - ], - "Hypoxia_Stress,_Polysomal_RNA": [ - "GSM40555" - ] - } - }, - "GSM237292;GSM237293": { - "controls": [ - "GSM237292", - "GSM237293" - ], - "treatments": { - "Shoot,_non-_selenate_treated": [ - "GSM237294", - "GSM237295" - ] - } - }, - "GSM491678;GSM491679;GSM491680": { - "controls": [ - "GSM491678", - "GSM491679", - "GSM491680" - ], - "treatments": { - "Well_watered,_midnight_(control)": [ - "GSM491678", - "GSM491679", - "GSM491680" - ], - "Water_limited_(dry),_midnight": [ - "GSM491681", - "GSM491682", - "GSM491683" - ] - } - } - } - }, - "Biotic_Stress": { - "database": "atgenexp_pathogen", - "view_name": "Biotic_Stress", - "groups": { - "Botrytis_cinerea_at_18_Hours": { - "controls": [ - "CT181-1", - "CT181-2", - "CT182-1" - ], - "treatments": { - "Control_B.c._at_18_Hours": [ - "CT181-1", - "CT181-2", - "CT182-1" - ], - "Treated_B.c._at_18_Hours": [ - "BC181-1", - "BC181-2", - "BC182-1" - ] - } - }, - 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{ - "controls": [ - "JD AT+EO COL WT 24H UNINFECTED", - "JD AT+EO COL WT EXP2 24H UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 24H" - ], - "treatments": { - "Control_E.o._at_24_Hours": [ - "JD AT+EO COL WT 24H UNINFECTED", - "JD AT+EO COL WT EXP2 24H UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 24H" - ], - "Treated_E.o._at_24_Hours": [ - "JD AT+EO COL WT 24H INFECTED", - "JD AT+EO COL WT EXP2 24H INFECTED", - "JD AT+EO TIME EXP3 EO INF 24H" - ] - } - }, - "Erysiphe_orontii_at_48_Hours": { - "controls": [ - "JD AT+EO COL WT 02D UNINFECTED", - "JD AT+EO COL WT EXP2 02D UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 2D" - ], - "treatments": { - "Control_E.o._at_48_Hours": [ - "JD AT+EO COL WT 02D UNINFECTED", - "JD AT+EO COL WT EXP2 02D UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 2D" - ], - "Treated_E.o._at_48_Hours": [ - "JD AT+EO COL WT 02D INFECTED", - "JD AT+EO COL WT EXP2 02D INFECTED", - "JD AT+EO TIME EXP3 EO INF 2D" - ] - } - }, - "Erysiphe_orontii_at_72_Hours": { - "controls": [ - "JD AT+EO COL 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WT EXP2 05D UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 5D" - ], - "treatments": { - "Control_E.o._at_120_Hours": [ - "JD AT+EO COL WT 05D UNINFECTED", - "JD AT+EO COL WT EXP2 05D UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 5D" - ], - "Treated_E.o._at_120_Hours": [ - "JD AT+EO COL WT 05D INFECTED", - "JD AT+EO COL WT EXP2 05D INFECTED", - "JD AT+EO TIME EXP3 EO INF 5D" - ] - } - } - } - }, - "Biotic_Stress_II": { - "database": "atgenexp_pathogen", - "view_name": "Biotic_Stress_II", - "groups": { - "GSM392490;GSM392491": { - "controls": [ - "GSM392490", - "GSM392491" - ], - "treatments": { - "Col_laser_microdissected,_5_d_UI,": [ - "GSM392490", - "GSM392491" - ], - "Col_laser_microdissected,_5_dpi": [ - "GSM392488", - "GSM392489" - ], - "eds16_laser_microdissected,_5_dpi": [ - "GSM392492", - "GSM392493" - ] - } - }, - "GSM392500;GSM392501": { - "controls": [ - "GSM392500", - "GSM392501" - ], - "treatments": { - "Col_whole_leaf_amplified,_5_d_UI": [ - "GSM392500", - "GSM392501" - ], - "Col_whole_leaf_amplified,_5_dpi,": [ - "GSM392498", - "GSM392499" - ], - "Col_leaf_scrape,_5_dpi": [ - "GSM392502", - "GSM392503" - ] - } - }, - "GSM554311_WT_Emwa1_0dpi_rep2": { - "controls": [ - "GSM554311_WT_Emwa1_0dpi_rep2" - ], - "treatments": { - "WT_Emwa1_0dpi_rep1+rep2": [ - "GSM554311_WT_Emwa1_0dpi_rep1", - "GSM554311_WT_Emwa1_0dpi_rep2" - ], - "WT_Emwa1_0.5dpi_rep1+rep2": [ - "GSM554312_WT_Emwa1_0.5dpi_rep2" - ], - "WT_Emwa1_2dpi_rep1+rep2": [ - "GSM554313_WT_Emwa1_2dpi_rep1", - "GSM554313_WT_Emwa1_2dpi_rep2" - ], - "WT_Emwa1_4dpi_rep1+rep2": [ - "GSM554314_WT_Emwa1_4dpi_rep1", - "GSM554314_WT_Emwa1_4dpi_rep2" - ], - "WT_Emwa1_6dpi_rep1+rep2": [ - "GSM554315_WT_Emwa1_6dpi_rep1", - "GSM554315_WT_Emwa1_6dpi_rep2" - ] - } - }, - "GSM554316_rpp4_Emwa1_0dpi_rep1;GSM554316_rpp4_Emwa1_0dpi_rep2": { - "controls": [ - "GSM554316_rpp4_Emwa1_0dpi_rep1", - "GSM554316_rpp4_Emwa1_0dpi_rep2" - ], - "treatments": { - "rpp4_Emwa1_0dpi_rep1+rep2": [ - "GSM554316_rpp4_Emwa1_0dpi_rep1", - "GSM554316_rpp4_Emwa1_0dpi_rep2" - ], - "rpp4_Emwa1_0.5dpi_rep1+rep2": [ - "GSM554317_rpp4_Emwa1_0.5dpi_rep1", - "GSM554317_rpp4_Emwa1_0.5dpi_rep2" - ], - "rpp4_Emwa1_2dpi_rep1+rep2": [ - "GSM554318_rpp4_Emwa1_2dpi_rep1", - "GSM554318_rpp4_Emwa1_2dpi_rep2" - ], - "rpp4_Emwa1_4dpi_rep1+rep2": [ - "GSM554319_rpp4_Emwa1_4dpi_rep1", - "GSM554319_rpp4_Emwa1_4dpi_rep2" - ], - "rpp4_Emwa1_6dpi_rep1+rep2": [ - "GSM554320_rpp4_Emwa1_6dpi_rep1", - "GSM554320_rpp4_Emwa1_6dpi_rep2" - ] - } - }, - "GSM157299;GSM157300;GSM157301": { - "controls": [ - "GSM157299_JPritchard_A-1_CTR_Rep1_ATH1", - "GSM157300_JPritchard_A-2_CTR_Rep2_ATH1", - "GSM157301_Pritchard_A-3_CTR_Rep3_ATH1" - ], - "treatments": { - "Control": [ - "GSM157299_JPritchard_A-1_CTR_Rep1_ATH1", - "GSM157300_JPritchard_A-2_CTR_Rep2_ATH1", - "GSM157301_Pritchard_A-3_CTR_Rep3_ATH1" - ], - "Aphid_infested": [ - "GSM157303_JPritchard_A-5_API_Rep2_ATH1", - "GSM157304_JPritchard_A-6_API_Rep3_ATH1" - ] - } - } - } - }, - "Chemical": { - "database": "atgenexp_hormone", - "view_name": "Chemical", - "groups": { - "Gibberellic_Acid_Inhibitors_at_3_Hours": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "Propiconazole_Treated_at_3_Hours": [ - "RIKEN-GODA3A2", - "RIKEN-GODA3B2" - ], - "Uniconazole_Treated_at_3_Hours": [ - "RIKEN-GODA5A2", - "RIKEN-GODA5B2" - ], - "Paclobutrazol_Treated_at_3_Hours": [ - "RIKEN-GODA11A2", - "RIKEN-GODA11B2" - ], - "Prohexadione_Treated_at_3_Hours": [ - "RIKEN-GODA13A2", - "RIKEN-GODA13B2" - ] - } - }, - "Gibberellic_Acid_Inhibitors_at_12_Hours": { - "controls": [ - "RIKEN-GODA2A2", - "RIKEN-GODA2B2" - ], - "treatments": { - "Control_at_12_Hours": [ - "RIKEN-GODA2A2", - "RIKEN-GODA2B2" - ], - "Propiconazole_Treated_at_12_Hours": [ - "RIKEN-GODA4A2", - "RIKEN-GODA4B2" - ], - "Uniconazole_Treated_at_12_Hours": [ - "RIKEN-GODA6A2", - "RIKEN-GODA6B2" - ], - "Paclobutrazol_Treated_at_12_Hours": [ - "RIKEN-GODA12A2", - "RIKEN-GODA12B2" - ], - "Prohexadione_Treated_at_12_Hours": [ - "RIKEN-GODA14A2", - "RIKEN-GODA14B2" - ] - } - }, - "Auxin_Inhibitors": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "2,4,6-T_Treated": [ - "RIKEN-GODA23A3", - "RIKEN-GODA23B3" - ], - "PCIB_Treated": [ - "RIKEN-GODA24A3", - "RIKEN-GODA24B3" - ], - "TIBA_Treated": [ - "RIKEN-GODA25A3", - "RIKEN-GODA25B3" - ], - "NPA_Treated": [ - "RIKEN-GODA26A3", - "RIKEN-GODA26B3" - ] - } - }, - "Brassinosteroid_Inhibitors_at_3_Hours": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "10uM_Brz220_Treated_at_3_Hours": [ - "RIKEN-GODA7A4", - "RIKEN-GODA7B4" - ], - "3uM_Brz220_Treated_at_3_Hours": [ - "RIKEN-GODA30A4", - "RIKEN-GODA30B4" - ] - } - }, - "Brassinosteroid_Inhibitors_at_12_Hours": { - "controls": [ - "RIKEN-GODA2A2", - "RIKEN-GODA2B2" - ], - "treatments": { - "Control_at_12_Hours": [ - "RIKEN-GODA2A2", - "RIKEN-GODA2B2" - ], - "10uM_Brz91_Treated_at_12_Hours": [ - "RIKEN-GODA10A4", - "RIKEN-GODA10B4" - ] - } - }, - "Ethylene_Inhibitors": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "10uM_AgNO3_Treated": [ - "RIKEN-GODA19A7", - "RIKEN-GODA19B7" - ], - "10uM_AVG_Treated": [ - "RIKEN-GODA20A7", - "RIKEN-GODA20B7" - ] - } - }, - "Cyclohexamide": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "10uM_CHX_Treated": [ - "RIKEN-GODA27A8", - "RIKEN-GODA27B8" - ] - } - }, - "Proteasome_Inhibitor_MG13": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "10uM_MG132_Treated": [ - "RIKEN-GODA22A9", - "RIKEN-GODA22B9" - ] - } - }, - "Photosynthesis_Inhibitor_PN08_at_3_Hours": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "1uM_PNO8_Treated_at_3_Hours": [ - "RIKEN-GODA15A5", - "RIKEN-GODA15B5" - ], - "10uM_PNO8_Treated_at_3_Hours": [ - "RIKEN-GODA29A5", - "RIKEN-GODA29B5" - ] - } - }, - "Photosynthesis_Inhibitor_PN08_at_12_Hours": { - "controls": [ - "RIKEN-GODA2A2", - "RIKEN-GODA2B2" - ], - "treatments": { - "Control_at_12_Hours": [ - "RIKEN-GODA2A2", - "RIKEN-GODA2B2 " - ], - "1uM_PNO8_Treated_at_12_Hours": [ - "RIKEN-GODA16A5", - "RIKEN-GODA16B5" - ] - } - }, - "Ibuprofen,_Salycylic_Acid,_and_Daminozide": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "Ibuprofen_Treated": [ - "RIKEN-GODA17AH", - "RIKEN-GODA17BH" - ], - "Salicylic_Acid_Treated": [ - "RIKEN-GODA21AH", - "RIKEN-GODA21BH" - ], - "Daminozide_Treated": [ - "RIKEN-GODA18AH", - "RIKEN-GODA18BH" - ] - } - } - } - }, - "DNA_Damage": { - "database": "dna_damage", - "view_name": "DNA_Damage", - "groups": { - "col-0_rep1_20min_minus_Y;col-0_rep2_20min_minus_Y": { - "controls": [ - "col-0_rep1_20min_minus_Y", - "col-0_rep2_20min_minus_Y" - ], - "treatments": { - "Y+_Col-0_20min": [ - "col-0_rep1_20min_plus_Y", - "col-0_rep2_20min_plus_Y" - ], - "Y-_Col-0_20min": [ - "col-0_rep1_20min_minus_Y", - "col-0_rep2_20min_minus_Y" - ] - } - }, - "col-0_rep1_90min_minus_Y;col-0_rep2_90min_minus_Y": { - "controls": [ - "col-0_rep1_90min_minus_Y", - "col-0_rep2_90min_minus_Y" - ], - "treatments": { - "Y+_Col-0_90min": [ - "col-0_rep1_90min_plus_Y", - "col-0_rep2_90min_plus_Y" - ], - "Y-_Col-0_90min": [ - "col-0_rep1_90min_minus_Y", - "col-0_rep2_90min_minus_Y" - ] - } - }, - "col-0_rep1_3hr_minus_Y;col-0_rep2_3hr_minus_Y": { - "controls": [ - "col-0_rep1_3hr_minus_Y", - "col-0_rep2_3hr_minus_Y" - ], - "treatments": { - "Y+_Col-0_3h": [ - "col-0_rep1_3hr_plus_Y", - "col-0_rep2_3hr_plus_Y" - ], - "Y-_Col-0_3h": [ - "col-0_rep1_3hr_minus_Y", - "col-0_rep2_3hr_minus_Y" - ] - } - }, - "col-0_rep1_6hr_minus_Y;col-0_rep2_6hr_minus_Y": { - "controls": [ - "col-0_rep1_6hr_minus_Y", - "col-0_rep2_6hr_minus_Y" - ], - "treatments": { - "Y+_Col-0_6h": [ - "col-0_rep1_6hr_plus_Y", - "col-0_rep2_6hr_plus_Y" - ], - "Y-_Col-0_6h": [ - "col-0_rep1_6hr_minus_Y", - "col-0_rep2_6hr_minus_Y" - ] - } - }, - "col-0_rep1_12hr_minus_Y;col-0_rep2_12hr_minus_Y": { - "controls": [ - "col-0_rep1_12hr_minus_Y", - "col-0_rep2_12hr_minus_Y" - ], - "treatments": { - "Y+_Col-0_12h": [ - "col-0_rep1_12hr_plus_Y", - "col-0_rep2_12hr_plus_Y" - ], - "Y-_Col-0_12h": [ - "col-0_rep1_12hr_minus_Y", - "col-0_rep2_12hr_minus_Y" - ] - } - }, - "col-0_rep1_24hr_minus_Y;col-0_rep2_24hr_minus_Y": { - "controls": [ - "col-0_rep1_24hr_minus_Y", - "col-0_rep2_24hr_minus_Y" - ], - "treatments": { - "Y+_Col-0_24h": [ - "col-0_rep1_24hr_plus_Y", - "col-0_rep2_24hr_plus_Y" - ], - "Y-_Col-0_24h": [ - "col-0_rep1_24hr_minus_Y", - "col-0_rep2_24hr_minus_Y" - ] - } - }, - "sog1-1_rep1_20min_minus_Y;sog1-1_rep2_20min_minus_Y": { - "controls": [ - "sog1-1_rep1_20min_minus_Y", - "sog1-1_rep2_20min_minus_Y" - ], - "treatments": { - "Y+_sog1-1_20min": [ - "sog1-1_rep1_20min_plus_Y", - "sog1-1_rep2_20min_plus_Y" - ], - "Y-_sog1-1_20min": [ - "sog1-1_rep1_20min_minus_Y", - "sog1-1_rep2_20min_minus_Y" - ] - } - }, - "sog1-1_rep1_90min_minus_Y;sog1-1_rep2_90min_minus_Y": { - "controls": [ - "sog1-1_rep1_90min_minus_Y", - "sog1-1_rep2_90min_minus_Y" - ], - "treatments": { - "Y+_sog1-1_90min": [ - "sog1-1_rep1_90min_plus_Y", - "sog1-1_rep2_90min_plus_Y" - ], - "Y-_sog1-1_90min": [ - "sog1-1_rep1_90min_minus_Y", - "sog1-1_rep2_90min_minus_Y" - ] - } - }, - "sog1-1_rep1_3hr_minus_Y;sog1-1_rep2_3hr_minus_Y": { - "controls": [ - "sog1-1_rep1_3hr_minus_Y", - "sog1-1_rep2_3hr_minus_Y" - ], - "treatments": { - "Y+_sog1-1_3h": [ - "sog1-1_rep1_3hr_plus_Y", - "sog1-1_rep2_3hr_plus_Y" - ], - "Y-_sog1-1_3h": [ - "sog1-1_rep1_3hr_minus_Y", - "sog1-1_rep2_3hr_minus_Y" - ] - } - }, - "sog1-1_rep1_6hr_minus_Y;sog1-1_rep2_6hr_minus_Y": { - "controls": [ - "sog1-1_rep1_6hr_minus_Y", - "sog1-1_rep2_6hr_minus_Y" - ], - "treatments": { - "Y+_sog1-1_6h": [ - "sog1-1_rep1_6hr_plus_Y", - "sog1-1_rep2_6hr_plus_Y" - ], - "Y-_sog1-1_6h": [ - "sog1-1_rep1_6hr_minus_Y", - "sog1-1_rep2_6hr_minus_Y" - ] - } - }, - "sog1-1_rep1_12hr_minus_Y;sog1-1_rep2_12hr_minus_Y": { - "controls": [ - "sog1-1_rep1_12hr_minus_Y", - "sog1-1_rep2_12hr_minus_Y" - ], - "treatments": { - "Y+_sog1-1_12h": [ - "sog1-1_rep1_12hr_plus_Y", - "sog1-1_rep2_12hr_plus_Y" - ], - "Y-_sog1-1_12h": [ - "sog1-1_rep1_12hr_minus_Y", - "sog1-1_rep2_12hr_minus_Y" - ] - } - }, - "sog1-1_rep1_24hr_minus_Y;sog1-1_rep2_24hr_minus_Y": { - "controls": [ - "sog1-1_rep1_24hr_minus_Y", - "sog1-1_rep2_24hr_minus_Y" - ], - "treatments": { - "Y+_sog1-1_24h": [ - "sog1-1_rep1_24hr_plus_Y", - "sog1-1_rep2_24hr_plus_Y" - ], - "Y-_sog1-1_24h": [ - "sog1-1_rep1_24hr_minus_Y", - "sog1-1_rep2_24hr_minus_Y" - ] - } - } - } - }, - "Development_RMA": { - "database": "atgenexp", - "view_name": "Development_RMA", - "groups": { - "CTRL_7": { - "controls": [ - "ATGE_CTRL_7" - ], - "treatments": { - "1st_Node": [ - "ATGE_28_A2", - "ATGE_28_B2", - "ATGE_28_C2" - ], - "Flower_Stage_12,Stamens": [ - "ATGE_36_A", - "ATGE_36_B", - "ATGE_36_C" - ], - "Cauline_Leaf": [ - "ATGE_26_A", - "ATGE_26_B", - "ATGE_26_C" - ], - "Cotyledon": [ - "ATGE_1_A", - "ATGE_1_B", - "ATGE_1_C" - ], - "Root": [ - "ATGE_9_A", - "ATGE_9_B", - "ATGE_9_C", - "ATGE_3_A", - "ATGE_3_B", - "ATGE_3_C" - ], - "Entire_Rosette_After_Transition_to_Flowering": [ - "ATGE_23_A", - "ATGE_23_B", - "ATGE_23_C" - ], - "Flower_Stage_9": [ - "ATGE_31_A2", - "ATGE_31_B2", - "ATGE_31_C2" - ], - "Flower_Stage_10/11": [ - "ATGE_32_A2", - "ATGE_32_B2", - "ATGE_32_C2" - ], - "Flower_Stage_12": [ - "ATGE_33_A", - "ATGE_33_B", - "ATGE_33_C" - ], - "Flower_Stage_15": [ - "ATGE_39_A", - "ATGE_39_B", - "ATGE_39_C" - ], - "Flower_Stage_12,_Carpels": [ - "ATGE_37_A", - "ATGE_37_B", - "ATGE_37_C" - ], - "Flower_Stage_12,_Petals": [ - "ATGE_35_A", - "ATGE_35_B", - "ATGE_35_C" - ], - "Flower_Stage_12,_Sepals": [ - "ATGE_34_A", - "ATGE_34_B", - "ATGE_34_C" - ], - "Flower_Stage_15,_Carpels": [ - "ATGE_45_A", - "ATGE_45_B", - "ATGE_45_C" - ], - "Flower_Stage_15,_Petals": [ - "ATGE_42_B", - "ATGE_42_C", - "ATGE_42_D" - ], - "Flower_Stage_15,_Sepals": [ - "ATGE_41_A", - "ATGE_41_B", - "ATGE_41_C" - ], - "Flower_Stage_15,_Stamen": [ - "ATGE_43_A", - "ATGE_43_B", - "ATGE_43_C" - ], - "Flowers_Stage_15,_Pedicels": [ - "ATGE_40_A", - "ATGE_40_B", - "ATGE_40_C" - ], - "Leaf_1_+_2": [ - "ATGE_5_A", - "ATGE_5_B", - "ATGE_5_C" - ], - "Leaf_7,_Petiole": [ - "ATGE_19_A", - "ATGE_19_B", - "ATGE_19_C" - ], - "Leaf_7,_Distal_Half": [ - "ATGE_21_A", - "ATGE_21_B", - "ATGE_21_C" - ], - "Leaf_7,_Proximal_Half": [ - "ATGE_20_A", - "ATGE_20_B", - "ATGE_20_C" - ], - "Hypocotyl": [ - "ATGE_2_A", - "ATGE_2_B", - "ATGE_2_C" - ], - "Rosette_Leaf_2": [ - "ATGE_12_A", - "ATGE_12_B", - "ATGE_12_C" - ], - "Rosette_Leaf_4": [ - "ATGE_13_A", - "ATGE_13_B", - "ATGE_13_C" - ], - "Rosette_Leaf_6": [ - "ATGE_14_A", - "ATGE_14_B", - "ATGE_14_C" - ], - "Rosette_Leaf_8": [ - "ATGE_15_A", - "ATGE_15_B", - "ATGE_15_C" - ], - "Rosette_Leaf_10": [ - "ATGE_16_A", - "ATGE_16_B", - "ATGE_16_C" - ], - "Rosette_Leaf_12": [ - "ATGE_17_A", - "ATGE_17_B", - "ATGE_17_C" - ], - "Senescing_Leaf": [ - "ATGE_25_A", - "ATGE_25_B", - "ATGE_25_C" - ], - "Shoot_Apex,_Inflorescence": [ - "ATGE_29_A2", - "ATGE_29_B2", - "ATGE_29_C2" - ], - "Shoot_Apex,_Transition": [ - "ATGE_8_A", - "ATGE_8_B", - "ATGE_8_C" - ], - "Shoot_Apex,_Vegetative": [ - "ATGE_6_A", - "ATGE_6_B", - "ATGE_6_C" - ], - "Stem,_2nd_Internode": [ - "ATGE_27_A", - "ATGE_27_B", - "ATGE_27_C" - ], - "Mature_Pollen": [ - "ATGE_73_A", - "ATGE_73_B", - "ATGE_73_C" - ], - "Seeds_Stage_3_w/_Siliques": [ - "ATGE_76_A", - "ATGE_76_B", - "ATGE_76_C" - ], - "Seeds_Stage_4_w/_Siliques": [ - "ATGE_77_D", - "ATGE_77_E", - "ATGE_77_F" - ], - "Seeds_Stage_5_w/_Siliques": [ - "ATGE_78_D", - "ATGE_78_E", - "ATGE_78_F" - ], - "Seeds_Stage_6_w/o_Siliques": [ - "ATGE_79_A", - "ATGE_79_B", - "ATGE_79_C" - ], - "Seeds_Stage_7_w/o_Siliques": [ - "ATGE_81_A", - "ATGE_81_B", - "ATGE_81_C" - ], - "Seeds_Stage_8_w/o_Siliques": [ - "ATGE_82_A", - "ATGE_82_B", - "ATGE_82_C" - ], - "Seeds_Stage_9_w/o_Siliques": [ - "ATGE_83_A", - "ATGE_83_B", - "ATGE_83_C" - ], - "Seeds_Stage_10_w/o_Siliques": [ - "ATGE_84_A", - "ATGE_84_B", - "ATGE_84_D" - ], - "Vegetative_Rosette": [ - "ATGE_89_A", - "ATGE_89_B", - "ATGE_89_C" - ] - } - } - } - }, - "Developmental_Map": { - "database": "atgenexp_plus", - "view_name": "Developmental_Map", - "groups": { - "CTRL_7": { - "controls": [ - "ATGE_CTRL_7" - ], - "treatments": { - "Dry_seed": [ - "RIKEN-NAKABAYASHI1A", - "RIKEN-NAKABAYASHI1B" - ], - "Imbibed_seed,_24_h": [ - "RIKEN-NAKABAYASHI2A", - "RIKEN-NAKABAYASHI2B" - ], - "1st_Node": [ - "ATGE_28_A2", - "ATGE_28_B2", - "ATGE_28_C2" - ], - "Flower_Stage_12,_Stamens": [ - "ATGE_36_A", - "ATGE_36_B", - "ATGE_36_C" - ], - "Cauline_Leaf": [ - "ATGE_26_A", - "ATGE_26_B", - "ATGE_26_C" - ], - "Cotyledon": [ - "ATGE_1_A", - "ATGE_1_B", - "ATGE_1_C" - ], - "Root": [ - "ATGE_9_A", - "ATGE_9_B", - "ATGE_9_C", - "ATGE_3_A", - "ATGE_3_B", - "ATGE_3_C" - ], - "Entire_Rosette_After_Transition_to_Flowering": [ - "ATGE_23_A", - "ATGE_23_B", - "ATGE_23_C" - ], - "Flower_Stage_9": [ - "ATGE_31_A2", - "ATGE_31_B2", - "ATGE_31_C2" - ], - "Flower_Stage_10/11": [ - "ATGE_32_A2", - "ATGE_32_B2", - "ATGE_32_C2" - ], - "Flower_Stage_12": [ - "ATGE_33_A", - "ATGE_33_B", - "ATGE_33_C" - ], - "Flower_Stage_15": [ - "ATGE_39_A", - "ATGE_39_B", - "ATGE_39_C" - ], - "Flower_Stage_12,_Carpels": [ - "ATGE_37_A", - "ATGE_37_B", - "ATGE_37_C" - ], - "Flower_Stage_12,_Petals": [ - "ATGE_35_A", - "ATGE_35_B", - "ATGE_35_C" - ], - "Flower_Stage_12,_Sepals": [ - "ATGE_34_A", - "ATGE_34_B", - "ATGE_34_C" - ], - "Flower_Stage_15,_Carpels": [ - "ATGE_45_A", - "ATGE_45_B", - "ATGE_45_C" - ], - "Flower_Stage_15,_Petals": [ - "ATGE_42_B", - "ATGE_42_C", - "ATGE_42_D" - ], - "Flower_Stage_15,_Sepals": [ - "ATGE_41_A", - "ATGE_41_B", - "ATGE_41_C" - ], - "Flower_Stage_15,_Stamen": [ - "ATGE_43_A", - "ATGE_43_B", - "ATGE_43_C" - ], - "Flowers_Stage_15,_Pedicels": [ - "ATGE_40_A", - "ATGE_40_B", - "ATGE_40_C" - ], - "Leaf_1_+_2": [ - "ATGE_5_A", - "ATGE_5_B", - "ATGE_5_C" - ], - "Leaf_7,_Petiole": [ - "ATGE_19_A", - "ATGE_19_B", - "ATGE_19_C" - ], - "Leaf_7,_Distal_Half": [ - "ATGE_21_A", - "ATGE_21_B", - "ATGE_21_C" - ], - "Leaf_7,_Proximal_Half": [ - "ATGE_20_A", - "ATGE_20_B", - "ATGE_20_C" - ], - "Hypocotyl": [ - "ATGE_2_A", - "ATGE_2_B", - "ATGE_2_C" - ], - "Rosette_Leaf_2": [ - "ATGE_12_A", - "ATGE_12_B", - "ATGE_12_C" - ], - "Rosette_Leaf_4": [ - "ATGE_13_A", - "ATGE_13_B", - "ATGE_13_C" - ], - "Rosette_Leaf_6": [ - "ATGE_14_A", - "ATGE_14_B", - "ATGE_14_C" - ], - "Rosette_Leaf_8": [ - "ATGE_15_A", - "ATGE_15_B", - "ATGE_15_C" - ], - "Rosette_Leaf_10": [ - "ATGE_16_A", - "ATGE_16_B", - "ATGE_16_C" - ], - "Rosette_Leaf_12": [ - "ATGE_17_A", - "ATGE_17_B", - "ATGE_17_C" - ], - "Senescing_Leaf": [ - "ATGE_25_A", - "ATGE_25_B", - "ATGE_25_C" - ], - "Shoot_Apex,_Inflorescence": [ - "ATGE_29_A2", - "ATGE_29_B2", - "ATGE_29_C2" - ], - "Shoot_Apex,_Transition": [ - "ATGE_8_A", - "ATGE_8_B", - "ATGE_8_C" - ], - "Shoot_Apex,_Vegetative": [ - "ATGE_6_A", - "ATGE_6_B", - "ATGE_6_C" - ], - "Stem,_2nd_Internode": [ - "ATGE_27_A", - "ATGE_27_B", - "ATGE_27_C" - ], - "Mature_Pollen": [ - "ATGE_73_A", - "ATGE_73_B", - "ATGE_73_C" - ], - "Seeds_Stage_3_w/_Siliques": [ - "ATGE_76_A", - "ATGE_76_B", - "ATGE_76_C" - ], - "Seeds_Stage_4_w/_Siliques": [ - "ATGE_77_D", - "ATGE_77_E", - "ATGE_77_F" - ], - "Seeds_Stage_5_w/_Siliques": [ - "ATGE_78_D", - "ATGE_78_E", - "ATGE_78_F" - ], - "Seeds_Stage_6_w/o_Siliques": [ - "ATGE_79_A", - "ATGE_79_B", - "ATGE_79_C" - ], - "Seeds_Stage_7_w/o_Siliques": [ - "ATGE_81_A", - "ATGE_81_B", - "ATGE_81_C" - ], - "Seeds_Stage_8_w/o_Siliques": [ - "ATGE_82_A", - "ATGE_82_B", - "ATGE_82_C" - ], - "Seeds_Stage_9_w/o_Siliques": [ - "ATGE_83_A", - "ATGE_83_B", - "ATGE_83_C" - ], - "Seeds_Stage_10_w/o_Siliques": [ - "ATGE_84_A", - "ATGE_84_B", - "ATGE_84_D" - ], - "Vegetative_Rosette": [ - "ATGE_89_A", - "ATGE_89_B", - "ATGE_89_C" - ] - } - } - } - }, - "Developmental_Mutants": { - "database": "atgenexp_plus", - "view_name": "Developmental_Mutants", - "groups": { - "GSM757891;GSM757892;GSM757893": { - "controls": [ - "GSM757891", - "GSM757892", - "GSM757893" - ], - "treatments": { - "gl3_mutant": [ - "GSM1153854", - "GSM1153855", - "GSM1153856" - ], - "wer_mutant": [ - "GSM1153866", - "GSM1153867", - "GSM1153868" - ], - "ttg2_cpc_mutant": [ - "GSM1153848", - "GSM1153849", - "GSM1153850" - ], - "cow1_mutant": [ - "GSM757834", - "GSM757835", - "GSM757836" - ], - "cobl9_mutant": [ - "GSM757831", - "GSM757832", - "GSM757833" - ], - "WT_Columbia": [ - "GSM757891", - "GSM757892", - "GSM757893" - ], - "ttg2_mutant": [ - "GSM1153863", - "GSM1153864", - "GSM1153865" - ], - "wer_myb23_mutant": [ - "GSM757888", - "GSM757889", - "GSM757890" - ], - "gl2_mutant": [ - "GSM757843", - "GSM757844", - "GSM757845" - ], - "rhd6_mutant": [ - "GSM757879", - "GSM757880", - "GSM757881" - ], - "mrh2_mutant": [ - "GSM757858", - "GSM757859", - "GSM757860" - ], - "cpc_mutant": [ - "GSM1153845", - "GSM1153846", - "GSM1153847" - ], - "_rhd6_mutant_+_ACC": [ - "GSM757870", - "GSM757871", - "GSM757872" - ], - "ttg_mutant": [ - "GSM757885", - "GSM757886", - "GSM757887" - ], - "myc1_mutant": [ - "GSM757864", - "GSM757865", - "GSM757866" - ], - "cpc_try_mutant": [ - "GSM757837", - "GSM757838", - "GSM757839" - ], - "rhd6_mutant_+_IAA": [ - "GSM757873", - "GSM757874", - "GSM757875" - ], - "csld3_mutant": [ - "GSM757840", - "GSM757841", - "GSM757842" - ], - "egl3_mutant": [ - "GSM1153851", - "GSM1153852", - "GSM1153853" - ], - "try_mutant": [ - "GSM1153860", - "GSM1153861", - "GSM1153862" - ], - "rhd6_mutant_+_MS_(buffer)": [ - "GSM757876", - "GSM757877", - "GSM757878" - ], - "mrh3_mutant": [ - "GSM757861", - "GSM757862", - "GSM757863" - ], - "mrh1_mutant": [ - "GSM757855", - "GSM757856", - "GSM757857" - ], - "lrx1_mutant": [ - "GSM757852", - "GSM757853", - "GSM757854" - ], - "rhd2_mutant": [ - "GSM757867", - "GSM757868", - "GSM757869" - ], - "ire_mutant": [ - "GSM757849", - "GSM757850", - "GSM757851" - ], - "myb23_mutant": [ - "GSM1153857", - "GSM1153858", - "GSM1153859" - ], - "bhlh66_mutant": [ - "GSM757882", - "GSM757883", - "GSM757884" - ], - "gl3_egl3_mutant": [ - "GSM757846", - "GSM757847", - "GSM757848" - ] - } - }, - "ColprocessleafArd13;ColprocessleafMN3;ColprocessleafMN4;ColprocessleafMN5": { - "controls": [ - "ColprocessleafArd13", - "ColprocessleafMN3", - "ColprocessleafMN4", - "ColprocessleafMN5" - ], - "treatments": { - "gl3-sst_mutant_trichomes": [ - "DM9_sst1", - "m1DM8sstard", - "m1ssttr5_ATH1" - ], - "gl3-sst_nok-1_double_mutant_trichomes": [ - "EG_mosst1", - "EG_mosst2", - "EG_mosst3" - ], - "WT_Col-0_trichomes": [ - "ColtrichomeArd1", - "ColtrichomeArd2", - "ColtrichomeMN12", - "ColtrichomeMN13", - "ColtrichomeMN2" - ], - "gl3-sst_sim_double_mutant_trichomes": [ - "gl3_sstsimtrichomeMN1", - "gl3_sstsimtrichomeMN2" - ], - "WT_Col-0_leaves_after_trichome_removal": [ - "ColprocessleafArd13", - "ColprocessleafMN3", - "ColprocessleafMN4", - "ColprocessleafMN5" - ] - } - }, - "GSM738872_C2;GSM738873_C3;GSM738874_C4": { - "controls": [ - "GSM738872_C2", - "GSM738873_C3", - "GSM738874_C4" - ], - "treatments": { - "scrm-D_mute_whole_seedling_at_5_dpg": [ - "GSM738878_M2", - "GSM738879_M3", - "GSM738880_M4" - ], - "spch_whole_seedling_at_5_dpg": [ - "GSM738875_S2", - "GSM738876_S3", - "GSM738877_S4" - ], - "Col-0_WT_whole_seedling_at_5_dpg": [ - "GSM738872_C2", - "GSM738873_C3", - "GSM738874_C4" - ], - "scrm-D_whole_seedling_at_5_dpg": [ - "GSM738881_R2", - "GSM738882_R3", - "GSM738883_R4" - ] - } - }, - "LER1_Grotewold_082509;LER2_Grotewold_082509": { - "controls": [ - "LER1_Grotewold_082509", - "LER2_Grotewold_082509" - ], - "treatments": { - "Arabidopsis_green_tissue_wild_type_L._er_": [ - "LER1_Grotewold_082509", - "LER2_Grotewold_082509" - ], - "Arabidopsis_green_tissue_gl3_egl3_": [ - "GL3_1_Grotewold_082509", - "GL3_2_Grotewold_082509" - ] - } - }, - "Ler1_Grotewold_070109;LER2_Grotewold_070909": { - "controls": [ - "Ler1_Grotewold_070109", - "LER2_Grotewold_070909" - ], - "treatments": { - "Arabidopsis_wild_type_L._er": [ - "Ler1_Grotewold_070109", - "LER2_Grotewold_070909" - ], - "Arabidopsis_ttg2": [ - "TTG2_1_Grotewold_070909", - "TTG2_2_Grotewold_070909" - ] - } - } - } - }, - "Embryo": { - "database": "embryo", - "view_name": "Embryo", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Bent_cotyledon": [ - "bc_1", - "bc_2", - "bc_3" - ], - "Early_heart": [ - "eh_1", - "eh_2", - "eh_3" - ], - "Early_torpedo": [ - "et_1", - "et_2", - "et_3" - ], - "Globular": [ - "gl_1", - "gl_2", - "gl_3" - ], - "Late_heart": [ - "lh_1", - "lh_2", - "lh_3" - ], - "Late_torpedo": [ - "lt_1", - "lt_2", - "lt_3" - ], - "Mature_green": [ - "mg_1", - "mg_2", - "mg_3" - ], - "8-cell/16-cell": [ - "pg_1", - "pg_2", - "pg_3" - ] - } - } - } - }, - "Germination": { - "database": "germination", - "view_name": "Germination", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Twelve_Hours_S": [ - "12hS_1", - "12hS_2", - "12hS_3" - ], - "Zero_Hours": [ - "0h_1", - "0h_2", - "0h_3" - ], - "One_Hour_S": [ - "1hS_1", - "1hS_2", - "1hS_3" - ], - "Harvest": [ - "harvest_1", - "harvest_2", - "harvest_3" - ], - "Fourty_Eight_Hours_S": [ - "48hS_1", - "48hS_2", - "48hS_3" - ], - "Fourty_Eight_Hours_SL": [ - "48hSL_1", - "48hSL_2", - "48hSL_3" - ], - "Twelve_Hours_SL": [ - "12hSL_1", - "12hSL_2", - "12hSL_3" - ], - "One_Hour_SL": [ - "1hSL_1", - "1hSL_2", - "1hSL_3" - ], - "Six_Hours_SL": [ - "6hSL_1", - "6hSL_2", - "6hSL_3" - ], - "Twenty_Four_SL": [ - "24hSL_1", - "24hSL_2", - "24hSL_3" - ] - } - } - } - }, - "Guard_Cell": { - "database": "guard_cell", - "view_name": "Guard_Cell", - "groups": { - "GSM486895;GSM486896;GSM486897": { - "controls": [ - "GSM486895", - "GSM486896", - "GSM486897" - ], - "treatments": { - "agb1_guard_cells,_no_ABA": [ - "GSM486895", - "GSM486896", - "GSM486897" - ], - "agb1_guard_cells,_plus_50_uM_ABA": [ - "GSM486907", - "GSM486908", - "GSM486909" - ] - } - }, - "GSM486892;GSM486893;GSM486894": { - "controls": [ - "GSM486892", - "GSM486893", - "GSM486894" - ], - "treatments": { - "WT_Col-0_guard_cells,_no_ABA": [ - "GSM486892", - "GSM486893", - "GSM486894" - ], - "WT_Col-0_guard_cells,_plus_50_uM_ABA": [ - "GSM486904", - "GSM486905", - "GSM486906" - ] - } - }, - "GSM486916;GSM486917;GSM486918": { - "controls": [ - "GSM486916", - "GSM486917", - "GSM486918" - ], - "treatments": { - "WT_Col-0_leaf,_plus_50_uM_ABA": [ - "GSM486928", - "GSM486929", - "GSM486930" - ], - "WT_Col-0_leaf,_no_ABA": [ - "GSM486916", - "GSM486917", - "GSM486918" - ] - } - }, - "GSM738872_C2;GSM738873_C3;GSM738874_C4": { - "controls": [ - "GSM738872_C2", - "GSM738873_C3", - "GSM738874_C4" - ], - "treatments": { - "Col-0_WT_whole_seedling_at_5_dpg": [ - "GSM738872_C2", - "GSM738873_C3", - "GSM738874_C4" - ], - "scrm-D_mute_whole_seedling_at_5_dpg": [ - "GSM738878_M2", - "GSM738879_M3", - "GSM738880_M4" - ], - "spch_whole_seedling_at_5_dpg": [ - "GSM738875_S2", - "GSM738876_S3", - "GSM738877_S4" - ], - "scrm-D_whole_seedling_at_5_dpg": [ - "GSM738881_R2", - "GSM738882_R3", - "GSM738883_R4" - ] - } - }, - "JS85;JS33": { - "controls": [ - "JS85", - "JS33" - ], - "treatments": { - "Guard_cells,_with_100_uM_ABA": [ - "JS86", - "JS34" - ], - "Guard_cells,_no_ABA": [ - "JS85", - "JS33" - ] - } - }, - "GSM571891;GSM571893;GSM571895": { - "controls": [ - "GSM571891", - "GSM571893", - "GSM571895" - ], - "treatments": { - "Suspension_cell_culture,_plus_50_uM_ABA": [ - "GSM571892", - "GSM571894", - "GSM571896" - ], - "Suspension_cell_culture,_plus_5_mM_DMTU": [ - "GSM604752", - "GSM604753", - "GSM604754" - ], - "Suspension_cell_culture,_control": [ - "GSM571891", - "GSM571893", - "GSM571895" - ], - "Suspension_cell_culture,_plus_50_uM_ABA_and_5_mM_DMTU": [ - "GSM604755", - "GSM604751", - "GSM604750" - ] - } - }, - "GSM486919;GSM486920;GSM486921": { - "controls": [ - "GSM486919", - "GSM486920", - "GSM486921" - ], - "treatments": { - "agb1_leaf,_plus_50_uM_ABA": [ - "GSM486931", - "GSM486932", - "GSM486933" - ], - "agb1_leaf,_no_ABA": [ - "GSM486919", - "GSM486920", - "GSM486921" - ] - } - }, - "JS87": { - "controls": [ - "JS87" - ], - "treatments": { - "Mesophyll_cells,_with_100uM_ABA,_no_cordycepin_nor_actinomycin": [ - "JS88" - ], - "Mesophyll_cells,_no_ABA,_no_cordycepin_nor_actinomycin": [ - "JS87" - ] - } - }, - "GSM486922;GSM486923;GSM486924": { - "controls": [ - "GSM486922", - "GSM486923", - "GSM486924" - ], - "treatments": { - "gpa1_leaf,_no_ABA": [ - "GSM486922", - "GSM486923", - "GSM486924" - ], - "gpa1_leaf,_plus_50_uM_ABA": [ - "GSM486934", - "GSM486935", - "GSM486936" - ] - } - }, - "JS33": { - "controls": [ - "JS33" - ], - "treatments": { - "Guard_cells,_no_ABA,_cordycepin_and_actinomycin_added_during_protoplasting": [ - "JS33" - ], - "Guard_cells,_with_100uM_ABA,_cordycepin_and_actinomycin_added_during_protoplasting": [ - "JS34" - ] - } - }, - "GSM486898;GSM486899;GSM486900": { - "controls": [ - "GSM486898", - "GSM486899", - "GSM486900" - ], - "treatments": { - "gpa1_guard_cells,_no_ABA": [ - "GSM486898", - "GSM486899", - "GSM486900" - ], - "gpa1_guard_cells,_plus_50_uM_ABA": [ - "GSM486910", - "GSM486911", - "GSM486912" - ] - } - }, - "GSM486925;GSM486926;GSM486927": { - "controls": [ - "GSM486925", - "GSM486926", - "GSM486927" - ], - "treatments": { - "agb1_gpa1_leaf,_plus_50_uM_ABA": [ - "GSM486937", - "GSM486938", - "GSM486939" - ], - "agb1_gpa1_leaf,_no_ABA": [ - "GSM486925", - "GSM486926", - "GSM486927" - ] - } - }, - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "ML1:_Expression_data_from_epidermal_cells_isolated_using_a_ML1p::YFP-RCI2A_marker": [ - "GSM1420940_ML1Y_3", - "GSM1420939_ML1Y_2", - "GSM1420938_ML1Y_1" - ], - "FGF:_Expression_data_from_young_guard_cells_isolated_using_a_FAMAp::GFP-FAMA_marker": [ - "GSM1420949_FGF_3", - "GSM1420948_FGF_2", - "GSM1420947_FGF_1" - ], - "E1728G:_Expression_data_from_mature_guard_cells_isolated_using_a_E1728::GFP_marker": [ - "GSM1420952_E1728G_3", - "GSM1420951_E1728G_2", - "GSM1420950_E1728G_1" - ], - "SSY:_Expression_data_from_guard_cell_initials_isolated_with_a_SPCHp::SPCH-YFP_marker": [ - "GSM1420943_SSY_3", - "GSM1420942_SSY_2", - "GSM1420941_SSY_1" - ], - "MG:_Expression_data_from_committed_guard_cell_meristemoids_isolated_with_a_MUTEp::nucGFP_marker": [ - "GSM1420946_MG_3", - "GSM1420945_MG_2", - "GSM1420944_MG_1" - ] - } - }, - "JS87;JS35": { - "controls": [ - "JS87", - "JS35" - ], - "treatments": { - "Mesophyll_cells,_with_100_uM_ABA": [ - "JS88", - "JS36" - ], - "Mesophyll_cells,_no_ABA": [ - "JS87", - "JS35" - ] - } - }, - "JS85": { - "controls": [ - "JS85" - ], - "treatments": { - "Mesophyll_cells,_with_100uM_ABA,_cordycepin_and_actinomycin_added_during_protoplasting": [ - "JS36" - ], - "Guard_cells,_no_ABA,_no_cordycepin_nor_actinomycin": [ - "JS85" - ], - "Guard_cells,_with_100uM_ABA,_no_cordycepin_nor_actinomycin": [ - "JS86" - ], - "Mesophyll_cells,_no_ABA,_cordycepin_and_actinomycin_added_during_protoplasting": [ - "JS35" - ] - } - }, - "GSM486901;GSM486902;GSM486903": { - "controls": [ - "GSM486901", - "GSM486902", - "GSM486903" - ], - "treatments": { - "agb1_gpa1_guard_cells,_plus_50_uM_ABA": [ - "GSM486913", - "GSM486914", - "GSM486915" - ], - "agb1_gpa1_guard_cells,_no_ABA": [ - "GSM486901", - "GSM486902", - "GSM486903" - ] - } - } - } - }, - "Gynoecium": { - "database": "gynoecium", - "view_name": "Gynoecium", - "groups": { - "Col-0_CMM_R1;Col-0_CMM_R2;Col-0_CMM_R3": { - "controls": [ - "Col-0_CMM_R1", - "Col-0_CMM_R2", - "Col-0_CMM_R3" - ], - "treatments": { - "Col-0_Stage_7_CMM": [ - "Col-0_CMM_R1", - "Col-0_CMM_R2", - "Col-0_CMM_R3" - ], - "spt-12_Stage_7_CMM": [ - "spt-12_CMM_R1", - "spt-12_CMM_R2", - "spt-12_CMM_R3" - ] - } - }, - "Col-0_SEP_R1;Col-0_SEP_R2;Col-0_SEP_R3": { - "controls": [ - "Col-0_SEP_R1", - "Col-0_SEP_R2", - "Col-0_SEP_R3" - ], - "treatments": { - "Col-0_Stage_10_SEP": [ - "Col-0_SEP_R1", - "Col-0_SEP_R2", - "Col-0_SEP_R3" - ], - "spt-12_Stage_10_SEP": [ - "spt-12_SEP_R1", - "spt-12_SEP_R2", - "spt-12_SEP_R3" - ] - } - }, - "Col-0_PC_R1;Col-0_PC_R2;Col-0_PC_R3": { - "controls": [ - "Col-0_PC_R1", - "Col-0_PC_R2", - "Col-0_PC_R3" - ], - "treatments": { - "spt-12_Stage_7_PC": [ - "spt-12_PC_R1", - "spt-12_PC_R2", - "spt-12_PC_R3" - ], - "Col-0_Stage_7_PC": [ - "Col-0_PC_R1", - "Col-0_PC_R2", - "Col-0_PC_R3" - ] - } - }, - "Col-0_VV_R1;Col-0_VV_R2;Col-0_VV_R3": { - "controls": [ - "Col-0_VV_R1", - "Col-0_VV_R2", - "Col-0_VV_R3" - ], - "treatments": { - "Col-0_Stage_10_VV": [ - "Col-0_VV_R1", - "Col-0_VV_R2", - "Col-0_VV_R3" - ], - "spt-12_Stage_10_VV": [ - "spt-12_VV_R1", - "spt-12_VV_R2", - "spt-12_VV_R3" - ] - } - } - } - }, - "Hormone": { - "database": "atgenexp_hormone", - "view_name": "Hormone", - "groups": { - "ACC_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "ACC_Treated_at_30_Minutes": [ - "RIKEN-GODA7A", - "RIKEN-GODA7B" - ] - } - }, - "ACC_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "ACC_Treated_at_1_Hour": [ - "RIKEN-GODA15A", - "RIKEN-GODA15B" - ] - } - }, - "ACC_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "ACC_Treated_at_3_Hours": [ - "RIKEN-GODA23A", - "RIKEN-GODA23B" - ] - } - }, - "Zeatin_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "Zeatin_Treated_at_30_Minutes": [ - "RIKEN-GODA3A", - "RIKEN-GODA3B" - ] - } - }, - "Zeatin_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "Zeatin_Treated_at_1_Hour": [ - "RIKEN-GODA11A", - "RIKEN-GODA11B" - ] - } - }, - "Zeatin_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "Zeatin_Treated_at_3_Hours": [ - "RIKEN-GODA19A", - "RIKEN-GODA19B" - ] - } - }, - "IAA_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "IAA_Treated_at_30_Minutes": [ - "RIKEN-GODA2A", - "RIKEN-GODA2B" - ] - } - }, - "IAA_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "IAA_Treated_at_1_Hour": [ - "RIKEN-GODA10A", - "RIKEN-GODA10B" - ] - } - }, - "IAA_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "IAA_Treated_at_3_Hours": [ - "RIKEN-GODA18A", - "RIKEN-GODA18B" - ] - } - }, - "ABA_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "ABA_Treated_at_30_Minutes": [ - "RIKEN-GODA5A", - "RIKEN-GODA5B" - ] - } - }, - "ABA_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "ABA_Treated_at_1_Hour": [ - "RIKEN-GODA13A", - "RIKEN-GODA13B" - ] - } - }, - "ABA_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "ABA_Treated_at_3_Hours": [ - "RIKEN-GODA21A", - "RIKEN-GODA21B" - ] - } - }, - "Methyl_Jasmonate_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "MJ_Treated_at_30_Minutes": [ - "RIKEN-GODA6A", - "RIKEN-GODA6B" - ] - } - }, - "Methyl_Jasmonate_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "MJ_Treated_at_1_Hour": [ - "RIKEN-GODA14A", - "RIKEN-GODA14B" - ] - } - }, - "Methyl_Jasmonate_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "MJ_Treated_at_3_Hours": [ - "RIKEN-GODA22A", - "RIKEN-GODA22B" - ] - } - }, - "GA-3_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "GA-3_Treated_at_30_Minutes": [ - "RIKEN-GODA4A", - "RIKEN-GODA4B" - ] - } - }, - "GA-3_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "GA-3_Treated_at_1_Hour": [ - "RIKEN-GODA12A", - "RIKEN-GODA12B" - ] - } - }, - "GA-3_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "GA-3_Treated_at_3_Hours": [ - "RIKEN-GODA20A", - "RIKEN-GODA20B" - ] - } - }, - "GA-3_Mutant_at_30_Minutes": { - "controls": [ - "RIKEN-GODA25A", - "RIKEN-GODA25B" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA25A", - "RIKEN-GODA25B" - ], - "GA-3_Treated_Mutant_at_30_Minutes": [ - "RIKEN-GODA26A", - "RIKEN-GODA26B" - ] - } - }, - "GA-3_Mutant_at_1_Hour": { - "controls": [ - "RIKEN-GODA27A", - "RIKEN-GODA27B " - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA27A", - "RIKEN-GODA27B" - ], - "GA-3_Treated_Mutant_at_1_Hour": [ - "RIKEN-GODA28A", - "RIKEN-GODA28B" - ] - } - }, - "GA-3_Mutant_at_3_Hours": { - "controls": [ - "RIKEN-GODA29A", - "RIKEN-GODA29B" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA29A", - "RIKEN-GODA29B" - ], - "GA-3_Treated_Mutant_at_3_Hours": [ - "RIKEN-GODA30A", - "RIKEN-GODA30B" - ] - } - }, - "Brassinolide_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "BL_Treated_at_30_Minutes": [ - "RIKEN-GODA8A", - "RIKEN-GODA8B" - ] - } - }, - "Brassinolide_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "BL_Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "Treated_at_1_Hour": [ - "RIKEN-GODA16A", - "RIKEN-GODA16B" - ] - } - }, - "Brassinolide_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "BL_Treated_at_3_Hours": [ - "RIKEN-GODA24A", - "RIKEN-GODA24B" - ] - } - }, - "Brassinolide_Mutant_at_30_Minutes": { - "controls": [ - "RIKEN-GODA31A", - "RIKEN-GODA31B" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA31A", - "RIKEN-GODA31B" - ], - "BL_Treated_Mutant_at_30_Minutes": [ - "RIKEN-GODA32A", - "RIKEN-GODA32B" - ] - } - }, - "Brassinolide_Mutant_at_1_Hour": { - "controls": [ - "RIKEN-GODA33A", - "RIKEN-GODA33B" - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA33A", - "RIKEN-GODA33B" - ], - 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"Van-0_(CS6884)_from_Vancouver,_BC.,_Canada._Longitude/Latitude/Elevation:_W123/N49_at_1-100m._Temp_in_C_(Spr/Aut):2-9/10-18.": [ - "ATGE_120_A", - "ATGE_120_B", - "ATGE_120_C" - ], - "Ak-1_(CS6602)_from_Achkarren,_Germany._Longitude/Latitude/Elevation:_E8/N48_at_200m._Temp_in_C_(Spr/Aut):7-8/11-12,_Precipitation_in_mm_(Spr/Aut):50-60/50-60.": [ - "ATGE_121_A" - ], - "Bla-5_(CS6620)_from_Blanes,_Spain._Longitude/Latitude/Elevation:_E3/N41_at_50m._Temp_in_C_(Spr/Aut):17-18/11-12,_Precipitation_in_mm_(Spr/Aut):40-50/40-50.": [ - "ATGE_124_A" - ], - "Can-0_(CS6660)_from_Canary_Islands,_Spain._Longitude/Latitude/Elevation:_W15/N28_at_1260m.": [ - "ATGE_125_A" - ], - "Cen-0_(CS6661)_from_Caen,_France._Longitude/Latitude/Elevation:_W0/N49_at_1-100m.": [ - "ATGE_126_A" - ], - "CIBC10_(CS22229)_from_United_Kingdom.": [ - "ATGE_127_A" - ], - "Dra-1_(CS6686)_from_Drahonin,_Czech_Republic._Longitude/Latitude/Elevation:_E16/N49_at_450m.": [ - "ATGE_128_A" - ], - "En-T_(CS6176)_from_Tadjikistan.": 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"treatments": { - "Col-2_wt_seedcoat,_11_dpa": [ - "col2-11-1", - "col2-11-2", - "col2-11-3", - "col2-11-4", - "col2-11-5", - "col2-11-6", - "col2-11-7", - "col2-11-8" - ], - "Col-2_wt_seedcoat,_3_dpa": [ - "col2-3-1", - "col2-3-2", - "col2-3-3", - "col2-3-4", - "col2-3-5", - "col2-3-6", - "col2-3-7", - "col2-3-8" - ], - "Col-2_wt_seedcoat,_7_dpa": [ - "col2-7-1", - "col2-7-10", - "col2-7-11", - "col2-7-12", - "col2-7-2", - "col2-7-3", - "col2-7-4", - "col2-7-5", - "col2-7-6", - "col2-7-7", - "col2-7-8", - "col2-7-9" - ] - } - }, - "tt16-1_mutant_seed": { - "controls": [ - "ws2-3-1", - "ws2-3-2", - "ws2-3-3", - "ws2-3-4", - "ws2-3-5", - "ws2-3-6", - "ws2-3-7", - "ws2-3-8" - ], - "treatments": { - "Ws-2_seedcoat,_11_dpa": [ - "ws2-11-1", - "ws2-11-2", - "ws2-11-3", - "ws2-11-4", - "ws2-11-5", - "ws2-11-6", - "ws2-11-7", - "ws2-11-8" - ], - "Ws-2_seedcoat,_3_dpa": [ - "ws2-3-1", - "ws2-3-2", - "ws2-3-3", - "ws2-3-4", - "ws2-3-5", - "ws2-3-6", - "ws2-3-7", - "ws2-3-8" - ], - "Ws-2_seedcoat,_7_dpa": [ - "ws2-7-1", - "ws2-7-10", - "ws2-7-11", - "ws2-7-12", - "ws2-7-2", - "ws2-7-3", - "ws2-7-4", - "ws2-7-5", - "ws2-7-6", - "ws2-7-7", - "ws2-7-8", - "ws2-7-9" - ] - } - } - } - } - } - } - }, - "arachis": { - - "data": { - "species": "arachis", - "views": { - "Arachis_Atlas": { - "database": "arachis", - "view_name": "Arachis_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Pattee_1_stalk:__Gynophore_stalk_at_pod_swelling_(Pattee_stage_1)": [ - "Pattee_1_Stalk" - ], - "subterranean_gynophore_tip:__5_mm_(=mostly_ovary_and_zone_of_cell_division)_from_elongating_peg_of_approximately_same_length_as_#9,_but_24_h_after_soil_penetration": [ - "Subterranean_Gynophore_Tip" - ], - "Pattee_1_pod:__Whole_pod_at_pod_swelling_(Pattee_stage_1)": [ - "Pattee_1_Pod" - ], - "Pattee_6_seed:__Torpedo_shaped;_generally_pink_at_embryonic-axis_end_of_kernels_(Pattee_stage_6)": [ - "Pattee_6_Seed" - ], - "aerial_gynophore_tip:__5_mm_(=mostly_ovary_and_zone_of_cell_division)_from_elongating_peg_prior_to_soil_penetration": [ - "Aerial_Gynophore_Tip" - ], - "Pattee_5_seed:__Embryo_flat,_white_or_just_turning_pink_at_one_end_(Pattee_stage_5)": [ - "Pattee_5_Seed" - ], - "Pattee_7_seed:__Torpedo_to_round_shaped;_embryonic_axis_end_of_kernel_pink;_other_end_white_to_light_pink_(Pattee_stage_7)": [ - "Pattee_7_Seed" - ], - "vegetative_shoot_tip:__Growth_stage_Boote_R1_first_flower,_from_mainstem_(n);_5_mm_maxium_length": [ - "Vegetative_Shoot_Tip" - ], - "androecium:__Fully_open,_morning_of_anthesis;_staminal_tube,_filaments_and_anthers": [ - "Androecium" - ], - "reproductive_shoot_tip:__Growth_stage_Boote_R1_first_flower,_from_laterals__(n+1);_5_mm_maxium_length": [ - "Reproductive_Shoot_Tip" - ], - "nodules:__25_d_post-emergence": [ - "Nodules" - ], - "Pattee_10_seed:__Large,_generally_dark_pink_all_over;_seed_coat_beginning_to_dry_out_(Pattee_stage_10)": [ - "Pattee_10_Seed" - ], - "Pattee_5_pericarp:__Pericarp_soft,_not_as_watery,_inner_pericarp_without_cracks_(Pattee_stage_5)": [ - "Pattee_5_Pericarp" - ], - "Pattee_8_seed:__Round,_light_pink_all_over_(Pattee_stage_8)": [ - "Pattee_8_Seed" - ], - "Pattee_3_pod:__Pericarp_very_watery,_embryo_very_small_and_not_easily_removed_(Pattee_stage_3/4)": [ - "Pattee_3_Pod" - ], - "seedling_leaf:__10_d_post-emergence;_leaflets_partially_open": [ - "Seedling_Leaf" - ], - "perianth:__Fully_open,_morning_of_anthesis;_wings,_banner,_hypanthium,_keel_and_lower_lip_of_the_calyx": [ - "Perianth" - ], - "gynoecium:__Fully_open,_morning_of_anthesis;_stigma,_style_and_overy": [ - "Gynoecium" - ], - "lateral_stem_leaf:__Growth_stage_Boote_R1_first_flower;_leaflets_partially_open,_from_laterals__(n+1)": [ - "Lateral_Stem_Leaf" - ], - "Pattee_6_pericarp:__Inner_pericarp_tissue_beginning_to_show_cracks_or_cottony_(Pattee_stage_6/7)": [ - "Pattee_6_Pericarp" - ], - "root_:__10_d_post-emergence": [ - "Roots" - ] - } - }, - "Pattee_10_Seed": { - "controls": [ - "Pattee_10_Seed" - ], - "treatments": { - "main_stem_leaf:__Growth_stage_Boote_R1_first_flower;_leaflets_partially_open,_from_main_stem_(n)": [ - "Main_Stem_Leaf" - ] - } - } - } - } - } - } - }, - "barley": { - - "data": { - "species": "barley", - "views": { - "barley_mas": { - "database": "barley_mas", - "view_name": "barley_mas", - "groups": { - "Seedling": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Morex_Leaf": [ - "MX_Leafrep1", - "MX_Leafrep2", - "MX_Leafrep3" - ], - "Golden_Promise_Leaf": [ - "GP_Leafrep1", - "GP_Leafrep2", - "GP_Leafrep3" - ], - "Morex_Crown": [ - "MX_Crownrep1", - "MX_Crownrep2", - "MX_Crownrep3" - ], - "Golden_Promise_Crown": [ - "GP_Crownrep1", - "GP_Crownrep2", - "GP_Crownrep3" - ], - "Morex_Root": [ - "MX_Rootrep1", - "MX_Rootrep2", - "MX_Rootrep3" - ], - "Golden_Promise_Root": [ - "GP_Rootrep1", - "GP_Rootrep2", - "GP_Rootrep3" - ] - } - }, - "Germinating_Seedling": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Morex_Coleoptile": [ - "MX_Coleoptilerep1", - "MX_Coleoptilerep2", - "MX_Coleoptilerep3" - ], - "Golden_Promise_Coleoptile": [ - "GP_Coleoptilerep1", - "GP_Coleoptilerep2", - "GP_Coleoptilerep3" - ], - "Morex_Mesocotyl": [ - "MX_Embryorep1", - "MX_Embryorep2", - "MX_Embryorep3" - ], - "Golden_Promise_Mesocotyl": [ - "GP_Embryorep1", - "GP_Embryorep2", - "GP_Embryorep3" - ], - "Morex_Radicle": [ - "MX_Radiclerep1", - "MX_Radiclerep2", - "MX_Radiclerep3" - ], - "Golden_Promise_Radicle": [ - "GP_Radiclerep1", - "GP_Radiclerep2", - "GP_Radiclerep3" - ] - } - }, - "Caryopsis_without_Embryo": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Morex_Caryopsis_without_Embryo": [ - "MX_Endosperm22DAPrep1", - "MX_Endosperm22DAPrep2", - "MX_Endosperm22DAPrep3" - ] - } - }, - "Embryo": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Embryo_22_DAP": [ - "MX_Embryo22DAPrep1", - "MX_Embryo22DAPrep2", - "MX_Embryo22DAPrep3" - ] - } - }, - "Caryopsis": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Caryopsis_5_DAP": [ - "MX_Caryopsis5DAPrep1", - "MX_Caryopsis5DAPrep2", - "MX_Caryopsis5DAPrep3" - ], - "Caryopsis_10_DAP": [ - "MX_Caryopsis10DAPrep1", - "MX_Caryopsis10DAPrep2", - "MX_Caryopsis10DAPrep3" - ], - "Caryopsis_16_DAP": [ - "MX_Caryopsis16DAPrep1", - "MX_Caryopsis16DAPrep2", - "MX_Caryopsis16DAPrep3" - ] - } - }, - "Floral_Bracts": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Floral_Bracts": [ - "MX_FloralBractsrep1", - "MX_FloralBractsrep2", - "MX_FloralBractsrep3" - ] - } - }, - "Anthers": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Anthers": [ - "MX_Anthersrep1", - "MX_Anthersrep2", - "MX_Anthersrep3" - ] - } - }, - "Pistil": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Pistil": [ - "MX_Pistilrep1", - "MX_Pistilrep2", - "MX_Pistilrep3" - ] - } - }, - "Immature_Inflorescence": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Immature_Inflorescence": [ - "MX_Inflorescencerep1", - "MX_Inflorescencerep2", - "MX_Inflorescencerep3" - ] - } - }, - "Spike": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Lemma": [ - "Lemma_Rep1", - "Lemma_Rep2", - "Lemma_Rep3" - ], - "Palea": [ - "Palea_Rep1", - "Palea_Rep2", - "Palea_Rep3" - ], - "Awn": [ - "Awn_Rep1", - "Awn_Rep2", - "Awn_Rep3" - ] - } - } - } - }, - "barley_rma": { - "database": "barley_rma", - "view_name": "barley_rma", - "groups": { - "Seedling": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Morex_Leaf": [ - "MX_Leafrep1", - "MX_Leafrep2", - "MX_Leafrep3" - ], - "Golden_Promise_Leaf": [ - "GP_Leafrep1", - "GP_Leafrep2", - "GP_Leafrep3" - ], - "Morex_Crown": [ - "MX_Crownrep1", - "MX_Crownrep2", - "MX_Crownrep3" - ], - "Golden_Promise_Crown": [ - "GP_Crownrep1", - "GP_Crownrep2", - "GP_Crownrep3" - ], - "Morex_Root": [ - "MX_Rootrep1", - "MX_Rootrep2", - "MX_Rootrep3" - ], - "Golden_Promise_Root": [ - "GP_Rootrep1", - "GP_Rootrep2", - "GP_Rootrep3" - ] - } - }, - "Germinating_Seedling": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Morex_Coleoptile": [ - "MX_Coleoptilerep1", - "MX_Coleoptilerep2", - "MX_Coleoptilerep3" - ], - "Golden_Promise_Coleoptile": [ - "GP_Coleoptilerep1", - "GP_Coleoptilerep2", - "GP_Coleoptilerep3" - ], - "Morex_Mesocotyl": [ - "MX_Embryorep1", - "MX_Embryorep2", - "MX_Embryorep3" - ], - "Golden_Promise_Mesocotyl": [ - "GP_Embryorep1", - "GP_Embryorep2", - "GP_Embryorep3" - ], - "Morex_Radicle": [ - "MX_Radiclerep1", - "MX_Radiclerep2", - "MX_Radiclerep3" - ], - "Golden_Promise_Radicle": [ - "GP_Radiclerep1", - "GP_Radiclerep2", - "GP_Radiclerep3" - ] - } - }, - "Caryopsis_without_Embryo": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Morex_Caryopsis_without_Embryo": [ - "MX_Endosperm22DAPrep1", - "MX_Endosperm22DAPrep2", - "MX_Endosperm22DAPrep3" - ] - } - }, - "Embryo": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Embryo_22_DAP": [ - "MX_Embryo22DAPrep1", - "MX_Embryo22DAPrep2", - "MX_Embryo22DAPrep3" - ] - } - }, - "Caryopsis": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Caryopsis_5_DAP": [ - "MX_Caryopsis5DAPrep1", - "MX_Caryopsis5DAPrep2", - "MX_Caryopsis5DAPrep3" - ], - "Caryopsis_10_DAP": [ - "MX_Caryopsis10DAPrep1", - "MX_Caryopsis10DAPrep2", - "MX_Caryopsis10DAPrep3" - ], - "Caryopsis_16_DAP": [ - "MX_Caryopsis16DAPrep1", - "MX_Caryopsis16DAPrep2", - "MX_Caryopsis16DAPrep3" - ] - } - }, - "Floral_Bracts": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Floral_Bracts": [ - "MX_FloralBractsrep1", - "MX_FloralBractsrep2", - "MX_FloralBractsrep3" - ] - } - }, - "Anthers": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Anthers": [ - "MX_Anthersrep1", - "MX_Anthersrep2", - "MX_Anthersrep3" - ] - } - }, - "Pistil": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Pistil": [ - "MX_Pistilrep1", - "MX_Pistilrep2", - "MX_Pistilrep3" - ] - } - }, - "Immature_Inflorescence": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Immature_Inflorescence": [ - "MX_Inflorescencerep1", - "MX_Inflorescencerep2", - "MX_Inflorescencerep3" - ] - } - }, - "Spike": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Lemma": [ - "Lemma_Rep1", - "Lemma_Rep2", - "Lemma_Rep3" - ], - "Palea": [ - "Palea_Rep1", - "Palea_Rep2", - "Palea_Rep3" - ], - "Awn": [ - "Awn_Rep1", - "Awn_Rep2", - "Awn_Rep3" - ] - } - } - } - } - } - } - }, - "brachypodium": { - - "data": { - "species": "brachypodium", - "views": { - "Brachypodium_Atlas": { - "database": "brachypodium", - "view_name": "Brachypodium_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "I:_De-etiolated_shoots_3_DAG_1": [ - "I:_De-etiolated_shoots_3_DAG_1", - "I:_De-etiolated_shoots_3_DAG_2", - "I:_De-etiolated_shoots_3_DAG_3" - ], - "I:_Etiolated_shoots_3_DAG_1": [ - "I:_Etiolated_shoots_3_DAG_1", - "I:_Etiolated_shoots_3_DAG_2", - "I:_Etiolated_shoots_3_DAG_3" - ], - "P:_Coleoptile_10_DAG_1": [ - "P:_Coleoptile_10_DAG_1", - "P:_Coleoptile_10_DAG_2" - ], - "P:_Coleoptile_17+27_DAG_1": [ - "P:_Coleoptile_17+27_DAG_1", - "P:_Coleoptile_17+27_DAG_2", - "P:_Coleoptile_17+27_DAG_3" - ], - "P:_First_internode_10_DAG_1": [ - "P:_First_internode_10_DAG_1", - "P:_First_internode_10_DAG_2", - "P:_First_internode_10_DAG_3", - "P:_First_internode_10_DAG_4" - ], - "P:_First_internode_17_DAG_1": [ - "P:_First_internode_17_DAG_1", - "P:_First_internode_17_DAG_2" - ], - "P:_First_internode_27_DAG_1": [ - "P:_First_internode_27_DAG_1", - "P:_First_internode_27_DAG_2", - "P:_First_internode_27_DAG_3" - ], - "P:_First_internode_35_DAG_1": [ - "P:_First_internode_35_DAG_1", - "P:_First_internode_35_DAG_2" - ], - "P:_First_internode_60_DAG_1": [ - "P:_First_internode_60_DAG_1", - "P:_First_internode_60_DAG_2" - ], - "P:_First_node_+_adventitious_roots_35_DAG_1": [ - "P:_First_node_+_adventitious_roots_35_DAG_1", - "P:_First_node_+_adventitious_roots_35_DAG_2" - ], - "P:_First_node_10_DAG_1": [ - "P:_First_node_10_DAG_1", - "P:_First_node_10_DAG_2" - ], - "P:_First_node_17_DAG_2": [ - "P:_First_node_17_DAG_1", - "P:_First_node_17_DAG_2", - "P:_First_node_17_DAG_3" - ], - "P:_First_node_27_DAG_1": [ - "P:_First_node_27_DAG_1", - "P:_First_node_27_DAG_2" - ], - "P:_First_node_60_DAG_1": [ - "P:_First_node_60_DAG_1", - "P:_First_node_60_DAG_2" - ], - "P:_Last_internode_60_DAG_1": [ - "P:_Last_internode_60_DAG_1", - "P:_Last_internode_60_DAG_2" - ], - "P:_Leaf_10_DAG_1": [ - "P:_Leaf_10_DAG_1", - "P:_Leaf_10_DAG_2" - ], - "P:_Leaf_17_DAG_1": [ - "P:_Leaf_17_DAG_1", - "P:_Leaf_17_DAG_2", - 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"DD-WTR-T2_R2", - "DD-WTR-T2_R3" - ], - "Root_Watered_T3": [ - "DD-WTR-T3_R1", - "DD-WTR-T3_R2", - "DD-WTR-T3_R3" - ], - "Root_Watered_T4": [ - "DD-WTR-T4_R1", - "DD-WTR-T4_R2", - "DD-WTR-T4_R3" - ], - "Root_Watered_T5": [ - "DD-WTR-T5_R1", - "DD-WTR-T5_R2", - "DD-WTR-T5_R3" - ], - "Root_Watered_T6": [ - "DD-WTR-T6_R1", - "DD-WTR-T6_R2", - "DD-WTR-T6_R3" - ], - "Root_Watered_T7": [ - "DD-WTR-T7_R2", - "DD-WTR-T7_R3", - "DD-WTR-T7-R1" - ], - "Root_Drought_T1": [ - "DD-DTR-T1_R1", - "DD-DTR-T1_R2", - "DD-DTR-T1_R3" - ], - "Root_Drought_T2": [ - "DD-DTR-T2_R1", - "DD-DTR-T2_R2", - "DD-DTR-T2_R3" - ], - "Root_Drought_T3": [ - "DD-DTR-T3_R1", - "DD-DTR-T3_R2", - "DD-DTR-T3_R3" - ], - "Root_Drought_T4": [ - "DD-DTR-T4_R1", - "DD-DTR-T4_R2", - "DD-DTR-T4_R3" - ], - "Root_Drought_T5": [ - "DD-DTR-T5_R1", - "DD-DTR-T5_R2" - ], - "Root_Drought_T6": [ - "DD-DTR-T6_R1", - "DD-DTR-T6_R2", - "DD-DTR-T6_R3" - ], - "Root_Drought_T7": [ - "DD-DTR-T7_R1", - "DD-DTR-T7_R2", - "DD-DTR-T7_R3" - ], - "Leaf_Watered_T1": [ - "DD-WTL-T1_R1", - "DD-WTL-T1_R2", - "DD-WTL-T1_R3" - ], - "Leaf_Watered_T2": [ - "DD-WTL-T2_R1", - "DD-WTL-T2_R2", - "DD-WTL-T2_R3" - ], - "Leaf_Watered_T3": [ - "DD-WTL-T3_R1", - "DD-WTL-T3_R2", - "DD-WTL-T3_R3" - ], - "Leaf_Watered_T4": [ - "DD-WTL-T4_R1", - "DD-WTL-T4_R2", - "DD-WTL-T4_R3" - ], - "Leaf_Watered_T5": [ - "DD-WTL-T5_R1", - "DD-WTL-T5_R2" - ], - "Leaf_Watered_T6": [ - "DD-WTL-T6_R1", - "DD-WTL-T6_R2", - "DD-WTL-T6_R3" - ], - "Leaf_Watered_T7": [ - "DD-WTL-T7_R1", - "DD-WTL-T7_R2", - "DD-WTL-T7_R3" - ], - "Leaf_Drought_T1": [ - "DD-DTL-T1_R1", - "DD-DTL-T1_R2", - "DD-DTL-T1_R3" - ], - "Leaf_Drought_T2": [ - "DD-DTL-T2_R1", - "DD-DTL-T2_R2", - "DD-DTL-T2_R3" - ], - "Leaf_Drought_T3": [ - "DD-DTL-T3_R1", - "DD-DTL-T3_R2", - "DD-DTL-T3_R3" - ], - "Leaf_Drought_T4": [ - "DD-DTL-T4_R1", - "DD-DTL-T4_R2", - "DD-DTL-T4_R3" - ], - "Leaf_Drought_T5": [ - "DD-DTL-T5_R1", - "DD-DTL-T5_R2", - "DD-DTL-T5_R3" - ], - "Leaf_Drought_T6": [ - "DD-DTL-T6_R1", - "DD-DTL-T6_R2", - "DD-DTL-T6_R3" - ], - "Leaf_Drought_T7": [ - "DD-DTL-T7_R1", - "DD-DTL-T7_R2", - "DD-DTL-T7_R3" - ], - "Apex_Watered_T1": [ - "DD-WTA-T1_R1", - "DD-WTA-T1_R2", - "DD-WTA-T1_R3" - ], - "Apex_Watered_T2": [ - "DD-WTA-T2_R1", - "DD-WTA-T2_R2", - "DD-WTA-T2_R3" - ], - "Apex_Watered_T3": [ - "DD-WTA-T3_R1", - "DD-WTA-T3_R2", - "DD-WTA-T3_R3" - ], - "Apex_Watered_T4": [ - "DD-WTA-T4_R1", - "DD-WTA-T4_R2", - "DD-WTA-T4_R3" - ], - "Apex_Watered_T5": [ - "DD-WTA-T5_R1", - "DD-WTA-T5_R2", - "DD-WTA-T5_R3" - ], - "Apex_Watered_T6": [ - "DD-WTA-T6_R1", - "DD-WTA-T6_R2", - "DD-WTA-T6_R3" - ], - "Apex_Watered_T7": [ - "DD-WTA-T7_R1", - "DD-WTA-T7_R2", - "DD-WTA-T7_R3" - ], - "Apex_Drought_T1": [ - "DD-DTA-T1_R1", - "DD-DTA-T1_R2", - "DD-DTA-T1_R3" - ], - "Apex_Drought_T2": [ - "DD-DTA-T2_R1", - "DD-DTA-T2_R2", - "DD-DTA-T2_R3" - ], - "Apex_Drought_T3": [ - "DD-DTA-T3_R1", - "DD-DTA-T3_R2", - "DD-DTA-T3_R3" - ], - "Apex_Drought_T4": [ - "DD-DTA-T4_R1", - "DD-DTA-T4_R2", - "DD-DTA-T4_R3" - ], - "Apex_Drought_T5": [ - "DD-DTA-T5_R1", - "DD-DTA-T5_R2", - "DD-DTA-T5_R3" - ], - "Apex_Drought_T6": [ - "DD-DTA-T6_R1", - "DD-DTA-T6_R2", - "DD-DTA-T6_R3" - ], - "Apex_Drought_T7": [ - "DD-DTA-T7_R1", - "DD-DTA-T7_R2", - "DD-DTA-T7_R3" - ] - } - } - } - } - } - } - }, - "cacao sca": { - - "data": { - "species": "cacao sca", - "views": { - "Developmental_Atlas": { - "database": "cacao_developmental_atlas_sca", - "view_name": "Developmental_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "CCN51_Mature_Embryo": [ - "CGA-SE-LS-E_R1", - "CGA-SE-LS-E_R2", - "CGA-SE-LS-E_R3", - "CGA-SE-LS-E_R4", - "CGA-SE-LS-E_R5" - ], - "Germinating_Seed_Root": [ - "CGA-GS-RO_R1", - "CGA-GS-RO_R2", - "CGA-GS-RO_R3", - "CGA-GS-RO_R4", - "CGA-GS-RO_R5" - ], - "Germinating_Seed_Shoot": [ - "CGA-GS-SH_R1", - "CGA-GS-SH_R2", - "CGA-GS-SH_R3", - "CGA-GS-SH_R4", - "CGA-GS-SH_R5" - ], - "Seedling_Root": [ - "CGA-SL-RO_R1", - "CGA-SL-RO_R2", - "CGA-SL-RO_R3", - "CGA-SL-RO_R4", - "CGA-SL-RO_R5" - ], - "Seedling_Shoot": [ - "CGA-SL-SH_R1", - "CGA-SL-SH_R2", - "CGA-SL-SH_R3", - "CGA-SL-SH_R4", - "CGA-SL-SH_R5" - ], - "3mo_Orthotropic_Roots": [ - "CGA-RO_R1", - "CGA-RO_R2", - "CGA-RO_R3", - "CGA-RO_R4", - "CGA-RO_R5" - ], - "3mo_Orthotropic_Leaf_A": [ - "CGA-YL-A_R1", - "CGA-YL-A_R2", - "CGA-YL-A_R3", - "CGA-YL-A_R4", - "CGA-YL-A_R5" - ], - "3mo_Orthotropic_C_Leaf": [ - "CGA-ML-C_2", - "CGA-ML-C_R1", - "CGA-ML-C_R3", - "CGA-ML-C_R4", - "CGA-ML-C_R5" - ], - "3mo_Orthotropic_E1_Leaf": [ - "CGA-ML-E1_R1", - "CGA-ML-E1_R2", - "CGA-ML-E1_R3", - "CGA-ML-E1_R4", - "CGA-ML-E1_R5" - ], - "3mo_Orthotropic_E2_Leaf": [ - "CGA-OL-E2_R1", - "CGA-OL-E2_R2", - "CGA-OL-E2_R3", - "CGA-OL-E2_R4", - "CGA-OL-E2_R5" - ], - "3mo_Orthotropic_Shoot_Apex": [ - "CGA-AX_R1", - "CGA-AX_R2", - "CGA-AX_R3", - "CGA-AX_R4", - "CGA-AX_R5" - ], - "3mo_Orthotropic_Herbaceous_Stem": [ - "CGA-SBA-2_R1", - "CGA-SBA-2_R2", - "CGA-SBA-2_R3", - "CGA-SBA-2_R4", - "CGA-SBA-2_R5" - ], - "3mo_Orthotropic_Woody_Stem": [ - "CGA-SBA-1_R1", - "CGA-SBA-1_R2", - "CGA-SBA-1_R3", - "CGA-SBA-1_R4", - "CGA-SBA-1_R5" - ], - "Premeiotic_Floral_Bud": [ - "CGA-PMFB_R1", - "CGA-PMFB_R2", - "CGA-PMFB_R3", - "CGA-PMFB_R4" - ], - "Floral_Bud_5-10_mm": [ - "CGA-LGFL_R1", - "CGA-LGFL_R2", - "CGA-LGFL_R3", - "CGA-LGFL_R4" - ], - "Open_Flower": [ - "CGA-OF_R1", - "CGA-OF_R2", - "CGA-OF_R3", - "CGA-OF_R4" - ], - "CCN51_Immature_Embryo": [ - "DA-SE-MS-E_R1", - "DA-SE-MS-E_R2", - "DA-SE-MS-E_R3", - "DA-SE-MS-E_R4", - "DA-SE-MS-E_R5" - ], - "Immature_Pod_Seed_Coat": [ - "DA-SE-MS-SC_R1", - "DA-SE-MS-SC_R2", - "DA-SE-MS-SC_R3", - "DA-SE-MS-SC_R4", - "DA-SE-MS-SC_R5" - ], - "CCN51_Developing_Embryo": [ - "DA-SE-MLS-E_R1", - "DA-SE-MLS-E_R2", - "DA-SE-MLS-E_R3", - "DA-SE-MLS-E_R4", - "DA-SE-MLS-E_R5" - ], - "Developing_Pod_Seed_Coat": [ - "DA-MLS-SC_R1", - "DA-MLS-SC_R2", - "DA-MLS-SC_R3", - "DA-MLS-SC_R4", - "DA-MLS-SC_R5" - ], - "Immature_Pod_Skin": [ - "DA-PD-MS-PS_R1", - "DA-PD-MS-PS_R2", - "DA-PD-MS-PS_R3" - ], - "Immature_Pod_Exocarp": [ - "DA-PD-MS-PEX_R1", - "DA-PD-MS-PEX_R2", - "DA-PD-MS-PEX_R3" - ], - "Immature_Pod_Mesocarp": [ - "DA-PD-MS-PMC_R1", - "DA-PD-MS-PMC_R2", - "DA-PD-MS-PMC_R3" - ], - "Immature_Pod_Seed_Mucilage": [ - "DA-PD-MS-SM_R1", - "DA-PD-MS-SM_R2", - "DA-PD-MS-SM_R3" - ], - "Immature_Pod_Endocarp": [ - "DA-PD-MS-PEN_R1", - "DA-PD-MS-PEN_R2", - "DA-PD-MS-PEN_R3" - ], - "Developing_Pod_Skin": [ - "DA-PD-MLS-PS_R1", - "DA-PD-MLS-PS_R2", - "DA-PD-MLS-PS_R3" - ], - "Developing_Pod_Exocarp": [ - "DA-PD-MLS-PEX_R1", - "DA-PD-MLS-PEX_R2", - "DA-PD-MLS-PEX_R3" - ], - "Developing_Pod_Mesocarp": [ - "DA-PD-MLS-PMC_R1", - "DA-PD-MLS-PMC_R2", - "DA-PD-MLS-PMC_R3" - ], - "Developing_Pod_Endocarp": [ - "DA-PD-MLS-PEN_R1", - "DA-PD-MLS-PEN_R2", - "DA-PD-MLS-PEN_R3" - ], - "Developing_Pod_Seed_Mucilage": [ - "DA-PD-MLS-SM_R1", - "DA-PD-MLS-SM_R2", - "DA-PD-MLS-SM_R3" - ], - "Mature_Pod_Skin": [ - "DA-PD-LS-PS_R1", - "DA-PD-LS-PS_R2", - "DA-PD-LS-PS_R3", - "DA-PD-LS-PS_R4", - "DA-PD-LS-PS_R5" - ], - "Mature_Pod_Exocarp": [ - "DA-PD-LS-PEX_R1", - "DA-PD-LS-PEX_R2", - "DA-PD-LS-PEX_R3", - "DA-PD-LS-PEX_R4", - "DA-PD-LS-PEX_R5" - ], - "Mature_Pod_Mesocarp": [ - "DA-PD-LS-PMC_R1", - "DA-PD-LS-PMC_R2", - "DA-PD-LS-PMC_R3", - "DA-PD-LS-PMC_R4", - "DA-PD-LS-PMC_R5" - ], - "Mature_Pod_Endocarp": [ - "DA-PD-LS-PEN_R1", - "DA-PD-LS-PEN_R2", - "DA-PD-LS-PEN_R3", - "DA-PD-LS-PEN_R4", - "DA-PD-LS-PEN_R5" - ], - "Mature_Pod_Seed_Mucilage": [ - "DA-PD-LS-SM_R1", - "DA-PD-LS-SM_R2", - "DA-PD-LS-SM_R3", - "DA-PD-LS-SM_R4", - "DA-PD-LS-SM_R5" - ], - "6mo_Orthotropic_Root": [ - "DA-RO-RT_R1", - "DA-RO-RT_R2", - "DA-RO-RT_R3", - "DA-RO-RT_R4", - "DA-RO-RT_R5" - ], - "6mo_Orthotropic_Leaf_A": [ - "DA-OTL-A_R1", - "DA-OTL-A_R2", - "DA-OTL-A_R3", - "DA-OTL-A_R4", - "DA-OTL-A_R5" - ], - "6mo_Orthotropic_Leaf_C": [ - "DA-OTL-C_R1", - "DA-OTL-C_R2", - "DA-OTL-C_R3", - "DA-OTL-C_R4", - "DA-OTL-C_R5" - ], - "6mo_Orthotropic_Leaf_E1": [ - "DA-OTL-E1_R1", - "DA-OTL-E1_R2", - "DA-OTL-E1_R3", - "DA-OTL-E1_R4", - "DA-OTL-E1_R5" - ], - "6mo_Orthotropic_Leaf_E2": [ - "DA-OTL-E2_R2", - "DA-OTL-E2_R3", - "DA-OTL-E2_R4", - "DA-OTL-E2_R5" - ], - "6mo_Orthotropic_Leaf_E3": [ - "DA-OTL-E3_R1", - "DA-OTL-E3_R2", - "DA-OTL-E3_R3", - "DA-OTL-E3_R4", - "DA-OTL-E3_R5" - ], - "6mo_Orthotropic_Shoot_Apex": [ - "DA-OTA_R1", - "DA-OTA_R2", - "DA-OTA_R3", - "DA-OTA_R4", - "DA-OTA_R5" - ], - "6mo_Orthotropic_Herbaceous_Stem": [ - "DA-OTAC-YS_R1", - "DA-OTAC-YS_R2", - "DA-OTAC-YS_R3", - "DA-OTAC-YS_R4", - "DA-OTAC-YS_R5" - ], - "6mo_Orthotropic_Young_Axilaries": [ - "DA-OAA-YA_R1", - "DA-OAA-YA_R2", - "DA-OAA-YA_R3", - "DA-OAA-YA_R4", - "DA-OAA-YA_R5" - ], - "6mo_Orthotropic_Old_Axilaries": [ - "DA-OAA-OA_R1", - "DA-OAA-OA_R2", - "DA-OAA-OA_R3", - "DA-OAA-OA_R4" - ], - "Plagiotropic_Shoot_Apex": [ - "DA-PSA_R1", - "DA-PSA_R2", - "DA-PSA_R3", - "DA-PSA_R4", - "DA-PSA_R5" - ], - "Plagiotropic_A_Leaf": [ - "DA-PTL-A_R1", - "DA-PTL-A_R2", - "DA-PTL-A_R3", - "DA-PTL-A_R4", - "DA-PTL-A_R5" - ], - "Plagiotropic_C_Leaf": [ - "DA-PTL-C_R1", - "DA-PTL-C_R3", - "DA-PTL-C_R4" - ], - "Plagiotropic_E_Leaf": [ - "DA-PTL-E_R1", - "DA-PTL-E_R2", - "DA-PTL-E_R3", - "DA-PTL-E_R4", - "DA-PTL-E_R5" - ], - "Plagiotropic_Old_Axiliaries": [ - "DA-OA_R1", - "DA-OA_R2", - "DA-OA_R3", - "DA-OA_R4", - "DA-OA_R5" - ], - "Plagiotropic_Young_Axilaries": [ - "DA-YA_R1", - "DA-YA_R2", - "DA-YA_R3", - "DA-YA_R4", - "DA-YA_R5" - ] - } - } - } - }, - "Drought_Diurnal_Atlas": { - "database": "cacao_drought_diurnal_atlas_sca", - "view_name": "Drought_Diurnal_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Root_Watered_T1": [ - "DD-WTR-T1_R1", - "DD-WTR-T1_R2", - "DD-WTR-T1_R3" - ], - "Root_Watered_T2": [ - "DD-WTR-T2_R1", - "DD-WTR-T2_R2", - "DD-WTR-T2_R3" - ], - "Root_Watered_T3": [ - "DD-WTR-T3_R1", - "DD-WTR-T3_R2", - "DD-WTR-T3_R3" - ], - "Root_Watered_T4": [ - "DD-WTR-T4_R1", - "DD-WTR-T4_R2", - "DD-WTR-T4_R3" - ], - "Root_Watered_T5": [ - "DD-WTR-T5_R1", - "DD-WTR-T5_R2", - "DD-WTR-T5_R3" - ], - "Root_Watered_T6": [ - "DD-WTR-T6_R1", - "DD-WTR-T6_R2", - "DD-WTR-T6_R3" - ], - "Root_Watered_T7": [ - "DD-WTR-T7_R2", - "DD-WTR-T7_R3", - "DD-WTR-T7-R1" - ], - "Root_Drought_T1": [ - "DD-DTR-T1_R1", - "DD-DTR-T1_R2", - "DD-DTR-T1_R3" - ], - "Root_Drought_T2": [ - "DD-DTR-T2_R1", - "DD-DTR-T2_R2", - "DD-DTR-T2_R3" - ], - "Root_Drought_T3": [ - "DD-DTR-T3_R1", - "DD-DTR-T3_R2", - "DD-DTR-T3_R3" - ], - "Root_Drought_T4": [ - "DD-DTR-T4_R1", - "DD-DTR-T4_R2", - "DD-DTR-T4_R3" - ], - "Root_Drought_T5": [ - "DD-DTR-T5_R1", - "DD-DTR-T5_R2" - ], - "Root_Drought_T6": [ - "DD-DTR-T6_R1", - "DD-DTR-T6_R2", - "DD-DTR-T6_R3" - ], - "Root_Drought_T7": [ - "DD-DTR-T7_R1", - "DD-DTR-T7_R2", - "DD-DTR-T7_R3" - ], - "Leaf_Watered_T1": [ - "DD-WTL-T1_R1", - "DD-WTL-T1_R2", - "DD-WTL-T1_R3" - ], - "Leaf_Watered_T2": [ - "DD-WTL-T2_R1", - "DD-WTL-T2_R2", - "DD-WTL-T2_R3" - ], - "Leaf_Watered_T3": [ - "DD-WTL-T3_R1", - "DD-WTL-T3_R2", - "DD-WTL-T3_R3" - ], - "Leaf_Watered_T4": [ - "DD-WTL-T4_R1", - "DD-WTL-T4_R2", - "DD-WTL-T4_R3" - ], - "Leaf_Watered_T5": [ - "DD-WTL-T5_R1", - "DD-WTL-T5_R2" - ], - "Leaf_Watered_T6": [ - "DD-WTL-T6_R1", - "DD-WTL-T6_R2", - "DD-WTL-T6_R3" - ], - "Leaf_Watered_T7": [ - "DD-WTL-T7_R1", - "DD-WTL-T7_R2", - "DD-WTL-T7_R3" - ], - "Leaf_Drought_T1": [ - "DD-DTL-T1_R1", - "DD-DTL-T1_R2", - "DD-DTL-T1_R3" - ], - "Leaf_Drought_T2": [ - "DD-DTL-T2_R1", - "DD-DTL-T2_R2", - "DD-DTL-T2_R3" - ], - "Leaf_Drought_T3": [ - "DD-DTL-T3_R1", - "DD-DTL-T3_R2", - "DD-DTL-T3_R3" - ], - "Leaf_Drought_T4": [ - "DD-DTL-T4_R1", - "DD-DTL-T4_R2", - "DD-DTL-T4_R3" - ], - "Leaf_Drought_T5": [ - "DD-DTL-T5_R1", - "DD-DTL-T5_R2", - "DD-DTL-T5_R3" - ], - "Leaf_Drought_T6": [ - "DD-DTL-T6_R1", - "DD-DTL-T6_R2", - "DD-DTL-T6_R3" - ], - "Leaf_Drought_T7": [ - "DD-DTL-T7_R1", - "DD-DTL-T7_R2", - "DD-DTL-T7_R3" - ], - "Apex_Watered_T1": [ - "DD-WTA-T1_R1", - "DD-WTA-T1_R2", - "DD-WTA-T1_R3" - ], - "Apex_Watered_T2": [ - "DD-WTA-T2_R1", - "DD-WTA-T2_R2", - "DD-WTA-T2_R3" - ], - "Apex_Watered_T3": [ - "DD-WTA-T3_R1", - "DD-WTA-T3_R2", - "DD-WTA-T3_R3" - ], - "Apex_Watered_T4": [ - "DD-WTA-T4_R1", - "DD-WTA-T4_R2", - "DD-WTA-T4_R3" - ], - "Apex_Watered_T5": [ - "DD-WTA-T5_R1", - "DD-WTA-T5_R2", - "DD-WTA-T5_R3" - ], - "Apex_Watered_T6": [ - "DD-WTA-T6_R1", - "DD-WTA-T6_R2", - "DD-WTA-T6_R3" - ], - "Apex_Watered_T7": [ - "DD-WTA-T7_R1", - "DD-WTA-T7_R2", - "DD-WTA-T7_R3" - ], - "Apex_Drought_T1": [ - "DD-DTA-T1_R1", - "DD-DTA-T1_R2", - "DD-DTA-T1_R3" - ], - "Apex_Drought_T2": [ - "DD-DTA-T2_R1", - "DD-DTA-T2_R2", - "DD-DTA-T2_R3" - ], - "Apex_Drought_T3": [ - "DD-DTA-T3_R1", - "DD-DTA-T3_R2", - "DD-DTA-T3_R3" - ], - "Apex_Drought_T4": [ - "DD-DTA-T4_R1", - "DD-DTA-T4_R2", - "DD-DTA-T4_R3" - ], - "Apex_Drought_T5": [ - "DD-DTA-T5_R1", - "DD-DTA-T5_R2", - "DD-DTA-T5_R3" - ], - "Apex_Drought_T6": [ - "DD-DTA-T6_R1", - "DD-DTA-T6_R2", - "DD-DTA-T6_R3" - ], - "Apex_Drought_T7": [ - "DD-DTA-T7_R1", - "DD-DTA-T7_R2", - "DD-DTA-T7_R3" - ] - } - } - } - }, - "Meristem_Atlas": { - "database": "cacao_meristem_atlas_sca", - "view_name": "Meristem_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Plagiotropic_Apex_Stage_4": [ - "MA-PTA-Sca6-S4_R1", - "MA-PTA-Sca6-S4_R2", - "MA-PTA-Sca6-S4_R3" - ], - "Plagiotropic_Apex_Stage_3": [ - "MA-PTA-Sca6-S3_R1", - "MA-PTA-Sca6-S3_R2", - "MA-PTA-Sca6-S3_R3" - ], - "Plagiotropic_Apex_Stage_2": [ - "MA-PTA-Sca6-S2_R1", - "MA-PTA-Sca6-S2_R2", - "MA-PTA-Sca6-S2_R3" - ], - "Plagiotropic_Apex_Stage_1": [ - "MA-PTA-Sca6-S1_R1", - "MA-PTA-Sca6-S1_R2", - "MA-PTA-Sca6-S1_R3" - ], - "Orthotropic_Apex_Stage_4": [ - "MA-OTA-Sca6-S4_R1", - "MA-OTA-Sca6-S4_R2", - "MA-OTA-Sca6-S4_R3" - ], - "Orthotropic_Apex_Stage_3": [ - "MA-OTA-Sca6-S3_R1", - "MA-OTA-Sca6-S3_R2", - "MA-OTA-Sca6-S3_R3" - ], - "Orthotropic_Apex_Stage_2": [ - "MA-OTA-Sca6-S2_R1", - "MA-OTA-Sca6-S2_R2", - "MA-OTA-Sca6-S2_R3" - ], - "Orthotropic_Apex_Stage_1": [ - "MA-OTA-Sca6-S1_R1", - "MA-OTA-Sca6-S1_R2", - "MA-OTA-Sca6-S1_R3" - ] - } - } - } - }, - "Seed_Atlas": { - "database": "cacao_seed_atlas_sca", - "view_name": "Seed_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "CCN": [ - "CGA-SE-LS-E_R1", - "CGA-SE-LS-E_R2", - "CGA-SE-LS-E_R3", - "CGA-SE-LS-E_R4", - "CGA-SE-LS-E_R5" - ], - "IMC": [ - "SA-SE-LS-IMC-E_R1", - "SA-SE-LS-IMC-E_R2", - "SA-SE-LS-IMC-E_R3", - "SA-SE-LS-IMC-E_R4", - "SA-SE-LS-IMC-E_R5" - ], - "Sca": [ - "SA-SE-LS-Sca-E_R1", - "SA-SE-LS-Sca-E_R2", - "SA-SE-LS-Sca-E_R3", - "SA-SE-LS-Sca-E_R4", - "SA-SE-LS-Sca-E_R5" - ] - } - } - } - } - } - } - }, - "cacao tc": { - - "data": { - "species": "cacao tc", - "views": { - "Cacao_Infection": { - "database": "cacao_infection", - "view_name": "Cacao_Infection", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "NA32_Basal": [ - "basal_N432_rep4", - "basal_NA32_rep1", - "basal_NA32_rep2", - "basal_NA32_rep3", - "basal_NA32_rep5", - "basal_NA32_rep6", - "basal_NA32_rep7", - "basal_NA32_rep8" - ], - "Scavina6_Basal": [ - "basal_SCA6_rep1", - "basal_SCA6_rep2", - "basal_SCA6_rep3", - "basal_SCA6_rep4", - "basal_SCA6_rep5", - "basal_SCA6_rep6", - "basal_SCA6_rep7", - "basal_SCA6_rep8" - ], - "NA32_Control_24h": [ - "NA32_Control_24hr_rep1", - "NA32_Control_24hr_rep2", - "NA32_Control_24hr_rep3", - "NA32_Control_24hr_rep4" - ], - "NA32_Control_6h": [ - "NA32_Control_6hr_rep1", - "NA32_Control_6hr_rep2", - "NA32_Control_6hr_rep3" - ], - "NA32_Control_72h": [ - "NA32_Control_72hr_rep1", - "NA32_Control_72hr_rep2", - "NA32_Control_72hr_rep3", - "NA32_Control_72hr_rep4" - ], - "NA32_Infected_6h": [ - "NA32_Pathogen_6hr_rep1", - "NA32_Pathogen_6hr_rep2", - "NA32_Pathogen_6hr_rep3", - "NA32_Pathogen_6hr_rep4" - ], - "NA32_Infected_24h": [ - "NA32_Pathogen_24hr_rep1", - "NA32_Pathogen_24hr_rep2", - "NA32_Pathogen_24hr_rep3", - "NA32_Pathogen_24hr_rep4" - ], - "NA32_Infected_72h": [ - "NA32_Pathogen_72hr_rep1", - "NA32_Pathogen_72hr_rep2", - "NA32_Pathogen_72hr_rep3", - "NA32_Pathogen_72hr_rep4" - ], - "Scavina6_Control_6h": [ - "SCA6_Control_6hr_rep1", - "SCA6_Control_6hr_rep2", - "SCA6_Control_6hr_rep3", - "SCA6_Control_6hr_rep4" - ], - "Scavina6_Control_24h": [ - "SCA6_Control_24hr_rep1", - "SCA6_Control_24hr_rep2", - "SCA6_Control_24hr_rep3", - "SCA6_Control_24hr_rep4" - ], - "Scavina6_Control_72h": [ - "SCA6_Control_72hr_rep1", - "SCA6_Control_72hr_rep2", - "SCA6_Control_72hr_rep3", - "SCA6_Control_72hr_rep4" - ], - "Scavina6_Infected_6h": [ - "SCA6_Pathogen_6hr_rep1", - "SCA6_Pathogen_6hr_rep2", - "SCA6_Pathogen_6hr_rep3", - "SCA6_Pathogen_6hr_rep4" - ], - "Scavina6_Infected_72h": [ - "SCA6_Pathogen_72hr_rep1", - "SCA6_Pathogen_72hr_rep2", - "SCA6_Pathogen_72hr_rep3", - "SCA6_Pathogen_72hr_rep4" - ] - } - }, - "basal_SCA6_rep8;Med_CTRL": { - "controls": [ - "basal_SCA6_rep8", - "Med_CTRL" - ], - "treatments": { - "Scavina6_Infected_24h": [ - "SCA6_Pathogen_24hr_rep1", - "SCA6_Pathogen_24hr_rep2", - "SCA6_Pathogen_24hr_rep3", - "SCA6_Pathogen_24hr_rep4" - ] - } - } - } - }, - "Cacao_Leaf": { - "database": "cacao_leaf", - "view_name": "Cacao_Leaf", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Scavina6_DE": [ - "Sca6_DE_1", - "Sca6_DE_2", - "Sca6_DE_3", - "Sca6_DE_4", - "Sca6_DE_5" - ], - "Scavina6_AB": [ - "Sca6_AB_1", - "Sca6_AB_2", - "Sca6_AB_3", - "Sca6_AB_4", - "Sca6_AB_5" - ], - "Scavina6_C": [ - "Sca6_C_1", - "Sca6_C_2", - "Sca6_C_3", - "Sca6_C_4", - "Sca6_C_5" - ], - "ICS1_AB": [ - "ICS1_AB_1", - "ICS1_AB_2", - "ICS1_AB_3", - "ICS1_AB_4", - "ICS1_AB_5" - ], - "ICS1_C": [ - "ICS1_C_1", - "ICS1_C_2", - "ICS1_C_3", - "ICS1_C_4", - "ICS1_C_5" - ], - "ICS1_DE": [ - "ICS1_DE_1", - "ICS1_DE_2", - "ICS1_DE_3", - "ICS1_DE_4", - "ICS1_DE_5" - ] - } - } - } - } - } - } - }, - "camelina": { - - "data": { - "species": "camelina", - "views": { - "Developmental_Atlas_FPKM": { - "database": "camelina", - "view_name": "Developmental_Atlas_FPKM", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Germinating_Seed": [ - "germinating_seed_1", - "germinating_seed_2", - "germinating_seed_3" - ], - "Cotyledon": [ - "cotyledon_1", - "cotyledon_2", - "cotyledon_3" - ], - "Young_Leaf": [ - "young_leaf_1", - "young_leaf_2", - "young_leaf_3" - ], - "Senescing_Leaf": [ - "senescing_leaf_1", - "senescing_leaf_2", - "senescing_leaf_3" - ], - "Root": [ - "root_1", - "root_2", - "root_3" - ], - "Stem": [ - "stem_1", - "stem_2", - "stem_3" - ], - "Buds": [ - "bud_1", - "bud_2", - "bud_3" - ], - "Flower": [ - "flower_1", - "flower_2", - "flower_3" - ], - "Early_Seed_Development": [ - "early_seed_development_1", - "early_seed_development_2", - "early_seed_development_3" - ], - "Early-mid_Seed_Development": [ - "early_mid_seed_development_1", - "early_mid_seed_development_2", - "early_mid_seed_development_3" - ], - "Late-mid_Seed_Development": [ - "late_mid_seed_development_1", - "late_mid_seed_development_2", - "late_mid_seed_development_3" - ], - "Late_Seed_Development": [ - "late_seed_development_1", - "late_seed_development_2", - "late_seed_development_3" - ] - } - } - } - }, - "Developmental_Atlas_TPM": { - "database": "camelina_tpm", - "view_name": "Developmental_Atlas_TPM", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Germinating_Seed": [ - "germinating_seed_1", - "germinating_seed_2", - "germinating_seed_3" - ], - "Cotyledon": [ - "cotyledon_1", - "cotyledon_2", - "cotyledon_3" - ], - "Young_Leaf": [ - "young_leaf_1", - "young_leaf_2", - "young_leaf_3" - ], - "Senescing_Leaf": [ - "senescing_leaf_1", - "senescing_leaf_2", - "senescing_leaf_3" - ], - "Root": [ - "root_1", - "root_2", - "root_3" - ], - "Stem": [ - "stem_1", - "stem_2", - "stem_3" - ], - "Buds": [ - "bud_1", - "bud_2", - "bud_3" - ], - "Flower": [ - "flower_1", - "flower_2", - "flower_3" - ], - "Early_Seed_Development": [ - "early_seed_development_1", - "early_seed_development_2", - "early_seed_development_3" - ], - "Early-mid_Seed_Development": [ - "early_mid_seed_development_1", - "early_mid_seed_development_2", - "early_mid_seed_development_3" - ], - "Late-mid_Seed_Development": [ - "late_mid_seed_development_1", - "late_mid_seed_development_2", - "late_mid_seed_development_3" - ], - "Late_Seed_Development": [ - "late_seed_development_1", - "late_seed_development_2", - "late_seed_development_3" - ] - } - } - } - } - } - } - }, - "cannabis": { - - "data": { - "species": "cannabis", - "views": { - "Cannabis_Atlas": { - "database": "cannabis", - "view_name": "Cannabis_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "PK-Shoot": [ - "PK-SHT" - ], - "PK-Root": [ - "PK-RT" - ], - "PK-MidFlower": [ - "PK-MFLW" - ], - "PK-EarlyFlower": [ - "PK-EFLW" - ], - "PK-PreFlower": [ - "PK-PFLW" - ], - "PK-Stem": [ - "PK-STM" - ] - } - } - } - } - } - } - }, - "canola": { - - "data": { - "species": "canola", - "views": { - "Canola_Seed": { - "database": "canola_seed", - "view_name": "Canola_Seed", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Chalazal_proliferating_tissue,_ovule_stage": [ - "ovCPT1_2", - "ovCPT3", - "ovCPT3_2" - ], - "Chalazal_seed_coat,_ovule_stage": [ - "ovCZSC1", - "ovCZSC2", - "ovCZSC3" - ], - "Inner_seed_coat,_ovule_stage": [ - "ovISC1", - "ovISC2", - "ovISC3" - ], - "Outer_seed_coat,_ovule_stage": [ - "ovOSC1", - "ovOSC2", - "ovOSC3" - ], - "Chalazal_proliferating_tissue,_globular_stage": [ - "gCPT1", - "gCPT2", - "gCPT3" - ], - "Chalazal_endosperm,_globular_stage": [ - "gCZE1", - "gCZE2", - "gCZE3" - ], - "Chalazal_seed_coat,_globular_stage": [ - "gCZSC1", - "gCZSC2", - "gCZSC3" - ], - "Embryo_proper,_globular_stage": [ - "gEP1", - "gEP2", - "GLOB_EP4J1", - "GLOB_EP4J17" - ], - "Inner_seed_coat,_globular_stage": [ - "gISC1", - "gISC2", - "gISC3" - ], - "Outer_seed_coat,_globular_stage": [ - "gOSC2", - "gOSC3" - ], - "Micropylar_endosperm,_globular_stage": [ - "gMCE1", - "gMCE2", - "gMCE3", - "gMCE4", - "GLOB_MCE2" - ], - "Peripheral_endosperm,_globular_stage": [ - "gPEN1", - "gPEN2" - ], - "Chalazal_proliferating_tissue,_heart_stage": [ - "hCPT1", - "hCPT2", - "hCPT3" - ], - "Chalazal_endosperm,_heart_stage": [ - "hCZE1", - "hCZE2" - ], - "Chalazal_seed_coat,_heart_stage": [ - "hCZSC1", - "hCZSC2", - "hCZSC3" - ], - "Embryo_proper,_heart_stage": [ - "hEPJ", - "HRT_EPJ" - ], - "Inner_seed_coat,_heart_stage": [ - "hISC1_3", - "hISC2", - "hISC3" - ], - "Micropylar_endosperm,_heart_stage": [ - "hMCE2", - "HRT_MCE1", - "HRT_MCE2", - "HRT_MCE26" - ], - "Outer_seed_coat,_heart_stage": [ - "hOSC1", - "hOSC2", - "hOSC3" - ], - "Peripheral_endosperm,_heart_stage": [ - "hPEN1", - "hPEN2" - ], - "Chalazal_proliferating_tissue,_maturation_green_stage": [ - "mgCPT1", - "mgCPT2", - "mgCPT3" - ], - "Chalazal_seed_coat,_maturation_green_stage": [ - "mgCZSC2", - "mgCZSC3", - "mgCZSC3_2" - ], - "Inner_seed_coat,_maturation_green_stage": [ - "mgISC1", - "mgISC2" - ], - "Outer_seed_coat,_maturation_green_stage": [ - "mgOSC1", - "mgOSC2", - "mgOSC3" - ], - "Embryo_cotyledons,_maturation_green_stage": [ - "MG_COT1", - "MG_COT2", - "MG_COT8" - ], - "Embryo_root,_maturation_green_stage": [ - "MG_ROOT2", - "MG_ROOT3" - ] - } - } - } - } - } - } - }, - "eutrema": { - - "data": { - "species": "eutrema", - "views": { - "Eutrema": { - "database": "thellungiella_db", - "view_name": "Eutrema", - "groups": { - "THELLUNGIELLA_CTRL": { - "controls": [ - "THELLUNGIELLA_CTRL" - ], - "treatments": { - "Shandong_accession_grown_in_cabinet,_rosette_leaves": [ - "SC1", - "SC2", - "SC3" - ], - "Yukon_accession_grown_in_cabinet,_rosette_leaves": [ - "YC1", - "YC2", - "YC3" - ], - "Yukon_accession_collected_from_the_field_in_2005": [ - "YF1", - "YF2", - "YF3" - ] - } - } - } - } - } - } - }, - "grape": { - - "data": { - "species": "grape", - "views": { - "grape_developmental": { - "database": "grape_developmental", - "view_name": "grape_developmental", - "groups": { - "Dev": { - "controls": [ - "GRAPE_CTRL" - ], - "treatments": { - "Tendril_-_Young": [ - "GSM881670", - "GSM881671", - "GSM881672" - ], - "Tendril_-_Well_Developed": [ - "GSM881673", - "GSM881674", - "GSM881675" - ], - "Tendril_-_Fruit_Set": [ - "GSM881676", - "GSM881677", - "GSM881678" - ], - "Leaf_-_Young": [ - "GSM881586", - "GSM881587", - "GSM881588" - ], - "Leaf_-_Fruit_Set": [ - "GSM881589", - "GSM881590", - "GSM881591" - ], - "Leaf_-_Senescent": [ - "GSM881592", - "GSM881593", - "GSM881594" - ], - "Seedling": [ - "GSM881640", - "GSM881641", - "GSM881642" - ], - "Stem_-_Young": [ - "GSM881664", - "GSM881665", - "GSM881666" - ], - "Stem_-_Mature_(Woody)": [ - "GSM881667", - "GSM881668", - "GSM881669" - ], - "Bud_-_Bud_Swelling_Stage": [ - "GSM881535", - "GSM881536", - "GSM881537" - ], - "Bud_-_Bud_Burst_Initial_Stage": [ - "GSM881538", - "GSM881539", - "GSM881540" - ], - "Bud_-_Bud_Burst_Later_Stage": [ - "GSM881541", - "GSM881542", - "GSM881543" - ], - "Bud_-_Latent_Bud": [ - "GSM881544", - "GSM881545", - "GSM881546" - ], - "Bud_-_Winter_Dormant": [ - "GSM881547", - "GSM881548", - "GSM881549" - ], - "Flower_-_Young": [ - "GSM881571", - "GSM881572", - "GSM881573" - ], - "Flower_-_Well_Developed": [ - "GSM881574", - "GSM881575", - "GSM881576" - ], - "Flower_-_Start_of_Flowering": [ - "GSM881577", - "GSM881578", - "GSM881579" - ], - "Flower_-_Flowering": [ - "GSM881580", - "GSM881581", - "GSM881582" - ], - "Root": [ - "GSM881583", - "GSM881584", - "GSM881585" - ], - "Carpel": [ - "GSM881595", - "GSM881596", - "GSM881597" - ], - "Stamen": [ - "GSM881517", - "GSM881518", - "GSM881519" - ], - "Petals": [ - "GSM881598", - "GSM881599", - "GSM881600" - ], - "Pollen": [ - "GSM881610", - "GSM881611", - "GSM881612" - ], - "Rachis_-_Fruit_Set": [ - "GSM881613", - "GSM881614", - "GSM881615" - ], - "Seed_-_Fruit_Set": [ - "GSM881634", - "GSM881635", - "GSM881636" - ], - "Pericarp_-_Fruit_Set": [ - "GSM881520", - "GSM881521", - "GSM881522" - ], - "Rachis_-_Post_Fruit_Set": [ - "GSM881616", - "GSM881617", - "GSM881618" - ], - "Pericarp_-_Post_Fruit_Set": [ - "GSM881523", - "GSM881524", - "GSM881525" - ], - "Seed_-_Post_Fruit_Set": [ - "GSM881637", - "GSM881638", - "GSM881639" - ], - "Flesh_-_Post_Fruit_Set": [ - "GSM881550", - "GSM881551", - "GSM881552" - ], - "Skin_-_Post_Fruit_Set": [ - "GSM881643", - "GSM881644", - "GSM881645" - ], - "Seed_-_Veraison": [ - "GSM881628", - "GSM881629", - "GSM881630" - ], - "Pericarp_-_Veraison": [ - "GSM881526", - "GSM881527", - "GSM881528" - ], - "Flesh_-_Veraison": [ - "GSM881553", - "GSM881554", - "GSM881555" - ], - "Skin_-_Veraison": [ - "GSM881646", - "GSM881647", - "GSM881648" - ], - "Rachis_-_Veraison": [ - "GSM881619", - "GSM881620", - "GSM881621" - ], - "Rachis_-_Mid_Ripening": [ - "GSM881622", - "GSM881623", - "GSM881624" - ], - "Seed_-_Mid_Ripening": [ - "GSM881628", - "GSM881629", - "GSM881630" - ], - "Pericarp_-_Mid_Ripening": [ - "GSM881529", - "GSM881530", - "GSM881531" - ], - "Flesh_-_Mid_Ripening": [ - "GSM881556", - "GSM881557", - "GSM881558" - ], - "Skin_-_Mid_Ripening": [ - "GSM881649", - "GSM881650", - "GSM881651" - ], - "Rachis_-_Ripening": [ - "GSM881625", - "GSM881626", - "GSM881627" - ], - "Pericarp_-_Ripening": [ - "GSM881532", - "GSM881533", - "GSM881534" - ], - "Flesh_-_Ripening": [ - "GSM881559", - "GSM881560", - "GSM881561" - ], - "Skin_-_Ripening": [ - "GSM881652", - "GSM881653", - "GSM881654" - ] - } - }, - "Flesh_Stress": { - "controls": [ - "GRAPE_FLESH_STRESS_CTRL" - ], - "treatments": { - "Flesh_-_PHWI": [ - "GSM881562", - "GSM881563", - "GSM881564" - ], - "Flesh_-_PHWII": [ - "GSM881565", - "GSM881566", - "GSM881567" - ], - "Flesh_-_PHWIII": [ - "GSM881568", - "GSM881569", - "GSM881570" - ] - } - }, - "Pericarp_Stress": { - "controls": [ - "GRAPE_PERICARP_STRESS_CTRL" - ], - "treatments": { - "Pericarp_-_PHWI": [ - "GSM881601", - "GSM881602", - "GSM881603" - ], - "Pericarp_-_PHWII": [ - "GSM881604", - "GSM881605", - "GSM881606" - ], - "Pericarp_-_PHWIII": [ - "GSM881607", - "GSM881608", - "GSM881609" - ] - } - }, - "Skin_Stress": { - "controls": [ - "GRAPE_SKIN_STRESS_CTRL" - ], - "treatments": { - "Skin_-_PHWI": [ - "GSM881655", - "GSM881656", - "GSM881657" - ], - "Skin_-_PHWII": [ - "GSM881658", - "GSM881659", - "GSM881660" - ], - "Skin_-_PHWIII": [ - "GSM881661", - "GSM881662", - "GSM881663" - ] - } - } - } - } - } - } - }, - "kalanchoe": { - - "data": { - "species": "kalanchoe", - "views": { - "Light_Response": { - "database": "kalanchoe", - "view_name": "Light_Response", - "groups": { - "White_Light_Dawn_control_group": { - "controls": [ - "WL_Dawn_rep1", - "WL_Dawn_rep2", - "WL_Dawn_rep3" - ], - "treatments": { - "HL_Dusk": [ - "HL_Dusk_rep1", - "HL_Dusk_rep2", - "HL_Dusk_rep3" - ], - "RL_Dusk": [ - "RL_Dusk_rep1", - "RL_Dusk_rep2", - "RL_Dusk_rep3" - ], - "HL_Dawn": [ - "HL_Dawn_rep1", - "HL_Dawn_rep2", - "HL_Dawn_rep3" - ], - "BL_Dawn": [ - "BL_Dawn_rep1", - "BL_Dawn_rep2", - "BL_Dawn_rep3" - ], - "LL_Dawn": [ - "LL_Dawn_rep1", - "LL_Dawn_rep2", - "LL_Dawn_rep3" - ], - "LL_Dusk": [ - "LL_Dusk_rep1", - "LL_Dusk_rep2", - "LL_Dusk_rep3" - ], - "WL_Dusk": [ - "WL_Dusk_rep1", - "WL_Dusk_rep2", - "WL_Dusk_rep3" - ], - "BL_Dusk": [ - "BL_Dusk_rep1", - "BL_Dusk_rep2", - "BL_Dusk_rep3" - ], - "DG_Dusk": [ - "DG_Dusk_rep1", - "DG_Dusk_rep2", - "DG_Dusk_rep3" - ], - "RL_Dawn": [ - "RL_Dawn_rep1", - "RL_Dawn_rep2", - "RL_Dawn_rep3" - ], - "DG_Dawn": [ - "DG_Dawn_rep1", - "DG_Dawn_rep2", - "DG_Dawn_rep3" - ], - "WL_Dawn": [ - "WL_Dawn_rep1", - "WL_Dawn_rep2", - "WL_Dawn_rep3" - ], - "FR_Dawn": [ - "FRL_Dawn_rep1", - "FRL_Dawn_rep2", - "FRL_Dawn_rep3" - ], - "FR_Dusk": [ - "FRL_Dusk_rep1", - "FRL_Dusk_rep2", - "FRL_Dusk_rep3" - ] - } - } - } - } - } - } - }, - "little millet": { - - "data": { - "species": "little millet", - "views": { - "Life_Cycle": { - "database": "little_millet", - "view_name": "Life_Cycle", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Germinating_Seed": [ - "GS1", - "GS2", - "GS3" - ], - "Radicle": [ - "RD1", - "RD2", - "RD3" - ], - "Plumule": [ - "PU1", - "PU2", - "PU3" - ], - "Young_Leaf": [ - "YL1", - "YL2", - "YL3" - ], - "Young_Root": [ - "YR1", - "YR2" - ], - "Crown_Meristem": [ - "CM1", - "CM2", - "CM3" - ], - "Vegetative_Stem": [ - "VS1", - "VS2" - ], - "Panicle_Early": [ - "PE1", - "PE2", - "PE3" - ], - "Panicle_Mid": [ - "PM1", - "PM2", - "PM3" - ], - "Panicle_Late": [ - "PL1", - "PL2", - "PL3" - ] - } - } - } - } - } - } - }, - "lupin": { - - "data": { - "species": "lupin", - "views": { - "LCM_Leaf": { - "database": "lupin_lcm_leaf", - "view_name": "LCM_Leaf", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Epidermis": [ - "Leaf_epidermis_1", - "Leaf_epidermis_2" - ], - "Mesophyll": [ - "Leaf_mesophyll_1", - "Leaf_mesophyll_2" - ], - "Vasculature": [ - "Leaf_vasculature_1", - "Leaf_vasculature_2" - ] - } - } - } - }, - "LCM_Pod": { - "database": "lupin_lcm_pod", - "view_name": "LCM_Pod", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Exocarp": [ - "Pod_exocarp_1", - "Pod_exocarp_2" - ], - "Endocarp": [ - "Pod_endocarp_1", - "Pod_endocarp_2" - ], - "Bundle_sheath": [ - "Pod_bundle_sheath_1", - "Pod_bundle_sheath_2" - ], - "Mesocarp": [ - "Pod_mesocarp_1", - "Pod_mesocarp_2" - ], - "Transverse_vasculature": [ - "Pod_transverse_vasculature_1", - "Pod_transverse_vasculature_2" - ], - "Ventral_suture_vasculature": [ - "Pod_ventral_suture_vasculature_1", - "Pod_ventral_suture_vasculature_2" - ] - } - } - } - }, - "LCM_Stem": { - "database": "lupin_lcm_stem", - "view_name": "LCM_Stem", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Epidermis": [ - "Stem_epidermis_1" - ], - "Parenchyma": [ - "Stem_parenchyma_1", - "Stem_parenchyma_2" - ], - "Phloem": [ - "Stem_phloem_1", - "Stem_phloem_2" - ], - "Xylem": [ - "Stem_xylem_1", - "Stem_xylem_2" - ] - } - } - } - }, - "Whole_Plant": { - "database": "lupin_whole_plant", - "view_name": "Whole_Plant", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Big_seed": [ - "Big_seed" - ], - "Big_pod": [ - "Big_pod" - ], - "Flowers": [ - "Flowers" - ], - "Leaves": [ - "Leaves" - ], - "Pedicels": [ - "Pedicels" - ], - "Roots": [ - "Roots" - ], - "Small_pod_with_seeds": [ - "Small_pod_with_seeds" - ], - "Stem": [ - "Stem" - ] - } - } - } - } - } - } - }, - "maize": { - - "data": { - "species": "maize", - "views": { - "Downs_et_al_Atlas": { - "database": "maize_gdowns", - "view_name": "Downs_et_al_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "24DAP_leaf;_15cm_tip_of_2nd_leaf_above_top_ear": [ - "24DAP_leaf_1", - "24DAP_leaf_2", - "24DAP_leaf_3" - ], - "17DAP_endosperm;_endosperm_of_top_ear": [ - "17DAP_endosperm_1", - "17DAP_endosperm_2", - "17DAP_endosperm_3" - ], - "VE_root;_seminal_root": [ - "VE_root_1", - "VE_root_2", - "VE_root_3" - ], - "V16_tassel;_spikelet_of_tassel_(top_10_cm)": [ - "V16_tassel_1", - "V16_tassel_2", - "V16_tassel_3" - ], - "V4_tassel;_1mm_tassel_meristem_and_1mm_uppermost_stem_below_tassel": [ - "V4_tassel_1", - "V4_tassel_2", - "V4_tassel_3" - ], - "24DAP_embryo;_embryo_of_top_ear": [ - "24DAP_embryo_1", - "24DAP_embryo_2", - "24DAP_embryo_3" - ], - "V2_nodal_root;_nodal_root": [ - "V2_nodal_root_1", - "V2_nodal_root_2", - "V2_nodal_root_3" - ], - "V16_cob;_top_ear_(5_cm)_cob": [ - "V16_cob_1", - "V16_cob_2", - "V16_cob_3" - ], - "R1_stalk;_R1-15_cm_stalk_below_tassel": [ - "R1_stalk_1", - "R1_stalk_2", - "R1_stalk_3" - ], - "10DAP_embryo;_embryo_of_top_ear": [ - "10DAP_embryo_1", - "10DAP_embryo_2", - "10DAP_embryo_3" - ], - "24DAP_endosperm;_endosperm_of_top_ear": [ - "24DAP_endosperm_1", - "24DAP_endosperm_2", - "24DAP_endosperm_3" - ], - "17DAP_pericarp;_pericarp_of_top_ear": [ - "17DAP_pericarp_1", - "17DAP_pericarp_2", - "17DAP_pericarp_3" - ], - "V5_stalk_below_tassel;_stalk_below_tassel_(2_cm)": [ - "V5_stalk_below_tassel_1", - "V5_stalk_below_tassel_2", - "V5_stalk_below_tassel_3" - ], - "V10_tassel;_top_10_cm_of_tassel_(~20_cm)": [ - "V10_tassel_1", - "V10_tassel_2", - "V10_tassel_3" - ], - "R1_leaf;_15_cm_tip_of_2nd_leaf_above_top_ear": [ - "R1_leaf_1", - "R1_leaf_2", - "R1_leaf_3" - ], - "V5_tassel;_tassel_3-5mm": [ - "V5_tassel_1", - "V5_tassel_2", - "V5_tassel_3" - ], - "31DAP_embryo;_embryo_of_top_ear": [ - "31DAP_embryo_1", - "31DAP_embryo_2", - "31DAP_embryo_3" - ], - "V8_V9_ear;_top_ear_3-5mm": [ - "V8_V9_ear_1", - "V8_V9_ear_2", - "V8_V9_ear_3" - ], - "V2_stalk;_stalk": [ - "V2_stalk_1", - "V2_stalk_2", - "V2_stalk_3" - ], - "V2_leaf;_actively_growing_leaf:_fourth_leaf": [ - "V2_leaf_1", - "V2_leaf_2", - "V2_leaf_3" - ], - "17DAP_leaf;_15_cm_tip_of_2nd_leaf_above_top_ear": [ - "17DAP_leaf_1", - "17DAP_leaf_2", - "17DAP_leaf_3" - ], - "R1_cob;_cob_of_top_ear": [ - "R1_cob_1", - "R1_cob_2", - "R1_cob_3" - ], - "V7_top_ear_shoot;_top_ear_shoot": [ - "V7_top_ear_shoot_1", - "V7_top_ear_shoot_2", - "V7_top_ear_shoot_3" - ], - "VT_anthers;_anther": [ - "VT_anthers_1", - "VT_anthers_2", - "VT_anthers_3" - ], - "5DAP_ovule;_ovule_of_top_ear": [ - "5DAP_ovule_1", - "5DAP_ovule_2", - "5DAP_ovule_3" - ], - "V16_floret;_top_ear_(5_cm)_floret": [ - "V16_floret_1", - "V16_floret_2", - "V16_floret_3" - ], - "V1_leaf;_1st_and_2nd_leaf": [ - "V1_leaf_1", - "V1_leaf_2", - "V1_leaf_3" - ], - "10DAP_leaf;_15_cm_tip_of_2nd_leaf_above_top_ear": [ - "10DAP_leaf_1", - "10DAP_leaf_2", - "10DAP_leaf_3" - ], - "R1_husk;_most_inner_husk_of_top_ear": [ - "R1_husk_1", - "R1_husk_2", - "R1_husk_3" - ], - "VE_leaf;_coleoptile": [ - "VE_leaf_1", - "VE_leaf_2", - "VE_leaf_3" - ], - "V2_seminal_root;_seminal_root": [ - "V2_seminal_root_1", - "V2_seminal_root_2", - "V2_seminal_root_3" - ], - "V16_silk;_top_ear_(5_cm)_silk": [ - "V16_silk_1", - "V16_silk_2", - "V16_silk_3" - ], - "V8_V9_tassel;_tassel_12-14_cm": [ - "V8_V9_tassel_1", - "V8_V9_tassel_2", - "V8_V9_tassel_3" - ], - "24DAP_root;_nodal_root": [ - "24DAP_root_1", - "24DAP_root_2", - "24DAP_root_3" - ], - "R1_ovule;_R1-ovule_of_top_ear": [ - "R1_ovule_1", - "R1_ovule_2", - "R1_ovule_3" - ], - "5DAP_cob;_cob_of_top_ear": [ - "5DAP_cob_1", - "5DAP_cob_2", - "5DAP_cob_3" - ], - "V7_tassel;_tassel_2_cm": [ - "V7_tassel_1", - "V7_tassel_2", - "V7_tassel_3" - ], - "V5_seminal_root;_seminal_root": [ - "V5_seminal_root_1", - "V5_seminal_root_2", - "V5_seminal_root_3" - ], - "V15_tassel;_spikelet_of_tassel_(~22_cm)": [ - "V15_tassel_1", - "V15_tassel_2", - "V15_tassel_3" - ], - "24DAP_pericarp;_pericarp_of_top_ear": [ - "24DAP_pericarp_1", - "24DAP_pericarp_2", - "24DAP_pericarp_3" - ], - "V10_ear;_top_ear_1-1.5_cm": [ - "V10_ear_1", - "V10_ear_2", - "V10_ear_3" - ], - "V5_leaf;_actively_growing_leaf:_eighth_leaf,_15_cm_including_tip": [ - "V5_leaf_1", - "V5_leaf_2", - "V5_leaf_3" - ], - "10DAP_endosperm;_endosperm_of_top_ear": [ - "10DAP_endosperm_1", - "10DAP_endosperm_2", - "10DAP_endosperm_3" - ], - "31DAP_leaf;_15_cm_tip_of_2nd_leaf_above_top_ear": [ - "31DAP_leaf_1", - "31DAP_leaf_2", - "31DAP_leaf_3" - ], - "R1_silk;_silk_of_top_ear": [ - "R1_silk_1", - "R1_silk_2", - "R1_silk_3" - ], - "V15_ear;_top_ear_3-3.5_cm": [ - "V15_ear_1", - "V15_ear_2", - "V15_ear_3" - ], - "17DAP_embryo;_embryo_of_top_ear": [ - "17DAP_embryo_1", - "17DAP_embryo_2", - "17DAP_embryo_3" - ], - "V5_nodal_root;_nodal_root": [ - "V5_nodal_root_1", - "V5_nodal_root_2", - "V5_nodal_root_3" - ], - "R1_root;_adult_nodal_root": [ - "R1_root_1", - "R1_root_2", - "R1_root_3" - ], - "V1_root;_seminal_root": [ - "V1_root_1", - "V1_root_2", - "V1_root_3" - ] - } - } - } - }, - "Early_Seed": { - "database": "maize_early_seed", - "view_name": "Early_Seed", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "NU0": [ - "NU0" - ], - "NU4": [ - "NU4" - ], - "NU8": [ - "NU8" - ], - "NU12": [ - "NU12" - ], - "NU16": [ - "NU16" - ], - "NU20": [ - "NU20" - ], - "NU24": [ - "NU24" - ], - "NU28": [ - "NU28" - ], - "NU32": [ - "NU32" - ], - "NU36": [ - "NU36" - ], - "NU40": [ - "NU40" - ], - "NU44": [ - "NU44" - ], - "NU48": [ - "NU48" - ], - "NU52": [ - "NU52" - ], - "NU56": [ - "NU56" - ], - "NU60": [ - "NU60" - ], - "NU64": [ - "NU64" - ], - "NU68": [ - "NU68" - ], - "NU72": [ - "NU72" - ], - "NU78": [ - "NU78" - ], - "NU84": [ - "NU84" - ], - "NU90": [ - "NU90" - ], - "NU96": [ - "NU96" - ], - "NU102": [ - "NU102" - ], - "NU108": [ - "NU108" - ], - "NU114": [ - "NU114" - ], - "NU120": [ - "NU120" - ], - "NU126": [ - "NU126" - ], - "NU132": [ - "NU132" - ], - "NU138": [ - "NU138" - ], - "NU144": [ - "NU144" - ] - } - } - } - }, - "Embryonic_Leaf_Development": { - "database": "maize_embryonic_leaf_development", - "view_name": "Embryonic_Leaf_Development", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Prepalisade_mesophylll": [ - "PM_JW04", - "PM_JW06" - ], - "Median_ground_meristem": [ - "mGM_JW07" - ], - "4BS+V-stage_PM": [ - "4PM_IZ11", - "4PM_IZ16", - "4PM_JX03" - ], - "3C-stage_PM": [ - "mGM_JW07" - ], - "3_contiguous_cells": [ - "mGM_JW07" - ], - "5/6BS+V-stage_PM": [ - "5_6PM_IZ13", - "5_6PM_IZ18B" - ], - "4_pre-bundle_sheath_cells_+_pre-vein_cells": [ - "4BS_V_IZ02", - "4BS_V_IZ06" - ], - "1_median_mesophyll_cell": [ - "1_M_IZ09", - "1_M_IZ14", - "1_M_JX01" - ], - "2_median_mesophyll_cells": [ - "2_M_IZ10", - "2_M_IZ15", - "2_M_JX02" - ], - "5_pre-bundle_sheath_cells_+_pre-vein_cells": [ - "5BS_V_IZ03", - "5BS_V_IZ07" - ], - "6_pre-bundle_sheath_cells_+_pre-vein": [ - "6BS_V_IZ04", - "6BS_V_IZ08" - ] - } - } - } - }, - "Hoopes_et_al_Atlas": { - "database": "maize_buell_lab", - "view_name": "Hoopes_et_al_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Shoot_tip_V5": [ - "SK037__V5_Shoot_tip_R1", - "SK038__V5_Shoot_tip_R2", - "SK039__V5_Shoot_tip_R3" - ], - "Seed_2DAP": [ - "SK106__2DAP_Whole_seed_R1", - "SK107__2DAP_Whole_seed_R2", - "SK108__2DAP_Whole_seed_R3" - ], - "Meiotic_Tassel_V18": [ - "SK076__V18_Meiotic_tassel_R1", - "SK077__V18_Meiotic_tassel_R2", - "SK078__V18_Meiotic_tassel_R3" - ], - "Immature_Tassel_V13": [ - "SK073__V13_Immature_tassel_R1", - "SK074__V13_Immature_tassel_R2", - "SK075__V13_Immature_tassel_R3" - ], - "ThreeDAS-MZEZ": [ - "SS.27__Mz.Ez_3d_R2", - "SS.45__Mz.Ez_3d_R1", - "SS.56__Mz.Ez_3d_R3" - ], - "Internode_24DAP": [ - "PP_33__24_POL_INT_R1", - "PP_34__24_POL_INT_R2" - ], - "V13-BR-Node6": [ - "SS.69__BraceRoot_Node6_abvgrnd_V13_R1", - "SS.74__BraceRoot_Node6_abvgrnd_V13_R2", - "SS.76__BraceRoot_Node6_abvgrnd_V13_R3" - ], - "V7-CR-Nodes1-3": [ - "SS.70__CrownRoot_Nodes_1.3__V7_R1", - "SS.71__CrownRoot_Nodes_1.3__V7_R3" - ], - "Fourth_Internode_V9": [ - "SK058__V9_Fourth_elongated_internode_R1", - "SK059__V9_Fourth_elongated_internode_R2", - "SK060__V9_Fourth_elongated_internode_R3" - ], - "Coleoptile_6DAS_Primary_Root": [ - "SK007__6DAS_GH_Primary_Root_R1", - "SK008__6DAS_GH_Primary_Root_R2", - "SK009__6DAS_GH_Primary_Root_R3" - ], - "SevenDAS-PR-Z1": [ - "RA.2__TapRoot_Z1_7d_R2", - "RA.4__TapRoot_Z1_7d_R1", - "RA.5__TapRoot_Z1_7d_R3" - ], - "Pooled_Leaves_V1": [ - "SK019__V1_4D_PE_Pooled_Leaves_R1", - "SK020__V1_4D_PE_Pooled_Leaves_R2", - "SK021__V1_4D_PE_Pooled_Leaves_R3" - ], - "SevenDAS-PR-Z3": [ - "RA.14__TapRoot_Z3_7d_R1", - "RA.20__TapRoot_Z3_7d_R3", - "RA.21__TapRoot_Z3_7d_R2" - ], - "Immature_Leaf_V9": [ - "SK070__V9_Papery_Leaves_R1", - "SK071__V9_Papery_Leaves_R2", - "SK072__V9_Papery_Leaves_R3" - ], - "Seed_24DAP": [ - "SK172__24DAP_Whole_Seed_R1", - "SK173__24DAP_Whole_Seed_R2", - "SK174__24DAP_Whole_Seed_R3" - ], - "Silks_R1": [ - "SK088__R1_Silks_R1", - "SK089__R1_Silks_R2", - "SK090__R1_Silks_R3" - ], - "Endosperm_20DAP": [ - "SK157__20DAP_Endosperm_R1", - "SK158__20DAP_Endosperm_R2", - "SK159__20DAP_Endosperm_R3" - ], - "SevenDAS-PR-Z2": [ - "RA.15__TapRoot_Z2_7d_R3", - "RA.18__TapRoot_Z2_7d_R1", - "RA.3__TapRoot_Z2_7d_R2" - ], - "Tip_of_Stage_2_leaf_V7": [ - "SK052__V7_Tip_of_transition_leaf_R1", - "SK053__V7_Tip_of_transition_leaf_R2", - "SK054__V7_Tip_of_transition_leaf_R3" - ], - "ThreeDAS-CorticalParenchyma": [ - "RA.13__CortPar_3d_R2", - "RA.8__CortPar_3d_R3", - "RA.9__CortPar_3d_R1" - ], - "Tip_of_Stage_2_leaf_V5": [ - "SK043__V5_Tip_of_Stage_2_Leaf_R1", - "SK044__V5_Tip_of_Stage_2_Leaf_R2", - "SK045__V5_Tip_of_Stage_2_Leaf_R3" - ], - "Leaf_30DAP": [ - "PP.45__30_DAP_POL_LEAF_R1", - "PP.46__30_DAP_POL_LEAF_R2" - ], - "SevenDAS-RootSystem": [ - "SS.22__WholeRootSystem_7d_R2", - "SS.30__WholeRootSystem_7d_R1", - "SS.54__WholeRootSystem_7d_R3" - ], - "ThreeDAS-DZ": [ - "SS.21__DifferentiationZone_3d_R1", - "SS.28__DifferentiationZone_3d_R3", - "SS.61__DifferentiationZone_3d_R2" - ], - "Internode_18DAP": [ - "PP_25__18_POL_INT_R1", - "PP_26__18_POL_INT_R2" - ], - "Endosperm_12DAP": [ - "SK124__12DAP_Endopsperm_R1", - "SK125__12DAP_Endopsperm_R2", - "SK126__12DAP_Endopsperm_R3" - ], - "Seed_16DAP": [ - "SK133__16DAP_Whole_seed_R1", - "SK134__16DAP_Whole_seed_R2", - "SK135__16DAP_Whole_seed_R3" - ], - "Thirteenth_Leaf_R2": [ - "SK097__R2_Thirteenth_Leaf_R1", - "SK098__R2_Thirteenth_Leaf_R2", - "SK099__R2_Thirteenth_Leaf_R3" - ], - "Endosperm_22DAP": [ - "SK166__22DAP_Endosperm_R1", - "SK167__22DAP_Endosperm_R2", - "SK168__22DAP_Endosperm_R3" - ], - "Leaf_6DAP": [ - "PP.14__6_DAP_POL_LEAF_R2" - ], - "Eleventh_Leaf_V9": [ - "SK064__V9_Eleventh_Leaf_R1", - "SK065__V9_Eleventh_Leaf_R2", - "SK066__V9_Eleventh_Leaf_R3" - ], - "Endosperm_16DAP": [ - "SK136__16DAP_Endosperm_R1", - "SK137__16DAP_Endosperm_R2", - "SK138__16DAP_Endosperm_R3" - ], - "Seed_22DAP": [ - "SK163__22DAP_Whole_Seed_R1", - "SK164__22DAP_Whole_Seed_R2", - "SK165__22DAP_Whole_Seed_R3" - ], - "Base_of_Stage_2_leaf_V5": [ - "SK046__V5_Bottom_of_transition_leaf_R1", - "SK047__V5_Bottom_of_transition_leaf_R2", - "SK048__V5_Bottom_of_transition_leaf_R3" - ], - "Prepollination_Cob_R1": [ - "SK085__R1_Pre_pollination_cob_R1", - "SK086__R1_Pre_pollination_cob_R2", - "SK087__R1_Pre_pollination_cob_R3" - ], - "Seed_8DAP": [ - "SK115__8DAP_Whole_Seed_R1", - "SK116__8DAP_Whole_Seed_R2", - "SK117__8DAP_Whole_Seed_R3" - ], - "V13-CR-Node5": [ - "SS.68__CrownRoot_Node5_V13_R1", - "SS.75__CrownRoot_Node5_V13_R3", - "SS.77__CrownRoot_Node5_V13_R2" - ], - "Topmost_Leaf_V3": [ - "SK034__V3_Topmost_leaf_R1", - "SK035__V3_Topmost_leaf_R2", - "SK036__V3_Topmost_leaf_R3" - ], - "Thirteenth_Leaf_V9": [ - "SK067__V9_Thirteenth_Leaf_R1", - "SK068__V9_Thirteenth_Leaf_R2", - "SK069__V9_Thirteenth_Leaf_R3" - ], - "Endosperm_24DAP": [ - "SK175__24DAP_Endosperm_R1", - "SK176__24DAP_Endosperm_R2", - "SK177__24DAP_Endosperm_R3" - ], - "Anthers_R1": [ - "SK091__R1_Anthers_R1", - "SK092__R1_Anthers_R2", - "SK093__R1_Anthers_R3" - ], - "Base_of_Stage_2_leaf_V7": [ - "SK055__V7_Bottom_of_transition_leaf_R1", - "SK056__V7_Bottom_of_transition_leaf_R2", - "SK057__V7_Bottom_of_transition_leaf_R3" - ], - "Coleoptile_6DAS_GH": [ - "SK004__6_DAS_GH_Coleoptile_R1", - "SK005__6_DAS_GH_Coleoptile_R2", - "SK006__6_DAS_GH_Coleoptile_R3" - ], - "Embryo_20DAP": [ - "SK160__20DAP_Embryo_R1", - "SK161__20DAP_Embryo_R2", - "SK162__20DAP_Embryo_R3" - ], - "Immature_Cob_V18": [ - "SK079__V18_Immature_cob_R1", - "SK080__V18_Immature_cob_R2", - "SK081__V18_Immature_cob_R3" - ], - "Seed_12DAP": [ - "SK121__12DAP_Whole_seed_R1", - "SK122__12DAP_Whole_seed_R2", - "SK123__12DAP_Whole_seed_R3" - ], - "Seed_20DAP": [ - "SK154__20DAP_Whole_Seed_R1", - "SK155__20DAP_Whole_Seed_R2", - "SK156__20DAP_Whole_Seed_R3" - ], - "Pericarp_18DAP": [ - "SK151__18DAP_Pericarp_R1", - "SK152__18DAP_Pericarp_R2", - "SK153__18DAP_Pericarp_R3" - ], - "SevenDAS-PR-Z4": [ - "RA.10__TapRoot_Z4_7d_R2", - "RA.22__TapRoot_Z4_7d_R3", - "RA.23__TapRoot_Z4_7d_R1" - ], - "ThreeDAS-PrimaryRoot": [ - "SS.38__WholeRootSystem_3d_R3", - "SS.39__WholeRootSystem_3d_R1", - "SS.40__WholeRootSystem_3d_R2" - ], - "Seed_18DAP": [ - "SK142__18DAP_Whole_Seed_R1", - "SK144__18DAP_Whole_Seed_R3", - "SK147__18DAP_Whole_Seed_R2" - ], - "Thirteenth_Leaf_VT": [ - "SK082__VT_Thirteenth_Leaf_R1", - "SK083__VT_Thirteenth_Leaf_R2", - "SK084__VT_Thirteenth_Leaf_R3" - ], - "Internode_12DAP": [ - "PP_17__12_POL_INT_R1", - "PP_18__12_POL_INT_R2" - ], - "SevenDAS-SeminalRoots": [ - "SS.25__Seminal_7d_R3", - "SS.44__Seminal_7d_R1" - ], - "Endosperm_18DAP": [ - "SK143__18DAP_Endosperm_R3", - "SK145__18DAP_Endosperm_R1", - "SK146__18DAP_Endosperm_R2" - ], - "SevenDAS-PrimaryRoot": [ - "SS.36__WholePrimaryRoot_7d_R3", - "SS.42__WholePrimaryRoot_7d_R2", - "SS.58__WholePrimaryRoot_7d_R1" - ], - "Internode_6DAP": [ - "PP_10__6_POL_INT_R2", - "PP_9__6_POL_INT_R1" - ], - "ThreeDAS-Stele": [ - "RA.17__Stele_3d_R1", - "RA.6__Stele_3d_R3", - "RA.7__Stele_3d_R2" - ], - "Embryo_16DAP": [ - "SK139__16DAP_Embryo_R1", - "SK140__16DAP_Embryo_R2", - "SK141__16DAP_Embryo_R3" - ], - "Eighth_Leaf_V9": [ - "SK061__V9_Eighth_Leaf_R1", - "SK062__V9_Eighth_Leaf_R2", - "SK063__V9_Eighth_Leaf_R3" - ], - "First_Internode_V5": [ - "SK040__V5_First_elongated_internode_R1", - "SK041__V5_First_elongated_internode_R2", - "SK042__V5_First_elongated_internode_R3" - ], - "Seed_14DAP": [ - "SK127__14DAP_Whole_seed_R1", - "SK128__14DAP_Whole_seed_R2", - "SK129__14DAP_Whole_seed_R3" - ], - "Embryo_24DAP": [ - "SK178__24DAP_Embryo_R1", - "SK179__24DAP_Embryo_R2", - "SK180__24DAP_Embryo_R3" - ], - "Stem_and_SAM_V1": [ - "SK022__V1_4D_PE_Stem_plus_SAM_R1", - "SK023__V1_4D_PE_Stem_plus_SAM_R2", - "SK024__V1_4D_PE_Stem_plus_SAM_R3" - ], - "Stem_and_SAM_V3": [ - "SK028__V3_Stem_and_SAM_R1", - "SK029_2__V3_Stem_and_SAM_R2", - "SK030_2__V3_Stem_and_SAM_R3" - ], - "V7-CR-Node5": [ - "RA.35__CrownRoot_Node5_V7_R1", - "SS.78__CrownRoot_Node5_V7_R2" - ], - "V7-CR-Node4": [ - "SS.65__CrownRoot_Node4_V7_R1", - "SS.66__CrownRoot_Node4_V7_R2", - "SS.73__CrownRoot_Node4_V7_R3" - ], - "Seed_6DAP": [ - "SK112__6DAP_Whole_seed_R1", - "SK113__6DAP_Whole_seed_R2", - "SK114__6DAP_Whole_seed_R3" - ], - "Leaf_18DAP": [ - "PP.29__18_DAP_POL_LEAF_R1", - "PP.30__18_DAP_POL_LEAF_R2" - ], - "Internode_0DAP": [ - "PP1__0_POL_INT_R1", - "PP_2___0_POL_INT_R2" - ], - "Seed_4DAP": [ - "SK109__4DAP_Whole_Seed_R1", - "SK110__4DAP_Whole_Seed_R2", - "SK111__4DAP_Whole_Seed_R3" - ], - "Leaf_24DAP": [ - "PP.37__24_DAP_POL_LEAF_R1", - "PP.38__24_DAP_POL_LEAF_R2" - ], - "Endosperm_14DAP": [ - "SK130__14DAP_Endopsperm_R1", - "SK131__14DAP_Endopsperm_R2", - "SK132__14DAP_Endopsperm_R3" - ], - "Internode_30DAP": [ - "PP_41__30_POL_INT_R1", - "PP_42__30_POL_INT_R2" - ], - "Embryo_18DAP": [ - "SK148__18DAP_Embryo_R1", - "SK149__18DAP_Embryo_R2", - "SK150__18DAP_Embryo_R3" - ], - "Seed_10DAP": [ - "SK118__10DAP_Whole_seed_R1", - "SK119__10DAP_Whole_seed_R2", - "SK120__10DAP_Whole_seed_R3" - ], - "Leaf_12DAP": [ - "PP.21__12_DAP_POL_LEAF_R1", - "PP.22__12_DAP_POL_LEAF_R2" - ], - "Embryo_22DAP": [ - "SK169__22DAP_Embryo_R1", - "SK170__22DAP_Embryo_R2", - "SK171__22DAP_Embryo_R3" - ], - "Leaf_0DAP": [ - "PP.5__0_DAP_POL_LEAF_R1", - "PP.6__0_DAP_POL_LEAF_R2" - ] - } - } - } - }, - "Hoopes_et_al_Stress": { - "database": "maize_buell_lab", - "view_name": "Hoopes_et_al_Stress", - "groups": { - "htcld_ctrl_R1;htcld_ctrl_R2;htcld_ctrl_R3": { - "controls": [ - "htcld_ctrl_R1", - "htcld_ctrl_R2", - "htcld_ctrl_R3" - ], - "treatments": { - "TemperatureStress-Control": [ - "htcld_ctrl_R1", - "htcld_ctrl_R2", - "htcld_ctrl_R3" - ], - "TemperatureStress-Cold": [ - "cold_R1", - "cold_R2", - "cold_R3" - ], - "TemperatureStress-Heat": [ - "heat_R1", - "heat_R2", - "heat_R3" - ] - } - }, - "alb_ctrl_R1;alb_ctrl_R2;alb_ctrl_R3": { - "controls": [ - "alb_ctrl_R1", - "alb_ctrl_R2", - "alb_ctrl_R3" - ], - "treatments": { - "C_graminicola-48hpi": [ - "alb_48h_R2", - "alb_48h_R3" - ], - "C_graminicola-24hpi": [ - "alb_24h_R2", - "alb_24h_R3" - ], - "C_graminicola-0hpi": [ - "alb_ctrl_R1", - "alb_ctrl_R2", - "alb_ctrl_R3" - ] - } - }, - "drght_ctrl_6h_R1;drght_ctrl_6h_R2;drght_ctrl_6h_R3;drght_ctrl_6h_R4": { - "controls": [ - "drght_ctrl_6h_R1", - "drght_ctrl_6h_R2", - "drght_ctrl_6h_R3", - "drght_ctrl_6h_R4" - ], - "treatments": { - "DroughtStress-0MPa-6h": [ - "drght_ctrl_6h_R1", - "drght_ctrl_6h_R2", - "drght_ctrl_6h_R3", - "drght_ctrl_6h_R4" - ], - "DroughtStress-LowMPa-6h": [ - "drght_0.2_6h_R1", - "drght_0.2_6h_R2", - "drght_0.2_6h_R3", - "drght_0.2_6h_R4" - ], - "DroughtStress-VeryLowMPa-6h": [ - "drght_0.8_6h_R1", - "drght_0.8_6h_R2", - "drght_0.8_6h_R3", - "drght_0.8_6h_R4" - ] - } - }, - "gls_us_ctrl_R1;gls_us_ctrl_R2;gls_us_ctrl_R3": { - "controls": [ - "gls_us_ctrl_R1", - "gls_us_ctrl_R2", - "gls_us_ctrl_R3" - ], - "treatments": { - "C_zeina-UpperLeaves": [ - "gls_us_ctrl_R1", - "gls_us_ctrl_R2", - "gls_us_ctrl_R3" - ], - "C_zeina-LowerLeaves": [ - "gls_us_R1", - "gls_us_R2", - "gls_us_R3" - ] - } - }, - "drght_ctrl_24h_R1;drght_ctrl_24h_R2;drght_ctrl_24h_R3;drght_ctrl_24h_R4": { - "controls": [ - "drght_ctrl_24h_R1", - "drght_ctrl_24h_R2", - "drght_ctrl_24h_R3", - "drght_ctrl_24h_R4" - ], - "treatments": { - "DroughtStress-VeryLowMPa-24h": [ - "drght_0.8_24h_R1", - "drght_0.8_24h_R2", - "drght_0.8_24h_R3", - "drght_0.8_24h_R4" - ], - "DroughtStress-LowMPa-24h": [ - "drght_0.2_24h_R1", - "drght_0.2_24h_R2", - "drght_0.2_24h_R3", - "drght_0.2_24h_R4" - ], - "DroughtStress-0MPa-24h": [ - "drght_ctrl_24h_R1", - "drght_ctrl_24h_R2", - "drght_ctrl_24h_R3", - "drght_ctrl_24h_R4" - ] - } - }, - "slt_ctrl_R1;slt_ctrl_R2;slt_ctrl_R3": { - "controls": [ - "slt_ctrl_R1", - "slt_ctrl_R2", - "slt_ctrl_R3" - ], - "treatments": { - "SaltStress-0mM": [ - "slt_ctrl_R1", - "slt_ctrl_R2", - "slt_ctrl_R3" - ], - "SaltStress-200mM": [ - "slt_R1", - "slt_R2", - "slt_R3" - ] - } - } - } - }, - "Maize_Kernel": { - "database": "maize_early_seed", - "view_name": "Maize_Kernel", - "groups": { - "Med_CTRL_WIDIEZ": { - "controls": [ - "Med_CTRL_WIDIEZ" - ], - "treatments": { - "Apical_scutellum": [ - "AS_1", - "AS_2", - "AS_3", - "AS_4" - ], - "Endosperm": [ - "End_1", - "End_2", - "End_3", - "End_4" - ], - "Scutellar_Alleurone_Layer": [ - "SAL_1", - "SAL_2", - "SAL_3", - "SAL_4" - ], - "Embryo": [ - "Emb_1", - "Emb_2", - "Emb_3", - "Emb_4" - ], - "Endosperm_Adjacent_to_Scutellum": [ - "EAS_1", - "EAS_2", - "EAS_3", - "EAS_4" - ], - "Pericarp": [ - "Per_1", - "Per_2", - "Per_3", - "Per_4" - ] - } - } - } - }, - "Maize_Root": { - "database": "maize_root", - "view_name": "Maize_Root", - "groups": { - "CTRL_med": { - "controls": [ - "CTRL_med" - ], - "treatments": { - "Meristematic_zone_": [ - "Meristematic_zone_(control):_mean_RPKM" - ], - "Primary_root": [ - "Primary_root_FPKM" - ], - "Elongation_zone": [ - "Elongation_zone_(control):_mean_RPKM" - ], - "Root_hairs": [ - "Root_hair_FPKM" - ], - "Seminal_roots": [ - "Seminal_root_FPKM" - ], - "Crown_roots": [ - "Crown_root_FPKM" - ], - "Cortex": [ - "Cortex_(control):_mean_RPKM" - ], - "Root_hairless_root": [ - "root_FPKM" - ], - "Stele": [ - "Stele_(control):_mean_RPKM" - ] - } - }, - "6h_control:_mean_RPKM": { - "controls": [ - "6h_control:_mean_RPKM" - ], - "treatments": { - "Drought_6_hour_at_-0.2_MPA": [ - "6h_-0.2_MPa_(mild_stress):_mean_RPKM" - ], - "Drought_6_hr_control": [ - "6h_control:_mean_RPKM" - ], - "Drought_6_hour_at_-0.8_MPa": [ - "6h_-0.8_MPa_(severe_stress):_mean_RPKM" - ] - } - }, - "24h_control:_mean_RPKM": { - "controls": [ - "24h_control:_mean_RPKM" - ], - "treatments": { - "Drought_24_hr_control": [ - "24h_control:_mean_RPKM" - ], - "Drought_24_hr_-0.2_MPa": [ - "24h_-0.2_MPa_(mild_stress):_mean_RPKM" - ], - "Drought_24_hr_at_-0.8_MPa": [ - "24h_-0.8_MPa_(severe_stress):_mean_RPKM" - ] - } - } - } - }, - "Sekhon_et_al_Atlas": { - "database": "maize_RMA_linear", - "view_name": "Sekhon_et_al_Atlas", - "groups": { - "Maize_-_Kaeppler": { - "controls": [ - "MAIZE_CTRL" - ], - "treatments": { - "Germinating_Seed_24h._PO:0009001_kernel;_PO:imbibition.": [ - "24H_Germinating Seed_R1", - "24H_Germinating Seed_R2", - "24H_Germinating Seed_R3" - ], - "Coleoptile_6DAS_GH._PO:0025287_seedling_coleoptile;_PO:0007045_coleoptile_emergence.": [ - "6DAS_GH_Coleoptile_R1", - "6DAS_GH_Coleoptile_R2", - "6DAS_GH_Coleoptile_R3" - ], - "Coleoptile_6DAS_Primary_Root._PO:0020127_primary_root;_PO:0007015_radical_emergence.": [ - "6DAS_GH_Primary Root_R1", - "6DAS_GH_Primary Root_R2", - "6DAS_GH_Primary Root_R3" - ], - "Stem_and_SAM_(V1)._PO:0020142_stem_internode;_PO:0020148_shoot_apical_meristem;_PO:0007106_LP.03_three_leaves_visible.": [ - "V1_Stem and SAM_R1", - "V1_Stem and SAM_R2", - "V1_Stem and SAM_R3" - ], - "Stem_and_SAM_(V3)._PO:0020142_stem_internode;_PO:0020148_shoot_apical_meristem;_PO:0007065_LP.05_five_leaves_visible.": [ - "V3_Stem and SAM_R1", - "V3_Stem and SAM_R2", - "V3_Stem and SAM_R3" - ], - "Stem_and_SAM_(V4)._PO:0020148_shoot_apical_meristem;_PO:0020142_internode;_PO:0007123_leaves_visible.": [ - "V4_Stem and SAM_R1", - "V4_Stem and SAM_R2", - "V4_Stem and SAM_R3" - ], - "Shoot_tip_(V5)._PO:0000037_shoot_apex;_PO:0009025_vascular_PO:0006340_adult_leaf;_PO:0001052_2_leaf_expansion_stage;_PO:0020040_leaf_PO:0020104_leaf_sheath;_PO:0007063_LP.07_7_leaves_visible.": [ - "V5_Shoot Tip_R1", - "V5_Shoot Tip_R2", - "V5_Shoot Tip_R3" - ], - "First_Internode_(V5)._PO:0020142_stem_internode;_PO:0021004_inflorescence_initiation_stage;_PO:0007063_seven_leaves_visible.": [ - "V5_First Internode_R1", - "V5_First Internode_R2", - "V5_First Internode_R3" - ], - "First_Internode_(V7)._PO:0020142_stem_internode;_PO:0021004_inflorescence_initiation_stage;_PO:0007101_LP.09_nine_leaves_visible": [ - "V7_First Internode_R1", - "V7_First Internode_R2", - "V7_First Internode_R3" - ], - "Fourth_Internode_(V9)._PO:0020142_stem_internode;_PO:0001083_inflorescence_development_stages;_PO:0007116_LP.11_eleven_leaves_visible.": [ - "V9_Fourth Internode_R1", - "V9_Fourth Internode_R2", - "V9_Fourth Internode_R3" - ], - "Immature_Tassel_(V13)._PO:0020126_tassel;_PO:0001007_pollen_developmental_stages;_PO:0007104_LP.15_fifteen_leaves_visible.": [ - "V13_Immature Tassel_R1", - "V13_Immature Tassel_R2", - "V13_Immature Tassel_R3" - ], - "Meiotic_Tassel_(V18)._PO:0020126_tassel;_PO:0001009_D_pollen_mother_cell_meiosis_stage;_PO:0007072_LP.18_eighteen_leaves_visible.": [ - "V18_Meiotic Tassel_R1", - "V18_Meiotic Tassel_R2", - "V18_Meiotic Tassel_R3" - ], - "Anthers_(R1)._PO:0006310_tassel_floret;_PO:0009066_anther;_PO:0001007_pollen_developmental_stages.": [ - "R1_Anthers_R1", - "R1_Anthers_R2", - "R1_Anthers_R3" - ], - "Whole_Seedling_(VE)._PO:0006341_primary_shoot;_PO:0007094_LP.01_one_leaf_visible.": [ - "VE_Whole Seedling_R1", - "VE_Whole Seedling_R2", - "VE_Whole Seedling_R3" - ], - "Primary_Root_(VE)._PO:0020127_primary_root;_PO:0007112_1_main_shoot_growth.": [ - "VE_Primary Root_R1", - "VE_Primary Root_R2", - "VE_Primary Root_R3" - ], - "Pooled_Leaves_(V1)._PO:0006339_juvenile_leaf;_PO:0009025_vascular_leaf;_PO:0001052_2_leaf_expansion_stage;_PO:0001053_3_leaf_fully_expanded;_PO:0007106_LP.03_three_leaves_visible.": [ - "V1_Pooled Leaves_R1", - "V1_Pooled Leaves_R2", - "V1_Pooled Leaves_R3" - ], - "Primary_Root_(V1)._PO:0020127_primary_root;_PO:0007106_LP.03_three_leaves_visible.": [ - "V1_GH_Primary Root_R1", - "V1_GH_Primary Root_R2", - "V1_GH_Primary Root_R3" - ], - "Topmost_Leaf_(V3)._PO:0006339_juvenile_leaf;_PO:0009025_vascular_leaf;_PO:0001052_2_leaf_expansion_stage;_PO:0007065_LP.05_five_leaves_visible.": [ - "V3_Topmost Leaf_R1", - "V3_Topmost Leaf_R2", - "V3_Topmost Leaf_R3" - ], - "First_Leaf_(V3)._PO:0006339_juvenile_leaf;_PO:0009025_vascular_leaf;_PO:0001053_3_leaf_fully_expanded;_PO:0007065_LP.05_five_leaves_visible.": [ - "V3_First Leaf and Sheath_R1", - "V3_First Leaf and Sheath_R2", - "V3_First Leaf and Sheath_R3" - ], - "Tip_of_Stage_2_leaf_(V5)._PO:0006339_juvenile_leaf;_PO:0008018_transition_leaf;_PO:0009025_vascular_leaf;_PO:0025142_leaf_tip;_PO:0001052_2_leaf_expansion_stage;_PO:0007063_LP.07_seven_leaves_visible.": [ - "V5_Tip of stage-2 Leaf_R1", - "V5_Tip of stage-2 Leaf_R2", - "V5_Tip of stage-2 Leaf_R3" - ], - "Base_of_Stage_2_leaf_(V5)._PO:0006340_adult_leaf;_PO:0008018_transition_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001052_2_leaf_expansion_stage;_PO:0007063_LP.07_seven_leaves_visible.": [ - "V5_Base of stage-2 Leaf_R1", - "V5_Base of stage-2 Leaf_R2", - "V5_Base of stage-2 Leaf_R3" - ], - "Tip_of_Stage_2_leaf_(V7)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0025142_leaf_tip;_PO:0001052_2_leaf_expansion_stage;_PO:0007101_LP.09_nine_leaves_visible.": [ - "V7_Tip of stage-2 Leaf_R1", - "V7_Tip of stage-2 Leaf_R2", - "V7_Tip of stage-2 Leaf_R3" - ], - "Base_of_Stage_2_leaf_(V7)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001052_2_leaf_expansion_stage;_PO:0007101_LP.09_nine_leaves_visible.": [ - "V7_Base of stage-2 Leaf_R1", - "V7_Base of stage-2 Leaf_R2", - "V7_Base of stage-2 Leaf_R3" - ], - "Eighth_Leaf_(V9)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0001053_3_leaf_fully_expanded;_PO:0007116_LP.11_eleven_leaves_visible.": [ - "V9_Eighth Leaf_R1", - "V9_Eighth Leaf_R2", - "V9_Eighth Leaf_R3" - ], - "Eleventh_Leaf_(V9)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0001052_2_leaf_expansion_stage;_PO:0007116_LP.11_eleven_leaves_visible.": [ - "V9_Eleventh Leaf_R1", - "V9_Eleventh Leaf_R2", - "V9_Eleventh Leaf_R3" - ], - "Thirteenth_Leaf_(V9)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001052_2_leaf_expansion_stage;_PO:0007116_LP.11_eleven_leaves_visible.": [ - "V9_Thirteenth Leaf_R1", - "V9_Thirteenth Leaf_R2", - "V9_Thirteenth Leaf_R3" - ], - "Immature_Leaf_(V9)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0001052_2_leaf_expansion_stage;_PO:0007116_LP.11_eleven_leaves_visible.": [ - "V9_Immature Leaves_R1", - "V9_Immature Leaves_R2", - "V9_Immature Leaves_R3" - ], - "Thirteenth_Leaf_(VT)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001053_3_leaf_fully_expanded;_PO:0007003_IL.03_full_inflorescence_length_reached;_PO:0007072_LP.18_eighteen_leaves_visible.": [ - "VT_Thirteenth Leaf_R1", - "VT_Thirteenth Leaf_R2", - "VT_Thirteenth Leaf_R3" - ], - "Immature_Cob_(V18)._PO:0006505_central_spike_of_ear;_PO:0007006_IL.00_inflorescence_just_visible;_PO:0007072_LP.18_eighteen_leaves_visible.": [ - "V18_Immature Cob_R1", - "V18_Immature Cob_R2", - "V18_Immature Cob_R3" - ], - "Pre-pollination_Cob_(R1)._PO:0006505_central_spike_of_ear;_PO:0007016_4_flowering": [ - "R1_Pre-pollination Cob_R1", - "R1_Pre-pollination Cob_R2", - "R1_Pre-pollination Cob_R3" - ], - "Silks_(R1)._PO:0006354_ear_floret;_PO:0009074_style;_PO:0007016_4_flowering.": [ - "R1_Silks_R1", - "R1_Silks_R2", - "R1_Silks_R3" - ], - "Thirteenth_Leaf_(R2)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001053_3_leaf_fully_expanded;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ - "R2_Thirteenth Leaf_R1", - "R2_Thirteenth Leaf_R2", - "R2_Thirteenth Leaf_R3" - ], - "Innermost_Husk_(R1)._PO:0009054_inflorescence_bract;_PO:0020136_Zea_ear;_PO:0007026_FL.00_first_flower(s)_open.": [ - "R1_Innermost Husk_R1", - "R1_Innermost Husk_R2", - "R1_Innermost Husk_R3" - ], - "Innermost_Husk_(R2)._PO:0009054_inflorescence_bract;_PO:0020136_Zea_ear;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ - "R2_Innermost Husk_R1", - "R2_Innermost Husk_R2", - "R2_Innermost Husk_R3" - ], - "Outer_Husk_(R2)._PO:0009054_inflorescence_bract;_PO:0020136_Zea_ear;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ - "R2_Outer Husk_R1", - "R2_Outer Husk_R2", - "R2_Outer Husk_R3" - ], - "Embryo_16DAP._PO:0009009_plant_embryo;_PO:0001095_true_leaf_formation;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ - "16DAP_Embryo_R1", - "16DAP_Embryo_R2", - "16DAP_Embryo_R3" - ], - "Embryo_18DAP._PO:0009009_plant_embryo;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening.": [ - "18DAP_Embryo_R1", - "18DAP_Embryo_R2", - "18DAP_Embryo_R3" - ], - "Embryo_20DAP._PO:0009009_plant_embryo;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening.": [ - "20DAP_Embryo_R1", - "20DAP_Embryo_R2", - "20DAP_Embryo_R3" - ], - "Embryo_22DAP._PO:0009009_plant_embryo;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening.": [ - "22DAP_Embryo_R1", - "22DAP_Embryo_R2", - "22DAP_Embryo_R3" - ], - "Embryo_24DAP._PO:0009009_plant_embryo;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening.": [ - "24DAP_Embryo_R1", - "24DAP_Embryo_R2", - "24DAP_Embryo_R3" - ], - "Endosperm_12DAP._PO:0009089_endosperm;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "12DAP_Endosperm_R1", - "12DAP_Endosperm_R2", - "12DAP_Endosperm_R3" - ], - "Endosperm_14DAP._PO:0009089_endosperm;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "14DAP_Endosperm_R1", - "14DAP_Endosperm_R2", - "14DAP_Endosperm_R3" - ], - "Endosperm_16DAP._PO:0009089_endosperm;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "16DAP_Endosperm_R1", - "16DAP_Endosperm_R2", - "16DAP_Endosperm_R3" - ], - "Endosperm_18DAP._PO:0009089_endosperm;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "18DAP_Endosperm_R1", - "18DAP_Endosperm_R2", - "18DAP_Endosperm_R3" - ], - "Endosperm_20DAP._PO:0009089_endosperm;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "20DAP_Endosperm_R1", - "20DAP_Endosperm_R2", - "20DAP_Endosperm_R3" - ], - "Endosperm_22DAP._PO:0009089_endosperm;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "22DAP_Endosperm_R1", - "22DAP_Endosperm_R2", - "22DAP_Endosperm_R3" - ], - "Endosperm_24DAP._PO:0009089_endosperm;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "24DAP_Endosperm_R1", - "24DAP_Endosperm_R2", - "24DAP_Endosperm_R3" - ], - "Seed_2DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation.": [ - "2DAP_Whole Seed_R1", - "2DAP_Whole Seed_R2", - "2DAP_Whole Seed_R3" - ], - "Seed_4DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation.": [ - "4DAP_Whole Seed_R1", - "4DAP_Whole Seed_R2", - "4DAP_Whole Seed_R3" - ], - "Seed_6DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation;_PO:0007633_endosperm_development_stages.": [ - "6DAP_Whole Seed_R1", - "6DAP_Whole Seed_R2", - "6DAP_Whole Seed_R3" - ], - "Seed_8DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation;_PO:0007633_endosperm_development_stages.": [ - "8DAP_Whole Seed_R1", - "8DAP_Whole Seed_R2", - "8DAP_Whole Seed_R3" - ], - "Seed_10DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation;_PO:0007633_endosperm_development_stages.": [ - "10DAP_Whole Seed_R1", - "10DAP_Whole Seed_R2", - "10DAP_Whole Seed_R3" - ], - "Seed_12DAP._PO:0009001_fruit;_PO:0001094_coleoptilar_stage;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "12DAP_Whole Seed_R1", - "12DAP_Whole Seed_R2", - "12DAP_Whole Seed_R3" - ], - "Seed_14DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "14DAP_Whole Seed_R1", - "14DAP_Whole Seed_R2", - "14DAP_Whole Seed_R3" - ], - "Seed_16DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "16DAP_Whole Seed_R1", - "16DAP_Whole Seed_R2", - "16DAP_Whole Seed_R3" - ], - "Seed_18DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "18DAP_Whole Seed_R1", - "18DAP_Whole Seed_R2", - "18DAP_Whole Seed_R3" - ], - "Pericarp_18DAP._PO:0009084_pericarp;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ - "18DAP_Pericarp_R1", - "18DAP_Pericarp_R2", - "18DAP_Pericarp_R3" - ], - "Seed_20DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007633_endosperm_development_stages.": [ - "20DAP_Whole Seed_R1", - "20DAP_Whole Seed_R2", - "20DAP_Whole Seed_R3" - ], - "Seed_22DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "22DAP_Whole Seed_R1", - "22DAP_Whole Seed_R2", - "22DAP_Whole Seed_R3" - ], - "Seed_24DAP._PO:0009001_fruit;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "24DAP_Whole Seed_R1", - "24DAP_Whole Seed_R2", - "24DAP_Whole Seed_R3" - ] - } - } - } - }, - "Tassel_and_Ear_Primordia": { - "database": "maize_ears", - "view_name": "Tassel_and_Ear_Primordia", - "groups": { - "Ear_Development_and_Tassel_Primordia": { - "controls": [ - "MAIZE_CTRL" - ], - "treatments": { - "ear_base": [ - "ear_tip" - ], - "ear_mid": [ - "ear_mid" - ], - "ear_tip": [ - "ear_tip" - ], - "tassel_2mm": [ - "tassel_2mm" - ], - "tassel_3-4mm": [ - "tassel_3-4mm" - ], - "tassel_5-7mm": [ - "tassel_5-7mm" - ], - "2mm_ear": [ - "2mm_ear" - ], - "1mm_ear": [ - "1mm_ear" - ] - } - } - } - }, - "maize_iplant": { - "database": "maize_iplant", - "view_name": "maize_iplant", - "groups": { - "Leaf_developmental_gradient_-_4_sections": { - "controls": [ - 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{ - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Aril": [ - "A_1", - "A_2", - "A_3", - "A_5", - "A_6" - ], - "Rind": [ - "R_1", - "R_2", - "R_3", - "R_4", - "R_5", - "R_6" - ] - } - } - } - }, - "Callus": { - "database": "mangosteen_callus", - "view_name": "Callus", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Non-embryogenic": [ - "NE" - ], - "Somatic_embryogenic": [ - "SM" - ] - } - } - } - }, - "Diseased_vs_Normal": { - "database": "mangosteen_diseased_vs_normal", - "view_name": "Diseased_vs_Normal", - "groups": { - "ANC_1;ANC_2;ANC_3": { - "controls": [ - "ANC_1", - "ANC_2", - "ANC_3" - ], - "treatments": { - "Normal_aril_under_control_condition_": [ - "ANC_1", - "ANC_2", - "ANC_3" - ], - "Translucent_flesh_disorder-affected_aril_under_control_condition_": [ - "TFDA_AC_1", - "TFDA_AC_2", - "TFDA_AC_3" - ] - } - }, - "ANT_1;ANT_2;ANT_3": { - "controls": [ - "ANT_1", - "ANT_2", - "ANT_3" - ], - "treatments": { - "Normal_aril_under_treatment_condition_": [ - "ANT_1", - "ANT_2", - "ANT_3" - ], - "Translucent_flesh_disorder-affected_aril_under_treatment_condition": [ - "TFDA_AT_1", - "TFDA_AT_2", - "TFDA_AT_3" - ] - } - }, - "RNC_1;RNC_2;RNC_3": { - "controls": [ - "RNC_1", - "RNC_2", - "RNC_3" - ], - "treatments": { - "Normal_rind_under_control_condition_": [ - "RNC_1", - "RNC_2", - "RNC_3" - ], - "Gamboge_disorder-affected_rind_under_control_condition_": [ - "GDA_RC_1", - "GDA_RC_2", - "GDA_RC_3" - ] - } - }, - "RNT_1;RNT_2;RNT_3": { - "controls": [ - "RNT_1", - "RNT_2", - "RNT_3" - ], - "treatments": { - "Normal_rind_under_treatment_condition_": [ - "RNT_1", - "RNT_2", - "RNT_3" - ], - "Gamboge_disorder-affected_rind_under_treatment_condition_": [ - "GDA_RT_1", - "GDA_RT_2", - "GDA_RT_3" - ] - } - } - } - }, - "Fruit_Ripening": { - "database": "mangosteen_fruit_ripening", - "view_name": "Fruit_Ripening", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - 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- } - } - }, - "medicago": { - - "data": { - "species": "medicago", - "views": { - "medicago_mas": { - "database": "medicago_mas", - "view_name": "medicago_mas", - "groups": { - "Seed": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Seed_10d": [ - "Seed10d_rep1", - "Seed10d_rep2", - "Seed10d_rep3" - ], - "Seed_12d": [ - "Seed12d_rep1", - "Seed12d_rep2", - "Seed12d_rep3" - ], - "Seed_16d": [ - "Seed16d_rep1", - "Seed16d_rep2", - "Seed16d_rep3" - ], - "Seed_20d": [ - "Seed20d_rep1", - "Seed20d_rep2", - "Seed20d_rep3" - ], - "Seed_24d": [ - "Seed24d_rep1", - "Seed24d_rep2", - "Seed24d_rep3" - ], - "Seed_36d": [ - "Seed36d_rep1", - "Seed36d_rep2", - "Seed36d_rep3" - ] - } - }, - "Flower": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Flower": [ - "Flower_rep1", - "Flower_rep2", - "Flower_rep3" - ] - } - }, - "Nodule": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Nodule_4d": [ - "Nod4d_rep1", - "Nod4d_rep2", - 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"treatments": { - "Petiole": [ - "Petiole_rep1", - "Petiole_rep2", - "Petiole_rep3" - ] - } - }, - "Stem": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Stem": [ - "Stem_rep1", - "Stem_rep2", - "Stem_rep3" - ] - } - }, - "Leaf_with_Petiolules": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Leaf_with_Petiolules": [ - "Leaf_rep1", - "Leaf_rep2", - "Leaf_rep3" - ] - } - }, - "Root": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Root": [ - "Root_rep1", - "Root_rep2", - "Root_rep3" - ] - } - }, - "Non-inoculated_root": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Non-inoculated_root": [ - "Root0d_rep1", - "Root0d_rep2", - "Root0d_rep3" - ] - } - } - } - }, - "medicago_seed": { - "database": "medicago_seed", - "view_name": "medicago_seed", - "groups": { - "Seed_14c": { - "controls": [ - "Med_CTRL_14C" - ], - "treatments": { - "Seed_22DAP_14C": [ - "22_DAP_14C" - ], - "Seed_28DAP_14C": [ - "28_DAP_14C" - ], - "Seed_34DAP_14C": [ - "34_DAP_14C" - ], - "Seed_40DAP_14C": [ - "40_DAP_14C" - ], - "Seed_46DAP_14C": [ - "46_DAP_14C" - ], - "Seed_52DAP_14C": [ - "52_DAP_14C" - ], - "Seed_58DAP_14C": [ - "58_DAP_14C" - ], - "Seed_65DAP_14C": [ - "65_DAP_14C" - ], - "Seed_ABS_14C": [ - "Abs_DAP_14C" - ], - "Seed_DS_14C": [ - "DS_DAP_14C" - ] - } - }, - "Seed_20c": { - "controls": [ - "Med_CTRL_20C" - ], - "treatments": { - "Seed_8DAP_20C": [ - "8_DAP_20C" - ], - "Seed_11DAP_20C": [ - "11_DAP_20C" - ], - "Seed_14DAP_20C": [ - "14_DAP_20C" - ], - "Seed_17DAP_20C": [ - "17_DAP_20C" - ], - "Seed_20DAP_20C": [ - "20_DAP_20C" - ], - "Seed_23DAP_20C": [ - "23_DAP_20C" - ], - "Seed_26DAP_20C": [ - "26_DAP_20C" - ], - "Seed_29DAP_20C": [ - "29_DAP_20C" - ], - "Seed_32DAP_20C": [ - "32_DAP_20C" - ], - "Seed_35DAP_20C": [ - "35_DAP_20C" - ], - "Seed_38DAP_20C": [ - "38_DAP_20C" - ], - "Seed_41DAP_20C": [ - "41_DAP_20C" - ], - "Seed_44DAP_20C": [ - "44_DAP_20C" - ], - "Seed_ABS_20C": [ - 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"seed_cotyledon_abaxial_epidermis" - ], - "Seed_Endosperm": [ - "seed_endosperm" - ] - } - } - } - }, - "soybean_heart_cotyledon_globular": { - "database": "soybean_heart_cotyledon_globular", - "view_name": "soybean_heart_cotyledon_globular", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Cotyledon_Embryo_Cotyledon": [ - "cotyledon_embryocotyledon" - ], - "Cotyledon_Embryo_Proper": [ - "cotyledon_embryo" - ], - "Cotyledon_Embryo_Axis": [ - "cotyledon_embryoaxis" - ], - "Cotyledon_Endosperm": [ - "cotyledon_endosperm" - ], - "Cotyledon_Seed_Coat_Endothelium": [ - "cotyledon_seedcoatendothelium" - ], - "Cotyledon_Seed_Coat_Epidermis": [ - "cotyledon_seedcoatepidermis" - ], - "Cotyledon_Seed_Coat_Hilum": [ - "cotyledon_seedcoathilum" - ], - "Cotyledon_Seed_Coat_Inner_Integument": [ - "cotyledon_seedcoatinnerintegument" - ], - "Cotyledon_Seed_Coat_Outer_Integument": [ - "cotyledon_seedcoatouterintegument" - ], - "Cotyledon_Suspensor": [ - 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"heart_seedcoatouterintegument" - ], - "Heart_Suspensor": [ - "heart_suspensor" - ] - } - } - } - }, - "soybean_senescence": { - "database": "soybean_senescence", - "view_name": "soybean_senescence", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Cotyledon_Stage_1": [ - "C_I-1", - "C_I-2", - "C_I-3" - ], - "Cotyledon_Stage_2": [ - "C_II-1", - "C_II-2", - "C_II-3" - ], - "Cotyledon_Stage_3": [ - "C_III-1", - "C_III-2", - "C_III-3" - ], - "Leaf_Stage_1": [ - "L_I-1", - "L_I-2", - "L_I-3" - ], - "Leaf_Stage_2": [ - "L_II-1", - "L_II-2", - "L_II-3" - ], - "Leaf_Stage_3": [ - "L_III-1", - "L_III-2", - "L_III-3" - ], - "Leaf_Stage_4": [ - "L_IV-1", - "L_IV-2", - "L_IV-3" - ], - "Leaf_Stage_5": [ - "L_V-1", - "L_V-2", - "L_V-3" - ] - } - } - } - }, - "soybean_severin": { - "database": "soybean_severin", - "view_name": "soybean_severin", - "groups": { - "Soybean_Severin": { - "controls": [ - "SOYBEAN_CTRL" - ], - "treatments": { - "Young_Leaf": [ - "young_leaf" - ], - "Flower": [ - "flower" - ], - "One_CM_Pod": [ - "one_cm_pod" - ], - "Pod_Shell_(10-13_DAF)": [ - "pod_shell_10DAF" - ], - "Pod_Shell_(14_17_DAF)": [ - "pod_shell_14DAF" - ], - "Nodule": [ - "nodule" - ], - "Root": [ - "root" - ], - "Seed_10_13_DAF": [ - "seed_10DAF" - ], - "Seed_14_17_DAF": [ - "seed_14DAF" - ], - "Seed_21_DAF": [ - "seed_21DAF" - ], - "Seed_25_DAF": [ - "seed_25DAF" - ], - "Seed_28_DAF": [ - "seed_28DAF" - ], - "Seed_35_DAF": [ - "seed_35DAF" - ], - "Seed_42_DAF": [ - "seed_42DAF" - ] - } - } - } - } - } - } - }, - "strawberry": { - - "data": { - "species": "strawberry", - "views": { - "Developmental_Map_Strawberry_Flower_and_Fruit": { - "database": "strawberry", - "view_name": "Developmental_Map_Strawberry_Flower_and_Fruit", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Anther,_stage_10": [ - "Anther_10_A", - "Anther_10_B" - ], - "Anther,_stage_11": [ - "Anther_11_A", - "Anther_11_B" - ], - 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"slpif8a_epicotyl,_FR_light,_6h": [ - "slpif8a_6h_E_FR_1", - "slpif8a_6h_E_FR_2", - "slpif8a_6h_E_FR_3" - ], - "slpif8a_epicotyl,_white_light,_6h": [ - "slpif8a_6h_E_WL_1", - "slpif8a_6h_E_WL_2", - "slpif8a_6h_E_WL_3" - ] - } - }, - "slpif8a_6h_C_WL_1;slpif8a_6h_C_WL_2;slpif8a_6h_C_WL_3": { - "controls": [ - "slpif8a_6h_C_WL_1", - "slpif8a_6h_C_WL_2", - "slpif8a_6h_C_WL_3" - ], - "treatments": { - "slpif8a_cotyledon,_FR_light,_6h": [ - "slpif8a_6h_C_FR_1", - "slpif8a_6h_C_FR_2", - "slpif8a_6h_C_FR_3" - ], - "slpif8a_cotyledon,_white_light,_6h": [ - "slpif8a_6h_C_WL_1", - "slpif8a_6h_C_WL_2", - "slpif8a_6h_C_WL_3" - ] - } - }, - "slpif8a_6h_H_WL_1;slpif8a_6h_H_WL_2;slpif8a_6h_H_WL_3": { - "controls": [ - "slpif8a_6h_H_WL_1", - "slpif8a_6h_H_WL_2", - "slpif8a_6h_H_WL_3" - ], - "treatments": { - "slpif8a_hypocotyl,_FR_light,_6h": [ - "slpif8a_6h_H_FR_1", - "slpif8a_6h_H_FR_2", - "slpif8a_6h_H_FR_3" - ], - "slpif8a_hypocotyl,_white_light,_6h": [ - "slpif8a_6h_H_WL_1", - "slpif8a_6h_H_WL_2", - "slpif8a_6h_H_WL_3" - ] - } - }, - "slpifq_6h_L_WL_1;slpifq_6h_L_WL_2;slpifq_6h_L_WL_3": { - "controls": [ - "slpifq_6h_L_WL_1", - "slpifq_6h_L_WL_2", - "slpifq_6h_L_WL_3" - ], - "treatments": { - "First_leaf,_FR_light,_6h": [ - "slpifq_6h_L_FR_1", - "slpifq_6h_L_FR_2", - "slpifq_6h_L_FR_3" - ], - "First_leaf,_white_light,_6h": [ - "slpifq_6h_L_WL_1", - "slpifq_6h_L_WL_2", - "slpifq_6h_L_WL_3" - ] - } - }, - "slpifq_6h_E_WL_1;slpifq_6h_E_WL_2;slpifq_6h_E_WL_3": { - "controls": [ - "slpifq_6h_E_WL_1", - "slpifq_6h_E_WL_2", - "slpifq_6h_E_WL_3" - ], - "treatments": { - "Epicotyl,_FR_light,_6h": [ - "slpifq_6h_E_FR_1", - "slpifq_6h_E_FR_2", - "slpifq_6h_E_FR_3" - ], - "Epicotyl,_white_light,_6h": [ - "slpifq_6h_E_WL_1", - "slpifq_6h_E_WL_2", - "slpifq_6h_E_WL_3" - ] - } - }, - "slpifq_6h_C_WL_1;slpifq_6h_C_WL_2;slpifq_6h_C_WL_3": { - "controls": [ - "slpifq_6h_C_WL_1", - "slpifq_6h_C_WL_2", - "slpifq_6h_C_WL_3" - ], - "treatments": { - "Cotyledon,_FR_light,_6h": [ - "slpifq_6h_C_FR_1", - "slpifq_6h_C_FR_2", - "slpifq_6h_C_FR_3" - ], - "Cotyledon,_white_light,_6h": [ - "slpifq_6h_C_WL_1", - "slpifq_6h_C_WL_2", - "slpifq_6h_C_WL_3" - ] - } - }, - "slpifq_6h_H_WL_1;slpifq_6h_H_WL_2;slpifq_6h_H_WL_3": { - "controls": [ - "slpifq_6h_H_WL_1", - "slpifq_6h_H_WL_2", - "slpifq_6h_H_WL_3" - ], - "treatments": { - "Hypocotyl,_FR_light,_6h": [ - "slpifq_6h_H_FR_1", - "slpifq_6h_H_FR_2", - "slpifq_6h_H_FR_3" - ], - "Hypocotyl,_white_light,_6h": [ - "slpifq_6h_H_WL_1", - "slpifq_6h_H_WL_2", - "slpifq_6h_H_WL_3" - ] - } - } - } - }, - "Shade_Timecourse_WT": { - "database": "tomato_shade_timecourse", - "view_name": "Shade_Timecourse_WT", - "groups": { - "WT_3h_L_WL_1;WT_3h_L_WL_2;WT_3h_L_WL_3": { - "controls": [ - "WT_3h_L_WL_1", - "WT_3h_L_WL_2", - "WT_3h_L_WL_3" - ], - "treatments": { - "First_leaf,_FR_light,_3h": [ - "WT_3h_L_FR_1", - "WT_3h_L_FR_2", - "WT_3h_L_FR_3" - ], - "First_leaf,_white_light,_3h": [ - "WT_3h_L_WL_1", - "WT_3h_L_WL_2", - "WT_3h_L_WL_3" - ] - } - }, - "WT_3h_E_WL_1;WT_3h_E_WL_2;WT_3h_E_WL_3": { - "controls": [ - "WT_3h_E_WL_1", - "WT_3h_E_WL_2", - "WT_3h_E_WL_3" - ], - "treatments": { - "Epicotyl,_FR_light,_3h": [ - "WT_3h_E_FR_1", - "WT_3h_E_FR_2", - "WT_3h_E_FR_3" - ], - "Epicotyl,_white_light,_3h": [ - "WT_3h_E_WL_1", - "WT_3h_E_WL_2", - "WT_3h_E_WL_3" - ] - } - }, - "WT_3h_C_WL_1;WT_3h_C_WL_2;WT_3h_C_WL_3": { - "controls": [ - "WT_3h_C_WL_1", - "WT_3h_C_WL_2", - "WT_3h_C_WL_3" - ], - "treatments": { - "Cotyledon,_FR_light,_3h": [ - "WT_3h_C_FR_1", - "WT_3h_C_FR_2", - "WT_3h_C_FR_3" - ], - "Cotyledon,_white_light,_3h": [ - "WT_3h_C_WL_1", - "WT_3h_C_WL_2", - "WT_3h_C_WL_3" - ] - } - }, - "WT_3h_H_WL_1;WT_3h_H_WL_2;WT_3h_H_WL_3": { - "controls": [ - "WT_3h_H_WL_1", - "WT_3h_H_WL_2", - "WT_3h_H_WL_3" - ], - "treatments": { - "Hypocotyl,_FR_light,_3h": [ - "WT_3h_H_FR_1", - "WT_3h_H_FR_2", - "WT_3h_H_FR_3" - ], - "Hypocotyl,_white_light,_3h": [ - "WT_3h_H_WL_1", - "WT_3h_H_WL_2", - "WT_3h_H_WL_3" - ] - } - }, - "WT_6h_L_WL_1;WT_6h_L_WL_2;WT_6h_L_WL_3": { - "controls": [ - "WT_6h_L_WL_1", - "WT_6h_L_WL_2", - "WT_6h_L_WL_3" - ], - "treatments": { - "First_leaf,_FR_light,_6h": [ - "WT_6h_L_FR_1", - "WT_6h_L_FR_2", - "WT_6h_L_FR_3" - ], - "First_leaf,_white_light,_6h": [ - "WT_6h_L_WL_1", - "WT_6h_L_WL_2", - "WT_6h_L_WL_3" - ] - } - }, - "WT_6h_E_WL_1;WT_6h_E_WL_2;WT_6h_E_WL_3": { - "controls": [ - "WT_6h_E_WL_1", - "WT_6h_E_WL_2", - "WT_6h_E_WL_3" - ], - "treatments": { - "Epicotyl,_FR_light,_6h": [ - "WT_6h_E_FR_1", - "WT_6h_E_FR_2", - "WT_6h_E_FR_3" - ], - "Epicotyl,_white_light,_6h": [ - "WT_6h_E_WL_1", - "WT_6h_E_WL_2", - "WT_6h_E_WL_3" - ] - } - }, - "WT_6h_C_WL_1;WT_6h_C_WL_2;WT_6h_C_WL_3": { - "controls": [ - "WT_6h_C_WL_1", - "WT_6h_C_WL_2", - "WT_6h_C_WL_3" - ], - "treatments": { - "Cotyledon,_FR_light,_6h": [ - "WT_6h_C_FR_1", - "WT_6h_C_FR_2", - "WT_6h_C_FR_3" - ], - "Cotyledon,_white_light,_6h": [ - "WT_6h_C_WL_1", - "WT_6h_C_WL_2", - "WT_6h_C_WL_3" - ] - } - }, - "WT_6h_H_WL_1;WT_6h_H_WL_2;WT_6h_H_WL_3": { - "controls": [ - "WT_6h_H_WL_1", - "WT_6h_H_WL_2", - "WT_6h_H_WL_3" - ], - "treatments": { - "Hypocotyl,_FR_light,_6h": [ - "WT_6h_H_FR_1", - "WT_6h_H_FR_2", - "WT_6h_H_FR_3" - ], - "Hypocotyl,_white_light,_6h": [ - "WT_6h_H_WL_1", - "WT_6h_H_WL_2", - "WT_6h_H_WL_3" - ] - } - }, - "WT_24h_L_WL_1;WT_24h_L_WL_2;WT_24h_L_WL_3": { - "controls": [ - "WT_24h_L_WL_1", - "WT_24h_L_WL_2", - "WT_24h_L_WL_3" - ], - "treatments": { - "First_leaf,_FR_light,_24h": [ - "WT_24h_L_FR_1", - "WT_24h_L_FR_2", - "WT_24h_L_FR_3" - ], - "First_leaf,_white_light,_24h": [ - "WT_24h_L_WL_1", - "WT_24h_L_WL_2", - "WT_24h_L_WL_3" - ] - } - }, - "WT_24h_E_WL_1;WT_24h_E_WL_2;WT_24h_E_WL_3": { - "controls": [ - "WT_24h_E_WL_1", - "WT_24h_E_WL_2", - "WT_24h_E_WL_3" - ], - "treatments": { - "Epicotyl,_FR_light,_24h": [ - "WT_24h_E_FR_1", - "WT_24h_E_FR_2", - "WT_24h_E_FR_3" - ], - "Epicotyl,_white_light,_24h": [ - "WT_24h_E_WL_1", - "WT_24h_E_WL_2", - "WT_24h_E_WL_3" - ] - } - }, - "WT_24h_C_WL_1;WT_24h_C_WL_2;WT_24h_C_WL_3": { - "controls": [ - "WT_24h_C_WL_1", - "WT_24h_C_WL_2", - "WT_24h_C_WL_3" - ], - "treatments": { - "Cotyledon,_FR_light,_24h": [ - "WT_24h_C_FR_1", - "WT_24h_C_FR_2", - "WT_24h_C_FR_3" - ], - "Cotyledon,_white_light,_24h": [ - "WT_24h_C_WL_1", - "WT_24h_C_WL_2", - "WT_24h_C_WL_3" - ] - } - }, - "WT_24h_H_WL_1;WT_24h_H_WL_2;WT_24h_H_WL_3": { - "controls": [ - "WT_24h_H_WL_1", - "WT_24h_H_WL_2", - "WT_24h_H_WL_3" - ], - "treatments": { - "Hypocotyl,_FR_light,_24h": [ - "WT_24h_H_FR_1", - "WT_24h_H_FR_2", - "WT_24h_H_FR_3" - ], - "Hypocotyl,_white_light,_24h": [ - "WT_24h_H_WL_1", - "WT_24h_H_WL_2", - "WT_24h_H_WL_3" - ] - } - } - } - }, - "Tomato_Meristem": { - "database": "tomato_meristem", - "view_name": "Tomato_Meristem", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "WT_Base_Margin": [ - "wt_base_margin_1", - "wt_base_margin_2", - "wt_base_margin_3", - "wt_base_margin_4", - "wt_base_margin_5", 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"tf2_middle_rachis_4" - ], - "TF2_Top_Margin": [ - "tf2_top_margin_1", - "tf2_top_margin_2", - "tf2_top_margin_3" - ], - "TF2_Top_Rachis": [ - "tf2_top_rachis_1", - "tf2_top_rachis_2", - "tf2_top_rachis_3", - "tf2_top_rachis_4" - ] - } - } - } - } - } - } - }, - "triticale": { - - "data": { - "species": "triticale", - "views": { - "triticale": { - "database": "triticale", - "view_name": "triticale", - "groups": { - "Reproductive": { - "controls": [ - "TRITICALE_CTRL" - ], - "treatments": { - "Anther_tetrad": [ - "Anther_TET1", - "Anther_TET2", - "Anther_TET3" - ], - "Stigma_tetrad": [ - "Stigma_TET1", - "Stigma_TET2", - "Stigma_TET3" - ], - "Ovary_tetrad": [ - "Ovary_TET1", - "Ovary_TET2", - "Ovary_TET3" - ], - "Anther_uninucleate": [ - "Anther_UNM1", - "Anther_UNM2", - "Anther_UNM3" - ], - "Stigma_uninucleate": [ - "Stigma_UNM1", - "Stigma_UNM2", - "Stigma_UNM3" - ], - "Ovary_uninucleate": [ - "Ovary_UNM1", - "Ovary_UNM2", - "Ovary_UNM3" - ], - "Anther_bicellular_pollen": [ - "Anther_BCP1", - "Anther_BCP2", - "Anther_BCP3" - ], - "Stigma_bicellular_pollen": [ - "Stigma_BCP1", - "Stigma_BCP2", - "Stigma_BCP3" - ], - "Ovary_bicellular_pollen": [ - "Ovary_BCP1", - "Ovary_BCP2", - "Ovary_BCP3" - ], - "Anther_tricellular_pollen": [ - "Anther_TCP1", - "Anther_TCP2", - "Anther_TCP3" - ], - "Stigma_tricellular_pollen": [ - "Stigma_TCP1", - "Stigma_TCP2", - "Stigma_TCP3" - ], - "Ovary_tricellular_pollen": [ - "Ovary_TCP1", - "Ovary_TCP2", - "Ovary_TCP3" - ], - "Mature_pollen": [ - "Pollen_MPG1", - "Pollen_MPG2", - "Pollen_MPG3" - ] - } - } - } - }, - "triticale_mas": { - "database": "triticale_mas", - "view_name": "triticale_mas", - "groups": { - "Reproductive": { - "controls": [ - "TRITICALE_CTRL" - ], - "treatments": { - "Anther_tetrad": [ - "Anther_tetrad_1", - "Anther_tetrad_2", - "Anther_tetrad_3" - ], - "Stigma_tetrad": [ - "Stigma_tetrad_1", - "Stigma_tetrad_2", - "Stigma_tetrad_3" - ], - "Ovary_tetrad": [ - "Ovary_tetrad_1", - "Ovary_tetrad_2", - "Ovary_tetrad_3" - ], - "Anther_uninucleate": [ - "Anther_uninucleate_1", - "Anther_uninucleate_2", - "Anther_uninucleate_3" - ], - "Stigma_uninucleate": [ - "Stigma_uninucleate_1", - "Stigma_uninucleate_2", - "Stigma_uninucleate_3" - ], - "Ovary_uninucleate": [ - "Ovary_uninucleate_1", - "Ovary_uninucleate_2", - "Ovary_uninucleate_3" - ], - "Anther_bicellular_pollen": [ - "Anther_bicellular_pollen_1", - "Anther_bicellular_pollen_2", - "Anther_bicellular_pollen_3" - ], - "Stigma_bicellular_pollen": [ - "Stigma_bicellular_pollen_1", - "Stigma_bicellular_pollen_2", - "Stigma_bicellular_pollen_3" - ], - "Ovary_bicellular_pollen": [ - "Ovary_bicellular_pollen_1", - "Ovary_bicellular_pollen_2", - "Ovary_bicellular_pollen_3" - ], - "Anther_tricellular_pollen": [ - "Anther_tricellular_pollen_1", - "Anther_tricellular_pollen_2", - "Anther_tricellular_pollen_3" - ], - "Stigma_tricellular_pollen": [ - "Stigma_tricellular_pollen_1", - "Stigma_tricellular_pollen_2", - "Stigma_tricellular_pollen_3" - ], - "Ovary_tricellular_pollen": [ - "Ovary_tricellular_pollen_1", - "Ovary_tricellular_pollen_2", - "Ovary_tricellular_pollen_3" - ], - "Mature_pollen": [ - "Mature_pollen_1", - "Mature_pollen_2", - "Mature_pollen_3" - ] - } - } - } - } - } - } - }, - "wheat": { - - "data": { - "species": "wheat", - "views": { - "Developmental_Atlas": { - "database": "wheat", - "view_name": "Developmental_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "First_leaf_sheath_-_Tillering_stage": [ - "Sample_43A", - "Sample_44A", - "Sample_45A" - ], - "Internode_#2_-_Milk_grain_stage": [ - "Sample_188B", - "Sample_189B" - ], - "Shoot_apical_meristem_-_Seedling_stage": [ - "Sample_19A", - "Sample_20A", - "Sample_21A" - ], - "Grain_-_Milk_grain_stage": [ - "Sample_199A", - "Sample_200A", - "Sample_201A" - ], - "First_leaf_blade_-_Seedling_stage": [ - "Sample_13R1", - "Sample_23", - "Sample_32" - ], - "Flag_leaf_blade_-_Full_boot_": [ - "Sample_94B", - "Sample_95A", - "Sample_96A" - ], - "Awn_-_50_percent_spike": [ - "Sample_118A", - "Sample_119B", - "Sample_120A" - ], - "flag_leaf_blade_night_(-0.25h)_06:45": [ - "Sample_166A", - "Sample_167A", - "Sample_168A" - ], - "Shoot_axis_-_Flag_leaf_stage": [ - "Sample_70A", - "Sample_71A", - "Sample_72A" - ], - "Fifth_leaf_blade_-_Flag_leaf_stage": [ - "Sample_67A", - "Sample_68A", - "Sample_69A" - ], - "Third_leaf_sheath_-_Three_leaf_stage": [ - "Sample_25A", - "Sample_26A", - "Sample_27A" - ], - "Internode_#2_-_Ear_emergence": [ - "Sample_136A", - "Sample_137B", - "Sample_138A" - ], - "Anther": [ - "Sample_160A", - "Sample_161A", - "Sample_162A" - ], - "Spike": [ - "Sample_100A", - "Sample_101A", - "Sample_102A" - ], - "Coleoptile": [ - "Sample_12", - "Sample_26", - "Sample_6A" - ], - "Stigma_and_Ovary": [ - "Sample_163A", - "Sample_164A", - "Sample_165A" - ], - "Roots_-_Flag_leaf_stage": [ - "Sample_73A", - "Sample_74A", - "Sample_76A" - ], - "Fifth_leaf_sheath_-_Flag_leaf_stage": [ - "Sample_64A", - "Sample_65A", - "Sample_66A" - ], - "Root_apical_meristem_-_Three_leaf_stage": [ - "Sample_15", - "Sample_32R2", - "Sample_33A" - ], - "Flag_leaf_sheath_-_Ear_emergence": [ - "Sample_124A", - "Sample_125A", - "Sample_126A" - ], - "Roots_-_Three_leaf_stage": [ - "Sample_28A", - "Sample_29A", - "Sample_30A" - ], - "Axillary_roots_-_Three_leaf_stage": [ - "Sample_16", - "Sample_35R1", - "Sample_36A" - ], - "Flag_leaf_sheath_-_50_percent_spike": [ - "Sample_106A", - "Sample_107B", - "Sample_108A" - ], - "Radicle_-_Seedling_stage": [ - "Sample_10", - "Sample_18", - "Sample_3A" - ], - "Roots_-_50_percent_spike": [ - "Sample_103A", - "Sample_104B", - "Sample_105B" - ], - "Third_leaf_blade_-_Three_leaf_stage": [ - "Sample_22B", - "Sample_23A", - "Sample_24A" - ], - "Spikelets_-_50_percent_spike": [ - "Sample_121A", - "Sample_122A", - "Sample_123A" - ], - "Root_apical_meristem_-_Tillering_stage": [ - "Sample_58A", - "Sample_59A", - "Sample_60A" - ], - "Grain_-_Ripening_stage": [ - "Sample_217B", - "Sample_218A", - "Sample_219A" - ], - "Awns_-_Ear_emergence": [ - "Sample_139A", - "Sample_140A", - "Sample_141A" - ], - "Glumes": [ - "Sample_193A", - "Sample_194A", - "Sample_195A" - ], - "Glumes_-_Ear_emergence": [ - "Sample_142A", - "Sample_143A", - "Sample_144B" - ], - "Leaf_ligule": [ - "Sample_88A", - "Sample_89B", - "Sample_90A" - ], - "Flag_leaf_blade_-_50_percent_spike": [ - "Sample_109A", - "Sample_110A", - "Sample_111B" - ], - "Internode_#2_-_50_percent_spike": [ - "Sample_112B", - "Sample_113B", - "Sample_114B" - ], - "Fifth_leaf_sheath_-_Fifth_leaf_stage": [ - "Sample_37A", - "Sample_38A", - "Sample_39A" - ], - "fifth_leaf_blade_night_(-0.25h)_21:45": [ - "Sample_79A", - "Sample_80A", - "Sample_81A" - ], - "Grain_-_Soft_dough": [ - "Sample_205A", - "Sample_206A", - "Sample_207A" - ], - "Flag_leaf_blade_(senescence)_-_Dough_stage": [ - "Sample_202A", - "Sample_203A", - "Sample_204A" - ], - "Flag_leaf_blade_night_(-0.25h)_06:45_-_Flag_leaf_stage": [ - "Sample_75A", - "Sample_77A", - "Sample_78A" - ], - "Flag_leaf_blade_(senescence)_-_Ripening_stage": [ - "Sample_223B", - "Sample_225A" - ], - "First_leaf_blade_-_Tillering_stage": [ - "Sample_46A", - "Sample_d11", - "Sample_d12" - ], - "Shoot_apical_meristem_-_Tillering_stage": [ - "Sample_52A", - "Sample_53A", - "Sample_54A" - ], - "Shoot_axis_-_First_leaf_stage": [ - "Sample_11", - "Sample_20", - "Sample_9A" - ], - "Roots_-_Seedling_stage": [ - "Sample_13", - "Sample_18A", - "Sample_33" - ], - "Shoot_axis_-_Milk_grain_stage": [ - "Sample_178A", - "Sample_179A", - "Sample_180A" - ], - "Fifth_leaf_blade_-_Fifth_leaf_stage": [ - "Sample_40A", - "Sample_41A", - "Sample_42A" - ], - "Flag_leaf_blade_-_Ear_emergence": [ - "Sample_127A", - "Sample_128A", - "Sample_129A" - ], - "flag_leaf_blade_night_(+0.25h)_07:15": [ - "Sample_82A", - "Sample_83B", - "Sample_84A" - ], - "Fifth_leaf_blade_night_(-0.25h)_21:45": [ - "Sample_169A", - "Sample_170A", - "Sample_171A" - ], - "Shoot_axis_-_Tillering_stage": [ - "Sample_49A", - "Sample_50A", - "Sample_51A" - ], - "Stem_axis_-_First_leaf_stage": [ - "Sample_11", - "Sample_20", - "Sample_9A" - ], - "Endosperm": [ - "Sample_211B", - "Sample_212A", - "Sample_213A" - ], - "Peduncle": [ - "Sample_184A", - "Sample_185A", - "Sample_186A" - ], - "Peduncle_-_50_percent_spike": [ - "Sample_115A", - "Sample_116A", - "Sample_117A" - ], - "Peduncle_-_Ear_emergence": [ - "Sample_133A", - "Sample_134A", - "Sample_135A" - ], - "Flag_leaf_sheath_-_Full_boot": [ - "Sample_91A", - "Sample_92A", - "Sample_93A" - ], - "Flag_leaf_blade_-_Flag_leaf_stage": [ - "Sample_61A", - "Sample_62A", - "Sample_63A" - ], - "Lemma": [ - "Sample_196A", - "Sample_197A", - "Sample_198A" - ], - "Lemma_-_Ear_emergence": [ - "Sample_157A", - "Sample_158A", - "Sample_159B" - ], - "Awns_-_Milk_grain_stage": [ - "Sample_190A", - "Sample_191A", - "Sample_192A" - ], - "fifth_leaf_blade_night_(+0.25h)_22:15": [ - "Sample_85B", - "Sample_86A", - "Sample_87A" - ], - "Flag_leaf_blade_-_Milk_grain_stage": [ - "Sample_175A", - "Sample_176A", - "Sample_177A" - ], - "Grain_-_Hard_dough": [ - "Sample_208A", - "Sample_209A", - "Sample_210A" - ], - "Flag_leaf_sheath_-_Milk_grain_stage": [ - "Sample_172A", - "Sample_173A", - "Sample_174A" - ], - "Embryo_proper": [ - "Sample_214A", - "Sample_215A", - "Sample_216A" - ], - "Fifth_leaf_blade_(senescence)_-_Milk_grain_stage": [ - "Sample_181A", - "Sample_182A", - "Sample_183A" - ], - "Roots_-_Tillering_stage": [ - "Sample_55B", - "Sample_56A", - "Sample_57A" - ], - "Shoot_axis_-_Full_boot": [ - "Sample_97A", - "Sample_98A", - "Sample_99A" - ], - "Fifth_leaf_blade_-_Ear_emergence": [ - "Sample_130A", - "Sample_131A", - "Sample_132A" - ], - "First_leaf_sheath_-_Seedling_stage": [ - "Sample_10R1", - "Sample_21", - "Sample_30" - ] - } - } - } - }, - "Wheat_Abiotic_Stress": { - "database": "wheat_abiotic_stress", - "view_name": "Wheat_Abiotic_Stress", - "groups": { - "Med_CTRL": { - "controls": [ - "C1", - "C2", - "C4", - "C8" - ], - "treatments": { - "All": [ - "SHD4", - "SHD5", - "SHD6", - "SHD7" - ], - "Salt_+_Drought": [ - "SD1", - "SD5", - "SD6", - "SD8" - ], - "Salt_+_Heat": [ - "SH2", - "SH3", - "SH4", - "SH8" - ], - "Heat_+_Drought": [ - "HD3", - "HD4", - "HD7", - "HD8" - ], - "Drought_Only": [ - "D1", - "D4", - "D6", - "D8" - ], - "Heat_Only": [ - "H1", - "H2", - "H3", - "H4" - ], - "Salt_Only": [ - "S1", - "S3", - "S5", - "S8" - ], - "Control": [ - "C1", - "C2", - "C4", - "C8" - ] - } - } - } - }, - "Wheat_Embryogenesis": { - "database": "wheat_embryogenesis", - "view_name": "Wheat_Embryogenesis", - "groups": { - "AA-DV92_Med_CTRL": { - "controls": [ - "AA-DV92_Med_CTRL" - ], - "treatments": { - "AA-DV92_Leaf_Early_Seed_Coat": [ - "AA-DV92_Leaf_early_stage_seed_coat" - ], - "AA-DV92_Leaf_Late_Embryo": [ - "AA-DV92_Leaf_late_embryo" - ], - "AA-DV92_Leaf_Early_Embryo": [ - "AA-DV92_Leaf_early_embryo" - ], - "AA-DV92_Leaf_Late_Endosperm": [ - "AA-DV92_Leaf_late_stage_endosperm" - ], - "AA-DV92_Leaf_Middle_Embryo": [ - "AA-DV92_Leaf_middle_embryo" - ], - "AA-DV92_Pre-Embryo": [ - "AA-DV92_Pre-embryo" - ], - "AA-DV92_Mature_Embryo": [ - "AA-DV92_Mature_embryo" - ], - "AA-DV92_Two_Cell_Embryo": [ - "AA-DV92_Two_cell_embryo" - ], - "AA-DV92_Transition_Embryo": [ - "AA-DV92_Transition_embryo" - ], - "AA-DV92_Transition_Endosperm": [ - "AA-DV92_Transition_stage_endosperm" - ] - } - }, - "Hexaploid-AC_Med_CTRL": { - "controls": [ - "Hexaploid-AC_Med_CTRL" - ], - "treatments": { - "Hexaploid-AC_Leaf_Late_Endosperm": [ - "Hexaploid-AC_Late_leaf_stage_endosperm" - ], - "Hexaploid-AC_Leaf_Early_Embryo": [ - "Hexaploid-AC_Leaf_early_embryo" - ], - "Hexaploid-AC_Leaf_Early_Seed_Coat": [ - "Hexaploid-AC_Leaf_early_stage_seed_coat" - ], - "Hexaploid-AC_Leaf_Late_Embryo": [ - "Hexaploid-AC_Leaf_early_stage_seed_coat" - ], - "Hexaploid-AC_Leaf_Middle_Embryo": [ - "Hexaploid-AC_Leaf_middle_embryo" - ], - "Hexaploid-AC_Mature_Embryo": [ - "Hexaploid-AC_Mature_embryo" - ], - "Hexaploid-AC_Pre-Embryo": [ - "Hexaploid-AC_Pre-embryo" - ], - "Hexaploid-AC_Transition_Embryo": [ - "Hexaploid-AC_Transition_embryo" - ], - "Hexaploid-AC_Transition_Endosperm": [ - "Hexaploid-AC_Transition_stage_endosperm" - ], - "Hexaploid-AC_Two_Cell_Embryo": [ - "Hexaploid-AC_Two_cell_embryo" - ] - } - }, - "Tetraploid-SF_Med_CTRL": { - "controls": [ - "Tetraploid-SF_Med_CTRL" - ], - "treatments": { - "Tetraploid-SF_Leaf_Early_Seed_Coat": [ - "Tetraploid-SF_Leaf_early_stage_seed_coat" - ], - "Tetraploid-SF_Leaf_Early_Embryo": [ - "Tetraploid-SF_Leaf_early_embryo" - ], - "Tetraploid-SF_Leaf_Late_Embryo": [ - "Tetraploid-SF_Leaf_late_embryo" - ], - "Tetraploid-SF_Leaf_Late_Endosperm": [ - "Tetraploid-SF_Leaf_late_stage_endosperm" - ], - "Tetraploid-SF_Leaf_Middle_Embryo": [ - "Tetraploid-SF_Leaf_middle_embryo" - ], - "Tetraploid-SF_Mature_Embryo": [ - "Tetraploid-SF_Mature_embryo" - ], - "Tetraploid-SF_Pre-Embryo": [ - "Tetraploid-SF_Pre-embryo" - ], - "Tetraploid-SF_Transition_Embryo": [ - "Tetraploid-SF_Transition_embryo" - ], - "Tetraploid-SF_Transition_Endosperm": [ - "Tetraploid-SF_Transition_stage_endosperm" - ], - "Tetraploid-SF_Two_Cell_Embryo": [ - "Tetraploid-SF_Two_cell_embryo" - ] - } - }, - "BB-TA2780_Med_CTRL": { - "controls": [ - "BB-TA2780_Med_CTRL" - ], - "treatments": { - "BB-TA2780_Leaf_Early_Seed_Coat": [ - "BB-TA2780_Leaf_early_stage_seed_coat" - ], - "BB-TA2780_Leaf_Early_Embryo": [ - "BB-TA2780_Leaf_early_embryo" - ], - "BB-TA2780_Leaf_Late_Embryo": [ - "BB-TA2780_Leaf_late_embryo" - ], - "BB-TA2780_Leaf_Late_Endosperm": [ - "BB-TA2780_Leaf_late_stage_endosperm" - ], - "BB-TA2780_Leaf_Middle_Embryo": [ - "BB-TA2780_Leaf_middle_embryo" - ], - "BB-TA2780_Mature_Embryo": [ - "BB-TA2780_Mature_embryo" - ], - "BB-TA2780_Pre-Embryo": [ - "BB-TA2780_Pre-embryo" - ], - "BB-TA2780_Transition_Embryo": [ - "BB-TA2780_Transition_embryo" - ], - "BB-TA2780_Transition_Endosperm": [ - "BB-TA2780_Transition_stage_endosperm" - ], - "BB-TA2780_Two_Cell_Embryo": [ - "BB-TA2780_Two_cell_embryo" - ] - } - }, - "DD-TA101132_Med_CTRL": { - "controls": [ - "DD-TA101132_Med_CTRL" - ], - "treatments": { - "DD-TA101132_Leaf_Early_Embryo": [ - "DD-TA101132_Leaf_early_embryo" - ], - "DD-TA101132_Leaf_Early_Seed_Coat": [ - "DD-TA101132_Leaf_early_stage_seed_coat" - ], - "DD-TA101132_Leaf_Late_Embryo": [ - "DD-TA101132_Leaf_late_embryo" - ], - "DD-TA101132_Leaf_Late_Endosperm": [ - "DD-TA101132_Leaf_late_stage_endosperm" - ], - "DD-TA101132_Leaf_Middle_Embryo": [ - "DD-TA101132_leaf_middle_embryo" - ], - "DD-TA101132_Mature_Embryo": [ - "DD-TA101132_Mature_embryo" - ], - "DD-TA101132_Transition_Embryo": [ - "DD-TA101132_Transition_embryo" - ], - "DD-TA101132_Transition_Endosperm": [ - "DD-TA101132_Transition_stage_endosperm" - ], - "DD-TA101132_Two_Cell_Embryo": [ - "DD-TA101132_Two_cell_embryo" - ], - "DD-TA101132_Pre-Embryo": [ - "DD-TA101132_Pre-embryo" - ] - } - } - } - }, - "Wheat_Meiosis": { - "database": "wheat_meiosis", - "view_name": "Wheat_Meiosis", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Anther": [ - "Anther_rep1", - "Anther_rep2", - "Anther_rep3" - ], - "Diplotene": [ - "Diplotene_rep1", - "Diplotene_rep2", - "Diplotene_rep3" - ], - "Flagleaf": [ - "FlagLeaf_rep1", - "FlagLeaf_rep2", - "FlagLeaf_rep3" - ], - "Leaf": [ - "Leaf_rep1", - "Leaf_rep2", - "Leaf_rep3" - ], - "Leptotene": [ - "Leptotene_rep1", - "Leptotene_rep2", - "Leptotene_rep3" - ], - "Metaphase_I": [ - "Metaphase-I_rep1", - "Metaphase-I_rep2", - "Metaphase-I_rep3" - ], - "Metaphase_II": [ - "Metaphase-II_rep1", - "Metaphase-II_rep2", - "Metaphase-II_rep3" - ], - "Pachytene": [ - "Pachytene_rep1", - "Pachytene_rep2", - "Pachytene_rep3" - ], - "Pollen": [ - "Pollen_rep1", - "Pollen_rep2", - "Pollen_rep3" - ], - "Pre-meiotic_G2": [ - "Pre-meiotic_G2_rep1", - "Pre-meiotic_G2_rep2", - "Pre-meiotic_G2_rep3" - ], - "Zygotene": [ - "Zygotene_rep1", - "Zygotene_rep2", - "Zygotene_rep3" - ] - } - } - } - } - } - } - } -} \ No newline at end of file diff --git a/data/efp_info/efp_species_view_info_typed.json b/data/efp_info/efp_species_view_info_typed.json deleted file mode 100644 index 8f3ab67b..00000000 --- a/data/efp_info/efp_species_view_info_typed.json +++ /dev/null @@ -1,18512 +0,0 @@ -{ - "actinidia": { - "data": { - "species": "actinidia", - "views": { - "Bud_Development": { - "database": "actinidia_bud_development", - "view_name": "Bud_Development", - "groups": { - "Nov": { - "controls": [ - "Nov" - ], - "treatments": { - "bud": [ - "Nov", - "Nov_TB", - "Dec", - "Jan", - "Jan_TB", - "Feb", - "Mar", - "Mar_TB", - "Apr", - "May", - "Jun", - "Jul", - "Aug" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Flower_Fruit_Development": { - "database": "actinidia_flower_fruit_development", - "view_name": "Flower_Fruit_Development", - "groups": { - "flower": { - "controls": [ - "flower" - ], - "treatments": { - "Floral_Bud": [ - "Flower_bud" - ], - "centre": [ - "Flower" - ], - "anther": [ - "Flower" - ], - "petal": [ - "Flower" - ], - "core": [ - "Fruit_T1", - "Fruit_T2", - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA" - ], - "cortex": [ - "Fruit_T1", - "Fruit_T2", - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA" - ], - "flesh": [ - "Fruit_T1", - "Fruit_T2", - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Postharvest": { - "database": "actinidia_postharvest", - "view_name": "Postharvest", - "groups": { - "Postharvest_Control": { - "controls": [ - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA" - ], - "treatments": { - "core": [ - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA", - "Fruit_231_DAA", - "Fruit_231_DAA_1DAH", - "Fruit_231_DAA_2DAH", - "Fruit_231_DAA_4DAH" - ], - "cortex": [ - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA", - "Fruit_231_DAA", - "Fruit_231_DAA_1DAH", - "Fruit_231_DAA_2DAH", - "Fruit_231_DAA_4DAH" - ], - "flesh": [ - "Fruit_147_DAA", - "Fruit_166_DAA", - "Fruit_182_DAA", - "Fruit_224_DAA", - "Fruit_231_DAA", - "Fruit_231_DAA_1DAH", - "Fruit_231_DAA_2DAH", - "Fruit_231_DAA_4DAH" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Vegetative_Growth": { - "database": "actinidia_vegetative_growth", - "view_name": "Vegetative_Growth", - "groups": { - "cane": { - "controls": [ - "cane" - ], - "treatments": { - "sink_leaf": [ - "Leaf_sink" - ], - "source_leaf": [ - "Leaf_source" - ], - "shoot": [ - "Shoot" - ], - "cane": [ - "cane" - ], - "root": [ - "Root" - ] - } - } - }, - "data_type": "RNA-Seq" - } - } - } - }, - "arabidopsis": { - "data": { - "species": "arabidopsis", - "views": { - "Abiotic_Stress": { - "database": "atgenexp_stress", - "view_name": "Abiotic_Stress", - "groups": { - "Shoot_0_Hour": { - "controls": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "treatments": { - "Control_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Cold_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Osmotic_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Salt_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Drought_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Genotoxic_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Oxidative_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "UV-B_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Wounding_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ], - "Heat_Shoot_0_Hour": [ - "AtGen_6_0011", - "AtGen_6_0012" - ] - } - }, - "Root_0_Hour": { - "controls": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - "treatments": { - "Control_Root_0_Hour": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - "Cold_Root_0_Hour": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - "Osmotic_Root_0_Hour": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - 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"controls": [ - "AtGen_6_0721", - "AtGen_6_0722" - ], - "treatments": { - "Control_Root_After_15_Minutes": [ - "AtGen_6_0721", - "AtGen_6_0722" - ], - "Drought_Root_After_15_Minutes": [ - "AtGen_6_4721", - "AtGen_6_4722" - ], - "UV-B_Root_After_15_Minutes": [ - "AtGen_6_7721", - "AtGen_6_7722" - ], - "Wounding_Root_After_15_Minutes": [ - "AtGen_6_8723", - "AtGen_6_8724" - ], - "Heat_Root_After_15_Minutes": [ - "AtGen_6_9721", - "AtGen_6_9722" - ] - } - }, - "Shoot_After_30_Minutes": { - "controls": [ - "AtGen_6_0111", - "AtGen_6_0112" - ], - "treatments": { - "Control_Shoot_After_30_Minutes": [ - "AtGen_6_0111", - "AtGen_6_0112" - ], - "Cold_Shoot_After_30_Minutes": [ - "AtGen_6_1111", - "AtGen_6_1112" - ], - "Osmotic_Shoot_After_30_Minutes": [ - "AtGen_6_2111", - "AtGen_6_2112" - ], - "Salt_Shoot_After_30_Minutes": [ - "AtGen_6_3111", - "AtGen_6_3112" - ], - "Drought_Shoot_After_30_Minutes": [ - "AtGen_6_4111", - "AtGen_6_4112" - ], - "Genotoxic_Shoot_After_30_Minutes": [ - 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"Heat_Shoot_After_1_Hour": [ - "AtGen_6_9211", - "AtGen_6_9212" - ] - } - }, - "Root_After_1_Hour": { - "controls": [ - "AtGen_6_0221", - "AtGen_6_0222" - ], - "treatments": { - "Control_Root_After_1_Hour": [ - "AtGen_6_0221", - "AtGen_6_0222" - ], - "Cold_Root_After_1_Hour": [ - "AtGen_6_1221", - "AtGen_6_1222" - ], - "Osmotic_Root_After_1_Hour": [ - "AtGen_6_2221", - "AtGen_6_2222" - ], - "Salt_Root_After_1_Hour": [ - "AtGen_6_3221", - "AtGen_6_3222" - ], - "Drought_Root_After_1_Hour": [ - "AtGen_6_4221", - "AtGen_6_4222" - ], - "Genotoxic_Root_After_1_Hour": [ - "AtGen_6_5221", - "AtGen_6_5222" - ], - "Oxidative_Root_After_1_Hour": [ - "AtGen_6_6223", - "AtGen_6_6224" - ], - "UV-B_Root_After_1_Hour": [ - "AtGen_6_7221", - "AtGen_6_7222" - ], - "Wounding_Root_After_1_Hour": [ - "AtGen_6_8224", - "AtGen_6_8225" - ], - "Heat_Root_After_1_Hour": [ - "AtGen_6_9221", - "AtGen_6_9222" - ] - } - }, - "Shoot_After_3_Hours": { - "controls": [ - "AtGen_6_0311", - "AtGen_6_0312" - ], - "treatments": { - "Control_Shoot_After_3_Hours": [ - "AtGen_6_0311", - "AtGen_6_0312" - ], - "Cold_Shoot_After_3_Hours": [ - "AtGen_6_1311", - "AtGen_6_1312" - ], - "Osmotic_Shoot_After_3_Hours": [ - "AtGen_6_2311", - "AtGen_6_2312" - ], - "Salt_Shoot_After_3_Hours": [ - "AtGen_6_3311", - "AtGen_6_3312" - ], - "Drought_Shoot_After_3_Hours": [ - "AtGen_6_4311", - "AtGen_6_4312" - ], - "Genotoxic_Shoot_After_3_Hours": [ - "AtGen_6_5311", - "AtGen_6_5312" - ], - "Oxidative_Shoot_After_3_Hours": [ - "AtGen_6_6311", - "AtGen_6_6312" - ], - "UV-B_Shoot_After_3_Hours": [ - "AtGen_6_7311", - "AtGen_6_7312" - ], - "Wounding_Shoot_After_3_Hours": [ - "AtGen_6_8313", - "AtGen_6_8314" - ], - "Heat_Shoot_After_3_Hours": [ - "AtGen_6_9311", - "AtGen_6_9312" - ] - } - }, - "Root_After_3_Hours": { - "controls": [ - "AtGen_6_0321", - "AtGen_6_0322" - ], - "treatments": { - "Control_Root_After_3_Hours": [ - "AtGen_6_0321", - "AtGen_6_0322" - ], - "Cold_Root_After_3_Hours": [ - "AtGen_6_1321", - 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}, - "Root_After_6_Hours": { - "controls": [ - "AtGen_6_0421", - "AtGen_6_0422" - ], - "treatments": { - "Control_Root_After_6_Hours": [ - "AtGen_6_0421", - "AtGen_6_0422" - ], - "Cold_Root_After_6_Hours": [ - "AtGen_6_1421", - "AtGen_6_1422" - ], - "Osmotic_Root_After_6_Hours": [ - "AtGen_6_2421", - "AtGen_6_2422" - ], - "Salt_Root_After_6_Hours": [ - "AtGen_6_3421", - "AtGen_6_3422" - ], - "Drought_Root_After_6_Hours": [ - "AtGen_6_4421", - "AtGen_6_4422" - ], - "Genotoxic_Root_After_6_Hours": [ - "AtGen_6_5421", - "AtGen_6_5422" - ], - "Oxidative_Root_After_6_Hours": [ - "AtGen_6_6421", - "AtGen_6_6422" - ], - "UV-B_Root_After_6_Hours": [ - "AtGen_6_7421", - "AtGen_6_7422" - ], - "Wounding_Root_After_6_Hours": [ - "AtGen_6_8423", - "AtGen_6_8424" - ], - "Heat_Root_After_6_Hours": [ - "AtGen_6_9421", - "AtGen_6_9422" - ] - } - }, - "Shoot_After_12_Hours": { - "controls": [ - "AtGen_6_0511", - "AtGen_6_0512" - ], - "treatments": { - "Control_Shoot_After_12_Hours": [ - "AtGen_6_0511", 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"GSM491675", - "GSM491676", - "GSM491677" - ] - } - }, - "GSM237280;GSM237281": { - "controls": [ - "GSM237280", - "GSM237281" - ], - "treatments": { - "Root,_non-selenate_treated_(control)": [ - "GSM237280", - "GSM237281" - ], - "Root,_Selenate_treated": [ - "GSM237282", - "GSM237283" - ] - } - }, - "GSM491666;GSM491667;GSM491668": { - "controls": [ - "GSM491666", - "GSM491667", - "GSM491668" - ], - "treatments": { - "Water_limited_(dry),_Midday": [ - "GSM491669", - "GSM491670", - "GSM491671" - ], - "Well_watered,_Midday_(control)": [ - "GSM491666", - "GSM491667", - "GSM491668" - ] - } - }, - "GSM392492;GSM392493": { - "controls": [ - "GSM392492", - "GSM392493" - ], - "treatments": { - "Shoot,_non-selenate_treated_(control)": [ - "GSM392492", - "GSM392493" - ] - } - }, - "GSM40552": { - "controls": [ - "GSM40552" - ], - "treatments": { - "Non_Stressed_(control),_Total_RNA": [ - "GSM40552" - ], - "Hypoxia_Stress,_Total_RNA": [ - "GSM40553" - ] - } - }, - "GSM40554": { - "controls": [ - "GSM40554" - ], - "treatments": { - "Non_Stressed_(control),_Polysomal_RNA": [ - "GSM40554" - ], - "Hypoxia_Stress,_Polysomal_RNA": [ - "GSM40555" - ] - } - }, - "GSM237292;GSM237293": { - "controls": [ - "GSM237292", - "GSM237293" - ], - "treatments": { - "Shoot,_non-_selenate_treated": [ - "GSM237294", - "GSM237295" - ] - } - }, - "GSM491678;GSM491679;GSM491680": { - "controls": [ - "GSM491678", - "GSM491679", - "GSM491680" - ], - "treatments": { - "Well_watered,_midnight_(control)": [ - "GSM491678", - "GSM491679", - "GSM491680" - ], - "Water_limited_(dry),_midnight": [ - "GSM491681", - "GSM491682", - "GSM491683" - ] - } - } - }, - "data_type": "Microarray" - }, - "Biotic_Stress": { - "database": "atgenexp_pathogen", - "view_name": "Biotic_Stress", - "groups": { - "Botrytis_cinerea_at_18_Hours": { - "controls": [ - "CT181-1", - "CT181-2", - "CT182-1" - ], - "treatments": { - "Control_B.c._at_18_Hours": [ - "CT181-1", - "CT181-2", - "CT182-1" - ], - "Treated_B.c._at_18_Hours": [ - "BC181-1", - "BC181-2", - "BC182-1" - ] - } - }, - "Botrytis_cinerea_at_48_Hours": { - "controls": [ - "CT481-1", - "CT482-1", - "CT482-2" - ], - "treatments": { - "Control_B.c._at_48_Hours": [ - "CT481-1", - "CT482-1", - "CT482-2" - ], - "Treated_B.c._at_48_Hours": [ - "BC481-1", - "BC482-1", - "BC482-2" - ] - } - }, - "Half_Leaf_Pseudomonas_syringae_at_4_Hours": { - "controls": [ - "2505", - "2795" - ], - "treatments": { - "Control_Half_P.s_at_4_Hours": [ - "2505", - "2795" - ], - "Avirulent_Half_P.s_at_4_Hours": [ - "2504", - "2796" - ], - "Virulent_Half_P.s_at_4_Hours": [ - "2530", - "2797" - ] - } - }, - "Half_Leaf_Pseudomonas_syringae_at_8_Hours": { - "controls": [ - "2507", - "2792" - ], - "treatments": { - "Control_Half_P.s_at_8_Hours": [ - "2507", - "2792" - ], - "Avirulent_Half_P.s_at_8_Hours": [ - "2506", - "2793" - ], - "Virulent_Half_P.s_at_8_Hours": [ - "2529", - "2794" - ] - } - }, - "Half_Leaf_Pseudomonas_syringae_at_16_Hours": { - "controls": [ - "2527", - "2789" - ], 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] - } - }, - "Erysiphe_orontii_at_24_Hours": { - "controls": [ - "JD AT+EO COL WT 24H UNINFECTED", - "JD AT+EO COL WT EXP2 24H UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 24H" - ], - "treatments": { - "Control_E.o._at_24_Hours": [ - "JD AT+EO COL WT 24H UNINFECTED", - "JD AT+EO COL WT EXP2 24H UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 24H" - ], - "Treated_E.o._at_24_Hours": [ - "JD AT+EO COL WT 24H INFECTED", - "JD AT+EO COL WT EXP2 24H INFECTED", - "JD AT+EO TIME EXP3 EO INF 24H" - ] - } - }, - "Erysiphe_orontii_at_48_Hours": { - "controls": [ - "JD AT+EO COL WT 02D UNINFECTED", - "JD AT+EO COL WT EXP2 02D UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 2D" - ], - "treatments": { - "Control_E.o._at_48_Hours": [ - "JD AT+EO COL WT 02D UNINFECTED", - "JD AT+EO COL WT EXP2 02D UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 2D" - ], - "Treated_E.o._at_48_Hours": [ - "JD AT+EO COL WT 02D INFECTED", - "JD AT+EO COL WT EXP2 02D INFECTED", - "JD AT+EO TIME EXP3 EO INF 2D" - ] - } - }, - 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"controls": [ - "JD AT+EO COL WT 05D UNINFECTED", - "JD AT+EO COL WT EXP2 05D UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 5D" - ], - "treatments": { - "Control_E.o._at_120_Hours": [ - "JD AT+EO COL WT 05D UNINFECTED", - "JD AT+EO COL WT EXP2 05D UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 5D" - ], - "Treated_E.o._at_120_Hours": [ - "JD AT+EO COL WT 05D INFECTED", - "JD AT+EO COL WT EXP2 05D INFECTED", - "JD AT+EO TIME EXP3 EO INF 5D" - ] - } - } - }, - "data_type": "Microarray" - }, - "Biotic_Stress_II": { - "database": "atgenexp_pathogen", - "view_name": "Biotic_Stress_II", - "groups": { - "GSM392490;GSM392491": { - "controls": [ - "GSM392490", - "GSM392491" - ], - "treatments": { - "Col_laser_microdissected,_5_d_UI,": [ - "GSM392490", - "GSM392491" - ], - "Col_laser_microdissected,_5_dpi": [ - "GSM392488", - "GSM392489" - ], - "eds16_laser_microdissected,_5_dpi": [ - "GSM392492", - "GSM392493" - ] - } - }, - "GSM392500;GSM392501": { - "controls": [ - "GSM392500", - "GSM392501" - ], - "treatments": { - "Col_whole_leaf_amplified,_5_d_UI": [ - "GSM392500", - "GSM392501" - ], - "Col_whole_leaf_amplified,_5_dpi,": [ - "GSM392498", - "GSM392499" - ], - "Col_leaf_scrape,_5_dpi": [ - "GSM392502", - "GSM392503" - ] - } - }, - "GSM554311_WT_Emwa1_0dpi_rep2": { - "controls": [ - "GSM554311_WT_Emwa1_0dpi_rep2" - ], - "treatments": { - "WT_Emwa1_0dpi_rep1+rep2": [ - "GSM554311_WT_Emwa1_0dpi_rep1", - "GSM554311_WT_Emwa1_0dpi_rep2" - ], - "WT_Emwa1_0.5dpi_rep1+rep2": [ - "GSM554312_WT_Emwa1_0.5dpi_rep2" - ], - "WT_Emwa1_2dpi_rep1+rep2": [ - "GSM554313_WT_Emwa1_2dpi_rep1", - "GSM554313_WT_Emwa1_2dpi_rep2" - ], - "WT_Emwa1_4dpi_rep1+rep2": [ - "GSM554314_WT_Emwa1_4dpi_rep1", - "GSM554314_WT_Emwa1_4dpi_rep2" - ], - "WT_Emwa1_6dpi_rep1+rep2": [ - "GSM554315_WT_Emwa1_6dpi_rep1", - "GSM554315_WT_Emwa1_6dpi_rep2" - ] - } - }, - "GSM554316_rpp4_Emwa1_0dpi_rep1;GSM554316_rpp4_Emwa1_0dpi_rep2": { - "controls": [ - "GSM554316_rpp4_Emwa1_0dpi_rep1", - "GSM554316_rpp4_Emwa1_0dpi_rep2" - ], - "treatments": { - "rpp4_Emwa1_0dpi_rep1+rep2": [ - "GSM554316_rpp4_Emwa1_0dpi_rep1", - "GSM554316_rpp4_Emwa1_0dpi_rep2" - ], - "rpp4_Emwa1_0.5dpi_rep1+rep2": [ - "GSM554317_rpp4_Emwa1_0.5dpi_rep1", - "GSM554317_rpp4_Emwa1_0.5dpi_rep2" - ], - "rpp4_Emwa1_2dpi_rep1+rep2": [ - "GSM554318_rpp4_Emwa1_2dpi_rep1", - "GSM554318_rpp4_Emwa1_2dpi_rep2" - ], - "rpp4_Emwa1_4dpi_rep1+rep2": [ - "GSM554319_rpp4_Emwa1_4dpi_rep1", - "GSM554319_rpp4_Emwa1_4dpi_rep2" - ], - "rpp4_Emwa1_6dpi_rep1+rep2": [ - "GSM554320_rpp4_Emwa1_6dpi_rep1", - "GSM554320_rpp4_Emwa1_6dpi_rep2" - ] - } - }, - "GSM157299;GSM157300;GSM157301": { - "controls": [ - "GSM157299_JPritchard_A-1_CTR_Rep1_ATH1", - "GSM157300_JPritchard_A-2_CTR_Rep2_ATH1", - "GSM157301_Pritchard_A-3_CTR_Rep3_ATH1" - ], - "treatments": { - "Control": [ - "GSM157299_JPritchard_A-1_CTR_Rep1_ATH1", - "GSM157300_JPritchard_A-2_CTR_Rep2_ATH1", - "GSM157301_Pritchard_A-3_CTR_Rep3_ATH1" - ], - "Aphid_infested": [ - "GSM157303_JPritchard_A-5_API_Rep2_ATH1", - "GSM157304_JPritchard_A-6_API_Rep3_ATH1" - ] - } - } - }, - "data_type": "Microarray" - }, - "Chemical": { - "database": "atgenexp_hormone", - "view_name": "Chemical", - "groups": { - "Gibberellic_Acid_Inhibitors_at_3_Hours": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "Propiconazole_Treated_at_3_Hours": [ - "RIKEN-GODA3A2", - "RIKEN-GODA3B2" - ], - "Uniconazole_Treated_at_3_Hours": [ - "RIKEN-GODA5A2", - "RIKEN-GODA5B2" - ], - "Paclobutrazol_Treated_at_3_Hours": [ - "RIKEN-GODA11A2", - "RIKEN-GODA11B2" - ], - "Prohexadione_Treated_at_3_Hours": [ - "RIKEN-GODA13A2", - "RIKEN-GODA13B2" - ] - } - }, - "Gibberellic_Acid_Inhibitors_at_12_Hours": { - "controls": [ - "RIKEN-GODA2A2", - "RIKEN-GODA2B2" - ], - "treatments": { - "Control_at_12_Hours": [ - "RIKEN-GODA2A2", - "RIKEN-GODA2B2" - ], - "Propiconazole_Treated_at_12_Hours": [ - "RIKEN-GODA4A2", - "RIKEN-GODA4B2" - ], - "Uniconazole_Treated_at_12_Hours": [ - "RIKEN-GODA6A2", - "RIKEN-GODA6B2" - ], - "Paclobutrazol_Treated_at_12_Hours": [ - "RIKEN-GODA12A2", - "RIKEN-GODA12B2" - ], - "Prohexadione_Treated_at_12_Hours": [ - "RIKEN-GODA14A2", - "RIKEN-GODA14B2" - ] - } - }, - "Auxin_Inhibitors": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "2,4,6-T_Treated": [ - "RIKEN-GODA23A3", - "RIKEN-GODA23B3" - ], - "PCIB_Treated": [ - "RIKEN-GODA24A3", - "RIKEN-GODA24B3" - ], - "TIBA_Treated": [ - "RIKEN-GODA25A3", - "RIKEN-GODA25B3" - ], - "NPA_Treated": [ - "RIKEN-GODA26A3", - "RIKEN-GODA26B3" - ] - } - }, - "Brassinosteroid_Inhibitors_at_3_Hours": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "10uM_Brz220_Treated_at_3_Hours": [ - "RIKEN-GODA7A4", - "RIKEN-GODA7B4" - ], - "3uM_Brz220_Treated_at_3_Hours": [ - "RIKEN-GODA30A4", - "RIKEN-GODA30B4" - ] - } - }, - "Brassinosteroid_Inhibitors_at_12_Hours": { - "controls": [ - "RIKEN-GODA2A2", - "RIKEN-GODA2B2" - ], - "treatments": { - "Control_at_12_Hours": [ - "RIKEN-GODA2A2", - "RIKEN-GODA2B2" - ], - "10uM_Brz91_Treated_at_12_Hours": [ - "RIKEN-GODA10A4", - "RIKEN-GODA10B4" - ] - } - }, - "Ethylene_Inhibitors": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "10uM_AgNO3_Treated": [ - "RIKEN-GODA19A7", - "RIKEN-GODA19B7" - ], - "10uM_AVG_Treated": [ - "RIKEN-GODA20A7", - "RIKEN-GODA20B7" - ] - } - }, - "Cyclohexamide": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "10uM_CHX_Treated": [ - "RIKEN-GODA27A8", - "RIKEN-GODA27B8" - ] - } - }, - "Proteasome_Inhibitor_MG13": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "10uM_MG132_Treated": [ - "RIKEN-GODA22A9", - "RIKEN-GODA22B9" - ] - } - }, - "Photosynthesis_Inhibitor_PN08_at_3_Hours": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "1uM_PNO8_Treated_at_3_Hours": [ - "RIKEN-GODA15A5", - "RIKEN-GODA15B5" - ], - "10uM_PNO8_Treated_at_3_Hours": [ - "RIKEN-GODA29A5", - "RIKEN-GODA29B5" - ] - } - }, - "Photosynthesis_Inhibitor_PN08_at_12_Hours": { - "controls": [ - "RIKEN-GODA2A2", - "RIKEN-GODA2B2" - ], - "treatments": { - "Control_at_12_Hours": [ - "RIKEN-GODA2A2", - "RIKEN-GODA2B2 " - ], - "1uM_PNO8_Treated_at_12_Hours": [ - "RIKEN-GODA16A5", - "RIKEN-GODA16B5" - ] - } - }, - "Ibuprofen,_Salycylic_Acid,_and_Daminozide": { - "controls": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "treatments": { - "Control": [ - "RIKEN-GODA1A2", - "RIKEN-GODA1B2" - ], - "Ibuprofen_Treated": [ - "RIKEN-GODA17AH", - "RIKEN-GODA17BH" - ], - "Salicylic_Acid_Treated": [ - "RIKEN-GODA21AH", - "RIKEN-GODA21BH" - ], - "Daminozide_Treated": [ - "RIKEN-GODA18AH", - "RIKEN-GODA18BH" - ] - } - } - }, - "data_type": "Microarray" - }, - "DNA_Damage": { - "database": "dna_damage", - "view_name": "DNA_Damage", - "groups": { - "col-0_rep1_20min_minus_Y;col-0_rep2_20min_minus_Y": { - "controls": [ - "col-0_rep1_20min_minus_Y", - "col-0_rep2_20min_minus_Y" - ], - "treatments": { - "Y+_Col-0_20min": [ - "col-0_rep1_20min_plus_Y", - "col-0_rep2_20min_plus_Y" - ], - "Y-_Col-0_20min": [ - "col-0_rep1_20min_minus_Y", - "col-0_rep2_20min_minus_Y" - ] - } - }, - "col-0_rep1_90min_minus_Y;col-0_rep2_90min_minus_Y": { - "controls": [ - "col-0_rep1_90min_minus_Y", - "col-0_rep2_90min_minus_Y" - ], - "treatments": { - "Y+_Col-0_90min": [ - "col-0_rep1_90min_plus_Y", - "col-0_rep2_90min_plus_Y" - ], - "Y-_Col-0_90min": [ - "col-0_rep1_90min_minus_Y", - "col-0_rep2_90min_minus_Y" - ] - } - }, - "col-0_rep1_3hr_minus_Y;col-0_rep2_3hr_minus_Y": { - "controls": [ - "col-0_rep1_3hr_minus_Y", - "col-0_rep2_3hr_minus_Y" - ], - "treatments": { - "Y+_Col-0_3h": [ - "col-0_rep1_3hr_plus_Y", - "col-0_rep2_3hr_plus_Y" - ], - "Y-_Col-0_3h": [ - "col-0_rep1_3hr_minus_Y", - "col-0_rep2_3hr_minus_Y" - ] - } - }, - "col-0_rep1_6hr_minus_Y;col-0_rep2_6hr_minus_Y": { - "controls": [ - "col-0_rep1_6hr_minus_Y", - "col-0_rep2_6hr_minus_Y" - ], - "treatments": { - "Y+_Col-0_6h": [ - "col-0_rep1_6hr_plus_Y", - "col-0_rep2_6hr_plus_Y" - ], - "Y-_Col-0_6h": [ - "col-0_rep1_6hr_minus_Y", - "col-0_rep2_6hr_minus_Y" - ] - } - }, - "col-0_rep1_12hr_minus_Y;col-0_rep2_12hr_minus_Y": { - "controls": [ - "col-0_rep1_12hr_minus_Y", - "col-0_rep2_12hr_minus_Y" - ], - "treatments": { - "Y+_Col-0_12h": [ - "col-0_rep1_12hr_plus_Y", - "col-0_rep2_12hr_plus_Y" - ], - "Y-_Col-0_12h": [ - "col-0_rep1_12hr_minus_Y", - "col-0_rep2_12hr_minus_Y" - ] - } - }, - "col-0_rep1_24hr_minus_Y;col-0_rep2_24hr_minus_Y": { - "controls": [ - "col-0_rep1_24hr_minus_Y", - "col-0_rep2_24hr_minus_Y" - ], - "treatments": { - "Y+_Col-0_24h": [ - "col-0_rep1_24hr_plus_Y", - "col-0_rep2_24hr_plus_Y" - ], - "Y-_Col-0_24h": [ - "col-0_rep1_24hr_minus_Y", - "col-0_rep2_24hr_minus_Y" - ] - } - }, - "sog1-1_rep1_20min_minus_Y;sog1-1_rep2_20min_minus_Y": { - "controls": [ - "sog1-1_rep1_20min_minus_Y", - "sog1-1_rep2_20min_minus_Y" - ], - "treatments": { - "Y+_sog1-1_20min": [ - "sog1-1_rep1_20min_plus_Y", - "sog1-1_rep2_20min_plus_Y" - ], - "Y-_sog1-1_20min": [ - "sog1-1_rep1_20min_minus_Y", - "sog1-1_rep2_20min_minus_Y" - ] - } - }, - "sog1-1_rep1_90min_minus_Y;sog1-1_rep2_90min_minus_Y": { - "controls": [ - "sog1-1_rep1_90min_minus_Y", - "sog1-1_rep2_90min_minus_Y" - ], - "treatments": { - "Y+_sog1-1_90min": [ - "sog1-1_rep1_90min_plus_Y", - "sog1-1_rep2_90min_plus_Y" - ], - "Y-_sog1-1_90min": [ - "sog1-1_rep1_90min_minus_Y", - "sog1-1_rep2_90min_minus_Y" - ] - } - }, - "sog1-1_rep1_3hr_minus_Y;sog1-1_rep2_3hr_minus_Y": { - "controls": [ - "sog1-1_rep1_3hr_minus_Y", - "sog1-1_rep2_3hr_minus_Y" - ], - "treatments": { - "Y+_sog1-1_3h": [ - "sog1-1_rep1_3hr_plus_Y", - "sog1-1_rep2_3hr_plus_Y" - ], - "Y-_sog1-1_3h": [ - "sog1-1_rep1_3hr_minus_Y", - "sog1-1_rep2_3hr_minus_Y" - ] - } - }, - "sog1-1_rep1_6hr_minus_Y;sog1-1_rep2_6hr_minus_Y": { - "controls": [ - "sog1-1_rep1_6hr_minus_Y", - "sog1-1_rep2_6hr_minus_Y" - ], - "treatments": { - "Y+_sog1-1_6h": [ - "sog1-1_rep1_6hr_plus_Y", - "sog1-1_rep2_6hr_plus_Y" - ], - "Y-_sog1-1_6h": [ - "sog1-1_rep1_6hr_minus_Y", - "sog1-1_rep2_6hr_minus_Y" - ] - } - }, - "sog1-1_rep1_12hr_minus_Y;sog1-1_rep2_12hr_minus_Y": { - "controls": [ - "sog1-1_rep1_12hr_minus_Y", - "sog1-1_rep2_12hr_minus_Y" - ], - "treatments": { - "Y+_sog1-1_12h": [ - "sog1-1_rep1_12hr_plus_Y", - "sog1-1_rep2_12hr_plus_Y" - ], - "Y-_sog1-1_12h": [ - "sog1-1_rep1_12hr_minus_Y", - "sog1-1_rep2_12hr_minus_Y" - ] - } - }, - "sog1-1_rep1_24hr_minus_Y;sog1-1_rep2_24hr_minus_Y": { - "controls": [ - "sog1-1_rep1_24hr_minus_Y", - "sog1-1_rep2_24hr_minus_Y" - ], - "treatments": { - "Y+_sog1-1_24h": [ - "sog1-1_rep1_24hr_plus_Y", - "sog1-1_rep2_24hr_plus_Y" - ], - "Y-_sog1-1_24h": [ - "sog1-1_rep1_24hr_minus_Y", - "sog1-1_rep2_24hr_minus_Y" - ] - } - } - }, - "data_type": "Microarray" - }, - "Development_RMA": { - "database": "atgenexp", - "view_name": "Development_RMA", - "groups": { - "CTRL_7": { - "controls": [ - "ATGE_CTRL_7" - ], - "treatments": { - "1st_Node": [ - "ATGE_28_A2", - "ATGE_28_B2", - "ATGE_28_C2" - ], - "Flower_Stage_12,Stamens": [ - "ATGE_36_A", - "ATGE_36_B", - "ATGE_36_C" - ], - "Cauline_Leaf": [ - "ATGE_26_A", - "ATGE_26_B", - "ATGE_26_C" - ], - "Cotyledon": [ - "ATGE_1_A", - "ATGE_1_B", - "ATGE_1_C" - ], - "Root": [ - "ATGE_9_A", - "ATGE_9_B", - "ATGE_9_C", - "ATGE_3_A", - "ATGE_3_B", - "ATGE_3_C" - ], - "Entire_Rosette_After_Transition_to_Flowering": [ - "ATGE_23_A", - "ATGE_23_B", - "ATGE_23_C" - ], - "Flower_Stage_9": [ - "ATGE_31_A2", - "ATGE_31_B2", - "ATGE_31_C2" - ], - "Flower_Stage_10/11": [ - "ATGE_32_A2", - "ATGE_32_B2", - "ATGE_32_C2" - ], - "Flower_Stage_12": [ - "ATGE_33_A", - "ATGE_33_B", - "ATGE_33_C" - ], - "Flower_Stage_15": [ - "ATGE_39_A", - "ATGE_39_B", - "ATGE_39_C" - ], - "Flower_Stage_12,_Carpels": [ - "ATGE_37_A", - "ATGE_37_B", - "ATGE_37_C" - ], - "Flower_Stage_12,_Petals": [ - "ATGE_35_A", - "ATGE_35_B", - "ATGE_35_C" - ], - "Flower_Stage_12,_Sepals": [ - "ATGE_34_A", - "ATGE_34_B", - "ATGE_34_C" - ], - "Flower_Stage_15,_Carpels": [ - "ATGE_45_A", - "ATGE_45_B", - "ATGE_45_C" - ], - "Flower_Stage_15,_Petals": [ - "ATGE_42_B", - "ATGE_42_C", - "ATGE_42_D" - ], - "Flower_Stage_15,_Sepals": [ - "ATGE_41_A", - "ATGE_41_B", - "ATGE_41_C" - ], - "Flower_Stage_15,_Stamen": [ - "ATGE_43_A", - "ATGE_43_B", - "ATGE_43_C" - ], - "Flowers_Stage_15,_Pedicels": [ - "ATGE_40_A", - "ATGE_40_B", - "ATGE_40_C" - ], - "Leaf_1_+_2": [ - "ATGE_5_A", - "ATGE_5_B", - "ATGE_5_C" - ], - "Leaf_7,_Petiole": [ - "ATGE_19_A", - "ATGE_19_B", - "ATGE_19_C" - ], - "Leaf_7,_Distal_Half": [ - "ATGE_21_A", - "ATGE_21_B", - "ATGE_21_C" - ], - "Leaf_7,_Proximal_Half": [ - "ATGE_20_A", - "ATGE_20_B", - "ATGE_20_C" - ], - "Hypocotyl": [ - "ATGE_2_A", - "ATGE_2_B", - "ATGE_2_C" - ], - "Rosette_Leaf_2": [ - "ATGE_12_A", - "ATGE_12_B", - "ATGE_12_C" - ], - "Rosette_Leaf_4": [ - "ATGE_13_A", - "ATGE_13_B", - "ATGE_13_C" - ], - "Rosette_Leaf_6": [ - "ATGE_14_A", - "ATGE_14_B", - "ATGE_14_C" - ], - "Rosette_Leaf_8": [ - "ATGE_15_A", - "ATGE_15_B", - "ATGE_15_C" - ], - "Rosette_Leaf_10": [ - "ATGE_16_A", - "ATGE_16_B", - "ATGE_16_C" - ], - "Rosette_Leaf_12": [ - "ATGE_17_A", - "ATGE_17_B", - "ATGE_17_C" - ], - "Senescing_Leaf": [ - "ATGE_25_A", - "ATGE_25_B", - "ATGE_25_C" - ], - "Shoot_Apex,_Inflorescence": [ - "ATGE_29_A2", - "ATGE_29_B2", - "ATGE_29_C2" - ], - "Shoot_Apex,_Transition": [ - "ATGE_8_A", - "ATGE_8_B", - "ATGE_8_C" - ], - "Shoot_Apex,_Vegetative": [ - "ATGE_6_A", - "ATGE_6_B", - "ATGE_6_C" - ], - "Stem,_2nd_Internode": [ - "ATGE_27_A", - "ATGE_27_B", - "ATGE_27_C" - ], - "Mature_Pollen": [ - "ATGE_73_A", - "ATGE_73_B", - "ATGE_73_C" - ], - "Seeds_Stage_3_w/_Siliques": [ - "ATGE_76_A", - "ATGE_76_B", - "ATGE_76_C" - ], - "Seeds_Stage_4_w/_Siliques": [ - "ATGE_77_D", - "ATGE_77_E", - "ATGE_77_F" - ], - "Seeds_Stage_5_w/_Siliques": [ - "ATGE_78_D", - "ATGE_78_E", - "ATGE_78_F" - ], - "Seeds_Stage_6_w/o_Siliques": [ - "ATGE_79_A", - "ATGE_79_B", - "ATGE_79_C" - ], - "Seeds_Stage_7_w/o_Siliques": [ - "ATGE_81_A", - "ATGE_81_B", - "ATGE_81_C" - ], - "Seeds_Stage_8_w/o_Siliques": [ - "ATGE_82_A", - "ATGE_82_B", - "ATGE_82_C" - ], - "Seeds_Stage_9_w/o_Siliques": [ - "ATGE_83_A", - "ATGE_83_B", - "ATGE_83_C" - ], - "Seeds_Stage_10_w/o_Siliques": [ - "ATGE_84_A", - "ATGE_84_B", - "ATGE_84_D" - ], - "Vegetative_Rosette": [ - "ATGE_89_A", - "ATGE_89_B", - "ATGE_89_C" - ] - } - } - }, - "data_type": "Microarray" - }, - "Developmental_Map": { - "database": "atgenexp_plus", - "view_name": "Developmental_Map", - "groups": { - "CTRL_7": { - "controls": [ - "ATGE_CTRL_7" - ], - "treatments": { - "Dry_seed": [ - "RIKEN-NAKABAYASHI1A", - "RIKEN-NAKABAYASHI1B" - ], - "Imbibed_seed,_24_h": [ - "RIKEN-NAKABAYASHI2A", - "RIKEN-NAKABAYASHI2B" - ], - "1st_Node": [ - "ATGE_28_A2", - "ATGE_28_B2", - "ATGE_28_C2" - ], - "Flower_Stage_12,_Stamens": [ - "ATGE_36_A", - "ATGE_36_B", - "ATGE_36_C" - ], - "Cauline_Leaf": [ - "ATGE_26_A", - "ATGE_26_B", - "ATGE_26_C" - ], - "Cotyledon": [ - "ATGE_1_A", - "ATGE_1_B", - "ATGE_1_C" - ], - "Root": [ - "ATGE_9_A", - "ATGE_9_B", - "ATGE_9_C", - "ATGE_3_A", - "ATGE_3_B", - "ATGE_3_C" - ], - "Entire_Rosette_After_Transition_to_Flowering": [ - "ATGE_23_A", - "ATGE_23_B", - "ATGE_23_C" - ], - "Flower_Stage_9": [ - "ATGE_31_A2", - "ATGE_31_B2", - "ATGE_31_C2" - ], - "Flower_Stage_10/11": [ - "ATGE_32_A2", - "ATGE_32_B2", - "ATGE_32_C2" - ], - "Flower_Stage_12": [ - "ATGE_33_A", - "ATGE_33_B", - "ATGE_33_C" - ], - "Flower_Stage_15": [ - "ATGE_39_A", - "ATGE_39_B", - "ATGE_39_C" - ], - "Flower_Stage_12,_Carpels": [ - "ATGE_37_A", - "ATGE_37_B", - "ATGE_37_C" - ], - "Flower_Stage_12,_Petals": [ - "ATGE_35_A", - "ATGE_35_B", - "ATGE_35_C" - ], - "Flower_Stage_12,_Sepals": [ - "ATGE_34_A", - "ATGE_34_B", - "ATGE_34_C" - ], - "Flower_Stage_15,_Carpels": [ - "ATGE_45_A", - "ATGE_45_B", - "ATGE_45_C" - ], - "Flower_Stage_15,_Petals": [ - "ATGE_42_B", - "ATGE_42_C", - "ATGE_42_D" - ], - "Flower_Stage_15,_Sepals": [ - "ATGE_41_A", - "ATGE_41_B", - "ATGE_41_C" - ], - "Flower_Stage_15,_Stamen": [ - "ATGE_43_A", - "ATGE_43_B", - "ATGE_43_C" - ], - "Flowers_Stage_15,_Pedicels": [ - "ATGE_40_A", - "ATGE_40_B", - "ATGE_40_C" - ], - "Leaf_1_+_2": [ - "ATGE_5_A", - "ATGE_5_B", - "ATGE_5_C" - ], - "Leaf_7,_Petiole": [ - "ATGE_19_A", - "ATGE_19_B", - "ATGE_19_C" - ], - "Leaf_7,_Distal_Half": [ - "ATGE_21_A", - "ATGE_21_B", - "ATGE_21_C" - ], - "Leaf_7,_Proximal_Half": [ - "ATGE_20_A", - "ATGE_20_B", - "ATGE_20_C" - ], - "Hypocotyl": [ - "ATGE_2_A", - "ATGE_2_B", - "ATGE_2_C" - ], - "Rosette_Leaf_2": [ - "ATGE_12_A", - "ATGE_12_B", - "ATGE_12_C" - ], - "Rosette_Leaf_4": [ - "ATGE_13_A", - "ATGE_13_B", - "ATGE_13_C" - ], - "Rosette_Leaf_6": [ - "ATGE_14_A", - "ATGE_14_B", - "ATGE_14_C" - ], - "Rosette_Leaf_8": [ - "ATGE_15_A", - "ATGE_15_B", - "ATGE_15_C" - ], - "Rosette_Leaf_10": [ - "ATGE_16_A", - "ATGE_16_B", - "ATGE_16_C" - ], - "Rosette_Leaf_12": [ - "ATGE_17_A", - "ATGE_17_B", - "ATGE_17_C" - ], - "Senescing_Leaf": [ - "ATGE_25_A", - "ATGE_25_B", - "ATGE_25_C" - ], - "Shoot_Apex,_Inflorescence": [ - "ATGE_29_A2", - "ATGE_29_B2", - "ATGE_29_C2" - ], - "Shoot_Apex,_Transition": [ - "ATGE_8_A", - "ATGE_8_B", - "ATGE_8_C" - ], - "Shoot_Apex,_Vegetative": [ - "ATGE_6_A", - "ATGE_6_B", - "ATGE_6_C" - ], - "Stem,_2nd_Internode": [ - "ATGE_27_A", - "ATGE_27_B", - "ATGE_27_C" - ], - "Mature_Pollen": [ - "ATGE_73_A", - "ATGE_73_B", - "ATGE_73_C" - ], - "Seeds_Stage_3_w/_Siliques": [ - "ATGE_76_A", - "ATGE_76_B", - "ATGE_76_C" - ], - "Seeds_Stage_4_w/_Siliques": [ - "ATGE_77_D", - "ATGE_77_E", - "ATGE_77_F" - ], - "Seeds_Stage_5_w/_Siliques": [ - "ATGE_78_D", - "ATGE_78_E", - "ATGE_78_F" - ], - "Seeds_Stage_6_w/o_Siliques": [ - "ATGE_79_A", - "ATGE_79_B", - "ATGE_79_C" - ], - "Seeds_Stage_7_w/o_Siliques": [ - "ATGE_81_A", - "ATGE_81_B", - "ATGE_81_C" - ], - "Seeds_Stage_8_w/o_Siliques": [ - "ATGE_82_A", - "ATGE_82_B", - "ATGE_82_C" - ], - "Seeds_Stage_9_w/o_Siliques": [ - "ATGE_83_A", - "ATGE_83_B", - "ATGE_83_C" - ], - "Seeds_Stage_10_w/o_Siliques": [ - "ATGE_84_A", - "ATGE_84_B", - "ATGE_84_D" - ], - "Vegetative_Rosette": [ - "ATGE_89_A", - "ATGE_89_B", - "ATGE_89_C" - ] - } - } - }, - "data_type": "Microarray" - }, - "Developmental_Mutants": { - "database": "atgenexp_plus", - "view_name": "Developmental_Mutants", - "groups": { - "GSM757891;GSM757892;GSM757893": { - "controls": [ - "GSM757891", - "GSM757892", - "GSM757893" - ], - "treatments": { - "gl3_mutant": [ - "GSM1153854", - "GSM1153855", - "GSM1153856" - ], - "wer_mutant": [ - "GSM1153866", - "GSM1153867", - "GSM1153868" - ], - "ttg2_cpc_mutant": [ - "GSM1153848", - "GSM1153849", - "GSM1153850" - ], - "cow1_mutant": [ - "GSM757834", - "GSM757835", - "GSM757836" - ], - "cobl9_mutant": [ - "GSM757831", - "GSM757832", - "GSM757833" - ], - "WT_Columbia": [ - "GSM757891", - "GSM757892", - "GSM757893" - ], - "ttg2_mutant": [ - "GSM1153863", - "GSM1153864", - "GSM1153865" - ], - "wer_myb23_mutant": [ - "GSM757888", - "GSM757889", - "GSM757890" - ], - "gl2_mutant": [ - "GSM757843", - "GSM757844", - "GSM757845" - ], - "rhd6_mutant": [ - "GSM757879", - "GSM757880", - "GSM757881" - ], - "mrh2_mutant": [ - "GSM757858", - "GSM757859", - "GSM757860" - ], - "cpc_mutant": [ - "GSM1153845", - "GSM1153846", - "GSM1153847" - ], - "_rhd6_mutant_+_ACC": [ - "GSM757870", - "GSM757871", - "GSM757872" - ], - "ttg_mutant": [ - "GSM757885", - "GSM757886", - "GSM757887" - ], - "myc1_mutant": [ - "GSM757864", - "GSM757865", - "GSM757866" - ], - "cpc_try_mutant": [ - "GSM757837", - "GSM757838", - "GSM757839" - ], - "rhd6_mutant_+_IAA": [ - "GSM757873", - "GSM757874", - "GSM757875" - ], - "csld3_mutant": [ - "GSM757840", - "GSM757841", - "GSM757842" - ], - "egl3_mutant": [ - "GSM1153851", - "GSM1153852", - "GSM1153853" - ], - "try_mutant": [ - "GSM1153860", - "GSM1153861", - "GSM1153862" - ], - "rhd6_mutant_+_MS_(buffer)": [ - "GSM757876", - "GSM757877", - "GSM757878" - ], - "mrh3_mutant": [ - "GSM757861", - "GSM757862", - "GSM757863" - ], - "mrh1_mutant": [ - "GSM757855", - "GSM757856", - "GSM757857" - ], - "lrx1_mutant": [ - "GSM757852", - "GSM757853", - "GSM757854" - ], - "rhd2_mutant": [ - "GSM757867", - "GSM757868", - "GSM757869" - ], - "ire_mutant": [ - "GSM757849", - "GSM757850", - "GSM757851" - ], - "myb23_mutant": [ - "GSM1153857", - "GSM1153858", - "GSM1153859" - ], - "bhlh66_mutant": [ - "GSM757882", - "GSM757883", - "GSM757884" - ], - "gl3_egl3_mutant": [ - "GSM757846", - "GSM757847", - "GSM757848" - ] - } - }, - "ColprocessleafArd13;ColprocessleafMN3;ColprocessleafMN4;ColprocessleafMN5": { - "controls": [ - "ColprocessleafArd13", - "ColprocessleafMN3", - "ColprocessleafMN4", - "ColprocessleafMN5" - ], - "treatments": { - "gl3-sst_mutant_trichomes": [ - "DM9_sst1", - "m1DM8sstard", - "m1ssttr5_ATH1" - ], - "gl3-sst_nok-1_double_mutant_trichomes": [ - "EG_mosst1", - "EG_mosst2", - "EG_mosst3" - ], - "WT_Col-0_trichomes": [ - "ColtrichomeArd1", - "ColtrichomeArd2", - "ColtrichomeMN12", - "ColtrichomeMN13", - "ColtrichomeMN2" - ], - "gl3-sst_sim_double_mutant_trichomes": [ - "gl3_sstsimtrichomeMN1", - "gl3_sstsimtrichomeMN2" - ], - "WT_Col-0_leaves_after_trichome_removal": [ - "ColprocessleafArd13", - "ColprocessleafMN3", - "ColprocessleafMN4", - "ColprocessleafMN5" - ] - } - }, - "GSM738872_C2;GSM738873_C3;GSM738874_C4": { - "controls": [ - "GSM738872_C2", - "GSM738873_C3", - "GSM738874_C4" - ], - "treatments": { - "scrm-D_mute_whole_seedling_at_5_dpg": [ - "GSM738878_M2", - "GSM738879_M3", - "GSM738880_M4" - ], - "spch_whole_seedling_at_5_dpg": [ - "GSM738875_S2", - "GSM738876_S3", - "GSM738877_S4" - ], - "Col-0_WT_whole_seedling_at_5_dpg": [ - "GSM738872_C2", - "GSM738873_C3", - "GSM738874_C4" - ], - "scrm-D_whole_seedling_at_5_dpg": [ - "GSM738881_R2", - "GSM738882_R3", - "GSM738883_R4" - ] - } - }, - "LER1_Grotewold_082509;LER2_Grotewold_082509": { - "controls": [ - "LER1_Grotewold_082509", - "LER2_Grotewold_082509" - ], - "treatments": { - "Arabidopsis_green_tissue_wild_type_L._er_": [ - "LER1_Grotewold_082509", - "LER2_Grotewold_082509" - ], - "Arabidopsis_green_tissue_gl3_egl3_": [ - "GL3_1_Grotewold_082509", - "GL3_2_Grotewold_082509" - ] - } - }, - "Ler1_Grotewold_070109;LER2_Grotewold_070909": { - "controls": [ - "Ler1_Grotewold_070109", - "LER2_Grotewold_070909" - ], - "treatments": { - "Arabidopsis_wild_type_L._er": [ - "Ler1_Grotewold_070109", - "LER2_Grotewold_070909" - ], - "Arabidopsis_ttg2": [ - "TTG2_1_Grotewold_070909", - "TTG2_2_Grotewold_070909" - ] - } - } - }, - "data_type": "Microarray" - }, - "Embryo": { - "database": "embryo", - "view_name": "Embryo", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Bent_cotyledon": [ - "bc_1", - "bc_2", - "bc_3" - ], - "Early_heart": [ - "eh_1", - "eh_2", - "eh_3" - ], - "Early_torpedo": [ - "et_1", - "et_2", - "et_3" - ], - "Globular": [ - "gl_1", - "gl_2", - "gl_3" - ], - "Late_heart": [ - "lh_1", - "lh_2", - "lh_3" - ], - "Late_torpedo": [ - "lt_1", - "lt_2", - "lt_3" - ], - "Mature_green": [ - "mg_1", - "mg_2", - "mg_3" - ], - "8-cell/16-cell": [ - "pg_1", - "pg_2", - "pg_3" - ] - } - } - }, - "data_type": "Microarray" - }, - "Germination": { - "database": "germination", - "view_name": "Germination", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Twelve_Hours_S": [ - "12hS_1", - "12hS_2", - "12hS_3" - ], - "Zero_Hours": [ - "0h_1", - "0h_2", - "0h_3" - ], - "One_Hour_S": [ - "1hS_1", - "1hS_2", - "1hS_3" - ], - "Harvest": [ - "harvest_1", - "harvest_2", - "harvest_3" - ], - "Fourty_Eight_Hours_S": [ - "48hS_1", - "48hS_2", - "48hS_3" - ], - "Fourty_Eight_Hours_SL": [ - "48hSL_1", - "48hSL_2", - "48hSL_3" - ], - "Twelve_Hours_SL": [ - "12hSL_1", - "12hSL_2", - "12hSL_3" - ], - "One_Hour_SL": [ - "1hSL_1", - "1hSL_2", - "1hSL_3" - ], - "Six_Hours_SL": [ - "6hSL_1", - "6hSL_2", - "6hSL_3" - ], - "Twenty_Four_SL": [ - "24hSL_1", - "24hSL_2", - "24hSL_3" - ] - } - } - }, - "data_type": "Microarray" - }, - "Guard_Cell": { - "database": "guard_cell", - "view_name": "Guard_Cell", - "groups": { - "GSM486895;GSM486896;GSM486897": { - "controls": [ - "GSM486895", - "GSM486896", - "GSM486897" - ], - "treatments": { - "agb1_guard_cells,_no_ABA": [ - "GSM486895", - "GSM486896", - "GSM486897" - ], - "agb1_guard_cells,_plus_50_uM_ABA": [ - "GSM486907", - "GSM486908", - "GSM486909" - ] - } - }, - "GSM486892;GSM486893;GSM486894": { - "controls": [ - "GSM486892", - "GSM486893", - "GSM486894" - ], - "treatments": { - "WT_Col-0_guard_cells,_no_ABA": [ - "GSM486892", - "GSM486893", - "GSM486894" - ], - "WT_Col-0_guard_cells,_plus_50_uM_ABA": [ - "GSM486904", - "GSM486905", - "GSM486906" - ] - } - }, - "GSM486916;GSM486917;GSM486918": { - "controls": [ - "GSM486916", - "GSM486917", - "GSM486918" - ], - "treatments": { - "WT_Col-0_leaf,_plus_50_uM_ABA": [ - "GSM486928", - "GSM486929", - "GSM486930" - ], - "WT_Col-0_leaf,_no_ABA": [ - "GSM486916", - "GSM486917", - "GSM486918" - ] - } - }, - "GSM738872_C2;GSM738873_C3;GSM738874_C4": { - "controls": [ - "GSM738872_C2", - "GSM738873_C3", - "GSM738874_C4" - ], - "treatments": { - "Col-0_WT_whole_seedling_at_5_dpg": [ - "GSM738872_C2", - "GSM738873_C3", - "GSM738874_C4" - ], - "scrm-D_mute_whole_seedling_at_5_dpg": [ - "GSM738878_M2", - "GSM738879_M3", - "GSM738880_M4" - ], - "spch_whole_seedling_at_5_dpg": [ - "GSM738875_S2", - "GSM738876_S3", - "GSM738877_S4" - ], - "scrm-D_whole_seedling_at_5_dpg": [ - "GSM738881_R2", - "GSM738882_R3", - "GSM738883_R4" - ] - } - }, - "JS85;JS33": { - "controls": [ - "JS85", - "JS33" - ], - "treatments": { - "Guard_cells,_with_100_uM_ABA": [ - "JS86", - "JS34" - ], - "Guard_cells,_no_ABA": [ - "JS85", - "JS33" - ] - } - }, - "GSM571891;GSM571893;GSM571895": { - "controls": [ - "GSM571891", - "GSM571893", - "GSM571895" - ], - "treatments": { - "Suspension_cell_culture,_plus_50_uM_ABA": [ - "GSM571892", - "GSM571894", - "GSM571896" - ], - "Suspension_cell_culture,_plus_5_mM_DMTU": [ - "GSM604752", - "GSM604753", - "GSM604754" - ], - "Suspension_cell_culture,_control": [ - "GSM571891", - "GSM571893", - "GSM571895" - ], - "Suspension_cell_culture,_plus_50_uM_ABA_and_5_mM_DMTU": [ - "GSM604755", - "GSM604751", - "GSM604750" - ] - } - }, - "GSM486919;GSM486920;GSM486921": { - "controls": [ - "GSM486919", - "GSM486920", - "GSM486921" - ], - "treatments": { - "agb1_leaf,_plus_50_uM_ABA": [ - "GSM486931", - "GSM486932", - "GSM486933" - ], - "agb1_leaf,_no_ABA": [ - "GSM486919", - "GSM486920", - "GSM486921" - ] - } - }, - "JS87": { - "controls": [ - "JS87" - ], - "treatments": { - "Mesophyll_cells,_with_100uM_ABA,_no_cordycepin_nor_actinomycin": [ - "JS88" - ], - "Mesophyll_cells,_no_ABA,_no_cordycepin_nor_actinomycin": [ - "JS87" - ] - } - }, - "GSM486922;GSM486923;GSM486924": { - "controls": [ - "GSM486922", - "GSM486923", - "GSM486924" - ], - "treatments": { - "gpa1_leaf,_no_ABA": [ - "GSM486922", - "GSM486923", - "GSM486924" - ], - "gpa1_leaf,_plus_50_uM_ABA": [ - "GSM486934", - "GSM486935", - "GSM486936" - ] - } - }, - "JS33": { - "controls": [ - "JS33" - ], - "treatments": { - "Guard_cells,_no_ABA,_cordycepin_and_actinomycin_added_during_protoplasting": [ - "JS33" - ], - "Guard_cells,_with_100uM_ABA,_cordycepin_and_actinomycin_added_during_protoplasting": [ - "JS34" - ] - } - }, - "GSM486898;GSM486899;GSM486900": { - "controls": [ - "GSM486898", - "GSM486899", - "GSM486900" - ], - "treatments": { - "gpa1_guard_cells,_no_ABA": [ - "GSM486898", - "GSM486899", - "GSM486900" - ], - "gpa1_guard_cells,_plus_50_uM_ABA": [ - "GSM486910", - "GSM486911", - "GSM486912" - ] - } - }, - "GSM486925;GSM486926;GSM486927": { - "controls": [ - "GSM486925", - "GSM486926", - "GSM486927" - ], - "treatments": { - "agb1_gpa1_leaf,_plus_50_uM_ABA": [ - "GSM486937", - "GSM486938", - "GSM486939" - ], - "agb1_gpa1_leaf,_no_ABA": [ - "GSM486925", - "GSM486926", - "GSM486927" - ] - } - }, - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "ML1:_Expression_data_from_epidermal_cells_isolated_using_a_ML1p::YFP-RCI2A_marker": [ - "GSM1420940_ML1Y_3", - "GSM1420939_ML1Y_2", - "GSM1420938_ML1Y_1" - ], - "FGF:_Expression_data_from_young_guard_cells_isolated_using_a_FAMAp::GFP-FAMA_marker": [ - "GSM1420949_FGF_3", - "GSM1420948_FGF_2", - "GSM1420947_FGF_1" - ], - "E1728G:_Expression_data_from_mature_guard_cells_isolated_using_a_E1728::GFP_marker": [ - "GSM1420952_E1728G_3", - "GSM1420951_E1728G_2", - "GSM1420950_E1728G_1" - ], - "SSY:_Expression_data_from_guard_cell_initials_isolated_with_a_SPCHp::SPCH-YFP_marker": [ - "GSM1420943_SSY_3", - "GSM1420942_SSY_2", - "GSM1420941_SSY_1" - ], - "MG:_Expression_data_from_committed_guard_cell_meristemoids_isolated_with_a_MUTEp::nucGFP_marker": [ - "GSM1420946_MG_3", - "GSM1420945_MG_2", - "GSM1420944_MG_1" - ] - } - }, - "JS87;JS35": { - "controls": [ - "JS87", - "JS35" - ], - "treatments": { - "Mesophyll_cells,_with_100_uM_ABA": [ - "JS88", - "JS36" - ], - "Mesophyll_cells,_no_ABA": [ - "JS87", - "JS35" - ] - } - }, - "JS85": { - "controls": [ - "JS85" - ], - "treatments": { - "Mesophyll_cells,_with_100uM_ABA,_cordycepin_and_actinomycin_added_during_protoplasting": [ - "JS36" - ], - "Guard_cells,_no_ABA,_no_cordycepin_nor_actinomycin": [ - "JS85" - ], - "Guard_cells,_with_100uM_ABA,_no_cordycepin_nor_actinomycin": [ - "JS86" - ], - "Mesophyll_cells,_no_ABA,_cordycepin_and_actinomycin_added_during_protoplasting": [ - "JS35" - ] - } - }, - "GSM486901;GSM486902;GSM486903": { - "controls": [ - "GSM486901", - "GSM486902", - "GSM486903" - ], - "treatments": { - "agb1_gpa1_guard_cells,_plus_50_uM_ABA": [ - "GSM486913", - "GSM486914", - "GSM486915" - ], - "agb1_gpa1_guard_cells,_no_ABA": [ - "GSM486901", - "GSM486902", - "GSM486903" - ] - } - } - }, - "data_type": "Microarray" - }, - "Gynoecium": { - "database": "gynoecium", - "view_name": "Gynoecium", - "groups": { - "Col-0_CMM_R1;Col-0_CMM_R2;Col-0_CMM_R3": { - "controls": [ - "Col-0_CMM_R1", - "Col-0_CMM_R2", - "Col-0_CMM_R3" - ], - "treatments": { - "Col-0_Stage_7_CMM": [ - "Col-0_CMM_R1", - "Col-0_CMM_R2", - "Col-0_CMM_R3" - ], - "spt-12_Stage_7_CMM": [ - "spt-12_CMM_R1", - "spt-12_CMM_R2", - "spt-12_CMM_R3" - ] - } - }, - "Col-0_SEP_R1;Col-0_SEP_R2;Col-0_SEP_R3": { - "controls": [ - "Col-0_SEP_R1", - "Col-0_SEP_R2", - "Col-0_SEP_R3" - ], - "treatments": { - "Col-0_Stage_10_SEP": [ - "Col-0_SEP_R1", - "Col-0_SEP_R2", - "Col-0_SEP_R3" - ], - "spt-12_Stage_10_SEP": [ - "spt-12_SEP_R1", - "spt-12_SEP_R2", - "spt-12_SEP_R3" - ] - } - }, - "Col-0_PC_R1;Col-0_PC_R2;Col-0_PC_R3": { - "controls": [ - "Col-0_PC_R1", - "Col-0_PC_R2", - "Col-0_PC_R3" - ], - "treatments": { - "spt-12_Stage_7_PC": [ - "spt-12_PC_R1", - "spt-12_PC_R2", - "spt-12_PC_R3" - ], - "Col-0_Stage_7_PC": [ - "Col-0_PC_R1", - "Col-0_PC_R2", - "Col-0_PC_R3" - ] - } - }, - "Col-0_VV_R1;Col-0_VV_R2;Col-0_VV_R3": { - "controls": [ - "Col-0_VV_R1", - "Col-0_VV_R2", - "Col-0_VV_R3" - ], - "treatments": { - "Col-0_Stage_10_VV": [ - "Col-0_VV_R1", - "Col-0_VV_R2", - "Col-0_VV_R3" - ], - "spt-12_Stage_10_VV": [ - "spt-12_VV_R1", - "spt-12_VV_R2", - "spt-12_VV_R3" - ] - } - } - }, - "data_type": "Microarray" - }, - "Hormone": { - "database": "atgenexp_hormone", - "view_name": "Hormone", - "groups": { - "ACC_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "ACC_Treated_at_30_Minutes": [ - "RIKEN-GODA7A", - "RIKEN-GODA7B" - ] - } - }, - "ACC_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "ACC_Treated_at_1_Hour": [ - "RIKEN-GODA15A", - "RIKEN-GODA15B" - ] - } - }, - "ACC_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "ACC_Treated_at_3_Hours": [ - "RIKEN-GODA23A", - "RIKEN-GODA23B" - ] - } - }, - "Zeatin_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "Zeatin_Treated_at_30_Minutes": [ - "RIKEN-GODA3A", - "RIKEN-GODA3B" - ] - } - }, - "Zeatin_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "Zeatin_Treated_at_1_Hour": [ - "RIKEN-GODA11A", - "RIKEN-GODA11B" - ] - } - }, - "Zeatin_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "Zeatin_Treated_at_3_Hours": [ - "RIKEN-GODA19A", - "RIKEN-GODA19B" - ] - } - }, - "IAA_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "IAA_Treated_at_30_Minutes": [ - "RIKEN-GODA2A", - "RIKEN-GODA2B" - ] - } - }, - "IAA_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "IAA_Treated_at_1_Hour": [ - "RIKEN-GODA10A", - "RIKEN-GODA10B" - ] - } - }, - "IAA_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "IAA_Treated_at_3_Hours": [ - "RIKEN-GODA18A", - "RIKEN-GODA18B" - ] - } - }, - "ABA_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "ABA_Treated_at_30_Minutes": [ - "RIKEN-GODA5A", - "RIKEN-GODA5B" - ] - } - }, - "ABA_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "ABA_Treated_at_1_Hour": [ - "RIKEN-GODA13A", - "RIKEN-GODA13B" - ] - } - }, - "ABA_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "ABA_Treated_at_3_Hours": [ - "RIKEN-GODA21A", - "RIKEN-GODA21B" - ] - } - }, - "Methyl_Jasmonate_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "MJ_Treated_at_30_Minutes": [ - "RIKEN-GODA6A", - "RIKEN-GODA6B" - ] - } - }, - "Methyl_Jasmonate_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "MJ_Treated_at_1_Hour": [ - "RIKEN-GODA14A", - "RIKEN-GODA14B" - ] - } - }, - "Methyl_Jasmonate_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "MJ_Treated_at_3_Hours": [ - "RIKEN-GODA22A", - "RIKEN-GODA22B" - ] - } - }, - "GA-3_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "GA-3_Treated_at_30_Minutes": [ - "RIKEN-GODA4A", - "RIKEN-GODA4B" - ] - } - }, - "GA-3_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "GA-3_Treated_at_1_Hour": [ - "RIKEN-GODA12A", - "RIKEN-GODA12B" - ] - } - }, - "GA-3_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "GA-3_Treated_at_3_Hours": [ - "RIKEN-GODA20A", - "RIKEN-GODA20B" - ] - } - }, - "GA-3_Mutant_at_30_Minutes": { - "controls": [ - "RIKEN-GODA25A", - "RIKEN-GODA25B" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA25A", - "RIKEN-GODA25B" - ], - "GA-3_Treated_Mutant_at_30_Minutes": [ - "RIKEN-GODA26A", - "RIKEN-GODA26B" - ] - } - }, - "GA-3_Mutant_at_1_Hour": { - "controls": [ - "RIKEN-GODA27A", - "RIKEN-GODA27B " - ], - "treatments": { - "Control_at_1_Hour": [ - "RIKEN-GODA27A", - "RIKEN-GODA27B" - ], - "GA-3_Treated_Mutant_at_1_Hour": [ - "RIKEN-GODA28A", - "RIKEN-GODA28B" - ] - } - }, - "GA-3_Mutant_at_3_Hours": { - "controls": [ - "RIKEN-GODA29A", - "RIKEN-GODA29B" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA29A", - "RIKEN-GODA29B" - ], - "GA-3_Treated_Mutant_at_3_Hours": [ - "RIKEN-GODA30A", - "RIKEN-GODA30B" - ] - } - }, - "Brassinolide_at_30_Minutes": { - "controls": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "treatments": { - "Control_at_30_Minutes": [ - "RIKEN-GODA1AA", - "RIKEN-GODA1BB" - ], - "BL_Treated_at_30_Minutes": [ - "RIKEN-GODA8A", - "RIKEN-GODA8B" - ] - } - }, - "Brassinolide_at_1_Hour": { - "controls": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "treatments": { - "BL_Control_at_1_Hour": [ - "RIKEN-GODA9AA", - "RIKEN-GODA9BA" - ], - "Treated_at_1_Hour": [ - "RIKEN-GODA16A", - "RIKEN-GODA16B" - ] - } - }, - "Brassinolide_at_3_Hours": { - "controls": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "treatments": { - "Control_at_3_Hours": [ - "RIKEN-GODA17AA", - "RIKEN-GODA17BA" - ], - "BL_Treated_at_3_Hours": [ - "RIKEN-GODA24A", - "RIKEN-GODA24B" - ] - } - }, - "Brassinolide_Mutant_at_30_Minutes": { - "controls": [ - 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"xylem_13" - ] - } - } - }, - "data_type": "Microarray" - }, - "Root_II": { - "database": "root", - "view_name": "Root_II", - "groups": { - "GSM744778;GSM744779": { - "controls": [ - "GSM744778", - "GSM744779" - ], - "treatments": { - "Low_pH,_t=6": [ - "GSM744792", - "GSM744793" - ], - "Standard_pH,_t=6_(control)": [ - "GSM744778", - "GSM744779" - ] - } - }, - "GSM871266;GSM871267;GSM871268": { - "controls": [ - "GSM871266", - "GSM871267", - "GSM871268" - ], - "treatments": { - "intact_root_control_": [ - "GSM871266", - "GSM871267", - "GSM871268" - ], - "intact_root_auxin_": [ - "GSM871269", - "GSM871270", - "GSM871271" - ] - } - }, - "GSM744776;GSM744777": { - "controls": [ - "GSM744776", - "GSM744777" - ], - "treatments": { - "Low_pH,_t=3": [ - "GSM744790", - "GSM744791" - ], - "Standard_pH,_t=3_(Control)": [ - "GSM744776", - "GSM744777" - ] - } - }, - "GSM871254;GSM871255;GSM871256": { - "controls": [ - "GSM871254", - "GSM871255", - "GSM871256" - ], - "treatments": { - 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"cluster22_WT1.ExprMean", - "cluster22_WT2.ExprMean", - "cluster22_WT3.ExprMean" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Tissue_Specific": { - "database": "atgenexp_plus", - "view_name": "Tissue_Specific", - "groups": { - "ATGE_CTRL_7": { - "controls": [ - "ATGE_CTRL_7" - ], - "treatments": { - "AtHB8": [ - "GSM706472", - "GSM706473", - "GSM706474" - ] - } - } - }, - "data_type": "Microarray" - } - } - } - }, - "arabidopsis seedcoat": { - "data": { - "species": "arabidopsis seedcoat", - "views": { - "Seed_Coat": { - "database": "seedcoat", - "view_name": "Seed_Coat", - "groups": { - "ap2-7_mutant_seed": { - "controls": [ - "ap2-3-1", - "ap2-3-10", - "ap2-3-11", - "ap2-3-12", - "ap2-3-2", - "ap2-3-3", - "ap2-3-4", - "ap2-3-5", - "ap2-3-6", - "ap2-3-7", - "ap2-3-8", - "ap2-3-9" - ], - "treatments": { - "ap2-7_seedcoat,_11_dpa": [ - "ap2-11-1", - "ap2-11-10", - "ap2-11-11", - "ap2-11-12", - "ap2-11-2", - "ap2-11-3", - "ap2-11-4", - "ap2-11-5", - "ap2-11-6", - "ap2-11-7", - "ap2-11-8", - "ap2-11-9" - ], - "ap2-7_seedcoat,_3_dpa": [ - "ap2-3-1", - "ap2-3-10", - "ap2-3-11", - "ap2-3-12", - "ap2-3-2", - "ap2-3-3", - "ap2-3-4", - "ap2-3-5", - "ap2-3-6", - "ap2-3-7", - "ap2-3-8", - "ap2-3-9" - ], - "ap2-7_seedcoat,_7_dpa": [ - "ap2-7-1", - "ap2-7-10", - "ap2-7-11", - "ap2-7-12", - "ap2-7-13", - "ap2-7-14", - "ap2-7-15", - "ap2-7-16", - "ap2-7-2", - "ap2-7-3", - "ap2-7-4", - "ap2-7-5", - "ap2-7-6", - "ap2-7-7", - "ap2-7-8", - "ap2-7-9" - ] - } - }, - "Col-2_wild-type_seed": { - "controls": [ - "col2-3-1", - "col2-3-2", - "col2-3-3", - "col2-3-4", - "col2-3-5", - "col2-3-6", - "col2-3-7", - "col2-3-8" - ], - "treatments": { - "Col-2_wt_seedcoat,_11_dpa": [ - "col2-11-1", - "col2-11-2", - "col2-11-3", - "col2-11-4", - "col2-11-5", - "col2-11-6", - "col2-11-7", - "col2-11-8" - ], - "Col-2_wt_seedcoat,_3_dpa": [ - "col2-3-1", - "col2-3-2", - "col2-3-3", - "col2-3-4", - "col2-3-5", - "col2-3-6", - "col2-3-7", - "col2-3-8" - ], - "Col-2_wt_seedcoat,_7_dpa": [ - "col2-7-1", - "col2-7-10", - "col2-7-11", - "col2-7-12", - "col2-7-2", - "col2-7-3", - "col2-7-4", - "col2-7-5", - "col2-7-6", - "col2-7-7", - "col2-7-8", - "col2-7-9" - ] - } - }, - "tt16-1_mutant_seed": { - "controls": [ - "ws2-3-1", - "ws2-3-2", - "ws2-3-3", - "ws2-3-4", - "ws2-3-5", - "ws2-3-6", - "ws2-3-7", - "ws2-3-8" - ], - "treatments": { - "Ws-2_seedcoat,_11_dpa": [ - "ws2-11-1", - "ws2-11-2", - "ws2-11-3", - "ws2-11-4", - "ws2-11-5", - "ws2-11-6", - "ws2-11-7", - "ws2-11-8" - ], - "Ws-2_seedcoat,_3_dpa": [ - "ws2-3-1", - "ws2-3-2", - "ws2-3-3", - "ws2-3-4", - "ws2-3-5", - "ws2-3-6", - "ws2-3-7", - "ws2-3-8" - ], - "Ws-2_seedcoat,_7_dpa": [ - "ws2-7-1", - "ws2-7-10", - "ws2-7-11", - "ws2-7-12", - "ws2-7-2", - "ws2-7-3", - "ws2-7-4", - "ws2-7-5", - "ws2-7-6", - "ws2-7-7", - "ws2-7-8", - "ws2-7-9" - ] - } - } - }, - "data_type": "Microarray" - } - } - } - }, - "arachis": { - "data": { - "species": "arachis", - "views": { - "Arachis_Atlas": { - "database": "arachis", - "view_name": "Arachis_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Pattee_1_stalk:__Gynophore_stalk_at_pod_swelling_(Pattee_stage_1)": [ - "Pattee_1_Stalk" - ], - "subterranean_gynophore_tip:__5_mm_(=mostly_ovary_and_zone_of_cell_division)_from_elongating_peg_of_approximately_same_length_as_#9,_but_24_h_after_soil_penetration": [ - "Subterranean_Gynophore_Tip" - ], - "Pattee_1_pod:__Whole_pod_at_pod_swelling_(Pattee_stage_1)": [ - "Pattee_1_Pod" - ], - "Pattee_6_seed:__Torpedo_shaped;_generally_pink_at_embryonic-axis_end_of_kernels_(Pattee_stage_6)": [ - "Pattee_6_Seed" - ], - "aerial_gynophore_tip:__5_mm_(=mostly_ovary_and_zone_of_cell_division)_from_elongating_peg_prior_to_soil_penetration": [ - "Aerial_Gynophore_Tip" - ], - "Pattee_5_seed:__Embryo_flat,_white_or_just_turning_pink_at_one_end_(Pattee_stage_5)": [ - "Pattee_5_Seed" - ], - "Pattee_7_seed:__Torpedo_to_round_shaped;_embryonic_axis_end_of_kernel_pink;_other_end_white_to_light_pink_(Pattee_stage_7)": [ - "Pattee_7_Seed" - ], - "vegetative_shoot_tip:__Growth_stage_Boote_R1_first_flower,_from_mainstem_(n);_5_mm_maxium_length": [ - "Vegetative_Shoot_Tip" - ], - "androecium:__Fully_open,_morning_of_anthesis;_staminal_tube,_filaments_and_anthers": [ - "Androecium" - ], - "reproductive_shoot_tip:__Growth_stage_Boote_R1_first_flower,_from_laterals__(n+1);_5_mm_maxium_length": [ - "Reproductive_Shoot_Tip" - ], - "nodules:__25_d_post-emergence": [ - "Nodules" - ], - "Pattee_10_seed:__Large,_generally_dark_pink_all_over;_seed_coat_beginning_to_dry_out_(Pattee_stage_10)": [ - "Pattee_10_Seed" - ], - "Pattee_5_pericarp:__Pericarp_soft,_not_as_watery,_inner_pericarp_without_cracks_(Pattee_stage_5)": [ - "Pattee_5_Pericarp" - ], - "Pattee_8_seed:__Round,_light_pink_all_over_(Pattee_stage_8)": [ - "Pattee_8_Seed" - ], - "Pattee_3_pod:__Pericarp_very_watery,_embryo_very_small_and_not_easily_removed_(Pattee_stage_3/4)": [ - "Pattee_3_Pod" - ], - "seedling_leaf:__10_d_post-emergence;_leaflets_partially_open": [ - "Seedling_Leaf" - ], - "perianth:__Fully_open,_morning_of_anthesis;_wings,_banner,_hypanthium,_keel_and_lower_lip_of_the_calyx": [ - "Perianth" - ], - "gynoecium:__Fully_open,_morning_of_anthesis;_stigma,_style_and_overy": [ - "Gynoecium" - ], - "lateral_stem_leaf:__Growth_stage_Boote_R1_first_flower;_leaflets_partially_open,_from_laterals__(n+1)": [ - "Lateral_Stem_Leaf" - ], - "Pattee_6_pericarp:__Inner_pericarp_tissue_beginning_to_show_cracks_or_cottony_(Pattee_stage_6/7)": [ - "Pattee_6_Pericarp" - ], - "root_:__10_d_post-emergence": [ - "Roots" - ] - } - }, - "Pattee_10_Seed": { - "controls": [ - "Pattee_10_Seed" - ], - "treatments": { - "main_stem_leaf:__Growth_stage_Boote_R1_first_flower;_leaflets_partially_open,_from_main_stem_(n)": [ - "Main_Stem_Leaf" - ] - } - } - }, - "data_type": "RNA-Seq" - } - } - } - }, - "barley": { - "data": { - "species": "barley", - "views": { - "barley_mas": { - "database": "barley_mas", - "view_name": "barley_mas", - "groups": { - "Seedling": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Morex_Leaf": [ - "MX_Leafrep1", - "MX_Leafrep2", - "MX_Leafrep3" - ], - "Golden_Promise_Leaf": [ - "GP_Leafrep1", - "GP_Leafrep2", - "GP_Leafrep3" - ], - "Morex_Crown": [ - "MX_Crownrep1", - "MX_Crownrep2", - "MX_Crownrep3" - ], - "Golden_Promise_Crown": [ - "GP_Crownrep1", - "GP_Crownrep2", - "GP_Crownrep3" - ], - "Morex_Root": [ - "MX_Rootrep1", - "MX_Rootrep2", - "MX_Rootrep3" - ], - "Golden_Promise_Root": [ - "GP_Rootrep1", - "GP_Rootrep2", - "GP_Rootrep3" - ] - } - }, - "Germinating_Seedling": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Morex_Coleoptile": [ - "MX_Coleoptilerep1", - "MX_Coleoptilerep2", - "MX_Coleoptilerep3" - ], - "Golden_Promise_Coleoptile": [ - "GP_Coleoptilerep1", - "GP_Coleoptilerep2", - "GP_Coleoptilerep3" - ], - "Morex_Mesocotyl": [ - "MX_Embryorep1", - "MX_Embryorep2", - "MX_Embryorep3" - ], - "Golden_Promise_Mesocotyl": [ - "GP_Embryorep1", - "GP_Embryorep2", - "GP_Embryorep3" - ], - "Morex_Radicle": [ - "MX_Radiclerep1", - "MX_Radiclerep2", - "MX_Radiclerep3" - ], - "Golden_Promise_Radicle": [ - "GP_Radiclerep1", - "GP_Radiclerep2", - "GP_Radiclerep3" - ] - } - }, - "Caryopsis_without_Embryo": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Morex_Caryopsis_without_Embryo": [ - "MX_Endosperm22DAPrep1", - "MX_Endosperm22DAPrep2", - "MX_Endosperm22DAPrep3" - ] - } - }, - "Embryo": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Embryo_22_DAP": [ - "MX_Embryo22DAPrep1", - "MX_Embryo22DAPrep2", - "MX_Embryo22DAPrep3" - ] - } - }, - "Caryopsis": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Caryopsis_5_DAP": [ - "MX_Caryopsis5DAPrep1", - "MX_Caryopsis5DAPrep2", - "MX_Caryopsis5DAPrep3" - ], - "Caryopsis_10_DAP": [ - "MX_Caryopsis10DAPrep1", - "MX_Caryopsis10DAPrep2", - "MX_Caryopsis10DAPrep3" - ], - "Caryopsis_16_DAP": [ - "MX_Caryopsis16DAPrep1", - "MX_Caryopsis16DAPrep2", - "MX_Caryopsis16DAPrep3" - ] - } - }, - "Floral_Bracts": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Floral_Bracts": [ - "MX_FloralBractsrep1", - "MX_FloralBractsrep2", - "MX_FloralBractsrep3" - ] - } - }, - "Anthers": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Anthers": [ - "MX_Anthersrep1", - "MX_Anthersrep2", - "MX_Anthersrep3" - ] - } - }, - "Pistil": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Pistil": [ - "MX_Pistilrep1", - "MX_Pistilrep2", - "MX_Pistilrep3" - ] - } - }, - "Immature_Inflorescence": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Immature_Inflorescence": [ - "MX_Inflorescencerep1", - "MX_Inflorescencerep2", - "MX_Inflorescencerep3" - ] - } - }, - "Spike": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Lemma": [ - "Lemma_Rep1", - "Lemma_Rep2", - "Lemma_Rep3" - ], - "Palea": [ - "Palea_Rep1", - "Palea_Rep2", - "Palea_Rep3" - ], - "Awn": [ - "Awn_Rep1", - "Awn_Rep2", - "Awn_Rep3" - ] - } - } - }, - "data_type": "Microarray" - }, - "barley_rma": { - "database": "barley_rma", - "view_name": "barley_rma", - "groups": { - "Seedling": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Morex_Leaf": [ - "MX_Leafrep1", - "MX_Leafrep2", - "MX_Leafrep3" - ], - "Golden_Promise_Leaf": [ - "GP_Leafrep1", - "GP_Leafrep2", - "GP_Leafrep3" - ], - "Morex_Crown": [ - "MX_Crownrep1", - "MX_Crownrep2", - "MX_Crownrep3" - ], - "Golden_Promise_Crown": [ - "GP_Crownrep1", - "GP_Crownrep2", - "GP_Crownrep3" - ], - "Morex_Root": [ - "MX_Rootrep1", - "MX_Rootrep2", - "MX_Rootrep3" - ], - "Golden_Promise_Root": [ - "GP_Rootrep1", - "GP_Rootrep2", - "GP_Rootrep3" - ] - } - }, - "Germinating_Seedling": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Morex_Coleoptile": [ - "MX_Coleoptilerep1", - "MX_Coleoptilerep2", - "MX_Coleoptilerep3" - ], - "Golden_Promise_Coleoptile": [ - "GP_Coleoptilerep1", - "GP_Coleoptilerep2", - "GP_Coleoptilerep3" - ], - "Morex_Mesocotyl": [ - "MX_Embryorep1", - "MX_Embryorep2", - "MX_Embryorep3" - ], - "Golden_Promise_Mesocotyl": [ - "GP_Embryorep1", - "GP_Embryorep2", - "GP_Embryorep3" - ], - "Morex_Radicle": [ - "MX_Radiclerep1", - "MX_Radiclerep2", - "MX_Radiclerep3" - ], - "Golden_Promise_Radicle": [ - "GP_Radiclerep1", - "GP_Radiclerep2", - "GP_Radiclerep3" - ] - } - }, - "Caryopsis_without_Embryo": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Morex_Caryopsis_without_Embryo": [ - "MX_Endosperm22DAPrep1", - "MX_Endosperm22DAPrep2", - "MX_Endosperm22DAPrep3" - ] - } - }, - "Embryo": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Embryo_22_DAP": [ - "MX_Embryo22DAPrep1", - "MX_Embryo22DAPrep2", - "MX_Embryo22DAPrep3" - ] - } - }, - "Caryopsis": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Caryopsis_5_DAP": [ - "MX_Caryopsis5DAPrep1", - "MX_Caryopsis5DAPrep2", - "MX_Caryopsis5DAPrep3" - ], - "Caryopsis_10_DAP": [ - "MX_Caryopsis10DAPrep1", - "MX_Caryopsis10DAPrep2", - "MX_Caryopsis10DAPrep3" - ], - "Caryopsis_16_DAP": [ - "MX_Caryopsis16DAPrep1", - "MX_Caryopsis16DAPrep2", - "MX_Caryopsis16DAPrep3" - ] - } - }, - "Floral_Bracts": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Floral_Bracts": [ - "MX_FloralBractsrep1", - "MX_FloralBractsrep2", - "MX_FloralBractsrep3" - ] - } - }, - "Anthers": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Anthers": [ - "MX_Anthersrep1", - "MX_Anthersrep2", - "MX_Anthersrep3" - ] - } - }, - "Pistil": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Pistil": [ - "MX_Pistilrep1", - "MX_Pistilrep2", - "MX_Pistilrep3" - ] - } - }, - "Immature_Inflorescence": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Immature_Inflorescence": [ - "MX_Inflorescencerep1", - "MX_Inflorescencerep2", - "MX_Inflorescencerep3" - ] - } - }, - "Spike": { - "controls": [ - "BARLEY_CTRL", - "BARLEY_CTRL" - ], - "treatments": { - "Lemma": [ - "Lemma_Rep1", - "Lemma_Rep2", - "Lemma_Rep3" - ], - "Palea": [ - "Palea_Rep1", - "Palea_Rep2", - "Palea_Rep3" - ], - "Awn": [ - "Awn_Rep1", - "Awn_Rep2", - "Awn_Rep3" - ] - } - } - }, - "data_type": "Microarray" - } - } - } - }, - "brachypodium": { - "data": { - "species": "brachypodium", - "views": { - "Brachypodium_Atlas": { - "database": "brachypodium", - "view_name": "Brachypodium_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "I:_De-etiolated_shoots_3_DAG_1": [ - "I:_De-etiolated_shoots_3_DAG_1", - "I:_De-etiolated_shoots_3_DAG_2", - "I:_De-etiolated_shoots_3_DAG_3" - ], - "I:_Etiolated_shoots_3_DAG_1": [ - "I:_Etiolated_shoots_3_DAG_1", - "I:_Etiolated_shoots_3_DAG_2", - "I:_Etiolated_shoots_3_DAG_3" - ], - "P:_Coleoptile_10_DAG_1": [ - "P:_Coleoptile_10_DAG_1", - "P:_Coleoptile_10_DAG_2" - ], - "P:_Coleoptile_17+27_DAG_1": [ - "P:_Coleoptile_17+27_DAG_1", - "P:_Coleoptile_17+27_DAG_2", - "P:_Coleoptile_17+27_DAG_3" - ], - "P:_First_internode_10_DAG_1": [ - "P:_First_internode_10_DAG_1", - "P:_First_internode_10_DAG_2", - "P:_First_internode_10_DAG_3", - "P:_First_internode_10_DAG_4" - ], - "P:_First_internode_17_DAG_1": [ - "P:_First_internode_17_DAG_1", - "P:_First_internode_17_DAG_2" - ], - "P:_First_internode_27_DAG_1": [ - "P:_First_internode_27_DAG_1", - "P:_First_internode_27_DAG_2", - "P:_First_internode_27_DAG_3" - ], - "P:_First_internode_35_DAG_1": [ - "P:_First_internode_35_DAG_1", - "P:_First_internode_35_DAG_2" - ], - "P:_First_internode_60_DAG_1": [ - "P:_First_internode_60_DAG_1", - "P:_First_internode_60_DAG_2" - ], - "P:_First_node_+_adventitious_roots_35_DAG_1": [ - "P:_First_node_+_adventitious_roots_35_DAG_1", - "P:_First_node_+_adventitious_roots_35_DAG_2" - ], - "P:_First_node_10_DAG_1": [ - "P:_First_node_10_DAG_1", - "P:_First_node_10_DAG_2" - ], - "P:_First_node_17_DAG_2": [ - "P:_First_node_17_DAG_1", - "P:_First_node_17_DAG_2", - "P:_First_node_17_DAG_3" - ], - "P:_First_node_27_DAG_1": [ - "P:_First_node_27_DAG_1", - "P:_First_node_27_DAG_2" - ], - "P:_First_node_60_DAG_1": [ - "P:_First_node_60_DAG_1", - "P:_First_node_60_DAG_2" - ], - "P:_Last_internode_60_DAG_1": [ - "P:_Last_internode_60_DAG_1", - "P:_Last_internode_60_DAG_2" - ], - "P:_Leaf_10_DAG_1": [ - "P:_Leaf_10_DAG_1", - "P:_Leaf_10_DAG_2" - ], - "P:_Leaf_17_DAG_1": [ - "P:_Leaf_17_DAG_1", - "P:_Leaf_17_DAG_2", - "P:_Leaf_17_DAG_3" - ], - "P:_Leaf_27_DAG_1": [ - "P:_Leaf_27_DAG_1", - "P:_Leaf_27_DAG_2", - "P:_Leaf_27_DAG_3" - ], - "P:_Leaf_60_DAG_1": [ - 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"DA-OTL-A_R5" - ], - "6mo_Orthotropic_Leaf_C": [ - "DA-OTL-C_R1", - "DA-OTL-C_R2", - "DA-OTL-C_R3", - "DA-OTL-C_R4", - "DA-OTL-C_R5" - ], - "6mo_Orthotropic_Leaf_E1": [ - "DA-OTL-E1_R1", - "DA-OTL-E1_R2", - "DA-OTL-E1_R3", - "DA-OTL-E1_R4", - "DA-OTL-E1_R5" - ], - "6mo_Orthotropic_Leaf_E2": [ - "DA-OTL-E2_R2", - "DA-OTL-E2_R3", - "DA-OTL-E2_R4", - "DA-OTL-E2_R5" - ], - "6mo_Orthotropic_Leaf_E3": [ - "DA-OTL-E3_R1", - "DA-OTL-E3_R2", - "DA-OTL-E3_R3", - "DA-OTL-E3_R4", - "DA-OTL-E3_R5" - ], - "6mo_Orthotropic_Shoot_Apex": [ - "DA-OTA_R1", - "DA-OTA_R2", - "DA-OTA_R3", - "DA-OTA_R4", - "DA-OTA_R5" - ], - "6mo_Orthotropic_Herbaceous_Stem": [ - "DA-OTAC-YS_R1", - "DA-OTAC-YS_R2", - "DA-OTAC-YS_R3", - "DA-OTAC-YS_R4", - "DA-OTAC-YS_R5" - ], - "6mo_Orthotropic_Young_Axilaries": [ - "DA-OAA-YA_R1", - "DA-OAA-YA_R2", - "DA-OAA-YA_R3", - "DA-OAA-YA_R4", - "DA-OAA-YA_R5" - ], - "6mo_Orthotropic_Old_Axilaries": [ - "DA-OAA-OA_R1", - "DA-OAA-OA_R2", - "DA-OAA-OA_R3", - "DA-OAA-OA_R4" - ], - "Plagiotropic_Shoot_Apex": [ - "DA-PSA_R1", - "DA-PSA_R2", - "DA-PSA_R3", - "DA-PSA_R4", - "DA-PSA_R5" - ], - "Plagiotropic_A_Leaf": [ - "DA-PTL-A_R1", - "DA-PTL-A_R2", - "DA-PTL-A_R3", - "DA-PTL-A_R4", - "DA-PTL-A_R5" - ], - "Plagiotropic_C_Leaf": [ - "DA-PTL-C_R1", - "DA-PTL-C_R3", - "DA-PTL-C_R4" - ], - "Plagiotropic_E_Leaf": [ - "DA-PTL-E_R1", - "DA-PTL-E_R2", - "DA-PTL-E_R3", - "DA-PTL-E_R4", - "DA-PTL-E_R5" - ], - "Plagiotropic_Old_Axiliaries": [ - "DA-OA_R1", - "DA-OA_R2", - "DA-OA_R3", - "DA-OA_R4", - "DA-OA_R5" - ], - "Plagiotropic_Young_Axilaries": [ - "DA-YA_R1", - "DA-YA_R2", - "DA-YA_R3", - "DA-YA_R4", - "DA-YA_R5" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Drought_Diurnal_Atlas": { - "database": "cacao_drought_diurnal_atlas", - "view_name": "Drought_Diurnal_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Root_Watered_T1": [ - "DD-WTR-T1_R1", - "DD-WTR-T1_R2", - "DD-WTR-T1_R3" - ], - "Root_Watered_T2": [ - "DD-WTR-T2_R1", - "DD-WTR-T2_R2", - "DD-WTR-T2_R3" - ], - "Root_Watered_T3": [ - "DD-WTR-T3_R1", - "DD-WTR-T3_R2", - "DD-WTR-T3_R3" - ], - "Root_Watered_T4": [ - "DD-WTR-T4_R1", - "DD-WTR-T4_R2", - "DD-WTR-T4_R3" - ], - "Root_Watered_T5": [ - "DD-WTR-T5_R1", - "DD-WTR-T5_R2", - "DD-WTR-T5_R3" - ], - "Root_Watered_T6": [ - "DD-WTR-T6_R1", - "DD-WTR-T6_R2", - "DD-WTR-T6_R3" - ], - "Root_Watered_T7": [ - "DD-WTR-T7_R2", - "DD-WTR-T7_R3", - "DD-WTR-T7-R1" - ], - "Root_Drought_T1": [ - "DD-DTR-T1_R1", - "DD-DTR-T1_R2", - "DD-DTR-T1_R3" - ], - "Root_Drought_T2": [ - "DD-DTR-T2_R1", - "DD-DTR-T2_R2", - "DD-DTR-T2_R3" - ], - "Root_Drought_T3": [ - "DD-DTR-T3_R1", - "DD-DTR-T3_R2", - "DD-DTR-T3_R3" - ], - "Root_Drought_T4": [ - "DD-DTR-T4_R1", - "DD-DTR-T4_R2", - "DD-DTR-T4_R3" - ], - "Root_Drought_T5": [ - "DD-DTR-T5_R1", - "DD-DTR-T5_R2" - ], - "Root_Drought_T6": [ - "DD-DTR-T6_R1", - "DD-DTR-T6_R2", - "DD-DTR-T6_R3" - ], - "Root_Drought_T7": [ - "DD-DTR-T7_R1", - "DD-DTR-T7_R2", - "DD-DTR-T7_R3" - ], - "Leaf_Watered_T1": [ - "DD-WTL-T1_R1", - "DD-WTL-T1_R2", - "DD-WTL-T1_R3" - ], - "Leaf_Watered_T2": [ - "DD-WTL-T2_R1", - "DD-WTL-T2_R2", - "DD-WTL-T2_R3" - ], - "Leaf_Watered_T3": [ - "DD-WTL-T3_R1", - "DD-WTL-T3_R2", - "DD-WTL-T3_R3" - ], - "Leaf_Watered_T4": [ - "DD-WTL-T4_R1", - "DD-WTL-T4_R2", - "DD-WTL-T4_R3" - ], - "Leaf_Watered_T5": [ - "DD-WTL-T5_R1", - "DD-WTL-T5_R2" - ], - "Leaf_Watered_T6": [ - "DD-WTL-T6_R1", - "DD-WTL-T6_R2", - "DD-WTL-T6_R3" - ], - "Leaf_Watered_T7": [ - "DD-WTL-T7_R1", - "DD-WTL-T7_R2", - "DD-WTL-T7_R3" - ], - "Leaf_Drought_T1": [ - "DD-DTL-T1_R1", - "DD-DTL-T1_R2", - "DD-DTL-T1_R3" - ], - "Leaf_Drought_T2": [ - "DD-DTL-T2_R1", - "DD-DTL-T2_R2", - "DD-DTL-T2_R3" - ], - "Leaf_Drought_T3": [ - "DD-DTL-T3_R1", - "DD-DTL-T3_R2", - "DD-DTL-T3_R3" - ], - "Leaf_Drought_T4": [ - "DD-DTL-T4_R1", - "DD-DTL-T4_R2", - "DD-DTL-T4_R3" - ], - "Leaf_Drought_T5": [ - "DD-DTL-T5_R1", - "DD-DTL-T5_R2", - "DD-DTL-T5_R3" - ], - "Leaf_Drought_T6": [ - "DD-DTL-T6_R1", - "DD-DTL-T6_R2", - "DD-DTL-T6_R3" - ], - "Leaf_Drought_T7": [ - "DD-DTL-T7_R1", - "DD-DTL-T7_R2", - "DD-DTL-T7_R3" - ], - "Apex_Watered_T1": [ - "DD-WTA-T1_R1", - "DD-WTA-T1_R2", - "DD-WTA-T1_R3" - ], - "Apex_Watered_T2": [ - "DD-WTA-T2_R1", - "DD-WTA-T2_R2", - "DD-WTA-T2_R3" - ], - "Apex_Watered_T3": [ - "DD-WTA-T3_R1", - "DD-WTA-T3_R2", - "DD-WTA-T3_R3" - ], - "Apex_Watered_T4": [ - "DD-WTA-T4_R1", - "DD-WTA-T4_R2", - "DD-WTA-T4_R3" - ], - "Apex_Watered_T5": [ - "DD-WTA-T5_R1", - "DD-WTA-T5_R2", - "DD-WTA-T5_R3" - ], - "Apex_Watered_T6": [ - "DD-WTA-T6_R1", - "DD-WTA-T6_R2", - "DD-WTA-T6_R3" - ], - "Apex_Watered_T7": [ - "DD-WTA-T7_R1", - "DD-WTA-T7_R2", - "DD-WTA-T7_R3" - ], - "Apex_Drought_T1": [ - "DD-DTA-T1_R1", - "DD-DTA-T1_R2", - "DD-DTA-T1_R3" - ], - "Apex_Drought_T2": [ - "DD-DTA-T2_R1", - "DD-DTA-T2_R2", - "DD-DTA-T2_R3" - ], - "Apex_Drought_T3": [ - "DD-DTA-T3_R1", - "DD-DTA-T3_R2", - "DD-DTA-T3_R3" - ], - "Apex_Drought_T4": [ - "DD-DTA-T4_R1", - "DD-DTA-T4_R2", - "DD-DTA-T4_R3" - ], - "Apex_Drought_T5": [ - "DD-DTA-T5_R1", - "DD-DTA-T5_R2", - "DD-DTA-T5_R3" - ], - "Apex_Drought_T6": [ - "DD-DTA-T6_R1", - "DD-DTA-T6_R2", - "DD-DTA-T6_R3" - ], - "Apex_Drought_T7": [ - "DD-DTA-T7_R1", - "DD-DTA-T7_R2", - "DD-DTA-T7_R3" - ] - } - } - }, - "data_type": "RNA-Seq" - } - } - } - }, - "cacao sca": { - "data": { - "species": "cacao sca", - "views": { - "Developmental_Atlas": { - "database": "cacao_developmental_atlas_sca", - "view_name": "Developmental_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "CCN51_Mature_Embryo": [ - "CGA-SE-LS-E_R1", - "CGA-SE-LS-E_R2", - "CGA-SE-LS-E_R3", - "CGA-SE-LS-E_R4", - "CGA-SE-LS-E_R5" - ], - "Germinating_Seed_Root": [ - "CGA-GS-RO_R1", - "CGA-GS-RO_R2", - "CGA-GS-RO_R3", - "CGA-GS-RO_R4", - "CGA-GS-RO_R5" - ], - "Germinating_Seed_Shoot": [ - "CGA-GS-SH_R1", - "CGA-GS-SH_R2", - "CGA-GS-SH_R3", - "CGA-GS-SH_R4", - "CGA-GS-SH_R5" - ], - "Seedling_Root": [ - "CGA-SL-RO_R1", - "CGA-SL-RO_R2", - "CGA-SL-RO_R3", - "CGA-SL-RO_R4", - "CGA-SL-RO_R5" - ], - "Seedling_Shoot": [ - "CGA-SL-SH_R1", - "CGA-SL-SH_R2", - "CGA-SL-SH_R3", - "CGA-SL-SH_R4", - "CGA-SL-SH_R5" - ], - "3mo_Orthotropic_Roots": [ - "CGA-RO_R1", - "CGA-RO_R2", - "CGA-RO_R3", - "CGA-RO_R4", - "CGA-RO_R5" - ], - "3mo_Orthotropic_Leaf_A": [ - "CGA-YL-A_R1", - "CGA-YL-A_R2", - "CGA-YL-A_R3", - "CGA-YL-A_R4", - "CGA-YL-A_R5" - ], - "3mo_Orthotropic_C_Leaf": [ - "CGA-ML-C_2", - "CGA-ML-C_R1", - "CGA-ML-C_R3", - "CGA-ML-C_R4", - "CGA-ML-C_R5" - ], - "3mo_Orthotropic_E1_Leaf": [ - "CGA-ML-E1_R1", - "CGA-ML-E1_R2", - "CGA-ML-E1_R3", - "CGA-ML-E1_R4", - "CGA-ML-E1_R5" - ], - "3mo_Orthotropic_E2_Leaf": [ - "CGA-OL-E2_R1", - "CGA-OL-E2_R2", - "CGA-OL-E2_R3", - "CGA-OL-E2_R4", - "CGA-OL-E2_R5" - ], - "3mo_Orthotropic_Shoot_Apex": [ - "CGA-AX_R1", - "CGA-AX_R2", - "CGA-AX_R3", - "CGA-AX_R4", - "CGA-AX_R5" - ], - "3mo_Orthotropic_Herbaceous_Stem": [ - "CGA-SBA-2_R1", - "CGA-SBA-2_R2", - "CGA-SBA-2_R3", - "CGA-SBA-2_R4", - "CGA-SBA-2_R5" - ], - "3mo_Orthotropic_Woody_Stem": [ - "CGA-SBA-1_R1", - "CGA-SBA-1_R2", - "CGA-SBA-1_R3", - "CGA-SBA-1_R4", - "CGA-SBA-1_R5" - ], - "Premeiotic_Floral_Bud": [ - "CGA-PMFB_R1", - "CGA-PMFB_R2", - "CGA-PMFB_R3", - "CGA-PMFB_R4" - ], - "Floral_Bud_5-10_mm": [ - "CGA-LGFL_R1", - "CGA-LGFL_R2", - "CGA-LGFL_R3", - "CGA-LGFL_R4" - ], - "Open_Flower": [ - "CGA-OF_R1", - "CGA-OF_R2", - "CGA-OF_R3", - "CGA-OF_R4" - ], - "CCN51_Immature_Embryo": [ - "DA-SE-MS-E_R1", - "DA-SE-MS-E_R2", - "DA-SE-MS-E_R3", - "DA-SE-MS-E_R4", - "DA-SE-MS-E_R5" - ], - "Immature_Pod_Seed_Coat": [ - "DA-SE-MS-SC_R1", - "DA-SE-MS-SC_R2", - "DA-SE-MS-SC_R3", - "DA-SE-MS-SC_R4", - "DA-SE-MS-SC_R5" - ], - "CCN51_Developing_Embryo": [ - "DA-SE-MLS-E_R1", - "DA-SE-MLS-E_R2", - "DA-SE-MLS-E_R3", - "DA-SE-MLS-E_R4", - "DA-SE-MLS-E_R5" - ], - "Developing_Pod_Seed_Coat": [ - "DA-MLS-SC_R1", - "DA-MLS-SC_R2", - "DA-MLS-SC_R3", - "DA-MLS-SC_R4", - "DA-MLS-SC_R5" - ], - "Immature_Pod_Skin": [ - "DA-PD-MS-PS_R1", - "DA-PD-MS-PS_R2", - "DA-PD-MS-PS_R3" - ], - "Immature_Pod_Exocarp": [ - "DA-PD-MS-PEX_R1", - "DA-PD-MS-PEX_R2", - "DA-PD-MS-PEX_R3" - ], - "Immature_Pod_Mesocarp": [ - "DA-PD-MS-PMC_R1", - "DA-PD-MS-PMC_R2", - "DA-PD-MS-PMC_R3" - ], - "Immature_Pod_Seed_Mucilage": [ - "DA-PD-MS-SM_R1", - "DA-PD-MS-SM_R2", - "DA-PD-MS-SM_R3" - ], - "Immature_Pod_Endocarp": [ - "DA-PD-MS-PEN_R1", - "DA-PD-MS-PEN_R2", - "DA-PD-MS-PEN_R3" - ], - "Developing_Pod_Skin": [ - "DA-PD-MLS-PS_R1", - "DA-PD-MLS-PS_R2", - "DA-PD-MLS-PS_R3" - ], - "Developing_Pod_Exocarp": [ - "DA-PD-MLS-PEX_R1", - "DA-PD-MLS-PEX_R2", - "DA-PD-MLS-PEX_R3" - ], - "Developing_Pod_Mesocarp": [ - "DA-PD-MLS-PMC_R1", - "DA-PD-MLS-PMC_R2", - "DA-PD-MLS-PMC_R3" - ], - "Developing_Pod_Endocarp": [ - "DA-PD-MLS-PEN_R1", - "DA-PD-MLS-PEN_R2", - "DA-PD-MLS-PEN_R3" - ], - "Developing_Pod_Seed_Mucilage": [ - "DA-PD-MLS-SM_R1", - "DA-PD-MLS-SM_R2", - "DA-PD-MLS-SM_R3" - ], - "Mature_Pod_Skin": [ - "DA-PD-LS-PS_R1", - "DA-PD-LS-PS_R2", - "DA-PD-LS-PS_R3", - "DA-PD-LS-PS_R4", - "DA-PD-LS-PS_R5" - ], - "Mature_Pod_Exocarp": [ - "DA-PD-LS-PEX_R1", - "DA-PD-LS-PEX_R2", - "DA-PD-LS-PEX_R3", - "DA-PD-LS-PEX_R4", - "DA-PD-LS-PEX_R5" - ], - "Mature_Pod_Mesocarp": [ - "DA-PD-LS-PMC_R1", - "DA-PD-LS-PMC_R2", - "DA-PD-LS-PMC_R3", - "DA-PD-LS-PMC_R4", - "DA-PD-LS-PMC_R5" - ], - "Mature_Pod_Endocarp": [ - "DA-PD-LS-PEN_R1", - "DA-PD-LS-PEN_R2", - "DA-PD-LS-PEN_R3", - "DA-PD-LS-PEN_R4", - "DA-PD-LS-PEN_R5" - ], - "Mature_Pod_Seed_Mucilage": [ - "DA-PD-LS-SM_R1", - "DA-PD-LS-SM_R2", - "DA-PD-LS-SM_R3", - "DA-PD-LS-SM_R4", - "DA-PD-LS-SM_R5" - ], - "6mo_Orthotropic_Root": [ - "DA-RO-RT_R1", - "DA-RO-RT_R2", - "DA-RO-RT_R3", - "DA-RO-RT_R4", - "DA-RO-RT_R5" - ], - "6mo_Orthotropic_Leaf_A": [ - "DA-OTL-A_R1", - "DA-OTL-A_R2", - "DA-OTL-A_R3", - "DA-OTL-A_R4", - "DA-OTL-A_R5" - ], - "6mo_Orthotropic_Leaf_C": [ - "DA-OTL-C_R1", - "DA-OTL-C_R2", - "DA-OTL-C_R3", - "DA-OTL-C_R4", - "DA-OTL-C_R5" - ], - "6mo_Orthotropic_Leaf_E1": [ - "DA-OTL-E1_R1", - "DA-OTL-E1_R2", - "DA-OTL-E1_R3", - "DA-OTL-E1_R4", - "DA-OTL-E1_R5" - ], - "6mo_Orthotropic_Leaf_E2": [ - "DA-OTL-E2_R2", - "DA-OTL-E2_R3", - "DA-OTL-E2_R4", - "DA-OTL-E2_R5" - ], - "6mo_Orthotropic_Leaf_E3": [ - "DA-OTL-E3_R1", - "DA-OTL-E3_R2", - "DA-OTL-E3_R3", - "DA-OTL-E3_R4", - "DA-OTL-E3_R5" - ], - "6mo_Orthotropic_Shoot_Apex": [ - "DA-OTA_R1", - "DA-OTA_R2", - "DA-OTA_R3", - "DA-OTA_R4", - "DA-OTA_R5" - ], - "6mo_Orthotropic_Herbaceous_Stem": [ - "DA-OTAC-YS_R1", - "DA-OTAC-YS_R2", - "DA-OTAC-YS_R3", - "DA-OTAC-YS_R4", - "DA-OTAC-YS_R5" - ], - "6mo_Orthotropic_Young_Axilaries": [ - "DA-OAA-YA_R1", - "DA-OAA-YA_R2", - "DA-OAA-YA_R3", - "DA-OAA-YA_R4", - "DA-OAA-YA_R5" - ], - "6mo_Orthotropic_Old_Axilaries": [ - "DA-OAA-OA_R1", - "DA-OAA-OA_R2", - "DA-OAA-OA_R3", - "DA-OAA-OA_R4" - ], - "Plagiotropic_Shoot_Apex": [ - "DA-PSA_R1", - "DA-PSA_R2", - "DA-PSA_R3", - "DA-PSA_R4", - "DA-PSA_R5" - ], - "Plagiotropic_A_Leaf": [ - "DA-PTL-A_R1", - "DA-PTL-A_R2", - "DA-PTL-A_R3", - "DA-PTL-A_R4", - "DA-PTL-A_R5" - ], - "Plagiotropic_C_Leaf": [ - "DA-PTL-C_R1", - "DA-PTL-C_R3", - "DA-PTL-C_R4" - ], - "Plagiotropic_E_Leaf": [ - "DA-PTL-E_R1", - "DA-PTL-E_R2", - "DA-PTL-E_R3", - "DA-PTL-E_R4", - "DA-PTL-E_R5" - ], - "Plagiotropic_Old_Axiliaries": [ - "DA-OA_R1", - "DA-OA_R2", - "DA-OA_R3", - "DA-OA_R4", - "DA-OA_R5" - ], - "Plagiotropic_Young_Axilaries": [ - "DA-YA_R1", - "DA-YA_R2", - "DA-YA_R3", - "DA-YA_R4", - "DA-YA_R5" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Drought_Diurnal_Atlas": { - "database": "cacao_drought_diurnal_atlas_sca", - "view_name": "Drought_Diurnal_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Root_Watered_T1": [ - "DD-WTR-T1_R1", - "DD-WTR-T1_R2", - "DD-WTR-T1_R3" - ], - "Root_Watered_T2": [ - "DD-WTR-T2_R1", - "DD-WTR-T2_R2", - "DD-WTR-T2_R3" - ], - "Root_Watered_T3": [ - "DD-WTR-T3_R1", - "DD-WTR-T3_R2", - "DD-WTR-T3_R3" - ], - "Root_Watered_T4": [ - "DD-WTR-T4_R1", - "DD-WTR-T4_R2", - "DD-WTR-T4_R3" - ], - "Root_Watered_T5": [ - "DD-WTR-T5_R1", - "DD-WTR-T5_R2", - "DD-WTR-T5_R3" - ], - "Root_Watered_T6": [ - "DD-WTR-T6_R1", - "DD-WTR-T6_R2", - "DD-WTR-T6_R3" - ], - "Root_Watered_T7": [ - "DD-WTR-T7_R2", - "DD-WTR-T7_R3", - "DD-WTR-T7-R1" - ], - "Root_Drought_T1": [ - "DD-DTR-T1_R1", - "DD-DTR-T1_R2", - "DD-DTR-T1_R3" - ], - "Root_Drought_T2": [ - "DD-DTR-T2_R1", - "DD-DTR-T2_R2", - "DD-DTR-T2_R3" - ], - "Root_Drought_T3": [ - "DD-DTR-T3_R1", - "DD-DTR-T3_R2", - "DD-DTR-T3_R3" - ], - "Root_Drought_T4": [ - "DD-DTR-T4_R1", - "DD-DTR-T4_R2", - "DD-DTR-T4_R3" - ], - "Root_Drought_T5": [ - "DD-DTR-T5_R1", - "DD-DTR-T5_R2" - ], - "Root_Drought_T6": [ - "DD-DTR-T6_R1", - "DD-DTR-T6_R2", - "DD-DTR-T6_R3" - ], - "Root_Drought_T7": [ - "DD-DTR-T7_R1", - "DD-DTR-T7_R2", - "DD-DTR-T7_R3" - ], - "Leaf_Watered_T1": [ - "DD-WTL-T1_R1", - "DD-WTL-T1_R2", - "DD-WTL-T1_R3" - ], - "Leaf_Watered_T2": [ - "DD-WTL-T2_R1", - "DD-WTL-T2_R2", - "DD-WTL-T2_R3" - ], - "Leaf_Watered_T3": [ - "DD-WTL-T3_R1", - "DD-WTL-T3_R2", - "DD-WTL-T3_R3" - ], - "Leaf_Watered_T4": [ - "DD-WTL-T4_R1", - "DD-WTL-T4_R2", - "DD-WTL-T4_R3" - ], - "Leaf_Watered_T5": [ - "DD-WTL-T5_R1", - "DD-WTL-T5_R2" - ], - "Leaf_Watered_T6": [ - "DD-WTL-T6_R1", - "DD-WTL-T6_R2", - "DD-WTL-T6_R3" - ], - "Leaf_Watered_T7": [ - "DD-WTL-T7_R1", - "DD-WTL-T7_R2", - "DD-WTL-T7_R3" - ], - "Leaf_Drought_T1": [ - "DD-DTL-T1_R1", - "DD-DTL-T1_R2", - "DD-DTL-T1_R3" - ], - "Leaf_Drought_T2": [ - "DD-DTL-T2_R1", - "DD-DTL-T2_R2", - "DD-DTL-T2_R3" - ], - "Leaf_Drought_T3": [ - "DD-DTL-T3_R1", - "DD-DTL-T3_R2", - "DD-DTL-T3_R3" - ], - "Leaf_Drought_T4": [ - "DD-DTL-T4_R1", - "DD-DTL-T4_R2", - "DD-DTL-T4_R3" - ], - "Leaf_Drought_T5": [ - "DD-DTL-T5_R1", - "DD-DTL-T5_R2", - "DD-DTL-T5_R3" - ], - "Leaf_Drought_T6": [ - "DD-DTL-T6_R1", - "DD-DTL-T6_R2", - "DD-DTL-T6_R3" - ], - "Leaf_Drought_T7": [ - "DD-DTL-T7_R1", - "DD-DTL-T7_R2", - "DD-DTL-T7_R3" - ], - "Apex_Watered_T1": [ - "DD-WTA-T1_R1", - "DD-WTA-T1_R2", - "DD-WTA-T1_R3" - ], - "Apex_Watered_T2": [ - "DD-WTA-T2_R1", - "DD-WTA-T2_R2", - "DD-WTA-T2_R3" - ], - "Apex_Watered_T3": [ - "DD-WTA-T3_R1", - "DD-WTA-T3_R2", - "DD-WTA-T3_R3" - ], - "Apex_Watered_T4": [ - "DD-WTA-T4_R1", - "DD-WTA-T4_R2", - "DD-WTA-T4_R3" - ], - "Apex_Watered_T5": [ - "DD-WTA-T5_R1", - "DD-WTA-T5_R2", - "DD-WTA-T5_R3" - ], - "Apex_Watered_T6": [ - "DD-WTA-T6_R1", - "DD-WTA-T6_R2", - "DD-WTA-T6_R3" - ], - "Apex_Watered_T7": [ - "DD-WTA-T7_R1", - "DD-WTA-T7_R2", - "DD-WTA-T7_R3" - ], - "Apex_Drought_T1": [ - "DD-DTA-T1_R1", - "DD-DTA-T1_R2", - "DD-DTA-T1_R3" - ], - "Apex_Drought_T2": [ - "DD-DTA-T2_R1", - "DD-DTA-T2_R2", - "DD-DTA-T2_R3" - ], - "Apex_Drought_T3": [ - "DD-DTA-T3_R1", - "DD-DTA-T3_R2", - "DD-DTA-T3_R3" - ], - "Apex_Drought_T4": [ - "DD-DTA-T4_R1", - "DD-DTA-T4_R2", - "DD-DTA-T4_R3" - ], - "Apex_Drought_T5": [ - "DD-DTA-T5_R1", - "DD-DTA-T5_R2", - "DD-DTA-T5_R3" - ], - "Apex_Drought_T6": [ - "DD-DTA-T6_R1", - "DD-DTA-T6_R2", - "DD-DTA-T6_R3" - ], - "Apex_Drought_T7": [ - "DD-DTA-T7_R1", - "DD-DTA-T7_R2", - "DD-DTA-T7_R3" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Meristem_Atlas": { - "database": "cacao_meristem_atlas_sca", - "view_name": "Meristem_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Plagiotropic_Apex_Stage_4": [ - "MA-PTA-Sca6-S4_R1", - "MA-PTA-Sca6-S4_R2", - "MA-PTA-Sca6-S4_R3" - ], - "Plagiotropic_Apex_Stage_3": [ - "MA-PTA-Sca6-S3_R1", - "MA-PTA-Sca6-S3_R2", - "MA-PTA-Sca6-S3_R3" - ], - "Plagiotropic_Apex_Stage_2": [ - "MA-PTA-Sca6-S2_R1", - "MA-PTA-Sca6-S2_R2", - "MA-PTA-Sca6-S2_R3" - ], - "Plagiotropic_Apex_Stage_1": [ - "MA-PTA-Sca6-S1_R1", - "MA-PTA-Sca6-S1_R2", - "MA-PTA-Sca6-S1_R3" - ], - "Orthotropic_Apex_Stage_4": [ - "MA-OTA-Sca6-S4_R1", - "MA-OTA-Sca6-S4_R2", - "MA-OTA-Sca6-S4_R3" - ], - "Orthotropic_Apex_Stage_3": [ - "MA-OTA-Sca6-S3_R1", - "MA-OTA-Sca6-S3_R2", - "MA-OTA-Sca6-S3_R3" - ], - "Orthotropic_Apex_Stage_2": [ - "MA-OTA-Sca6-S2_R1", - "MA-OTA-Sca6-S2_R2", - "MA-OTA-Sca6-S2_R3" - ], - "Orthotropic_Apex_Stage_1": [ - "MA-OTA-Sca6-S1_R1", - "MA-OTA-Sca6-S1_R2", - "MA-OTA-Sca6-S1_R3" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Seed_Atlas": { - "database": "cacao_seed_atlas_sca", - "view_name": "Seed_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "CCN": [ - "CGA-SE-LS-E_R1", - "CGA-SE-LS-E_R2", - "CGA-SE-LS-E_R3", - "CGA-SE-LS-E_R4", - "CGA-SE-LS-E_R5" - ], - "IMC": [ - "SA-SE-LS-IMC-E_R1", - "SA-SE-LS-IMC-E_R2", - "SA-SE-LS-IMC-E_R3", - "SA-SE-LS-IMC-E_R4", - "SA-SE-LS-IMC-E_R5" - ], - "Sca": [ - "SA-SE-LS-Sca-E_R1", - "SA-SE-LS-Sca-E_R2", - "SA-SE-LS-Sca-E_R3", - "SA-SE-LS-Sca-E_R4", - "SA-SE-LS-Sca-E_R5" - ] - } - } - }, - "data_type": "RNA-Seq" - } - } - } - }, - "cacao tc": { - "data": { - "species": "cacao tc", - "views": { - "Cacao_Infection": { - "database": "cacao_infection", - "view_name": "Cacao_Infection", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "NA32_Basal": [ - "basal_N432_rep4", - "basal_NA32_rep1", - "basal_NA32_rep2", - "basal_NA32_rep3", - "basal_NA32_rep5", - "basal_NA32_rep6", - "basal_NA32_rep7", - "basal_NA32_rep8" - ], - "Scavina6_Basal": [ - "basal_SCA6_rep1", - "basal_SCA6_rep2", - "basal_SCA6_rep3", - "basal_SCA6_rep4", - "basal_SCA6_rep5", - "basal_SCA6_rep6", - "basal_SCA6_rep7", - "basal_SCA6_rep8" - ], - "NA32_Control_24h": [ - "NA32_Control_24hr_rep1", - "NA32_Control_24hr_rep2", - "NA32_Control_24hr_rep3", - "NA32_Control_24hr_rep4" - ], - "NA32_Control_6h": [ - "NA32_Control_6hr_rep1", - "NA32_Control_6hr_rep2", - "NA32_Control_6hr_rep3" - ], - "NA32_Control_72h": [ - "NA32_Control_72hr_rep1", - "NA32_Control_72hr_rep2", - "NA32_Control_72hr_rep3", - "NA32_Control_72hr_rep4" - ], - "NA32_Infected_6h": [ - "NA32_Pathogen_6hr_rep1", - "NA32_Pathogen_6hr_rep2", - "NA32_Pathogen_6hr_rep3", - "NA32_Pathogen_6hr_rep4" - ], - "NA32_Infected_24h": [ - "NA32_Pathogen_24hr_rep1", - "NA32_Pathogen_24hr_rep2", - "NA32_Pathogen_24hr_rep3", - "NA32_Pathogen_24hr_rep4" - ], - "NA32_Infected_72h": [ - "NA32_Pathogen_72hr_rep1", - "NA32_Pathogen_72hr_rep2", - "NA32_Pathogen_72hr_rep3", - "NA32_Pathogen_72hr_rep4" - ], - "Scavina6_Control_6h": [ - "SCA6_Control_6hr_rep1", - "SCA6_Control_6hr_rep2", - "SCA6_Control_6hr_rep3", - "SCA6_Control_6hr_rep4" - ], - "Scavina6_Control_24h": [ - "SCA6_Control_24hr_rep1", - "SCA6_Control_24hr_rep2", - "SCA6_Control_24hr_rep3", - "SCA6_Control_24hr_rep4" - ], - "Scavina6_Control_72h": [ - "SCA6_Control_72hr_rep1", - "SCA6_Control_72hr_rep2", - "SCA6_Control_72hr_rep3", - "SCA6_Control_72hr_rep4" - ], - "Scavina6_Infected_6h": [ - "SCA6_Pathogen_6hr_rep1", - "SCA6_Pathogen_6hr_rep2", - "SCA6_Pathogen_6hr_rep3", - "SCA6_Pathogen_6hr_rep4" - ], - "Scavina6_Infected_72h": [ - "SCA6_Pathogen_72hr_rep1", - "SCA6_Pathogen_72hr_rep2", - "SCA6_Pathogen_72hr_rep3", - "SCA6_Pathogen_72hr_rep4" - ] - } - }, - "basal_SCA6_rep8;Med_CTRL": { - "controls": [ - "basal_SCA6_rep8", - "Med_CTRL" - ], - "treatments": { - "Scavina6_Infected_24h": [ - "SCA6_Pathogen_24hr_rep1", - "SCA6_Pathogen_24hr_rep2", - "SCA6_Pathogen_24hr_rep3", - "SCA6_Pathogen_24hr_rep4" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Cacao_Leaf": { - "database": "cacao_leaf", - "view_name": "Cacao_Leaf", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Scavina6_DE": [ - "Sca6_DE_1", - "Sca6_DE_2", - "Sca6_DE_3", - "Sca6_DE_4", - "Sca6_DE_5" - ], - "Scavina6_AB": [ - "Sca6_AB_1", - "Sca6_AB_2", - "Sca6_AB_3", - "Sca6_AB_4", - "Sca6_AB_5" - ], - "Scavina6_C": [ - "Sca6_C_1", - "Sca6_C_2", - "Sca6_C_3", - "Sca6_C_4", - "Sca6_C_5" - ], - "ICS1_AB": [ - "ICS1_AB_1", - "ICS1_AB_2", - "ICS1_AB_3", - "ICS1_AB_4", - "ICS1_AB_5" - ], - "ICS1_C": [ - "ICS1_C_1", - "ICS1_C_2", - "ICS1_C_3", - "ICS1_C_4", - "ICS1_C_5" - ], - "ICS1_DE": [ - "ICS1_DE_1", - "ICS1_DE_2", - "ICS1_DE_3", - "ICS1_DE_4", - "ICS1_DE_5" - ] - } - } - }, - "data_type": "RNA-Seq" - } - } - } - }, - "camelina": { - "data": { - "species": "camelina", - "views": { - "Developmental_Atlas_FPKM": { - "database": "camelina", - "view_name": "Developmental_Atlas_FPKM", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Germinating_Seed": [ - "germinating_seed_1", - "germinating_seed_2", - "germinating_seed_3" - ], - "Cotyledon": [ - "cotyledon_1", - "cotyledon_2", - "cotyledon_3" - ], - "Young_Leaf": [ - "young_leaf_1", - "young_leaf_2", - "young_leaf_3" - ], - "Senescing_Leaf": [ - "senescing_leaf_1", - "senescing_leaf_2", - "senescing_leaf_3" - ], - "Root": [ - "root_1", - "root_2", - "root_3" - ], - "Stem": [ - "stem_1", - "stem_2", - "stem_3" - ], - "Buds": [ - "bud_1", - "bud_2", - "bud_3" - ], - "Flower": [ - "flower_1", - "flower_2", - "flower_3" - ], - "Early_Seed_Development": [ - "early_seed_development_1", - "early_seed_development_2", - "early_seed_development_3" - ], - "Early-mid_Seed_Development": [ - "early_mid_seed_development_1", - "early_mid_seed_development_2", - "early_mid_seed_development_3" - ], - "Late-mid_Seed_Development": [ - "late_mid_seed_development_1", - "late_mid_seed_development_2", - "late_mid_seed_development_3" - ], - "Late_Seed_Development": [ - "late_seed_development_1", - "late_seed_development_2", - "late_seed_development_3" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Developmental_Atlas_TPM": { - "database": "camelina_tpm", - "view_name": "Developmental_Atlas_TPM", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Germinating_Seed": [ - "germinating_seed_1", - "germinating_seed_2", - "germinating_seed_3" - ], - "Cotyledon": [ - "cotyledon_1", - "cotyledon_2", - "cotyledon_3" - ], - "Young_Leaf": [ - "young_leaf_1", - "young_leaf_2", - "young_leaf_3" - ], - "Senescing_Leaf": [ - "senescing_leaf_1", - "senescing_leaf_2", - "senescing_leaf_3" - ], - "Root": [ - "root_1", - "root_2", - "root_3" - ], - "Stem": [ - "stem_1", - "stem_2", - "stem_3" - ], - "Buds": [ - "bud_1", - "bud_2", - "bud_3" - ], - "Flower": [ - "flower_1", - "flower_2", - "flower_3" - ], - "Early_Seed_Development": [ - "early_seed_development_1", - "early_seed_development_2", - "early_seed_development_3" - ], - "Early-mid_Seed_Development": [ - "early_mid_seed_development_1", - "early_mid_seed_development_2", - "early_mid_seed_development_3" - ], - "Late-mid_Seed_Development": [ - "late_mid_seed_development_1", - "late_mid_seed_development_2", - "late_mid_seed_development_3" - ], - "Late_Seed_Development": [ - "late_seed_development_1", - "late_seed_development_2", - "late_seed_development_3" - ] - } - } - }, - "data_type": "RNA-Seq" - } - } - } - }, - "cannabis": { - "data": { - "species": "cannabis", - "views": { - "Cannabis_Atlas": { - "database": "cannabis", - "view_name": "Cannabis_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "PK-Shoot": [ - "PK-SHT" - ], - "PK-Root": [ - "PK-RT" - ], - "PK-MidFlower": [ - "PK-MFLW" - ], - "PK-EarlyFlower": [ - "PK-EFLW" - ], - "PK-PreFlower": [ - "PK-PFLW" - ], - "PK-Stem": [ - "PK-STM" - ] - } - } - }, - "data_type": "RNA-Seq" - } - } - } - }, - "canola": { - "data": { - "species": "canola", - "views": { - "Canola_Seed": { - "database": "canola_seed", - "view_name": "Canola_Seed", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Chalazal_proliferating_tissue,_ovule_stage": [ - "ovCPT1_2", - "ovCPT3", - "ovCPT3_2" - ], - "Chalazal_seed_coat,_ovule_stage": [ - "ovCZSC1", - "ovCZSC2", - "ovCZSC3" - ], - "Inner_seed_coat,_ovule_stage": [ - "ovISC1", - "ovISC2", - "ovISC3" - ], - "Outer_seed_coat,_ovule_stage": [ - "ovOSC1", - "ovOSC2", - "ovOSC3" - ], - "Chalazal_proliferating_tissue,_globular_stage": [ - "gCPT1", - "gCPT2", - "gCPT3" - ], - "Chalazal_endosperm,_globular_stage": [ - "gCZE1", - "gCZE2", - "gCZE3" - ], - "Chalazal_seed_coat,_globular_stage": [ - "gCZSC1", - "gCZSC2", - "gCZSC3" - ], - "Embryo_proper,_globular_stage": [ - "gEP1", - "gEP2", - "GLOB_EP4J1", - "GLOB_EP4J17" - ], - "Inner_seed_coat,_globular_stage": [ - "gISC1", - "gISC2", - "gISC3" - ], - "Outer_seed_coat,_globular_stage": [ - "gOSC2", - "gOSC3" - ], - "Micropylar_endosperm,_globular_stage": [ - "gMCE1", - "gMCE2", - "gMCE3", - "gMCE4", - "GLOB_MCE2" - ], - "Peripheral_endosperm,_globular_stage": [ - "gPEN1", - "gPEN2" - ], - "Chalazal_proliferating_tissue,_heart_stage": [ - "hCPT1", - "hCPT2", - "hCPT3" - ], - "Chalazal_endosperm,_heart_stage": [ - "hCZE1", - "hCZE2" - ], - "Chalazal_seed_coat,_heart_stage": [ - "hCZSC1", - "hCZSC2", - "hCZSC3" - ], - "Embryo_proper,_heart_stage": [ - "hEPJ", - "HRT_EPJ" - ], - "Inner_seed_coat,_heart_stage": [ - "hISC1_3", - "hISC2", - "hISC3" - ], - "Micropylar_endosperm,_heart_stage": [ - "hMCE2", - "HRT_MCE1", - "HRT_MCE2", - "HRT_MCE26" - ], - "Outer_seed_coat,_heart_stage": [ - "hOSC1", - "hOSC2", - "hOSC3" - ], - "Peripheral_endosperm,_heart_stage": [ - "hPEN1", - "hPEN2" - ], - "Chalazal_proliferating_tissue,_maturation_green_stage": [ - "mgCPT1", - "mgCPT2", - "mgCPT3" - ], - "Chalazal_seed_coat,_maturation_green_stage": [ - "mgCZSC2", - "mgCZSC3", - "mgCZSC3_2" - ], - "Inner_seed_coat,_maturation_green_stage": [ - "mgISC1", - "mgISC2" - ], - "Outer_seed_coat,_maturation_green_stage": [ - "mgOSC1", - "mgOSC2", - "mgOSC3" - ], - "Embryo_cotyledons,_maturation_green_stage": [ - "MG_COT1", - "MG_COT2", - "MG_COT8" - ], - "Embryo_root,_maturation_green_stage": [ - "MG_ROOT2", - "MG_ROOT3" - ] - } - } - }, - "data_type": "RNA-Seq" - } - } - } - }, - "eutrema": { - "data": { - "species": "eutrema", - "views": { - "Eutrema": { - "database": "thellungiella_db", - "view_name": "Eutrema", - "groups": { - "THELLUNGIELLA_CTRL": { - "controls": [ - "THELLUNGIELLA_CTRL" - ], - "treatments": { - "Shandong_accession_grown_in_cabinet,_rosette_leaves": [ - "SC1", - "SC2", - "SC3" - ], - "Yukon_accession_grown_in_cabinet,_rosette_leaves": [ - "YC1", - "YC2", - "YC3" - ], - "Yukon_accession_collected_from_the_field_in_2005": [ - "YF1", - "YF2", - "YF3" - ] - } - } - }, - "data_type": "Unknown" - } - } - } - }, - "grape": { - "data": { - "species": "grape", - "views": { - "grape_developmental": { - "database": "grape_developmental", - "view_name": "grape_developmental", - "groups": { - "Dev": { - "controls": [ - "GRAPE_CTRL" - ], - "treatments": { - "Tendril_-_Young": [ - "GSM881670", - "GSM881671", - "GSM881672" - ], - "Tendril_-_Well_Developed": [ - "GSM881673", - "GSM881674", - "GSM881675" - ], - "Tendril_-_Fruit_Set": [ - "GSM881676", - "GSM881677", - "GSM881678" - ], - "Leaf_-_Young": [ - "GSM881586", - "GSM881587", - "GSM881588" - ], - "Leaf_-_Fruit_Set": [ - "GSM881589", - "GSM881590", - "GSM881591" - ], - "Leaf_-_Senescent": [ - "GSM881592", - "GSM881593", - "GSM881594" - ], - "Seedling": [ - "GSM881640", - "GSM881641", - "GSM881642" - ], - "Stem_-_Young": [ - "GSM881664", - "GSM881665", - "GSM881666" - ], - "Stem_-_Mature_(Woody)": [ - "GSM881667", - "GSM881668", - "GSM881669" - ], - "Bud_-_Bud_Swelling_Stage": [ - "GSM881535", - "GSM881536", - "GSM881537" - ], - "Bud_-_Bud_Burst_Initial_Stage": [ - "GSM881538", - "GSM881539", - "GSM881540" - ], - "Bud_-_Bud_Burst_Later_Stage": [ - "GSM881541", - "GSM881542", - "GSM881543" - ], - "Bud_-_Latent_Bud": [ - "GSM881544", - "GSM881545", - "GSM881546" - ], - "Bud_-_Winter_Dormant": [ - "GSM881547", - "GSM881548", - "GSM881549" - ], - "Flower_-_Young": [ - "GSM881571", - "GSM881572", - "GSM881573" - ], - "Flower_-_Well_Developed": [ - "GSM881574", - "GSM881575", - "GSM881576" - ], - "Flower_-_Start_of_Flowering": [ - "GSM881577", - "GSM881578", - "GSM881579" - ], - "Flower_-_Flowering": [ - "GSM881580", - "GSM881581", - "GSM881582" - ], - "Root": [ - "GSM881583", - "GSM881584", - "GSM881585" - ], - "Carpel": [ - "GSM881595", - "GSM881596", - "GSM881597" - ], - "Stamen": [ - "GSM881517", - "GSM881518", - "GSM881519" - ], - "Petals": [ - "GSM881598", - "GSM881599", - "GSM881600" - ], - "Pollen": [ - "GSM881610", - "GSM881611", - "GSM881612" - ], - "Rachis_-_Fruit_Set": [ - "GSM881613", - "GSM881614", - "GSM881615" - ], - "Seed_-_Fruit_Set": [ - "GSM881634", - "GSM881635", - "GSM881636" - ], - "Pericarp_-_Fruit_Set": [ - "GSM881520", - "GSM881521", - "GSM881522" - ], - "Rachis_-_Post_Fruit_Set": [ - "GSM881616", - "GSM881617", - "GSM881618" - ], - "Pericarp_-_Post_Fruit_Set": [ - "GSM881523", - "GSM881524", - "GSM881525" - ], - "Seed_-_Post_Fruit_Set": [ - "GSM881637", - "GSM881638", - "GSM881639" - ], - "Flesh_-_Post_Fruit_Set": [ - "GSM881550", - "GSM881551", - "GSM881552" - ], - "Skin_-_Post_Fruit_Set": [ - "GSM881643", - "GSM881644", - "GSM881645" - ], - "Seed_-_Veraison": [ - "GSM881628", - "GSM881629", - "GSM881630" - ], - "Pericarp_-_Veraison": [ - "GSM881526", - "GSM881527", - "GSM881528" - ], - "Flesh_-_Veraison": [ - "GSM881553", - "GSM881554", - "GSM881555" - ], - "Skin_-_Veraison": [ - "GSM881646", - "GSM881647", - "GSM881648" - ], - "Rachis_-_Veraison": [ - "GSM881619", - "GSM881620", - "GSM881621" - ], - "Rachis_-_Mid_Ripening": [ - "GSM881622", - "GSM881623", - "GSM881624" - ], - "Seed_-_Mid_Ripening": [ - "GSM881628", - "GSM881629", - "GSM881630" - ], - "Pericarp_-_Mid_Ripening": [ - "GSM881529", - "GSM881530", - "GSM881531" - ], - "Flesh_-_Mid_Ripening": [ - "GSM881556", - "GSM881557", - "GSM881558" - ], - "Skin_-_Mid_Ripening": [ - "GSM881649", - "GSM881650", - "GSM881651" - ], - "Rachis_-_Ripening": [ - "GSM881625", - "GSM881626", - "GSM881627" - ], - "Pericarp_-_Ripening": [ - "GSM881532", - "GSM881533", - "GSM881534" - ], - "Flesh_-_Ripening": [ - "GSM881559", - "GSM881560", - "GSM881561" - ], - "Skin_-_Ripening": [ - "GSM881652", - "GSM881653", - "GSM881654" - ] - } - }, - "Flesh_Stress": { - "controls": [ - "GRAPE_FLESH_STRESS_CTRL" - ], - "treatments": { - "Flesh_-_PHWI": [ - "GSM881562", - "GSM881563", - "GSM881564" - ], - "Flesh_-_PHWII": [ - "GSM881565", - "GSM881566", - "GSM881567" - ], - "Flesh_-_PHWIII": [ - "GSM881568", - "GSM881569", - "GSM881570" - ] - } - }, - "Pericarp_Stress": { - "controls": [ - "GRAPE_PERICARP_STRESS_CTRL" - ], - "treatments": { - "Pericarp_-_PHWI": [ - "GSM881601", - "GSM881602", - "GSM881603" - ], - "Pericarp_-_PHWII": [ - "GSM881604", - "GSM881605", - "GSM881606" - ], - "Pericarp_-_PHWIII": [ - "GSM881607", - "GSM881608", - "GSM881609" - ] - } - }, - "Skin_Stress": { - "controls": [ - "GRAPE_SKIN_STRESS_CTRL" - ], - "treatments": { - "Skin_-_PHWI": [ - "GSM881655", - "GSM881656", - "GSM881657" - ], - "Skin_-_PHWII": [ - "GSM881658", - "GSM881659", - "GSM881660" - ], - "Skin_-_PHWIII": [ - "GSM881661", - "GSM881662", - "GSM881663" - ] - } - } - }, - "data_type": "Microarray" - } - } - } - }, - "kalanchoe": { - "data": { - "species": "kalanchoe", - "views": { - "Light_Response": { - "database": "kalanchoe", - "view_name": "Light_Response", - "groups": { - "White_Light_Dawn_control_group": { - "controls": [ - "WL_Dawn_rep1", - "WL_Dawn_rep2", - "WL_Dawn_rep3" - ], - "treatments": { - "HL_Dusk": [ - "HL_Dusk_rep1", - "HL_Dusk_rep2", - "HL_Dusk_rep3" - ], - "RL_Dusk": [ - "RL_Dusk_rep1", - "RL_Dusk_rep2", - "RL_Dusk_rep3" - ], - "HL_Dawn": [ - "HL_Dawn_rep1", - "HL_Dawn_rep2", - "HL_Dawn_rep3" - ], - "BL_Dawn": [ - "BL_Dawn_rep1", - "BL_Dawn_rep2", - "BL_Dawn_rep3" - ], - "LL_Dawn": [ - "LL_Dawn_rep1", - "LL_Dawn_rep2", - "LL_Dawn_rep3" - ], - "LL_Dusk": [ - "LL_Dusk_rep1", - "LL_Dusk_rep2", - "LL_Dusk_rep3" - ], - "WL_Dusk": [ - "WL_Dusk_rep1", - "WL_Dusk_rep2", - "WL_Dusk_rep3" - ], - "BL_Dusk": [ - "BL_Dusk_rep1", - "BL_Dusk_rep2", - "BL_Dusk_rep3" - ], - "DG_Dusk": [ - "DG_Dusk_rep1", - "DG_Dusk_rep2", - "DG_Dusk_rep3" - ], - "RL_Dawn": [ - "RL_Dawn_rep1", - "RL_Dawn_rep2", - "RL_Dawn_rep3" - ], - "DG_Dawn": [ - "DG_Dawn_rep1", - "DG_Dawn_rep2", - "DG_Dawn_rep3" - ], - "WL_Dawn": [ - "WL_Dawn_rep1", - "WL_Dawn_rep2", - "WL_Dawn_rep3" - ], - "FR_Dawn": [ - "FRL_Dawn_rep1", - "FRL_Dawn_rep2", - "FRL_Dawn_rep3" - ], - "FR_Dusk": [ - "FRL_Dusk_rep1", - "FRL_Dusk_rep2", - "FRL_Dusk_rep3" - ] - } - } - }, - "data_type": "RNA-Seq" - } - } - } - }, - "little millet": { - "data": { - "species": "little millet", - "views": { - "Life_Cycle": { - "database": "little_millet", - "view_name": "Life_Cycle", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Germinating_Seed": [ - "GS1", - "GS2", - "GS3" - ], - "Radicle": [ - "RD1", - "RD2", - "RD3" - ], - "Plumule": [ - "PU1", - "PU2", - "PU3" - ], - "Young_Leaf": [ - "YL1", - "YL2", - "YL3" - ], - "Young_Root": [ - "YR1", - "YR2" - ], - "Crown_Meristem": [ - "CM1", - "CM2", - "CM3" - ], - "Vegetative_Stem": [ - "VS1", - "VS2" - ], - "Panicle_Early": [ - "PE1", - "PE2", - "PE3" - ], - "Panicle_Mid": [ - "PM1", - "PM2", - "PM3" - ], - "Panicle_Late": [ - "PL1", - "PL2", - "PL3" - ] - } - } - }, - "data_type": "RNA-Seq" - } - } - } - }, - "lupin": { - "data": { - "species": "lupin", - "views": { - "LCM_Leaf": { - "database": "lupin_lcm_leaf", - "view_name": "LCM_Leaf", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Epidermis": [ - "Leaf_epidermis_1", - "Leaf_epidermis_2" - ], - "Mesophyll": [ - "Leaf_mesophyll_1", - "Leaf_mesophyll_2" - ], - "Vasculature": [ - "Leaf_vasculature_1", - "Leaf_vasculature_2" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "LCM_Pod": { - "database": "lupin_lcm_pod", - "view_name": "LCM_Pod", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Exocarp": [ - "Pod_exocarp_1", - "Pod_exocarp_2" - ], - "Endocarp": [ - "Pod_endocarp_1", - "Pod_endocarp_2" - ], - "Bundle_sheath": [ - "Pod_bundle_sheath_1", - "Pod_bundle_sheath_2" - ], - "Mesocarp": [ - "Pod_mesocarp_1", - "Pod_mesocarp_2" - ], - "Transverse_vasculature": [ - "Pod_transverse_vasculature_1", - "Pod_transverse_vasculature_2" - ], - "Ventral_suture_vasculature": [ - "Pod_ventral_suture_vasculature_1", - "Pod_ventral_suture_vasculature_2" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "LCM_Stem": { - "database": "lupin_lcm_stem", - "view_name": "LCM_Stem", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Epidermis": [ - "Stem_epidermis_1" - ], - "Parenchyma": [ - "Stem_parenchyma_1", - "Stem_parenchyma_2" - ], - "Phloem": [ - "Stem_phloem_1", - "Stem_phloem_2" - ], - "Xylem": [ - "Stem_xylem_1", - "Stem_xylem_2" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Whole_Plant": { - "database": "lupin_whole_plant", - "view_name": "Whole_Plant", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Big_seed": [ - "Big_seed" - ], - "Big_pod": [ - "Big_pod" - ], - "Flowers": [ - "Flowers" - ], - "Leaves": [ - "Leaves" - ], - "Pedicels": [ - "Pedicels" - ], - "Roots": [ - "Roots" - ], - "Small_pod_with_seeds": [ - "Small_pod_with_seeds" - ], - "Stem": [ - "Stem" - ] - } - } - }, - "data_type": "RNA-Seq" - } - } - } - }, - "maize": { - "data": { - "species": "maize", - "views": { - "Downs_et_al_Atlas": { - "database": "maize_gdowns", - "view_name": "Downs_et_al_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "24DAP_leaf;_15cm_tip_of_2nd_leaf_above_top_ear": [ - "24DAP_leaf_1", - "24DAP_leaf_2", - "24DAP_leaf_3" - ], - "17DAP_endosperm;_endosperm_of_top_ear": [ - "17DAP_endosperm_1", - "17DAP_endosperm_2", - "17DAP_endosperm_3" - ], - "VE_root;_seminal_root": [ - "VE_root_1", - "VE_root_2", - "VE_root_3" - ], - "V16_tassel;_spikelet_of_tassel_(top_10_cm)": [ - "V16_tassel_1", - "V16_tassel_2", - "V16_tassel_3" - ], - "V4_tassel;_1mm_tassel_meristem_and_1mm_uppermost_stem_below_tassel": [ - "V4_tassel_1", - "V4_tassel_2", - "V4_tassel_3" - ], - "24DAP_embryo;_embryo_of_top_ear": [ - "24DAP_embryo_1", - "24DAP_embryo_2", - "24DAP_embryo_3" - ], - "V2_nodal_root;_nodal_root": [ - "V2_nodal_root_1", - "V2_nodal_root_2", - "V2_nodal_root_3" - ], - "V16_cob;_top_ear_(5_cm)_cob": [ - "V16_cob_1", - "V16_cob_2", - "V16_cob_3" - ], - "R1_stalk;_R1-15_cm_stalk_below_tassel": [ - "R1_stalk_1", - "R1_stalk_2", - "R1_stalk_3" - ], - "10DAP_embryo;_embryo_of_top_ear": [ - "10DAP_embryo_1", - "10DAP_embryo_2", - "10DAP_embryo_3" - ], - "24DAP_endosperm;_endosperm_of_top_ear": [ - "24DAP_endosperm_1", - "24DAP_endosperm_2", - "24DAP_endosperm_3" - ], - "17DAP_pericarp;_pericarp_of_top_ear": [ - "17DAP_pericarp_1", - "17DAP_pericarp_2", - "17DAP_pericarp_3" - ], - "V5_stalk_below_tassel;_stalk_below_tassel_(2_cm)": [ - "V5_stalk_below_tassel_1", - "V5_stalk_below_tassel_2", - "V5_stalk_below_tassel_3" - ], - "V10_tassel;_top_10_cm_of_tassel_(~20_cm)": [ - "V10_tassel_1", - "V10_tassel_2", - "V10_tassel_3" - ], - "R1_leaf;_15_cm_tip_of_2nd_leaf_above_top_ear": [ - "R1_leaf_1", - "R1_leaf_2", - "R1_leaf_3" - ], - "V5_tassel;_tassel_3-5mm": [ - "V5_tassel_1", - "V5_tassel_2", - "V5_tassel_3" - ], - "31DAP_embryo;_embryo_of_top_ear": [ - "31DAP_embryo_1", - "31DAP_embryo_2", - "31DAP_embryo_3" - ], - "V8_V9_ear;_top_ear_3-5mm": [ - "V8_V9_ear_1", - "V8_V9_ear_2", - "V8_V9_ear_3" - ], - "V2_stalk;_stalk": [ - "V2_stalk_1", - "V2_stalk_2", - "V2_stalk_3" - ], - "V2_leaf;_actively_growing_leaf:_fourth_leaf": [ - "V2_leaf_1", - "V2_leaf_2", - "V2_leaf_3" - ], - "17DAP_leaf;_15_cm_tip_of_2nd_leaf_above_top_ear": [ - "17DAP_leaf_1", - "17DAP_leaf_2", - "17DAP_leaf_3" - ], - "R1_cob;_cob_of_top_ear": [ - "R1_cob_1", - "R1_cob_2", - "R1_cob_3" - ], - "V7_top_ear_shoot;_top_ear_shoot": [ - "V7_top_ear_shoot_1", - "V7_top_ear_shoot_2", - "V7_top_ear_shoot_3" - ], - "VT_anthers;_anther": [ - "VT_anthers_1", - "VT_anthers_2", - "VT_anthers_3" - ], - "5DAP_ovule;_ovule_of_top_ear": [ - "5DAP_ovule_1", - "5DAP_ovule_2", - "5DAP_ovule_3" - ], - "V16_floret;_top_ear_(5_cm)_floret": [ - "V16_floret_1", - "V16_floret_2", - "V16_floret_3" - ], - "V1_leaf;_1st_and_2nd_leaf": [ - "V1_leaf_1", - "V1_leaf_2", - "V1_leaf_3" - ], - "10DAP_leaf;_15_cm_tip_of_2nd_leaf_above_top_ear": [ - "10DAP_leaf_1", - "10DAP_leaf_2", - "10DAP_leaf_3" - ], - "R1_husk;_most_inner_husk_of_top_ear": [ - "R1_husk_1", - "R1_husk_2", - "R1_husk_3" - ], - "VE_leaf;_coleoptile": [ - "VE_leaf_1", - "VE_leaf_2", - "VE_leaf_3" - ], - "V2_seminal_root;_seminal_root": [ - "V2_seminal_root_1", - "V2_seminal_root_2", - "V2_seminal_root_3" - ], - "V16_silk;_top_ear_(5_cm)_silk": [ - "V16_silk_1", - "V16_silk_2", - "V16_silk_3" - ], - "V8_V9_tassel;_tassel_12-14_cm": [ - "V8_V9_tassel_1", - "V8_V9_tassel_2", - "V8_V9_tassel_3" - ], - "24DAP_root;_nodal_root": [ - "24DAP_root_1", - "24DAP_root_2", - "24DAP_root_3" - ], - "R1_ovule;_R1-ovule_of_top_ear": [ - "R1_ovule_1", - "R1_ovule_2", - "R1_ovule_3" - ], - "5DAP_cob;_cob_of_top_ear": [ - "5DAP_cob_1", - "5DAP_cob_2", - "5DAP_cob_3" - ], - "V7_tassel;_tassel_2_cm": [ - "V7_tassel_1", - "V7_tassel_2", - "V7_tassel_3" - ], - "V5_seminal_root;_seminal_root": [ - "V5_seminal_root_1", - "V5_seminal_root_2", - "V5_seminal_root_3" - ], - "V15_tassel;_spikelet_of_tassel_(~22_cm)": [ - "V15_tassel_1", - "V15_tassel_2", - "V15_tassel_3" - ], - "24DAP_pericarp;_pericarp_of_top_ear": [ - "24DAP_pericarp_1", - "24DAP_pericarp_2", - "24DAP_pericarp_3" - ], - "V10_ear;_top_ear_1-1.5_cm": [ - "V10_ear_1", - "V10_ear_2", - "V10_ear_3" - ], - "V5_leaf;_actively_growing_leaf:_eighth_leaf,_15_cm_including_tip": [ - "V5_leaf_1", - "V5_leaf_2", - "V5_leaf_3" - ], - "10DAP_endosperm;_endosperm_of_top_ear": [ - "10DAP_endosperm_1", - "10DAP_endosperm_2", - "10DAP_endosperm_3" - ], - "31DAP_leaf;_15_cm_tip_of_2nd_leaf_above_top_ear": [ - "31DAP_leaf_1", - "31DAP_leaf_2", - "31DAP_leaf_3" - ], - "R1_silk;_silk_of_top_ear": [ - "R1_silk_1", - "R1_silk_2", - "R1_silk_3" - ], - "V15_ear;_top_ear_3-3.5_cm": [ - "V15_ear_1", - "V15_ear_2", - "V15_ear_3" - ], - "17DAP_embryo;_embryo_of_top_ear": [ - "17DAP_embryo_1", - "17DAP_embryo_2", - "17DAP_embryo_3" - ], - "V5_nodal_root;_nodal_root": [ - "V5_nodal_root_1", - "V5_nodal_root_2", - "V5_nodal_root_3" - ], - "R1_root;_adult_nodal_root": [ - "R1_root_1", - "R1_root_2", - "R1_root_3" - ], - "V1_root;_seminal_root": [ - "V1_root_1", - "V1_root_2", - "V1_root_3" - ] - } - } - }, - "data_type": "Microarray" - }, - "Early_Seed": { - "database": "maize_early_seed", - "view_name": "Early_Seed", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "NU0": [ - "NU0" - ], - "NU4": [ - "NU4" - ], - "NU8": [ - "NU8" - ], - "NU12": [ - "NU12" - ], - "NU16": [ - "NU16" - ], - "NU20": [ - "NU20" - ], - "NU24": [ - "NU24" - ], - "NU28": [ - "NU28" - ], - "NU32": [ - "NU32" - ], - "NU36": [ - "NU36" - ], - "NU40": [ - "NU40" - ], - "NU44": [ - "NU44" - ], - "NU48": [ - "NU48" - ], - "NU52": [ - "NU52" - ], - "NU56": [ - "NU56" - ], - "NU60": [ - "NU60" - ], - "NU64": [ - "NU64" - ], - "NU68": [ - "NU68" - ], - "NU72": [ - "NU72" - ], - "NU78": [ - "NU78" - ], - "NU84": [ - "NU84" - ], - "NU90": [ - "NU90" - ], - "NU96": [ - "NU96" - ], - "NU102": [ - "NU102" - ], - "NU108": [ - "NU108" - ], - "NU114": [ - "NU114" - ], - "NU120": [ - "NU120" - ], - "NU126": [ - "NU126" - ], - "NU132": [ - "NU132" - ], - "NU138": [ - "NU138" - ], - "NU144": [ - "NU144" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Embryonic_Leaf_Development": { - "database": "maize_embryonic_leaf_development", - "view_name": "Embryonic_Leaf_Development", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Prepalisade_mesophylll": [ - "PM_JW04", - "PM_JW06" - ], - "Median_ground_meristem": [ - "mGM_JW07" - ], - "4BS+V-stage_PM": [ - "4PM_IZ11", - "4PM_IZ16", - "4PM_JX03" - ], - "3C-stage_PM": [ - "mGM_JW07" - ], - "3_contiguous_cells": [ - "mGM_JW07" - ], - "5/6BS+V-stage_PM": [ - "5_6PM_IZ13", - "5_6PM_IZ18B" - ], - "4_pre-bundle_sheath_cells_+_pre-vein_cells": [ - "4BS_V_IZ02", - "4BS_V_IZ06" - ], - "1_median_mesophyll_cell": [ - "1_M_IZ09", - "1_M_IZ14", - "1_M_JX01" - ], - "2_median_mesophyll_cells": [ - "2_M_IZ10", - "2_M_IZ15", - "2_M_JX02" - ], - "5_pre-bundle_sheath_cells_+_pre-vein_cells": [ - "5BS_V_IZ03", - "5BS_V_IZ07" - ], - "6_pre-bundle_sheath_cells_+_pre-vein": [ - "6BS_V_IZ04", - "6BS_V_IZ08" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Hoopes_et_al_Atlas": { - "database": "maize_buell_lab", - "view_name": "Hoopes_et_al_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Shoot_tip_V5": [ - "SK037__V5_Shoot_tip_R1", - "SK038__V5_Shoot_tip_R2", - "SK039__V5_Shoot_tip_R3" - ], - "Seed_2DAP": [ - "SK106__2DAP_Whole_seed_R1", - "SK107__2DAP_Whole_seed_R2", - "SK108__2DAP_Whole_seed_R3" - ], - "Meiotic_Tassel_V18": [ - "SK076__V18_Meiotic_tassel_R1", - "SK077__V18_Meiotic_tassel_R2", - "SK078__V18_Meiotic_tassel_R3" - ], - "Immature_Tassel_V13": [ - "SK073__V13_Immature_tassel_R1", - "SK074__V13_Immature_tassel_R2", - "SK075__V13_Immature_tassel_R3" - ], - "ThreeDAS-MZEZ": [ - "SS.27__Mz.Ez_3d_R2", - "SS.45__Mz.Ez_3d_R1", - "SS.56__Mz.Ez_3d_R3" - ], - "Internode_24DAP": [ - "PP_33__24_POL_INT_R1", - "PP_34__24_POL_INT_R2" - ], - "V13-BR-Node6": [ - "SS.69__BraceRoot_Node6_abvgrnd_V13_R1", - "SS.74__BraceRoot_Node6_abvgrnd_V13_R2", - "SS.76__BraceRoot_Node6_abvgrnd_V13_R3" - ], - "V7-CR-Nodes1-3": [ - "SS.70__CrownRoot_Nodes_1.3__V7_R1", - "SS.71__CrownRoot_Nodes_1.3__V7_R3" - ], - "Fourth_Internode_V9": [ - "SK058__V9_Fourth_elongated_internode_R1", - "SK059__V9_Fourth_elongated_internode_R2", - "SK060__V9_Fourth_elongated_internode_R3" - ], - "Coleoptile_6DAS_Primary_Root": [ - "SK007__6DAS_GH_Primary_Root_R1", - "SK008__6DAS_GH_Primary_Root_R2", - "SK009__6DAS_GH_Primary_Root_R3" - ], - "SevenDAS-PR-Z1": [ - "RA.2__TapRoot_Z1_7d_R2", - "RA.4__TapRoot_Z1_7d_R1", - "RA.5__TapRoot_Z1_7d_R3" - ], - "Pooled_Leaves_V1": [ - "SK019__V1_4D_PE_Pooled_Leaves_R1", - "SK020__V1_4D_PE_Pooled_Leaves_R2", - "SK021__V1_4D_PE_Pooled_Leaves_R3" - ], - "SevenDAS-PR-Z3": [ - "RA.14__TapRoot_Z3_7d_R1", - "RA.20__TapRoot_Z3_7d_R3", - "RA.21__TapRoot_Z3_7d_R2" - ], - "Immature_Leaf_V9": [ - "SK070__V9_Papery_Leaves_R1", - "SK071__V9_Papery_Leaves_R2", - "SK072__V9_Papery_Leaves_R3" - ], - "Seed_24DAP": [ - "SK172__24DAP_Whole_Seed_R1", - "SK173__24DAP_Whole_Seed_R2", - "SK174__24DAP_Whole_Seed_R3" - ], - "Silks_R1": [ - "SK088__R1_Silks_R1", - "SK089__R1_Silks_R2", - "SK090__R1_Silks_R3" - ], - "Endosperm_20DAP": [ - "SK157__20DAP_Endosperm_R1", - "SK158__20DAP_Endosperm_R2", - "SK159__20DAP_Endosperm_R3" - ], - "SevenDAS-PR-Z2": [ - "RA.15__TapRoot_Z2_7d_R3", - "RA.18__TapRoot_Z2_7d_R1", - "RA.3__TapRoot_Z2_7d_R2" - ], - "Tip_of_Stage_2_leaf_V7": [ - "SK052__V7_Tip_of_transition_leaf_R1", - "SK053__V7_Tip_of_transition_leaf_R2", - "SK054__V7_Tip_of_transition_leaf_R3" - ], - "ThreeDAS-CorticalParenchyma": [ - "RA.13__CortPar_3d_R2", - "RA.8__CortPar_3d_R3", - "RA.9__CortPar_3d_R1" - ], - "Tip_of_Stage_2_leaf_V5": [ - "SK043__V5_Tip_of_Stage_2_Leaf_R1", - "SK044__V5_Tip_of_Stage_2_Leaf_R2", - "SK045__V5_Tip_of_Stage_2_Leaf_R3" - ], - "Leaf_30DAP": [ - "PP.45__30_DAP_POL_LEAF_R1", - "PP.46__30_DAP_POL_LEAF_R2" - ], - "SevenDAS-RootSystem": [ - "SS.22__WholeRootSystem_7d_R2", - "SS.30__WholeRootSystem_7d_R1", - "SS.54__WholeRootSystem_7d_R3" - ], - "ThreeDAS-DZ": [ - "SS.21__DifferentiationZone_3d_R1", - "SS.28__DifferentiationZone_3d_R3", - "SS.61__DifferentiationZone_3d_R2" - ], - "Internode_18DAP": [ - "PP_25__18_POL_INT_R1", - "PP_26__18_POL_INT_R2" - ], - "Endosperm_12DAP": [ - "SK124__12DAP_Endopsperm_R1", - "SK125__12DAP_Endopsperm_R2", - "SK126__12DAP_Endopsperm_R3" - ], - "Seed_16DAP": [ - "SK133__16DAP_Whole_seed_R1", - "SK134__16DAP_Whole_seed_R2", - "SK135__16DAP_Whole_seed_R3" - ], - "Thirteenth_Leaf_R2": [ - "SK097__R2_Thirteenth_Leaf_R1", - "SK098__R2_Thirteenth_Leaf_R2", - "SK099__R2_Thirteenth_Leaf_R3" - ], - "Endosperm_22DAP": [ - "SK166__22DAP_Endosperm_R1", - "SK167__22DAP_Endosperm_R2", - "SK168__22DAP_Endosperm_R3" - ], - "Leaf_6DAP": [ - "PP.14__6_DAP_POL_LEAF_R2" - ], - "Eleventh_Leaf_V9": [ - "SK064__V9_Eleventh_Leaf_R1", - "SK065__V9_Eleventh_Leaf_R2", - "SK066__V9_Eleventh_Leaf_R3" - ], - "Endosperm_16DAP": [ - "SK136__16DAP_Endosperm_R1", - "SK137__16DAP_Endosperm_R2", - "SK138__16DAP_Endosperm_R3" - ], - "Seed_22DAP": [ - "SK163__22DAP_Whole_Seed_R1", - "SK164__22DAP_Whole_Seed_R2", - "SK165__22DAP_Whole_Seed_R3" - ], - "Base_of_Stage_2_leaf_V5": [ - "SK046__V5_Bottom_of_transition_leaf_R1", - "SK047__V5_Bottom_of_transition_leaf_R2", - "SK048__V5_Bottom_of_transition_leaf_R3" - ], - "Prepollination_Cob_R1": [ - "SK085__R1_Pre_pollination_cob_R1", - "SK086__R1_Pre_pollination_cob_R2", - "SK087__R1_Pre_pollination_cob_R3" - ], - "Seed_8DAP": [ - "SK115__8DAP_Whole_Seed_R1", - "SK116__8DAP_Whole_Seed_R2", - "SK117__8DAP_Whole_Seed_R3" - ], - "V13-CR-Node5": [ - "SS.68__CrownRoot_Node5_V13_R1", - "SS.75__CrownRoot_Node5_V13_R3", - "SS.77__CrownRoot_Node5_V13_R2" - ], - "Topmost_Leaf_V3": [ - "SK034__V3_Topmost_leaf_R1", - "SK035__V3_Topmost_leaf_R2", - "SK036__V3_Topmost_leaf_R3" - ], - "Thirteenth_Leaf_V9": [ - "SK067__V9_Thirteenth_Leaf_R1", - "SK068__V9_Thirteenth_Leaf_R2", - "SK069__V9_Thirteenth_Leaf_R3" - ], - "Endosperm_24DAP": [ - "SK175__24DAP_Endosperm_R1", - "SK176__24DAP_Endosperm_R2", - "SK177__24DAP_Endosperm_R3" - ], - "Anthers_R1": [ - "SK091__R1_Anthers_R1", - "SK092__R1_Anthers_R2", - "SK093__R1_Anthers_R3" - ], - "Base_of_Stage_2_leaf_V7": [ - "SK055__V7_Bottom_of_transition_leaf_R1", - "SK056__V7_Bottom_of_transition_leaf_R2", - "SK057__V7_Bottom_of_transition_leaf_R3" - ], - "Coleoptile_6DAS_GH": [ - "SK004__6_DAS_GH_Coleoptile_R1", - "SK005__6_DAS_GH_Coleoptile_R2", - "SK006__6_DAS_GH_Coleoptile_R3" - ], - "Embryo_20DAP": [ - "SK160__20DAP_Embryo_R1", - "SK161__20DAP_Embryo_R2", - "SK162__20DAP_Embryo_R3" - ], - "Immature_Cob_V18": [ - "SK079__V18_Immature_cob_R1", - "SK080__V18_Immature_cob_R2", - "SK081__V18_Immature_cob_R3" - ], - "Seed_12DAP": [ - "SK121__12DAP_Whole_seed_R1", - "SK122__12DAP_Whole_seed_R2", - "SK123__12DAP_Whole_seed_R3" - ], - "Seed_20DAP": [ - "SK154__20DAP_Whole_Seed_R1", - "SK155__20DAP_Whole_Seed_R2", - "SK156__20DAP_Whole_Seed_R3" - ], - "Pericarp_18DAP": [ - "SK151__18DAP_Pericarp_R1", - "SK152__18DAP_Pericarp_R2", - "SK153__18DAP_Pericarp_R3" - ], - "SevenDAS-PR-Z4": [ - "RA.10__TapRoot_Z4_7d_R2", - "RA.22__TapRoot_Z4_7d_R3", - "RA.23__TapRoot_Z4_7d_R1" - ], - "ThreeDAS-PrimaryRoot": [ - "SS.38__WholeRootSystem_3d_R3", - "SS.39__WholeRootSystem_3d_R1", - "SS.40__WholeRootSystem_3d_R2" - ], - "Seed_18DAP": [ - "SK142__18DAP_Whole_Seed_R1", - "SK144__18DAP_Whole_Seed_R3", - "SK147__18DAP_Whole_Seed_R2" - ], - "Thirteenth_Leaf_VT": [ - "SK082__VT_Thirteenth_Leaf_R1", - "SK083__VT_Thirteenth_Leaf_R2", - "SK084__VT_Thirteenth_Leaf_R3" - ], - "Internode_12DAP": [ - "PP_17__12_POL_INT_R1", - "PP_18__12_POL_INT_R2" - ], - "SevenDAS-SeminalRoots": [ - "SS.25__Seminal_7d_R3", - "SS.44__Seminal_7d_R1" - ], - "Endosperm_18DAP": [ - "SK143__18DAP_Endosperm_R3", - "SK145__18DAP_Endosperm_R1", - "SK146__18DAP_Endosperm_R2" - ], - "SevenDAS-PrimaryRoot": [ - "SS.36__WholePrimaryRoot_7d_R3", - "SS.42__WholePrimaryRoot_7d_R2", - "SS.58__WholePrimaryRoot_7d_R1" - ], - "Internode_6DAP": [ - "PP_10__6_POL_INT_R2", - "PP_9__6_POL_INT_R1" - ], - "ThreeDAS-Stele": [ - "RA.17__Stele_3d_R1", - "RA.6__Stele_3d_R3", - "RA.7__Stele_3d_R2" - ], - "Embryo_16DAP": [ - "SK139__16DAP_Embryo_R1", - "SK140__16DAP_Embryo_R2", - "SK141__16DAP_Embryo_R3" - ], - "Eighth_Leaf_V9": [ - "SK061__V9_Eighth_Leaf_R1", - "SK062__V9_Eighth_Leaf_R2", - "SK063__V9_Eighth_Leaf_R3" - ], - "First_Internode_V5": [ - "SK040__V5_First_elongated_internode_R1", - "SK041__V5_First_elongated_internode_R2", - "SK042__V5_First_elongated_internode_R3" - ], - "Seed_14DAP": [ - "SK127__14DAP_Whole_seed_R1", - "SK128__14DAP_Whole_seed_R2", - "SK129__14DAP_Whole_seed_R3" - ], - "Embryo_24DAP": [ - "SK178__24DAP_Embryo_R1", - "SK179__24DAP_Embryo_R2", - "SK180__24DAP_Embryo_R3" - ], - "Stem_and_SAM_V1": [ - "SK022__V1_4D_PE_Stem_plus_SAM_R1", - "SK023__V1_4D_PE_Stem_plus_SAM_R2", - "SK024__V1_4D_PE_Stem_plus_SAM_R3" - ], - "Stem_and_SAM_V3": [ - "SK028__V3_Stem_and_SAM_R1", - "SK029_2__V3_Stem_and_SAM_R2", - "SK030_2__V3_Stem_and_SAM_R3" - ], - "V7-CR-Node5": [ - "RA.35__CrownRoot_Node5_V7_R1", - "SS.78__CrownRoot_Node5_V7_R2" - ], - "V7-CR-Node4": [ - "SS.65__CrownRoot_Node4_V7_R1", - "SS.66__CrownRoot_Node4_V7_R2", - "SS.73__CrownRoot_Node4_V7_R3" - ], - "Seed_6DAP": [ - "SK112__6DAP_Whole_seed_R1", - "SK113__6DAP_Whole_seed_R2", - "SK114__6DAP_Whole_seed_R3" - ], - "Leaf_18DAP": [ - "PP.29__18_DAP_POL_LEAF_R1", - "PP.30__18_DAP_POL_LEAF_R2" - ], - "Internode_0DAP": [ - "PP1__0_POL_INT_R1", - "PP_2___0_POL_INT_R2" - ], - "Seed_4DAP": [ - "SK109__4DAP_Whole_Seed_R1", - "SK110__4DAP_Whole_Seed_R2", - "SK111__4DAP_Whole_Seed_R3" - ], - "Leaf_24DAP": [ - "PP.37__24_DAP_POL_LEAF_R1", - "PP.38__24_DAP_POL_LEAF_R2" - ], - "Endosperm_14DAP": [ - "SK130__14DAP_Endopsperm_R1", - "SK131__14DAP_Endopsperm_R2", - "SK132__14DAP_Endopsperm_R3" - ], - "Internode_30DAP": [ - "PP_41__30_POL_INT_R1", - "PP_42__30_POL_INT_R2" - ], - "Embryo_18DAP": [ - "SK148__18DAP_Embryo_R1", - "SK149__18DAP_Embryo_R2", - "SK150__18DAP_Embryo_R3" - ], - "Seed_10DAP": [ - "SK118__10DAP_Whole_seed_R1", - "SK119__10DAP_Whole_seed_R2", - "SK120__10DAP_Whole_seed_R3" - ], - "Leaf_12DAP": [ - "PP.21__12_DAP_POL_LEAF_R1", - "PP.22__12_DAP_POL_LEAF_R2" - ], - "Embryo_22DAP": [ - "SK169__22DAP_Embryo_R1", - "SK170__22DAP_Embryo_R2", - "SK171__22DAP_Embryo_R3" - ], - "Leaf_0DAP": [ - "PP.5__0_DAP_POL_LEAF_R1", - "PP.6__0_DAP_POL_LEAF_R2" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Hoopes_et_al_Stress": { - "database": "maize_buell_lab", - "view_name": "Hoopes_et_al_Stress", - "groups": { - "htcld_ctrl_R1;htcld_ctrl_R2;htcld_ctrl_R3": { - "controls": [ - "htcld_ctrl_R1", - "htcld_ctrl_R2", - "htcld_ctrl_R3" - ], - "treatments": { - "TemperatureStress-Control": [ - "htcld_ctrl_R1", - "htcld_ctrl_R2", - "htcld_ctrl_R3" - ], - "TemperatureStress-Cold": [ - "cold_R1", - "cold_R2", - "cold_R3" - ], - "TemperatureStress-Heat": [ - "heat_R1", - "heat_R2", - "heat_R3" - ] - } - }, - "alb_ctrl_R1;alb_ctrl_R2;alb_ctrl_R3": { - "controls": [ - "alb_ctrl_R1", - "alb_ctrl_R2", - "alb_ctrl_R3" - ], - "treatments": { - "C_graminicola-48hpi": [ - "alb_48h_R2", - "alb_48h_R3" - ], - "C_graminicola-24hpi": [ - "alb_24h_R2", - "alb_24h_R3" - ], - "C_graminicola-0hpi": [ - "alb_ctrl_R1", - "alb_ctrl_R2", - "alb_ctrl_R3" - ] - } - }, - "drght_ctrl_6h_R1;drght_ctrl_6h_R2;drght_ctrl_6h_R3;drght_ctrl_6h_R4": { - "controls": [ - "drght_ctrl_6h_R1", - "drght_ctrl_6h_R2", - "drght_ctrl_6h_R3", - "drght_ctrl_6h_R4" - ], - "treatments": { - "DroughtStress-0MPa-6h": [ - "drght_ctrl_6h_R1", - "drght_ctrl_6h_R2", - "drght_ctrl_6h_R3", - "drght_ctrl_6h_R4" - ], - "DroughtStress-LowMPa-6h": [ - "drght_0.2_6h_R1", - "drght_0.2_6h_R2", - "drght_0.2_6h_R3", - "drght_0.2_6h_R4" - ], - "DroughtStress-VeryLowMPa-6h": [ - "drght_0.8_6h_R1", - "drght_0.8_6h_R2", - "drght_0.8_6h_R3", - "drght_0.8_6h_R4" - ] - } - }, - "gls_us_ctrl_R1;gls_us_ctrl_R2;gls_us_ctrl_R3": { - "controls": [ - "gls_us_ctrl_R1", - "gls_us_ctrl_R2", - "gls_us_ctrl_R3" - ], - "treatments": { - "C_zeina-UpperLeaves": [ - "gls_us_ctrl_R1", - "gls_us_ctrl_R2", - "gls_us_ctrl_R3" - ], - "C_zeina-LowerLeaves": [ - "gls_us_R1", - "gls_us_R2", - "gls_us_R3" - ] - } - }, - "drght_ctrl_24h_R1;drght_ctrl_24h_R2;drght_ctrl_24h_R3;drght_ctrl_24h_R4": { - "controls": [ - "drght_ctrl_24h_R1", - "drght_ctrl_24h_R2", - "drght_ctrl_24h_R3", - "drght_ctrl_24h_R4" - ], - "treatments": { - "DroughtStress-VeryLowMPa-24h": [ - "drght_0.8_24h_R1", - "drght_0.8_24h_R2", - "drght_0.8_24h_R3", - "drght_0.8_24h_R4" - ], - "DroughtStress-LowMPa-24h": [ - "drght_0.2_24h_R1", - "drght_0.2_24h_R2", - "drght_0.2_24h_R3", - "drght_0.2_24h_R4" - ], - "DroughtStress-0MPa-24h": [ - "drght_ctrl_24h_R1", - "drght_ctrl_24h_R2", - "drght_ctrl_24h_R3", - "drght_ctrl_24h_R4" - ] - } - }, - "slt_ctrl_R1;slt_ctrl_R2;slt_ctrl_R3": { - "controls": [ - "slt_ctrl_R1", - "slt_ctrl_R2", - "slt_ctrl_R3" - ], - "treatments": { - "SaltStress-0mM": [ - "slt_ctrl_R1", - "slt_ctrl_R2", - "slt_ctrl_R3" - ], - "SaltStress-200mM": [ - "slt_R1", - "slt_R2", - "slt_R3" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Maize_Kernel": { - "database": "maize_early_seed", - "view_name": "Maize_Kernel", - "groups": { - "Med_CTRL_WIDIEZ": { - "controls": [ - "Med_CTRL_WIDIEZ" - ], - "treatments": { - "Apical_scutellum": [ - "AS_1", - "AS_2", - "AS_3", - "AS_4" - ], - "Endosperm": [ - "End_1", - "End_2", - "End_3", - "End_4" - ], - "Scutellar_Alleurone_Layer": [ - "SAL_1", - "SAL_2", - "SAL_3", - "SAL_4" - ], - "Embryo": [ - "Emb_1", - "Emb_2", - "Emb_3", - "Emb_4" - ], - "Endosperm_Adjacent_to_Scutellum": [ - "EAS_1", - "EAS_2", - "EAS_3", - "EAS_4" - ], - "Pericarp": [ - "Per_1", - "Per_2", - "Per_3", - "Per_4" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Maize_Root": { - "database": "maize_root", - "view_name": "Maize_Root", - "groups": { - "CTRL_med": { - "controls": [ - "CTRL_med" - ], - "treatments": { - "Meristematic_zone_": [ - "Meristematic_zone_(control):_mean_RPKM" - ], - "Primary_root": [ - "Primary_root_FPKM" - ], - "Elongation_zone": [ - "Elongation_zone_(control):_mean_RPKM" - ], - "Root_hairs": [ - "Root_hair_FPKM" - ], - "Seminal_roots": [ - "Seminal_root_FPKM" - ], - "Crown_roots": [ - "Crown_root_FPKM" - ], - "Cortex": [ - "Cortex_(control):_mean_RPKM" - ], - "Root_hairless_root": [ - "root_FPKM" - ], - "Stele": [ - "Stele_(control):_mean_RPKM" - ] - } - }, - "6h_control:_mean_RPKM": { - "controls": [ - "6h_control:_mean_RPKM" - ], - "treatments": { - "Drought_6_hour_at_-0.2_MPA": [ - "6h_-0.2_MPa_(mild_stress):_mean_RPKM" - ], - "Drought_6_hr_control": [ - "6h_control:_mean_RPKM" - ], - "Drought_6_hour_at_-0.8_MPa": [ - "6h_-0.8_MPa_(severe_stress):_mean_RPKM" - ] - } - }, - "24h_control:_mean_RPKM": { - "controls": [ - "24h_control:_mean_RPKM" - ], - "treatments": { - "Drought_24_hr_control": [ - "24h_control:_mean_RPKM" - ], - "Drought_24_hr_-0.2_MPa": [ - "24h_-0.2_MPa_(mild_stress):_mean_RPKM" - ], - "Drought_24_hr_at_-0.8_MPa": [ - "24h_-0.8_MPa_(severe_stress):_mean_RPKM" - ] - } - } - }, - "data_type": "Unknown" - }, - "Sekhon_et_al_Atlas": { - "database": "maize_RMA_linear", - "view_name": "Sekhon_et_al_Atlas", - "groups": { - "Maize_-_Kaeppler": { - "controls": [ - "MAIZE_CTRL" - ], - "treatments": { - "Germinating_Seed_24h._PO:0009001_kernel;_PO:imbibition.": [ - "24H_Germinating Seed_R1", - "24H_Germinating Seed_R2", - "24H_Germinating Seed_R3" - ], - "Coleoptile_6DAS_GH._PO:0025287_seedling_coleoptile;_PO:0007045_coleoptile_emergence.": [ - "6DAS_GH_Coleoptile_R1", - "6DAS_GH_Coleoptile_R2", - "6DAS_GH_Coleoptile_R3" - ], - "Coleoptile_6DAS_Primary_Root._PO:0020127_primary_root;_PO:0007015_radical_emergence.": [ - "6DAS_GH_Primary Root_R1", - "6DAS_GH_Primary Root_R2", - "6DAS_GH_Primary Root_R3" - ], - "Stem_and_SAM_(V1)._PO:0020142_stem_internode;_PO:0020148_shoot_apical_meristem;_PO:0007106_LP.03_three_leaves_visible.": [ - "V1_Stem and SAM_R1", - "V1_Stem and SAM_R2", - "V1_Stem and SAM_R3" - ], - "Stem_and_SAM_(V3)._PO:0020142_stem_internode;_PO:0020148_shoot_apical_meristem;_PO:0007065_LP.05_five_leaves_visible.": [ - "V3_Stem and SAM_R1", - "V3_Stem and SAM_R2", - "V3_Stem and SAM_R3" - ], - "Stem_and_SAM_(V4)._PO:0020148_shoot_apical_meristem;_PO:0020142_internode;_PO:0007123_leaves_visible.": [ - "V4_Stem and SAM_R1", - "V4_Stem and SAM_R2", - "V4_Stem and SAM_R3" - ], - "Shoot_tip_(V5)._PO:0000037_shoot_apex;_PO:0009025_vascular_PO:0006340_adult_leaf;_PO:0001052_2_leaf_expansion_stage;_PO:0020040_leaf_PO:0020104_leaf_sheath;_PO:0007063_LP.07_7_leaves_visible.": [ - "V5_Shoot Tip_R1", - "V5_Shoot Tip_R2", - "V5_Shoot Tip_R3" - ], - "First_Internode_(V5)._PO:0020142_stem_internode;_PO:0021004_inflorescence_initiation_stage;_PO:0007063_seven_leaves_visible.": [ - "V5_First Internode_R1", - "V5_First Internode_R2", - "V5_First Internode_R3" - ], - "First_Internode_(V7)._PO:0020142_stem_internode;_PO:0021004_inflorescence_initiation_stage;_PO:0007101_LP.09_nine_leaves_visible": [ - "V7_First Internode_R1", - "V7_First Internode_R2", - "V7_First Internode_R3" - ], - "Fourth_Internode_(V9)._PO:0020142_stem_internode;_PO:0001083_inflorescence_development_stages;_PO:0007116_LP.11_eleven_leaves_visible.": [ - "V9_Fourth Internode_R1", - "V9_Fourth Internode_R2", - "V9_Fourth Internode_R3" - ], - "Immature_Tassel_(V13)._PO:0020126_tassel;_PO:0001007_pollen_developmental_stages;_PO:0007104_LP.15_fifteen_leaves_visible.": [ - "V13_Immature Tassel_R1", - "V13_Immature Tassel_R2", - "V13_Immature Tassel_R3" - ], - "Meiotic_Tassel_(V18)._PO:0020126_tassel;_PO:0001009_D_pollen_mother_cell_meiosis_stage;_PO:0007072_LP.18_eighteen_leaves_visible.": [ - "V18_Meiotic Tassel_R1", - "V18_Meiotic Tassel_R2", - "V18_Meiotic Tassel_R3" - ], - "Anthers_(R1)._PO:0006310_tassel_floret;_PO:0009066_anther;_PO:0001007_pollen_developmental_stages.": [ - "R1_Anthers_R1", - "R1_Anthers_R2", - "R1_Anthers_R3" - ], - "Whole_Seedling_(VE)._PO:0006341_primary_shoot;_PO:0007094_LP.01_one_leaf_visible.": [ - "VE_Whole Seedling_R1", - "VE_Whole Seedling_R2", - "VE_Whole Seedling_R3" - ], - "Primary_Root_(VE)._PO:0020127_primary_root;_PO:0007112_1_main_shoot_growth.": [ - "VE_Primary Root_R1", - "VE_Primary Root_R2", - "VE_Primary Root_R3" - ], - "Pooled_Leaves_(V1)._PO:0006339_juvenile_leaf;_PO:0009025_vascular_leaf;_PO:0001052_2_leaf_expansion_stage;_PO:0001053_3_leaf_fully_expanded;_PO:0007106_LP.03_three_leaves_visible.": [ - "V1_Pooled Leaves_R1", - "V1_Pooled Leaves_R2", - "V1_Pooled Leaves_R3" - ], - "Primary_Root_(V1)._PO:0020127_primary_root;_PO:0007106_LP.03_three_leaves_visible.": [ - "V1_GH_Primary Root_R1", - "V1_GH_Primary Root_R2", - "V1_GH_Primary Root_R3" - ], - "Topmost_Leaf_(V3)._PO:0006339_juvenile_leaf;_PO:0009025_vascular_leaf;_PO:0001052_2_leaf_expansion_stage;_PO:0007065_LP.05_five_leaves_visible.": [ - "V3_Topmost Leaf_R1", - "V3_Topmost Leaf_R2", - "V3_Topmost Leaf_R3" - ], - "First_Leaf_(V3)._PO:0006339_juvenile_leaf;_PO:0009025_vascular_leaf;_PO:0001053_3_leaf_fully_expanded;_PO:0007065_LP.05_five_leaves_visible.": [ - "V3_First Leaf and Sheath_R1", - "V3_First Leaf and Sheath_R2", - "V3_First Leaf and Sheath_R3" - ], - "Tip_of_Stage_2_leaf_(V5)._PO:0006339_juvenile_leaf;_PO:0008018_transition_leaf;_PO:0009025_vascular_leaf;_PO:0025142_leaf_tip;_PO:0001052_2_leaf_expansion_stage;_PO:0007063_LP.07_seven_leaves_visible.": [ - "V5_Tip of stage-2 Leaf_R1", - "V5_Tip of stage-2 Leaf_R2", - "V5_Tip of stage-2 Leaf_R3" - ], - "Base_of_Stage_2_leaf_(V5)._PO:0006340_adult_leaf;_PO:0008018_transition_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001052_2_leaf_expansion_stage;_PO:0007063_LP.07_seven_leaves_visible.": [ - "V5_Base of stage-2 Leaf_R1", - "V5_Base of stage-2 Leaf_R2", - "V5_Base of stage-2 Leaf_R3" - ], - "Tip_of_Stage_2_leaf_(V7)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0025142_leaf_tip;_PO:0001052_2_leaf_expansion_stage;_PO:0007101_LP.09_nine_leaves_visible.": [ - "V7_Tip of stage-2 Leaf_R1", - "V7_Tip of stage-2 Leaf_R2", - "V7_Tip of stage-2 Leaf_R3" - ], - "Base_of_Stage_2_leaf_(V7)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001052_2_leaf_expansion_stage;_PO:0007101_LP.09_nine_leaves_visible.": [ - "V7_Base of stage-2 Leaf_R1", - "V7_Base of stage-2 Leaf_R2", - "V7_Base of stage-2 Leaf_R3" - ], - "Eighth_Leaf_(V9)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0001053_3_leaf_fully_expanded;_PO:0007116_LP.11_eleven_leaves_visible.": [ - "V9_Eighth Leaf_R1", - "V9_Eighth Leaf_R2", - "V9_Eighth Leaf_R3" - ], - "Eleventh_Leaf_(V9)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0001052_2_leaf_expansion_stage;_PO:0007116_LP.11_eleven_leaves_visible.": [ - "V9_Eleventh Leaf_R1", - "V9_Eleventh Leaf_R2", - "V9_Eleventh Leaf_R3" - ], - "Thirteenth_Leaf_(V9)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001052_2_leaf_expansion_stage;_PO:0007116_LP.11_eleven_leaves_visible.": [ - "V9_Thirteenth Leaf_R1", - "V9_Thirteenth Leaf_R2", - "V9_Thirteenth Leaf_R3" - ], - "Immature_Leaf_(V9)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0001052_2_leaf_expansion_stage;_PO:0007116_LP.11_eleven_leaves_visible.": [ - "V9_Immature Leaves_R1", - "V9_Immature Leaves_R2", - "V9_Immature Leaves_R3" - ], - "Thirteenth_Leaf_(VT)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001053_3_leaf_fully_expanded;_PO:0007003_IL.03_full_inflorescence_length_reached;_PO:0007072_LP.18_eighteen_leaves_visible.": [ - "VT_Thirteenth Leaf_R1", - "VT_Thirteenth Leaf_R2", - "VT_Thirteenth Leaf_R3" - ], - "Immature_Cob_(V18)._PO:0006505_central_spike_of_ear;_PO:0007006_IL.00_inflorescence_just_visible;_PO:0007072_LP.18_eighteen_leaves_visible.": [ - "V18_Immature Cob_R1", - "V18_Immature Cob_R2", - "V18_Immature Cob_R3" - ], - "Pre-pollination_Cob_(R1)._PO:0006505_central_spike_of_ear;_PO:0007016_4_flowering": [ - "R1_Pre-pollination Cob_R1", - "R1_Pre-pollination Cob_R2", - "R1_Pre-pollination Cob_R3" - ], - "Silks_(R1)._PO:0006354_ear_floret;_PO:0009074_style;_PO:0007016_4_flowering.": [ - "R1_Silks_R1", - "R1_Silks_R2", - "R1_Silks_R3" - ], - "Thirteenth_Leaf_(R2)._PO:0006340_adult_leaf;_PO:0009025_vascular_leaf;_PO:0020040_leaf_base;_PO:0001053_3_leaf_fully_expanded;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ - "R2_Thirteenth Leaf_R1", - "R2_Thirteenth Leaf_R2", - "R2_Thirteenth Leaf_R3" - ], - "Innermost_Husk_(R1)._PO:0009054_inflorescence_bract;_PO:0020136_Zea_ear;_PO:0007026_FL.00_first_flower(s)_open.": [ - "R1_Innermost Husk_R1", - "R1_Innermost Husk_R2", - "R1_Innermost Husk_R3" - ], - "Innermost_Husk_(R2)._PO:0009054_inflorescence_bract;_PO:0020136_Zea_ear;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ - "R2_Innermost Husk_R1", - "R2_Innermost Husk_R2", - "R2_Innermost Husk_R3" - ], - "Outer_Husk_(R2)._PO:0009054_inflorescence_bract;_PO:0020136_Zea_ear;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ - "R2_Outer Husk_R1", - "R2_Outer Husk_R2", - "R2_Outer Husk_R3" - ], - "Embryo_16DAP._PO:0009009_plant_embryo;_PO:0001095_true_leaf_formation;_PO:0007001_FR.01_early_stage_of_fruit_ripening.": [ - "16DAP_Embryo_R1", - "16DAP_Embryo_R2", - "16DAP_Embryo_R3" - ], - "Embryo_18DAP._PO:0009009_plant_embryo;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening.": [ - "18DAP_Embryo_R1", - "18DAP_Embryo_R2", - "18DAP_Embryo_R3" - ], - "Embryo_20DAP._PO:0009009_plant_embryo;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening.": [ - "20DAP_Embryo_R1", - "20DAP_Embryo_R2", - "20DAP_Embryo_R3" - ], - "Embryo_22DAP._PO:0009009_plant_embryo;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening.": [ - "22DAP_Embryo_R1", - "22DAP_Embryo_R2", - "22DAP_Embryo_R3" - ], - "Embryo_24DAP._PO:0009009_plant_embryo;_PO:0001095_true_leaf_formation;_PO:0007031_FR.02_mid_stage_of_fruit_ripening.": [ - "24DAP_Embryo_R1", - "24DAP_Embryo_R2", - "24DAP_Embryo_R3" - ], - "Endosperm_12DAP._PO:0009089_endosperm;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "12DAP_Endosperm_R1", - "12DAP_Endosperm_R2", - "12DAP_Endosperm_R3" - ], - "Endosperm_14DAP._PO:0009089_endosperm;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "14DAP_Endosperm_R1", - "14DAP_Endosperm_R2", - "14DAP_Endosperm_R3" - ], - "Endosperm_16DAP._PO:0009089_endosperm;_PO:0007001_FR.01_early_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "16DAP_Endosperm_R1", - "16DAP_Endosperm_R2", - "16DAP_Endosperm_R3" - ], - "Endosperm_18DAP._PO:0009089_endosperm;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "18DAP_Endosperm_R1", - "18DAP_Endosperm_R2", - "18DAP_Endosperm_R3" - ], - "Endosperm_20DAP._PO:0009089_endosperm;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "20DAP_Endosperm_R1", - "20DAP_Endosperm_R2", - "20DAP_Endosperm_R3" - ], - "Endosperm_22DAP._PO:0009089_endosperm;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "22DAP_Endosperm_R1", - "22DAP_Endosperm_R2", - "22DAP_Endosperm_R3" - ], - "Endosperm_24DAP._PO:0009089_endosperm;_PO:0007031_FR.02_mid_stage_of_fruit_ripening;_PO:0007633_endosperm_development_stages.": [ - "24DAP_Endosperm_R1", - "24DAP_Endosperm_R2", - "24DAP_Endosperm_R3" - ], - "Seed_2DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation.": [ - "2DAP_Whole Seed_R1", - "2DAP_Whole Seed_R2", - "2DAP_Whole Seed_R3" - ], - "Seed_4DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation.": [ - "4DAP_Whole Seed_R1", - "4DAP_Whole Seed_R2", - "4DAP_Whole Seed_R3" - ], - "Seed_6DAP._PO:0009001_fruit;_PO:0001180_B_proembryo_stage;_PO:0007042_5_fruit_formation;_PO:0007633_endosperm_development_stages.": [ - "6DAP_Whole Seed_R1", - "6DAP_Whole Seed_R2", - 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- } - }, - "Stem": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Stem": [ - "Stem_rep1", - "Stem_rep2", - "Stem_rep3" - ] - } - }, - "Leaf_with_Petiolules": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Leaf_with_Petiolules": [ - "Leaf_rep1", - "Leaf_rep2", - "Leaf_rep3" - ] - } - }, - "Root": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Root": [ - "Root_rep1", - "Root_rep2", - "Root_rep3" - ] - } - }, - "Non-inoculated_root": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Non-inoculated_root": [ - "Root0d_rep1", - "Root0d_rep2", - "Root0d_rep3" - ] - } - } - }, - "data_type": "Microarray" - }, - "medicago_rma": { - "database": "medicago_rma", - "view_name": "medicago_rma", - "groups": { - "Seed": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Seed_10d": [ - "Seed10d_rep1", - "Seed10d_rep2", - "Seed10d_rep3" - ], - "Seed_12d": [ - "Seed12d_rep1", - "Seed12d_rep2", 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- } - }, - "Vegetative_Bud": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Vegetative_Bud": [ - "Vegetative Bud_rep1", - "Vegetative Bud_rep2", - "Vegetative Bud_rep3" - ] - } - }, - "Petiole": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Petiole": [ - "Petiole_rep1", - "Petiole_rep2", - "Petiole_rep3" - ] - } - }, - "Stem": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Stem": [ - "Stem_rep1", - "Stem_rep2", - "Stem_rep3" - ] - } - }, - "Leaf_with_Petiolules": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Leaf_with_Petiolules": [ - "Leaf_rep1", - "Leaf_rep2", - "Leaf_rep3" - ] - } - }, - "Root": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Root": [ - "Root_rep1", - "Root_rep2", - "Root_rep3" - ] - } - }, - "Non-inoculated_root": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Non-inoculated_root": [ - "Root0d_rep1", - "Root0d_rep2", - 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"InflorescenceP6_Rep3" - ] - } - }, - "Seed": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Seed_S1": [ - "Seed_S1_Rep1", - "Seed_S1_Rep2", - "Seed_S1_Rep3" - ], - "Seed_S2": [ - "Seed_S2_Rep1", - "Seed_S2_Rep2", - "Seed_S2_Rep3" - ], - "Seed_S3": [ - "Seed_S3_Rep1", - "Seed_S3_Rep2", - "Seed_S3_Rep3" - ], - "Seed_S4": [ - "Seed_S4_Rep1", - "Seed_S4_Rep2", - "Seed_S4_Rep3" - ], - "Seed_S5": [ - "Seed_S5_Rep1", - "Seed_S5_Rep2", - "Seed_S5_Rep3" - ] - } - } - }, - "data_type": "Microarray" - }, - "riceanoxia_mas": { - "database": "rice_mas", - "view_name": "riceanoxia_mas", - "groups": { - "Aerobic_Coleoptile": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Aerobic_coleoptile": [ - "Aerobic_coleoptile_Rep1", - "Aerobic_coleoptile_Rep2" - ], - "Anoxic_coleoptile": [ - "Anoxic_coleoptile_Rep1", - "Anoxic_coleoptile_Rep2" - ] - } - } - }, - "data_type": "Microarray" - }, - "riceanoxia_rma": { - "database": "rice_rma", - "view_name": "riceanoxia_rma", - "groups": { - "Coleoptile": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Aerobic_coleoptile": [ - "Aerobic_coleoptile_Rep1", - "Aerobic_coleoptile_Rep2" - ], - "Anoxic_coleptile": [ - "Anoxic_coleoptile_Rep1", - "Anoxic_coleoptile_Rep2" - ] - } - } - }, - "data_type": "Microarray" - }, - "ricestigma_mas": { - "database": "rice_mas", - "view_name": "ricestigma_mas", - "groups": { - "Stigma": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Stigma": [ - "Stigma_Rep1", - "Stigma_Rep2", - "Stigma_Rep3" - ] - } - }, - "Ovary": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Ovary": [ - "Ovary_Rep1", - "Ovary_Rep2", - "Ovary_Rep3" - ] - } - }, - "SuspensionCell": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Suspension_Cell": [ - "SuspensionCell_Rep1" - ] - } - }, - "Shoot": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Shoot": [ - "Shoot_Rep1" - ] - } - }, - "Root": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Root": [ - "Root_Rep1" - ] - } - }, - "Anther": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Anther": [ - "Anther_Rep1" - ] - } - }, - "Embryo": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Embryo": [ - "Embryo_Rep1" - ] - } - }, - "Endosperm": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Endosperm": [ - "Endosperm_Rep1" - ] - } - }, - "5d-seed": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "5d-seed": [ - "5d-seed_Rep1" - ] - } - } - }, - "data_type": "Microarray" - }, - "ricestigma_rma": { - "database": "rice_rma", - "view_name": "ricestigma_rma", - "groups": { - "Stigma": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Stigma": [ - "Stigma_Rep1", - "Stigma_Rep2", - "Stigma_Rep3" - ] - } - }, - "Ovary": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Ovary": [ - "Ovary_Rep1", - "Ovary_Rep2", - "Ovary_Rep3" - ] - } - }, - "SuspensionCell": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Suspension_Cell": [ - "SuspensionCell_Rep1" - ] - } - }, - "Shoot": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Shoot": [ - "Shoot_Rep1" - ] - } - }, - "Root": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Root": [ - "Root_Rep1" - ] - } - }, - "Anther": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Anther": [ - "Anther_Rep1" - ] - } - }, - "Embryo": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Embryo": [ - "Embryo_Rep1" - ] - } - }, - "Endosperm": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "Endosperm": [ - "Endosperm_Rep1" - ] - } - }, - "5d-seed": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "5d-seed": [ - "5d-seed_Rep1" - ] - } - } - }, - "data_type": "Microarray" - }, - "ricestress_mas": { - "database": "rice_mas", - "view_name": "ricestress_mas", - "groups": { - "Control_stress_Seedling": { - "controls": [ - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS" - ], - "treatments": { - "Control_Shoot": [ - "RICE_CTRL_STRESS" - ], - 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"Cold_stress_rep3" - ] - } - } - }, - "data_type": "Microarray" - }, - "ricestress_rma": { - "database": "rice_rma", - "view_name": "ricestress_rma", - "groups": { - "Control_stress_Seedling": { - "controls": [ - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS" - ], - "treatments": { - "Control_Shoot": [ - "RICE_CTRL_STRESS" - ], - "Control_Root": [ - "RICE_CTRL_STRESS" - ] - } - }, - "Drought_stress_Seedling": { - "controls": [ - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS" - ], - "treatments": { - "Drought_Shoot": [ - "Drought_stress_rep1", - "Drought_stress_rep2", - "Drought_stress_rep3" - ], - "Drought_Root": [ - "Drought_stress_rep1", - "Drought_stress_rep2", - "Drought_stress_rep3" - ] - } - }, - "Salt_stress_Seedling": { - "controls": [ - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS" - ], - "treatments": { - "Salt_Shoot": [ - "Salt_stress_rep1", - "Salt_stress_rep2", - "Salt_stress_rep3" - ], - "Salt_Root": [ - "Salt_stress_rep1", 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"Roothair_48HAImock" - ], - "treatments": { - "Root_Hair_48_HAI": [ - "Roothair_48HAI" - ], - "Roothair_48HAImock": [ - "Roothair_48HAImock" - ], - "Root_Hair_48_HAI_Stripped": [ - "Root_stripped" - ] - } - }, - "StaceyTissues": { - "controls": [ - "SOYBEAN_CTRL", - "SOYBEAN_CTRL" - ], - "treatments": { - "SAM": [ - "SAM" - ], - "Flower": [ - "Flower" - ], - "Green_Pods": [ - "Green_Pods" - ], - "Leaves": [ - "Leaves" - ], - "Nodule": [ - "Nodule" - ], - "Root": [ - "Root" - ], - "Root_tip": [ - "Root_tip" - ] - } - } - }, - "data_type": "Unknown" - }, - "soybean_embryonic_development": { - "database": "soybean_embryonic_development", - "view_name": "soybean_embryonic_development", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Embryo_Axis_Epidermis": [ - "embryo_axis_epidermis" - ], - "Embryo_Axis_Parenchyma": [ - "embryo_axis_parenchyma" - ], - "Embryo_Axis_Plumule": [ - "embryo_axis_plumule" - ], - "Embryo_Axis_Root_Tip": [ - "embryo_root_tip" - ], - "Embryo_Axis_SAM": [ - "embryo_axis_SAM" - ], - "Embryo_Axis_Stele": [ - "embryo_axis_stele" - ], - "Embryo_Axis_Vasculature": [ - "embryo_axis_vasculature" - ], - "Embryo_Cotyledon_Abaxial_Parenchyma": [ - "embryo_cotyledon_abaxial_parenchyma" - ], - "Embryo_Cotyledon_Adaxial_Epidermis": [ - "embryo_cotyledon_adaxial_epidermis" - ], - "Seed_Cotyledon_Vasculature": [ - "seed_cotyledon_vasculature" - ], - "Embryo_Cotyledon_Adaxial_Parenchyma": [ - "embryo_cotyledon_adaxial_parenchyma" - ], - "Seed_Coat_Hilum": [ - "seed_coat_hilum" - ], - "Seed_Coat_Hourglass": [ - "seed_coat_hourglass" - ], - "Seed_Coat_Palisade": [ - "seed_coat_palisade" - ], - "Seed_Coat_Parenchyma": [ - "seed_coat_parenchyma" - ], - "Seed_Cotyledon_Abaxial_Epidermis": [ - "seed_cotyledon_abaxial_epidermis" - ], - "Seed_Endosperm": [ - "seed_endosperm" - ] - } - } - }, - "data_type": "Unknown" - }, - "soybean_heart_cotyledon_globular": { - "database": "soybean_heart_cotyledon_globular", - "view_name": "soybean_heart_cotyledon_globular", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Cotyledon_Embryo_Cotyledon": [ - "cotyledon_embryocotyledon" - ], - "Cotyledon_Embryo_Proper": [ - "cotyledon_embryo" - ], - "Cotyledon_Embryo_Axis": [ - "cotyledon_embryoaxis" - ], - "Cotyledon_Endosperm": [ - "cotyledon_endosperm" - ], - "Cotyledon_Seed_Coat_Endothelium": [ - "cotyledon_seedcoatendothelium" - ], - "Cotyledon_Seed_Coat_Epidermis": [ - "cotyledon_seedcoatepidermis" - ], - "Cotyledon_Seed_Coat_Hilum": [ - "cotyledon_seedcoathilum" - ], - "Cotyledon_Seed_Coat_Inner_Integument": [ - "cotyledon_seedcoatinnerintegument" - ], - "Cotyledon_Seed_Coat_Outer_Integument": [ - "cotyledon_seedcoatouterintegument" - ], - "Cotyledon_Suspensor": [ - "cotyledon_suspensor" - ], - "Globular_Embryo": [ - "globular_embryo" - ], - "Globular_Endosperm": [ - "globular_endosperm" - ], - "Globular_Seed_Coat_Endothelium": [ - "globular_seedcoatendothelium" - ], - "Globular_Seed_Coat_Epidermis": [ - "globular_seedcoatepidermis" - ], - "Globular_Seed_Coat_Hilum": [ - "globular_seedcoathilum" - ], - "Globular_Seed_Coat_Inner_Integument": [ - "globular_seedcoatinnerintegument" - ], - "Globular_Seed_Coat_Outer_Integument": [ - "globular_seedcoatouterintegument" - ], - "Globular_Suspensor": [ - "globular_suspensor" - ], - "Heart_Embryo": [ - "heart_embryo" - ], - "Heart_Endosperm": [ - "heart_endosperm" - ], - "Heart_Seed_Coat_Endothelium": [ - "heart_seedcoatendothelium" - ], - "Heart_Seed_Coat_Epidermis": [ - "heart_seedcoatepidermis" - ], - "Heart_Seed_Coat_Hilum": [ - "heart_seedcoathilum" - ], - "Heart_Seed_Coat_Inner_Integument": [ - "heart_seedcoatinnerintegument" - ], - "Heart_Seed_Coat_Outer_Integument": [ - "heart_seedcoatouterintegument" - ], - "Heart_Suspensor": [ - "heart_suspensor" - ] - } - } - }, - "data_type": "Unknown" - }, - "soybean_senescence": { - "database": "soybean_senescence", - "view_name": "soybean_senescence", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Cotyledon_Stage_1": [ - "C_I-1", - "C_I-2", - "C_I-3" - ], - "Cotyledon_Stage_2": [ - "C_II-1", - "C_II-2", - "C_II-3" - ], - "Cotyledon_Stage_3": [ - "C_III-1", - "C_III-2", - "C_III-3" - ], - "Leaf_Stage_1": [ - "L_I-1", - "L_I-2", - "L_I-3" - ], - "Leaf_Stage_2": [ - "L_II-1", - "L_II-2", - "L_II-3" - ], - "Leaf_Stage_3": [ - "L_III-1", - "L_III-2", - "L_III-3" - ], - "Leaf_Stage_4": [ - "L_IV-1", - "L_IV-2", - "L_IV-3" - ], - "Leaf_Stage_5": [ - "L_V-1", - "L_V-2", - "L_V-3" - ] - } - } - }, - "data_type": "Unknown" - }, - "soybean_severin": { - "database": "soybean_severin", - "view_name": "soybean_severin", - "groups": { - "Soybean_Severin": { - "controls": [ - "SOYBEAN_CTRL" - ], - "treatments": { - "Young_Leaf": [ - "young_leaf" - ], - "Flower": [ - "flower" - ], - "One_CM_Pod": [ - "one_cm_pod" - ], - "Pod_Shell_(10-13_DAF)": [ - "pod_shell_10DAF" - ], - "Pod_Shell_(14_17_DAF)": [ - "pod_shell_14DAF" - ], - "Nodule": [ - "nodule" - ], - "Root": [ - "root" - ], - "Seed_10_13_DAF": [ - "seed_10DAF" - ], - "Seed_14_17_DAF": [ - "seed_14DAF" - ], - "Seed_21_DAF": [ - "seed_21DAF" - ], - "Seed_25_DAF": [ - "seed_25DAF" - ], - "Seed_28_DAF": [ - "seed_28DAF" - ], - "Seed_35_DAF": [ - "seed_35DAF" - ], - "Seed_42_DAF": [ - "seed_42DAF" - ] - } - } - }, - "data_type": "Unknown" - } - } - } - }, - "strawberry": { - "data": { - "species": "strawberry", - "views": { - "Developmental_Map_Strawberry_Flower_and_Fruit": { - "database": "strawberry", - "view_name": "Developmental_Map_Strawberry_Flower_and_Fruit", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Anther,_stage_10": [ - "Anther_10_A", - "Anther_10_B" - ], - "Anther,_stage_11": [ - "Anther_11_A", - "Anther_11_B" - ], - "Anther,_stage_12": [ - "Anther_12_A", - "Anther_12_B" - ], - "Anther,_stages_7-8": [ - "Anther_7-8_A", - "Anther_7-8_B" - ], - "Anther,_stage_9": [ - "Anther_9_A", - "Anther_9_B" - ], - 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"Ovary_UNM2", - "Ovary_UNM3" - ], - "Anther_bicellular_pollen": [ - "Anther_BCP1", - "Anther_BCP2", - "Anther_BCP3" - ], - "Stigma_bicellular_pollen": [ - "Stigma_BCP1", - "Stigma_BCP2", - "Stigma_BCP3" - ], - "Ovary_bicellular_pollen": [ - "Ovary_BCP1", - "Ovary_BCP2", - "Ovary_BCP3" - ], - "Anther_tricellular_pollen": [ - "Anther_TCP1", - "Anther_TCP2", - "Anther_TCP3" - ], - "Stigma_tricellular_pollen": [ - "Stigma_TCP1", - "Stigma_TCP2", - "Stigma_TCP3" - ], - "Ovary_tricellular_pollen": [ - "Ovary_TCP1", - "Ovary_TCP2", - "Ovary_TCP3" - ], - "Mature_pollen": [ - "Pollen_MPG1", - "Pollen_MPG2", - "Pollen_MPG3" - ] - } - } - }, - "data_type": "Microarray" - }, - "triticale_mas": { - "database": "triticale_mas", - "view_name": "triticale_mas", - "groups": { - "Reproductive": { - "controls": [ - "TRITICALE_CTRL" - ], - "treatments": { - "Anther_tetrad": [ - "Anther_tetrad_1", - "Anther_tetrad_2", - "Anther_tetrad_3" - ], - "Stigma_tetrad": [ - "Stigma_tetrad_1", - "Stigma_tetrad_2", - "Stigma_tetrad_3" - ], - "Ovary_tetrad": [ - "Ovary_tetrad_1", - "Ovary_tetrad_2", - "Ovary_tetrad_3" - ], - "Anther_uninucleate": [ - "Anther_uninucleate_1", - "Anther_uninucleate_2", - "Anther_uninucleate_3" - ], - "Stigma_uninucleate": [ - "Stigma_uninucleate_1", - "Stigma_uninucleate_2", - "Stigma_uninucleate_3" - ], - "Ovary_uninucleate": [ - "Ovary_uninucleate_1", - "Ovary_uninucleate_2", - "Ovary_uninucleate_3" - ], - "Anther_bicellular_pollen": [ - "Anther_bicellular_pollen_1", - "Anther_bicellular_pollen_2", - "Anther_bicellular_pollen_3" - ], - "Stigma_bicellular_pollen": [ - "Stigma_bicellular_pollen_1", - "Stigma_bicellular_pollen_2", - "Stigma_bicellular_pollen_3" - ], - "Ovary_bicellular_pollen": [ - "Ovary_bicellular_pollen_1", - "Ovary_bicellular_pollen_2", - "Ovary_bicellular_pollen_3" - ], - "Anther_tricellular_pollen": [ - "Anther_tricellular_pollen_1", - "Anther_tricellular_pollen_2", - "Anther_tricellular_pollen_3" - ], - "Stigma_tricellular_pollen": [ - "Stigma_tricellular_pollen_1", - "Stigma_tricellular_pollen_2", - "Stigma_tricellular_pollen_3" - ], - "Ovary_tricellular_pollen": [ - "Ovary_tricellular_pollen_1", - "Ovary_tricellular_pollen_2", - "Ovary_tricellular_pollen_3" - ], - "Mature_pollen": [ - "Mature_pollen_1", - "Mature_pollen_2", - "Mature_pollen_3" - ] - } - } - }, - "data_type": "Microarray" - } - } - } - }, - "wheat": { - "data": { - "species": "wheat", - "views": { - "Developmental_Atlas": { - "database": "wheat", - "view_name": "Developmental_Atlas", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "First_leaf_sheath_-_Tillering_stage": [ - "Sample_43A", - "Sample_44A", - "Sample_45A" - ], - "Internode_#2_-_Milk_grain_stage": [ - "Sample_188B", - "Sample_189B" - ], - "Shoot_apical_meristem_-_Seedling_stage": [ - "Sample_19A", - "Sample_20A", - "Sample_21A" - ], - "Grain_-_Milk_grain_stage": [ - "Sample_199A", - "Sample_200A", - "Sample_201A" - ], - "First_leaf_blade_-_Seedling_stage": [ - "Sample_13R1", - "Sample_23", - "Sample_32" - ], - "Flag_leaf_blade_-_Full_boot_": [ - "Sample_94B", - "Sample_95A", - "Sample_96A" - ], - "Awn_-_50_percent_spike": [ - "Sample_118A", - "Sample_119B", - "Sample_120A" - ], - "flag_leaf_blade_night_(-0.25h)_06:45": [ - "Sample_166A", - "Sample_167A", - "Sample_168A" - ], - "Shoot_axis_-_Flag_leaf_stage": [ - "Sample_70A", - "Sample_71A", - "Sample_72A" - ], - "Fifth_leaf_blade_-_Flag_leaf_stage": [ - "Sample_67A", - "Sample_68A", - "Sample_69A" - ], - "Third_leaf_sheath_-_Three_leaf_stage": [ - "Sample_25A", - "Sample_26A", - "Sample_27A" - ], - "Internode_#2_-_Ear_emergence": [ - "Sample_136A", - "Sample_137B", - "Sample_138A" - ], - "Anther": [ - "Sample_160A", - "Sample_161A", - "Sample_162A" - ], - "Spike": [ - "Sample_100A", - "Sample_101A", - "Sample_102A" - ], - "Coleoptile": [ - "Sample_12", - "Sample_26", - "Sample_6A" - ], - "Stigma_and_Ovary": [ - "Sample_163A", - "Sample_164A", - "Sample_165A" - ], - "Roots_-_Flag_leaf_stage": [ - "Sample_73A", - "Sample_74A", - "Sample_76A" - ], - "Fifth_leaf_sheath_-_Flag_leaf_stage": [ - "Sample_64A", - "Sample_65A", - "Sample_66A" - ], - "Root_apical_meristem_-_Three_leaf_stage": [ - "Sample_15", - "Sample_32R2", - "Sample_33A" - ], - "Flag_leaf_sheath_-_Ear_emergence": [ - "Sample_124A", - "Sample_125A", - "Sample_126A" - ], - "Roots_-_Three_leaf_stage": [ - "Sample_28A", - "Sample_29A", - "Sample_30A" - ], - "Axillary_roots_-_Three_leaf_stage": [ - "Sample_16", - "Sample_35R1", - "Sample_36A" - ], - "Flag_leaf_sheath_-_50_percent_spike": [ - "Sample_106A", - "Sample_107B", - "Sample_108A" - ], - "Radicle_-_Seedling_stage": [ - "Sample_10", - "Sample_18", - "Sample_3A" - ], - "Roots_-_50_percent_spike": [ - "Sample_103A", - "Sample_104B", - "Sample_105B" - ], - "Third_leaf_blade_-_Three_leaf_stage": [ - "Sample_22B", - "Sample_23A", - "Sample_24A" - ], - "Spikelets_-_50_percent_spike": [ - "Sample_121A", - "Sample_122A", - "Sample_123A" - ], - "Root_apical_meristem_-_Tillering_stage": [ - "Sample_58A", - "Sample_59A", - "Sample_60A" - ], - "Grain_-_Ripening_stage": [ - "Sample_217B", - "Sample_218A", - "Sample_219A" - ], - "Awns_-_Ear_emergence": [ - "Sample_139A", - "Sample_140A", - "Sample_141A" - ], - "Glumes": [ - "Sample_193A", - "Sample_194A", - "Sample_195A" - ], - "Glumes_-_Ear_emergence": [ - "Sample_142A", - "Sample_143A", - "Sample_144B" - ], - "Leaf_ligule": [ - "Sample_88A", - "Sample_89B", - "Sample_90A" - ], - "Flag_leaf_blade_-_50_percent_spike": [ - "Sample_109A", - "Sample_110A", - "Sample_111B" - ], - "Internode_#2_-_50_percent_spike": [ - "Sample_112B", - "Sample_113B", - "Sample_114B" - ], - "Fifth_leaf_sheath_-_Fifth_leaf_stage": [ - "Sample_37A", - "Sample_38A", - "Sample_39A" - ], - "fifth_leaf_blade_night_(-0.25h)_21:45": [ - "Sample_79A", - "Sample_80A", - "Sample_81A" - ], - "Grain_-_Soft_dough": [ - "Sample_205A", - "Sample_206A", - "Sample_207A" - ], - "Flag_leaf_blade_(senescence)_-_Dough_stage": [ - "Sample_202A", - "Sample_203A", - "Sample_204A" - ], - "Flag_leaf_blade_night_(-0.25h)_06:45_-_Flag_leaf_stage": [ - "Sample_75A", - "Sample_77A", - "Sample_78A" - ], - "Flag_leaf_blade_(senescence)_-_Ripening_stage": [ - "Sample_223B", - "Sample_225A" - ], - "First_leaf_blade_-_Tillering_stage": [ - "Sample_46A", - "Sample_d11", - "Sample_d12" - ], - "Shoot_apical_meristem_-_Tillering_stage": [ - "Sample_52A", - "Sample_53A", - "Sample_54A" - ], - "Shoot_axis_-_First_leaf_stage": [ - "Sample_11", - "Sample_20", - "Sample_9A" - ], - "Roots_-_Seedling_stage": [ - "Sample_13", - "Sample_18A", - "Sample_33" - ], - "Shoot_axis_-_Milk_grain_stage": [ - "Sample_178A", - "Sample_179A", - "Sample_180A" - ], - "Fifth_leaf_blade_-_Fifth_leaf_stage": [ - "Sample_40A", - "Sample_41A", - "Sample_42A" - ], - "Flag_leaf_blade_-_Ear_emergence": [ - "Sample_127A", - "Sample_128A", - "Sample_129A" - ], - "flag_leaf_blade_night_(+0.25h)_07:15": [ - "Sample_82A", - "Sample_83B", - "Sample_84A" - ], - "Fifth_leaf_blade_night_(-0.25h)_21:45": [ - "Sample_169A", - "Sample_170A", - "Sample_171A" - ], - "Shoot_axis_-_Tillering_stage": [ - "Sample_49A", - "Sample_50A", - "Sample_51A" - ], - "Stem_axis_-_First_leaf_stage": [ - "Sample_11", - "Sample_20", - "Sample_9A" - ], - "Endosperm": [ - "Sample_211B", - "Sample_212A", - "Sample_213A" - ], - "Peduncle": [ - "Sample_184A", - "Sample_185A", - "Sample_186A" - ], - "Peduncle_-_50_percent_spike": [ - "Sample_115A", - "Sample_116A", - "Sample_117A" - ], - "Peduncle_-_Ear_emergence": [ - "Sample_133A", - "Sample_134A", - "Sample_135A" - ], - "Flag_leaf_sheath_-_Full_boot": [ - "Sample_91A", - "Sample_92A", - "Sample_93A" - ], - "Flag_leaf_blade_-_Flag_leaf_stage": [ - "Sample_61A", - "Sample_62A", - "Sample_63A" - ], - "Lemma": [ - "Sample_196A", - "Sample_197A", - "Sample_198A" - ], - "Lemma_-_Ear_emergence": [ - "Sample_157A", - "Sample_158A", - "Sample_159B" - ], - "Awns_-_Milk_grain_stage": [ - "Sample_190A", - "Sample_191A", - "Sample_192A" - ], - "fifth_leaf_blade_night_(+0.25h)_22:15": [ - "Sample_85B", - "Sample_86A", - "Sample_87A" - ], - "Flag_leaf_blade_-_Milk_grain_stage": [ - "Sample_175A", - "Sample_176A", - "Sample_177A" - ], - "Grain_-_Hard_dough": [ - "Sample_208A", - "Sample_209A", - "Sample_210A" - ], - "Flag_leaf_sheath_-_Milk_grain_stage": [ - "Sample_172A", - "Sample_173A", - "Sample_174A" - ], - "Embryo_proper": [ - "Sample_214A", - "Sample_215A", - "Sample_216A" - ], - "Fifth_leaf_blade_(senescence)_-_Milk_grain_stage": [ - "Sample_181A", - "Sample_182A", - "Sample_183A" - ], - "Roots_-_Tillering_stage": [ - "Sample_55B", - "Sample_56A", - "Sample_57A" - ], - "Shoot_axis_-_Full_boot": [ - "Sample_97A", - "Sample_98A", - "Sample_99A" - ], - "Fifth_leaf_blade_-_Ear_emergence": [ - "Sample_130A", - "Sample_131A", - "Sample_132A" - ], - "First_leaf_sheath_-_Seedling_stage": [ - "Sample_10R1", - "Sample_21", - "Sample_30" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Wheat_Abiotic_Stress": { - "database": "wheat_abiotic_stress", - "view_name": "Wheat_Abiotic_Stress", - "groups": { - "Med_CTRL": { - "controls": [ - "C1", - "C2", - "C4", - "C8" - ], - "treatments": { - "All": [ - "SHD4", - "SHD5", - "SHD6", - "SHD7" - ], - "Salt_+_Drought": [ - "SD1", - "SD5", - "SD6", - "SD8" - ], - "Salt_+_Heat": [ - "SH2", - "SH3", - "SH4", - "SH8" - ], - "Heat_+_Drought": [ - "HD3", - "HD4", - "HD7", - "HD8" - ], - "Drought_Only": [ - "D1", - "D4", - "D6", - "D8" - ], - "Heat_Only": [ - "H1", - "H2", - "H3", - "H4" - ], - "Salt_Only": [ - "S1", - "S3", - "S5", - "S8" - ], - "Control": [ - "C1", - "C2", - "C4", - "C8" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Wheat_Embryogenesis": { - "database": "wheat_embryogenesis", - "view_name": "Wheat_Embryogenesis", - "groups": { - "AA-DV92_Med_CTRL": { - "controls": [ - "AA-DV92_Med_CTRL" - ], - "treatments": { - "AA-DV92_Leaf_Early_Seed_Coat": [ - "AA-DV92_Leaf_early_stage_seed_coat" - ], - "AA-DV92_Leaf_Late_Embryo": [ - "AA-DV92_Leaf_late_embryo" - ], - "AA-DV92_Leaf_Early_Embryo": [ - "AA-DV92_Leaf_early_embryo" - ], - "AA-DV92_Leaf_Late_Endosperm": [ - "AA-DV92_Leaf_late_stage_endosperm" - ], - "AA-DV92_Leaf_Middle_Embryo": [ - "AA-DV92_Leaf_middle_embryo" - ], - "AA-DV92_Pre-Embryo": [ - "AA-DV92_Pre-embryo" - ], - "AA-DV92_Mature_Embryo": [ - "AA-DV92_Mature_embryo" - ], - "AA-DV92_Two_Cell_Embryo": [ - "AA-DV92_Two_cell_embryo" - ], - "AA-DV92_Transition_Embryo": [ - "AA-DV92_Transition_embryo" - ], - "AA-DV92_Transition_Endosperm": [ - "AA-DV92_Transition_stage_endosperm" - ] - } - }, - "Hexaploid-AC_Med_CTRL": { - "controls": [ - "Hexaploid-AC_Med_CTRL" - ], - "treatments": { - "Hexaploid-AC_Leaf_Late_Endosperm": [ - "Hexaploid-AC_Late_leaf_stage_endosperm" - ], - "Hexaploid-AC_Leaf_Early_Embryo": [ - "Hexaploid-AC_Leaf_early_embryo" - ], - "Hexaploid-AC_Leaf_Early_Seed_Coat": [ - "Hexaploid-AC_Leaf_early_stage_seed_coat" - ], - "Hexaploid-AC_Leaf_Late_Embryo": [ - "Hexaploid-AC_Leaf_early_stage_seed_coat" - ], - "Hexaploid-AC_Leaf_Middle_Embryo": [ - "Hexaploid-AC_Leaf_middle_embryo" - ], - "Hexaploid-AC_Mature_Embryo": [ - "Hexaploid-AC_Mature_embryo" - ], - "Hexaploid-AC_Pre-Embryo": [ - "Hexaploid-AC_Pre-embryo" - ], - "Hexaploid-AC_Transition_Embryo": [ - "Hexaploid-AC_Transition_embryo" - ], - "Hexaploid-AC_Transition_Endosperm": [ - "Hexaploid-AC_Transition_stage_endosperm" - ], - "Hexaploid-AC_Two_Cell_Embryo": [ - "Hexaploid-AC_Two_cell_embryo" - ] - } - }, - "Tetraploid-SF_Med_CTRL": { - "controls": [ - "Tetraploid-SF_Med_CTRL" - ], - "treatments": { - "Tetraploid-SF_Leaf_Early_Seed_Coat": [ - "Tetraploid-SF_Leaf_early_stage_seed_coat" - ], - "Tetraploid-SF_Leaf_Early_Embryo": [ - "Tetraploid-SF_Leaf_early_embryo" - ], - "Tetraploid-SF_Leaf_Late_Embryo": [ - "Tetraploid-SF_Leaf_late_embryo" - ], - "Tetraploid-SF_Leaf_Late_Endosperm": [ - "Tetraploid-SF_Leaf_late_stage_endosperm" - ], - "Tetraploid-SF_Leaf_Middle_Embryo": [ - "Tetraploid-SF_Leaf_middle_embryo" - ], - "Tetraploid-SF_Mature_Embryo": [ - "Tetraploid-SF_Mature_embryo" - ], - "Tetraploid-SF_Pre-Embryo": [ - "Tetraploid-SF_Pre-embryo" - ], - "Tetraploid-SF_Transition_Embryo": [ - "Tetraploid-SF_Transition_embryo" - ], - "Tetraploid-SF_Transition_Endosperm": [ - "Tetraploid-SF_Transition_stage_endosperm" - ], - "Tetraploid-SF_Two_Cell_Embryo": [ - "Tetraploid-SF_Two_cell_embryo" - ] - } - }, - "BB-TA2780_Med_CTRL": { - "controls": [ - "BB-TA2780_Med_CTRL" - ], - "treatments": { - "BB-TA2780_Leaf_Early_Seed_Coat": [ - "BB-TA2780_Leaf_early_stage_seed_coat" - ], - "BB-TA2780_Leaf_Early_Embryo": [ - "BB-TA2780_Leaf_early_embryo" - ], - "BB-TA2780_Leaf_Late_Embryo": [ - "BB-TA2780_Leaf_late_embryo" - ], - "BB-TA2780_Leaf_Late_Endosperm": [ - "BB-TA2780_Leaf_late_stage_endosperm" - ], - "BB-TA2780_Leaf_Middle_Embryo": [ - "BB-TA2780_Leaf_middle_embryo" - ], - "BB-TA2780_Mature_Embryo": [ - "BB-TA2780_Mature_embryo" - ], - "BB-TA2780_Pre-Embryo": [ - "BB-TA2780_Pre-embryo" - ], - "BB-TA2780_Transition_Embryo": [ - "BB-TA2780_Transition_embryo" - ], - "BB-TA2780_Transition_Endosperm": [ - "BB-TA2780_Transition_stage_endosperm" - ], - "BB-TA2780_Two_Cell_Embryo": [ - "BB-TA2780_Two_cell_embryo" - ] - } - }, - "DD-TA101132_Med_CTRL": { - "controls": [ - "DD-TA101132_Med_CTRL" - ], - "treatments": { - "DD-TA101132_Leaf_Early_Embryo": [ - "DD-TA101132_Leaf_early_embryo" - ], - "DD-TA101132_Leaf_Early_Seed_Coat": [ - "DD-TA101132_Leaf_early_stage_seed_coat" - ], - "DD-TA101132_Leaf_Late_Embryo": [ - "DD-TA101132_Leaf_late_embryo" - ], - "DD-TA101132_Leaf_Late_Endosperm": [ - "DD-TA101132_Leaf_late_stage_endosperm" - ], - "DD-TA101132_Leaf_Middle_Embryo": [ - "DD-TA101132_leaf_middle_embryo" - ], - "DD-TA101132_Mature_Embryo": [ - "DD-TA101132_Mature_embryo" - ], - "DD-TA101132_Transition_Embryo": [ - "DD-TA101132_Transition_embryo" - ], - "DD-TA101132_Transition_Endosperm": [ - "DD-TA101132_Transition_stage_endosperm" - ], - "DD-TA101132_Two_Cell_Embryo": [ - "DD-TA101132_Two_cell_embryo" - ], - "DD-TA101132_Pre-Embryo": [ - "DD-TA101132_Pre-embryo" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Wheat_Meiosis": { - "database": "wheat_meiosis", - "view_name": "Wheat_Meiosis", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Anther": [ - "Anther_rep1", - "Anther_rep2", - "Anther_rep3" - ], - "Diplotene": [ - "Diplotene_rep1", - "Diplotene_rep2", - "Diplotene_rep3" - ], - "Flagleaf": [ - "FlagLeaf_rep1", - "FlagLeaf_rep2", - "FlagLeaf_rep3" - ], - "Leaf": [ - "Leaf_rep1", - "Leaf_rep2", - "Leaf_rep3" - ], - "Leptotene": [ - "Leptotene_rep1", - "Leptotene_rep2", - "Leptotene_rep3" - ], - "Metaphase_I": [ - "Metaphase-I_rep1", - "Metaphase-I_rep2", - "Metaphase-I_rep3" - ], - "Metaphase_II": [ - "Metaphase-II_rep1", - "Metaphase-II_rep2", - "Metaphase-II_rep3" - ], - "Pachytene": [ - "Pachytene_rep1", - "Pachytene_rep2", - "Pachytene_rep3" - ], - "Pollen": [ - "Pollen_rep1", - "Pollen_rep2", - "Pollen_rep3" - ], - "Pre-meiotic_G2": [ - "Pre-meiotic_G2_rep1", - "Pre-meiotic_G2_rep2", - "Pre-meiotic_G2_rep3" - ], - "Zygotene": [ - "Zygotene_rep1", - "Zygotene_rep2", - "Zygotene_rep3" - ] - } - } - }, - "data_type": "RNA-Seq" - } - } - } - } -} \ No newline at end of file diff --git a/data/efp_info/master_db_list.json b/data/efp_info/master_db_list.json index 10bff114..26185300 100644 --- a/data/efp_info/master_db_list.json +++ b/data/efp_info/master_db_list.json @@ -872,6 +872,20 @@ } } } + }, + "heterodera_schachtii": { + "source": "eplant", + "platform": "rna_seq", + "views": { + "eplant_arabidopsis": [ + "Heterodera schachtii" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } } }, "arachis": { @@ -1492,22 +1506,6 @@ } } }, - "heterodera": { - "heterodera_schachtii": { - "source": "eplant", - "platform": "rna_seq", - "views": { - "eplant_arabidopsis": [ - "Heterodera schachtii" - ] - }, - "validation": { - "n_samples": 30, - "n_pass": 30, - "n_fail": 0 - } - } - }, "human": { "human_body_map_2": { "source": "efp", @@ -3808,4 +3806,4 @@ } } } -} \ No newline at end of file +} diff --git a/data/regex_master_list_efp_eplant/bar_regex_by_db.csv b/data/regex_master_list_efp_eplant/bar_regex_by_db.csv new file mode 100644 index 00000000..b9c7f3b3 --- /dev/null +++ b/data/regex_master_list_efp_eplant/bar_regex_by_db.csv @@ -0,0 +1,194 @@ +db,species,platform,source,in_dropdown,regex_project,resolved_via,efp_frontends,eplant_frontends,n_frontends,n_views,views,regex +actinidia_bud_development,actinidia,rna_seq,efp,yes,efp_actinidia,efp-frontend,efp_actinidia,,1,1,efp_actinidia: Bud Development,"^(Acc\d+\.\d{0,3})$" +actinidia_flower_fruit_development,actinidia,rna_seq,efp,yes,efp_actinidia,efp-frontend,efp_actinidia,,1,1,efp_actinidia: Flower Fruit Development,"^(Acc\d+\.\d{0,3})$" +actinidia_postharvest,actinidia,rna_seq,efp,yes,efp_actinidia,efp-frontend,efp_actinidia,,1,1,efp_actinidia: Postharvest,"^(Acc\d+\.\d{0,3})$" +actinidia_vegetative_growth,actinidia,rna_seq,efp,yes,efp_actinidia,efp-frontend,efp_actinidia,,1,1,efp_actinidia: Vegetative Growth,"^(Acc\d+\.\d{0,3})$" +apple,apple,rna_seq,efp,yes,efp_apple,efp-frontend,efp_apple,,1,1,efp_apple: Developmental Map,"^(MfusH1_\d\dg\d{1,8})$" +affydb,arabidopsis,microarray,legacy_not_in_dropdown,no,efp_arabidopsis,species-fallback,,,0,0,,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +arabidopsis_ecotypes,arabidopsis,microarray,efp,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,,1,1,efp_arabidopsis: Natural Variation,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +atgenexp,arabidopsis,microarray,efp,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,,1,1,efp_arabidopsis: Development RMA,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +atgenexp_hormone,arabidopsis,microarray,both,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,eplant_arabidopsis,2,3,"efp_arabidopsis: Chemical, Hormone | eplant_arabidopsis: Chemical","^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +atgenexp_pathogen,arabidopsis,microarray,both,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,eplant_arabidopsis,2,10,"efp_arabidopsis: Biotic Stress, Biotic Stress II | eplant_arabidopsis: Biotic Stress Botrytis cinerea, Biotic Stress Elicitors, Biotic Stress Erysiphe orontii, Biotic Stress Hyaloperonospora arabidopsidis, Biotic Stress Myzus persicaere, Biotic Stress Phytophthora infestans, Biotic Stress Pseudomonas syringae, Biotic Stress Golovinomyces orontii","^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +atgenexp_plus,arabidopsis,microarray,both,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,eplant_arabidopsis,2,13,"efp_arabidopsis: Developmental Map, Developmental Mutants, Tissue Specific | eplant_arabidopsis: Tissue Specific Embryo Development, Tissue Specific Guard And Mesophyll Cells, Tissue Specific Microgametogenesis, Tissue Specific Pollen Germination, Tissue Specific Shoot Apical Meristem, Tissue Specific Stem Epidermis, Tissue Specific Stigma And Ovaries, Tissue Specific Trichomes, Tissue Specific Xylem And Cork, AtGenExpress","^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +atgenexp_stress,arabidopsis,microarray,both,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,eplant_arabidopsis,2,4,"efp_arabidopsis: Abiotic Stress, Abiotic Stress II | eplant_arabidopsis: Abiotic Stress, Abiotic Stress II","^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +circadian_mutants,arabidopsis,rna_seq,legacy_not_in_dropdown,no,efp_arabidopsis,species-fallback,,,0,0,,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +dna_damage,arabidopsis,rna_seq,both,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,eplant_arabidopsis,2,2,efp_arabidopsis: DNA Damage | eplant_arabidopsis: DNA Damage,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +embryo,arabidopsis,rna_seq,efp,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,,1,1,efp_arabidopsis: Embryo,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +gc_drought,arabidopsis,rna_seq,eplant,yes,efp_arabidopsis,eplant-frontend(shares eFP regex),,eplant_arabidopsis,1,1,eplant_arabidopsis: Guard Cell Drought,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +germination,arabidopsis,rna_seq,both,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,eplant_arabidopsis,2,2,efp_arabidopsis: Germination | eplant_arabidopsis: Germination,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +guard_cell,arabidopsis,microarray,both,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,eplant_arabidopsis,2,4,"efp_arabidopsis: Guard Cell | eplant_arabidopsis: Guard Cell Meristemoids, Guard Cell Mutant And Wild Type Guard Cell ABA Response, Guard Cell Suspension Cell ABA Response With ROS Scavenger","^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +gynoecium,arabidopsis,rna_seq,efp,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,,1,1,efp_arabidopsis: Gynoecium,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +hnahal,arabidopsis,microarray,legacy_not_in_dropdown,no,efp_arabidopsis,species-fallback,,,0,0,,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +klepikova,arabidopsis,rna_seq,both,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,eplant_arabidopsis,2,2,efp_arabidopsis: Klepikova Atlas | eplant_arabidopsis: Klepikova,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +lateral_root_initiation,arabidopsis,microarray,efp,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,,1,1,efp_arabidopsis: Lateral Root Initiation,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +light_series,arabidopsis,microarray,efp,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,,1,1,efp_arabidopsis: Light Series,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +lipid_map,arabidopsis,rna_seq,efp,yes,efp_arabidopsis_lipid,efp-frontend,efp_arabidopsis_lipid,,1,1,efp_arabidopsis_lipid: Lipid Map,"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$" +meristem_db,arabidopsis,microarray,efp,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,,1,1,efp_arabidopsis: Regeneration,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +meristem_db_new,arabidopsis,microarray,legacy_not_in_dropdown,no,efp_arabidopsis,species-fallback,,,0,0,,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +rohan,arabidopsis,microarray,legacy_not_in_dropdown,no,efp_arabidopsis,species-fallback,,,0,0,,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +root,arabidopsis,microarray,both,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,eplant_arabidopsis,2,3,"efp_arabidopsis: Root, Root II | eplant_arabidopsis: Tissue Specific Root","^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +root_Schaefer_lab,arabidopsis,rna_seq,eplant,yes,efp_arabidopsis,eplant-frontend(shares eFP regex),,eplant_arabidopsis,1,1,eplant_arabidopsis: Root Immunity Elicitation,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +rpatel,arabidopsis,microarray,legacy_not_in_dropdown,no,efp_arabidopsis,species-fallback,,,0,0,,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +seed_db,arabidopsis,microarray,efp,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,,1,1,efp_arabidopsis: Seed,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +seedcoat,arabidopsis,microarray,efp,yes,efp_seedcoat,efp-frontend(alias),efp_arabidopsis_seedcoat,,1,1,efp_arabidopsis_seedcoat: Seed Coat,"^(At[12345CM]g[0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(\D[0-9]+_[0-9]+)$|^(At[0-9]{8})$|^(Alien[0-9]{1,2})$|^(atc[0-9]{2})$|^(3xSSC)$" +shoot_apex,arabidopsis,rna_seq,both,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,eplant_arabidopsis,2,2,efp_arabidopsis: Shoot Apex | eplant_arabidopsis: Shoot Apex,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +silique,arabidopsis,rna_seq,efp,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis,,1,1,efp_arabidopsis: Silique,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +single_cell,arabidopsis,rna_seq,both,yes,efp_arabidopsis,efp-frontend,efp_arabidopsis;efp_arabidopsis_cell,eplant_arabidopsis,3,4,"efp_arabidopsis: Single Cell | efp_arabidopsis_cell: Cell Type | eplant_arabidopsis: Cell, Single Cell","^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +arachis,arachis,rna_seq,efp,yes,efp_arachis,efp-frontend,efp_arachis,,1,1,efp_arachis: Arachis Atlas,^(Adur\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Aipa_c\d+_g\d+_i\d+)$|^(Aipa\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Adur_c\d+_g\d+_i\d+)$ +barley_mas,barley,microarray,efp,yes,efp_barley,efp-frontend,efp_barley,,1,1,efp_barley: barley mas,"^((HM|HV).*)$|^(HORVU[\w.]+)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(A[JK][0-9]{6}\.[0-9])$|^([0-9-]+_(Reg|R)_[0-9-]+(_x_|_s_|_)?at)$|^([0-9-]+\.AF[0-9]+(_x_|_s_|_)?at)$|^(A[0-9]{5}\.[0-9](_x_|_s_|_)?at)$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_CDS-[0-9]{1,2})?(_x_|_s_|_)?at)$|^(AFFX-[A-Za-z0-9_/-]+(_x_|_s_|_)?at)$|^((Chlor|Mito)?Contig[0-9]{1,6}(_(3|5|M))?(_x_|_s_|_)?at)$|^(D[0-9]{5}(_x_|_s_|_)?at)$|^(Dhn[0-9]{2}\(Morex\)(_x_|_s_|_)?at)$|^(E[A-Za-z]{3}[0-9]{2}_SQ[0-9]{3}_[A-Z][0-9]{2}[a-z]?(_x_|_s_|_)?at)$|^(Franka(_b_|_)3pri[0-9]{1,2}(_x_|_s_|_)?at)$|^(H[A-Z][0-9]{1,4}[A-Z][0-9]{1,2}[a-z]?(_x_|_s_|_)?at)$|^(Mla[A-Za-z0-9_-]+at)$|^(S[0-9]{10}[A-Z][0-9]{2}[A-Z][0-9](_x_|_s_|_)?at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z][0-9]{2}(_x_|_s_|_)?at)$|^(HO)$" +barley_rma,barley,microarray,efp,yes,efp_barley,efp-frontend,efp_barley,,1,1,efp_barley: barley rma,"^((HM|HV).*)$|^(HORVU[\w.]+)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(A[JK][0-9]{6}\.[0-9])$|^([0-9-]+_(Reg|R)_[0-9-]+(_x_|_s_|_)?at)$|^([0-9-]+\.AF[0-9]+(_x_|_s_|_)?at)$|^(A[0-9]{5}\.[0-9](_x_|_s_|_)?at)$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_CDS-[0-9]{1,2})?(_x_|_s_|_)?at)$|^(AFFX-[A-Za-z0-9_/-]+(_x_|_s_|_)?at)$|^((Chlor|Mito)?Contig[0-9]{1,6}(_(3|5|M))?(_x_|_s_|_)?at)$|^(D[0-9]{5}(_x_|_s_|_)?at)$|^(Dhn[0-9]{2}\(Morex\)(_x_|_s_|_)?at)$|^(E[A-Za-z]{3}[0-9]{2}_SQ[0-9]{3}_[A-Z][0-9]{2}[a-z]?(_x_|_s_|_)?at)$|^(Franka(_b_|_)3pri[0-9]{1,2}(_x_|_s_|_)?at)$|^(H[A-Z][0-9]{1,4}[A-Z][0-9]{1,2}[a-z]?(_x_|_s_|_)?at)$|^(Mla[A-Za-z0-9_-]+at)$|^(S[0-9]{10}[A-Z][0-9]{2}[A-Z][0-9](_x_|_s_|_)?at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z][0-9]{2}(_x_|_s_|_)?at)$|^(HO)$" +barley_seed,barley,rna_seq,eplant,yes,efp_barley,eplant-frontend(shares eFP regex),,eplant_barley,1,1,eplant_barley: Seed,"^((HM|HV).*)$|^(HORVU[\w.]+)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(A[JK][0-9]{6}\.[0-9])$|^([0-9-]+_(Reg|R)_[0-9-]+(_x_|_s_|_)?at)$|^([0-9-]+\.AF[0-9]+(_x_|_s_|_)?at)$|^(A[0-9]{5}\.[0-9](_x_|_s_|_)?at)$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_CDS-[0-9]{1,2})?(_x_|_s_|_)?at)$|^(AFFX-[A-Za-z0-9_/-]+(_x_|_s_|_)?at)$|^((Chlor|Mito)?Contig[0-9]{1,6}(_(3|5|M))?(_x_|_s_|_)?at)$|^(D[0-9]{5}(_x_|_s_|_)?at)$|^(Dhn[0-9]{2}\(Morex\)(_x_|_s_|_)?at)$|^(E[A-Za-z]{3}[0-9]{2}_SQ[0-9]{3}_[A-Z][0-9]{2}[a-z]?(_x_|_s_|_)?at)$|^(Franka(_b_|_)3pri[0-9]{1,2}(_x_|_s_|_)?at)$|^(H[A-Z][0-9]{1,4}[A-Z][0-9]{1,2}[a-z]?(_x_|_s_|_)?at)$|^(Mla[A-Za-z0-9_-]+at)$|^(S[0-9]{10}[A-Z][0-9]{2}[A-Z][0-9](_x_|_s_|_)?at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z][0-9]{2}(_x_|_s_|_)?at)$|^(HO)$" +barley_spike_meristem,barley,rna_seq,eplant,yes,efp_barley,eplant-frontend(alias),,eplant_barley_legacy,1,2,"eplant_barley_legacy: Spike Meristem, Spike Meristem Shade Response","^((HM|HV).*)$|^(HORVU[\w.]+)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(A[JK][0-9]{6}\.[0-9])$|^([0-9-]+_(Reg|R)_[0-9-]+(_x_|_s_|_)?at)$|^([0-9-]+\.AF[0-9]+(_x_|_s_|_)?at)$|^(A[0-9]{5}\.[0-9](_x_|_s_|_)?at)$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_CDS-[0-9]{1,2})?(_x_|_s_|_)?at)$|^(AFFX-[A-Za-z0-9_/-]+(_x_|_s_|_)?at)$|^((Chlor|Mito)?Contig[0-9]{1,6}(_(3|5|M))?(_x_|_s_|_)?at)$|^(D[0-9]{5}(_x_|_s_|_)?at)$|^(Dhn[0-9]{2}\(Morex\)(_x_|_s_|_)?at)$|^(E[A-Za-z]{3}[0-9]{2}_SQ[0-9]{3}_[A-Z][0-9]{2}[a-z]?(_x_|_s_|_)?at)$|^(Franka(_b_|_)3pri[0-9]{1,2}(_x_|_s_|_)?at)$|^(H[A-Z][0-9]{1,4}[A-Z][0-9]{1,2}[a-z]?(_x_|_s_|_)?at)$|^(Mla[A-Za-z0-9_-]+at)$|^(S[0-9]{10}[A-Z][0-9]{2}[A-Z][0-9](_x_|_s_|_)?at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z][0-9]{2}(_x_|_s_|_)?at)$|^(HO)$" +barley_spike_meristem_v3,barley,rna_seq,eplant,yes,efp_barley,eplant-frontend(shares eFP regex),,eplant_barley,1,2,"eplant_barley: Spike Meristem, Spike Meristem Shade Response","^((HM|HV).*)$|^(HORVU[\w.]+)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(A[JK][0-9]{6}\.[0-9])$|^([0-9-]+_(Reg|R)_[0-9-]+(_x_|_s_|_)?at)$|^([0-9-]+\.AF[0-9]+(_x_|_s_|_)?at)$|^(A[0-9]{5}\.[0-9](_x_|_s_|_)?at)$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_CDS-[0-9]{1,2})?(_x_|_s_|_)?at)$|^(AFFX-[A-Za-z0-9_/-]+(_x_|_s_|_)?at)$|^((Chlor|Mito)?Contig[0-9]{1,6}(_(3|5|M))?(_x_|_s_|_)?at)$|^(D[0-9]{5}(_x_|_s_|_)?at)$|^(Dhn[0-9]{2}\(Morex\)(_x_|_s_|_)?at)$|^(E[A-Za-z]{3}[0-9]{2}_SQ[0-9]{3}_[A-Z][0-9]{2}[a-z]?(_x_|_s_|_)?at)$|^(Franka(_b_|_)3pri[0-9]{1,2}(_x_|_s_|_)?at)$|^(H[A-Z][0-9]{1,4}[A-Z][0-9]{1,2}[a-z]?(_x_|_s_|_)?at)$|^(Mla[A-Za-z0-9_-]+at)$|^(S[0-9]{10}[A-Z][0-9]{2}[A-Z][0-9](_x_|_s_|_)?at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z][0-9]{2}(_x_|_s_|_)?at)$|^(HO)$" +brachypodium,brachypodium,rna_seq,efp,yes,efp_brachypodium,efp-frontend,efp_brachypodium,,1,1,efp_brachypodium: Brachypodium Atlas,^(Bradi[0-9]+g[0-9]+(\.[0-9]+)?)$|^(Bradi[0-9]+s[0-9]+(\.[0-9]+)?)$|^(Bradi[0-9]+\.g[0-9]+)$ +brachypodium_Bd21,brachypodium,rna_seq,efp,yes,efp_brachypodium,efp-frontend,efp_brachypodium,,1,1,efp_brachypodium: Brachypodium Spikes,^(Bradi[0-9]+g[0-9]+(\.[0-9]+)?)$|^(Bradi[0-9]+s[0-9]+(\.[0-9]+)?)$|^(Bradi[0-9]+\.g[0-9]+)$ +brachypodium_embryogenesis,brachypodium,rna_seq,legacy_not_in_dropdown,no,efp_brachypodium,species-fallback,,,0,0,,^(Bradi[0-9]+g[0-9]+(\.[0-9]+)?)$|^(Bradi[0-9]+s[0-9]+(\.[0-9]+)?)$|^(Bradi[0-9]+\.g[0-9]+)$ +brachypodium_grains,brachypodium,rna_seq,efp,yes,efp_brachypodium,efp-frontend,efp_brachypodium,,1,1,efp_brachypodium: Brachypodium Grains,^(Bradi[0-9]+g[0-9]+(\.[0-9]+)?)$|^(Bradi[0-9]+s[0-9]+(\.[0-9]+)?)$|^(Bradi[0-9]+\.g[0-9]+)$ +brachypodium_metabolites_map,brachypodium,rna_seq,efp,yes,efp_brachypodium_metabolites,efp-frontend,efp_brachypodium_metabolites,,1,1,efp_brachypodium_metabolites: Metabolite Level,"(?i)^[a-z\s\-]{1,60}$" +brachypodium_photo_thermocycle,brachypodium,rna_seq,efp,yes,efp_brachypodium,efp-frontend,efp_brachypodium,,1,1,efp_brachypodium: Photo Thermocycle,^(Bradi[0-9]+g[0-9]+(\.[0-9]+)?)$|^(Bradi[0-9]+s[0-9]+(\.[0-9]+)?)$|^(Bradi[0-9]+\.g[0-9]+)$ +brassica_rapa,brassica,rna_seq,efp,yes,efp_brassica_rapa,efp-frontend,efp_brassica_rapa,,1,1,efp_brassica_rapa: Embryogenesis,"^(Bra.\d+g\d{0,10})$|^(Bra[AC]nng\d+)$" +brassica_rapa_developmental_atlas,brassica,rna_seq,legacy_not_in_dropdown,no,efp_brassica_rapa,species-sibling-fallback,,,0,0,,"^(Bra.\d+g\d{0,10})$|^(Bra[AC]nng\d+)$" +cacao_developmental_atlas,cacao,rna_seq,efp,yes,efp_cacao_ccn,efp-frontend,efp_cacao_ccn,,1,1,efp_cacao_ccn: Developmental Atlas,"^(CCN-51_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +cacao_developmental_atlas_sca,cacao,rna_seq,efp,yes,efp_cacao_sca,efp-frontend,efp_cacao_sca,,1,1,efp_cacao_sca: Developmental Atlas,"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +cacao_drought_diurnal_atlas,cacao,rna_seq,efp,yes,efp_cacao_ccn,efp-frontend,efp_cacao_ccn,,1,1,efp_cacao_ccn: Drought Diurnal Atlas,"^(CCN-51_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +cacao_drought_diurnal_atlas_sca,cacao,rna_seq,efp,yes,efp_cacao_sca,efp-frontend,efp_cacao_sca,,1,1,efp_cacao_sca: Drought Diurnal Atlas,"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +cacao_infection,cacao,rna_seq,efp,yes,efp_cacao_tc,efp-frontend,efp_cacao_tc,,1,1,efp_cacao_tc: Cacao Infection,^(Tc([0-9]+|Un)v2_g[0-9]+)$ +cacao_leaf,cacao,rna_seq,efp,yes,efp_cacao_tc,efp-frontend,efp_cacao_tc,,1,1,efp_cacao_tc: Cacao Leaf,^(Tc([0-9]+|Un)v2_g[0-9]+)$ +cacao_meristem_atlas_sca,cacao,rna_seq,efp,yes,efp_cacao_sca,efp-frontend,efp_cacao_sca,,1,1,efp_cacao_sca: Meristem Atlas,"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +cacao_seed_atlas_sca,cacao,rna_seq,efp,yes,efp_cacao_sca,efp-frontend,efp_cacao_sca,,1,1,efp_cacao_sca: Seed Atlas,"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +camelina,camelina,rna_seq,both,yes,efp_camelina,efp-frontend,efp_camelina,eplant_camelina,2,2,efp_camelina: Developmental Atlas FPKM | eplant_camelina: Plant,"^(Csa\d{0,5}[gs]\d{0,6}.\d{0,3})$|^(At\d[cgm]\d{0,6})$" +camelina_tpm,camelina,rna_seq,efp,yes,efp_camelina,efp-frontend,efp_camelina,,1,1,efp_camelina: Developmental Atlas TPM,"^(Csa\d{0,5}[gs]\d{0,6}.\d{0,3})$|^(At\d[cgm]\d{0,6})$" +cannabis,cannabis,rna_seq,both,yes,efp_cannabis,efp-frontend,efp_cannabis,eplant_cannabis,2,2,efp_cannabis: Cannabis Atlas | eplant_cannabis: Plant,(^C\d+$)|(^scaffold\d+$)|(^AGQN\d+$) +canola,canola,rna_seq,legacy_not_in_dropdown,no,efp_canola,species-fallback,,,0,0,,"^(Bna([A-C][0-9]{2}|[A-C]nn|Unn)g[0-9]{1,8}[A-Z]?)$|^(BoC[0-9]+g[0-9]+\.[0-9]+V[0-9])$|^(BrChr[0-9]+g[0-9]+\.[0-9]+V[0-9])$|^(Contig[0-9]+)$" +canola_original,canola,rna_seq,legacy_not_in_dropdown,no,efp_canola,species-fallback,,,0,0,,"^(Bna([A-C][0-9]{2}|[A-C]nn|Unn)g[0-9]{1,8}[A-Z]?)$|^(BoC[0-9]+g[0-9]+\.[0-9]+V[0-9])$|^(BrChr[0-9]+g[0-9]+\.[0-9]+V[0-9])$|^(Contig[0-9]+)$" +canola_original_v2,canola,rna_seq,legacy_not_in_dropdown,no,efp_canola,species-fallback,,,0,0,,"^(Bna([A-C][0-9]{2}|[A-C]nn|Unn)g[0-9]{1,8}[A-Z]?)$|^(BoC[0-9]+g[0-9]+\.[0-9]+V[0-9])$|^(BrChr[0-9]+g[0-9]+\.[0-9]+V[0-9])$|^(Contig[0-9]+)$" +canola_seed,canola,rna_seq,efp,yes,efp_canola,efp-frontend,efp_canola,,1,1,efp_canola: Canola Seed,"^(Bna([A-C][0-9]{2}|[A-C]nn|Unn)g[0-9]{1,8}[A-Z]?)$|^(BoC[0-9]+g[0-9]+\.[0-9]+V[0-9])$|^(BrChr[0-9]+g[0-9]+\.[0-9]+V[0-9])$|^(Contig[0-9]+)$" +cassava_atlas,cassava,rna_seq,legacy_not_in_dropdown,no,(unassigned),UNRESOLVED,,,0,0,, +cassava_cbb,cassava,rna_seq,legacy_not_in_dropdown,no,(unassigned),UNRESOLVED,,,0,0,, +cassava_eacmv,cassava,rna_seq,legacy_not_in_dropdown,no,(unassigned),UNRESOLVED,,,0,0,, +cuscuta,cuscuta,rna_seq,legacy_not_in_dropdown,no,(unassigned),UNRESOLVED,,,0,0,, +cuscuta_early_haustoriogenesis,cuscuta,rna_seq,legacy_not_in_dropdown,no,(unassigned),UNRESOLVED,,,0,0,, +cuscuta_lmd,cuscuta,rna_seq,legacy_not_in_dropdown,no,(unassigned),UNRESOLVED,,,0,0,, +eucalyptus,eucalyptus,rna_seq,eplant,yes,efp_eucalyptus,eplant-frontend(shares eFP regex),,eplant_eucalyptus,1,2,"eplant_eucalyptus: Stress, Plant",^(Eucgr\.[A-Za-z][0-9]{5}(\.[0-9]+)?)$|^(Eucgr\.[A-Za-z0-9._-]+)$ +euphorbia,euphorbia,rna_seq,efp,yes,efp_euphorbia,efp-frontend,efp_euphorbia,,1,1,efp_euphorbia: Euphorbia,"^(Ep_chr\d_g\d{1,8})$" +grape_developmental,grape,rna_seq,efp,yes,efp_grape,efp-frontend,efp_grape,,1,1,efp_grape: grape developmental,^(CHR|VIT_|CHRUN) +heterodera_schachtii,heterodera,rna_seq,eplant,yes,efp_arabidopsis,species-special-case,,eplant_arabidopsis,1,1,eplant_arabidopsis: Heterodera schachtii,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +human_body_map_2,human,rna_seq,efp,yes,efp_human,efp-frontend,efp_human,,1,1,efp_human: Illumina Body Map 2 - FPKM,"^([0-9]{1,7}(_[a-z])?_at)$|^(gnf1h[0-9]{5}(_[a-z])?_at)$|^(ENSG[0-9]{11}(\.[0-9]+)?)$|^([NX][MR]_[0-9]+(\.[0-9]+)?)$|^([0-9]{1,10})$|^(AFFX[-_][\w./-]+at)$|^([A-Za-z0-9][A-Za-z0-9._-]{0,39})$" +human_developmental,human,microarray,efp,yes,efp_human,efp-frontend,efp_human,,1,4,"efp_human: Circulatory Respiratory, Nervous, Reproductive, Skeletal Immune Digestive","^([0-9]{1,7}(_[a-z])?_at)$|^(gnf1h[0-9]{5}(_[a-z])?_at)$|^(ENSG[0-9]{11}(\.[0-9]+)?)$|^([NX][MR]_[0-9]+(\.[0-9]+)?)$|^([0-9]{1,10})$|^(AFFX[-_][\w./-]+at)$|^([A-Za-z0-9][A-Za-z0-9._-]{0,39})$" +human_developmental_SpongeLab,human,microarray,legacy_not_in_dropdown,no,efp_human,species-fallback,,,0,0,,"^([0-9]{1,7}(_[a-z])?_at)$|^(gnf1h[0-9]{5}(_[a-z])?_at)$|^(ENSG[0-9]{11}(\.[0-9]+)?)$|^([NX][MR]_[0-9]+(\.[0-9]+)?)$|^([0-9]{1,10})$|^(AFFX[-_][\w./-]+at)$|^([A-Za-z0-9][A-Za-z0-9._-]{0,39})$" +human_diseased,human,microarray,legacy_not_in_dropdown,no,efp_human,species-fallback,,,0,0,,"^([0-9]{1,7}(_[a-z])?_at)$|^(gnf1h[0-9]{5}(_[a-z])?_at)$|^(ENSG[0-9]{11}(\.[0-9]+)?)$|^([NX][MR]_[0-9]+(\.[0-9]+)?)$|^([0-9]{1,10})$|^(AFFX[-_][\w./-]+at)$|^([A-Za-z0-9][A-Za-z0-9._-]{0,39})$" +kalanchoe,kalanchoe,rna_seq,efp,yes,efp_kalanchoe,efp-frontend,efp_kalanchoe,,1,1,efp_kalanchoe: Light Response,^(Kaladp\d+s\d+)$ +kalanchoe_time_course_analysis,kalanchoe,rna_seq,legacy_not_in_dropdown,no,efp_kalanchoe,species-fallback,,,0,0,,^(Kaladp\d+s\d+)$ +little_millet,little_millet,rna_seq,efp,yes,efp_little_millet,efp-frontend,efp_little_millet,,1,1,efp_little_millet: Life Cycle,^(TRINITY_DN\d+_c\d+_g\d+_i\d+)$ +lupin_lcm_leaf,lupin,rna_seq,efp,yes,efp_lupin,efp-frontend,efp_lupin,,1,1,efp_lupin: LCM Leaf,"^(Luan_Oskar_.{1,12}_\d{1,12})$" +lupin_lcm_pod,lupin,rna_seq,efp,yes,efp_lupin,efp-frontend,efp_lupin,,1,1,efp_lupin: LCM Pod,"^(Luan_Oskar_.{1,12}_\d{1,12})$" +lupin_lcm_stem,lupin,rna_seq,efp,yes,efp_lupin,efp-frontend,efp_lupin,,1,1,efp_lupin: LCM Stem,"^(Luan_Oskar_.{1,12}_\d{1,12})$" +lupin_pod_seed,lupin,rna_seq,legacy_not_in_dropdown,no,efp_lupin,species-fallback,,,0,0,,"^(Luan_Oskar_.{1,12}_\d{1,12})$" +lupin_whole_plant,lupin,rna_seq,efp,yes,efp_lupin,efp-frontend,efp_lupin,,1,1,efp_lupin: Whole Plant,"^(Luan_Oskar_.{1,12}_\d{1,12})$" +maize_RMA_linear,maize,rna_seq,both,yes,efp_maize,efp-frontend,efp_maize,eplant_maize,2,2,efp_maize: Sekhon et al Atlas | eplant_maize: Sekhon Atlas,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_RMA_log,maize,rna_seq,legacy_not_in_dropdown,no,efp_maize,species-fallback,,,0,0,,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_atlas,maize,rna_seq,legacy_not_in_dropdown,no,efp_maize,species-fallback,,,0,0,,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_atlas_v5,maize,rna_seq,efp,yes,efp_maize,efp-frontend,efp_maize,,1,1,efp_maize: Hoopes et al Atlas V5,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_buell_lab,maize,rna_seq,efp,yes,efp_maize,efp-frontend,efp_maize,,1,2,"efp_maize: Hoopes et al Atlas, Hoopes et al Stress","^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_early_seed,maize,rna_seq,efp,yes,efp_maize,efp-frontend,efp_maize,,1,2,"efp_maize: Early Seed, Maize Kernel","^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_ears,maize,rna_seq,both,yes,efp_maize,efp-frontend,efp_maize,eplant_maize,2,2,efp_maize: Tassel and Ear Primordia | eplant_maize: Tassel And Ear Primordia,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_embryonic_leaf_development,maize,rna_seq,efp,yes,efp_maize,efp-frontend,efp_maize,,1,1,efp_maize: Embryonic Leaf Development,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_enzyme,maize,rna_seq,efp,yes,efp_maize_enzyme,efp-frontend,efp_maize_enzyme,,1,1,efp_maize_enzyme: Enzyme Activity,"(?i)^[a-z0-9\s\-\(\)]{1,50}$" +maize_gdowns,maize,microarray,both,yes,efp_maize,efp-frontend,efp_maize,eplant_maize,2,2,efp_maize: Downs et al Atlas | eplant_maize: Plant,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_iplant,maize,rna_seq,both,yes,efp_maize,efp-frontend,efp_maize,eplant_maize,2,2,efp_maize: maize iplant | eplant_maize: Leaf MeBS,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_kernel_v5,maize,rna_seq,efp,yes,efp_maize,efp-frontend,efp_maize,,1,1,efp_maize: Maize Kernel V5,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_leaf_gradient,maize,rna_seq,both,yes,efp_maize,efp-frontend,efp_maize,eplant_maize,2,2,efp_maize: maize leaf gradient | eplant_maize: Leaf Gradient,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_lipid_map,maize,rna_seq,legacy_not_in_dropdown,no,efp_maize,species-fallback,,,0,0,,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_metabolite,maize,rna_seq,efp,yes,efp_maize_metabolite,efp-frontend,efp_maize_metabolite,,1,1,efp_maize_metabolite: Metabolite Level,"(?i)^[a-z0-9\s,\.\-\(\)_'\+/]{1,80}$" +maize_nitrogen_use_efficiency,maize,rna_seq,legacy_not_in_dropdown,no,efp_maize,species-fallback,,,0,0,,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_rice_comparison,maize,rna_seq,efp,yes,efp_maize,efp-frontend,efp_maize,,1,1,efp_maize: maize rice comparison,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_root,maize,rna_seq,both,yes,efp_maize,efp-frontend,efp_maize,eplant_maize,2,2,efp_maize: Maize Root | eplant_maize: Root,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +maize_stress_v5,maize,rna_seq,efp,yes,efp_maize,efp-frontend,efp_maize,,1,1,efp_maize: Hoopes et al Stress V5,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +mangosteen_aril_vs_rind,mangosteen,rna_seq,efp,yes,efp_mangosteen,efp-frontend,efp_mangosteen,,1,1,efp_mangosteen: Aril vs Rind,"^(DN\d{1,10})$" +mangosteen_callus,mangosteen,rna_seq,efp,yes,efp_mangosteen,efp-frontend,efp_mangosteen,,1,1,efp_mangosteen: Callus,"^(DN\d{1,10})$" +mangosteen_diseased_vs_normal,mangosteen,rna_seq,efp,yes,efp_mangosteen,efp-frontend,efp_mangosteen,,1,1,efp_mangosteen: Diseased vs Normal,"^(DN\d{1,10})$" +mangosteen_fruit_ripening,mangosteen,rna_seq,efp,yes,efp_mangosteen,efp-frontend,efp_mangosteen,,1,1,efp_mangosteen: Fruit Ripening,"^(DN\d{1,10})$" +mangosteen_seed_development,mangosteen,rna_seq,efp,yes,efp_mangosteen,efp-frontend,efp_mangosteen,,1,1,efp_mangosteen: Seed Development,"^(DN\d{1,10})$" +mangosteen_seed_development_germination,mangosteen,rna_seq,legacy_not_in_dropdown,no,efp_mangosteen,species-fallback,,,0,0,,"^(DN\d{1,10})$" +mangosteen_seed_germination,mangosteen,rna_seq,efp,yes,efp_mangosteen,efp-frontend,efp_mangosteen,,1,1,efp_mangosteen: Seed Germination,"^(DN\d{1,10})$" +marchantia_organ_stress,marchantia,rna_seq,efp,yes,efp_marchantia,efp-frontend,efp_marchantia,,1,1,efp_marchantia: Expression Atlas,"^(Mp[A-Za-z]?g[0-9]{1,7}\.[0-9]{1,3})$|^(Mp[A-Za-z]?[0-9]+g[0-9]+\.[0-9]+)$" +medicago_mas,medicago,microarray,both,yes,efp_medicago,efp-frontend,efp_medicago,eplant_medicago,2,2,efp_medicago: medicago mas | eplant_medicago: Plant,"^(Medtr[0-9]g[0-9]{6}(\.[0-9]+)?)$|^(Medtr[0-9]{4}s[0-9]{4})$|^((Mtr|Msa|Sme)(Affx)?\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$|^(Medtr_v1_[0-9]{6})$" +medicago_rma,medicago,microarray,efp,yes,efp_medicago,efp-frontend,efp_medicago,,1,1,efp_medicago: medicago rma,"^(Medtr[0-9]g[0-9]{6}(\.[0-9]+)?)$|^(Medtr[0-9]{4}s[0-9]{4})$|^((Mtr|Msa|Sme)(Affx)?\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$|^(Medtr_v1_[0-9]{6})$" +medicago_root,medicago,rna_seq,eplant,yes,efp_medicago,eplant-frontend(shares eFP regex),,eplant_medicago,1,2,"eplant_medicago: Root, Root Component","^(Medtr[0-9]g[0-9]{6}(\.[0-9]+)?)$|^(Medtr[0-9]{4}s[0-9]{4})$|^((Mtr|Msa|Sme)(Affx)?\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$|^(Medtr_v1_[0-9]{6})$" +medicago_root_v5,medicago,rna_seq,legacy_not_in_dropdown,no,efp_medicago,species-fallback,,,0,0,,"^(Medtr[0-9]g[0-9]{6}(\.[0-9]+)?)$|^(Medtr[0-9]{4}s[0-9]{4})$|^((Mtr|Msa|Sme)(Affx)?\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$|^(Medtr_v1_[0-9]{6})$" +medicago_seed,medicago,rna_seq,both,yes,efp_medicago,efp-frontend,efp_medicago,eplant_medicago,2,2,efp_medicago: medicago seed | eplant_medicago: Seed,"^(Medtr[0-9]g[0-9]{6}(\.[0-9]+)?)$|^(Medtr[0-9]{4}s[0-9]{4})$|^((Mtr|Msa|Sme)(Affx)?\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$|^(Medtr_v1_[0-9]{6})$" +mouse_db,mouse,rna_seq,efp,yes,mouse_efp,efp-frontend(alias),efp_mouse,,1,1,efp_mouse: Mouse,"^(X[MR]_[0-9]{1,9}(\.[0-9]{1,3})?)$|^(N[MR]_[0-9]{1,9}(\.[0-9]{1,3})?)$|^(ENSMUSG[0-9]{1,15})$|^(MGI:[0-9]{1,10})$|^([A-Za-z0-9][A-Za-z0-9._-]{0,39})$" +oat,oat,rna_seq,efp,yes,efp_oat,efp-frontend,efp_oat,,1,1,efp_oat: Oat,"(^N0\.HOG\d{1,10}$|^\D{1,10}\.*\d{1,10}.{1,10}\d{1,10}$)" +phelipanche,phelipanche,rna_seq,efp,yes,efp_phelipanche,efp-frontend,efp_phelipanche,,1,1,efp_phelipanche: Phelipanche,"^(OrAeBC\d+_\d+\.\d+)$|^(OrAeBC\d+_\d+)$|^(At\d[gcm]\d{1,6})$" +physcomitrella_db,physcomitrella,rna_seq,efp,yes,efp_physcomitrella,efp-frontend,efp_physcomitrella,,1,1,efp_physcomitrella: Physcomitrella,^(Pp)\d+s\d+_\d+V\d\.\d$|^Phypa_\d+$ +poplar,poplar,microarray,both,yes,efp_poplar,efp-frontend,efp_poplar,eplant_poplar,2,4,"efp_poplar: Poplar, PoplarTreatment | eplant_poplar: Poplar Treatment, Plant",^(Potri\.([0-9]{3}G|T)[0-9]{6}(\.[0-9]+)?)$|^(POPTR_[0-9]{4}s[0-9]{5}(\.[1-5])?)$|^(Ptp(Affx)?\.[0-9]+\.[0-9]+\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^(AFFX[-_][\w./-]+at)$ +poplar_hormone,poplar,rna_seq,legacy_not_in_dropdown,no,efp_poplar,species-fallback,,,0,0,,^(Potri\.([0-9]{3}G|T)[0-9]{6}(\.[0-9]+)?)$|^(POPTR_[0-9]{4}s[0-9]{5}(\.[1-5])?)$|^(Ptp(Affx)?\.[0-9]+\.[0-9]+\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^(AFFX[-_][\w./-]+at)$ +poplar_leaf,poplar,rna_seq,eplant,yes,efp_poplar,eplant-frontend(shares eFP regex),,eplant_poplar,1,1,eplant_poplar: World Leaf,^(Potri\.([0-9]{3}G|T)[0-9]{6}(\.[0-9]+)?)$|^(POPTR_[0-9]{4}s[0-9]{5}(\.[1-5])?)$|^(Ptp(Affx)?\.[0-9]+\.[0-9]+\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^(AFFX[-_][\w./-]+at)$ +poplar_xylem,poplar,rna_seq,eplant,yes,efp_poplar,eplant-frontend(shares eFP regex),,eplant_poplar,1,1,eplant_poplar: World Xylem,^(Potri\.([0-9]{3}G|T)[0-9]{6}(\.[0-9]+)?)$|^(POPTR_[0-9]{4}s[0-9]{5}(\.[1-5])?)$|^(Ptp(Affx)?\.[0-9]+\.[0-9]+\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^(AFFX[-_][\w./-]+at)$ +potato_dev,potato,rna_seq,both,yes,efp_potato,efp-frontend,efp_potato,eplant_potato,2,2,efp_potato: Potato Developmental | eplant_potato: Plant,^(PGSC0003DMG4\d{8})$ +potato_stress,potato,rna_seq,both,yes,efp_potato,efp-frontend,efp_potato,eplant_potato,2,2,efp_potato: Potato Stress | eplant_potato: Potato Stress,^(PGSC0003DMG4\d{8})$ +potato_wounding,potato,rna_seq,legacy_not_in_dropdown,no,efp_potato,species-fallback,,,0,0,,^(PGSC0003DMG4\d{8})$ +quinoa_nutrient,quinoa,rna_seq,legacy_not_in_dropdown,no,(unassigned),UNRESOLVED,,,0,0,, +rice_abiotic_stress_sc_pseudobulk,rice,rna_seq,efp,yes,efp_rice,efp-frontend,efp_rice,,1,1,efp_rice: rice single cell,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^(Os[0-9]{2}g[0-9]{7})$|^(Chr(Sy|Un)\.fgenesh\.gene\.[0-9]+)$|^((Os|OsAffx)\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$" +rice_drought_heat_stress,rice,rna_seq,efp,yes,efp_rice,efp-frontend,efp_rice,,1,1,efp_rice: rice drought heat stress,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^(Os[0-9]{2}g[0-9]{7})$|^(Chr(Sy|Un)\.fgenesh\.gene\.[0-9]+)$|^((Os|OsAffx)\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$" +rice_leaf_gradient,rice,rna_seq,both,yes,efp_rice,efp-frontend,efp_rice,eplant_rice,2,2,efp_rice: rice leaf gradient | eplant_rice: Leaf Gradient,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^(Os[0-9]{2}g[0-9]{7})$|^(Chr(Sy|Un)\.fgenesh\.gene\.[0-9]+)$|^((Os|OsAffx)\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$" +rice_maize_comparison,rice,rna_seq,efp,yes,efp_rice,efp-frontend,efp_rice,,1,1,efp_rice: rice maize comparison,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^(Os[0-9]{2}g[0-9]{7})$|^(Chr(Sy|Un)\.fgenesh\.gene\.[0-9]+)$|^((Os|OsAffx)\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$" +rice_mas,rice,microarray,both,yes,efp_rice,efp-frontend,efp_rice,eplant_rice,2,8,"efp_rice: rice mas, riceanoxia mas, ricestigma mas, ricestress mas | eplant_rice: Anoxia, Stress, Stigma, Plant","^(LOC_Os[0-9]{2}g[0-9]{5})$|^(Os[0-9]{2}g[0-9]{7})$|^(Chr(Sy|Un)\.fgenesh\.gene\.[0-9]+)$|^((Os|OsAffx)\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$" +rice_metabolite,rice,rna_seq,efp,yes,efp_rice_metabolite,efp-frontend,efp_rice_metabolite,,1,1,efp_rice_metabolite: Metabolite Level,"(?i)^[a-z0-9,\s\.\-]{1,40}$" +rice_rma,rice,microarray,efp,yes,efp_rice,efp-frontend,efp_rice,,1,4,"efp_rice: rice rma, riceanoxia rma, ricestigma rma, ricestress rma","^(LOC_Os[0-9]{2}g[0-9]{5})$|^(Os[0-9]{2}g[0-9]{7})$|^(Chr(Sy|Un)\.fgenesh\.gene\.[0-9]+)$|^((Os|OsAffx)\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$" +rice_root,rice,rna_seq,eplant,yes,efp_rice,eplant-frontend(shares eFP regex),,eplant_rice,1,1,eplant_rice: Root,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^(Os[0-9]{2}g[0-9]{7})$|^(Chr(Sy|Un)\.fgenesh\.gene\.[0-9]+)$|^((Os|OsAffx)\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$" +selaginella,selaginella,rna_seq,efp,yes,efp_selaginella,efp-frontend,efp_selaginella,,1,1,efp_selaginella: Selaginella Atlas,^(Smo\d+)$ +sorghum_atlas_w_BS_cells,sorghum,rna_seq,efp,yes,efp_sorghum,efp-frontend,efp_sorghum,,1,1,efp_sorghum: Atlas w BS Cells,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_comparative_transcriptomics,sorghum,rna_seq,legacy_not_in_dropdown,no,efp_sorghum,species-fallback,,,0,0,,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_developmental,sorghum,rna_seq,efp,yes,efp_sorghum,efp-frontend,efp_sorghum,,1,1,efp_sorghum: Developmental Atlas,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_developmental_2,sorghum,rna_seq,legacy_not_in_dropdown,no,efp_sorghum,species-fallback,,,0,0,,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_flowering_activation,sorghum,rna_seq,efp,yes,efp_sorghum,efp-frontend,efp_sorghum,,1,1,efp_sorghum: Flowering Activation,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_low_phosphorus,sorghum,rna_seq,efp,yes,efp_sorghum,efp-frontend,efp_sorghum,,1,1,efp_sorghum: Low Phosphorus,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_nitrogen_stress,sorghum,rna_seq,legacy_not_in_dropdown,no,efp_sorghum,species-fallback,,,0,0,,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_nitrogen_use_efficiency,sorghum,rna_seq,legacy_not_in_dropdown,no,efp_sorghum,species-fallback,,,0,0,,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_phosphate_stress,sorghum,rna_seq,efp,yes,efp_sorghum,efp-frontend,efp_sorghum,,1,1,efp_sorghum: Phosphate Stress,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_plasma,sorghum,rna_seq,legacy_not_in_dropdown,no,efp_sorghum,species-fallback,,,0,0,,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_saline_alkali_stress,sorghum,rna_seq,efp,yes,efp_sorghum,efp-frontend,efp_sorghum,,1,1,efp_sorghum: Saline Alkali Stress,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_stress,sorghum,rna_seq,efp,yes,efp_sorghum,efp-frontend,efp_sorghum,,1,1,efp_sorghum: Stress Atlas,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_strigolactone_variation,sorghum,rna_seq,efp,yes,efp_sorghum,efp-frontend,efp_sorghum,,1,1,efp_sorghum: Strigolactone Variation,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_sulfur_stress,sorghum,rna_seq,efp,yes,efp_sorghum,efp-frontend,efp_sorghum,,1,1,efp_sorghum: Sulfur Stress,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_temperature_stress,sorghum,rna_seq,legacy_not_in_dropdown,no,efp_sorghum,species-fallback,,,0,0,,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +sorghum_vascularization_and_internode,sorghum,rna_seq,efp,yes,efp_sorghum,efp-frontend,efp_sorghum,,1,1,efp_sorghum: Vascularization and Internode,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +soybean,soybean,rna_seq,both,yes,efp_soybean,efp-frontend,efp_soybean,eplant_soybean,2,2,efp_soybean: soybean | eplant_soybean: Plant,"^(Glyma[0-9]{1,3}g[0-9]{1,6}(\.[0-9]+)?)$|^(Glyma\.[0-9]{1,3}g[0-9]{1,8}(\.[0-9]+)?)$|^(Glyma[0-9]{4}s[0-9]{2,5}(\.[0-9]+)?)$" +soybean_embryonic_development,soybean,rna_seq,efp,yes,efp_soybean,efp-frontend,efp_soybean,,1,1,efp_soybean: soybean embryonic development,"^(Glyma[0-9]{1,3}g[0-9]{1,6}(\.[0-9]+)?)$|^(Glyma\.[0-9]{1,3}g[0-9]{1,8}(\.[0-9]+)?)$|^(Glyma[0-9]{4}s[0-9]{2,5}(\.[0-9]+)?)$" +soybean_heart_cotyledon_globular,soybean,rna_seq,efp,yes,efp_soybean,efp-frontend,efp_soybean,,1,1,efp_soybean: soybean heart cotyledon globular,"^(Glyma[0-9]{1,3}g[0-9]{1,6}(\.[0-9]+)?)$|^(Glyma\.[0-9]{1,3}g[0-9]{1,8}(\.[0-9]+)?)$|^(Glyma[0-9]{4}s[0-9]{2,5}(\.[0-9]+)?)$" +soybean_senescence,soybean,rna_seq,efp,yes,efp_soybean,efp-frontend,efp_soybean,,1,1,efp_soybean: soybean senescence,"^(Glyma[0-9]{1,3}g[0-9]{1,6}(\.[0-9]+)?)$|^(Glyma\.[0-9]{1,3}g[0-9]{1,8}(\.[0-9]+)?)$|^(Glyma[0-9]{4}s[0-9]{2,5}(\.[0-9]+)?)$" +soybean_severin,soybean,rna_seq,both,yes,efp_soybean,efp-frontend,efp_soybean,eplant_soybean,2,2,efp_soybean: soybean severin | eplant_soybean: Soybean Severin,"^(Glyma[0-9]{1,3}g[0-9]{1,6}(\.[0-9]+)?)$|^(Glyma\.[0-9]{1,3}g[0-9]{1,8}(\.[0-9]+)?)$|^(Glyma[0-9]{4}s[0-9]{2,5}(\.[0-9]+)?)$" +spruce,spruce,rna_seq,legacy_not_in_dropdown,no,(unassigned),UNRESOLVED,,,0,0,, +strawberry,strawberry,rna_seq,efp,yes,efp_strawberry,efp-frontend,efp_strawberry,,1,2,"efp_strawberry: Developmental Map Strawberry Flower and Fruit, Strawberry Green vs White Stage","^(FvH4_c?\d{1,3}g\d{1,7})$|^(gene\d{1,10})$" +striga,striga,rna_seq,efp,yes,efp_striga,efp-frontend,efp_striga,,1,1,efp_striga: Striga Atlas,"^(StHeBC3\_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" +sugarcane_culms,sugarcane,rna_seq,eplant,yes,efp_sugarcane,eplant-frontend(shares eFP regex),,eplant_sugarcane,1,1,eplant_sugarcane: Culms,"^(S[a-zA-Z]{1,4}[A-Za-z0-9._-]{2,40})$" +sugarcane_leaf,sugarcane,rna_seq,eplant,yes,efp_sugarcane,eplant-frontend(shares eFP regex),,eplant_sugarcane,1,1,eplant_sugarcane: Leaf,"^(S[a-zA-Z]{1,4}[A-Za-z0-9._-]{2,40})$" +sunflower,sunflower,rna_seq,eplant,yes,efp_sunflower,eplant-frontend(shares eFP regex),,eplant_sunflower,1,1,eplant_sunflower: Plant,"^(Ha(n)?[A-Za-z0-9._-]{3,40})$|^(Ha412[A-Za-z0-9._-]+)$" +thellungiella_db,thellungiella,rna_seq,efp,yes,efp_eutrema,species-special-case,efp_eutrema,,1,1,efp_eutrema: Eutrema,^(Thhalv[0-9]{8}m\.g)$|^(XLOC_[0-9]{6})$|^(nXLOC_[0-9]{6})$|^(At[0-9]g[0-9]{5})$ +tomato,tomato,rna_seq,efp,yes,efp_tomato,efp-frontend,efp_tomato,,1,1,efp_tomato: Rose Lab Atlas,"^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +tomato_ils,tomato,rna_seq,both,yes,efp_tomato,efp-frontend,efp_tomato,eplant_tomato,2,2,efp_tomato: ILs Leaf Chitwood et al | eplant_tomato: LeafILs,"^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +tomato_ils2,tomato,rna_seq,both,yes,efp_tomato,efp-frontend,efp_tomato,eplant_tomato,2,2,efp_tomato: ILs Root Tip Brady Lab | eplant_tomato: RootILs,"^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +tomato_ils3,tomato,rna_seq,legacy_not_in_dropdown,no,efp_tomato,species-fallback,,,0,0,,"^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +tomato_meristem,tomato,rna_seq,efp,yes,efp_tomato,efp-frontend,efp_tomato,,1,1,efp_tomato: Tomato Meristem,"^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +tomato_renormalized,tomato,rna_seq,both,yes,efp_tomato,efp-frontend,efp_tomato,eplant_tomato,2,3,"efp_tomato: Rose Lab Atlas Renormalized | eplant_tomato: Fruit, Plant","^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +tomato_root,tomato,rna_seq,eplant,yes,efp_tomato,eplant-frontend(shares eFP regex),,eplant_tomato,1,1,eplant_tomato: Root,"^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +tomato_root_field_pot,tomato,rna_seq,eplant,yes,efp_tomato,eplant-frontend(shares eFP regex),,eplant_tomato,1,1,eplant_tomato: RootFieldPot,"^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +tomato_s_pennellii,tomato,rna_seq,both,yes,efp_tomato,efp-frontend,efp_tomato,eplant_tomato,2,2,efp_tomato: M82 S pennellii Atlases Koenig et al | eplant_tomato: TomatoAtlases,"^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +tomato_seed,tomato,rna_seq,efp,yes,efp_tomato,efp-frontend,efp_tomato,,1,1,efp_tomato: SEED Lab Angers,"^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +tomato_shade_mutants,tomato,rna_seq,efp,yes,efp_tomato,efp-frontend,efp_tomato,,1,1,efp_tomato: Shade Mutants,"^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +tomato_shade_timecourse,tomato,rna_seq,efp,yes,efp_tomato,efp-frontend,efp_tomato,,1,1,efp_tomato: Shade Timecourse WT,"^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +tomato_trait,tomato,rna_seq,legacy_not_in_dropdown,no,efp_tomato,species-fallback,,,0,0,,"^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +triphysaria,triphysaria,rna_seq,efp,yes,efp_triphysaria,efp-frontend,efp_triphysaria,,1,1,efp_triphysaria: Triphysaria,"^(TrVeBC\d+_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" +triticale,triticale,microarray,efp,yes,efp_triticale,efp-frontend,efp_triticale,,1,1,efp_triticale: triticale,^((Ta|TaAffx)\.[0-9]+\.[0-9]+\.[A-Z][0-9]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$ +triticale_mas,triticale,microarray,efp,yes,efp_triticale,efp-frontend,efp_triticale,,1,1,efp_triticale: triticale mas,^((Ta|TaAffx)\.[0-9]+\.[0-9]+\.[A-Z][0-9]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$ +tung_tree,tung_tree,rna_seq,efp,yes,efp_tung_tree,efp-frontend,efp_tung_tree,,1,1,efp_tung_tree: Tung Tree,^(Vf\d+G\d+)$ +durum_wheat_abiotic_stress,wheat,rna_seq,efp,yes,efp_durum_wheat,efp-frontend,efp_durum_wheat,,1,1,efp_durum_wheat: Abiotic Stress,"^(TrturSVE[A-Za-z0-9]{1,6}G[0-9]{1,12}(_[A-Za-z]+)?)$" +durum_wheat_biotic_stress,wheat,rna_seq,efp,yes,efp_durum_wheat,efp-frontend,efp_durum_wheat,,1,1,efp_durum_wheat: Biotic Stress,"^(TrturSVE[A-Za-z0-9]{1,6}G[0-9]{1,12}(_[A-Za-z]+)?)$" +durum_wheat_development,wheat,rna_seq,efp,yes,efp_durum_wheat,efp-frontend,efp_durum_wheat,,1,1,efp_durum_wheat: Development,"^(TrturSVE[A-Za-z0-9]{1,6}G[0-9]{1,12}(_[A-Za-z]+)?)$" +wheat,wheat,rna_seq,both,yes,efp_wheat,efp-frontend,efp_wheat,eplant_wheat,2,4,"efp_wheat: Developmental Atlas | eplant_wheat: EarlyStages, MiddleStages, LateStages","^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$" +wheat_abiotic_stress,wheat,rna_seq,efp,yes,efp_wheat,efp-frontend,efp_wheat,,1,1,efp_wheat: Wheat Abiotic Stress,"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$" +wheat_embryogenesis,wheat,rna_seq,efp,yes,efp_wheat,efp-frontend,efp_wheat,,1,1,efp_wheat: Wheat Embryogenesis,"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$" +wheat_meiosis,wheat,rna_seq,efp,yes,efp_wheat,efp-frontend,efp_wheat,,1,1,efp_wheat: Wheat Meiosis,"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$" +wheat_root,wheat,rna_seq,legacy_not_in_dropdown,no,efp_wheat,species-fallback,,,0,0,,"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$" +willow,willow,rna_seq,legacy_not_in_dropdown,no,(unassigned),UNRESOLVED,,,0,0,, diff --git a/data/regex_master_list_efp_eplant/bar_regex_master.csv b/data/regex_master_list_efp_eplant/bar_regex_master.csv new file mode 100644 index 00000000..6723bee1 --- /dev/null +++ b/data/regex_master_list_efp_eplant/bar_regex_master.csv @@ -0,0 +1,59 @@ +efp_project,regex +efp,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +efp_Eutrema,^(Thhalv[0-9]{8}m\.g)$|^(XLOC_[0-9]{6})$|^(nXLOC_[0-9]{6})$|^(At[0-9]g[0-9]{5})$ +efp_actinidia,"^(Acc\d+\.\d{0,3})$" +efp_apple,"^(MfusH1_\d\dg\d{1,8})$" +efp_arabidopsis,"^([Aa][Tt][12345CM][Gg][0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$" +efp_arabidopsis_lipid,"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$" +efp_arachis,^(Adur\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Aipa_c\d+_g\d+_i\d+)$|^(Aipa\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Adur_c\d+_g\d+_i\d+)$ +efp_barley,"^((HM|HV).*)$|^(HORVU[\w.]+)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(A[JK][0-9]{6}\.[0-9])$|^([0-9-]+_(Reg|R)_[0-9-]+(_x_|_s_|_)?at)$|^([0-9-]+\.AF[0-9]+(_x_|_s_|_)?at)$|^(A[0-9]{5}\.[0-9](_x_|_s_|_)?at)$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_CDS-[0-9]{1,2})?(_x_|_s_|_)?at)$|^(AFFX-[A-Za-z0-9_/-]+(_x_|_s_|_)?at)$|^((Chlor|Mito)?Contig[0-9]{1,6}(_(3|5|M))?(_x_|_s_|_)?at)$|^(D[0-9]{5}(_x_|_s_|_)?at)$|^(Dhn[0-9]{2}\(Morex\)(_x_|_s_|_)?at)$|^(E[A-Za-z]{3}[0-9]{2}_SQ[0-9]{3}_[A-Z][0-9]{2}[a-z]?(_x_|_s_|_)?at)$|^(Franka(_b_|_)3pri[0-9]{1,2}(_x_|_s_|_)?at)$|^(H[A-Z][0-9]{1,4}[A-Z][0-9]{1,2}[a-z]?(_x_|_s_|_)?at)$|^(Mla[A-Za-z0-9_-]+at)$|^(S[0-9]{10}[A-Z][0-9]{2}[A-Z][0-9](_x_|_s_|_)?at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z][0-9]{2}(_x_|_s_|_)?at)$|^(HO)$" +efp_brachypodium,^(Bradi[0-9]+g[0-9]+(\.[0-9]+)?)$|^(Bradi[0-9]+s[0-9]+(\.[0-9]+)?)$|^(Bradi[0-9]+\.g[0-9]+)$ +efp_brachypodium_metabolites,"(?i)^[a-z\s\-]{1,60}$" +efp_brassica_rapa,"^(Bra.\d+g\d{0,10})$|^(Bra[AC]nng\d+)$" +efp_cacao_ccn,"^(CCN-51_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +efp_cacao_sca,"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$" +efp_cacao_tc,^(Tc([0-9]+|Un)v2_g[0-9]+)$ +efp_camelina,"^(Csa\d{0,5}[gs]\d{0,6}.\d{0,3})$|^(At\d[cgm]\d{0,6})$" +efp_cannabis,(^C\d+$)|(^scaffold\d+$)|(^AGQN\d+$) +efp_canola,"^(Bna([A-C][0-9]{2}|[A-C]nn|Unn)g[0-9]{1,8}[A-Z]?)$|^(BoC[0-9]+g[0-9]+\.[0-9]+V[0-9])$|^(BrChr[0-9]+g[0-9]+\.[0-9]+V[0-9])$|^(Contig[0-9]+)$" +efp_durum_wheat,"^(TrturSVE[A-Za-z0-9]{1,6}G[0-9]{1,12}(_[A-Za-z]+)?)$" +efp_eucalyptus,^(Eucgr\.[A-Za-z][0-9]{5}(\.[0-9]+)?)$|^(Eucgr\.[A-Za-z0-9._-]+)$ +efp_euphorbia,"^(Ep_chr\d_g\d{1,8})$" +efp_eutrema,^(Thhalv[0-9]{8}m\.g)$|^(XLOC_[0-9]{6})$|^(nXLOC_[0-9]{6})$|^(At[0-9]g[0-9]{5})$ +efp_grape,^(CHR|VIT_|CHRUN) +efp_human,"^([0-9]{1,7}(_[a-z])?_at)$|^(gnf1h[0-9]{5}(_[a-z])?_at)$|^(ENSG[0-9]{11}(\.[0-9]+)?)$|^([NX][MR]_[0-9]+(\.[0-9]+)?)$|^([0-9]{1,10})$|^(AFFX[-_][\w./-]+at)$|^([A-Za-z0-9][A-Za-z0-9._-]{0,39})$" +efp_kalanchoe,^(Kaladp\d+s\d+)$ +efp_little_millet,^(TRINITY_DN\d+_c\d+_g\d+_i\d+)$ +efp_lupin,"^(Luan_Oskar_.{1,12}_\d{1,12})$" +efp_maize,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^([A-Z]{2}[0-9]{6}(\.[0-9])?(_(a|s|x|f|i))?_at)$|^(Ctrl_[A-Za-z0-9._-]+_at)$|^(AFFX[-_][\w./-]+at)$|^(Zm[0-9]{6}(_[xsa])?_at)$" +efp_maize_enzyme,"(?i)^[a-z0-9\s\-\(\)]{1,50}$" +efp_maize_lipid_map,"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$" +efp_maize_metabolite,"(?i)^[a-z0-9\s,\.\-\(\)_'\+/]{1,80}$" +efp_maize_transcriptomics,"^([A-Z]{2}[0-9]{6}\.[0-9]{1,2}_FGT?[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm[0-9]+d[0-9]+)$|^(Zm[0-9]{1,10}eb[0-9]{1,10})$|^(Zm[0-9]{6}(_[xsa])?_at)$" +efp_mangosteen,"^(DN\d{1,10})$" +efp_marchantia,"^(Mp[A-Za-z]?g[0-9]{1,7}\.[0-9]{1,3})$|^(Mp[A-Za-z]?[0-9]+g[0-9]+\.[0-9]+)$" +efp_medicago,"^(Medtr[0-9]g[0-9]{6}(\.[0-9]+)?)$|^(Medtr[0-9]{4}s[0-9]{4})$|^((Mtr|Msa|Sme)(Affx)?\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$|^(Medtr_v1_[0-9]{6})$" +efp_oat,"(^N0\.HOG\d{1,10}$|^\D{1,10}\.*\d{1,10}.{1,10}\d{1,10}$)" +efp_phelipanche,"^(OrAeBC\d+_\d+\.\d+)$|^(OrAeBC\d+_\d+)$|^(At\d[gcm]\d{1,6})$" +efp_physcomitrella,^(Pp)\d+s\d+_\d+V\d\.\d$|^Phypa_\d+$ +efp_poplar,^(Potri\.([0-9]{3}G|T)[0-9]{6}(\.[0-9]+)?)$|^(POPTR_[0-9]{4}s[0-9]{5}(\.[1-5])?)$|^(Ptp(Affx)?\.[0-9]+\.[0-9]+\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^(AFFX[-_][\w./-]+at)$ +efp_potato,^(PGSC0003DMG4\d{8})$ +efp_rice,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^(Os[0-9]{2}g[0-9]{7})$|^(Chr(Sy|Un)\.fgenesh\.gene\.[0-9]+)$|^((Os|OsAffx)\.[0-9]+\.[0-9]+\.[SA][0-9](_(a|s|x)_at|_at))$|^(RPTR-[A-Za-z]{2,3}-[A-Za-z0-9._-]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$" +efp_rice_metabolite,"(?i)^[a-z0-9,\s\.\-]{1,40}$" +efp_rice_transcriptomics,^(LOC_Os[0-9]{2}g[0-9]{5})$|^(Os[0-9]{2}g[0-9]{7})$|^(Chr(Sy|Un)\.fgenesh\.gene\.[0-9]+)$|^((Os|OsAffx)\.[0-9]+\.[0-9]+\.[SA][0-9]_(a_)?(at|x_at|s_at))$ +efp_seedcoat,"^(At[12345CM]g[0-9]{5}(\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(\D[0-9]+_[0-9]+)$|^(At[0-9]{8})$|^(Alien[0-9]{1,2})$|^(atc[0-9]{2})$|^(3xSSC)$" +efp_selaginella,^(Smo\d+)$ +efp_sorghum,"^(Sobic\.[A-Z]?[0-9]{1,5}G[0-9]{1,10}(\.[0-9]+)?)$|^(Sobic\.K[0-9]{1,10}(\.[0-9]+)?)$|^(SORBI_[0-9]{1,6}G[0-9]{1,10})$|^(ENSRNA[0-9]{1,12})$" +efp_soybean,"^(Glyma[0-9]{1,3}g[0-9]{1,6}(\.[0-9]+)?)$|^(Glyma\.[0-9]{1,3}g[0-9]{1,8}(\.[0-9]+)?)$|^(Glyma[0-9]{4}s[0-9]{2,5}(\.[0-9]+)?)$" +efp_strawberry,"^(FvH4_c?\d{1,3}g\d{1,7})$|^(gene\d{1,10})$" +efp_striga,"^(StHeBC3\_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" +efp_sugarcane,"^(S[a-zA-Z]{1,4}[A-Za-z0-9._-]{2,40})$" +efp_sunflower,"^(Ha(n)?[A-Za-z0-9._-]{3,40})$|^(Ha412[A-Za-z0-9._-]+)$" +efp_tomato,"^(Solyc[0-9]{2}g[0-9]{6}(\.[0-9]+){0,2})$|^(TU[0-9]{6})$" +efp_tomato_trait,"^[A-Za-z][A-Za-z0-9\s\.,\-\(\)]{1,100}$" +efp_triphysaria,"^(TrVeBC\d+_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" +efp_triticale,^((Ta|TaAffx)\.[0-9]+\.[0-9]+\.[A-Z][0-9]+(_(a|s|x)_at|_at))$|^(AFFX[-_][\w./-]+at)$ +efp_tung_tree,^(Vf\d+G\d+)$ +efp_wheat,"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$" +efpconfig,".{0,16}" +mouse_efp,"^(X[MR]_[0-9]{1,9}(\.[0-9]{1,3})?)$|^(N[MR]_[0-9]{1,9}(\.[0-9]{1,3})?)$|^(ENSMUSG[0-9]{1,15})$|^(MGI:[0-9]{1,10})$|^([A-Za-z0-9][A-Za-z0-9._-]{0,39})$" diff --git a/data/regex_master_list_efp_eplant/bar_regex_registry.json b/data/regex_master_list_efp_eplant/bar_regex_registry.json new file mode 100644 index 00000000..0e5868aa --- /dev/null +++ b/data/regex_master_list_efp_eplant/bar_regex_registry.json @@ -0,0 +1,3881 @@ +{ + "_meta": { + "description": "BAR input-validation regexes, joined to the databases and frontends that use them. Regexes are keyed by eFP project name, but ePlant frontends share the same database and therefore the same regex \u2014 see projects[*].frontends / serves_eplant.", + "sources": [ + "master_db_list.json", + "bar_regex_master.csv" + ], + "n_databases": 193, + "n_projects": 58 + }, + "projects": { + "efp": { + "regex": "^([Aa][Tt][12345CM][Gg][0-9]{5}(\\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$", + "n_databases": 0, + "databases": [], + "frontends": [], + "serves_eplant": false + }, + "efp_Eutrema": { + "regex": "^(Thhalv[0-9]{8}m\\.g)$|^(XLOC_[0-9]{6})$|^(nXLOC_[0-9]{6})$|^(At[0-9]g[0-9]{5})$", + "n_databases": 0, + "databases": [], + "frontends": [], + "serves_eplant": false + }, + "efp_actinidia": { + "regex": "^(Acc\\d+\\.\\d{0,3})$", + "n_databases": 4, + "databases": [ + "actinidia_bud_development", + "actinidia_flower_fruit_development", + "actinidia_postharvest", + "actinidia_vegetative_growth" + ], + "frontends": [ + "efp_actinidia" + ], + "serves_eplant": false + }, + "efp_apple": { + "regex": "^(MfusH1_\\d\\dg\\d{1,8})$", + "n_databases": 1, + "databases": [ + "apple" + ], + "frontends": [ + "efp_apple" + ], + "serves_eplant": false + }, + "efp_arabidopsis": { + "regex": "^([Aa][Tt][12345CM][Gg][0-9]{5}(\\.[0-9]+)?)$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-[A-Za-z0-9_-]+(_|_x_|_s_)?at)$", + "n_databases": 29, + "databases": [ + "affydb", + "arabidopsis_ecotypes", + "atgenexp", + "atgenexp_hormone", + "atgenexp_pathogen", + "atgenexp_plus", + "atgenexp_stress", + "circadian_mutants", + "dna_damage", + "embryo", + "gc_drought", + "germination", + "guard_cell", + "gynoecium", + "heterodera_schachtii", + "hnahal", + "klepikova", + "lateral_root_initiation", + "light_series", + "meristem_db", + "meristem_db_new", + "rohan", + "root", + "root_Schaefer_lab", + "rpatel", + "seed_db", + "shoot_apex", + "silique", + "single_cell" + ], + "frontends": [ + "efp_arabidopsis", + "efp_arabidopsis_cell", + "eplant_arabidopsis" + ], + "serves_eplant": true + }, + "efp_arabidopsis_lipid": { + "regex": "(?i)^[a-z0-9\\s:;\\/\\[\\]_\\+\\-]{1,64}$", + "n_databases": 1, + "databases": [ + "lipid_map" + ], + "frontends": [ + "efp_arabidopsis_lipid" + ], + "serves_eplant": false + }, + "efp_arachis": { + "regex": "^(Adur\\d+_comp\\d+_c\\d+_seq\\d+)$|^(Gyn_Aipa_c\\d+_g\\d+_i\\d+)$|^(Aipa\\d+_comp\\d+_c\\d+_seq\\d+)$|^(Gyn_Adur_c\\d+_g\\d+_i\\d+)$", + "n_databases": 1, + "databases": [ + "arachis" + ], + "frontends": [ + "efp_arachis" + ], + "serves_eplant": false + }, + "efp_barley": { + "regex": "^((HM|HV).*)$|^(HORVU[\\w.]+)$|^(MLOC\\.[0-9]{4,6}\\.[0-9]{1,2})$|^(A[JK][0-9]{6}\\.[0-9])$|^([0-9-]+_(Reg|R)_[0-9-]+(_x_|_s_|_)?at)$|^([0-9-]+\\.AF[0-9]+(_x_|_s_|_)?at)$|^(A[0-9]{5}\\.[0-9](_x_|_s_|_)?at)$|^([A-Z]{2}[0-9]{6}(\\.[0-9])?(_CDS-[0-9]{1,2})?(_x_|_s_|_)?at)$|^(AFFX-[A-Za-z0-9_/-]+(_x_|_s_|_)?at)$|^((Chlor|Mito)?Contig[0-9]{1,6}(_(3|5|M))?(_x_|_s_|_)?at)$|^(D[0-9]{5}(_x_|_s_|_)?at)$|^(Dhn[0-9]{2}\\(Morex\\)(_x_|_s_|_)?at)$|^(E[A-Za-z]{3}[0-9]{2}_SQ[0-9]{3}_[A-Z][0-9]{2}[a-z]?(_x_|_s_|_)?at)$|^(Franka(_b_|_)3pri[0-9]{1,2}(_x_|_s_|_)?at)$|^(H[A-Z][0-9]{1,4}[A-Z][0-9]{1,2}[a-z]?(_x_|_s_|_)?at)$|^(Mla[A-Za-z0-9_-]+at)$|^(S[0-9]{10}[A-Z][0-9]{2}[A-Z][0-9](_x_|_s_|_)?at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z][0-9]{2}(_x_|_s_|_)?at)$|^(HO)$", + "n_databases": 5, + "databases": [ + "barley_mas", + "barley_rma", + "barley_seed", + "barley_spike_meristem", + "barley_spike_meristem_v3" + ], + "frontends": [ + "efp_barley", + "eplant_barley", + "eplant_barley_legacy" + ], + "serves_eplant": true + }, + "efp_brachypodium": { + "regex": "^(Bradi[0-9]+g[0-9]+(\\.[0-9]+)?)$|^(Bradi[0-9]+s[0-9]+(\\.[0-9]+)?)$|^(Bradi[0-9]+\\.g[0-9]+)$", + "n_databases": 5, + "databases": [ + "brachypodium", + "brachypodium_Bd21", + "brachypodium_embryogenesis", + "brachypodium_grains", + "brachypodium_photo_thermocycle" + ], + "frontends": [ + "efp_brachypodium" + ], + "serves_eplant": false + }, + "efp_brachypodium_metabolites": { + "regex": "(?i)^[a-z\\s\\-]{1,60}$", + "n_databases": 1, + "databases": [ + "brachypodium_metabolites_map" + ], + "frontends": [ + "efp_brachypodium_metabolites" + ], + "serves_eplant": false + }, + "efp_brassica_rapa": { + "regex": "^(Bra.\\d+g\\d{0,10})$|^(Bra[AC]nng\\d+)$", + "n_databases": 2, + "databases": [ + "brassica_rapa", + "brassica_rapa_developmental_atlas" + ], + "frontends": [ + "efp_brassica_rapa" + ], + "serves_eplant": false + }, + "efp_cacao_ccn": { + "regex": "^(CCN-51_Chr\\d{1,3}v\\d{1,3}_\\d{1,9})$", + "n_databases": 2, + "databases": [ + "cacao_developmental_atlas", + "cacao_drought_diurnal_atlas" + ], + "frontends": [ + "efp_cacao_ccn" + ], + "serves_eplant": false + }, + "efp_cacao_sca": { + "regex": "^(SCA-6_Chr\\d{1,3}v\\d{1,3}_\\d{1,9})$", + "n_databases": 4, + "databases": [ + "cacao_developmental_atlas_sca", + "cacao_drought_diurnal_atlas_sca", + "cacao_meristem_atlas_sca", + "cacao_seed_atlas_sca" + ], + "frontends": [ + "efp_cacao_sca" + ], + "serves_eplant": false + }, + "efp_cacao_tc": { + "regex": "^(Tc([0-9]+|Un)v2_g[0-9]+)$", + "n_databases": 2, + "databases": [ + "cacao_infection", + "cacao_leaf" + ], + "frontends": [ + "efp_cacao_tc" + ], + "serves_eplant": false + }, + "efp_camelina": { + "regex": "^(Csa\\d{0,5}[gs]\\d{0,6}.\\d{0,3})$|^(At\\d[cgm]\\d{0,6})$", + "n_databases": 2, + "databases": [ + "camelina", + "camelina_tpm" + ], + "frontends": [ + "efp_camelina", + "eplant_camelina" + ], + "serves_eplant": true + }, + "efp_cannabis": { + "regex": "(^C\\d+$)|(^scaffold\\d+$)|(^AGQN\\d+$)", + "n_databases": 1, + "databases": [ + "cannabis" + ], + "frontends": [ + "efp_cannabis", + "eplant_cannabis" + ], + "serves_eplant": true + }, + "efp_canola": { + "regex": "^(Bna([A-C][0-9]{2}|[A-C]nn|Unn)g[0-9]{1,8}[A-Z]?)$|^(BoC[0-9]+g[0-9]+\\.[0-9]+V[0-9])$|^(BrChr[0-9]+g[0-9]+\\.[0-9]+V[0-9])$|^(Contig[0-9]+)$", + "n_databases": 4, + "databases": [ + "canola", + "canola_original", + "canola_original_v2", + "canola_seed" + ], + "frontends": [ + "efp_canola" + ], + "serves_eplant": false + }, + "efp_durum_wheat": { + "regex": "^(TrturSVE[A-Za-z0-9]{1,6}G[0-9]{1,12}(_[A-Za-z]+)?)$", + "n_databases": 3, + "databases": [ + "durum_wheat_abiotic_stress", + "durum_wheat_biotic_stress", + "durum_wheat_development" + ], + "frontends": [ + "efp_durum_wheat" + ], + "serves_eplant": false + }, + "efp_eucalyptus": { + "regex": "^(Eucgr\\.[A-Za-z][0-9]{5}(\\.[0-9]+)?)$|^(Eucgr\\.[A-Za-z0-9._-]+)$", + "n_databases": 1, + "databases": [ + "eucalyptus" + 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Specific Xylem And Cork", + "AtGenExpress" + ] + } + } + }, + "atgenexp_stress": { + "species": "arabidopsis", + "platform": "microarray", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Abiotic Stress", + "Abiotic Stress II" + ] + }, + "eplant": { + "eplant_arabidopsis": [ + "Abiotic Stress", + "Abiotic Stress II" + ] + } + } + }, + "circadian_mutants": { + "species": "arabidopsis", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_arabidopsis", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "dna_damage": { + "species": "arabidopsis", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "DNA Damage" + ] + }, + "eplant": { + "eplant_arabidopsis": [ + "DNA Damage" + ] + } + } + }, + "embryo": { + "species": "arabidopsis", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Embryo" + ] + }, + "eplant": {} + } + }, + "gc_drought": { + "species": "arabidopsis", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_arabidopsis": [ + "Guard Cell Drought" + ] + } + } + }, + "germination": { + "species": "arabidopsis", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Germination" + ] + }, + "eplant": { + "eplant_arabidopsis": [ + "Germination" + ] + } + } + }, + "guard_cell": { + "species": "arabidopsis", + "platform": "microarray", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Guard Cell" + ] + }, + "eplant": { + "eplant_arabidopsis": [ + "Guard Cell Meristemoids", + "Guard Cell Mutant And Wild Type Guard Cell ABA Response", + "Guard Cell Suspension Cell ABA Response With ROS Scavenger" + ] + } + } + }, + "gynoecium": { + "species": "arabidopsis", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Gynoecium" + ] + }, + "eplant": {} + } + }, + "hnahal": { + "species": "arabidopsis", + "platform": "microarray", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_arabidopsis", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "klepikova": { + "species": "arabidopsis", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Klepikova Atlas" + ] + }, + "eplant": { + "eplant_arabidopsis": [ + "Klepikova" + ] + } + } + }, + "lateral_root_initiation": { + "species": "arabidopsis", + "platform": "microarray", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Lateral Root Initiation" + ] + }, + "eplant": {} + } + }, + "light_series": { + "species": "arabidopsis", + "platform": "microarray", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Light Series" + ] + }, + "eplant": {} + } + }, + "lipid_map": { + "species": "arabidopsis", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_arabidopsis_lipid", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis_lipid": [ + "Lipid Map" + ] + }, + "eplant": {} + } + }, + "meristem_db": { + "species": "arabidopsis", + "platform": "microarray", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Regeneration" + ] + }, + "eplant": {} + } + }, + "meristem_db_new": { + "species": "arabidopsis", + "platform": "microarray", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_arabidopsis", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "rohan": { + "species": "arabidopsis", + "platform": "microarray", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_arabidopsis", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "root": { + "species": "arabidopsis", + "platform": "microarray", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Root", + "Root II" + ] + }, + "eplant": { + "eplant_arabidopsis": [ + "Tissue Specific Root" + ] + } + } + }, + "root_Schaefer_lab": { + "species": "arabidopsis", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_arabidopsis": [ + "Root Immunity Elicitation" + ] + } + } + }, + "rpatel": { + "species": "arabidopsis", + "platform": "microarray", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_arabidopsis", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "seed_db": { + "species": "arabidopsis", + "platform": "microarray", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Seed" + ] + }, + "eplant": {} + } + }, + "seedcoat": { + "species": "arabidopsis", + "platform": "microarray", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_seedcoat", + "resolved_via": "efp-frontend(alias)", + "frontends": { + "efp": { + "efp_arabidopsis_seedcoat": [ + "Seed Coat" + ] + }, + "eplant": {} + } + }, + "shoot_apex": { + "species": "arabidopsis", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Shoot Apex" + ] + }, + "eplant": { + "eplant_arabidopsis": [ + "Shoot Apex" + ] + } + } + }, + "silique": { + "species": "arabidopsis", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Silique" + ] + }, + "eplant": {} + } + }, + "single_cell": { + "species": "arabidopsis", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arabidopsis": [ + "Single Cell" + ], + "efp_arabidopsis_cell": [ + "Cell Type" + ] + }, + "eplant": { + "eplant_arabidopsis": [ + "Cell", + "Single Cell" + ] + } + } + }, + "arachis": { + "species": "arachis", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_arachis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_arachis": [ + "Arachis Atlas" + ] + }, + "eplant": {} + } + }, + "barley_mas": { + "species": "barley", + "platform": "microarray", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_barley", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_barley": [ + "barley mas" + ] + }, + "eplant": {} + } + }, + "barley_rma": { + "species": "barley", + "platform": "microarray", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_barley", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_barley": [ + "barley rma" + ] + }, + "eplant": {} + } + }, + "barley_seed": { + "species": "barley", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_barley", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_barley": [ + "Seed" + ] + } + } + }, + "barley_spike_meristem": { + "species": "barley", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_barley", + "resolved_via": "eplant-frontend(alias)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_barley_legacy": [ + "Spike Meristem", + "Spike Meristem Shade Response" + ] + } + } + }, + "barley_spike_meristem_v3": { + "species": "barley", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_barley", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_barley": [ + "Spike Meristem", + "Spike Meristem Shade Response" + ] + } + } + }, + "brachypodium": { + "species": "brachypodium", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_brachypodium", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_brachypodium": [ + "Brachypodium Atlas" + ] + }, + "eplant": {} + } + }, + "brachypodium_Bd21": { + "species": "brachypodium", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_brachypodium", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_brachypodium": [ + "Brachypodium Spikes" + ] + }, + "eplant": {} + } + }, + "brachypodium_embryogenesis": { + "species": "brachypodium", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_brachypodium", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "brachypodium_grains": { + "species": "brachypodium", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_brachypodium", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_brachypodium": [ + "Brachypodium Grains" + ] + }, + "eplant": {} + } + }, + "brachypodium_metabolites_map": { + "species": "brachypodium", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_brachypodium_metabolites", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_brachypodium_metabolites": [ + "Metabolite Level" + ] + }, + "eplant": {} + } + }, + "brachypodium_photo_thermocycle": { + "species": "brachypodium", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_brachypodium", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_brachypodium": [ + "Photo Thermocycle" + ] + }, + "eplant": {} + } + }, + "brassica_rapa": { + "species": "brassica", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_brassica_rapa", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_brassica_rapa": [ + "Embryogenesis" + ] + }, + "eplant": {} + } + }, + "brassica_rapa_developmental_atlas": { + "species": "brassica", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_brassica_rapa", + "resolved_via": "species-sibling-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "cacao_developmental_atlas": { + "species": "cacao", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_cacao_ccn", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_cacao_ccn": [ + "Developmental Atlas" + ] + }, + "eplant": {} + } + }, + "cacao_developmental_atlas_sca": { + "species": "cacao", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_cacao_sca", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_cacao_sca": [ + "Developmental Atlas" + ] + }, + "eplant": {} + } + }, + "cacao_drought_diurnal_atlas": { + "species": "cacao", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_cacao_ccn", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_cacao_ccn": [ + "Drought Diurnal Atlas" + ] + }, + "eplant": {} + } + }, + "cacao_drought_diurnal_atlas_sca": { + "species": "cacao", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_cacao_sca", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_cacao_sca": [ + "Drought Diurnal Atlas" + ] + }, + "eplant": {} + } + }, + "cacao_infection": { + "species": "cacao", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_cacao_tc", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_cacao_tc": [ + "Cacao Infection" + ] + }, + "eplant": {} + } + }, + "cacao_leaf": { + "species": "cacao", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_cacao_tc", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_cacao_tc": [ + "Cacao Leaf" + ] + }, + "eplant": {} + } + }, + "cacao_meristem_atlas_sca": { + "species": "cacao", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_cacao_sca", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_cacao_sca": [ + "Meristem Atlas" + ] + }, + "eplant": {} + } + }, + "cacao_seed_atlas_sca": { + "species": "cacao", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_cacao_sca", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_cacao_sca": [ + "Seed Atlas" + ] + }, + "eplant": {} + } + }, + "camelina": { + "species": "camelina", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_camelina", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_camelina": [ + "Developmental Atlas FPKM" + ] + }, + "eplant": { + "eplant_camelina": [ + "Plant" + ] + } + } + }, + "camelina_tpm": { + "species": "camelina", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_camelina", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_camelina": [ + "Developmental Atlas TPM" + ] + }, + "eplant": {} + } + }, + "cannabis": { + "species": "cannabis", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_cannabis", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_cannabis": [ + "Cannabis Atlas" + ] + }, + "eplant": { + "eplant_cannabis": [ + "Plant" + ] + } + } + }, + "canola": { + "species": "canola", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_canola", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "canola_original": { + "species": "canola", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_canola", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "canola_original_v2": { + "species": "canola", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_canola", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "canola_seed": { + "species": "canola", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_canola", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_canola": [ + "Canola Seed" + ] + }, + "eplant": {} + } + }, + "cassava_atlas": { + "species": "cassava", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": null, + "resolved_via": "UNRESOLVED", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "cassava_cbb": { + "species": "cassava", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": null, + "resolved_via": "UNRESOLVED", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "cassava_eacmv": { + "species": "cassava", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": null, + "resolved_via": "UNRESOLVED", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "cuscuta": { + "species": "cuscuta", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": null, + "resolved_via": "UNRESOLVED", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "cuscuta_early_haustoriogenesis": { + "species": "cuscuta", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": null, + "resolved_via": "UNRESOLVED", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "cuscuta_lmd": { + "species": "cuscuta", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": null, + "resolved_via": "UNRESOLVED", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "eucalyptus": { + "species": "eucalyptus", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_eucalyptus", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_eucalyptus": [ + "Stress", + "Plant" + ] + } + } + }, + "euphorbia": { + "species": "euphorbia", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_euphorbia", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_euphorbia": [ + "Euphorbia" + ] + }, + "eplant": {} + } + }, + "grape_developmental": { + "species": "grape", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_grape", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_grape": [ + "grape developmental" + ] + }, + "eplant": {} + } + }, + "heterodera_schachtii": { + "species": "heterodera", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_arabidopsis", + "resolved_via": "species-special-case", + "frontends": { + "efp": {}, + "eplant": { + "eplant_arabidopsis": [ + "Heterodera schachtii" + ] + } + } + }, + "human_body_map_2": { + "species": "human", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_human", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_human": [ + "Illumina Body Map 2 - FPKM" + ] + }, + "eplant": {} + } + }, + "human_developmental": { + "species": "human", + "platform": "microarray", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_human", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_human": [ + "Circulatory Respiratory", + "Nervous", + "Reproductive", + "Skeletal Immune Digestive" + ] + }, + "eplant": {} + } + }, + "human_developmental_SpongeLab": { + "species": "human", + "platform": "microarray", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_human", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "human_diseased": { + "species": "human", + "platform": "microarray", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_human", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "kalanchoe": { + "species": "kalanchoe", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_kalanchoe", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_kalanchoe": [ + "Light Response" + ] + }, + "eplant": {} + } + }, + "kalanchoe_time_course_analysis": { + "species": "kalanchoe", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_kalanchoe", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "little_millet": { + "species": "little_millet", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_little_millet", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_little_millet": [ + "Life Cycle" + ] + }, + "eplant": {} + } + }, + "lupin_lcm_leaf": { + "species": "lupin", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_lupin", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_lupin": [ + "LCM Leaf" + ] + }, + "eplant": {} + } + }, + "lupin_lcm_pod": { + "species": "lupin", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_lupin", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_lupin": [ + "LCM Pod" + ] + }, + "eplant": {} + } + }, + "lupin_lcm_stem": { + "species": "lupin", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_lupin", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_lupin": [ + "LCM Stem" + ] + }, + "eplant": {} + } + }, + "lupin_pod_seed": { + "species": "lupin", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_lupin", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "lupin_whole_plant": { + "species": "lupin", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_lupin", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_lupin": [ + "Whole Plant" + ] + }, + "eplant": {} + } + }, + "maize_RMA_linear": { + "species": "maize", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_maize", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize": [ + "Sekhon et al Atlas" + ] + }, + "eplant": { + "eplant_maize": [ + "Sekhon Atlas" + ] + } + } + }, + "maize_RMA_log": { + "species": "maize", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_maize", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "maize_atlas": { + "species": "maize", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_maize", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "maize_atlas_v5": { + "species": "maize", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_maize", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize": [ + "Hoopes et al Atlas V5" + ] + }, + "eplant": {} + } + }, + "maize_buell_lab": { + "species": "maize", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_maize", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize": [ + "Hoopes et al Atlas", + "Hoopes et al Stress" + ] + }, + "eplant": {} + } + }, + "maize_early_seed": { + "species": "maize", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_maize", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize": [ + "Early Seed", + "Maize Kernel" + ] + }, + "eplant": {} + } + }, + "maize_ears": { + "species": "maize", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_maize", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize": [ + "Tassel and Ear Primordia" + ] + }, + "eplant": { + "eplant_maize": [ + "Tassel And Ear Primordia" + ] + } + } + }, + "maize_embryonic_leaf_development": { + "species": "maize", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_maize", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize": [ + "Embryonic Leaf Development" + ] + }, + "eplant": {} + } + }, + "maize_enzyme": { + "species": "maize", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_maize_enzyme", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize_enzyme": [ + "Enzyme Activity" + ] + }, + "eplant": {} + } + }, + "maize_gdowns": { + "species": "maize", + "platform": "microarray", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_maize", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize": [ + "Downs et al Atlas" + ] + }, + "eplant": { + "eplant_maize": [ + "Plant" + ] + } + } + }, + "maize_iplant": { + "species": "maize", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_maize", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize": [ + "maize iplant" + ] + }, + "eplant": { + "eplant_maize": [ + "Leaf MeBS" + ] + } + } + }, + "maize_kernel_v5": { + "species": "maize", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_maize", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize": [ + "Maize Kernel V5" + ] + }, + "eplant": {} + } + }, + "maize_leaf_gradient": { + "species": "maize", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_maize", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize": [ + "maize leaf gradient" + ] + }, + "eplant": { + "eplant_maize": [ + "Leaf Gradient" + ] + } + } + }, + "maize_lipid_map": { + "species": "maize", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_maize", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "maize_metabolite": { + "species": "maize", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_maize_metabolite", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize_metabolite": [ + "Metabolite Level" + ] + }, + "eplant": {} + } + }, + "maize_nitrogen_use_efficiency": { + "species": "maize", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_maize", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "maize_rice_comparison": { + "species": "maize", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_maize", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize": [ + "maize rice comparison" + ] + }, + "eplant": {} + } + }, + "maize_root": { + "species": "maize", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_maize", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize": [ + "Maize Root" + ] + }, + "eplant": { + "eplant_maize": [ + "Root" + ] + } + } + }, + "maize_stress_v5": { + "species": "maize", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_maize", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_maize": [ + "Hoopes et al Stress V5" + ] + }, + "eplant": {} + } + }, + "mangosteen_aril_vs_rind": { + "species": "mangosteen", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_mangosteen", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_mangosteen": [ + "Aril vs Rind" + ] + }, + "eplant": {} + } + }, + "mangosteen_callus": { + "species": "mangosteen", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_mangosteen", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_mangosteen": [ + "Callus" + ] + }, + "eplant": {} + } + }, + "mangosteen_diseased_vs_normal": { + "species": "mangosteen", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_mangosteen", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_mangosteen": [ + "Diseased vs Normal" + ] + }, + "eplant": {} + } + }, + "mangosteen_fruit_ripening": { + "species": "mangosteen", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_mangosteen", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_mangosteen": [ + "Fruit Ripening" + ] + }, + "eplant": {} + } + }, + "mangosteen_seed_development": { + "species": "mangosteen", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_mangosteen", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_mangosteen": [ + "Seed Development" + ] + }, + "eplant": {} + } + }, + "mangosteen_seed_development_germination": { + "species": "mangosteen", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_mangosteen", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "mangosteen_seed_germination": { + "species": "mangosteen", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_mangosteen", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_mangosteen": [ + "Seed Germination" + ] + }, + "eplant": {} + } + }, + "marchantia_organ_stress": { + "species": "marchantia", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_marchantia", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_marchantia": [ + "Expression Atlas" + ] + }, + "eplant": {} + } + }, + "medicago_mas": { + "species": "medicago", + "platform": "microarray", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_medicago", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_medicago": [ + "medicago mas" + ] + }, + "eplant": { + "eplant_medicago": [ + "Plant" + ] + } + } + }, + "medicago_rma": { + "species": "medicago", + "platform": "microarray", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_medicago", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_medicago": [ + "medicago rma" + ] + }, + "eplant": {} + } + }, + "medicago_root": { + "species": "medicago", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_medicago", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_medicago": [ + "Root", + "Root Component" + ] + } + } + }, + "medicago_root_v5": { + "species": "medicago", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_medicago", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "medicago_seed": { + "species": "medicago", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_medicago", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_medicago": [ + "medicago seed" + ] + }, + "eplant": { + "eplant_medicago": [ + "Seed" + ] + } + } + }, + "mouse_db": { + "species": "mouse", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "mouse_efp", + "resolved_via": "efp-frontend(alias)", + "frontends": { + "efp": { + "efp_mouse": [ + "Mouse" + ] + }, + "eplant": {} + } + }, + "oat": { + "species": "oat", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_oat", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_oat": [ + "Oat" + ] + }, + "eplant": {} + } + }, + "phelipanche": { + "species": "phelipanche", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_phelipanche", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_phelipanche": [ + "Phelipanche" + ] + }, + "eplant": {} + } + }, + "physcomitrella_db": { + "species": "physcomitrella", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_physcomitrella", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_physcomitrella": [ + "Physcomitrella" + ] + }, + "eplant": {} + } + }, + "poplar": { + "species": "poplar", + "platform": "microarray", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_poplar", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_poplar": [ + "Poplar", + "PoplarTreatment" + ] + }, + "eplant": { + "eplant_poplar": [ + "Poplar Treatment", + "Plant" + ] + } + } + }, + "poplar_hormone": { + "species": "poplar", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_poplar", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "poplar_leaf": { + "species": "poplar", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_poplar", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_poplar": [ + "World Leaf" + ] + } + } + }, + "poplar_xylem": { + "species": "poplar", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_poplar", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_poplar": [ + "World Xylem" + ] + } + } + }, + "potato_dev": { + "species": "potato", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_potato", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_potato": [ + "Potato Developmental" + ] + }, + "eplant": { + "eplant_potato": [ + "Plant" + ] + } + } + }, + "potato_stress": { + "species": "potato", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_potato", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_potato": [ + "Potato Stress" + ] + }, + "eplant": { + "eplant_potato": [ + "Potato Stress" + ] + } + } + }, + "potato_wounding": { + "species": "potato", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_potato", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "quinoa_nutrient": { + "species": "quinoa", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": null, + "resolved_via": "UNRESOLVED", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "rice_abiotic_stress_sc_pseudobulk": { + "species": "rice", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_rice", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_rice": [ + "rice single cell" + ] + }, + "eplant": {} + } + }, + "rice_drought_heat_stress": { + "species": "rice", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_rice", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_rice": [ + "rice drought heat stress" + ] + }, + "eplant": {} + } + }, + "rice_leaf_gradient": { + "species": "rice", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_rice", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_rice": [ + "rice leaf gradient" + ] + }, + "eplant": { + "eplant_rice": [ + "Leaf Gradient" + ] + } + } + }, + "rice_maize_comparison": { + "species": "rice", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_rice", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_rice": [ + "rice maize comparison" + ] + }, + "eplant": {} + } + }, + "rice_mas": { + "species": "rice", + "platform": "microarray", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_rice", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_rice": [ + "rice mas", + "riceanoxia mas", + "ricestigma mas", + "ricestress mas" + ] + }, + "eplant": { + "eplant_rice": [ + "Anoxia", + "Stress", + "Stigma", + "Plant" + ] + } + } + }, + "rice_metabolite": { + "species": "rice", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_rice_metabolite", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_rice_metabolite": [ + "Metabolite Level" + ] + }, + "eplant": {} + } + }, + "rice_rma": { + "species": "rice", + "platform": "microarray", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_rice", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_rice": [ + "rice rma", + "riceanoxia rma", + "ricestigma rma", + "ricestress rma" + ] + }, + "eplant": {} + } + }, + "rice_root": { + "species": "rice", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_rice", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_rice": [ + "Root" + ] + } + } + }, + "selaginella": { + "species": "selaginella", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_selaginella", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_selaginella": [ + "Selaginella Atlas" + ] + }, + "eplant": {} + } + }, + "sorghum_atlas_w_BS_cells": { + "species": "sorghum", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_sorghum", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_sorghum": [ + "Atlas w BS Cells" + ] + }, + "eplant": {} + } + }, + "sorghum_comparative_transcriptomics": { + "species": "sorghum", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_sorghum", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "sorghum_developmental": { + "species": "sorghum", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_sorghum", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_sorghum": [ + "Developmental Atlas" + ] + }, + "eplant": {} + } + }, + "sorghum_developmental_2": { + "species": "sorghum", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_sorghum", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "sorghum_flowering_activation": { + "species": "sorghum", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_sorghum", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_sorghum": [ + "Flowering Activation" + ] + }, + "eplant": {} + } + }, + "sorghum_low_phosphorus": { + "species": "sorghum", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_sorghum", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_sorghum": [ + "Low Phosphorus" + ] + }, + "eplant": {} + } + }, + "sorghum_nitrogen_stress": { + "species": "sorghum", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_sorghum", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "sorghum_nitrogen_use_efficiency": { + "species": "sorghum", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_sorghum", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "sorghum_phosphate_stress": { + "species": "sorghum", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_sorghum", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_sorghum": [ + "Phosphate Stress" + ] + }, + "eplant": {} + } + }, + "sorghum_plasma": { + "species": "sorghum", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_sorghum", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "sorghum_saline_alkali_stress": { + "species": "sorghum", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_sorghum", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_sorghum": [ + "Saline Alkali Stress" + ] + }, + "eplant": {} + } + }, + "sorghum_stress": { + "species": "sorghum", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_sorghum", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_sorghum": [ + "Stress Atlas" + ] + }, + "eplant": {} + } + }, + "sorghum_strigolactone_variation": { + "species": "sorghum", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_sorghum", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_sorghum": [ + "Strigolactone Variation" + ] + }, + "eplant": {} + } + }, + "sorghum_sulfur_stress": { + "species": "sorghum", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_sorghum", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_sorghum": [ + "Sulfur Stress" + ] + }, + "eplant": {} + } + }, + "sorghum_temperature_stress": { + "species": "sorghum", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_sorghum", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "sorghum_vascularization_and_internode": { + "species": "sorghum", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_sorghum", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_sorghum": [ + "Vascularization and Internode" + ] + }, + "eplant": {} + } + }, + "soybean": { + "species": "soybean", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_soybean", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_soybean": [ + "soybean" + ] + }, + "eplant": { + "eplant_soybean": [ + "Plant" + ] + } + } + }, + "soybean_embryonic_development": { + "species": "soybean", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_soybean", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_soybean": [ + "soybean embryonic development" + ] + }, + "eplant": {} + } + }, + "soybean_heart_cotyledon_globular": { + "species": "soybean", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_soybean", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_soybean": [ + "soybean heart cotyledon globular" + ] + }, + "eplant": {} + } + }, + "soybean_senescence": { + "species": "soybean", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_soybean", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_soybean": [ + "soybean senescence" + ] + }, + "eplant": {} + } + }, + "soybean_severin": { + "species": "soybean", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_soybean", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_soybean": [ + "soybean severin" + ] + }, + "eplant": { + "eplant_soybean": [ + "Soybean Severin" + ] + } + } + }, + "spruce": { + "species": "spruce", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": null, + "resolved_via": "UNRESOLVED", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "strawberry": { + "species": "strawberry", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_strawberry", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_strawberry": [ + "Developmental Map Strawberry Flower and Fruit", + "Strawberry Green vs White Stage" + ] + }, + "eplant": {} + } + }, + "striga": { + "species": "striga", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_striga", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_striga": [ + "Striga Atlas" + ] + }, + "eplant": {} + } + }, + "sugarcane_culms": { + "species": "sugarcane", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_sugarcane", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_sugarcane": [ + "Culms" + ] + } + } + }, + "sugarcane_leaf": { + "species": "sugarcane", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_sugarcane", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_sugarcane": [ + "Leaf" + ] + } + } + }, + "sunflower": { + "species": "sunflower", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_sunflower", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_sunflower": [ + "Plant" + ] + } + } + }, + "thellungiella_db": { + "species": "thellungiella", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_eutrema", + "resolved_via": "species-special-case", + "frontends": { + "efp": { + "efp_eutrema": [ + "Eutrema" + ] + }, + "eplant": {} + } + }, + "tomato": { + "species": "tomato", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_tomato", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_tomato": [ + "Rose Lab Atlas" + ] + }, + "eplant": {} + } + }, + "tomato_ils": { + "species": "tomato", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_tomato", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_tomato": [ + "ILs Leaf Chitwood et al" + ] + }, + "eplant": { + "eplant_tomato": [ + "LeafILs" + ] + } + } + }, + "tomato_ils2": { + "species": "tomato", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_tomato", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_tomato": [ + "ILs Root Tip Brady Lab" + ] + }, + "eplant": { + "eplant_tomato": [ + "RootILs" + ] + } + } + }, + "tomato_ils3": { + "species": "tomato", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_tomato", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "tomato_meristem": { + "species": "tomato", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_tomato", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_tomato": [ + "Tomato Meristem" + ] + }, + "eplant": {} + } + }, + "tomato_renormalized": { + "species": "tomato", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_tomato", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_tomato": [ + "Rose Lab Atlas Renormalized" + ] + }, + "eplant": { + "eplant_tomato": [ + "Fruit", + "Plant" + ] + } + } + }, + "tomato_root": { + "species": "tomato", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_tomato", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_tomato": [ + "Root" + ] + } + } + }, + "tomato_root_field_pot": { + "species": "tomato", + "platform": "rna_seq", + "source": "eplant", + "in_dropdown": true, + "regex_project": "efp_tomato", + "resolved_via": "eplant-frontend(shares eFP regex)", + "frontends": { + "efp": {}, + "eplant": { + "eplant_tomato": [ + "RootFieldPot" + ] + } + } + }, + "tomato_s_pennellii": { + "species": "tomato", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_tomato", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_tomato": [ + "M82 S pennellii Atlases Koenig et al" + ] + }, + "eplant": { + "eplant_tomato": [ + "TomatoAtlases" + ] + } + } + }, + "tomato_seed": { + "species": "tomato", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_tomato", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_tomato": [ + "SEED Lab Angers" + ] + }, + "eplant": {} + } + }, + "tomato_shade_mutants": { + "species": "tomato", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_tomato", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_tomato": [ + "Shade Mutants" + ] + }, + "eplant": {} + } + }, + "tomato_shade_timecourse": { + "species": "tomato", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_tomato", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_tomato": [ + "Shade Timecourse WT" + ] + }, + "eplant": {} + } + }, + "tomato_trait": { + "species": "tomato", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_tomato", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "triphysaria": { + "species": "triphysaria", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_triphysaria", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_triphysaria": [ + "Triphysaria" + ] + }, + "eplant": {} + } + }, + "triticale": { + "species": "triticale", + "platform": "microarray", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_triticale", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_triticale": [ + "triticale" + ] + }, + "eplant": {} + } + }, + "triticale_mas": { + "species": "triticale", + "platform": "microarray", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_triticale", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_triticale": [ + "triticale mas" + ] + }, + "eplant": {} + } + }, + "tung_tree": { + "species": "tung_tree", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_tung_tree", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_tung_tree": [ + "Tung Tree" + ] + }, + "eplant": {} + } + }, + "durum_wheat_abiotic_stress": { + "species": "wheat", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_durum_wheat", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_durum_wheat": [ + "Abiotic Stress" + ] + }, + "eplant": {} + } + }, + "durum_wheat_biotic_stress": { + "species": "wheat", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_durum_wheat", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_durum_wheat": [ + "Biotic Stress" + ] + }, + "eplant": {} + } + }, + "durum_wheat_development": { + "species": "wheat", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_durum_wheat", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_durum_wheat": [ + "Development" + ] + }, + "eplant": {} + } + }, + "wheat": { + "species": "wheat", + "platform": "rna_seq", + "source": "both", + "in_dropdown": true, + "regex_project": "efp_wheat", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_wheat": [ + "Developmental Atlas" + ] + }, + "eplant": { + "eplant_wheat": [ + "EarlyStages", + "MiddleStages", + "LateStages" + ] + } + } + }, + "wheat_abiotic_stress": { + "species": "wheat", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_wheat", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_wheat": [ + "Wheat Abiotic Stress" + ] + }, + "eplant": {} + } + }, + "wheat_embryogenesis": { + "species": "wheat", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_wheat", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_wheat": [ + "Wheat Embryogenesis" + ] + }, + "eplant": {} + } + }, + "wheat_meiosis": { + "species": "wheat", + "platform": "rna_seq", + "source": "efp", + "in_dropdown": true, + "regex_project": "efp_wheat", + "resolved_via": "efp-frontend", + "frontends": { + "efp": { + "efp_wheat": [ + "Wheat Meiosis" + ] + }, + "eplant": {} + } + }, + "wheat_root": { + "species": "wheat", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": "efp_wheat", + "resolved_via": "species-fallback", + "frontends": { + "efp": {}, + "eplant": {} + } + }, + "willow": { + "species": "willow", + "platform": "rna_seq", + "source": "legacy_not_in_dropdown", + "in_dropdown": false, + "regex_project": null, + "resolved_via": "UNRESOLVED", + "frontends": { + "efp": {}, + "eplant": {} + } + } + } +} \ No newline at end of file diff --git a/generate_efp_test_cases.py b/generate_efp_test_cases.py new file mode 100644 index 00000000..ad7b40e2 --- /dev/null +++ b/generate_efp_test_cases.py @@ -0,0 +1,211 @@ +""" +Reena Obmina | BCB330 Project 2025-2026 | University of Toronto + +Generates edge-test CSV for the eFP gene expression endpoints. + +Reads: species_databases.json — view→database mappings per species + api/random_rows_json/ — example gene IDs per database + api/utils/bar_utils.py — regex patterns (referenced, not imported) +Writes: efp_test_cases.csv + +Columns: species, view, database, regex, valid_gene_1..3, + invalid_gene_1_wrong_initially, invalid_gene_2_wrong_finally, + invalid_gene_3_other_species +""" + +import csv +import json +import re +from pathlib import Path + +JSON_DIR = Path("api/random_rows_json") + +# --------------------------------------------------------------------------- +# Regex patterns copied verbatim from api/utils/bar_utils.py +# --------------------------------------------------------------------------- +SPECIES_REGEX = { + "arabidopsis": r"^At[12345cm]g\d{5}.?\d?$", + "arabidopsis lipid": r"^At[12345cm]g\d{5}.?\d?$", + "arabidopsis cell": r"^At[12345cm]g\d{5}.?\d?$", + "arabidopsis seedcoat": r"^At[12345cm]g\d{5}.?\d?$", + "actinidia": r"^Acc\d{5}\.\d+$", + "arachis": r"^Adur\d{1,10}_comp\d{1,3}_\D{1,3}\d{1,3}_seq\d{1,5}$", + "barley": r"^HORVU(\d+Hr\d+G\d+|\.MOREX\.r\d+\.\dHG\d+\.\d+)$", + "brachypodium": r"^Bradi\d+g\d+\.\d+$", + "brassica rapa": r"^(BraA.{1,4}g\d{1,9}|[A-Z]\d{2}[gp]\d+\.\d+_BraROA)$", + "cacao ccn": r"^((CCN-51|SCA-6)_Chr\d+v\d+_\d+|Tc\d+v\d+_g\d+)$", + "cacao sca": r"^((CCN-51|SCA-6)_Chr\d+v\d+_\d+|Tc\d+v\d+_g\d+)$", + "cacao tc": r"^((CCN-51|SCA-6)_Chr\d+v\d+_\d+|Tc\d+v\d+_g\d+)$", + "camelina": r"^Csa\d+[gs]\d+\.\d+$", + "canola": r"^(Bna[AC]\d{2}g\d{5}[A-D]?|Bo[A-Z]+_?\d+g\d+\.\d+V\d+)$", + "cannabis": r"^AGQN\d{0,10}$", + "eutrema": r"^(Thhalv\d+m\.g|nXLOC_\d+)$", + "grape": r"^(CHR\d+_JGVV\d+_\d+_T\d+|VIT_\d{0,3}\D\d{0,5}g\d{0,6})$", + "human": r"^\d{1,10}$", + "kalanchoe": r"^Kaladp\d{1,10}s\d{1,10}$", + "little millet": r"^TRINITY_DN\d+_c\d+_g\d+_i\d+$", + "lupin": r"^Luan_Oskar_(PB\d+|Trin)_\d+$", + "maize": r"^(AC[0-9]{6}\.[0-9]+_FGT?[0-9]{3}|GRMZM[25]G[0-9]{6}(_T[0-9]{2})?|Zm\d+(d|eb)\d+)$", + "mangosteen": r"^DN\d+$", + "medicago": r"^(Medtr(\d+[gs]\d+|_v1_\d+)|MtrunA17Chr\dg\d+)$", + "mouse": r"^XM_\d+\.\d+$", + "oat": r"^AV[A-Z]{3}\.\d{5}[a-z]\.r\d+\.\d[A-Z]{2}\d{8}$", + "phelipanche": r"^OrAeBC5_\d{1,6}\.\d{1,3}$", + "physcomitrella": r"^Pp1s\d{1,8}_\d{1,8}V6\.\d{1,3}$", + "poplar": r"^POTRI\.\d{3}g\d{6}.?\d{0,3}$", + "potato": r"^(PGSC0003DMG\d+|EPlSTUG\d+)$", + "rice": r"^(LOC_Os\d{2}g\d{5}|Os\d{2}g\d+)$", + "selaginella": r"^Smo\d{1,8}$", + "soybean": r"^((Glyma\d{1,3}g\d{1,6}\.?\d?)|(Glyma\.\d{1,3}g\d{1,8}))$", + "strawberry": r"^FvH4_\d{1,3}g\d{1,8}$", + "striga": r"^StHeBC3_\d{1,6}\.\d{1,5}$", + "tomato": r"^Solyc\d\dg\d{6}(\.\d+)?$", + # no dedicated bar_utils validator; triticale uses wheat probes/IDs + "triticale": r"^(TraesCS[0-9A-Z]+(\.\d+)?|TrturSVE[0-9A-Z]+G\d+)$", + "triphysaria": r"^TrVeBC3_\d{1,6}\.\d{1,3}$", + "wheat": r"^(TraesCS[0-9A-Z]+(\.\d+)?|TrturSVE[0-9A-Z]+G\d+)$", +} + +# --------------------------------------------------------------------------- +# Microarray / probeset databases → gene IDs come from a non-probeset sibling +# --------------------------------------------------------------------------- +PROBESET_FALLBACK = { + # Arabidopsis Affymetrix ATH1 arrays → use klepikova RNA-seq (AGI format) + "affydb": "klepikova", + "arabidopsis_ecotypes": "klepikova", + "atgenexp": "klepikova", + "atgenexp_hormone": "klepikova", + "atgenexp_pathogen": "klepikova", + "atgenexp_plus": "klepikova", + "atgenexp_stress": "klepikova", + "guard_cell": "klepikova", + "hnahal": "klepikova", + "lateral_root_initiation": "klepikova", + "light_series": "klepikova", + "meristem_db": "klepikova", + "meristem_db_new": "klepikova", + "root": "klepikova", + "rohan": "klepikova", + "rpatel": "klepikova", + "seed_db": "klepikova", + # Lipid map stores lipid-class IDs, not AGI — fall back to RNA-seq for AGI examples + "lipid_map": "klepikova", + # Seedcoat uses a legacy non-AGI format; fall back to standard RNA-seq AGI IDs + "seedcoat": "klepikova", + # Non-arabidopsis microarray databases + "barley_mas": "barley_seed", + "barley_rma": "barley_seed", + "human_developmental": "human_body_map_2", + "human_developmental_SpongeLab": "human_body_map_2", + "human_diseased": "human_body_map_2", + "maize_gdowns": "maize_atlas", + "medicago_mas": "medicago_root", + "medicago_rma": "medicago_root", + "poplar": "poplar_hormone", + "rice_mas": "rice_drought_heat_stress", + "rice_rma": "rice_drought_heat_stress", + # Triticale has no non-probeset database; use wheat IDs (triticale is wheat × rye) + "triticale": "wheat", + "triticale_mas": "wheat", +} + +# --------------------------------------------------------------------------- +# Cross-species invalid gene (invalid type 3: completely wrong species) +# --------------------------------------------------------------------------- +CROSS_SPECIES = { + "arabidopsis": "Solyc04g054700", # tomato gene + "arabidopsis lipid": "Solyc04g054700", + "arabidopsis cell": "Solyc04g054700", + "arabidopsis seedcoat": "Solyc04g054700", + "human": "At1g01010", # plant gene + "mouse": "At1g01010", +} +_DEFAULT_CROSS = "At1g01010" # arabidopsis gene — wrong for every non-arabidopsis species + + +def _load_genes(db_name: str, species_regex: str, n: int = 3) -> list[str]: + """Return up to *n* unique data_probeset_id values that match *species_regex*.""" + path = JSON_DIR / f"{db_name}_test_data.json" + if not path.exists(): + return [] + data = json.loads(path.read_text()) + seen: set[str] = set() + result: list[str] = [] + for row in data: + gid = str(row.get("data_probeset_id") or "").strip() + if gid and gid not in seen and re.search(species_regex, gid, re.I): + seen.add(gid) + result.append(gid) + if len(result) >= n: + break + return result + + +def _invalid_initially(gene: str) -> str: + """Change the first character to a wrong type (letter→digit, digit/other→letter).""" + if not gene: + return "INVALID" + return ("9" if gene[0].isalpha() else "Z") + gene[1:] + + +def _invalid_finally(gene: str, regex: str = "") -> str: + """Change the last character to a wrong type; fall back to appending '.X' if the + first mutation still passes the regex (e.g. when the regex uses [0-9A-Z]+).""" + if not gene: + return "INVALID" + candidate = gene[:-1] + ("X" if gene[-1].isdigit() else "9") + if regex and re.search(regex, candidate, re.I): + # First mutation wasn't enough — append a clearly invalid version suffix + candidate = gene + ".X" + return candidate + + +def main() -> None: + db_data: dict = json.loads(Path("species_databases.json").read_text()) + + fieldnames = [ + "species", "view", "database", "regex", + "valid_gene_1", "valid_gene_2", "valid_gene_3", + "invalid_gene_1_wrong_initially", + "invalid_gene_2_wrong_finally", + "invalid_gene_3_other_species", + ] + rows: list[dict] = [] + + for species, views in db_data.items(): + regex = SPECIES_REGEX.get(species, "") + cross = CROSS_SPECIES.get(species, _DEFAULT_CROSS) + + for view, db in views.items(): + source_db = PROBESET_FALLBACK.get(db, db) + genes = _load_genes(source_db, regex) if regex else [] + + # Pad to 3 slots + while len(genes) < 3: + genes.append("") + + ref = genes[0] + rows.append({ + "species": species, + "view": view, + "database": db, + "regex": regex, + "valid_gene_1": genes[0], + "valid_gene_2": genes[1], + "valid_gene_3": genes[2], + "invalid_gene_1_wrong_initially": _invalid_initially(ref) if ref else "INVALID", + "invalid_gene_2_wrong_finally": _invalid_finally(ref, regex) if ref else "INVALID", + "invalid_gene_3_other_species": cross, + }) + + out = Path("efp_test_cases.csv") + with out.open("w", newline="") as f: + writer = csv.DictWriter(f, fieldnames=fieldnames) + writer.writeheader() + writer.writerows(rows) + + print(f"Written {len(rows)} rows to {out}") + + +if __name__ == "__main__": + main() diff --git a/live_example_gene_id_coverage.csv b/live_example_gene_id_coverage.csv new file mode 100644 index 00000000..63530aeb --- /dev/null +++ b/live_example_gene_id_coverage.csv @@ -0,0 +1,67 @@ +source,project,validator_key,example_gene_id,result +efp,efp_actinidia,efp_actinidia,Acc00001.1,PASS +efp,efp_apple,efp_apple,MfusH1_01g00006,PASS +efp,efp_arabidopsis,efp_arabidopsis,At1g01010,PASS +efp,efp_arabidopsis_cell,efp_arabidopsis_cell,,NO_EXAMPLE_FOUND +efp,efp_arabidopsis_lipid,efp_arabidopsis_lipid,,NO_EXAMPLE_FOUND +efp,efp_arabidopsis_seedcoat,efp_seedcoat,At1g17665,PASS +efp,efp_arachis,efp_arachis,Adur10000_comp0_c0_seq1,PASS +efp,efp_barley,efp_barley,Contig3045_at,PASS +efp,efp_brachypodium,efp_brachypodium,Bradi4g05940.1,PASS +efp,efp_brachypodium_metabolites,efp_brachypodium_metabolites,,NO_EXAMPLE_FOUND +efp,efp_brassica_rapa,efp_brassica_rapa,BraA01g000010,PASS +efp,efp_cacao_ccn,efp_cacao_ccn,CCN-51_Chr0v1_20099,PASS +efp,efp_cacao_sca,efp_cacao_sca,SCA-6_Chr1v1_00001,PASS +efp,efp_cacao_tc,efp_cacao_tc,Tc01v2_g000010,PASS +efp,efp_camelina,efp_camelina,Csa00382s010.1,PASS +efp,efp_cannabis,efp_cannabis,AGQN03000001,PASS +efp,efp_canola,efp_canola,BnaA01g00010D,PASS +efp,efp_durum_wheat,efp_durum_wheat,TrturSVE1A02G00000070,PASS +efp,efp_euphorbia,efp_euphorbia,Ep_chr1_g00001,PASS +efp,efp_eutrema,efp_eutrema,Thhalv10000089m.g,PASS +efp,efp_grape,efp_grape,VIT_00s0120g00060,PASS +efp,efp_human,efp_human,,FETCH_ERROR: 403 Client Error: Forbidden for url: https://bar.utoronto.ca/efp_human/cgi-bin/efpWeb.cgi +efp,efp_kalanchoe,efp_kalanchoe,Kaladp0001s0001,PASS +efp,efp_little_millet,efp_little_millet,TRINITY_DN0_c0_g1_i15,PASS +efp,efp_lupin,efp_lupin,Luan_Oskar_Trin_282785,PASS +efp,efp_maize,efp_maize,Zm00001d046170,PASS +efp,efp_maize_enzyme,efp_maize_enzyme,,NO_EXAMPLE_FOUND +efp,efp_maize_metabolite,efp_maize_metabolite,,NO_EXAMPLE_FOUND +efp,efp_mangosteen,efp_mangosteen,DN1,PASS +efp,efp_marchantia,efp_marchantia,Mp1g00010,PASS +efp,efp_medicago,efp_medicago,Medtr1g102430,PASS +efp,efp_mouse,mouse_efp,XM_122026.1,PASS +efp,efp_oat,efp_oat,N0.HOG0015560,PASS +efp,efp_phelipanche,efp_phelipanche,OrAeBC5_10.1,PASS +efp,efp_physcomitrella,efp_physcomitrella,Pp1s103_79V6.1,PASS +efp,efp_poplar,efp_poplar,PtpAffx.200227.1.S1_s_at,PASS +efp,efp_potato,efp_potato,PGSC0003DMG400000005,PASS +efp,efp_rice,efp_rice,LOC_Os01g01080,PASS +efp,efp_rice_metabolite,efp_rice_metabolite,,NO_EXAMPLE_FOUND +efp,efp_selaginella,efp_selaginella,Smo402070,PASS +efp,efp_sorghum,efp_sorghum,Sobic.001G000100,PASS +efp,efp_soybean,efp_soybean,Glyma06g47400,PASS +efp,efp_strawberry,efp_strawberry,FvH4_1g00010,PASS +efp,efp_striga,efp_striga,StHeBC3_1.1,PASS +efp,efp_tomato,efp_tomato,Solyc04g014530,PASS +efp,efp_triphysaria,efp_triphysaria,TrVeBC3_1.1,PASS +efp,efp_triticale,efp_triticale,Ta.10026.1.A1_at,PASS +efp,efp_tung_tree,efp_tung_tree,Vf03G1621,PASS +efp,efp_wheat,efp_wheat,TraesCS1A01G000100,PASS +eplant,eplant_arabidopsis,arabidopsis,ABI3,FAIL +eplant,eplant_barley,barley,HORVU.MOREX.r3.1HG0000030,PASS +eplant,eplant_barley_legacy,barley,HORVU1Hr1G000010,PASS +eplant,eplant_camelina,camelina,Csa01g001040,PASS +eplant,eplant_cannabis,cannabis,AGQN03000001,PASS +eplant,eplant_eucalyptus,eucalyptus,Eucgr.A00001,PASS +eplant,eplant_maize,maize,GRMZM2G158252,PASS +eplant,eplant_medicago,medicago,Medtr8g043970,PASS +eplant,eplant_poplar,poplar,Potri.003G172600,PASS +eplant,eplant_potato,potato,PGSC0003DMG400000005,PASS +eplant,eplant_rice,rice,LOC_Os01g01080,PASS +eplant,eplant_soybean,soybean,Glyma.06G202300,PASS +eplant,eplant_sugarcane,sugarcane,Sh01_g000010,PASS +eplant,eplant_sunflower,sunflower,HanXRQChr12g0384141,FAIL +eplant,eplant_tomato,tomato,Solyc04g014530,PASS +eplant,eplant_wheat,wheat,TraesCS1A01G000100,PASS +eplant,eplant_willow,willow,SapurV1A.0035s0010,FAIL diff --git a/mysql_dbs.txt b/mysql_dbs.txt new file mode 100644 index 00000000..3738f468 --- /dev/null +++ b/mysql_dbs.txt @@ -0,0 +1,212 @@ +Database +actinidia_bud_development +actinidia_flower_fruit_development +actinidia_postharvest +actinidia_vegetative_growth +affydb +annotations_lookup +apple +arabidopsis_ecotypes +arachis +atgenexp +atgenexp_hormone +atgenexp_pathogen +atgenexp_plus +atgenexp_stress +barley_mas +barley_rma +barley_seed +barley_spike_meristem +barley_spike_meristem_v3 +brachypodium +brachypodium_Bd21 +brachypodium_embryogenesis +brachypodium_grains +brachypodium_metabolites_map +brachypodium_photo_thermocycle +brassica_rapa +cacao_developmental_atlas +cacao_developmental_atlas_sca +cacao_drought_diurnal_atlas +cacao_drought_diurnal_atlas_sca +cacao_infection +cacao_leaf +cacao_meristem_atlas_sca +cacao_seed_atlas_sca +camelina +camelina_tpm +cannabis +canola +canola_nssnp +canola_original +canola_original_v2 +canola_seed +cassava_atlas +cassava_cbb +cassava_eacmv +circadian_mutants +cuscuta +cuscuta_early_haustoriogenesis +cuscuta_lmd +dna_damage +durum_wheat_abiotic_stress +durum_wheat_biotic_stress +durum_wheat_development +embryo +eplant2 +eplant_poplar +eplant_rice +eplant_soybean +eplant_tomato +eucalyptus +euphorbia +fastpheno +gc_drought +germination +grape_developmental +guard_cell +gynoecium +heterodera_schachtii +hnahal +homologs_db +human_body_map_2 +human_developmental +human_developmental_SpongeLab +human_diseased +information_schema +interactions_vincent_v2 +kalanchoe +kalanchoe_time_course_analysis +klepikova +lateral_root_initiation +light_series +lipid_map +little_millet +llama3 +lupin_lcm_leaf +lupin_lcm_pod +lupin_lcm_stem +lupin_pod_seed +lupin_whole_plant +maize_RMA_linear +maize_RMA_log +maize_atlas +maize_atlas_v5 +maize_buell_lab +maize_early_seed +maize_ears +maize_embryonic_leaf_development +maize_enzyme +maize_gdowns +maize_iplant +maize_kernel_v5 +maize_leaf_gradient +maize_lipid_map +maize_metabolite +maize_nitrogen_use_efficiency +maize_rice_comparison +maize_root +maize_stress_v5 +mangosteen_aril_vs_rind +mangosteen_callus +mangosteen_diseased_vs_normal +mangosteen_fruit_ripening +mangosteen_seed_development +mangosteen_seed_development_germination +mangosteen_seed_germination +marchantia_organ_stress +medicago_mas +medicago_rma +medicago_root +medicago_root_v5 +medicago_seed +meristem_db +meristem_db_new +mouse_db +mysql +oat +performance_schema +phelipanche +physcomitrella_db +poplar +poplar_hormone +poplar_leaf +poplar_nssnp +poplar_xylem +potato_dev +potato_stress +potato_wounding +rice_abiotic_stress_sc_pseudobulk +rice_drought_heat_stress +rice_interactions +rice_leaf_gradient +rice_maize_comparison +rice_mas +rice_metabolite +rice_rma +rice_root +rohan +root +root_Schaefer_lab +rpatel +seed_db +seedcoat +selaginella +shoot_apex +silique +single_cell +sorghum_atlas_w_BS_cells +sorghum_comparative_transcriptomics +sorghum_developmental +sorghum_developmental_2 +sorghum_flowering_activation +sorghum_low_phosphorus +sorghum_nitrogen_stress 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+import matplotlib.ticker as ticker + +# ── Collected data ──────────────────────────────────────────────────────────── +with open("/tmp/speed_results.pkl", "rb") as f: + measured = pickle.load(f) + +DBS = ["embryo", "klepikova", "shoot_apex"] +DB_LABELS = ["Embryo", "Klepikova", "Shoot Apex"] + +# Real measured data +local = {db: measured[(db, "local")] for db in DBS} +cgi = {db: measured[(db, "legacy_cgi")] for db in DBS} + +# Real ngrok data (mirna-undeliberate-rachael.ngrok-free.dev → localhost:5000) +rng = np.random.default_rng(42) +ngrok = {db: measured[(db, "ngrok")] for db in DBS} +NGROK_ESTIMATED = False + +# ── Colours ─────────────────────────────────────────────────────────────────── +C_LOCAL = "#2196F3" # blue +C_NGROK = "#FF9800" # orange +C_CGI = "#9C27B0" # purple + +# ============================================================================= +# FIGURE 1 — Bar chart (averages) with broken y-axis at 2000 ms +# ============================================================================= +CLIP = 2000 # ms — y-axis ceiling + +fig1, (ax_top, ax_bot) = plt.subplots( + 2, 1, figsize=(9, 6), + gridspec_kw={"height_ratios": [1.6, 2.8], "hspace": 0.08} +) + +x = np.arange(len(DBS)) +W = 0.25 + +def bar_group(ax, vals_dict, clip=None): + """Draw grouped bars; returns bar objects.""" + bars = {} + for i, (key, color) in enumerate( + [("local", C_LOCAL), ("ngrok", C_NGROK), ("cgi", C_CGI)] + ): + data = {"local": local, "ngrok": ngrok, "cgi": cgi}[key] + means = [np.mean(data[db]) for db in DBS] + sds = [np.std(data[db]) for db in DBS] + if clip: + means_plot = [min(m, clip) for m in means] + else: + means_plot = means + b = ax.bar(x + (i - 1) * W, means_plot, W, + color=color, alpha=0.88, zorder=3, + yerr=sds if clip is None else None, + capsize=3, error_kw={"elinewidth": 1, "zorder": 4}) + bars[key] = (b, means) + return bars + +# ── Top panel: 1800–2800 ms range (shows CGI bars poking above clip) ────────── +TOP_LO, TOP_HI = 1800, 2800 +ax_top.set_ylim(TOP_LO, TOP_HI) +bar_group(ax_top, {}, clip=None) + +for i, (key, color) in enumerate( + [("local", C_LOCAL), ("ngrok", C_NGROK), ("cgi", C_CGI)]): + data = {"local": local, "ngrok": ngrok, "cgi": cgi}[key] + means = [np.mean(data[db]) for db in DBS] + sds = [np.std(data[db]) for db in DBS] + ax_top.bar(x + (i - 1) * W, means, W, color=color, alpha=0.88, zorder=3) + ax_top.errorbar(x + (i - 1) * W, means, yerr=sds, + fmt="none", color="black", capsize=3, + elinewidth=1, zorder=5) + +ax_top.set_ylim(TOP_LO, TOP_HI) +ax_top.set_yticks([1800, 2000, 2200, 2400, 2600, 2800]) +ax_top.tick_params(bottom=False, labelbottom=False) +ax_top.spines["bottom"].set_visible(False) +ax_top.set_facecolor("#fafafa") +ax_top.grid(axis="y", linestyle="--", alpha=0.4, zorder=0) + +# Annotate the outlier above the top panel +outlier_val = max(max(cgi[db]) for db in DBS) +ax_top.annotate( + f"outlier ≈ {outlier_val/1000:.1f} s\n(not shown)", + xy=(0.97, 0.97), xycoords="axes fraction", + ha="right", va="top", fontsize=7.5, + color="#666", style="italic" +) + +# ── Bottom panel: 0–CLIP ms ─────────────────────────────────────────────────── +for i, (key, color) in enumerate( + [("local", C_LOCAL), ("ngrok", C_NGROK), ("cgi", C_CGI)]): + data = {"local": local, "ngrok": ngrok, "cgi": cgi}[key] + means = [np.mean(data[db]) for db in DBS] + sds = [np.std(data[db]) for db in DBS] + capped = [min(m, CLIP) for m in means] + ax_bot.bar(x + (i - 1) * W, capped, W, color=color, alpha=0.88, zorder=3) + ax_bot.errorbar(x + (i - 1) * W, capped, yerr=sds, + fmt="none", color="black", capsize=3, + elinewidth=1, zorder=5) + # Draw squiggly break on bars that exceed CLIP + for j, (cap, real) in enumerate(zip(capped, means)): + if real > CLIP: + bx = x[j] + (i - 1) * W + for yy in np.linspace(CLIP - 60, CLIP + 10, 5): + ax_bot.plot([bx - W / 2 + 0.01, bx + W / 2 - 0.01], + [yy, yy + 18 * (1 if j % 2 == 0 else -1)], + color="white", lw=1.8, zorder=6) + +ax_bot.set_ylim(0, CLIP + 80) +ax_bot.set_xticks(x) +ax_bot.set_xticklabels(DB_LABELS, fontsize=11) +ax_bot.spines["top"].set_visible(False) +ax_bot.set_facecolor("#fafafa") +ax_bot.grid(axis="y", linestyle="--", alpha=0.4, zorder=0) +ax_bot.set_ylabel("Response time (ms)", fontsize=11, labelpad=8) +ax_bot.yaxis.set_label_coords(-0.08, 1.1) + +# Broken-axis diagonal tick marks +d = 0.012 +kwargs = dict(transform=fig1.transFigure, color="black", clip_on=False, lw=1.2) +# Get axes positions +pos_top = ax_top.get_position() +pos_bot = ax_bot.get_position() +y_break = pos_bot.y1 # top of bottom axes = bottom of top axes +for xi in [pos_top.x0 - 0.005, pos_top.x0 + 0.005]: + fig1.add_artist(plt.Line2D([xi - d, xi + d], + [y_break - d * 1.5, y_break + d * 1.5], **kwargs)) + +# Legend +legend_handles = [ + mpatches.Patch(color=C_LOCAL, label="Local API (localhost:5000)"), + mpatches.Patch(color=C_NGROK, + label="ngrok Tunnel" + (" [estimated]" if NGROK_ESTIMATED else "")), + mpatches.Patch(color=C_CGI, label="Legacy BAR CGI"), +] +ax_bot.legend(handles=legend_handles, fontsize=9, + loc="upper right", framealpha=0.9) + +fig1.suptitle("Gene Expression — Average HTTP Response Time", fontsize=13, + fontweight="bold", y=0.98) +ax_top.set_title("(y-axis clipped to 2000 ms; CGI bars shown in upper panel)", + fontsize=8, color="#555", pad=4) + +plt.savefig("/Users/reenamarieobmina/BAR_API/speed_bar_chart.png", + dpi=150, bbox_inches="tight") +plt.close() +print("Fig 1 saved: speed_bar_chart.png") + +# ============================================================================= +# FIGURE 2 — Box plots (all individual trials) +# ============================================================================= +fig2, axes = plt.subplots(1, 3, figsize=(13, 5), sharey=False) + +for col, (db, db_label) in enumerate(zip(DBS, DB_LABELS)): + ax = axes[col] + + endpoint_data = [local[db], ngrok[db], cgi[db]] + endpoint_labels = [ + "Local\nAPI", + "ngrok\nTunnel" + ("\n[est.]" if NGROK_ESTIMATED else ""), + "Legacy\nCGI", + ] + colors = [C_LOCAL, C_NGROK, C_CGI] + + bp = ax.boxplot( + endpoint_data, + patch_artist=True, + widths=0.45, + medianprops=dict(color="white", linewidth=2), + whiskerprops=dict(linewidth=1.2), + capprops=dict(linewidth=1.2), + flierprops=dict(marker="o", markersize=4, alpha=0.6), + zorder=3, + ) + for patch, color in zip(bp["boxes"], colors): + patch.set_facecolor(color) + patch.set_alpha(0.82) + + # Scatter individual points + for idx, (vals, color) in enumerate(zip(endpoint_data, colors), start=1): + jitter = rng.uniform(-0.12, 0.12, len(vals)) + ax.scatter([idx + j for j in jitter], vals, + color=color, s=18, alpha=0.7, zorder=4, edgecolors="white", linewidths=0.4) + + ax.set_xticks([1, 2, 3]) + ax.set_xticklabels(endpoint_labels, fontsize=9) + ax.set_title(db_label, fontsize=11, fontweight="bold") + ax.set_facecolor("#fafafa") + ax.grid(axis="y", linestyle="--", alpha=0.4, zorder=0) + ax.spines["top"].set_visible(False) + ax.spines["right"].set_visible(False) + + if col == 0: + ax.set_ylabel("Response time (ms)", fontsize=10) + + # Show n + ax.text(0.98, 0.98, f"n={len(local[db])} trials", + transform=ax.transAxes, ha="right", va="top", + fontsize=7.5, color="#777") + +fig2.suptitle("Gene Expression — Response Time Distribution", fontsize=13, + fontweight="bold") +fig2.tight_layout(rect=[0, 0, 1, 0.95]) +plt.savefig("/Users/reenamarieobmina/BAR_API/speed_box_plots.png", + dpi=150, bbox_inches="tight") +plt.close() +print("Fig 2 saved: speed_box_plots.png") diff --git a/tests/resources/test_microarray_expression.py b/tests/resources/test_microarray_expression.py index 8fd0a4dc..2756d280 100644 --- a/tests/resources/test_microarray_expression.py +++ b/tests/resources/test_microarray_expression.py @@ -1,4 +1,5 @@ from api import app +from api.utils.master_data_utils import load_combined_master from unittest import TestCase from json import load @@ -34,3 +35,77 @@ def test_get_world_eFP_expression(self): "error": "There are no data found for the given gene", } self.assertEqual(response.json, expected) + + +class TestGetDatabases(TestCase): + """/microarray_gene_expression//databases -- sourced from combined_master.json.""" + + def setUp(self): + self.app_client = app.test_client() + self.master = load_combined_master() + + def test_valid_species_matches_master_json(self): + response = self.app_client.get("/microarray_gene_expression/arabidopsis/databases") + self.assertTrue(response.json["wasSuccessful"]) + data = response.json["data"] + + expected_dbs = { + db_name for db_name, info in self.master["databases"].items() + if info["species"] == "arabidopsis" + } + self.assertEqual(data["num_databases"], len(expected_dbs)) + # Only databases with at least one live frontend view (used_by) can + # appear in a view-name -> database mapping; legacy/hidden databases + # (e.g. affydb, rohan) are counted in num_databases but have no view. + expected_dbs_with_views = { + db_name for db_name in expected_dbs + if self.master["databases"][db_name]["used_by"] + } + self.assertEqual(set(data["databases"].values()), expected_dbs_with_views) + + def test_species_case_insensitive(self): + response = self.app_client.get("/microarray_gene_expression/Arabidopsis/databases") + self.assertTrue(response.json["wasSuccessful"]) + + def test_species_previously_split_across_fake_subspecies_is_unified(self): + """cacao_ccn/cacao_sca/cacao_tc databases used to be modelled as three + fake pseudo-species ("cacao ccn", "cacao sca", "cacao tc"); the + master-JSON-backed endpoint reports them under the one real species.""" + response = self.app_client.get("/microarray_gene_expression/cacao/databases") + self.assertTrue(response.json["wasSuccessful"]) + data = response.json["data"] + self.assertGreaterEqual(data["num_databases"], 6) + + def test_invalid_species_rejected(self): + response = self.app_client.get("/microarray_gene_expression/not_a_real_species/databases") + self.assertEqual(response.json, {"wasSuccessful": False, "error": "Invalid species"}) + + +class TestGetSamples(TestCase): + """/microarray_gene_expression///samples -- sourced from combined_master.json.""" + + def setUp(self): + self.app_client = app.test_client() + + def test_single_view_returns_groups(self): + response = self.app_client.get("/microarray_gene_expression/arabidopsis/Abiotic_Stress/samples") + self.assertTrue(response.json["wasSuccessful"]) + data = response.json["data"] + self.assertEqual(data["database"], "atgenexp_stress") + self.assertIn("groups", data) + self.assertTrue(len(data["groups"]) > 0) + + def test_all_views_returns_every_view_for_species(self): + response = self.app_client.get("/microarray_gene_expression/arabidopsis/all/samples") + self.assertTrue(response.json["wasSuccessful"]) + self.assertIn("Abiotic_Stress", response.json["data"]["views"]) + + def test_invalid_view_rejected(self): + response = self.app_client.get("/microarray_gene_expression/arabidopsis/NotARealView/samples") + self.assertEqual( + response.json, {"wasSuccessful": False, "error": "Invalid view for this species"} + ) + + def test_invalid_species_rejected(self): + response = self.app_client.get("/microarray_gene_expression/not_a_real_species/Abiotic_Stress/samples") + self.assertEqual(response.json, {"wasSuccessful": False, "error": "Invalid species"}) diff --git a/validate_live_example_gene_ids.py b/validate_live_example_gene_ids.py new file mode 100644 index 00000000..1cacfad1 --- /dev/null +++ b/validate_live_example_gene_ids.py @@ -0,0 +1,182 @@ +""" +Reena Obmina | BCB330 Project 2025-2026 | University of Toronto + +Task (Jul 2026): test the production gene ID validators against each live +efp/eplant project's OWN example gene ID, instead of only against Vincent's +curated sample dumps in api/random_rows_json/. + +Motivation: api/random_rows_json/ only has data for the databases Vincent +happened to sample, and even where it does, the specific IDs picked can miss +edge cases -- e.g. every barley_spike_meristem_v3 sample happened to include +a trailing isoform suffix (HORVU.MOREX.r3.2HG0105390.1), which masked a real +gap: BAR's own eplant_barley (v3) page uses a bare gene ID with no suffix +(HORVU.MOREX.r3.1HG0000030) as its canonical example, and that failed +is_barley_gene_valid until this test caught it (see git history/PR for the fix). + +Each species view's datasource XML (data/{view}.xml) does NOT contain gene +IDs at all -- it only has tissue/sample/group names for the diagram -- so +that's not usable as a source here. The actual live, authoritative example +gene ID for a project lives in the page HTML itself: + - eFP (efpWeb.cgi, server-rendered): the "Primary Gene ID" default. + - ePlant (client-rendered SPA): a static "Example: ID" search hint + baked into the page shell (present even before any JS runs). + +Reads (live, over HTTP): every project in EFP_SITES and EPLANT_SITES +Reads (local): api/utils/bar_utils.py -- EFP_PROJECT_REGEXES, BARUtils + api/utils/gene_id_utils.py -- GeneIdUtils.validate_gene_id +Writes: live_example_gene_id_coverage.csv -- one row per project: the live + example ID, which validator it was checked against, and the result. +""" + +import csv +import re +import sys +import types +from concurrent.futures import ThreadPoolExecutor, as_completed + +import requests + +# importing api.utils.* normally runs api/__init__.py's create_app(), which +# tries to connect to MySQL even for this standalone script. Pre-register +# empty stand-in packages so Python loads the submodules directly instead. +sys.modules.setdefault("api", types.ModuleType("api")) +sys.modules["api"].__path__ = ["api"] +sys.modules.setdefault("api.utils", types.ModuleType("api.utils")) +sys.modules["api.utils"].__path__ = ["api/utils"] + +from api.utils.bar_utils import EFP_PROJECT_REGEXES, BARUtils # noqa: E402 +from api.utils.gene_id_utils import GeneIdUtils, _VALIDATORS # noqa: E402 + +from scrape_view_databases import EFP_SITES, EPLANT_SITES # noqa: E402 + +REQUEST_TIMEOUT = 20 + +# EFP_SITES keys that map straight to "efp_" + key.replace(" ", "_") in +# EFP_PROJECT_REGEXES for every project EXCEPT these two. +EFP_PROJECT_KEY_OVERRIDES = { + "arabidopsis seedcoat": "efp_seedcoat", + "mouse": "mouse_efp", +} + +PRIMARY_GENE_RE = re.compile(r']*name="primaryGene"[^>]*>', re.IGNORECASE) +VALUE_ATTR_RE = re.compile(r'value="([^"]*)"') +EPLANT_EXAMPLE_RE = re.compile(r"Example:\s*]*>([^<]+)", re.IGNORECASE) + + +def efp_project_key(species): + return EFP_PROJECT_KEY_OVERRIDES.get(species, f"efp_{species.replace(' ', '_')}") + + +def eplant_species_key(site): + """eplant_barley_legacy -> barley, eplant_maize -> maize, etc.""" + return site.removeprefix("eplant_").removesuffix("_legacy") + + +def fetch(url): + resp = requests.get(url, timeout=REQUEST_TIMEOUT) + resp.raise_for_status() + return resp.text + + +def check_efp_project(species, efp_url): + project_key = efp_project_key(species) + row = { + "source": "efp", + "project": f"efp_{species.replace(' ', '_')}", + "validator_key": project_key, + "example_gene_id": "", + "result": "", + } + try: + html = fetch(efp_url) + except Exception as e: + row["result"] = f"FETCH_ERROR: {e}" + return row + + tag_match = PRIMARY_GENE_RE.search(html) + value_match = VALUE_ATTR_RE.search(tag_match.group(0)) if tag_match else None + if not value_match or not value_match.group(1): + row["result"] = "NO_EXAMPLE_FOUND" + return row + + example_id = value_match.group(1) + row["example_gene_id"] = example_id + + if project_key not in EFP_PROJECT_REGEXES: + row["result"] = "NO_REGEX_MAPPING" + return row + + row["result"] = "PASS" if BARUtils.is_efp_gene_valid(example_id, project_key) else "FAIL" + return row + + +def check_eplant_project(site, base_url): + species_key = eplant_species_key(site) + row = { + "source": "eplant", + "project": site, + "validator_key": species_key, + "example_gene_id": "", + "result": "", + } + try: + html = fetch(base_url) + except Exception as e: + row["result"] = f"FETCH_ERROR: {e}" + return row + + match = EPLANT_EXAMPLE_RE.search(html) + if not match: + row["result"] = "NO_EXAMPLE_FOUND" + return row + + example_id = match.group(1).strip() + row["example_gene_id"] = example_id + + if species_key not in _VALIDATORS: + row["result"] = "NO_VALIDATOR_MAPPING" + return row + + row["result"] = "PASS" if GeneIdUtils.validate_gene_id(example_id, species_key) else "FAIL" + return row + + +def main(): + rows = [] + with ThreadPoolExecutor(max_workers=10) as pool: + futures = {pool.submit(check_efp_project, species, url): species for species, url in EFP_SITES.items()} + futures.update( + {pool.submit(check_eplant_project, site, url): site for site, url in EPLANT_SITES.items()} + ) + for future in as_completed(futures): + rows.append(future.result()) + + rows.sort(key=lambda r: (r["source"], r["project"])) + + out_file = "live_example_gene_id_coverage.csv" + with open(out_file, "w", newline="") as f: + writer = csv.DictWriter(f, fieldnames=["source", "project", "validator_key", "example_gene_id", "result"]) + writer.writeheader() + writer.writerows(rows) + + counts = {} + for row in rows: + key = row["result"].split(":")[0] + counts[key] = counts.get(key, 0) + 1 + + print(f"Checked {len(rows)} projects ({sum(1 for r in rows if r['source'] == 'efp')} efp, " + f"{sum(1 for r in rows if r['source'] == 'eplant')} eplant).") + for key, count in sorted(counts.items()): + print(f" {key}: {count}") + print(f"Report written to {out_file}") + + fails = [r for r in rows if r["result"] == "FAIL"] + if fails: + print("\nFAILURES (live example ID rejected by production validator):") + for r in fails: + print(f" {r['project']:30s} example={r['example_gene_id']!r:35s} validator={r['validator_key']}") + + +if __name__ == "__main__": + main() diff --git a/vincent_regex_summary_jun_25_2026.md b/vincent_regex_summary_jun_25_2026.md new file mode 100644 index 00000000..d6b54f0d --- /dev/null +++ b/vincent_regex_summary_jun_25_2026.md @@ -0,0 +1,178 @@ +# BAR eFP Regex Validation Summary for Vincent +**Date:** June 25, 2026 +**Prepared by:** Reena Obmina +**For:** Vincent (Production Database Validation) + +--- + +## Summary + +All eFP project regexes have been consolidated and are ready for production validation. These regexes validate both **canonical gene IDs AND microarray probeset IDs** where applicable. + +### Key Deliverables + +#### 1. **Master JSON File** ✅ +- **File:** `data/efp_info/combined_master.json` +- **Contents:** + - 48 species with standardized scientific names + - 193 databases with complete metadata + - SQL column structure for each database's sample_data table + - Schema variants (rnaseq_simple, legacy_microarray_projinfo) + - Frontend usage mapping for each database + - Sample groups and experimental design + +#### 2. **Consolidated Regex Dictionary** ✅ +- **File:** `api/utils/bar_utils.py` (lines 8-177) +- **Dictionary:** `EFP_PROJECT_REGEXES` +- **Total Patterns:** 50+ eFP project keys +- **Coverage:** All RNA-seq and microarray platforms + +--- + +## Regex Coverage by Platform + +### RNA-seq Projects (Gene Models) +- `efp_arabidopsis` - AGI gene IDs (At1g12345) +- `efp_barley` - HM/HV identifiers +- `efp_rice` - LOC_Os identifiers +- `efp_medicago` - Medtr identifiers +- `efp_poplar` - Potri identifiers +- `efp_soybean` - Glyma identifiers +- `efp_maize` - GRMZM identifiers +- `efp_wheat` - TraesCS identifiers +- And 20+ more species (apple, cacao, grape, potato, etc.) + +### Microarray Projects (Probeset IDs) +- `efp_arabidopsis` - Also accepts Affymetrix probeset IDs (123456_at, 123456_s_at) +- `efp_barley` - HV/HM array probes +- `efp_rice` - Affymetrix Rice array +- `efp_medicago` - Mtr/Msa/Sme array probes +- `efp_poplar` - Ptp array probes + +### Special Cases +- `efp_seedcoat` - Accepts CATMA probes (At\d{8}) + ATH1 Affymetrix +- `efp_arabidopsis_lipid` - Lipid species names (freeform text) +- `efp_maize_metabolite` - Metabolite names (freeform text) +- `efp_human` - Human probeset IDs (e.g., 202019_s_at) +- `efp` - Generic Arabidopsis validator (fallback) + +--- + +## Known Issues & Decisions Needed + +### ⚠️ Tomato Regex Issue + +**Current Status:** One generic regex for all tomato databases +``` +"efp_tomato": r"^(Solyc\d{2}g\d{6}\.?\d{0,3})$|^(TU\d{6})$" +``` + +**Database Mapping:** +``` +DATABASE_EFP_PROJECT = { + "tomato": "efp_tomato", + "tomato_ils": "efp_tomato", + "tomato_ils2": "efp_tomato", + "tomato_ils3": "efp_tomato", + "tomato_meristem": "efp_tomato", + "tomato_renormalized": "efp_tomato", + "tomato_root": "efp_tomato", + "tomato_root_field_pot": "efp_tomato", + "tomato_s_pennellii": "efp_tomato", + "tomato_seed": "efp_tomato", + "tomato_shade_mutants": "efp_tomato", + "tomato_shade_timecourse": "efp_tomato", + "tomato_trait": "efp_tomato_trait", (special case) +} +``` + +**Problem:** Different tomato databases may have different gene ID formats or probesets. + +**Options for Resolution:** +1. **Per-Species Approach (Current):** Keep one regex per species, validate all databases the same way +2. **Per-Database Approach:** Create individual regex patterns for each tomato database variant + +**Action Needed:** Vincent will consult with Asher about which approach to take. + +--- + +## What Reena Still Needs + +1. **`efp_human` regex** ✅ Already exists in bar_utils.py (line 125) + ```python + "efp_human": r"^(\d{6,7}(_[xsa])?_at)$|^(\D{0,12}\d{0,12})$|^(\d{1,12})$" + ``` + +2. **`efp` (generic) regex** ✅ Already exists in bar_utils.py (line 9) + ```python + "efp": ( + r"^([Aa][Tt][12345CM][Gg][0-9]{5})$" + r"|^([0-9]{6}(_[xsfi])?_at)$" + r"|^([0-9]{6,9})$" + r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$" + r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" + ) + ``` + +--- + +## Production Database Validation Steps + +### For Vincent: + +1. **Run the regexes against production BAR database** + - Validate gene IDs in `sample_data.data_probeset_id` column + - Check all 193 databases for ID format compliance + - Generate coverage report + +2. **Identify any edge cases or failures** + - Sample IDs that don't match regex patterns + - New ID formats not yet covered + - Per-database vs per-species mismatches (especially tomato) + +3. **Generate validation report** + - Which databases pass 100% validation + - Which databases have edge cases + - Recommendations for regex refinements + +### Expected Outputs: +- ✅ `efp_regex_audit_prod.csv` (already in repo) +- ✅ `db_regex_coverage_report.csv` (already in repo) +- 📊 New validation report from production scan + +--- + +## Files Ready for Production Use + +``` +api/utils/bar_utils.py + ├── EFP_PROJECT_REGEXES dict (lines 8-177) + └── is_efp_gene_valid() validator function + +api/utils/gene_id_utils.py + ├── DATABASE_EFP_PROJECT mapping + └── validate_gene_for_database() function + +data/efp_info/combined_master.json + └── Single source of truth for all database metadata +``` + +--- + +## Next Steps + +1. **Vincent:** Run production validation scan against all databases +2. **Vincent → Asher:** Consult on tomato database regex strategy (per-species vs per-database) +3. **Reena:** Once decision is made, update `DATABASE_EFP_PROJECT` mapping if needed +4. **Team:** Merge validated regex patterns into production codebase + +--- + +## Contact + +For questions about: +- **Regex patterns:** Reena Obmina (rmobmina@gmail.com) +- **Production validation:** Vincent +- **Architecture decision:** Asher + +**Generated:** June 25, 2026 From afd8c63c046c8f0f081868e8a8e75e549c81b098 Mon Sep 17 00:00:00 2001 From: Reena Date: Fri, 17 Jul 2026 13:34:26 -0400 Subject: [PATCH 3/3] Remove scratch CSVs, MDs, and one-off analysis files from repo root These were leftover exploratory outputs (regex audit dumps, coverage CSVs, speed benchmark plots, old email drafts) not consumed by any script in the active build pipeline. db_regex_coverage_report.csv is kept since build_master_db_list.py reads it as an input. --- ALL_EFP_REGEXES.csv | 58 ---- ALL_REGEXES_FOR_VINCENT.csv | 56 ---- EMAIL_FOR_VINCENT.txt | 55 ---- EMAIL_TO_VINCENT_JUL_17_2026.txt | 72 ----- EMAIL_TO_VINCENT_JUN_25_2026.txt | 69 ----- VINCENT_REGEX_PACKAGE_JUN25.md | 143 ---------- ...fp-projects-views-with-lookup-settings.txt | 268 ------------------ all_gene_id_regexes.csv | 108 ------- cfg_dbs.txt | 48 ---- efp_regex_audit_prod.csv | 60 ---- generate_efp_test_cases.py | 211 -------------- live_example_gene_id_coverage.csv | 67 ----- mysql_dbs.txt | 212 -------------- speed_bar_chart.png | Bin 81974 -> 0 bytes speed_box_plots.png | Bin 87920 -> 0 bytes speed_graphs.py | 217 -------------- validate_live_example_gene_ids.py | 182 ------------ vincent_regex_summary_jun_25_2026.md | 178 ------------ 18 files changed, 2004 deletions(-) delete mode 100644 ALL_EFP_REGEXES.csv delete mode 100644 ALL_REGEXES_FOR_VINCENT.csv delete mode 100644 EMAIL_FOR_VINCENT.txt delete mode 100644 EMAIL_TO_VINCENT_JUL_17_2026.txt delete mode 100644 EMAIL_TO_VINCENT_JUN_25_2026.txt delete mode 100644 VINCENT_REGEX_PACKAGE_JUN25.md delete mode 100644 all-efp-projects-views-with-lookup-settings.txt delete mode 100644 all_gene_id_regexes.csv delete mode 100644 cfg_dbs.txt delete mode 100644 efp_regex_audit_prod.csv delete mode 100644 generate_efp_test_cases.py delete mode 100644 live_example_gene_id_coverage.csv delete mode 100644 mysql_dbs.txt delete mode 100644 speed_bar_chart.png delete mode 100644 speed_box_plots.png delete mode 100644 speed_graphs.py delete mode 100644 validate_live_example_gene_ids.py delete mode 100644 vincent_regex_summary_jun_25_2026.md diff --git a/ALL_EFP_REGEXES.csv b/ALL_EFP_REGEXES.csv deleted file mode 100644 index 5a6e5173..00000000 --- a/ALL_EFP_REGEXES.csv +++ /dev/null @@ -1,58 +0,0 @@ -project,regex -efp,"(r"^([Aa][Tt][12345CM][Gg][0-9]{5})$"r"|^([0-9]{6}(_[xsfi])?_at)$"r"|^([0-9]{6,9})$"# ATH1 Affymetrix bacterial/control spike-in probes, shared by all Affy platformsr"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$"r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$")" -efp_arabidopsis,"(r"^([Aa][Tt][12345CM][Gg][0-9]{5})$"r"|^([0-9]{6}(_[xsfi])?_at)$"r"|^([0-9]{6,9})$"r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$"r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$")# Seedcoat uses CATMA probes (At\d{8}) and AROS probes (\D\d+_\d+) in addition to ATH1" -efp_seedcoat,"(r"^(At[12345CM]g[0-9]{5})$"r"|^([0-9]{6}(_[xsfi])?_at)$"r"|^([0-9]{6,9})$"r"|^(\D\d+_\d+)$"r"|^(At\d{8})$")" -efp_barley,"(r"^((HM|HV).*)$|^(HV.*_at)$"r"|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4})_at)$"r"|^([0-9]{4,5}\.AF[0-9]{5}(_|_x_)at)$"r"|^(A[0-9]{5}\.[0-9]{1}(_|_x_|_s_)at)$"r"|^(([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)(_|_x_|_s_|_CDS-[0-9]{1,2}_|_CDS-[0-9]{1,2}_s_)at)$"r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$"r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$"r"|^(ChlorContig[0-9]{1,2}(_|_x_|_s_)at)$"r"|^(((MitoContig|Contig)[0-9]{1,6})(_|_x_|_s_)at)$"r"|^(D[0-9]{5}_at)$"r"|^(Dhn[0-9]{2}\(Morex\)(_|_s_)at)$"r"|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2}(_|_s_|_x_)at)$"r"|^(Franka(_|_b_)3pri[0-9]{1,2}(_|_s_|_x_)at)$"r"|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$"r"|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$"r"|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru](_|_x_|_s_)at)$"r"|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1}(_|_x_|_s_)at)$"r"|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2}(_|_x_|_s_)at)$"r"|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4}))$"r"|^([0-9]{4,5}\.AF[0-9]{5})$"r"|^(A[0-9]{5}\.[0-9]{1})$"r"|^([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)$"r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX))$"r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre))$"r"|^(ChlorContig[0-9]{1,2})$"r"|^((MitoContig|Contig)[0-9]{1,6})$"r"|^(D[0-9]{5})$"r"|^(Dhn[0-9]{2}\(Morex\))$"r"|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2})$"r"|^(Franka(_|_b_)3pri[0-9]{1,2})$"r"|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$"r"|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$"r"|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru])$"r"|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1})$"r"|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2})$"r"|^(HO)$"r"|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$"r"|^(AK[0-9]{6}\.1)$"r"|^(AJ[0-9]{6}\.1)$")" -efp_rice,"(r"^(LOC_Os[0-9]{2}g[0-9]{5})$"r"|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$"r"|^(AFFX-OS-(18SrRNA|25SrRNA|5\.8SrRNA)_(s_at|at))$"r"|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$"r"|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$"r"|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$"r"|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$"r"|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$")" -efp_medicago,"(r"^(Medtr\d{1}g\d{6})$"r"|^(Medtr\d{1}g\d{6}\.[0-9]{1})$"" -# Medicago array probesets,"Mtr/Msa/Sme prefix, any Affymetrix suffix variantr"|^(Mtr\.\d{4,5}\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$"r"|^(Msa\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$"r"|^(Sme\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$"r"|^(AFFX-(Bio|Cre|Dap|Lys|Phe|Thr|Trpn)(B|C|Dn|X)-(3|5|M)_at)$"r"|^(AFFX-(Msa|Mtr)-(actin|gapc|gsta|ubq11|TrpnX)-(3|5|M)_(at|x_at|s_at))$"r"|^(AFFX-r2-(Bs|Ec|P1)-(cre|dap|lys|phe|thr|bioB|bioC|bioD)-(3|5|M)_(at|s_at|x_at))$"r"|^(AFFX-Mtr-ubq11-(3|5|M)_(at|s_at|x_at))$"r"|^(AFFX-r2-Tag[A-Z]{1,2}_at)$"r"|^(Medtr_v1_\d{6})$")" -efp_poplar,"(r"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$"r"|^((eugene3)\.\d{6,12})$"r"|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$"r"|^((grail3\.)\d{8,12})$"r"|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$"r"|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$"r"|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$"# poplar_hormone's real sample IDs omit the transcript suffix entirelyr"|^(Potri\.[0-9]{3}G[0-9]{6}(\.[0-9]{1})?)$")" -efp_soybean,"(r"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$"r"|^(Glyma\.\d{1,3}g\d{1,8}))$")" -efp_maize,"(r"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$"r"|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$"r"|^(GRMZM(2|5)G[0-9]{6})$"r"|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$"r"|^(Zm\d+d\d+)$"r"|^(Zm\d{1,10}eb\d{1,10})$"# Maize Affymetrix probeset IDs, e.g. Zm011368_at, Zm039842_s_atr"|^(Zm\d{6}(_[xsa])?_at)$")# TaAffx.* probes occur alongside Ta.* — handle both prefixes" -efp_triticale,"r"^((Ta|TaAffx)\.\d+\.\d+\.[A-Z]\d+_(at|s_at|x_at|a_at))$"# Affymetrix human probeset IDs (1557575_at, 202019_s_at) plus a loose fallback" -efp_human,"r"^(\d{6,7}(_[xsa])?_at)$|^(\D{0,12}\d{0,12})$|^(\d{1,12})$"# Remaining eFP projects, sourced verbatim from Vincent's efp_regex_audit_prod.csv" -efp_Eutrema,"r"^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$"" -efp_actinidia,"r"^(Acc\d+\.\d{0,3})$"" -efp_apple,"r"^(MfusH1_\d\dg\d{1,8})$"" -# CSV pattern is lowercase-only; lipid species names use mixed case (e.g. "TG 54,"5; ...")" -efp_arabidopsis_lipid,"r"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$"" -efp_arachis,"r"^(Adur\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Aipa_c\d+_g\d+_i\d+)$|^(Aipa\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Adur_c\d+_g\d+_i\d+)$"" -efp_brachypodium,"r"^(Bradi\d+g\d+.\d)$|^(Bradi\d+s\d+.\d)$|^(Bradi\d+.g\d+)$"" -efp_brachypodium_metabolites,"r"(?i)^[a-z\s\-]{1,60}$"" -efp_brassica_rapa,"r"^(Bra.\d+g\d{0,10})$"" -efp_cacao_ccn,"r"^(CCN-51_Chr\d{1,3}v\d{1,3}_\d{1,9})$"" -efp_cacao_sca,"r"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$"" -efp_cacao_tc,"r"^(Tc\d+v2_g\d+)$"" -efp_camelina,"r"^(Csa\d{0,5}[gs]\d{0,6}.\d{0,3})$|^(At\d[cgm]\d{0,6})$"" -efp_cannabis,"r"(^C\d+$)|(^scaffold\d+$)|(^AGQN\d+$)"" -efp_canola,"r"^(Bna\D\d{1,3}g\d{1,8}\D)$|^(Bna\Dnng\d{1,8}\D)$"" -efp_durum_wheat,"r"^(TrturSVE\d\D\d{1,3}G\d{1,12})$|^(TrturSVE\d\D\d{1,3}G\d{1,12}_ncBOCREA)$"" -efp_euphorbia,"r"^(Ep_chr\d_g\d{1,8})$"" -efp_eutrema,"r"^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$"" -efp_grape,"r"^(VIT_\d{1,2}s\d{4}g\d{5})$|^CHRUN[a-z0-9_]{1,20}$|^CHR\d{1,2}[a-z0-9_]{1,2}$"" -efp_kalanchoe,"r"^(Kaladp\d+s\d+)$"" -efp_little_millet,"r"^(TRINITY_DN\d+_c\d+_g\d+_i\d+)$"" -efp_lupin,"r"^(Luan_Oskar_.{1,12}_\d{1,12})$"# is_efp_gene_valid matches without re.IGNORECASE, so these freeform-text# patterns (enzyme/metabolite/category NAMES, not gene IDs) need an explicit# (?i) -- real sample data is mixed-case ("GAPDH (NAD)", "Citric Acid")." -efp_maize_enzyme,"r"(?i)^[a-z0-9\s\-\(\)]{1,50}$"" -efp_maize_metabolite,"r"(?i)^[a-z0-9\s,\.\-\(\)_'\+]{1,60}$"# Lipid species names (TG_52_1, MGDG_38_6), same freeform style as efp_arabidopsis_lipid" -efp_maize_lipid_map,"r"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$"# tomato_trait stores root-architecture trait descriptions, not gene IDs" -efp_tomato_trait,"r"^[A-Za-z][A-Za-z0-9\s\.,\-\(\)]{1,100}$"" -efp_maize_transcriptomics,"r"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$"" -efp_mangosteen,"r"^(DN\d{1,10})$"" -efp_marchantia,"r"^(Mp.{1,3}g\d{1,7}\.?\d{1,3}?)$"" -efp_oat,"r"(^N0\.HOG\d{1,10}$|^\D{1,10}\.*\d{1,10}.{1,10}\d{1,10}$)"" -efp_phelipanche,"r"^(OrAeBC\d+_\d+\.\d{1,5})|(At\d[gcm]\d{1,6})$"" -efp_physcomitrella,"r"^(Pp)\d+s\d+_\d+V\d\.\d$|^Phypa_\d+$"" -efp_potato,"r"^(PGSC0003DMG4\d{8})$"" -efp_rice_metabolite,"r"(?i)^[a-z0-9,\s\.\-]{1,40}$"" -efp_rice_transcriptomics,"r"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$"" -efp_selaginella,"r"^(Smo\d+)$"" -efp_sorghum,"r"^(Sobic.\d{0,5}G\d{0,10}$|^Sobic.K\d{0,10}$|^ENSRNA\d{0,12}$|^SORBI_\d{1,6}G\d{1,10})$"" -efp_strawberry,"r"^(FvH4_c?\d{1,3}g\d{1,7})$|^(gene\d{1,10})$"" -efp_striga,"r"^(StHeBC3\_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$"" -efp_tomato,"r"^(Solyc\d{2}g\d{6}\.?\d{0,3})$|^(TU\d{6})$"" -efp_triphysaria,"r"^(TrVeBC\d+_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$"" -efp_tung_tree,"r"^(Vf\d+G\d+)$"" -efp_wheat,"r"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$"" -efpconfig,"r".{0,16}"" -mouse_efp,"r"^(XM_\d{0,8}\.\d{0,3})$|^(\d{1,10}\D\d{0,4}\D{0,4})$|^(\D{1,8}\d{0,8}\D{0,8})$|^(ENSMUSG\d{1,15})$|^(NM_\d{0,12}\d.\d{0,3})$"" diff --git a/ALL_REGEXES_FOR_VINCENT.csv b/ALL_REGEXES_FOR_VINCENT.csv deleted file mode 100644 index c1ef7265..00000000 --- a/ALL_REGEXES_FOR_VINCENT.csv +++ /dev/null @@ -1,56 +0,0 @@ -efp_project,regex -efp,"^([Aa][Tt][12345CM][Gg][0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" -efp_arabidopsis,"^([Aa][Tt][12345CM][Gg][0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" -efp_seedcoat,"^(At[12345CM]g[0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(\D\d+_\d+)$|^(At\d{8})$" -efp_barley,"^(Contig|HM|HV|[A-Z][A-Za-z0-9]+_|[A-Z]{1,3}\d+_)" -efp_rice,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^(Os\.\d+\.\d+\.(S1|A1|S2)_(at|x_at|s_at|a_at))$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5\.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" -efp_medicago,"^(Medtr\d{1}g\d{6})$|^(Medtr\d{1}g\d{6}\.[0-9]{1})$|^(Mtr\.\d{4,5}\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(Msa\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(Sme\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(AFFX-(Bio|Cre|Dap|Lys|Phe|Thr|Trpn)(B|C|Dn|X)-(3|5|M)_at)$|^(AFFX-(Msa|Mtr)-(actin|gapc|gsta|ubq11|TrpnX)-(3|5|M)_(at|x_at|s_at))$|^(AFFX-r2-(Bs|Ec|P1)-(cre|dap|lys|phe|thr|bioB|bioC|bioD)-(3|5|M)_(at|s_at|x_at))$|^(AFFX-Mtr-ubq11-(3|5|M)_(at|s_at|x_at))$|^(AFFX-r2-Tag[A-Z]{1,2}_at)$|^(Medtr_v1_\d{6})$" -efp_poplar,"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^((eugene3)\.\d{6,12})$|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$|^((grail3\.)\d{8,12})$|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$|^(Potri\.[0-9]{3}G[0-9]{6}(\.[0-9]{1})?)$" -efp_soybean,"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$|^(Glyma\.\d{1,3}g\d{1,8}))$" -efp_maize,"^(AC[0-9]{6}\.[0-9]{1,2}_(FG|FGT)[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6}(_T[0-9]{2})?)$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$" -efp_triticale,^((Ta|TaAffx)\.\d+\.\d+\.[A-Z]\d+_(at|s_at|x_at|a_at))$ -efp_human,^([A-Z0-9]|MIR) -efp_Eutrema,^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$ -efp_actinidia,"^(Acc\d+\.\d{0,3})$" -efp_apple,"^(MfusH1_\d\dg\d{1,8})$" -efp_arabidopsis_lipid,"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$" -efp_arachis,^(Adur\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Aipa_c\d+_g\d+_i\d+)$|^(Aipa\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Adur_c\d+_g\d+_i\d+)$ -efp_brachypodium,^(Bradi\d+g\d+.\d)$|^(Bradi\d+s\d+.\d)$|^(Bradi\d+.g\d+)$ -efp_brachypodium_metabolites,"(?i)^[a-z\s\-]{1,60}$" -efp_brassica_rapa,"^(Bra.\d+g\d{0,10})$|^(Bra[AC]nng\d+)$" -efp_cacao_ccn,"^(CCN-51_Chr\d{1,3}v\d{1,3}_\d{1,9})$" -efp_cacao_sca,"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$" -efp_cacao_tc,^(Tc\d+v2_g\d+)$ -efp_camelina,"^(Csa\d{0,5}[gs]\d{0,6}.\d{0,3})$|^(At\d[cgm]\d{0,6})$" -efp_cannabis,(^C\d+$)|(^scaffold\d+$)|(^AGQN\d+$) -efp_canola,"^(Bna\D\d{1,3}g\d{1,8}\D)$|^(BoC\d+g\d+\.\d+V\d)$|^(BrChr\d+g\d+\.\d+V\d)$|^(Contig\d+)$" -efp_durum_wheat,"^(TrturSVE\d\D\d{1,3}G\d{1,12})$|^(TrturSVE\d\D\d{1,3}G\d{1,12}_ncBOCREA)$" -efp_euphorbia,"^(Ep_chr\d_g\d{1,8})$" -efp_eutrema,^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$ -efp_grape,^(CHR|VIT_|CHRUN) -efp_kalanchoe,^(Kaladp\d+s\d+)$ -efp_little_millet,^(TRINITY_DN\d+_c\d+_g\d+_i\d+)$ -efp_lupin,"^(Luan_Oskar_.{1,12}_\d{1,12})$" -efp_maize_enzyme,"(?i)^[a-z0-9\s\-\(\)]{1,50}$" -efp_maize_metabolite,"(?i)^[a-z0-9\s,\.\-\(\)_'\+]{1,60}$" -efp_maize_lipid_map,"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$" -efp_tomato_trait,"^[A-Za-z][A-Za-z0-9\s\.,\-\(\)]{1,100}$" -efp_maize_transcriptomics,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$" -efp_mangosteen,"^(DN\d{1,10})$" -efp_marchantia,^(Mp[a-z]?g\d+\.\d+)$|^(Mp[a-z]?\d+g\d+\.\d+)$ -efp_oat,"(^N0\.HOG\d{1,10}$|^\D{1,10}\.*\d{1,10}.{1,10}\d{1,10}$)" -efp_phelipanche,"^(OrAeBC\d+_\d+\.\d+)$|^(OrAeBC\d+_\d+)$|^(At\d[gcm]\d{1,6})$" -efp_physcomitrella,^(Pp)\d+s\d+_\d+V\d\.\d$|^Phypa_\d+$ -efp_potato,^(PGSC0003DMG4\d{8})$ -efp_rice_metabolite,"(?i)^[a-z0-9,\s\.\-]{1,40}$" -efp_rice_transcriptomics,^(LOC_Os[0-9]{2}g[0-9]{5})$|^(Os(Affx)?\.\d+\.\d+\.(S1|A1|S2)_(at|x_at|s_at|a_at))$ -efp_selaginella,^(Smo\d+)$ -efp_sorghum,"^(Sobic.\d{0,5}G\d{0,10}$|^Sobic.K\d{0,10}$|^ENSRNA\d{0,12}$|^SORBI_\d{1,6}G\d{1,10})$" -efp_strawberry,"^(FvH4_c?\d{1,3}g\d{1,7})$|^(gene\d{1,10})$" -efp_striga,"^(StHeBC3\_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" -efp_tomato,"^(Solyc\d{2}g\d{6}\.?\d{0,3})$|^(TU\d{6})$" -efp_triphysaria,"^(TrVeBC\d+_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" -efp_tung_tree,^(Vf\d+G\d+)$ -efp_wheat,"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$" -efpconfig,".{0,16}" -mouse_efp,"^(XM_\d{0,8}\.\d{0,3})$|^(\d{1,10}\D\d{0,4}\D{0,4})$|^(\D{1,8}\d{0,8}\D{0,8})$|^(ENSMUSG\d{1,15})$|^(NM_\d{0,12}\d.\d{0,3})$" diff --git a/EMAIL_FOR_VINCENT.txt b/EMAIL_FOR_VINCENT.txt deleted file mode 100644 index 005e4024..00000000 --- a/EMAIL_FOR_VINCENT.txt +++ /dev/null @@ -1,55 +0,0 @@ -Subject: eFP Regex Package & Production Database Validation Request - -Hi Vincent, - -Per the June 25 tasks, I've compiled all the eFP regex patterns from the endpoint-creation branch for your production database validation scan. - -## What's Ready ✅ - -1. **Regex Reference (JSON)** - - File: data/efp_info/efp_regex_endpoint_creation.json - - 20+ species/validators with descriptions, examples, and regex patterns - - Machine-readable format for production scanning - -2. **Source Code** - - File: api/utils/bar_utils.py (endpoint-creation branch) - - Individual validator functions for each species - - All patterns with proper case-sensitivity flags - -3. **Master Database Metadata** - - File: data/efp_info/combined_master.json - - 48 species, 193 databases, SQL schemas - - Use as single source of truth for database mapping - -4. **Complete Package Guide** - - File: VINCENT_REGEX_PACKAGE_JUN25.md - - Full reference with usage instructions - -## What I Need From You - -Please run production database validation: -1. Scan all gene IDs in sample_data tables against their assigned regex patterns -2. Generate coverage report (which databases pass/fail/have warnings) -3. Identify any new ID formats not yet covered -4. Flag the tomato database issue for Asher - -## Tomato Database Question - -Multiple tomato database variants currently share one regex. Consult with Asher: -- Per-species approach (current): Same regex for all tomato databases -- Per-database approach: Different regexes for each variant - -## Files Location - -All files are in the current repo: -- data/efp_info/efp_regex_endpoint_creation.json -- data/efp_info/combined_master.json -- VINCENT_REGEX_PACKAGE_JUN25.md - -Let me know if you need additional formats or data extractions for the validation scan. - -Best, -Reena - ---- -June 25, 2026 diff --git a/EMAIL_TO_VINCENT_JUL_17_2026.txt b/EMAIL_TO_VINCENT_JUL_17_2026.txt deleted file mode 100644 index 655e157a..00000000 --- a/EMAIL_TO_VINCENT_JUL_17_2026.txt +++ /dev/null @@ -1,72 +0,0 @@ -Subject: Regex package integrated + updated master JSON for a brief check - -Hi Vincent, - -Thanks for the regex_master_list_efp_eplant package -- I've integrated it into -the BAR API on the cleaned-endpoint branch. Quick summary of what changed and -a few things I found while wiring it in that you may want to know about. - -## What's integrated - -1. **bar_regex_registry.json is now the single source of truth for input - validation**, embedded into data/efp_info/combined_master.json at build - time (see build_combined_master_json.py -> get_validation_patterns()). - - 58 grouped eFP-project regex patterns (down from 193 per-database), same - grouping you did (e.g. all 4 actinidia databases share efp_actinidia). - - Every database's "regex_project" field in combined_master.json says - which pattern validates it. - -2. **General injection checker added before the probeset-shape check** - (api/utils/bar_utils.py -> BARUtils.is_injection_attempt()), wired in - ahead of GeneIdUtils.is_probeset_id() in the /gene_expression endpoint per - your note. It looks for actual attack syntax (SQL comment/statement- - chaining sequences, tautologies, UNION SELECT, script tags) rather than - blacklisting individual characters, since some of your freeform projects - (efp_maize_lipid_map, efp_maize_metabolite, etc.) legitimately use ';', - "'", "-" in real sample data. Verified zero false positives against all - 5,790 real IDs in api/random_rows_json/. - -## Things I found while validating against real sample data - -I ran every database's assigned regex_project against its own real sample -dump (api/random_rows_json/) before trusting the assignment. Two things worth -a look on your end: - -- **3 databases got demoted back to species-level validation** because their - assigned project scored 0% against real data: brachypodium_embryogenesis, - brassica_rapa_developmental_atlas, medicago_root_v5. All three are hidden/ - legacy databases (not in any current frontend dropdown) using an older or - alternate ID scheme than their species' main project -- e.g. - brachypodium_embryogenesis's real IDs are uppercase ("BRADI3G43400.1") - where efp_brachypodium expects "Bradi...". Not urgent since the species - validator already handles them correctly, but flagging in case that - matters for the comprehensive list you're finishing. - -- **maize_lipid_map and tomato_trait were assigned their species' main gene-ID - project** (efp_maize, efp_tomato) instead of the freeform-text projects that - already exist in your registry for exactly this data (efp_maize_lipid_map, - efp_tomato_trait) -- real values are lipid names ("TG 54:5; ...") and trait - descriptions ("Area of Stele"), not gene IDs. I corrected these two locally - since the right project was obviously already in your registry. - -- **Two small known gaps, ~99.9% overall pass rate** (5,790 real IDs - checked): canola_original has 2/30 real IDs in an older Brassica-prefix - format (BrBA_/BoBC_) efp_canola doesn't cover, and potato_wounding has 2/30 - in what looks like an Ensembl Plants ID format (EPlSTUG...) efp_potato - doesn't cover. Both are legacy/hidden databases, low priority, but exact - values are in the sample dumps if useful. - -## Master JSON for your check - -data/efp_info/combined_master.json is attached/in the repo (cleaned-endpoint -branch) -- 47 species, 193 databases, all schema_verified against real -column data, all regex_project assignments verified against real sample IDs. -Would appreciate a brief look before we move on to the next endpoint. - -Let me know if anything above needs a closer look on your end. - -Best, -Reena - ---- -July 17, 2026 diff --git a/EMAIL_TO_VINCENT_JUN_25_2026.txt b/EMAIL_TO_VINCENT_JUN_25_2026.txt deleted file mode 100644 index 9e8e9a3e..00000000 --- a/EMAIL_TO_VINCENT_JUN_25_2026.txt +++ /dev/null @@ -1,69 +0,0 @@ -Subject: eFP Regex Validation Materials & Production Database Scan Request - -Hi Vincent, - -Per our June 25 tasks, I've consolidated the complete eFP regex reference and master database metadata for production validation. Everything is ready for your production database scan. - -## What's Ready - -1. **Master Database JSON** ✅ - - File: data/efp_info/combined_master.json - - Contains: 48 species, 193 databases, SQL schemas, sample metadata - - Use this as the single source of truth for all database/species/frontend mapping - -2. **Regex Reference Materials** ✅ - - File: vincent_regex_summary_jun_25_2026.md - - File: data/efp_info/efp_regex_reference.json - - Contains: All 50+ eFP project regex patterns with descriptions and coverage details - -3. **Regex Dictionary** ✅ - - File: api/utils/bar_utils.py (lines 8-177) - - Dictionary: EFP_PROJECT_REGEXES - - All patterns validate both gene IDs and microarray probeset IDs where applicable - -4. **Database-to-Regex Mapping** ✅ - - File: api/utils/gene_id_utils.py (lines 214+) - - Dictionary: DATABASE_EFP_PROJECT - - Maps all 193 databases to their corresponding regex patterns - -## What I Need From You - -Please run a production database validation scan: -1. Validate all gene IDs in sample_data.data_probeset_id columns against their assigned regex patterns -2. Generate coverage report: which databases pass 100%, which have edge cases -3. Identify any new ID formats not yet covered by our regexes -4. Flag per-database vs per-species issues (especially for tomato) - -## Tomato Database Issue — Decision Needed - -Currently, all tomato database variants (tomato, tomato_ils, tomato_ils2, etc.) share one generic regex pattern. This may not be sufficient if each database uses different ID formats or probesets. - -**Please consult with Asher about:** -- Should we map regexes per-species (current approach) or per-database? -- Do different tomato database variants require different validation rules? - -Once you two decide, I'll update the DATABASE_EFP_PROJECT mapping accordingly. - -## Regex Highlights for Reference - -All regexes are in api/utils/bar_utils.py: -- ✅ **efp_human** (line 125) - Already complete for Reena's needs -- ✅ **efp** generic (line 9) - Already complete for Reena's needs -- ✅ All 50+ other eFP projects - Complete coverage - -## Files to Use - -``` -data/efp_info/combined_master.json ← Master truth JSON -data/efp_info/efp_regex_reference.json ← Regex descriptions & metadata -vincent_regex_summary_jun_25_2026.md ← Complete summary & next steps -api/utils/bar_utils.py ← Actual regex patterns (production-ready) -``` - -Let me know if you need any additional data or want me to extract specific regex patterns for a particular subset of databases. - -Best, -Reena - ---- -Generated: June 25, 2026 diff --git a/VINCENT_REGEX_PACKAGE_JUN25.md b/VINCENT_REGEX_PACKAGE_JUN25.md deleted file mode 100644 index 59a2612e..00000000 --- a/VINCENT_REGEX_PACKAGE_JUN25.md +++ /dev/null @@ -1,143 +0,0 @@ -# eFP Regex Validation Package for Vincent -**Source Branch:** endpoint-creation -**Date:** June 25, 2026 -**For:** Production Database Validation - ---- - -## 📦 What You're Getting - -### 1. **Regex Reference JSON** ✅ -- **File:** `data/efp_info/efp_regex_endpoint_creation.json` -- **Content:** All 20+ regex patterns extracted from endpoint-creation branch -- **Format:** Machine-readable with descriptions and examples -- **Coverage:** 20 species/validators - -### 2. **Source Code** ✅ -- **File:** `api/utils/bar_utils.py` (endpoint-creation branch) -- **Lines:** Individual validator functions for each species -- **Note:** Each function is independent, no consolidated dictionary - -### 3. **Master Database JSON** ✅ -- **File:** `data/efp_info/combined_master.json` -- **Content:** 48 species, 193 databases, SQL schemas -- **Source:** Generated from cleaned-endpoint branch - ---- - -## 📋 Species/Regex Coverage - -| Species | Regex Pattern | Function | Examples | -|---------|--------------|----------|----------| -| Arabidopsis | `^At[12345cm]g\d{5}.?\d?$` | `is_arabidopsis_gene_valid()` | At1g12345, At2g05123 | -| Rice | `^LOC_Os\d{2}g\d{5}(\.\d{1,2})?$` | `is_rice_gene_valid()` | LOC_Os01g01010, LOC_Os01g01010.1 | -| Maize | `^(AC[0-9]{6}\.[0-9]{1}_FG...)` | `is_maize_gene_valid()` | AC233276.1_FG001, GRMZM2G000010 | -| Poplar | `^POTRI\.\d{3}g\d{6}.?\d{0,3}$` | `is_poplar_gene_valid()` | POTRI.001g000010 | -| Grape | `^VIT_\d{0,3}\D\d{0,5}g\d{0,6}$` | `is_grape_gene_valid()` | VIT_00s0120g00060 | -| Tomato | `^Solyc\d\dg\d{6}(\.\d+)?$` | `is_tomato_gene_valid()` | Solyc01g000010, Solyc01g000010.1 | -| Soybean | `^((Glyma\d{1,3}g...)` | `is_soybean_gene_valid()` | Glyma06g47400, Glyma.06g000010 | -| Canola | `^Bna[AC]\d{2}g\d{5}[A-D]?$` | `is_canola_gene_valid()` | BnaC07g42830D | -| Sorghum | `^(Sobic.\d{0,5}G...)` | `is_sorghum_gene_valid()` | Sobic.001G000010 | -| Strawberry | `^FvH4_\d{1,3}g\d{1,8}$` | `is_strawberry_gene_valid()` | FvH4_1g00010 | -| Kalanchoe | `^Kaladp\d{1,10}s\d{1,10}$` | `is_kalanchoe_gene_valid()` | Kaladp000001s000001 | -| Cannabis | `^AGQN\d{0,10}$` | `is_cannabis_gene_valid()` | AGQN03000001 | -| Arachis | `^Adur\d{1,10}_comp...` | `is_arachis_gene_valid()` | Adur10000_comp0_c0_seq1 | -| Brassica rapa | `^BraA.{1,4}g\d{1,9}$` | `is_brassica_rapa_gene_valid()` | BraA01g000010 | -| Physcomitrella | `^Pp1s\d{1,8}_\d{1,8}V6...` | `is_physcomitrella_gene_valid()` | Pp1s9_70V6.1 | -| Phelipanche | `^OrAeBC5_\d{1,6}\.\d{1,3}$` | `is_phelipanche_gene_valid()` | OrAeBC5_9992.10 | -| Thellungiella | `^Thhalv\d+m\.g$\|^nXLOC...` | `is_thellungiella_gene_valid()` | Thhalv10000089m.g, nXLOC_003010 | -| Striga | `^StHeBC3_\d{1,6}\.\d{1,5}$` | `is_striga_gene_valid()` | StHeBC3_9993.10 | -| Triphysaria | `^TrVeBC3_\d{1,6}\.\d{1,3}$` | `is_triphysaria_gene_valid()` | TrVeBC3_9999.18 | -| Selaginella | `^Smo\d{1,8}$` | `is_selaginella_gene_valid()` | Smo402070 | - ---- - -## ⚠️ Known Issues - -### Tomato Database Mapping Question -Multiple tomato databases use the same regex: -- tomato -- tomato_ils -- tomato_ils2 -- tomato_ils3 -- tomato_meristem -- tomato_renormalized -- tomato_root -- tomato_root_field_pot -- tomato_s_pennellii -- tomato_seed -- tomato_shade_mutants -- tomato_shade_timecourse - -**Action Needed:** Consult with Asher on whether these should have: -1. **Per-species mapping** (current): One regex for all tomato databases -2. **Per-database mapping**: Different regexes for each variant based on actual data - ---- - -## 🎯 Production Validation Steps - -### Step 1: Scan All Databases -Run regexes against production BAR database: -- Check `sample_data.data_probeset_id` columns -- Validate gene IDs against assigned regex patterns -- All 193 databases - -### Step 2: Generate Coverage Report -``` -Which databases: ✅ PASS (100% ID validation) -Which databases: ⚠️ WARNING (some IDs don't match) -Which databases: ❌ FAIL (significant ID mismatches) -``` - -### Step 3: Identify Edge Cases -- New ID formats not yet covered -- Per-database regex issues (especially tomato) -- Microarray vs RNA-seq format differences - -### Step 4: Report Findings -Provide: -- List of databases needing regex updates -- Recommended new patterns for edge cases -- Decision on tomato database mapping approach - ---- - -## 📁 Files Provided - -``` -endpoint-creation branch: -├── api/utils/bar_utils.py (Source code with validators) -└── data/efp_info/ - ├── efp_regex_endpoint_creation.json (All regexes extracted & formatted) - ├── combined_master.json (Database metadata) - └── efp_regex_reference.json (Alternative format) -``` - ---- - -## 💡 Usage Notes - -Each regex in the JSON file includes: -- **regex:** The actual pattern to use -- **function:** Source function name from bar_utils.py -- **description:** What the regex validates -- **case_insensitive:** Whether regex uses re.I flag -- **examples:** Sample IDs that should match -- **notes:** Any special considerations - -All regexes are extracted with original case-sensitivity settings from the functions. - ---- - -## ✅ Next Steps - -1. **Vincent:** Run production database scan -2. **Vincent → Asher:** Decide on tomato database mapping strategy -3. **Reena:** Update DATABASE_EFP_PROJECT mapping once decision is made -4. **Team:** Deploy validated regexes to production - ---- - -**Contact:** Reena Obmina (rmobmina@gmail.com) -**Questions:** About regex patterns, production validation, or architecture decisions diff --git a/all-efp-projects-views-with-lookup-settings.txt b/all-efp-projects-views-with-lookup-settings.txt deleted file mode 100644 index d31d68a9..00000000 --- a/all-efp-projects-views-with-lookup-settings.txt +++ /dev/null @@ -1,268 +0,0 @@ -PROJECT VIEW LOOKUP ORTHO DB_LOOKUP_TABLE ----------------------------- ------------------------------------- ------ ----- ---------------------- -efp atgenexp 1 — at_agi_lookup -efp atgenexp_plus 1 — at_agi_lookup -efp seed_db 1 — at_agi_lookup -efp atgenexp_hormone 1 — at_agi_lookup -efp light_series 1 — at_agi_lookup -efp arabidopsis_ecotypes 1 — at_agi_lookup -efp root 1 — at_agi_lookup -efp atgenexp_stress 1 — at_agi_lookup -efp atgenexp_pathogen 1 — at_agi_lookup -efp guard_cell 1 — at_agi_lookup -efp atTax 1 — at_agi_lookup -efp meristem_db 1 — at_agi_lookup -efp lateral_root_initiation 1 — at_agi_lookup -efp shoot_apex 0 — at_agi_lookup -efp klepikova 0 — at_agi_lookup -efp germination 0 — at_agi_lookup -efp gynoecium 0 — at_agi_lookup -efp embryo 0 — at_agi_lookup -efp silique 0 — at_agi_lookup -efp single_cell 0 — at_agi_lookup -efp dna_damage 0 — at_agi_lookup - -efp_Eutrema thellungiella_db 1 yes tsa_arabidopsis_lookup - -efp_actinidia actinidia_bud_development 0 — — -efp_actinidia actinidia_flower_fruit_development 0 — — -efp_actinidia actinidia_postharvest 0 — — -efp_actinidia actinidia_vegetative_growth 0 — — - -efp_apple apple 0 — — - -efp_arabidopsis atgenexp 1 — at_agi_lookup -efp_arabidopsis atgenexp_plus 1 — at_agi_lookup -efp_arabidopsis seed_db 1 — at_agi_lookup -efp_arabidopsis atgenexp_hormone 1 — at_agi_lookup -efp_arabidopsis light_series 1 — at_agi_lookup -efp_arabidopsis arabidopsis_ecotypes 1 — at_agi_lookup -efp_arabidopsis root 1 — at_agi_lookup -efp_arabidopsis atgenexp_stress 1 — at_agi_lookup -efp_arabidopsis atgenexp_pathogen 1 — at_agi_lookup -efp_arabidopsis guard_cell 1 — at_agi_lookup -efp_arabidopsis atTax 1 — at_agi_lookup -efp_arabidopsis meristem_db 1 — at_agi_lookup -efp_arabidopsis lateral_root_initiation 1 — at_agi_lookup -efp_arabidopsis shoot_apex 0 — at_agi_lookup -efp_arabidopsis klepikova 0 — at_agi_lookup -efp_arabidopsis germination 0 — at_agi_lookup -efp_arabidopsis gynoecium 0 — at_agi_lookup -efp_arabidopsis embryo 0 — at_agi_lookup -efp_arabidopsis silique 0 — at_agi_lookup -efp_arabidopsis single_cell 0 — at_agi_lookup -efp_arabidopsis dna_damage 0 — at_agi_lookup - -efp_arabidopsis_lipid lipid_map 1 — — - -efp_arachis arachis 0 — — - -efp_barley barley_mas 1 — at_bar_lookup -efp_barley barley_rma 1 — at_bar_lookup - -efp_brachypodium brachypodium 0 — — -efp_brachypodium brachypodium_photo_thermocycle 0 — — -efp_brachypodium brachypodium_grains 0 — — -efp_brachypodium brachypodium_Bd21 0 — — - -efp_brachypodium_metabolites brachypodium_metabolites_map 1 — — - -efp_brassica_rapa brassica_rapa 0 — — - -efp_cacao_ccn cacao_drought_diurnal_atlas 0 — — -efp_cacao_ccn cacao_developmental_atlas 0 — — - -efp_cacao_sca cacao_meristem_atlas_sca 0 — — -efp_cacao_sca cacao_developmental_atlas_sca 0 — — -efp_cacao_sca cacao_drought_diurnal_atlas_sca 0 — — -efp_cacao_sca cacao_seed_atlas_sca 0 — — - -efp_cacao_tc cacao_leaf 0 — — -efp_cacao_tc cacao_infection 0 — — - -efp_camelina camelina 1 yes camelina_lookup -efp_camelina camelina_tpm 0 yes camelina_lookup - -efp_cannabis cannabis 0 — — - -efp_canola canola_seed 0 — — - -efp_durum_wheat durum_wheat_development 0 — — - -efp_euphorbia euphorbia 0 — — - -efp_eutrema thellungiella_db 1 yes tsa_arabidopsis_lookup - -efp_grape grape_developmental 1 — grape_probeset_lookup - -efp_human human_developmental 1 — gene_probeset_lookup -efp_human human_body_map_2 0 — gene_probeset_lookup - -efp_kalanchoe kalanchoe 0 — — - -efp_little_millet little_millet 0 — — - -efp_lupin lupin_whole_plant 0 — — -efp_lupin lupin_lcm_leaf 0 — — -efp_lupin lupin_lcm_pod 0 — — -efp_lupin lupin_lcm_stem 0 — — - -efp_maize maize_iplant 0 — — -efp_maize maize_ears 0 — — -efp_maize Sekhon_et_al_Atlas 0 — — -efp_maize maize_leaf_gradient 0 — — -efp_maize maize_rice_comparison 0 — — -efp_maize Maize_Root 0 — — -efp_maize Maize_Kernel 0 — — -efp_maize Hoopes_et_al_Atlas 0 — — -efp_maize Hoopes_et_al_Stress 0 — — -efp_maize Early_Seed 0 — — -efp_maize maize_embryonic_leaf_development 0 — — -efp_maize maize_atlas_v5 0 — — -efp_maize maize_kernel_v5 0 — — -efp_maize maize_stress_v5 0 — — - -efp_maize_enzyme maize_enzyme 0 — — - -efp_maize_metabolite maize_metabolite 0 — — - -efp_maize_transcriptomics maize_iplant 0 — — -efp_maize_transcriptomics maize_ears 0 — — -efp_maize_transcriptomics Sekhon_et_al_Atlas 0 — — -efp_maize_transcriptomics maize_leaf_gradient 0 — — -efp_maize_transcriptomics maize_rice_comparison 0 — — -efp_maize_transcriptomics Maize_Root 0 — — -efp_maize_transcriptomics Maize_Kernel 0 — — -efp_maize_transcriptomics Hoopes_et_al_Atlas 0 — — -efp_maize_transcriptomics Hoopes_et_al_Stress 0 — — -efp_maize_transcriptomics Early_Seed 0 — — -efp_maize_transcriptomics maize_embryonic_leaf_development 0 — — -efp_maize_transcriptomics maize_atlas_v5 0 — — -efp_maize_transcriptomics maize_kernel_v5 0 — — -efp_maize_transcriptomics maize_stress_v5 0 — — - -efp_mangosteen mangosteen_fruit_ripening 0 — — -efp_mangosteen mangosteen_callus 0 — — -efp_mangosteen mangosteen_seed_development 0 — — -efp_mangosteen mangosteen_seed_germination 0 — — -efp_mangosteen mangosteen_aril_vs_rind 0 — — -efp_mangosteen mangosteen_diseased_vs_normal 0 — — - -efp_marchantia marchantia_organ_stress 0 — — - -efp_medicago medicago_mas 1 — at_mtgi_lookup_merged -efp_medicago medicago_rma 1 — at_mtgi_lookup_merged -efp_medicago medicago_seed 1 — at_mtgi_lookup_merged - -efp_oat oat 0 — — - -efp_phelipanche phelipanche 1 yes phelipanche_lookup - -efp_physcomitrella physcomitrella_db 1 — physcomitrella_lookup - -efp_poplar poplar 1 — at_pgi_lookup - -efp_potato potato_dev 1 — gene_protein_lookup -efp_potato potato_stress 1 — gene_protein_lookup - -efp_rice rice_leaf_gradient 0 — at_loc_lookup -efp_rice rice_maize_comparison 0 — at_loc_lookup -efp_rice rice_mas 1 — at_loc_lookup -efp_rice ricestigma_mas 1 — at_loc_lookup -efp_rice riceanoxia_mas 1 — at_loc_lookup -efp_rice ricestress_mas 1 — at_loc_lookup -efp_rice rice_rma 1 — at_loc_lookup -efp_rice ricestigma_rma 1 — at_loc_lookup -efp_rice riceanoxia_rma 1 — at_loc_lookup -efp_rice ricestress_rma 1 — at_loc_lookup -efp_rice rice_drought_heat_stress 0 — at_loc_lookup - -efp_rice_metabolite rice_metabolite 0 — at_loc_lookup - -efp_rice_transcriptomics rice_leaf_gradient 0 — at_loc_lookup -efp_rice_transcriptomics rice_maize_comparison 0 — at_loc_lookup -efp_rice_transcriptomics rice_mas 1 — at_loc_lookup -efp_rice_transcriptomics ricestigma_mas 1 — at_loc_lookup -efp_rice_transcriptomics riceanoxia_mas 1 — at_loc_lookup -efp_rice_transcriptomics ricestress_mas 1 — at_loc_lookup -efp_rice_transcriptomics rice_rma 1 — at_loc_lookup -efp_rice_transcriptomics ricestigma_rma 1 — at_loc_lookup -efp_rice_transcriptomics riceanoxia_rma 1 — at_loc_lookup -efp_rice_transcriptomics ricestress_rma 1 — at_loc_lookup -efp_rice_transcriptomics rice_drought_heat_stress 0 — at_loc_lookup - -efp_seedcoat seedcoat 1 — pbi_agi_lookup - -efp_selaginella selaginella 0 — — - -efp_sorghum sorghum_stress 0 — — -efp_sorghum sorghum_developmental 0 — — -efp_sorghum sorghum_vascularization_and_internode 0 — — -efp_sorghum sorghum_low_phosphorus 0 — — -efp_sorghum sorghum_atlas_w_BS_cells 0 — — -efp_sorghum sorghum_saline_alkali_stress 0 — — -efp_sorghum sorghum_flowering_activation 0 — — -efp_sorghum sorghum_strigolactone_variation 0 — — -efp_sorghum sorghum_sulfur_stress 0 — — -efp_sorghum sorghum_phosphate_stress 0 — — - -efp_soybean soybean 1 — gene_probeset_lookup -efp_soybean soybean_severin 1 — gene_probeset_lookup -efp_soybean soybean_senescence 1 — gene_probeset_lookup -efp_soybean soybean_embryonic_development 1 — gene_probeset_lookup -efp_soybean soybean_heart_cotyledon_globular 1 — gene_probeset_lookup - -efp_strawberry strawberry 1 yes strawberry_lookup - -efp_striga striga 1 yes striga_lookup - -efp_tomato tomato 0 — 454_Illumina_lookup -efp_tomato tomato_renormalized 0 — 454_Illumina_lookup -efp_tomato tomato_ils 1 — 454_Illumina_lookup -efp_tomato tomato_ils2 1 — 454_Illumina_lookup -efp_tomato tomato_s_pennellii 1 — 454_Illumina_lookup -efp_tomato tomato_meristem 0 — 454_Illumina_lookup -efp_tomato tomato_seed 0 — 454_Illumina_lookup -efp_tomato tomato_shade_mutants 0 — 454_Illumina_lookup -efp_tomato tomato_shade_timecourse 0 — 454_Illumina_lookup - -efp_triphysaria triphysaria 1 yes triphysaria_lookup - -efp_triticale triticale 1 — triticale_lookup -efp_triticale triticale_mas 1 — triticale_lookup - -efp_tung_tree tung_tree 0 — — - -efp_wheat wheat 0 — — -efp_wheat wheat_embryogenesis 0 — — -efp_wheat wheat_meiosis 0 — — -efp_wheat wheat_abiotic_stress 0 — — - -efpbarley barley_mas 1 — at_bar_lookup -efpbarley barley_rma 1 — at_bar_lookup - -efpconfig (no LOOKUP dict) ? — at_agi_lookup - -efpmedicago medicago_mas 1 — at_mtgi_lookup_merged -efpmedicago medicago_rma 1 — at_mtgi_lookup_merged -efpmedicago medicago_seed 1 — at_mtgi_lookup_merged - -efppop poplar 1 — at_pgi_lookup - -efprice rice_leaf_gradient 0 — at_loc_lookup -efprice rice_maize_comparison 0 — at_loc_lookup -efprice rice_mas 1 — at_loc_lookup -efprice ricestigma_mas 1 — at_loc_lookup -efprice riceanoxia_mas 1 — at_loc_lookup -efprice ricestress_mas 1 — at_loc_lookup -efprice rice_rma 1 — at_loc_lookup -efprice ricestigma_rma 1 — at_loc_lookup -efprice riceanoxia_rma 1 — at_loc_lookup -efprice ricestress_rma 1 — at_loc_lookup -efprice rice_drought_heat_stress 0 — at_loc_lookup - -efpsoybean soybean 1 — gene_probeset_lookup -efpsoybean soybean_severin 1 — gene_probeset_lookup -efpsoybean soybean_senescence 1 — gene_probeset_lookup -efpsoybean soybean_embryonic_development 1 — gene_probeset_lookup -efpsoybean soybean_heart_cotyledon_globular 1 — gene_probeset_lookup \ No newline at end of file diff --git a/all_gene_id_regexes.csv b/all_gene_id_regexes.csv deleted file mode 100644 index 554f1d56..00000000 --- a/all_gene_id_regexes.csv +++ /dev/null @@ -1,108 +0,0 @@ -key,regex -efp,"^([Aa][Tt][12345CM][Gg][0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" -efp_Eutrema,^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$ -efp_actinidia,"^(Acc\d+\.\d{0,3})$" -efp_apple,"^(MfusH1_\d\dg\d{1,8})$" -efp_arabidopsis,"^([Aa][Tt][12345CM][Gg][0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" -efp_arabidopsis_lipid,"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$" -efp_arachis,^(Adur\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Aipa_c\d+_g\d+_i\d+)$|^(Aipa\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Adur_c\d+_g\d+_i\d+)$ -efp_barley,"^((HM|HV).*)$|^(HV.*_at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4})_at)$|^([0-9]{4,5}\.AF[0-9]{5}(_|_x_)at)$|^(A[0-9]{5}\.[0-9]{1}(_|_x_|_s_)at)$|^(([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)(_|_x_|_s_|_CDS-[0-9]{1,2}_|_CDS-[0-9]{1,2}_s_)at)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^(ChlorContig[0-9]{1,2}(_|_x_|_s_)at)$|^(((MitoContig|Contig)[0-9]{1,6})(_|_x_|_s_)at)$|^(D[0-9]{5}_at)$|^(Dhn[0-9]{2}\(Morex\)(_|_s_)at)$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2}(_|_s_|_x_)at)$|^(Franka(_|_b_)3pri[0-9]{1,2}(_|_s_|_x_)at)$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru](_|_x_|_s_)at)$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1}(_|_x_|_s_)at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2}(_|_x_|_s_)at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4}))$|^([0-9]{4,5}\.AF[0-9]{5})$|^(A[0-9]{5}\.[0-9]{1})$|^([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX))$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre))$|^(ChlorContig[0-9]{1,2})$|^((MitoContig|Contig)[0-9]{1,6})$|^(D[0-9]{5})$|^(Dhn[0-9]{2}\(Morex\))$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2})$|^(Franka(_|_b_)3pri[0-9]{1,2})$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru])$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1})$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2})$|^(HO)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(AK[0-9]{6}\.1)$|^(AJ[0-9]{6}\.1)$" -efp_brachypodium,^(Bradi\d+g\d+.\d)$|^(Bradi\d+s\d+.\d)$|^(Bradi\d+.g\d+)$ -efp_brachypodium_metabolites,"(?i)^[a-z\s\-]{1,60}$" -efp_brassica_rapa,"^(Bra.\d+g\d{0,10})$" -efp_cacao_ccn,"^(CCN-51_Chr\d{1,3}v\d{1,3}_\d{1,9})$" -efp_cacao_sca,"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$" -efp_cacao_tc,^(Tc\d+v2_g\d+)$ -efp_camelina,"^(Csa\d{0,5}[gs]\d{0,6}.\d{0,3})$|^(At\d[cgm]\d{0,6})$" -efp_cannabis,(^C\d+$)|(^scaffold\d+$)|(^AGQN\d+$) -efp_canola,"^(Bna\D\d{1,3}g\d{1,8}\D)$|^(Bna\Dnng\d{1,8}\D)$" -efp_durum_wheat,"^(TrturSVE\d\D\d{1,3}G\d{1,12})$|^(TrturSVE\d\D\d{1,3}G\d{1,12}_ncBOCREA)$" -efp_euphorbia,"^(Ep_chr\d_g\d{1,8})$" -efp_eutrema,^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$ -efp_grape,"^(VIT_\d{1,2}s\d{4}g\d{5})$|^CHRUN[a-z0-9_]{1,20}$|^CHR\d{1,2}[a-z0-9_]{1,2}$" -efp_human,"^(\d{6,7}(_[xsa])?_at)$|^(\D{0,12}\d{0,12})$|^(\d{1,12})$" -efp_kalanchoe,^(Kaladp\d+s\d+)$ -efp_little_millet,^(TRINITY_DN\d+_c\d+_g\d+_i\d+)$ -efp_lupin,"^(Luan_Oskar_.{1,12}_\d{1,12})$" -efp_maize,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$" -efp_maize_enzyme,"(?i)^[a-z0-9\s\-\(\)]{1,50}$" -efp_maize_lipid_map,"(?i)^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$" -efp_maize_metabolite,"(?i)^[a-z0-9\s,\.\-\(\)_'\+]{1,60}$" -efp_maize_transcriptomics,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$" -efp_mangosteen,"^(DN\d{1,10})$" -efp_marchantia,"^(Mp.{1,3}g\d{1,7}\.?\d{1,3}?)$" -efp_medicago,"^(Medtr\d{1}g\d{6})$|^(Medtr\d{1}g\d{6}\.[0-9]{1})$|^(Mtr\.\d{4,5}\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(Msa\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(Sme\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(AFFX-(Bio|Cre|Dap|Lys|Phe|Thr|Trpn)(B|C|Dn|X)-(3|5|M)_at)$|^(AFFX-(Msa|Mtr)-(actin|gapc|gsta|ubq11|TrpnX)-(3|5|M)_(at|x_at|s_at))$|^(AFFX-r2-(Bs|Ec|P1)-(cre|dap|lys|phe|thr|bioB|bioC|bioD)-(3|5|M)_(at|s_at|x_at))$|^(AFFX-Mtr-ubq11-(3|5|M)_(at|s_at|x_at))$|^(AFFX-r2-Tag[A-Z]{1,2}_at)$|^(Medtr_v1_\d{6})$" -efp_oat,"(^N0\.HOG\d{1,10}$|^\D{1,10}\.*\d{1,10}.{1,10}\d{1,10}$)" -efp_phelipanche,"^(OrAeBC\d+_\d+\.\d{1,5})|(At\d[gcm]\d{1,6})$" -efp_physcomitrella,^(Pp)\d+s\d+_\d+V\d\.\d$|^Phypa_\d+$ -efp_poplar,"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^((eugene3)\.\d{6,12})$|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$|^((grail3\.)\d{8,12})$|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$|^(Potri\.[0-9]{3}G[0-9]{6}(\.[0-9]{1})?)$" -efp_potato,^(PGSC0003DMG4\d{8})$ -efp_rice,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5\.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" -efp_rice_metabolite,"(?i)^[a-z0-9,\s\.\-]{1,40}$" -efp_rice_transcriptomics,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" -efp_seedcoat,"^(At[12345CM]g[0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(\D\d+_\d+)$|^(At\d{8})$" -efp_selaginella,^(Smo\d+)$ -efp_sorghum,"^(Sobic.\d{0,5}G\d{0,10}$|^Sobic.K\d{0,10}$|^ENSRNA\d{0,12}$|^SORBI_\d{1,6}G\d{1,10})$" -efp_soybean,"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$|^(Glyma\.\d{1,3}g\d{1,8}))$" -efp_strawberry,"^(FvH4_c?\d{1,3}g\d{1,7})$|^(gene\d{1,10})$" -efp_striga,"^(StHeBC3\_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" -efp_tomato,"^(Solyc\d{2}g\d{6}\.?\d{0,3})$|^(TU\d{6})$" -efp_tomato_trait,"^[A-Za-z][A-Za-z0-9\s\.,\-\(\)]{1,100}$" -efp_triphysaria,"^(TrVeBC\d+_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" -efp_triticale,^((Ta|TaAffx)\.\d+\.\d+\.[A-Z]\d+_(at|s_at|x_at|a_at))$ -efp_tung_tree,^(Vf\d+G\d+)$ -efp_wheat,"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$" -efpbarley,"^((HM|HV).*)$|^(HV.*_at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4})_at)$|^([0-9]{4,5}\.AF[0-9]{5}(_|_x_)at)$|^(A[0-9]{5}\.[0-9]{1}(_|_x_|_s_)at)$|^(([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)(_|_x_|_s_|_CDS-[0-9]{1,2}_|_CDS-[0-9]{1,2}_s_)at)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^(ChlorContig[0-9]{1,2}(_|_x_|_s_)at)$|^(((MitoContig|Contig)[0-9]{1,6})(_|_x_|_s_)at)$|^(D[0-9]{5}_at)$|^(Dhn[0-9]{2}\(Morex\)(_|_s_)at)$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2}(_|_s_|_x_)at)$|^(Franka(_|_b_)3pri[0-9]{1,2}(_|_s_|_x_)at)$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru](_|_x_|_s_)at)$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1}(_|_x_|_s_)at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2}(_|_x_|_s_)at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4}))$|^([0-9]{4,5}\.AF[0-9]{5})$|^(A[0-9]{5}\.[0-9]{1})$|^([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX))$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre))$|^(ChlorContig[0-9]{1,2})$|^((MitoContig|Contig)[0-9]{1,6})$|^(D[0-9]{5})$|^(Dhn[0-9]{2}\(Morex\))$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2})$|^(Franka(_|_b_)3pri[0-9]{1,2})$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}[ru])$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1})$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2})$|^(HO)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(AK[0-9]{6}\.1)$|^(AJ[0-9]{6}\.1)$" -efpconfig,".{0,16}" -efpmedicago,"^(Medtr\d{1}g\d{6})$|^(Medtr\d{1}g\d{6}\.[0-9]{1})$|^(Mtr\.\d{4,5}\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(Msa\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(Sme\.\d+\.\d+\.(S1|A1|S2)_(at|s_at|x_at|a_at))$|^(AFFX-(Bio|Cre|Dap|Lys|Phe|Thr|Trpn)(B|C|Dn|X)-(3|5|M)_at)$|^(AFFX-(Msa|Mtr)-(actin|gapc|gsta|ubq11|TrpnX)-(3|5|M)_(at|x_at|s_at))$|^(AFFX-r2-(Bs|Ec|P1)-(cre|dap|lys|phe|thr|bioB|bioC|bioD)-(3|5|M)_(at|s_at|x_at))$|^(AFFX-Mtr-ubq11-(3|5|M)_(at|s_at|x_at))$|^(AFFX-r2-Tag[A-Z]{1,2}_at)$|^(Medtr_v1_\d{6})$" -efppop,"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^((eugene3)\.\d{6,12})$|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$|^((grail3\.)\d{8,12})$|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$|^(Potri\.[0-9]{3}G[0-9]{6}(\.[0-9]{1})?)$" -efprice,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5\.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" -efpsoybean,"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$|^(Glyma\.\d{1,3}g\d{1,8}))$" -maizeefp,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$|^(Zm\d{6}(_[xsa])?_at)$" -mouse_efp,"^(XM_\d{0,8}\.\d{0,3})$|^(\d{1,10}\D\d{0,4}\D{0,4})$|^(\D{1,8}\d{0,8}\D{0,8})$|^(ENSMUSG\d{1,15})$|^(NM_\d{0,12}\d.\d{0,3})$" -actinidia,^Acc\d{5}\.\d+$ -apple,^MfusH1_\d{2}g\d{5}$ -arabidopsgene_valid,^At[12345cm]g\d{5}.?\d?$ -arachgene_valid,"^Adur\d{1,10}_comp\d{1,3}_\D{1,3}\d{1,3}_seq\d{1,5}$" -barley,^HORVU(\d+Hr\d+G\d+|\.MOREX\.r\d+\.(\dH|Un)G\d+(\.\d+)?)$ -brachypodium,^Bradi\d+g\d+\.\d+$ -brassica_rapa,"^(BraA.{1,4}g\d{1,9}|[A-Z]\d{2}[gp]\d+\.\d+_BraROA)$" -cacao,^((CCN-51|SCA-6)_Chr\d+v\d+_\d+|Tc\d+v\d+_g\d+)$ -camelina,^Csa\d+[gs]\d+(\.\d+)?$ -cannabgene_valid,"^AGQN\d{0,10}$" -canola,"^(Bna[AC]\d{2}g\d{5}[A-D]?|Bo[A-Z]+_?\d+g\d+\.\d+V\d+|Br(Chr\d{1,2}|BA_\d+)g\d{5}\.\d{2}V\d|Contig\d+)$" -cassava,^Manes\.\d{2}G\d+\.v\d+\.\d+$ -cuscuta,^Cc\d+(\.t\d+)?$ -eucalyptus,^Eucgr\.[A-Z]\d+$ -euphorbia,^Ep_chr\d+_g\d+$ -grape,"^(CHR(\d+|UN)_[A-Z]+\d+(_\d+)?_T\d+|VIT_\d{0,3}\D\d{0,5}g\d{0,6})$" -human,"^\d{1,10}$|^[A-Z][A-Z0-9]{1,9}(-\d{1,3})?$|^[A-Z]{2,4}\d{0,3}-\d{2,4}[A-Z]\d{1,3}\.\d{1,3}$|^A[CL]\d{6}\.\d{1,3}$" -kalanchoe,"^Kaladp\d{1,10}s\d{1,10}$" -little_millet,^TRINITY_DN\d+_c\d+_g\d+_i\d+$ -lupin,^Luan_Oskar_(PB\d+|Trin)_\d+$ -maize,^(AC[0-9]{6}\.[0-9]+_FGT?[0-9]{3}|GRMZM[25]G[0-9]{6}(_T[0-9]{2})?|Zm\d+(d|eb)\d+)$ -mangosteen,^DN\d+$ -marchantia,"^Mp\w{1,3}g\d+\.\d+$" -medicago,^(Medtr(\d+[gs]\d+|_v1_\d+)|MtrunA17Chr\dg\d+)$ -mouse,^XM_\d+\.\d+$ -oat,^AV[A-Z]{3}\.\d{5}[a-z]\.r\d+\.\d[A-Z]{2}\d{8}$ -phelipanche,"^OrAeBC5_\d{1,6}\.\d{1,3}$" -physcomitrella,"^Pp1s\d{1,8}_\d{1,8}V6\.\d{1,3}$" -poplar,"^POTRI\.(\d{3}G\d{6}\.?\d{0,3}|T\d{6})$" -potato,^(PGSC0003DMG\d+|EPlSTUG\d+)$ -quinoa,^CquiG\d+$ -rice,"^LOC_Os\d{2}g\d{5}\.\d{1,2}$|^LOC_Os\d{2}g\d{5}$|^Os\d{2}g\d+$" -selaginella,"^Smo\d{1,8}$" -sorghum,^(Sobic\.\d+G\d+(\.\d+)?|Sobic\.K\d+|SORBI_\d+G\d+|ENSRNA\d+)$ -soybean,"^((Glyma\d{1,3}g\d{1,6}\.?\d?)|(Glyma\.\d{1,3}g\d{1,8}))$" -spruce,"^(GQ|WS)\d{4,5}_[A-Z]\d{2}\.\d+$" -strawberry,"^FvH4_\d{1,3}g\d{1,8}$" -striga,"^StHeBC3_\d{1,6}\.\d{1,5}$" -sugarcane,^(Sh\d+_g\d+|Sh_[A-Z0-9]+(_contig-\d+)?_g\d+)$ -sunflower,^Ha\d+_\d+$ -thellungiella,^Thhalv\d+m\.g$|^nXLOC_\d+$ -tomato,^Solyc\d\dg\d{6}\.\d\.\d$|^Solyc\d\dg\d{6}(\.\d+)?$ -triphysaria,"^TrVeBC3_\d{1,6}\.\d{1,3}$" -tung_tree,^Vf\d+G\d+$ -wheat,^(TraesCS[0-9A-Z]+(\.\d+)?|TrturSVE[0-9A-Z]+G\d+)$ -willow,^comp\d+_c\d+_seq\d+$ diff --git a/cfg_dbs.txt b/cfg_dbs.txt deleted file mode 100644 index 69f7735b..00000000 --- a/cfg_dbs.txt +++ /dev/null @@ -1,48 +0,0 @@ -annotations_lookup', -arabidopsis_ecotypes', -arachis', -brachypodium_dump', -camelina_dump', -cannabis', -canola_nssnp', -dna_damage', -embryo', -eplant2', -eplant_poplar', -eplant_rice', -eplant_soybean', -eplant_tomato', -fastpheno', -germination', -homologs_db', -interactions_vincent_v2', -kalanchoe', -klepikova', -light_series', -llama3', -maize_RMA_linear', -medicago_mas_dump', -meristem_db', -phelipanche', -physcomitrella_db', -poplar', -poplar_nssnp', -potato_stress', -rice_interactions', -rice_mas', -seedcoat', -selaginella', -shoot_apex', -silique', -single_cell', -soybean', -soybean', -soybean_nssnp', -soybean_severin', -strawberry', -striga', -thellungiella', -tomato_nssnp', -tomato_sequence', -triphysaria', -triticale', diff --git a/efp_regex_audit_prod.csv b/efp_regex_audit_prod.csv deleted file mode 100644 index 81912863..00000000 --- a/efp_regex_audit_prod.csv +++ /dev/null @@ -1,60 +0,0 @@ -project,inputRegEx -efp,"^([Aa][Tt][12345CM][Gg][0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$" -efp_Eutrema,^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$ -efp_actinidia,"^(Acc\d+\.\d{0,3})$" -efp_apple,"^(MfusH1_\d\dg\d{1,8})$" -efp_arabidopsis,"^([Aa][Tt][12345CM][Gg][0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$" -efp_arabidopsis_lipid,"^[a-z0-9\s:;\/\[\]_\+\-]{1,64}$" -efp_arachis,^(Adur\d+_comp\d+_c\d+_seq\d+)$|^(Gyn_Aipa_c\d+_g\d+_i\d+)$|^(Aipa\d+_comp\d+_c\d+_seq\d+)$ -efp_barley,"^((HM|HV).*)$|^(HV.*_at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4})_at)$|^([0-9]{4,5}\.AF[0-9]{5}(_|_x_)at)$|^(A[0-9]{5}\.[0-9]{1}(_|_x_|_s_)at)$|^(([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)(_|_x_|_s_|_CDS-[0-9]{1,2}_|_CDS-[0-9]{1,2}_s_)at)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^(ChlorContig[0-9]{1,2}(_|_x_|_s_)at)$|^(((MitoContig|Contig)[0-9]{1,6})(_|_x_|_s_)at)$|^(D[0-9]{5}_at)$|^(Dhn[0-9]{2}\(Morex\)(_|_s_)at)$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2}(_|_s_|_x_)at)$|^(Franka(_|_b_)3pri[0-9]{1,2}(_|_s_|_x_)at)$|^(H[A-Z]{1}[0-9]{1-4}[A-Z]{1}[0-9]{1,2}[a-z]{1}(_|_x_|_s_)at)$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}r(_|_x_|_s_)at)$|^(Mla([0-9]{1,2}|[0-9]{1,2}DH)(_orf_|_div5_|_5pri_|_5pri-|_consrvd_|_3pri12_)(3pri12|3pr|UTR_intron2|UTR_intron1|5pri_end)(_|_x_|_s_)at)$|^((Mla|Mlk)(_div5|_3pri12)(_|_x_|_s__at))$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1}(_|_x_|_s_)at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2}(_|_x_|_s_)at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4}))$|^([0-9]{4,5}\.AF[0-9]{5})$|^(A[0-9]{5}\.[0-9]{1})$|^([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX))$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre))$|^(ChlorContig[0-9]{1,2})$|^((MitoContig|Contig)[0-9]{1,6})$|^(D[0-9]{5})$|^(Dhn[0-9]{2}\(Morex\))$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2})$|^(Franka(_|_b_)3pri[0-9]{1,2})$|^(H[A-Z]{1}[0-9]{1-4}[A-Z]{1}[0-9]{1,2}[a-z]{1})$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}r)$|^(Mla([0-9]{1,2}|[0-9]{1,2}DH)(_orf_|_div5_|_5pri_|_5pri-|_consrvd_|_3pri12_)(3pri12|3pr|UTR_intron2|UTR_intron1|5pri_end))$|^((Mla|Mlk)(_div5|_3pri12))$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1})$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2})$|^(HO)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(AK[0-9]{6}\.1)$|^(AJ[0-9]{6}\.1)$" -efp_brachypodium,^(Bradi\d+g\d+.\d)$|^(Bradi\d+s\d+.\d)$|^(Bradi\d+.g\d+)$ -efp_brachypodium_metabolites,"^[a-z\s]{0,40}$" -efp_brassica_rapa,"^(Bra.\d+g\d{0,10})$" -efp_cacao_ccn,"^(CCN-51_Chr\d{1,3}v\d{1,3}_\d{1,9})$" -efp_cacao_sca,"^(SCA-6_Chr\d{1,3}v\d{1,3}_\d{1,9})$" -efp_cacao_tc,^(Tc\d+v2_g\d+)$ -efp_camelina,"^(Csa\d{0,5}[gs]\d{0,6}.\d{0,3})$|^(At\d[cgm]\d{0,6})$" -efp_cannabis,(^C\d+$)|(^scaffold\d+$)|(^AGQN\d+$) -efp_canola,"^(Bna\D\d{1,3}g\d{1,8}\D)$|^(Bna\Dnng\d{1,8}\D)$" -efp_durum_wheat,"^(TrturSVE\d\D\d{1,3}G\d{1,12})$|^(TrturSVE\d\D\d{1,3}G\d{1,12}_ncBOCREA)$" -efp_euphorbia,"^(Ep_chr\d_g\d{1,8})$" -efp_eutrema,^(Thhalv\d{8}m\.g)$|^(XLOC_\d{6})$|^(nXLOC\d{6})$|^(At\dg\d{5})$ -efp_grape,"^(VIT_\d{1,2}s\d{4}g\d{5})$|^CHRUN[a-z0-9_]{1,20}$|^CHR\d{1,2}[a-z0-9_]{1,2}$" -efp_human,"^(\D{0,12}\d{0,12})$|^(\d{1,12})$" -efp_kalanchoe,^(Kaladp\d+s\d+)$ -efp_little_millet,^(TRINITY_DN\d+_c\d+_g\d+_i\d+)$ -efp_lupin,"^(Luan_Oskar_.{1,12}_\d{1,12})$" -efp_maize,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$" -efp_maize_enzyme,"^[a-z\-\(\)\s]{0,37}$" -efp_maize_metabolite,"^[a-z0-9,\s\-\(\)]{0,40}$" -efp_maize_transcriptomics,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$" -efp_mangosteen,"^(DN\d{1,10})$" -efp_marchantia,"^(Mp.{1,3}g\d{1,7}\.?\d{1,3}?)$" -efp_medicago,"^(Medtr\d{1}g\d{6})$|^(Medtr\d{1}g\d{6}\.[0-9]{1})$|^(Mtr.\d{4,5}.1.[S1|S1_x|s1|s1_x]_at)$|^(AFFX-[Bio|Cre|Dap|Lys|Phe|Thr|Trpn][B|C|Dn|X]-[3|5|M]_at)$|^(AFFX-[Msa|Mtr]-[actin|gapc|gsta|ubq11|TrpnX]-[3|5|M]_[at|x_at|s_at])$|^(AFFX-Mtr|AFFX-r2-[Bs|Ec|P1]-[cre|dap|lys|phe|thr|bioB|bioC|bioD]-[3|5|M]_[at|s_at|x_at])$|^(AFFX-Mtr-ubq11-[3|5|M]_[at|s_at|x_at])$|^(AFFX-r2-Tag[A-Z]{1,2}_at|-3_at|-5_at|-M_at)$|^(Medtr_v1_\d{6})$" -efp_oat,"(^N0\.HOG\d{1,10}$|^\D{1,10}\.*\d{1,10}.{1,10}\d{1,10}$)" -efp_phelipanche,"^(OrAeBC\d+_\d+\.\d{1,5})|(At\d[gcm]\d{1,6})$" -efp_physcomitrella,^(Pp)\d+s\d+_\d+V\d\.\d$|^Phypa_\d+$ -efp_poplar,"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^((eugene3)\.e{6,12})$|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$|^((grail3.)\d{8,12})$|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$|^(Potri\.[0-9]{3}G[0-9]{6}\.[0-9]{1})$" -efp_potato,^(PGSC0003DMG4\d{8})$ -efp_rice,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" -efp_rice_metabolite,"^[a-z0-9,\s\-]{0,30}$" -efp_rice_transcriptomics,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" -efp_seedcoat,"^(At[12345CM]g[0-9]{5})$|^([0-9]{6}(_[xsfi])?_at)$|^([0-9]{6,9})$|^(\D\d+_\d+)$" -efp_selaginella,^(Smo\d+)$ -efp_sorghum,"^(Sobic.\d{0,5}G\d{0,10}$|^Sobic.K\d{0,10}$|^ENSRNA\d{0,12}$|^SORBI_\d{1,6}G\d{1,10})$" -efp_soybean,"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$|^(Glyma\.\d{1,3}g\d{1,8}))$" -efp_strawberry,"^(FvH4_c?\d{1,3}g\d{1,7})$|^(gene\d{1,10})$" -efp_striga,"^(StHeBC3\_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" -efp_tomato,"^(Solyc\d{2}g\d{6}\.?\d{0,3})$|^(TU\d{6})$" -efp_triphysaria,"^(TrVeBC\d+_\d+\.\d{1,5})$|^(At\d[gcm]\d{1,6})$" -efp_triticale,^(Ta.\d+.\d+.\D+\d+_at)$ -efp_tung_tree,^(Vf\d+G\d+)$ -efp_wheat,"^(TraesCS\d\D\d{0,2}[G]\d{0,6}L*C*\.*\d*)$|^(TraesCSU\d+G\d+L*C*\.*\d*)$" -efpbarley,"^((HM|HV).*)$|^(HV.*_at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4})_at)$|^([0-9]{4,5}\.AF[0-9]{5}(_|_x_)at)$|^(A[0-9]{5}\.[0-9]{1}(_|_x_|_s_)at)$|^(([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)(_|_x_|_s_|_CDS-[0-9]{1,2}_|_CDS-[0-9]{1,2}_s_)at)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^(ChlorContig[0-9]{1,2}(_|_x_|_s_)at)$|^(((MitoContig|Contig)[0-9]{1,6})(_|_x_|_s_)at)$|^(D[0-9]{5}_at)$|^(Dhn[0-9]{2}\(Morex\)(_|_s_)at)$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2}(_|_s_|_x_)at)$|^(Franka(_|_b_)3pri[0-9]{1,2}(_|_s_|_x_)at)$|^(H[A-Z]{1}[0-9]{1-4}[A-Z]{1}[0-9]{1,2}[a-z]{1}(_|_x_|_s_)at)$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f)(_|_x_|_s_)at)$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}r(_|_x_|_s_)at)$|^(Mla([0-9]{1,2}|[0-9]{1,2}DH)(_orf_|_div5_|_5pri_|_5pri-|_consrvd_|_3pri12_)(3pri12|3pr|UTR_intron2|UTR_intron1|5pri_end)(_|_x_|_s_)at)$|^((Mla|Mlk)(_div5|_3pri12)(_|_x_|_s__at))$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1}(_|_x_|_s_)at)$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2}(_|_x_|_s_)at)$|^(([0-9]{4,7})_(Reg|R)_([0-9]{2,4})-([0-9]{4}))$|^([0-9]{4,5}\.AF[0-9]{5})$|^(A[0-9]{5}\.[0-9]{1})$|^([A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.1)$|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX))$|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre))$|^(ChlorContig[0-9]{1,2})$|^((MitoContig|Contig)[0-9]{1,6})$|^(D[0-9]{5})$|^(Dhn[0-9]{2}\(Morex\))$|^(E(Ban|Bca|Bed|Bem|Bes|Bma|Bpi|Bro)[0-9]{2}_SQ[0-9]{3}_[A-Z]{1}[0-9]{2})$|^(Franka(_|_b_)3pri[0-9]{1,2})$|^(H[A-Z]{1}[0-9]{1-4}[A-Z]{1}[0-9]{1,2}[a-z]{1})$|^(HVSME[a-z]{1}[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(HV_CEa[0-9]{4}[A-Z]{1}[0-9]{2}(r2|f))$|^(H[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{2}r)$|^(Mla([0-9]{1,2}|[0-9]{1,2}DH)(_orf_|_div5_|_5pri_|_5pri-|_consrvd_|_3pri12_)(3pri12|3pr|UTR_intron2|UTR_intron1|5pri_end))$|^((Mla|Mlk)(_div5|_3pri12))$|^(S[0-9]{10}[A-Z]{1}[0-9]{2}[A-Z]{1}[0-9]{1})$|^((b|rb)(aak|aal|ags|ah|asd)[0-9]{1,2}[a-z]{1}[0-9]{2})$|^(HO)$|^(MLOC\.[0-9]{4,6}\.[0-9]{1,2})$|^(AK[0-9]{6}\.1)$|^(AJ[0-9]{6}\.1)$" -efpconfig,".{0,16}" -efpmedicago,"^(Medtr\d{1}g\d{6})$|^(Medtr\d{1}g\d{6}\.[0-9]{1})$|^(Mtr.\d{4,5}.1.[S1|S1_x|s1|s1_x]_at)$|^(AFFX-[Bio|Cre|Dap|Lys|Phe|Thr|Trpn][B|C|Dn|X]-[3|5|M]_at)$|^(AFFX-[Msa|Mtr]-[actin|gapc|gsta|ubq11|TrpnX]-[3|5|M]_[at|x_at|s_at])$|^(AFFX-Mtr|AFFX-r2-[Bs|Ec|P1]-[cre|dap|lys|phe|thr|bioB|bioC|bioD]-[3|5|M]_[at|s_at|x_at])$|^(AFFX-Mtr-ubq11-[3|5|M]_[at|s_at|x_at])$|^(AFFX-r2-Tag[A-Z]{1,2}_at|-3_at|-5_at|-M_at)$|^(Medtr_v1_\d{6})$" -efppop,"^(Ptp(Affx)?\.\d{1,6}\.\d{1,6}\.(A1|A2|S1|S2)_(x_at|s_at|at|a_at))$|^((eugene3)\.e{6,12})$|^((estExt_)(Genewise|fgenesh)(1|4)\_(v1|kg|pg|pm)(\.|\_v1\.)C_LG_\w{6,10})$|^((grail3.)\d{8,12})$|^((fgenesh)(1|4)\_(kg|pg|pm)\.C\_(scaffold|LG)\_\w{7,12})$|^((gw1)\.\w{1,6}\.\w{1,4}\.1)$|^((POPTR)\_[0-9]{4}s[0-9]{5}\.*[1-5]{0,1})$|^(Potri\.[0-9]{3}G[0-9]{6}\.[0-9]{1})$" -efprice,"^(LOC_Os[0-9]{2}g[0-9]{5})$|^((AFFX|AFFX-Os)(-|_)(Ubiquitin|Actin|Cyph|Gapdh|BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX|ef1a|gapdh)(-|_)(3|5|M)_(at|x_at|s_at))$|^(AFFX-OS-(18SrRNA|25SrRNA|5.8SrRNA)_(s_at|at))$|^((AFFX-Mgr-(actin|ef1a|gapdh)-(3|5|M))_(at|x_at|s_at))$|^(AFFX-r2-Tag(A|B|C|D|E|F|G|H)_at)$|^(AFFX-r2-Tag(IN|I|J|O|Q)-(3|5|M)_at)$|^((AFFX|AFFX-Os)-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$|^((Os|OsAffx)\.[0-9]{1,5}\.[0-9]{1}\.(S1|A1|S2)_(at|x_at|s_at|a_at))$" -efpsoybean,"^((Glyma\d{1,3}g\d{1,6}\.?\d?)$|^(Glyma\.\d{1,3}g\d{1,8}))$" -maizeefp,"^(AC[0-9]{6}\.[0-9]{1}_FG[0-9]{3})$|^(AC[0-9]{6}\.[0-9]{1}_FGT[0-9]{3})$|^(GRMZM(2|5)G[0-9]{6})$|^(GRMZM(2|5)G[0-9]{6}_T[0-9]{2})$|^(Zm\d+d\d+)$|^(Zm\d{1,10}eb\d{1,10})$" -mouse_efp,"^(XM_\d{0,8}\.\d{0,3})$|^(\d{1,10}\D\d{0,4}\D{0,4})$|^(\D{1,8}\d{0,8}\D{0,8})$|^(ENSMUSG\d{1,15})$|^(NM_\d{0,12}\d.\d{0,3})$" \ No newline at end of file diff --git a/generate_efp_test_cases.py b/generate_efp_test_cases.py deleted file mode 100644 index ad7b40e2..00000000 --- a/generate_efp_test_cases.py +++ /dev/null @@ -1,211 +0,0 @@ -""" -Reena Obmina | BCB330 Project 2025-2026 | University of Toronto - -Generates edge-test CSV for the eFP gene expression endpoints. - -Reads: species_databases.json — view→database mappings per species - api/random_rows_json/ — example gene IDs per database - api/utils/bar_utils.py — regex patterns (referenced, not imported) -Writes: efp_test_cases.csv - -Columns: species, view, database, regex, valid_gene_1..3, - invalid_gene_1_wrong_initially, invalid_gene_2_wrong_finally, - invalid_gene_3_other_species -""" - -import csv -import json -import re -from pathlib import Path - -JSON_DIR = Path("api/random_rows_json") - -# --------------------------------------------------------------------------- -# Regex patterns copied verbatim from api/utils/bar_utils.py -# --------------------------------------------------------------------------- -SPECIES_REGEX = { - "arabidopsis": r"^At[12345cm]g\d{5}.?\d?$", - "arabidopsis lipid": r"^At[12345cm]g\d{5}.?\d?$", - "arabidopsis cell": r"^At[12345cm]g\d{5}.?\d?$", - "arabidopsis seedcoat": r"^At[12345cm]g\d{5}.?\d?$", - "actinidia": r"^Acc\d{5}\.\d+$", - "arachis": r"^Adur\d{1,10}_comp\d{1,3}_\D{1,3}\d{1,3}_seq\d{1,5}$", - "barley": r"^HORVU(\d+Hr\d+G\d+|\.MOREX\.r\d+\.\dHG\d+\.\d+)$", - "brachypodium": r"^Bradi\d+g\d+\.\d+$", - "brassica rapa": r"^(BraA.{1,4}g\d{1,9}|[A-Z]\d{2}[gp]\d+\.\d+_BraROA)$", - "cacao ccn": r"^((CCN-51|SCA-6)_Chr\d+v\d+_\d+|Tc\d+v\d+_g\d+)$", - "cacao sca": r"^((CCN-51|SCA-6)_Chr\d+v\d+_\d+|Tc\d+v\d+_g\d+)$", - "cacao tc": r"^((CCN-51|SCA-6)_Chr\d+v\d+_\d+|Tc\d+v\d+_g\d+)$", - "camelina": r"^Csa\d+[gs]\d+\.\d+$", - "canola": r"^(Bna[AC]\d{2}g\d{5}[A-D]?|Bo[A-Z]+_?\d+g\d+\.\d+V\d+)$", - "cannabis": r"^AGQN\d{0,10}$", - "eutrema": r"^(Thhalv\d+m\.g|nXLOC_\d+)$", - "grape": r"^(CHR\d+_JGVV\d+_\d+_T\d+|VIT_\d{0,3}\D\d{0,5}g\d{0,6})$", - "human": r"^\d{1,10}$", - "kalanchoe": r"^Kaladp\d{1,10}s\d{1,10}$", - "little millet": r"^TRINITY_DN\d+_c\d+_g\d+_i\d+$", - "lupin": r"^Luan_Oskar_(PB\d+|Trin)_\d+$", - "maize": r"^(AC[0-9]{6}\.[0-9]+_FGT?[0-9]{3}|GRMZM[25]G[0-9]{6}(_T[0-9]{2})?|Zm\d+(d|eb)\d+)$", - "mangosteen": r"^DN\d+$", - "medicago": r"^(Medtr(\d+[gs]\d+|_v1_\d+)|MtrunA17Chr\dg\d+)$", - "mouse": r"^XM_\d+\.\d+$", - "oat": r"^AV[A-Z]{3}\.\d{5}[a-z]\.r\d+\.\d[A-Z]{2}\d{8}$", - "phelipanche": r"^OrAeBC5_\d{1,6}\.\d{1,3}$", - "physcomitrella": r"^Pp1s\d{1,8}_\d{1,8}V6\.\d{1,3}$", - "poplar": r"^POTRI\.\d{3}g\d{6}.?\d{0,3}$", - "potato": r"^(PGSC0003DMG\d+|EPlSTUG\d+)$", - "rice": r"^(LOC_Os\d{2}g\d{5}|Os\d{2}g\d+)$", - "selaginella": r"^Smo\d{1,8}$", - "soybean": r"^((Glyma\d{1,3}g\d{1,6}\.?\d?)|(Glyma\.\d{1,3}g\d{1,8}))$", - "strawberry": r"^FvH4_\d{1,3}g\d{1,8}$", - "striga": r"^StHeBC3_\d{1,6}\.\d{1,5}$", - "tomato": r"^Solyc\d\dg\d{6}(\.\d+)?$", - # no dedicated bar_utils validator; triticale uses wheat probes/IDs - "triticale": r"^(TraesCS[0-9A-Z]+(\.\d+)?|TrturSVE[0-9A-Z]+G\d+)$", - "triphysaria": r"^TrVeBC3_\d{1,6}\.\d{1,3}$", - "wheat": r"^(TraesCS[0-9A-Z]+(\.\d+)?|TrturSVE[0-9A-Z]+G\d+)$", -} - -# --------------------------------------------------------------------------- -# Microarray / probeset databases → gene IDs come from a non-probeset sibling -# --------------------------------------------------------------------------- -PROBESET_FALLBACK = { - # Arabidopsis Affymetrix ATH1 arrays → use klepikova RNA-seq (AGI format) - "affydb": "klepikova", - "arabidopsis_ecotypes": "klepikova", - "atgenexp": "klepikova", - "atgenexp_hormone": "klepikova", - "atgenexp_pathogen": "klepikova", - "atgenexp_plus": "klepikova", - "atgenexp_stress": "klepikova", - "guard_cell": "klepikova", - "hnahal": "klepikova", - "lateral_root_initiation": "klepikova", - "light_series": "klepikova", - "meristem_db": "klepikova", - "meristem_db_new": "klepikova", - "root": "klepikova", - "rohan": "klepikova", - "rpatel": "klepikova", - "seed_db": "klepikova", - # Lipid map stores lipid-class IDs, not AGI — fall back to RNA-seq for AGI examples - "lipid_map": "klepikova", - # Seedcoat uses a legacy non-AGI format; fall back to standard RNA-seq AGI IDs - "seedcoat": "klepikova", - # Non-arabidopsis microarray databases - "barley_mas": "barley_seed", - "barley_rma": "barley_seed", - "human_developmental": "human_body_map_2", - "human_developmental_SpongeLab": "human_body_map_2", - "human_diseased": "human_body_map_2", - "maize_gdowns": "maize_atlas", - "medicago_mas": "medicago_root", - "medicago_rma": "medicago_root", - "poplar": "poplar_hormone", - "rice_mas": "rice_drought_heat_stress", - "rice_rma": "rice_drought_heat_stress", - # Triticale has no non-probeset database; use wheat IDs (triticale is wheat × rye) - "triticale": "wheat", - "triticale_mas": "wheat", -} - -# --------------------------------------------------------------------------- -# Cross-species invalid gene (invalid type 3: completely wrong species) -# --------------------------------------------------------------------------- -CROSS_SPECIES = { - "arabidopsis": "Solyc04g054700", # tomato gene - "arabidopsis lipid": "Solyc04g054700", - "arabidopsis cell": "Solyc04g054700", - "arabidopsis seedcoat": "Solyc04g054700", - "human": "At1g01010", # plant gene - "mouse": "At1g01010", -} -_DEFAULT_CROSS = "At1g01010" # arabidopsis gene — wrong for every non-arabidopsis species - - -def _load_genes(db_name: str, species_regex: str, n: int = 3) -> list[str]: - """Return up to *n* unique data_probeset_id values that match *species_regex*.""" - path = JSON_DIR / f"{db_name}_test_data.json" - if not path.exists(): - return [] - data = json.loads(path.read_text()) - seen: set[str] = set() - result: list[str] = [] - for row in data: - gid = str(row.get("data_probeset_id") or "").strip() - if gid and gid not in seen and re.search(species_regex, gid, re.I): - seen.add(gid) - result.append(gid) - if len(result) >= n: - break - return result - - -def _invalid_initially(gene: str) -> str: - """Change the first character to a wrong type (letter→digit, digit/other→letter).""" - if not gene: - return "INVALID" - return ("9" if gene[0].isalpha() else "Z") + gene[1:] - - -def _invalid_finally(gene: str, regex: str = "") -> str: - """Change the last character to a wrong type; fall back to appending '.X' if the - first mutation still passes the regex (e.g. when the regex uses [0-9A-Z]+).""" - if not gene: - return "INVALID" - candidate = gene[:-1] + ("X" if gene[-1].isdigit() else "9") - if regex and re.search(regex, candidate, re.I): - # First mutation wasn't enough — append a clearly invalid version suffix - candidate = gene + ".X" - return candidate - - -def main() -> None: - db_data: dict = json.loads(Path("species_databases.json").read_text()) - - fieldnames = [ - "species", "view", "database", "regex", - "valid_gene_1", "valid_gene_2", "valid_gene_3", - "invalid_gene_1_wrong_initially", - "invalid_gene_2_wrong_finally", - "invalid_gene_3_other_species", - ] - rows: list[dict] = [] - - for species, views in db_data.items(): - regex = SPECIES_REGEX.get(species, "") - cross = CROSS_SPECIES.get(species, _DEFAULT_CROSS) - - for view, db in views.items(): - source_db = PROBESET_FALLBACK.get(db, db) - genes = _load_genes(source_db, regex) if regex else [] - - # Pad to 3 slots - while len(genes) < 3: - genes.append("") - - ref = genes[0] - rows.append({ - "species": species, - "view": view, - "database": db, - "regex": regex, - "valid_gene_1": genes[0], - "valid_gene_2": genes[1], - "valid_gene_3": genes[2], - "invalid_gene_1_wrong_initially": _invalid_initially(ref) if ref else "INVALID", - "invalid_gene_2_wrong_finally": _invalid_finally(ref, regex) if ref else "INVALID", - "invalid_gene_3_other_species": cross, - }) - - out = Path("efp_test_cases.csv") - with out.open("w", newline="") as f: - writer = csv.DictWriter(f, fieldnames=fieldnames) - writer.writeheader() - writer.writerows(rows) - - print(f"Written {len(rows)} rows to {out}") - - -if __name__ == "__main__": - main() diff --git a/live_example_gene_id_coverage.csv b/live_example_gene_id_coverage.csv deleted file mode 100644 index 63530aeb..00000000 --- a/live_example_gene_id_coverage.csv +++ /dev/null @@ -1,67 +0,0 @@ -source,project,validator_key,example_gene_id,result -efp,efp_actinidia,efp_actinidia,Acc00001.1,PASS -efp,efp_apple,efp_apple,MfusH1_01g00006,PASS -efp,efp_arabidopsis,efp_arabidopsis,At1g01010,PASS -efp,efp_arabidopsis_cell,efp_arabidopsis_cell,,NO_EXAMPLE_FOUND -efp,efp_arabidopsis_lipid,efp_arabidopsis_lipid,,NO_EXAMPLE_FOUND -efp,efp_arabidopsis_seedcoat,efp_seedcoat,At1g17665,PASS -efp,efp_arachis,efp_arachis,Adur10000_comp0_c0_seq1,PASS -efp,efp_barley,efp_barley,Contig3045_at,PASS -efp,efp_brachypodium,efp_brachypodium,Bradi4g05940.1,PASS -efp,efp_brachypodium_metabolites,efp_brachypodium_metabolites,,NO_EXAMPLE_FOUND -efp,efp_brassica_rapa,efp_brassica_rapa,BraA01g000010,PASS -efp,efp_cacao_ccn,efp_cacao_ccn,CCN-51_Chr0v1_20099,PASS -efp,efp_cacao_sca,efp_cacao_sca,SCA-6_Chr1v1_00001,PASS -efp,efp_cacao_tc,efp_cacao_tc,Tc01v2_g000010,PASS -efp,efp_camelina,efp_camelina,Csa00382s010.1,PASS -efp,efp_cannabis,efp_cannabis,AGQN03000001,PASS -efp,efp_canola,efp_canola,BnaA01g00010D,PASS -efp,efp_durum_wheat,efp_durum_wheat,TrturSVE1A02G00000070,PASS -efp,efp_euphorbia,efp_euphorbia,Ep_chr1_g00001,PASS -efp,efp_eutrema,efp_eutrema,Thhalv10000089m.g,PASS -efp,efp_grape,efp_grape,VIT_00s0120g00060,PASS -efp,efp_human,efp_human,,FETCH_ERROR: 403 Client Error: Forbidden for url: https://bar.utoronto.ca/efp_human/cgi-bin/efpWeb.cgi -efp,efp_kalanchoe,efp_kalanchoe,Kaladp0001s0001,PASS -efp,efp_little_millet,efp_little_millet,TRINITY_DN0_c0_g1_i15,PASS -efp,efp_lupin,efp_lupin,Luan_Oskar_Trin_282785,PASS -efp,efp_maize,efp_maize,Zm00001d046170,PASS -efp,efp_maize_enzyme,efp_maize_enzyme,,NO_EXAMPLE_FOUND -efp,efp_maize_metabolite,efp_maize_metabolite,,NO_EXAMPLE_FOUND -efp,efp_mangosteen,efp_mangosteen,DN1,PASS -efp,efp_marchantia,efp_marchantia,Mp1g00010,PASS -efp,efp_medicago,efp_medicago,Medtr1g102430,PASS -efp,efp_mouse,mouse_efp,XM_122026.1,PASS -efp,efp_oat,efp_oat,N0.HOG0015560,PASS -efp,efp_phelipanche,efp_phelipanche,OrAeBC5_10.1,PASS -efp,efp_physcomitrella,efp_physcomitrella,Pp1s103_79V6.1,PASS -efp,efp_poplar,efp_poplar,PtpAffx.200227.1.S1_s_at,PASS -efp,efp_potato,efp_potato,PGSC0003DMG400000005,PASS -efp,efp_rice,efp_rice,LOC_Os01g01080,PASS -efp,efp_rice_metabolite,efp_rice_metabolite,,NO_EXAMPLE_FOUND -efp,efp_selaginella,efp_selaginella,Smo402070,PASS -efp,efp_sorghum,efp_sorghum,Sobic.001G000100,PASS -efp,efp_soybean,efp_soybean,Glyma06g47400,PASS -efp,efp_strawberry,efp_strawberry,FvH4_1g00010,PASS -efp,efp_striga,efp_striga,StHeBC3_1.1,PASS -efp,efp_tomato,efp_tomato,Solyc04g014530,PASS -efp,efp_triphysaria,efp_triphysaria,TrVeBC3_1.1,PASS -efp,efp_triticale,efp_triticale,Ta.10026.1.A1_at,PASS -efp,efp_tung_tree,efp_tung_tree,Vf03G1621,PASS -efp,efp_wheat,efp_wheat,TraesCS1A01G000100,PASS -eplant,eplant_arabidopsis,arabidopsis,ABI3,FAIL -eplant,eplant_barley,barley,HORVU.MOREX.r3.1HG0000030,PASS -eplant,eplant_barley_legacy,barley,HORVU1Hr1G000010,PASS -eplant,eplant_camelina,camelina,Csa01g001040,PASS -eplant,eplant_cannabis,cannabis,AGQN03000001,PASS -eplant,eplant_eucalyptus,eucalyptus,Eucgr.A00001,PASS -eplant,eplant_maize,maize,GRMZM2G158252,PASS -eplant,eplant_medicago,medicago,Medtr8g043970,PASS -eplant,eplant_poplar,poplar,Potri.003G172600,PASS -eplant,eplant_potato,potato,PGSC0003DMG400000005,PASS -eplant,eplant_rice,rice,LOC_Os01g01080,PASS -eplant,eplant_soybean,soybean,Glyma.06G202300,PASS -eplant,eplant_sugarcane,sugarcane,Sh01_g000010,PASS -eplant,eplant_sunflower,sunflower,HanXRQChr12g0384141,FAIL -eplant,eplant_tomato,tomato,Solyc04g014530,PASS -eplant,eplant_wheat,wheat,TraesCS1A01G000100,PASS -eplant,eplant_willow,willow,SapurV1A.0035s0010,FAIL diff --git a/mysql_dbs.txt b/mysql_dbs.txt deleted file mode 100644 index 3738f468..00000000 --- a/mysql_dbs.txt +++ /dev/null @@ -1,212 +0,0 @@ -Database -actinidia_bud_development -actinidia_flower_fruit_development -actinidia_postharvest -actinidia_vegetative_growth -affydb -annotations_lookup -apple -arabidopsis_ecotypes -arachis -atgenexp -atgenexp_hormone -atgenexp_pathogen -atgenexp_plus -atgenexp_stress -barley_mas -barley_rma -barley_seed -barley_spike_meristem -barley_spike_meristem_v3 -brachypodium -brachypodium_Bd21 -brachypodium_embryogenesis -brachypodium_grains -brachypodium_metabolites_map -brachypodium_photo_thermocycle -brassica_rapa -cacao_developmental_atlas -cacao_developmental_atlas_sca -cacao_drought_diurnal_atlas -cacao_drought_diurnal_atlas_sca -cacao_infection -cacao_leaf -cacao_meristem_atlas_sca -cacao_seed_atlas_sca -camelina -camelina_tpm -cannabis -canola -canola_nssnp -canola_original -canola_original_v2 -canola_seed -cassava_atlas -cassava_cbb -cassava_eacmv -circadian_mutants -cuscuta -cuscuta_early_haustoriogenesis -cuscuta_lmd -dna_damage -durum_wheat_abiotic_stress -durum_wheat_biotic_stress -durum_wheat_development -embryo -eplant2 -eplant_poplar -eplant_rice -eplant_soybean -eplant_tomato -eucalyptus -euphorbia -fastpheno -gc_drought -germination -grape_developmental -guard_cell -gynoecium -heterodera_schachtii -hnahal -homologs_db -human_body_map_2 -human_developmental -human_developmental_SpongeLab -human_diseased -information_schema -interactions_vincent_v2 -kalanchoe -kalanchoe_time_course_analysis -klepikova -lateral_root_initiation -light_series -lipid_map -little_millet -llama3 -lupin_lcm_leaf -lupin_lcm_pod -lupin_lcm_stem -lupin_pod_seed -lupin_whole_plant -maize_RMA_linear -maize_RMA_log -maize_atlas -maize_atlas_v5 -maize_buell_lab -maize_early_seed -maize_ears -maize_embryonic_leaf_development -maize_enzyme -maize_gdowns -maize_iplant -maize_kernel_v5 -maize_leaf_gradient -maize_lipid_map -maize_metabolite -maize_nitrogen_use_efficiency -maize_rice_comparison -maize_root -maize_stress_v5 -mangosteen_aril_vs_rind -mangosteen_callus -mangosteen_diseased_vs_normal -mangosteen_fruit_ripening -mangosteen_seed_development -mangosteen_seed_development_germination -mangosteen_seed_germination -marchantia_organ_stress -medicago_mas -medicago_rma -medicago_root -medicago_root_v5 -medicago_seed -meristem_db -meristem_db_new -mouse_db -mysql -oat -performance_schema -phelipanche -physcomitrella_db -poplar -poplar_hormone -poplar_leaf -poplar_nssnp -poplar_xylem -potato_dev -potato_stress -potato_wounding -rice_abiotic_stress_sc_pseudobulk -rice_drought_heat_stress -rice_interactions -rice_leaf_gradient -rice_maize_comparison -rice_mas -rice_metabolite -rice_rma -rice_root -rohan -root -root_Schaefer_lab -rpatel -seed_db -seedcoat -selaginella -shoot_apex -silique -single_cell -sorghum_atlas_w_BS_cells -sorghum_comparative_transcriptomics -sorghum_developmental -sorghum_developmental_2 -sorghum_flowering_activation -sorghum_low_phosphorus -sorghum_nitrogen_stress -sorghum_nitrogen_use_efficiency -sorghum_phosphate_stress -sorghum_plasma -sorghum_saline_alkali_stress -sorghum_stress -sorghum_strigolactone_variation -sorghum_sulfur_stress -sorghum_temperature_stress -sorghum_vascularization_and_internode -soybean -soybean_embryonic_development -soybean_heart_cotyledon_globular -soybean_nssnp -soybean_senescence -soybean_severin -spruce -strawberry -striga -sugarcane_culms -sugarcane_leaf -sunflower -sys -thellungiella_db -tomato -tomato_ils -tomato_ils2 -tomato_ils3 -tomato_meristem -tomato_nssnp -tomato_renormalized -tomato_root -tomato_root_field_pot -tomato_s_pennellii -tomato_seed -tomato_sequence -tomato_shade_mutants -tomato_shade_timecourse -tomato_trait -triphysaria -triticale -triticale_mas -tung_tree -wheat -wheat_abiotic_stress -wheat_embryogenesis -wheat_meiosis -wheat_root 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zKgqlY4afTz5wz##ZXJK2_X8j50i$LJCobRt@_m0^YbeT>v;oRGYkasPcf21qS;)Vs z0#vWJa1+AAbCT_FGZOzaW5x{7fb5dr#JG1iFz+GCf6sQS7(~^D6&m z47*ZOQAO3Nlr2{^Y?nF0<;{Z;yY~BJl)o6O`*PfiX*7fjH+b(v@rWjTe0)2t3yA&M z1D~-*{?<}6i#J}z^Xp%0v}jb+9f`GJWBVVR1tzbw?C!iOst5*(sl2a= zczXgxS(Plf0S$n*X^lFq2&$A=aVP{sQ(y-+5e#UnH208@=foJt4fWi~d-(i3pBuqU z5CcN#Tmv_;ywN@#!2Ilx)wpGD#O}%<{~Td@39$rLVF~oRG{~QKW-!GW&CF4|op~*a z9{;6$@Zl_{ns!NvrXnGuOPLX z3AXboDx%^BYIwwr!g;&lBs g)W7~O{o%yiTyr<2>wyD(^hH`b^tPvL{pHMm0uof?OaK4? diff --git a/speed_graphs.py b/speed_graphs.py deleted file mode 100644 index fbf2a0ac..00000000 --- a/speed_graphs.py +++ /dev/null @@ -1,217 +0,0 @@ -""" -Speed comparison: Local Flask API vs ngrok tunnel vs Legacy BAR eFP CGI -Run after collecting real ngrok data by replacing NGROK_DATA below. -""" -import pickle -import numpy as np -import matplotlib -matplotlib.use("Agg") -import matplotlib.pyplot as plt -import matplotlib.patches as mpatches -from matplotlib.patches import FancyBboxPatch -import matplotlib.ticker as ticker - -# ── Collected data ──────────────────────────────────────────────────────────── -with open("/tmp/speed_results.pkl", "rb") as f: - measured = pickle.load(f) - -DBS = ["embryo", "klepikova", "shoot_apex"] -DB_LABELS = ["Embryo", "Klepikova", "Shoot Apex"] - -# Real measured data -local = {db: measured[(db, "local")] for db in DBS} -cgi = {db: measured[(db, "legacy_cgi")] for db in DBS} - -# Real ngrok data (mirna-undeliberate-rachael.ngrok-free.dev → localhost:5000) -rng = np.random.default_rng(42) -ngrok = {db: measured[(db, "ngrok")] for db in DBS} -NGROK_ESTIMATED = False - -# ── Colours ─────────────────────────────────────────────────────────────────── -C_LOCAL = "#2196F3" # blue -C_NGROK = "#FF9800" # orange -C_CGI = "#9C27B0" # purple - -# ============================================================================= -# FIGURE 1 — Bar chart (averages) with broken y-axis at 2000 ms -# ============================================================================= -CLIP = 2000 # ms — y-axis ceiling - -fig1, (ax_top, ax_bot) = plt.subplots( - 2, 1, figsize=(9, 6), - gridspec_kw={"height_ratios": [1.6, 2.8], "hspace": 0.08} -) - -x = np.arange(len(DBS)) -W = 0.25 - -def bar_group(ax, vals_dict, clip=None): - """Draw grouped bars; returns bar objects.""" - bars = {} - for i, (key, color) in enumerate( - [("local", C_LOCAL), ("ngrok", C_NGROK), ("cgi", C_CGI)] - ): - data = {"local": local, "ngrok": ngrok, "cgi": cgi}[key] - means = [np.mean(data[db]) for db in DBS] - sds = [np.std(data[db]) for db in DBS] - if clip: - means_plot = [min(m, clip) for m in means] - else: - means_plot = means - b = ax.bar(x + (i - 1) * W, means_plot, W, - color=color, alpha=0.88, zorder=3, - yerr=sds if clip is None else None, - capsize=3, error_kw={"elinewidth": 1, "zorder": 4}) - bars[key] = (b, means) - return bars - -# ── Top panel: 1800–2800 ms range (shows CGI bars poking above clip) ────────── -TOP_LO, TOP_HI = 1800, 2800 -ax_top.set_ylim(TOP_LO, TOP_HI) -bar_group(ax_top, {}, clip=None) - -for i, (key, color) in enumerate( - [("local", C_LOCAL), ("ngrok", C_NGROK), ("cgi", C_CGI)]): - data = {"local": local, "ngrok": ngrok, "cgi": cgi}[key] - means = [np.mean(data[db]) for db in DBS] - sds = [np.std(data[db]) for db in DBS] - ax_top.bar(x + (i - 1) * W, means, W, color=color, alpha=0.88, zorder=3) - ax_top.errorbar(x + (i - 1) * W, means, yerr=sds, - fmt="none", color="black", capsize=3, - elinewidth=1, zorder=5) - -ax_top.set_ylim(TOP_LO, TOP_HI) -ax_top.set_yticks([1800, 2000, 2200, 2400, 2600, 2800]) -ax_top.tick_params(bottom=False, labelbottom=False) -ax_top.spines["bottom"].set_visible(False) -ax_top.set_facecolor("#fafafa") -ax_top.grid(axis="y", linestyle="--", alpha=0.4, zorder=0) - -# Annotate the outlier above the top panel -outlier_val = max(max(cgi[db]) for db in DBS) -ax_top.annotate( - f"outlier ≈ {outlier_val/1000:.1f} s\n(not shown)", - xy=(0.97, 0.97), xycoords="axes fraction", - ha="right", va="top", fontsize=7.5, - color="#666", style="italic" -) - -# ── Bottom panel: 0–CLIP ms ─────────────────────────────────────────────────── -for i, (key, color) in enumerate( - [("local", C_LOCAL), ("ngrok", C_NGROK), ("cgi", C_CGI)]): - data = {"local": local, "ngrok": ngrok, "cgi": cgi}[key] - means = [np.mean(data[db]) for db in DBS] - sds = [np.std(data[db]) for db in DBS] - capped = [min(m, CLIP) for m in means] - ax_bot.bar(x + (i - 1) * W, capped, W, color=color, alpha=0.88, zorder=3) - ax_bot.errorbar(x + (i - 1) * W, capped, yerr=sds, - fmt="none", color="black", capsize=3, - elinewidth=1, zorder=5) - # Draw squiggly break on bars that exceed CLIP - for j, (cap, real) in enumerate(zip(capped, means)): - if real > CLIP: - bx = x[j] + (i - 1) * W - for yy in np.linspace(CLIP - 60, CLIP + 10, 5): - ax_bot.plot([bx - W / 2 + 0.01, bx + W / 2 - 0.01], - [yy, yy + 18 * (1 if j % 2 == 0 else -1)], - color="white", lw=1.8, zorder=6) - -ax_bot.set_ylim(0, CLIP + 80) -ax_bot.set_xticks(x) -ax_bot.set_xticklabels(DB_LABELS, fontsize=11) -ax_bot.spines["top"].set_visible(False) -ax_bot.set_facecolor("#fafafa") -ax_bot.grid(axis="y", linestyle="--", alpha=0.4, zorder=0) -ax_bot.set_ylabel("Response time (ms)", fontsize=11, labelpad=8) -ax_bot.yaxis.set_label_coords(-0.08, 1.1) - -# Broken-axis diagonal tick marks -d = 0.012 -kwargs = dict(transform=fig1.transFigure, color="black", clip_on=False, lw=1.2) -# Get axes positions -pos_top = ax_top.get_position() -pos_bot = ax_bot.get_position() -y_break = pos_bot.y1 # top of bottom axes = bottom of top axes -for xi in [pos_top.x0 - 0.005, pos_top.x0 + 0.005]: - fig1.add_artist(plt.Line2D([xi - d, xi + d], - [y_break - d * 1.5, y_break + d * 1.5], **kwargs)) - -# Legend -legend_handles = [ - mpatches.Patch(color=C_LOCAL, label="Local API (localhost:5000)"), - mpatches.Patch(color=C_NGROK, - label="ngrok Tunnel" + (" [estimated]" if NGROK_ESTIMATED else "")), - mpatches.Patch(color=C_CGI, label="Legacy BAR CGI"), -] -ax_bot.legend(handles=legend_handles, fontsize=9, - loc="upper right", framealpha=0.9) - -fig1.suptitle("Gene Expression — Average HTTP Response Time", fontsize=13, - fontweight="bold", y=0.98) -ax_top.set_title("(y-axis clipped to 2000 ms; CGI bars shown in upper panel)", - fontsize=8, color="#555", pad=4) - -plt.savefig("/Users/reenamarieobmina/BAR_API/speed_bar_chart.png", - dpi=150, bbox_inches="tight") -plt.close() -print("Fig 1 saved: speed_bar_chart.png") - -# ============================================================================= -# FIGURE 2 — Box plots (all individual trials) -# ============================================================================= -fig2, axes = plt.subplots(1, 3, figsize=(13, 5), sharey=False) - -for col, (db, db_label) in enumerate(zip(DBS, DB_LABELS)): - ax = axes[col] - - endpoint_data = [local[db], ngrok[db], cgi[db]] - endpoint_labels = [ - "Local\nAPI", - "ngrok\nTunnel" + ("\n[est.]" if NGROK_ESTIMATED else ""), - "Legacy\nCGI", - ] - colors = [C_LOCAL, C_NGROK, C_CGI] - - bp = ax.boxplot( - endpoint_data, - patch_artist=True, - widths=0.45, - medianprops=dict(color="white", linewidth=2), - whiskerprops=dict(linewidth=1.2), - capprops=dict(linewidth=1.2), - flierprops=dict(marker="o", markersize=4, alpha=0.6), - zorder=3, - ) - for patch, color in zip(bp["boxes"], colors): - patch.set_facecolor(color) - patch.set_alpha(0.82) - - # Scatter individual points - for idx, (vals, color) in enumerate(zip(endpoint_data, colors), start=1): - jitter = rng.uniform(-0.12, 0.12, len(vals)) - ax.scatter([idx + j for j in jitter], vals, - color=color, s=18, alpha=0.7, zorder=4, edgecolors="white", linewidths=0.4) - - ax.set_xticks([1, 2, 3]) - ax.set_xticklabels(endpoint_labels, fontsize=9) - ax.set_title(db_label, fontsize=11, fontweight="bold") - ax.set_facecolor("#fafafa") - ax.grid(axis="y", linestyle="--", alpha=0.4, zorder=0) - ax.spines["top"].set_visible(False) - ax.spines["right"].set_visible(False) - - if col == 0: - ax.set_ylabel("Response time (ms)", fontsize=10) - - # Show n - ax.text(0.98, 0.98, f"n={len(local[db])} trials", - transform=ax.transAxes, ha="right", va="top", - fontsize=7.5, color="#777") - -fig2.suptitle("Gene Expression — Response Time Distribution", fontsize=13, - fontweight="bold") -fig2.tight_layout(rect=[0, 0, 1, 0.95]) -plt.savefig("/Users/reenamarieobmina/BAR_API/speed_box_plots.png", - dpi=150, bbox_inches="tight") -plt.close() -print("Fig 2 saved: speed_box_plots.png") diff --git a/validate_live_example_gene_ids.py b/validate_live_example_gene_ids.py deleted file mode 100644 index 1cacfad1..00000000 --- a/validate_live_example_gene_ids.py +++ /dev/null @@ -1,182 +0,0 @@ -""" -Reena Obmina | BCB330 Project 2025-2026 | University of Toronto - -Task (Jul 2026): test the production gene ID validators against each live -efp/eplant project's OWN example gene ID, instead of only against Vincent's -curated sample dumps in api/random_rows_json/. - -Motivation: api/random_rows_json/ only has data for the databases Vincent -happened to sample, and even where it does, the specific IDs picked can miss -edge cases -- e.g. every barley_spike_meristem_v3 sample happened to include -a trailing isoform suffix (HORVU.MOREX.r3.2HG0105390.1), which masked a real -gap: BAR's own eplant_barley (v3) page uses a bare gene ID with no suffix -(HORVU.MOREX.r3.1HG0000030) as its canonical example, and that failed -is_barley_gene_valid until this test caught it (see git history/PR for the fix). - -Each species view's datasource XML (data/{view}.xml) does NOT contain gene -IDs at all -- it only has tissue/sample/group names for the diagram -- so -that's not usable as a source here. The actual live, authoritative example -gene ID for a project lives in the page HTML itself: - - eFP (efpWeb.cgi, server-rendered): the "Primary Gene ID" default. - - ePlant (client-rendered SPA): a static "Example: ID" search hint - baked into the page shell (present even before any JS runs). - -Reads (live, over HTTP): every project in EFP_SITES and EPLANT_SITES -Reads (local): api/utils/bar_utils.py -- EFP_PROJECT_REGEXES, BARUtils - api/utils/gene_id_utils.py -- GeneIdUtils.validate_gene_id -Writes: live_example_gene_id_coverage.csv -- one row per project: the live - example ID, which validator it was checked against, and the result. -""" - -import csv -import re -import sys -import types -from concurrent.futures import ThreadPoolExecutor, as_completed - -import requests - -# importing api.utils.* normally runs api/__init__.py's create_app(), which -# tries to connect to MySQL even for this standalone script. Pre-register -# empty stand-in packages so Python loads the submodules directly instead. -sys.modules.setdefault("api", types.ModuleType("api")) -sys.modules["api"].__path__ = ["api"] -sys.modules.setdefault("api.utils", types.ModuleType("api.utils")) -sys.modules["api.utils"].__path__ = ["api/utils"] - -from api.utils.bar_utils import EFP_PROJECT_REGEXES, BARUtils # noqa: E402 -from api.utils.gene_id_utils import GeneIdUtils, _VALIDATORS # noqa: E402 - -from scrape_view_databases import EFP_SITES, EPLANT_SITES # noqa: E402 - -REQUEST_TIMEOUT = 20 - -# EFP_SITES keys that map straight to "efp_" + key.replace(" ", "_") in -# EFP_PROJECT_REGEXES for every project EXCEPT these two. -EFP_PROJECT_KEY_OVERRIDES = { - "arabidopsis seedcoat": "efp_seedcoat", - "mouse": "mouse_efp", -} - -PRIMARY_GENE_RE = re.compile(r']*name="primaryGene"[^>]*>', re.IGNORECASE) -VALUE_ATTR_RE = re.compile(r'value="([^"]*)"') -EPLANT_EXAMPLE_RE = re.compile(r"Example:\s*]*>([^<]+)", re.IGNORECASE) - - -def efp_project_key(species): - return EFP_PROJECT_KEY_OVERRIDES.get(species, f"efp_{species.replace(' ', '_')}") - - -def eplant_species_key(site): - """eplant_barley_legacy -> barley, eplant_maize -> maize, etc.""" - return site.removeprefix("eplant_").removesuffix("_legacy") - - -def fetch(url): - resp = requests.get(url, timeout=REQUEST_TIMEOUT) - resp.raise_for_status() - return resp.text - - -def check_efp_project(species, efp_url): - project_key = efp_project_key(species) - row = { - "source": "efp", - "project": f"efp_{species.replace(' ', '_')}", - "validator_key": project_key, - "example_gene_id": "", - "result": "", - } - try: - html = fetch(efp_url) - except Exception as e: - row["result"] = f"FETCH_ERROR: {e}" - return row - - tag_match = PRIMARY_GENE_RE.search(html) - value_match = VALUE_ATTR_RE.search(tag_match.group(0)) if tag_match else None - if not value_match or not value_match.group(1): - row["result"] = "NO_EXAMPLE_FOUND" - return row - - example_id = value_match.group(1) - row["example_gene_id"] = example_id - - if project_key not in EFP_PROJECT_REGEXES: - row["result"] = "NO_REGEX_MAPPING" - return row - - row["result"] = "PASS" if BARUtils.is_efp_gene_valid(example_id, project_key) else "FAIL" - return row - - -def check_eplant_project(site, base_url): - species_key = eplant_species_key(site) - row = { - "source": "eplant", - "project": site, - "validator_key": species_key, - "example_gene_id": "", - "result": "", - } - try: - html = fetch(base_url) - except Exception as e: - row["result"] = f"FETCH_ERROR: {e}" - return row - - match = EPLANT_EXAMPLE_RE.search(html) - if not match: - row["result"] = "NO_EXAMPLE_FOUND" - return row - - example_id = match.group(1).strip() - row["example_gene_id"] = example_id - - if species_key not in _VALIDATORS: - row["result"] = "NO_VALIDATOR_MAPPING" - return row - - row["result"] = "PASS" if GeneIdUtils.validate_gene_id(example_id, species_key) else "FAIL" - return row - - -def main(): - rows = [] - with ThreadPoolExecutor(max_workers=10) as pool: - futures = {pool.submit(check_efp_project, species, url): species for species, url in EFP_SITES.items()} - futures.update( - {pool.submit(check_eplant_project, site, url): site for site, url in EPLANT_SITES.items()} - ) - for future in as_completed(futures): - rows.append(future.result()) - - rows.sort(key=lambda r: (r["source"], r["project"])) - - out_file = "live_example_gene_id_coverage.csv" - with open(out_file, "w", newline="") as f: - writer = csv.DictWriter(f, fieldnames=["source", "project", "validator_key", "example_gene_id", "result"]) - writer.writeheader() - writer.writerows(rows) - - counts = {} - for row in rows: - key = row["result"].split(":")[0] - counts[key] = counts.get(key, 0) + 1 - - print(f"Checked {len(rows)} projects ({sum(1 for r in rows if r['source'] == 'efp')} efp, " - f"{sum(1 for r in rows if r['source'] == 'eplant')} eplant).") - for key, count in sorted(counts.items()): - print(f" {key}: {count}") - print(f"Report written to {out_file}") - - fails = [r for r in rows if r["result"] == "FAIL"] - if fails: - print("\nFAILURES (live example ID rejected by production validator):") - for r in fails: - print(f" {r['project']:30s} example={r['example_gene_id']!r:35s} validator={r['validator_key']}") - - -if __name__ == "__main__": - main() diff --git a/vincent_regex_summary_jun_25_2026.md b/vincent_regex_summary_jun_25_2026.md deleted file mode 100644 index d6b54f0d..00000000 --- a/vincent_regex_summary_jun_25_2026.md +++ /dev/null @@ -1,178 +0,0 @@ -# BAR eFP Regex Validation Summary for Vincent -**Date:** June 25, 2026 -**Prepared by:** Reena Obmina -**For:** Vincent (Production Database Validation) - ---- - -## Summary - -All eFP project regexes have been consolidated and are ready for production validation. These regexes validate both **canonical gene IDs AND microarray probeset IDs** where applicable. - -### Key Deliverables - -#### 1. **Master JSON File** ✅ -- **File:** `data/efp_info/combined_master.json` -- **Contents:** - - 48 species with standardized scientific names - - 193 databases with complete metadata - - SQL column structure for each database's sample_data table - - Schema variants (rnaseq_simple, legacy_microarray_projinfo) - - Frontend usage mapping for each database - - Sample groups and experimental design - -#### 2. **Consolidated Regex Dictionary** ✅ -- **File:** `api/utils/bar_utils.py` (lines 8-177) -- **Dictionary:** `EFP_PROJECT_REGEXES` -- **Total Patterns:** 50+ eFP project keys -- **Coverage:** All RNA-seq and microarray platforms - ---- - -## Regex Coverage by Platform - -### RNA-seq Projects (Gene Models) -- `efp_arabidopsis` - AGI gene IDs (At1g12345) -- `efp_barley` - HM/HV identifiers -- `efp_rice` - LOC_Os identifiers -- `efp_medicago` - Medtr identifiers -- `efp_poplar` - Potri identifiers -- `efp_soybean` - Glyma identifiers -- `efp_maize` - GRMZM identifiers -- `efp_wheat` - TraesCS identifiers -- And 20+ more species (apple, cacao, grape, potato, etc.) - -### Microarray Projects (Probeset IDs) -- `efp_arabidopsis` - Also accepts Affymetrix probeset IDs (123456_at, 123456_s_at) -- `efp_barley` - HV/HM array probes -- `efp_rice` - Affymetrix Rice array -- `efp_medicago` - Mtr/Msa/Sme array probes -- `efp_poplar` - Ptp array probes - -### Special Cases -- `efp_seedcoat` - Accepts CATMA probes (At\d{8}) + ATH1 Affymetrix -- `efp_arabidopsis_lipid` - Lipid species names (freeform text) -- `efp_maize_metabolite` - Metabolite names (freeform text) -- `efp_human` - Human probeset IDs (e.g., 202019_s_at) -- `efp` - Generic Arabidopsis validator (fallback) - ---- - -## Known Issues & Decisions Needed - -### ⚠️ Tomato Regex Issue - -**Current Status:** One generic regex for all tomato databases -``` -"efp_tomato": r"^(Solyc\d{2}g\d{6}\.?\d{0,3})$|^(TU\d{6})$" -``` - -**Database Mapping:** -``` -DATABASE_EFP_PROJECT = { - "tomato": "efp_tomato", - "tomato_ils": "efp_tomato", - "tomato_ils2": "efp_tomato", - "tomato_ils3": "efp_tomato", - "tomato_meristem": "efp_tomato", - "tomato_renormalized": "efp_tomato", - "tomato_root": "efp_tomato", - "tomato_root_field_pot": "efp_tomato", - "tomato_s_pennellii": "efp_tomato", - "tomato_seed": "efp_tomato", - "tomato_shade_mutants": "efp_tomato", - "tomato_shade_timecourse": "efp_tomato", - "tomato_trait": "efp_tomato_trait", (special case) -} -``` - -**Problem:** Different tomato databases may have different gene ID formats or probesets. - -**Options for Resolution:** -1. **Per-Species Approach (Current):** Keep one regex per species, validate all databases the same way -2. **Per-Database Approach:** Create individual regex patterns for each tomato database variant - -**Action Needed:** Vincent will consult with Asher about which approach to take. - ---- - -## What Reena Still Needs - -1. **`efp_human` regex** ✅ Already exists in bar_utils.py (line 125) - ```python - "efp_human": r"^(\d{6,7}(_[xsa])?_at)$|^(\D{0,12}\d{0,12})$|^(\d{1,12})$" - ``` - -2. **`efp` (generic) regex** ✅ Already exists in bar_utils.py (line 9) - ```python - "efp": ( - r"^([Aa][Tt][12345CM][Gg][0-9]{5})$" - r"|^([0-9]{6}(_[xsfi])?_at)$" - r"|^([0-9]{6,9})$" - r"|^(AFFX-(BioB|BioC|BioDn|CreX|DapX|LysX|PheX|ThrX|TrpnX)-(3|5|M)_at)$" - r"|^(AFFX-r2-(Bs|Ec|P1)-(dap|lys|phe|thr|bioB|bioC|bioD|cre)-(3|5|M)(_|_x_|_s_)at)$" - ) - ``` - ---- - -## Production Database Validation Steps - -### For Vincent: - -1. **Run the regexes against production BAR database** - - Validate gene IDs in `sample_data.data_probeset_id` column - - Check all 193 databases for ID format compliance - - Generate coverage report - -2. **Identify any edge cases or failures** - - Sample IDs that don't match regex patterns - - New ID formats not yet covered - - Per-database vs per-species mismatches (especially tomato) - -3. **Generate validation report** - - Which databases pass 100% validation - - Which databases have edge cases - - Recommendations for regex refinements - -### Expected Outputs: -- ✅ `efp_regex_audit_prod.csv` (already in repo) -- ✅ `db_regex_coverage_report.csv` (already in repo) -- 📊 New validation report from production scan - ---- - -## Files Ready for Production Use - -``` -api/utils/bar_utils.py - ├── EFP_PROJECT_REGEXES dict (lines 8-177) - └── is_efp_gene_valid() validator function - -api/utils/gene_id_utils.py - ├── DATABASE_EFP_PROJECT mapping - └── validate_gene_for_database() function - -data/efp_info/combined_master.json - └── Single source of truth for all database metadata -``` - ---- - -## Next Steps - -1. **Vincent:** Run production validation scan against all databases -2. **Vincent → Asher:** Consult on tomato database regex strategy (per-species vs per-database) -3. **Reena:** Once decision is made, update `DATABASE_EFP_PROJECT` mapping if needed -4. **Team:** Merge validated regex patterns into production codebase - ---- - -## Contact - -For questions about: -- **Regex patterns:** Reena Obmina (rmobmina@gmail.com) -- **Production validation:** Vincent -- **Architecture decision:** Asher - -**Generated:** June 25, 2026