diff --git a/api/models/efp_schemas.py b/api/models/efp_schemas.py index 4bcbdd2b..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"), @@ -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/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", + "data_signal": 4.03641, + "data_bot_id": "Mar_TB" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 5, + "data_probeset_id": "Acc24053.1", + "data_signal": 2.99612, + "data_bot_id": "Jan" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 12, + "data_probeset_id": "Acc19198.1", + "data_signal": 1.28844, + "data_bot_id": "Nov" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "Acc06107.1", + "data_signal": 0.428198, + "data_bot_id": "Apr" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 4, + "data_probeset_id": "Acc18350.1", + "data_signal": 4.16934, + "data_bot_id": "Feb" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 8, + "data_probeset_id": "Acc33448.1", + "data_signal": 1.79429, + "data_bot_id": "Jun" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 1, + "data_probeset_id": "Acc08927.1", + "data_signal": 2.33835, + "data_bot_id": "Apr" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 13, + "data_probeset_id": "Acc18447.1", + "data_signal": 0.0179441, + "data_bot_id": "Nov_TB" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 12, + "data_probeset_id": "Acc24973.1", + "data_signal": 3.48936, + "data_bot_id": "Nov" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 11, + "data_probeset_id": "Acc09777.1", + "data_signal": 0.0298628, + "data_bot_id": "May" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 11, + "data_probeset_id": "Acc09117.1", + "data_signal": 0.612542, + "data_bot_id": "May" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 7, + "data_probeset_id": "Acc02018.1", + "data_signal": 3.17797, + "data_bot_id": "Jul" + }, + { + "db": "actinidia_bud_development", + "proj_id": "1", + "sample_id": 8, + "data_probeset_id": "Acc14238.1", + "data_signal": 6.29684, + "data_bot_id": "Jun" + } +] \ No newline at end of file diff --git a/api/random_rows_json/actinidia_flower_fruit_development_test_data.json b/api/random_rows_json/actinidia_flower_fruit_development_test_data.json new file mode 100644 index 00000000..1288df55 --- /dev/null +++ b/api/random_rows_json/actinidia_flower_fruit_development_test_data.json @@ -0,0 +1,242 @@ +[ + { + "db": "actinidia_flower_fruit_development", + "proj_id": "1", + "sample_id": 4, + "data_probeset_id": "Acc09964.1", + "data_signal": 1.01904, + "data_bot_id": "Fruit_166_DAA" + }, + { + "db": "actinidia_flower_fruit_development", + "proj_id": "1", + "sample_id": 5, + "data_probeset_id": "Acc11080.1", + "data_signal": 0.0, + "data_bot_id": "Fruit_182_DAA" + }, + { + "db": "actinidia_flower_fruit_development", + "proj_id": "1", + "sample_id": 4, + "data_probeset_id": "Acc07661.1", + "data_signal": 6.3982, + "data_bot_id": "Fruit_166_DAA" + }, + { + "db": "actinidia_flower_fruit_development", + "proj_id": "1", + "sample_id": 8, + "data_probeset_id": "Acc15908.1", + "data_signal": 11.3977, + "data_bot_id": "Fruit_T2" + }, + { + "db": "actinidia_flower_fruit_development", + "proj_id": "1", + "sample_id": 6, + "data_probeset_id": "Acc11990.2", + "data_signal": 0.0, + "data_bot_id": "Fruit_224_DAA" + }, + { + "db": "actinidia_flower_fruit_development", + "proj_id": "1", + "sample_id": 7, + "data_probeset_id": "Acc15127.1", + "data_signal": 0.00812621, + "data_bot_id": "Fruit_T1" + }, + { + "db": "actinidia_flower_fruit_development", + "proj_id": "1", + "sample_id": 2, + "data_probeset_id": "Acc01084.1", + "data_signal": 0.0174041, + "data_bot_id": "Flower_bud" + }, + { + "db": "actinidia_flower_fruit_development", + "proj_id": "1", + "sample_id": 6, + "data_probeset_id": "Acc17398.1", + "data_signal": 0.0, + "data_bot_id": "Fruit_224_DAA" + }, + { + "db": "actinidia_flower_fruit_development", + "proj_id": "1", + "sample_id": 7, + "data_probeset_id": "Acc26364.1", + "data_signal": 0.687388, + "data_bot_id": "Fruit_T1" + }, + { + "db": "actinidia_flower_fruit_development", + "proj_id": "1", + "sample_id": 8, + "data_probeset_id": "Acc32192.1", + "data_signal": 0.328406, + "data_bot_id": "Fruit_T2" + }, + { + "db": "actinidia_flower_fruit_development", + "proj_id": "1", + "sample_id": 6, + "data_probeset_id": "Acc19552.1", + "data_signal": 21.2664, + "data_bot_id": "Fruit_224_DAA" + }, + { + "db": "actinidia_flower_fruit_development", + "proj_id": "1", + "sample_id": 5, + "data_probeset_id": "Acc00716.1", + "data_signal": 0.0239965, + "data_bot_id": "Fruit_182_DAA" + }, + { + "db": "actinidia_flower_fruit_development", + "proj_id": "1", + "sample_id": 7, + "data_probeset_id": "Acc00384.1", + "data_signal": 0.607365, + "data_bot_id": "Fruit_T1" + }, + { + "db": "actinidia_flower_fruit_development", + 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"data_probeset_id": "Acc15071.1", + "data_signal": 2.13413, + "data_bot_id": "Fruit_147_DAA" + } +] \ No newline at end of file diff --git a/api/random_rows_json/actinidia_postharvest_test_data.json b/api/random_rows_json/actinidia_postharvest_test_data.json new file mode 100644 index 00000000..5f5b73a6 --- /dev/null +++ b/api/random_rows_json/actinidia_postharvest_test_data.json @@ -0,0 +1,242 @@ +[ + { + "db": "actinidia_postharvest", + "proj_id": "1", + "sample_id": 7, + "data_probeset_id": "Acc27567.1", + "data_signal": 0.153958, + "data_bot_id": "Fruit_231_DAA_2DAH" + }, + { + "db": "actinidia_postharvest", + "proj_id": "1", + "sample_id": 2, + "data_probeset_id": "Acc05462.1", + "data_signal": 0.0, + "data_bot_id": "Fruit_166_DAA" + }, + { + "db": "actinidia_postharvest", + "proj_id": "1", + "sample_id": 5, + "data_probeset_id": "Acc17253.1", + "data_signal": 3.76794, + "data_bot_id": "Fruit_231_DAA" + }, + { + "db": "actinidia_postharvest", + "proj_id": "1", + "sample_id": 3, + 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index 00000000..12a6a812 --- /dev/null +++ b/api/random_rows_json/potato_stress_test_data.json @@ -0,0 +1,242 @@ +[ + { + "db": "potato_stress", + "sample_id": 8, + "proj_id": "1", + "data_probeset_id": "PGSC0003DMG400044115", + "data_signal": 0.0, + "data_bot_id": "BV_P_F" + }, + { + "db": "potato_stress", + "sample_id": 13, + "proj_id": "1", + "data_probeset_id": "PGSC0003DMG400037252", + "data_signal": 0.0, + "data_bot_id": "PE_BV_P_I" + }, + { + "db": "potato_stress", + "sample_id": 1, + "proj_id": "1", + "data_probeset_id": "PGSC0003DMG400046978", + "data_signal": 0.0, + "data_bot_id": "BV_A" + }, + { + "db": "potato_stress", + "sample_id": 11, + "proj_id": "1", + "data_probeset_id": "PGSC0003DMG400030510", + "data_signal": 1.79647, + "data_bot_id": "BV_P_M" + }, + { + "db": "potato_stress", + "sample_id": 12, + "proj_id": "1", + "data_probeset_id": "PGSC0003DMG400026715", + "data_signal": 44.2706, + "data_bot_id": "BV_Z" + }, + { + "db": "potato_stress", + "sample_id": 11, + 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"data_bot_id": "R3" + } +] \ No newline at end of file diff --git a/api/random_rows_json/rice_rma_test_data.json b/api/random_rows_json/rice_rma_test_data.json new file mode 100644 index 00000000..699d8a11 --- /dev/null +++ b/api/random_rows_json/rice_rma_test_data.json @@ -0,0 +1,332 @@ +[ + { + "db": "rice_rma", + "sample_id": 37, + "proj_id": "1", + "sample_file_name": "Seed_S3_Rep1.txt", + "data_probeset_id": "Os.12223.2.S1_at", + "data_signal": 8.46885, + "data_call": null, + "data_p_val": 0.0, + "data_bot_id": "Seed_S3_Rep1" + }, + { + "db": "rice_rma", + "sample_id": 33, + "proj_id": "1", + "sample_file_name": "Seed_S1_Rep3.txt", + "data_probeset_id": "Os.73.1.S1_at", + "data_signal": 8.46956, + "data_call": null, + "data_p_val": 0.0, + "data_bot_id": "Seed_S1_Rep3" + }, + { + "db": "rice_rma", + "sample_id": 1, + "proj_id": "1", + "sample_file_name": "Seedling_Root_Rep1.txt", + "data_probeset_id": "OsAffx.13653.1.S1_at", + "data_signal": 3.31508, + "data_call": null, + 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/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", + "sample_id": 22, + "data_probeset_id": "Glyma09g00346.2", + "data_signal": 4.45432, + "data_bot_id": "L_V-1" + }, + { + "db": "soybean_senescence", + "proj_id": "1", + "sample_id": 21, 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"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 d777e3e5..4f3cfe78 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 +32,24 @@ ) 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 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: - # 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/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 fcf75af1..210d6721 100644 --- a/api/utils/bar_utils.py +++ b/api/utils/bar_utils.py @@ -2,6 +2,46 @@ import redis import os +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"] + +# 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: @staticmethod @@ -43,41 +83,140 @@ 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.r3.1HG0000030 (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+)?)$", gene, re.I) + ) + + @staticmethod + def is_brachypodium_gene_valid(gene): + """Validates Brachypodium gene IDs: Bradi1g04930.1""" + return bool(gene and re.search(r"^Bradi\d+g\d+\.\d+$", 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+)$", gene)) + + @staticmethod + def is_camelina_gene_valid(gene): + """Validates Camelina gene IDs: Csa01g001040 (bare gene, BAR's own live example), + Csa01g012560.1, Csa00462s060.1 (with isoform suffix)""" + return bool(gene and re.search(r"^Csa\d+[gs]\d+(\.\d+)?$", gene, re.I)) + + @staticmethod + def is_cassava_gene_valid(gene): + """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 +227,7 @@ 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+)?$", gene, re.I): return True else: return False @@ -106,14 +245,18 @@ def is_cannabis_gene_valid(gene): @staticmethod def is_canola_gene_valid(gene): - """This function verifies if canola gene (BnaC07g42830D) is valid - :param gene: - :return: - """ - if re.search(r"^Bna[AC]\d{2}g\d{5}[A-D]?$", 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+)$", + gene, + re.I, + ) + ) @staticmethod def is_arachis_gene_valid(gene): @@ -128,14 +271,77 @@ def is_arachis_gene_valid(gene): @staticmethod def is_brassica_rapa_gene_valid(gene): - """This function verifies if Brassica rapa gene is valid: BraA01g000010 - :param gene: - :return: True if valid - """ - if gene and re.search(r"^BraA.{1,4}g\d{1,9}$", 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 +356,25 @@ 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 +483,40 @@ 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. + + 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 + """ + if BARUtils.is_injection_attempt(gene): + return False + 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..47f28013 100644 --- a/api/utils/gene_id_utils.py +++ b/api/utils/gene_id_utils.py @@ -1,50 +1,25 @@ -""" -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) +from api.utils.master_data_utils import load_combined_master -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)) +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") + } -# --------------------------------------------------------------------------- -# Database → species map -# --------------------------------------------------------------------------- +_PROBESET_RE = re.compile(r"^.+_at$", re.IGNORECASE) +_AROS_PROBESET_RE = re.compile(r"^A\d{6}_\d{2}$", re.IGNORECASE) +# 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 +46,29 @@ 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 +77,38 @@ 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 + "heterodera_schachtii": "arabidopsis", "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 +118,7 @@ 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 +128,6 @@ 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 +135,33 @@ 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 +178,18 @@ 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 +203,125 @@ 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 -} - - -# --------------------------------------------------------------------------- -# 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 +# 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() -# --------------------------------------------------------------------------- -# 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, + "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 + """ + 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) + 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/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/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/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", + "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": 18 + }, + "legacy_microarray_projinfo_minus_sample_file_name": { + "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", + "role": "value" + }, + "proj_id": { + "type": "varchar", + "role": "project" + }, + "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": 3 + }, + "legacy_microarray_projinfo_plus_sample_tissue": { + "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", + "role": "value" + }, + "proj_id": { + "type": "varchar", + "role": "project" + }, + "sample_file_name": { + "type": "varchar", + "role": "provenance" + }, + "sample_id": { + "type": "int", + "role": "row_id" + }, + "sample_tissue": { + "type": "varchar", + "role": "tissue" + } + } + }, + "proj_info": { + "columns": { + "proj_id": { + "role": "project" + }, + "proj_title": {}, + "proj_pi": {}, + "proj_res_area": {}, + "proj_num_samps": {} + } + } + }, + "assigned_databases": 3 + }, + "rnaseq_simple_plus_sample_file_name": { + "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_file_name": { + "type": "varchar", + "role": "provenance" + }, + "sample_id": { + "type": "int", + "role": "row_id" + } + } + } + }, + "assigned_databases": 3 + }, + "rnaseq_simple_plus_data_call_data_p_val_sample_file_name_sample_tissue": { + "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", + "role": "value" + }, + "proj_id": { + "type": "varchar", + "role": "project" + }, + "sample_file_name": { + "type": "varchar", + "role": "provenance" + }, + "sample_id": { + "type": "int", + "role": "row_id" + }, + "sample_tissue": { + "type": "varchar", + "role": "tissue" + } + } + } + }, + "assigned_databases": 5 + }, + "legacy_microarray_projinfo_plus_channel_minus_data_call_data_p_val": { + "tables": { + "sample_data": { + "columns": { + "channel": { + "type": "varchar", + "role": "channel" + }, + "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_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": 3 + }, + "rnaseq_simple_plus_data_call_data_p_val_sample_file_name": { + "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", + "role": "value" + }, + "proj_id": { + "type": "varchar", + "role": "project" + }, + "sample_file_name": { + "type": "varchar", + "role": "provenance" + }, + "sample_id": { + "type": "int", + "role": "row_id" + } + } + } + }, + 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"^(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})$|^([A-Za-z0-9][A-Za-z0-9._-]{0,39})$" + }, + "databases": { + "actinidia_bud_development": { + "species": "actinidia", + "instance_families": [ + "efp_actinidia" + ], + "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_actinidia", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_actinidia", + "view": "Bud Development" + } + ], + "views": { + "efp_actinidia::Bud Development": { + "frontend": "efp", + "instance": "efp_actinidia", + "display_name": "Bud 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"display_name": "Chemical", + "proj_ids": [], + "sample_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" + ] + } + }, + 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"RIKEN-GODA18AH", + "RIKEN-GODA18BH" + ] + } + } + } + }, + "efp_arabidopsis::Hormone": { + "frontend": "efp", + "instance": "efp_arabidopsis", + "display_name": "Hormone", + "proj_ids": [], + "sample_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" + ], + "BL_Treated_Mutant_at_1_Hour": [ + "RIKEN-GODA34A", + "RIKEN-GODA34B" + ] + } + }, + "Brassinolide_Mutant_at_3_Hours": { + "controls": [ + "RIKEN-GODA35A", + "RIKEN-GODA35B" + ], + "treatments": { + "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" + ], + "6-deoxocastasterone_Treated": [ + "RIKEN-GODA11A-6", + "RIKEN-GODA11B-6" + ], + "castasterone_Treated": [ + "RIKEN-GODA12A-6", + "RIKEN-GODA12B-6" + ], + "brassinolide_Treated": [ + "RIKEN-GODA13A-6", + "RIKEN-GODA13B-6" + ] + } + }, + "Cytokinin_on_Wild-Type": { + "controls": [ + "NO.10", + "NO.11", + "NO.12" + ], + "treatments": { + "Control_Wild-Type": [ + "NO.10", + "NO.11", + "NO.12" + ], + "t-zeatin_Treated_Wild-Type": [ + "NO.19-2", + "NO.20-2", + "NO.21-2" + ] + } + }, + "Cytokinin_on_ARR22_Overexpressed": { + "controls": [ + "NO.28", + "NO.29", + "NO.30" + ], + "treatments": { + "Control_ARR22_Overexpressed": [ + "NO.28", + "NO.29", + "NO.30" + ], + "t-zeatin_Treated_ARR22_Overexpressed": [ + "NO.31", + "NO.32", + "NO.33" + ] + } + }, + "ABA_during_Seed_Imbibtion": { + "controls": [ + "RIKEN-NAKABAYASHI2A", + "RIKEN-NAKABAYASHI2B" + ], + "treatments": { + "No_Treatment": [ + "RIKEN-NAKABAYASHI1A", + "RIKEN-NAKABAYASHI1B" + ], + "Treated_with_Water": [ + "RIKEN-NAKABAYASHI2A", 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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", + 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} + }, + "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" + ], + 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"display_name": "Biotic Stress Pseudomonas syringae", + "proj_ids": [], + "sample_groups": { + "Half_Leaf_Pseudomonas_syringae_at_4_Hours": { + "controls": [ + "2505", + "2795" + ], + "treatments": { + "Control_Half_Leaf_Pseudomonas_syringae_at_4_Hours": [ + "2505", + "2795" + ], + "Avirulent_Half_Leaf_Pseudomonas_syringae_at_4_Hours": [ + "2504", + "2796" + ], + "Virulent_Half_Leaf_Pseudomonas_syringae_at_4_Hours": [ + "2530", + "2797" + ] + } + }, + "Half_Leaf_Pseudomonas_syringae_at_8_Hours": { + "controls": [ + "2507", + "2792" + ], + "treatments": { + "Control_Half_Leaf_Pseudomonas_syringae_at_8_Hours": [ + "2507", + "2792" + ], + "Avirulent_Half_Leaf_Pseudomonas_syringae_at_8_Hours": [ + "2506", + "2793" + ], + "Virulent_Half_Leaf_Pseudomonas_syringae_at_8_Hours": [ + "2529", + "2794" + ] + } + }, + "Half_Leaf_Pseudomonas_syringae_at_16_Hours": { + "controls": [ + "2527", + "2789" + ], + "treatments": { + "Control_Half_Leaf_Pseudomonas_syringae_at_16_Hours": [ + "2527", + "2789" 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"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": { + "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" + ] + } + } + } + }, + "efp_arabidopsis::Abiotic Stress": { + "frontend": "efp", + "instance": "efp_arabidopsis", + "display_name": "Abiotic Stress", + "proj_ids": [], + "sample_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", + 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"UV-B_Root_0_Hour": [ + "AtGen_6_0021", + "AtGen_6_0022" + ], + "Wounding_Root_0_Hour": [ + "AtGen_6_0021", + "AtGen_6_0022" + ], + "Heat_Root_0_Hour": [ + "AtGen_6_0021", + "AtGen_6_0022" + ] + } + }, + "Shoot_After_15_Minutes": { + "controls": [ + "AtGen_6_0711", + "AtGen_6_0712" + ], + "treatments": { + "Control_Shoot_After_15_Minutes": [ + "AtGen_6_0711", + "AtGen_6_0712" + ], + "Drought_Shoot_After_15_Minutes": [ + "AtGen_6_4711", + "AtGen_6_4712" + ], + "UV-B_Shoot_After_15_Minutes": [ + "AtGen_6_7711", + "AtGen_6_7712" + ], + "Wounding_Shoot_After_15_Minutes": [ + "AtGen_6_8715", + "AtGen_6_8712" + ], + "Heat_Shoot_After_15_Minutes": [ + "AtGen_6_9711", + "AtGen_6_9712" + ] + } + }, + "Root_After_15_Minutes": { + "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": [ + 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"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" + ] + } + } + } + } + } + }, + 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], + "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" + ] + } + }, + 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"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", + "SP_CS_5_tpm", + "SP_CS_6_tpm" + ], + "l-sp-LSM": [ + "SP_LS_1_tpm", + "SP_LS_2_tpm", + "SP_LS_3_tpm", + "SP_LS_4_tpm", + "SP_LS_5_tpm", + "SP_LS_6_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" + ] + } + } + } + }, + "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", + 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"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", + 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+ "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": "Meristem Atlas" + } + ], + "views": { + "efp_cacao_sca::Meristem Atlas": { + "frontend": "efp", + "instance": "efp_cacao_sca", + "display_name": "Meristem Atlas", + "proj_ids": [], + "sample_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" + ], + 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+ "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" + ], + 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"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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"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 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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, + 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"Peduncle,_5DPA": [ + "ped_5DPA_R1", + "ped_5DPA_R2", + "ped_5DPA_R3" + ], + "Peduncle,_16DPA": [ + "ped_16DPA_R1", + "ped_16DPA_R2", + "ped_16DPA_R3" + ], + "Peduncle,_30DPA": [ + "ped_30DPA_R1", + "ped_30DPA_R2", + "ped_30DPA_R3" + ], + "Root_maturation_zone,_1st_leaf_stage": [ + "root_mat_R1", + "root_mat_R2", + "root_mat_R3" + ] + } + } + } + } + } + }, + "wheat": { + "species": "wheat", + "instance_families": [ + "efp_wheat", + "eplant_wheat" + ], + "source": "both", + "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": "Developmental Atlas" + }, + { + "frontend": "eplant", + "instance": "eplant_wheat", + "view": "MiddleStages" + }, + { + "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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"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", + 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"SS-Coleoptile": [ + "Sample_12", + "Sample_26", + "Sample_6A" + ], + "SS-Radicle": [ + "Sample_10", + "Sample_18", + "Sample_3A" + ], + "SS-1LBlade": [ + "Sample_13R1", + "Sample_23", + "Sample_32" + ], + "SS-1LSheath": [ + "Sample_10R1", + "Sample_21", + "Sample_30" + ], + "SS-SAM": [ + "Sample_19A", + "Sample_20A", + "Sample_21A" + ], + "SS-StemAxis": [ + "Sample_11", + "Sample_20", + "Sample_9A" + ], + "SS-Roots": [ + "Sample_13", + "Sample_18A", + "Sample_33" + ], + "ThirdLS-3LBlade": [ + "Sample_22B", + "Sample_23A", + "Sample_24A" + ], + "ThirdLS-3LSheath": [ + "Sample_25A", + "Sample_26A", + "Sample_27A" + ], + "ThirdLS-RAM": [ + "Sample_15", + "Sample_32R2", + "Sample_33A" + ], + "ThirdLS-Roots": [ + "Sample_28A", + "Sample_29A", + "Sample_30A" + ], + "ThirdLS-AxillaryRoots": [ + "Sample_16", + "Sample_35R1", + "Sample_36A" + ], + "FifthLS-5LSheath": [ + "Sample_37A", + "Sample_38A", + "Sample_39A" + ], + "FifthLS-5LBlade": [ + "Sample_40A", + "Sample_41A", + "Sample_42A" + ], 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+ "Med_CTRL" + ], + "treatments": { + "A-Anther": [ + "Sample_160A", + "Sample_161A", + "Sample_162A" + ], + "A-StigmaOvary": [ + "Sample_163A", + "Sample_164A", + "Sample_165A" + ], + "A-FLBladeNight": [ + "Sample_166A", + "Sample_167A", + "Sample_168A" + ], + "A-5LBladeNight": [ + "Sample_169A", + "Sample_170A", + "Sample_171A" + ], + "MGS-Grain": [ + "Sample_199A", + "Sample_200A", + "Sample_201A" + ], + "MGS-Awns": [ + "Sample_190A", + "Sample_191A", + "Sample_192A" + ], + "MGS-Lemma": [ + "Sample_196A", + "Sample_197A", + "Sample_198A" + ], + "MGS-Glumes": [ + "Sample_193A", + "Sample_194A", + "Sample_195A" + ], + "MGS-Peduncle": [ + "Sample_184A", + "Sample_185A", + "Sample_186A" + ], + "MGS-FLBlade": [ + "Sample_175A", + "Sample_176A", + "Sample_177A" + ], + "MGS-FLSheath": [ + "Sample_172A", + "Sample_173A", + "Sample_174A" + ], + "MGS-5LBladeSenescent": [ + "Sample_181A", + "Sample_182A", + "Sample_183A" + ], + "MGS-IN2": [ + "Sample_188B", + "Sample_189B" + ], + 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"gene_model", + "gene_id_namespace": null, + "regex_project": "efp_wheat", + "used_by": [ + { + "frontend": "efp", + "instance": "efp_wheat", + "view": "Wheat Abiotic Stress" + } + ], + "views": { + "efp_wheat::Wheat Abiotic Stress": { + "frontend": "efp", + "instance": "efp_wheat", + "display_name": "Wheat Abiotic Stress", + "proj_ids": [], + "sample_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": { + "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 Embryogenesis" + } + ], + "views": { + "efp_wheat::Wheat Embryogenesis": { + "frontend": "efp", + "instance": "efp_wheat", + "display_name": "Wheat Embryogenesis", + "proj_ids": [], + "sample_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": [ + 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], + "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" + ] + } + } + } + } + } + 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"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/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..7e21645e --- /dev/null +++ b/data/efp_info/efp_eplant_species_view_info.json @@ -0,0 +1,36376 @@ +{ + "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": { + 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"Circadian_experiment_-_plants_grown_under_12h_light-dark_cycle_and_constant_temperature,_then_sampled_under_continuous_light_and_constant_temperature,_44h": [ + "LL_LDHH_SH_44" + ] + } + }, + "LL_LDHH_AM_26": { + "controls": [ + "LL_LDHH_AM_26" + ], + "treatments": { + "Circadian_experiment_-_plants_grown_under_12h_light-dark_cycle_and_constant_temperature,_then_sampled_under_continuous_light_and_constant_temperature,_0h": [ + "LL_LDHH_AM_26" + ], + "Circadian_experiment_-_plants_grown_under_12h_light-dark_cycle_and_constant_temperature,_then_sampled_under_continuous_light_and_constant_temperature,_4h": [ + "LL_LDHH_AM_30" + ], + "Circadian_experiment_-_plants_grown_under_12h_light-dark_cycle_and_constant_temperature,_then_sampled_under_continuous_light_and_constant_temperature,_8h": [ + "LL_LDHH_AM_34" + ], + "Circadian_experiment_-_plants_grown_under_12h_light-dark_cycle_and_constant_temperature,_then_sampled_under_continuous_light_and_constant_temperature,_12h": [ + "LL_LDHH_AM_38" 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"Voss_1-9_27h_after-lateral-root-initiation_Rep1" + ], + "VossAndBennet_30h_after_bending": [ + "Voss_1-10_30h_after-lateral-root-initiation_Rep1", + "Voss_1-28_30h_after-lateral-root-initiation_Rep2", + "Voss_1-46_30h_after-lateral-root-initiation_Rep3", + "Voss_1-64_30h_after-lateral-root-initiation_Rep4" + ], + "VossAndBennet_33h_after_bending": [ + "Voss_1-11_33h_after-lateral-root-initiation_Rep1", + "Voss_1-29_33h_after-lateral-root-initiation_Rep2", + "Voss_1-47_33h_after-lateral-root-initiation_Rep3", + "Voss_1-65_33h_after-lateral-root-initiation_Rep4" + ], + "VossAndBennet_36h_after_bending": [ + "Voss_1-12_36h_after-lateral-root-initiation_Rep1", + "Voss_1-30_36h_after-lateral-root-initiation_Rep2", + "Voss_1-48_36h_after-lateral-root-initiation_Rep3", + "Voss_1-66_36h_after-lateral-root-initiation_Rep4" + ], + "VossAndBennet_39h_after_bending": [ + "Voss_1-13_39h_after-lateral-root-initiation_Rep1", + "Voss_1-31_39h_after-lateral-root-initiation_Rep2", + 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"Voss_1-35_51h_after-lateral-root-initiation_Rep2", + "Voss_1-53_51h_after-lateral-root-initiation_Rep3", + "Voss_1-71_51h_after-lateral-root-initiation_Rep4" + ], + "VossAndBennet_54h_after_bending": [ + "Voss_1-18_54h_after-lateral-root-initiation_Rep1", + "Voss_1-36_54h_after-lateral-root-initiation_Rep2", + "Voss_1-54_54h_after-lateral-root-initiation_Rep3", + "Voss_1-72_54h_after-lateral-root-initiation_Rep4" + ] + } + } + } + }, + { + "source": "efp", + "species": "arabidopsis", + "database": "meristem_db", + "view_name": "Regeneration", + "view_file": "Regeneration", + "groups": { + "0d_rep1;0d_rep2": { + "controls": [ + "0d_rep1", + "0d_rep2" + ], + "treatments": { + "Che_et_al.,_0_day_root_explants": [ + "0d_rep1", + "0d_rep2" + ], + "Che_et_al._expt,_2_days_CIM": [ + "2d_CIM_rep1", + "2d_CIM_rep2" + ], + "Che_et_al.,_4_days_CIM": [ + "4d_CIM_rep1", + "4d_CIM_rep2" + ], + "Che_et_al.,_7_days_CIM": [ + "7d_CIM_rep1", + "7d_CIM_rep2" + ], + "Che_el_al.,_10_days_CIM": [ + 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"Sugimoto_et_al.,_root_tissue_prior_to_callus-induction_treatment": [ + "GSM496071_d0", + "GSM496067_d0", + "GSM496076_d0", + "GSM496073_d0" + ], + "Sugimoto_et_al.,_root_derived_callus": [ + "GSM496067", + "GSM496076", + "GSM496073", + "GSM496071" + ] + } + }, + "GSM496084_d0;GSM496083_d0;GSM496082_d0;GSM496081_d0": { + "controls": [ + "GSM496084_d0", + "GSM496083_d0", + "GSM496082_d0", + "GSM496081_d0" + ], + "treatments": { + "Sugimoto_et_al.,_petal_tissue_prior_to_callus_induction": [ + "GSM496084_d0", + "GSM496083_d0", + "GSM496082_d0", + "GSM496081_d0" + ], + "Sugimoto_et_al.,_petal_derived_callus": [ + "GSM496084", + "GSM496083", + "GSM496082", + "GSM496081" + ] + } + }, + "GSM252663;GSM252664;GSM252665;GSM252666": { + "controls": [ + "GSM252663", + "GSM252664", + "GSM252665", + "GSM252666" + ], + "treatments": { + "Sena_et_al.,_130_mm_of_root_tip_(uncut_control)": [ + "GSM252663", + "GSM252664", + "GSM252665", + "GSM252666" + ], + 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"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" + ] + } + } + } + }, + { + "source": "eplant", + "project": "eplant_barley", + "species": "Hordeum_vulgare", + "family": "experiment", + "database": "barley_spike_meristem_v3", + "view_name": "Spike Meristem", + "view_folder": "SpikeMeristem", + "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": [ + 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"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", + 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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" + ], + "Leaf_-_Methyl_Jasmonate_6h": [ + "Leaf_JA_6h_rep1", + "Leaf_JA_6h_rep2", + "Leaf_JA_6h_rep3" + ], + "Leaf_-_Methyl_Jasmonate_24h": [ + "Leaf_JA_24h_rep1", + "Leaf_JA_24h_rep2", + "Leaf_JA_24h_rep3" + ], + "Leaf_-_Methyl_Jasmonate_168h": [ + "Leaf_JA_168h_rep1", + "Leaf_JA_168h_rep2", + "Leaf_JA_168h_rep3" + ], + "Leaf_-_Salt_1h": [ + "Leaf_NaCl_1h_rep1", + "Leaf_NaCl_1h_rep2", + "Leaf_NaCl_1h_rep3" + ], + "Leaf_-_Salt_6h": [ + "Leaf_NaCl_6h_rep1", + "Leaf_NaCl_6h_rep2", + "Leaf_NaCl_6h_rep3" + ], + "Leaf_-_Salt_24h": [ + "Leaf_NaCl_24h_rep1", + "Leaf_NaCl_24h_rep2", + "Leaf_NaCl_24h_rep3" + ], + "Leaf_-_Salt_168h": [ + "Leaf_NaCl_168h_rep1", + "Leaf_NaCl_168h_rep2", + "Leaf_NaCl_168h_rep3" + ] + } + }, + "Root": { + "controls": [ + "Root_Mock_rep1", + "Root_Mock_rep2", + "Root_Mock_rep3" + ], + "treatments": { + "Root_-_Control": [ + "Root_Mock_rep1", + "Root_Mock_rep2", + "Root_Mock_rep3" + ], + "Root_-_Phosphate_deficiency_6h": [ + "Root_Pidef_6h_rep1", + "Root_Pidef_6h_rep2", + "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" + ], + "Tree_6mo_-_Leaf_Young": [ + "YoungLeaf_SemiannualPlant_rep1", + "YoungLeaf_SemiannualPlant_rep2", + "YoungLeaf_SemiannualPlant_rep3" + ], + "Tree_6mo_-_Leaf_Adult": [ + "AdultLeaf_SemiannualPlant_rep1", + "AdultLeaf_SemiannualPlant_rep2", + "AdultLeaf_SemiannualPlant_rep3" + ], + "Tree_6mo_-_Root": [ + "Root_SemiannualPlant_rep1", + "Root_SemiannualPlant_rep2", + "Root_SemiannualPlant_rep3" + ], + "Tree_6mo_-_Apex": [ + "StemApex_SemiannualPlant_rep1", + "StemApex_SemiannualPlant_rep2", + "StemApex_SemiannualPlant_rep3" + ], + "Tree_6mo_-_Xylem": [ + "Xylem_SemiannualPlant_rep1", + "Xylem_SemiannualPlant_rep2", + "Xylem_SemiannualPlant_rep3" + ], + "Tree_6mo_-_Phloem": [ + "Phloem_SemiannualPlant_rep1", + "Phloem_SemiannualPlant_rep2", + "Phloem_SemiannualPlant_rep3" + ], + "Tree_3yo_-_Leaf_Young": [ + "YoungLeaf_3yPlant_rep1", + "YoungLeaf_3yPlant_rep2", + "YoungLeaf_3yPlant_rep3" + ], + "Tree_3yo_-_Leaf_Adult": [ + "AdultLeaf_3yPlant_rep1", + "AdultLeaf_3yPlant_rep2", + "AdultLeaf_3yPlant_rep3" + ], + "Tree_3yo_-_Flower": [ + "Flower_3yPlant_rep1", + "Flower_3yPlant_rep2", + "Flower_3yPlant_rep3" + ], + "Tree_3yo_-_Branch": [ + "LateralBranch_3yPlant_rep1", + "LateralBranch_3yPlant_rep2", + "LateralBranch_3yPlant_rep3" + ], + "Tree_3yo_-_Xylem": [ + "Xylem_3yPlant_rep2", + "Xylem_3yPlant_rep2", + "Xylem_3yPlant_rep2" + ], + "Tree_3yo_-_Phloem": [ + "Phloem_3yPlant_rep1", + "Phloem_3yPlant_rep2", + "Phloem_3yPlant_rep3" + ], + "Tree_6yo_-_Xylem": [ + "Xylem_6yPlant_rep2", + "Xylem_6yPlant_rep2", + "Xylem_6yPlant_rep2" + ], + "Tree_6yo_-_Phloem": [ + "Phloem_6yPlant_rep1", + "Phloem_6yPlant_rep2", + "Phloem_6yPlant_rep3" + ], + "Root_Induction_0h": [ + "StemBase_RootInduce_0h_rep1", + "StemBase_RootInduce_0h_rep2", + "StemBase_RootInduce_0h_rep3" + ], + "Root_Induction_1h": [ + "StemBase_RootInduce_1h_rep1", + "StemBase_RootInduce_1h_rep2", + "StemBase_RootInduce_1h_rep3" + ], + "Root_Induction_6h": [ + "StemBase_RootInduce_6h_rep1", + "StemBase_RootInduce_6h_rep2", + "StemBase_RootInduce_6h_rep3" + ], + "Root_Induction_24h": [ + "StemBase_RootInduce_24h_rep1", + "StemBase_RootInduce_24h_rep2", + "StemBase_RootInduce_24h_rep3" + ], + "Root_Induction_48h": [ + "StemBase_RootInduce_48h_rep1", + "StemBase_RootInduce_48h_rep2", + "StemBase_RootInduce_48h_rep3" + ], + "Root_Induction_72h": [ + "StemBase_RootInduce_72h_rep1", + "StemBase_RootInduce_72h_rep2", + "StemBase_RootInduce_72h_rep3" + ], + "Root_Induction_96h": [ + "StemBase_RootInduce_96h_rep1", + "StemBase_RootInduce_96h_rep2", + "StemBase_RootInduce_96h_rep3" + ], + "Root_Induction_7d": [ + "Root_AdventitiousRootInduce_168h_rep1", + "Root_AdventitiousRootInduce_168h_rep2", + "Root_AdventitiousRootInduce_168h_rep3" + ], + "Root_Induction_20d": [ + "Root_AdventitiousRootInduce_20d_rep1", + "Root_AdventitiousRootInduce_20d_rep2", + "Root_AdventitiousRootInduce_20d_rep3" + ] + } + } + } + } + ], + "eplant_rice": [ + { + "source": "eplant", + "project": "eplant_rice", + "species": "Oryza_sativa", + "family": "experiment", + "database": "rice_mas", + "view_name": "Anoxia", + "view_folder": "Anoxia", + "groups": { + "Aerobic_Coleoptile": { + "controls": [ + "RICE_CTRL" + ], + "treatments": { + "Aerobic_coleoptile": [ + "Aerobic_coleoptile_Rep1", + "Aerobic_coleoptile_Rep2" + ], + "Anoxic_coleoptile": [ + "Anoxic_coleoptile_Rep1", + "Anoxic_coleoptile_Rep2" + ] + } + } + } + }, + { + "source": "eplant", + "project": "eplant_rice", + "species": "Oryza_sativa", + "family": "experiment", + "database": "rice_mas", + "view_name": "Stigma", + "view_folder": "Stigma", + "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" + ] + } + } + } + }, + { + "source": "eplant", + "project": "eplant_rice", + "species": "Oryza_sativa", + "family": "experiment", + "database": "rice_mas", + "view_name": "Stress", + "view_folder": "Stress", + "groups": { + "Control_stress_Seedling": { + "controls": [ + "RICE_CTRL_STRESS", + "RICE_CTRL_STRESS", + "RICE_CTRL_STRESS" + ], + "treatments": { + "Control_Shoot": [ + "RICE_CTRL_STRESS", + "RICE_CTRL_STRESS", + "RICE_CTRL_STRESS" + ], + "Control_Root": [ + "RICE_CTRL_STRESS", + "RICE_CTRL_STRESS", + "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", + "Salt_stress_rep2", + "Salt_stress_rep3" + ] + } + }, + "Cold_stress_Seedling": { + "controls": [ + "RICE_CTRL_STRESS", + "RICE_CTRL_STRESS", + 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"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": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - "Drought_Root_0_Hour": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - "Genotoxic_Root_0_Hour": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - "Oxidative_Root_0_Hour": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - "UV-B_Root_0_Hour": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - "Wounding_Root_0_Hour": [ - "AtGen_6_0021", - "AtGen_6_0022" - ], - "Heat_Root_0_Hour": [ - "AtGen_6_0021", - "AtGen_6_0022" - ] - } - }, - "Shoot_After_15_Minutes": { - "controls": [ - "AtGen_6_0711", - "AtGen_6_0712" - ], - "treatments": { - 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- "AtGen_C-16_1-Pi-24_REP1_ATH1", - "AtGen_C-17_2-Pi-24_REP2_ATH1", - "AtGen_C-18_3-Pi-24_REP3_ATH1" - ] - } - }, - "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_E.o._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_E.o._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_E.o._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_E.o._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_E.o._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_E.o._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_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 WT 03D UNINFECTED", - "JD AT+EO COL WT EXP2 03D UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 3D" - ], - "treatments": { - "Control_E.o._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_E.o._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_E.o._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_E.o._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_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", - 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"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", - 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"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" - ], - 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{ - "Control_series_-_plants_grown_in_constant_dark_but_with_a_temperature_cycle_applied._Samples_taken_in_constant_dark_and_temperature,_0h": [ - "DD_DDHC_00" - ], - "Control_series_-_plants_grown_in_constant_dark_but_with_a_temperature_cycle_applied._Samples_taken_in_constant_dark_and_temperature,_4h": [ - "DD_DDHC_04" - ], - "Control_series_-_plants_grown_in_constant_dark_but_with_a_temperature_cycle_applied._Samples_taken_in_constant_dark_and_temperature,_8h": [ - "DD_DDHC_08" - ], - "Control_series_-_plants_grown_in_constant_dark_but_with_a_temperature_cycle_applied._Samples_taken_in_constant_dark_and_temperature,_12h": [ - "DD_DDHC_12" - ], - "Control_series_-_plants_grown_in_constant_dark_but_with_a_temperature_cycle_applied._Samples_taken_in_constant_dark_and_temperature,_16h": [ - "DD_DDHC_16" - ], - "Control_series_-_plants_grown_in_constant_dark_but_with_a_temperature_cycle_applied._Samples_taken_in_constant_dark_and_temperature,_20h": [ - "DD_DDHC_20" - ], - 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"Bay-0_(CS6608)_from_Bayreuth,_Germany._Longitude/Latitude/Elevation:_E11/N50_at_~300m.": [ - "ATGE_111_A", - "ATGE_111_B", - "ATGE_111_C" - ], - "C24_(CS906)_from_unknown.": [ - "ATGE_112_A", - "ATGE_112_C", - "ATGE_112_D" - ], - "Col-0_(N1092)_from_Columbia,_Missouri,_USA._Longitude/Latitude/Elevation:_W93/N38_at_1-100m._Temp_in_C_(Spr/Aut):15-16/21-2,_Precipitation_in_mm_(Spr/Aut):60-70/30-40.": [ - "ATGE_113_A", - "ATGE_113_C", - "ATGE_113_D" - ], - "Cvi-1_(CS8580)_from_Cape_Verde_Islands._Longitude/Latitude/Elevation:_W24/N16_at_1-100m.": [ - "ATGE_114_A", - "ATGE_114_B", - "ATGE_114_C" - ], - "Est_(CS6173)_from_Estonia._Longitude/Latitude/Elevation:_E25/N59_at_100-200m.": [ - "ATGE_115_A", - "ATGE_115_B", - "ATGE_115_D" - ], - "Kin-0_(CS6755)_from_Kindalville,_Michigan,_USA._Longitude/Latitude/Elevation:_W85/N43_at_200-300m.": [ - "ATGE_116_A", - "ATGE_116_B", - "ATGE_116_C" - ], - "Ler-2_(CS8581)_from_Landsberg,_Germany._Longitude/Latitude/Elevation:_E15/N53_at_100-200m.": [ - "ATGE_117_B", - "ATGE_117_C", - "ATGE_117_D" - ], - "Nd-1_(CS1636)_from_Niederzenz,_Germany._Longitude/Latitude/Elevation:_at_200-300m._Temp_in_C_(Spr/Aut):5-6/9-10,_Precipitation_in_mm_(Spr/Aut):20-30/30-40.": [ - "ATGE_118_A", - "ATGE_118_B", - "ATGE_118_C" - ], - "Sha_(CS6180)_from_Pamiro-Alay,_Tajikistan._Longitude/Latitude/Elevation:_E71/N39_at_3400m.": [ - "ATGE_119_A", - "ATGE_119_C", - "ATGE_119_D" - ], - "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.": [ - "ATGE_129_A" - ], - "Er-0_(CS6698)_from_Erlangen,_Germany._Longitude/Latitude/Elevation:_E11/N49_at_200-300m._Temp_in_C_(Spr/Aut):5-6/9-10,_Precipitation_in_mm_(Spr/Aut):30-40/30-40.": [ - "ATGE_130_A" - ], - "Fr-2_(CS6708)_from_Frankfurt,_Germany._Longitude/Latitude/Elevation:_E8/N50_at_0-100m._Temp_in_C_(Spr/Aut):7-8/9-10,_Precipitation_in_mm_(Spr/Aut):20-30/30-40.": [ - "ATGE_131_A" - ], - "GOT1_(CS22277)_from_Goettingen,_Germany._Longitude/Latitude:_E10/N51.": [ - "ATGE_132_A" - ], - "HR-5_(CS22205)_from_United_Kingdom.": [ - "ATGE_133_A" 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"treatments": { - "AtHB8": [ - "GSM706472", - "GSM706473", - "GSM706474" - ] - } - } - } - } - } - } - }, - "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" - ] - } - } - } - } - } - } - }, - "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": [ 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"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" - ], - 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"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", - "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" - ] - } - } - } - } - } - } - }, - "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": [ - "MAIZE_CTRL" - ], - "treatments": { - "Base": [ - "Base" - ], - "-1_from_ligule": [ - "Ligule+4" - ], - "+4_from_ligule": [ - "Ligule+9" - ], - "-1_from_tip": [ - "Tip_-1" - ] - } - }, - "LCM_ME_vs_BS_at_tip": { - "controls": [ - "MAIZE_CTRL" - ], - "treatments": { - "Tip_BS": [ - "Tip_BS" - ], - "Tip_ME": [ - "Tip_ME" - ] - } - } - } - }, - "maize_leaf_gradient": { - "database": "maize_leaf_gradient", - "view_name": "maize_leaf_gradient", - "groups": { - "Maize_Leaf_Gradient": { - "controls": [ - "MAIZE_CTRL" - ], - "treatments": { - "M1": [ - "M1" - ], - "M2": [ - "M2" - ], - "M3": [ - "M3" - ], - "M4": [ - "M4" - ], - "M5": [ - "M5" - ], - "M6": [ - "M6" - ], - "M7": [ - "M7" - ], - "M8": [ - "M8" - ], - "M9": [ - "M9" - ], - "M10": [ - "M10" - ], - "M11": [ - "M11" - ], - "M12": [ - "M12" - ], - "M13": [ - "M13" - ], - "M14": [ - "M14" - ], - "M15": [ - "M15" - ] - } - } - } - }, - "maize_rice_comparison": { - "database": "maize_rice_comparison", - "view_name": "maize_rice_comparison", - "groups": { - "Maize_Leaf_Gradient": { - "controls": [ - "MAIZE_CTRL" - ], - "treatments": { - "M1": [ - "M1" - ], - "M2": [ - "M2" - ], - "M3": [ - "M3" - ], - "M4": [ - "M4" - ], - "M5": [ - "M5" - ], - "M6": [ - "M6" - ], - "M7": [ - "M7" - ], - "M8": [ - "M8" - ], - "M9": [ - "M9" - ], - "M10": [ - "M10" - ], - "M11": [ - "M11" - ], - "M12": [ - "M12" - ], - "M13": [ - "M13" - ], - "M14": [ - "M14" - ], - "M15": [ - "M15" - ] - } - }, - "Rice": { - "controls": [ - "RICE_CTRL" - ], - "treatments": { - "R1": [ - "R1" - ], - "R2": [ - "R2" - ], - "R3": [ - "R3" - ], - "R4": [ - "R4" - ], - "R5": [ - "R5" - ], - "R6": [ - "R6" - ], - "R7": [ - "R7" - ], - "R8": [ - "R8" - ], - "R9": [ - "R9" - ], - "R10": [ - "R10" - ], - "R11": [ - "R11" - ] - } - } - } - } - } - } - }, - "mangosteen": { - - "data": { - "species": "mangosteen", - "views": { - "Aril_vs_Rind": { - "database": "mangosteen_aril_vs_rind", - "view_name": "Aril_vs_Rind", - "groups": { - "Med_CTRL": { - "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": 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"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", - "Nod4d_rep3" - ], - "Nodule_10d": [ - "Nod10d_rep1", - "Nod10d_rep2", - "Nod10d_rep3" - ], - "Nodule_14d": [ - "Nod14d_rep1", - "Nod14d_rep2", - "Nod14d_rep3" - ], - "Nodule_Mature_(4w)": [ - "Nodule_rep1", - "Nodule_rep2", - "Nodule_rep3" - ] - } - }, - "Pod": { - "controls": [ - "MED_CTRL", - "MED_CTRL" - ], - "treatments": { - "Pod": [ - "Pod_rep1", - "Pod_rep2", - "Pod_rep3" - ] - } - }, - "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" - ] - } - } - } - }, - "medicago_rma": { - "database": "medicago_rma", - "view_name": 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"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" - ], - 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"InflorescenceP6_Rep2", - "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" - ] - } - } - } - }, - "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" - ] - } - } - } - }, - "riceanoxia_rma": { - "database": "rice_rma", - "view_name": "riceanoxia_rma", - "groups": { - "Coleoptile": { - "controls": [ 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"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" - ] - } - } - } - }, - "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": [ 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"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", - "Salt_stress_rep2", - "Salt_stress_rep3" - ] - } - }, - "Cold_stress_Seedling": { - "controls": [ - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS" - ], - "treatments": { - "Cold_Shoot": [ - "Cold_stress_rep1", - "Cold_stress_rep2", - "Cold_stress_rep3" - ], - "Cold_Root": [ - "Cold_stress_rep1", - "Cold_stress_rep2", - "Cold_stress_rep3" - ] - } - } - } - } - } - } - }, - "soybean": { - - "data": { - "species": "soybean", - "views": { - "soybean": { - "database": "soybean", - "view_name": "soybean", - "groups": { - "Root_Hair_12HAI": { - "controls": [ - "Roothair_12HAImock" - ], - "treatments": { - "Root_Hair_12HAI": [ - "Roothair_12HAI" - ], - "Roothair_12HAImock": [ - "Roothair_12HAImock" - ] - } - }, - "Root_Hair_24HAI": { - "controls": [ - "Roothair_24HAImock" - ], - "treatments": { - "Root_Hair_24_HAI": [ - "Roothair_24HAI" - ], - "Roothair_24HAImock": [ - "Roothair_24HAImock" - ] - } - }, - "Root_Hair_48HAI": { - "controls": [ - "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" - ] - } - } - } - }, - "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" - ] - } - } - } - }, - "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" - ] - } - } - } - }, - "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" - ], - "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" - ], - "Carpel,_stage_10": [ - "Carpel_10_A", - "Carpel_10_B" - ], - "Carpel,_stage_12": [ - "Carpel_12_A", - "Carpel_12_B" - ], - "Carpel,_stages_7-8": [ - "Carpel_7-8_A", - "Carpel_7-8_B" - ], - "Carpel,_stage_9": [ - "Carpel_9_A", - "Carpel_9_B" - 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"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" - ], - 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"controls": [ - "AtGen_6_0711", - "AtGen_6_0712" - ], - "treatments": { - "Control_Shoot_After_15_Minutes": [ - "AtGen_6_0711", - "AtGen_6_0712" - ], - "Drought_Shoot_After_15_Minutes": [ - "AtGen_6_4711", - "AtGen_6_4712" - ], - "UV-B_Shoot_After_15_Minutes": [ - "AtGen_6_7711", - "AtGen_6_7712" - ], - "Wounding_Shoot_After_15_Minutes": [ - "AtGen_6_8715", - "AtGen_6_8712" - ], - "Heat_Shoot_After_15_Minutes": [ - "AtGen_6_9711", - "AtGen_6_9712" - ] - } - }, - "Root_After_15_Minutes": { - "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": 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], - "Drought_Shoot_After_6_Hours": [ - "AtGen_6_4411", - "AtGen_6_4412" - ], - "Genotoxic_Shoot_After_6_Hours": [ - "AtGen_6_5411", - "AtGen_6_5412" - ], - "Oxidative_Shoot_After_6_Hours": [ - "AtGen_6_6411", - "AtGen_6_6412" - ], - "UV-B_Shoot_After_6_Hours": [ - "AtGen_6_7411", - "AtGen_6_7412" - ], - "Wounding_Shoot_After_6_Hours": [ - "AtGen_6_8411", - "AtGen_6_8412" - ], - "Heat_Shoot_After_6_Hours": [ - "AtGen_6_9411", - "AtGen_6_9412" - ] - } - }, - "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", - "AtGen_6_0512" - ], - "Cold_Shoot_After_12_Hours": [ - "AtGen_6_1511", - "AtGen_6_1512" - ], - "Osmotic_Shoot_After_12_Hours": [ - "AtGen_6_2511", - "AtGen_6_2512" - ], - "Salt_Shoot_After_12_Hours": [ - "AtGen_6_3511", - "AtGen_6_3512" - ], - "Drought_Shoot_After_12_Hours": [ - "AtGen_6_4511", - "AtGen_6_4512" - ], - "Genotoxic_Shoot_After_12_Hours": [ - "AtGen_6_5511", - "AtGen_6_5512" - ], - "Oxidative_Shoot_After_12_Hours": [ - "AtGen_6_6511", - "AtGen_6_6512" - ], - "UV-B_Shoot_After_12_Hours": [ - "AtGen_6_7511", - "AtGen_6_7512" - ], - "Wounding_Shoot_After_12_Hours": [ - "AtGen_6_8511", - "AtGen_6_8512" - ], - "Heat_Shoot_After_12_Hours": [ - "AtGen_6_9511", - "AtGen_6_9512" - ] - } - }, - "Root_After_12_Hours": { - "controls": [ - "AtGen_6_0521", - "AtGen_6_0522" - ], - "treatments": { - "Control_Root_After_12_Hours": [ - "AtGen_6_0521", - "AtGen_6_0522" - ], - "Cold_Root_After_12_Hours": [ - "AtGen_6_1521", - "AtGen_6_1522" - ], - "Osmotic_Root_After_12_Hours": [ - "AtGen_6_2521", - "AtGen_6_2522" - ], - "Salt_Root_After_12_Hours": [ - "AtGen_6_3521", - "AtGen_6_3522" - ], - "Drought_Root_After_12_Hours": [ - "AtGen_6_4521", - "AtGen_6_4522" - ], - "Genotoxic_Root_After_12_Hours": [ - "AtGen_6_5521", - "AtGen_6_5522" - ], - "Oxidative_Root_After_12_Hours": [ - "AtGen_6_6523", - "AtGen_6_6524" - ], - "UV-B_Root_After_12_Hours": [ - "AtGen_6_7521", - "AtGen_6_7522" - ], - "Wounding_Root_After_12_Hours": [ - "AtGen_6_8524", - "AtGen_6_8525" - ], - "Heat_Root_After_12_Hours": [ - "AtGen_6_9521", - "AtGen_6_9522" - ] - } - }, - "Shoot_After_24_Hours": { - "controls": [ - "AtGen_6_0611", - "AtGen_6_0612" - ], - "treatments": { - "Control_Shoot_After_24_Hours": [ - "AtGen_6_0611", - "AtGen_6_0612" - ], - "Cold_Shoot_After_24_Hours": [ - "AtGen_6_1611", - "AtGen_6_1612" - ], - "Osmotic_Shoot_After_24_Hours": [ - "AtGen_6_2611", - "AtGen_6_2612" - ], - "Salt_Shoot_After_24_Hours": [ - "AtGen_6_3611", - "AtGen_6_3612" - ], - "Drought_Shoot_After_24_Hours": [ - "AtGen_6_4611", - "AtGen_6_4612" - ], - "Genotoxic_Shoot_After_24_Hours": [ - "AtGen_6_5611", - "AtGen_6_5612" - ], - "Oxidative_Shoot_After_24_Hours": [ - "AtGen_6_6611", - "AtGen_6_6612" - ], - "UV-B_Shoot_After_24_Hours": [ - "AtGen_6_7611", - "AtGen_6_7612" - ], - "Wounding_Shoot_After_24_Hours": [ - "AtGen_6_8611", - "AtGen_6_8612" - ], - "Heat_Shoot_After_24_Hours": [ - "AtGen_6_9611", - "AtGen_6_9612" - ] - } - }, - "Root_After_24_Hours": { - "controls": [ - "AtGen_6_0621", - "AtGen_6_0622" - ], - "treatments": { - "Control_Root_After_24_Hours": [ - "AtGen_6_0621", - "AtGen_6_0622" - ], - "Cold_Root_After_24_Hours": [ - "AtGen_6_1621", - "AtGen_6_1622" - ], - "Osmotic_Root_After_24_Hours": [ - "AtGen_6_2621", - "AtGen_6_2622" - ], - "Salt_Root_After_24_Hours": [ - "AtGen_6_3621", - "AtGen_6_3622" - ], - "Drought_Root_After_24_Hours": [ - "AtGen_6_4621", - "AtGen_6_4622" - ], - "Genotoxic_Root_After_24_Hours": [ - "AtGen_6_5621", - "AtGen_6_5622" - ], - "Oxidative_Root_After_24_Hours": [ - "AtGen_6_6621", - "AtGen_6_6625" - ], - "UV-B_Root_After_24_Hours": [ - "AtGen_6_7621", - "AtGen_6_7622" - ], - "Wounding_Root_After_24_Hours": [ - "AtGen_6_8621", - "AtGen_6_8622" - ], - "Heat_Root_After_24_Hours": [ - "AtGen_6_9621", - "AtGen_6_9622" - ] - } - } - }, - "data_type": "Microarray" - }, - "Abiotic_Stress_II": { - "database": "atgenexp_stress", - "view_name": "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" - ] - } - } - }, - "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" - ], - "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": [ - "AtGen_A-29_27-1_REP1_ATH1", - "AtGen_A-30_27-2_REP2_ATH1", - "AtGen_A-31-27-3_REP3_ATH1" - ], - 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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_E.o._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_E.o._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_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 WT 03D UNINFECTED", - "JD AT+EO COL WT EXP2 03D UNINFECTED", - "JD AT+EO TIME EXP3 UNINF 3D" - ], - "treatments": { - "Control_E.o._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_E.o._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_E.o._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_E.o._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_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": [ - "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" - ], - "BL_Treated_Mutant_at_1_Hour": [ - "RIKEN-GODA34A", - 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"4_d_darkness_then_4_h_continuous_blue_light": [ - "AtGen_D-5_1-BL_REP1_ATH1", - "AtGen_D-21_2-BL_REP2_ATH1", - "AtGen_D-37_3-BL_REP3_ATH1" - ], - "4_d_darkness_then_4_h_continuous_white_light": [ - "AtGen_D-8_1-WL_REP1_ATH1", - "AtGen_D-24_2-WL_REP2_ATH1", - "AtGen_D-40_3-WL_REP3_ATH1" - ], - "dark_control_4h": [ - "AtGen_D-33_3-DL_REP3_ATH1", - "AtGen_D-1_1-DL_REP1_ATH1", - "AtGen_D-17_2-DL_REP2_ATH1" - ] - } - } - }, - "data_type": "Microarray" - }, - "Natural_Variation": { - "database": "arabidopsis_ecotypes", - "view_name": "Natural_Variation", - "groups": { - "Natural_Variation_Set": { - "controls": [ - "ATGE_113_A", - "ATGE_113_C", - "ATGE_113_D" - ], - "treatments": { - "Bay-0_(CS6608)_from_Bayreuth,_Germany._Longitude/Latitude/Elevation:_E11/N50_at_~300m.": [ - "ATGE_111_A", - "ATGE_111_B", - "ATGE_111_C" - ], - "C24_(CS906)_from_unknown.": [ - "ATGE_112_A", - "ATGE_112_C", - "ATGE_112_D" - ], - 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"ATGE_118_B", - "ATGE_118_C" - ], - "Sha_(CS6180)_from_Pamiro-Alay,_Tajikistan._Longitude/Latitude/Elevation:_E71/N39_at_3400m.": [ - "ATGE_119_A", - "ATGE_119_C", - "ATGE_119_D" - ], - "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.": [ - "ATGE_129_A" - ], - "Er-0_(CS6698)_from_Erlangen,_Germany._Longitude/Latitude/Elevation:_E11/N49_at_200-300m._Temp_in_C_(Spr/Aut):5-6/9-10,_Precipitation_in_mm_(Spr/Aut):30-40/30-40.": [ - "ATGE_130_A" - ], - "Fr-2_(CS6708)_from_Frankfurt,_Germany._Longitude/Latitude/Elevation:_E8/N50_at_0-100m._Temp_in_C_(Spr/Aut):7-8/9-10,_Precipitation_in_mm_(Spr/Aut):20-30/30-40.": [ - "ATGE_131_A" - ], - "GOT1_(CS22277)_from_Goettingen,_Germany._Longitude/Latitude:_E10/N51.": [ - "ATGE_132_A" - ], - "HR-5_(CS22205)_from_United_Kingdom.": [ - "ATGE_133_A" - ], - "Is-0_(CS6741)_from_Isenburg,_Germany._Longitude/Latitude/Elevation:_E7/N50_at_100-200m._Temp_in_C_(Spr/Aut):7-8/11-12.": [ - "ATGE_134_A" - ], - "Li-2:1_(CS6772)_from_Limburg,_Germany._Longitude/Latitude/Elevation:_E8/N50_at_100-200m._Temp_in_C_(Spr/Aut):3-4/9-10,_Precipitation_in_mm_(Spr/Aut):30-40/30-40.": [ - "ATGE_136_A" - ], - "M7323S_(CS6184)_from_unknown.": [ - "ATGE_141_A" - ], - "MS-0_(CS6797)_from_Moscow,_Russia.": [ - "ATGE_142_A" - ], - "NFE1_(CS22163)_from_United_Kingdom.": [ - "ATGE_138_A" - ], - "Nok-1_(CS6808)_from_Noordwijk,_Netherlands._Longitude/Latitude/Elevation:_E4/N52_at_0-100m._Temp_in_C_(Spr/Aut):3-4/13-14.": [ - "ATGE_139_A" - ], - "Nw-1_(CS6812)_from_Neuweilnau,_Germany._Longitude/Latitude/Elevation:_E8/N50_at_100-200m._Temp_in_C_(Spr/Aut):5-6/9-10.": [ - "ATGE_140_A" - ], - "Old-2_(CS6821)_from_Oldenburg,_Germany._Longitude/Latitude/Elevation:_E8/N53_at_1-100m.": [ - "ATGE_144_A" - ], - "Ove-0_(CS6823)_from_Ovelgoenne,_Germany._Longitude/Latitude/Elevation:_E8/N53_at_1-100m._Temp_in_C_(Spr/Aut):5-6/9-10.": [ - "ATGE_145_A" - ], - 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"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" - ], 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"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", - "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" - ], - 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{ - "Aril_vs_Rind": { - "database": "mangosteen_aril_vs_rind", - "view_name": "Aril_vs_Rind", - "groups": { - "Med_CTRL": { - "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" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "Callus": { - "database": "mangosteen_callus", - "view_name": "Callus", - "groups": { - "Med_CTRL": { - "controls": [ - "Med_CTRL" - ], - "treatments": { - "Non-embryogenic": [ - "NE" - ], - "Somatic_embryogenic": [ - "SM" - ] - } - } - }, - "data_type": "RNA-Seq" - }, - "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_": [ - 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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" - ], - "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", - "Salt_stress_rep2", - "Salt_stress_rep3" - ] - } - }, - "Cold_stress_Seedling": { - "controls": [ - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS" - ], - "treatments": { - "Cold_Shoot": [ - "Cold_stress_rep1", - "Cold_stress_rep2", - "Cold_stress_rep3" - ], - "Cold_Root": [ - "Cold_stress_rep1", - "Cold_stress_rep2", - "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", - "Salt_stress_rep2", - "Salt_stress_rep3" - ] - } - }, - "Cold_stress_Seedling": { - "controls": [ - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS", - "RICE_CTRL_STRESS" - ], - "treatments": { - "Cold_Shoot": [ - "Cold_stress_rep1", - "Cold_stress_rep2", - "Cold_stress_rep3" - ], - "Cold_Root": [ - "Cold_stress_rep1", - "Cold_stress_rep2", - "Cold_stress_rep3" - ] - } - } - }, - "data_type": "Microarray" - } - } - } - }, - "soybean": { - "data": { - "species": "soybean", - "views": { - "soybean": { - "database": "soybean", - "view_name": "soybean", - "groups": { - "Root_Hair_12HAI": { - "controls": [ - "Roothair_12HAImock" - ], - "treatments": { - "Root_Hair_12HAI": [ - "Roothair_12HAI" - ], - "Roothair_12HAImock": [ - "Roothair_12HAImock" - ] - } - }, - "Root_Hair_24HAI": { - "controls": [ - "Roothair_24HAImock" - ], - "treatments": { - "Root_Hair_24_HAI": [ - "Roothair_24HAI" - ], - "Roothair_24HAImock": [ - "Roothair_24HAImock" - ] - } - }, - "Root_Hair_48HAI": { - "controls": [ - "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" - ], 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"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": [ - 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"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 new file mode 100644 index 00000000..26185300 --- /dev/null +++ b/data/efp_info/master_db_list.json @@ -0,0 +1,3809 @@ +{ + "actinidia": { + "actinidia_bud_development": { + "source": "efp", + "platform": "rna_seq", + "views": { + "efp_actinidia": [ + "Bud Development" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + }, + "actinidia_flower_fruit_development": { + "source": "efp", + "platform": "rna_seq", + "views": { + "efp_actinidia": [ + "Flower Fruit Development" + ] + }, + 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"tomato_root": { + "source": "eplant", + "platform": "rna_seq", + "views": { + "eplant_tomato": [ + "Root" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + }, + "tomato_root_field_pot": { + "source": "eplant", + "platform": "rna_seq", + "views": { + "eplant_tomato": [ + "RootFieldPot" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + }, + "tomato_s_pennellii": { + "source": "both", + "platform": "rna_seq", + "views": { + "efp_tomato": [ + "M82 S pennellii Atlases Koenig et al" + ], + "eplant_tomato": [ + "TomatoAtlases" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + }, + "proj_id_breakdown": { + "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" + ] + } + } + } + }, + "tomato_seed": { + "source": "efp", + "platform": "rna_seq", + "views": { + "efp_tomato": [ + "SEED Lab Angers" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + }, + "tomato_shade_mutants": { + "source": "efp", + "platform": "rna_seq", + "views": { + "efp_tomato": [ + "Shade Mutants" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + }, + "tomato_shade_timecourse": { + "source": "efp", + "platform": "rna_seq", + "views": { + "efp_tomato": [ + "Shade Timecourse WT" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + }, + "tomato_trait": { + "source": "legacy_not_in_dropdown", + "platform": "rna_seq", + "views": {}, + "validation": { + "n_samples": 16, + "n_pass": 16, + "n_fail": 0 + } + } + }, + "triphysaria": { + "triphysaria": { + "source": "efp", + "platform": "rna_seq", + "views": { + "efp_triphysaria": [ + "Triphysaria" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + } + }, + "triticale": { + "triticale": { + "source": "efp", + "platform": "microarray", + "views": { + "efp_triticale": [ + "triticale" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + }, + "triticale_mas": { + "source": "efp", + "platform": "microarray", + "views": { + "efp_triticale": [ + "triticale mas" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + } + }, + "tung_tree": { + "tung_tree": { + "source": "efp", + "platform": "rna_seq", + "views": { + "efp_tung_tree": [ + "Tung Tree" + ] + }, + "validation": { + "n_samples": 30, + "n_pass": 30, + "n_fail": 0 + } + } + }, + "wheat": { + "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 + } + } + } +} 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" + ], + "frontends": [ + "eplant_eucalyptus" + ], + "serves_eplant": true + }, + "efp_euphorbia": { + "regex": "^(Ep_chr\\d_g\\d{1,8})$", + "n_databases": 1, + "databases": [ + "euphorbia" + ], + "frontends": [ + "efp_euphorbia" + ], + "serves_eplant": false + }, + "efp_eutrema": { + "regex": "^(Thhalv[0-9]{8}m\\.g)$|^(XLOC_[0-9]{6})$|^(nXLOC_[0-9]{6})$|^(At[0-9]g[0-9]{5})$", + "n_databases": 1, + "databases": [ + "thellungiella_db" + ], + "frontends": [ + "efp_eutrema" + ], + "serves_eplant": false + }, + "efp_grape": { + "regex": "^(CHR|VIT_|CHRUN)", + "n_databases": 1, + "databases": [ + "grape_developmental" + ], + "frontends": [ + "efp_grape" + ], + "serves_eplant": false + }, + "efp_human": { + "regex": "^([0-9]{1,7}(_[a-z])?_at)$|^(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)$|^([A-Za-z0-9][A-Za-z0-9._-]{0,39})$", + "n_databases": 4, + "databases": [ + "human_body_map_2", + "human_developmental", + "human_developmental_SpongeLab", + "human_diseased" + ], + "frontends": [ + "efp_human" + ], + "serves_eplant": false + }, + "efp_kalanchoe": { + "regex": "^(Kaladp\\d+s\\d+)$", + "n_databases": 2, + "databases": [ + "kalanchoe", + "kalanchoe_time_course_analysis" + ], + "frontends": [ + "efp_kalanchoe" + ], + "serves_eplant": false + }, + "efp_little_millet": { + "regex": "^(TRINITY_DN\\d+_c\\d+_g\\d+_i\\d+)$", + "n_databases": 1, + "databases": [ + "little_millet" + ], + "frontends": [ + "efp_little_millet" + ], + "serves_eplant": false + }, + "efp_lupin": { + "regex": "^(Luan_Oskar_.{1,12}_\\d{1,12})$", + "n_databases": 5, + "databases": [ + "lupin_lcm_leaf", + "lupin_lcm_pod", + "lupin_lcm_stem", + "lupin_pod_seed", + "lupin_whole_plant" + ], + "frontends": [ + "efp_lupin" + ], + "serves_eplant": false + }, + "efp_maize": { + "regex": "^([A-Z]{2}[0-9]{6}\\.[0-9]{1,2}_FGT?[0-9]{3})$|^(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)$", + "n_databases": 17, + "databases": [ + "maize_RMA_linear", + "maize_RMA_log", + "maize_atlas", + "maize_atlas_v5", + "maize_buell_lab", + "maize_early_seed", + "maize_ears", + "maize_embryonic_leaf_development", + "maize_gdowns", + "maize_iplant", + "maize_kernel_v5", + "maize_leaf_gradient", + "maize_lipid_map", + "maize_nitrogen_use_efficiency", + "maize_rice_comparison", + "maize_root", + "maize_stress_v5" + ], + "frontends": [ + "efp_maize", + "eplant_maize" + ], + "serves_eplant": true + }, + "efp_maize_enzyme": { + "regex": "(?i)^[a-z0-9\\s\\-\\(\\)]{1,50}$", + "n_databases": 1, + "databases": [ + "maize_enzyme" + ], + "frontends": [ + "efp_maize_enzyme" + ], + "serves_eplant": false + }, + "efp_maize_lipid_map": { + "regex": "(?i)^[a-z0-9\\s:;\\/\\[\\]_\\+\\-]{1,64}$", + "n_databases": 0, + "databases": [], + "frontends": [], + "serves_eplant": false + }, + "efp_maize_metabolite": { + "regex": "(?i)^[a-z0-9\\s,\\.\\-\\(\\)_'\\+/]{1,80}$", + "n_databases": 1, + "databases": [ + "maize_metabolite" + ], + "frontends": [ + "efp_maize_metabolite" + ], + "serves_eplant": false + }, + "efp_maize_transcriptomics": { + "regex": "^([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)$", + "n_databases": 0, + "databases": [], + "frontends": [], + "serves_eplant": false + }, + "efp_mangosteen": { + "regex": "^(DN\\d{1,10})$", + "n_databases": 7, + "databases": [ + "mangosteen_aril_vs_rind", + "mangosteen_callus", + "mangosteen_diseased_vs_normal", + "mangosteen_fruit_ripening", + "mangosteen_seed_development", + "mangosteen_seed_development_germination", + "mangosteen_seed_germination" + ], + "frontends": [ + "efp_mangosteen" + ], + "serves_eplant": false + }, + "efp_marchantia": { + "regex": "^(Mp[A-Za-z]?g[0-9]{1,7}\\.[0-9]{1,3})$|^(Mp[A-Za-z]?[0-9]+g[0-9]+\\.[0-9]+)$", + "n_databases": 1, + "databases": [ + "marchantia_organ_stress" + ], + "frontends": [ + "efp_marchantia" + ], + "serves_eplant": false + }, + "efp_medicago": { + "regex": "^(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)$|^(Medtr_v1_[0-9]{6})$", + "n_databases": 5, + "databases": [ + "medicago_mas", + "medicago_rma", + "medicago_root", + "medicago_root_v5", + "medicago_seed" + ], + "frontends": [ + "efp_medicago", + "eplant_medicago" + ], + "serves_eplant": true + }, + "efp_oat": { + "regex": "(^N0\\.HOG\\d{1,10}$|^\\D{1,10}\\.*\\d{1,10}.{1,10}\\d{1,10}$)", + "n_databases": 1, + "databases": [ + "oat" + ], + "frontends": [ + "efp_oat" + ], + "serves_eplant": false + }, + "efp_phelipanche": { + "regex": "^(OrAeBC\\d+_\\d+\\.\\d+)$|^(OrAeBC\\d+_\\d+)$|^(At\\d[gcm]\\d{1,6})$", + "n_databases": 1, + "databases": [ + "phelipanche" + ], + "frontends": [ + "efp_phelipanche" + ], + "serves_eplant": false + }, + "efp_physcomitrella": { + "regex": "^(Pp)\\d+s\\d+_\\d+V\\d\\.\\d$|^Phypa_\\d+$", + "n_databases": 1, + "databases": [ + "physcomitrella_db" + ], + "frontends": [ + "efp_physcomitrella" + ], + "serves_eplant": false + }, + "efp_poplar": { + "regex": "^(Potri\\.([0-9]{3}G|T)[0-9]{6}(\\.[0-9]+)?)$|^(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)$", + "n_databases": 4, + "databases": [ + "poplar", + "poplar_hormone", + "poplar_leaf", + "poplar_xylem" + ], + "frontends": [ + "efp_poplar", + "eplant_poplar" + ], + "serves_eplant": true + }, + "efp_potato": { + "regex": "^(PGSC0003DMG4\\d{8})$", + "n_databases": 3, + "databases": [ + "potato_dev", + "potato_stress", + "potato_wounding" + ], + "frontends": [ + "efp_potato", + "eplant_potato" + ], + "serves_eplant": true + }, + "efp_rice": { + "regex": "^(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))$|^(AFFX[-_][\\w./-]+at)$", + "n_databases": 7, + "databases": [ + "rice_abiotic_stress_sc_pseudobulk", + "rice_drought_heat_stress", + "rice_leaf_gradient", + "rice_maize_comparison", + "rice_mas", + "rice_rma", + "rice_root" + ], + "frontends": [ + "efp_rice", + "eplant_rice" + ], + "serves_eplant": true + }, + "efp_rice_metabolite": { + "regex": "(?i)^[a-z0-9,\\s\\.\\-]{1,40}$", + "n_databases": 1, + "databases": [ + "rice_metabolite" + ], + "frontends": [ + "efp_rice_metabolite" + ], + "serves_eplant": false + }, + "efp_rice_transcriptomics": { + "regex": "^(LOC_Os[0-9]{2}g[0-9]{5})$|^(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))$", + "n_databases": 0, + "databases": [], + "frontends": [], + "serves_eplant": false + }, + "efp_seedcoat": { + "regex": "^(At[12345CM]g[0-9]{5}(\\.[0-9]+)?)$|^([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)$", + "n_databases": 1, + "databases": [ + "seedcoat" + ], + "frontends": [ + "efp_arabidopsis_seedcoat" + ], + "serves_eplant": false + }, + "efp_selaginella": { + "regex": "^(Smo\\d+)$", + "n_databases": 1, + "databases": [ + "selaginella" + ], + "frontends": [ + "efp_selaginella" + ], + "serves_eplant": false + }, + "efp_sorghum": { + "regex": "^(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})$|^(ENSRNA[0-9]{1,12})$", + "n_databases": 16, + "databases": [ + 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"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/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, +actinidia_vegetative_growth,efp,True,True,False,30,30,0,False, +affydb,legacy_not_in_dropdown,False,True,True,30,30,0,True, +apple,efp,True,True,False,30,30,0,False, +arabidopsis_ecotypes,efp,True,True,True,30,30,0,True, +arachis,efp,True,True,True,30,30,0,False, +atgenexp,efp,True,True,True,30,30,0,True, +atgenexp_hormone,both,True,True,True,30,30,0,True, +atgenexp_pathogen,both,True,True,True,30,30,0,True, +atgenexp_plus,both,True,True,True,30,30,0,True, +atgenexp_stress,both,True,True,True,30,30,0,True, +barley_mas,efp,True,True,True,30,30,0,True, +barley_rma,efp,True,True,True,30,30,0,True, +barley_seed,eplant,True,True,False,30,30,0,False, +barley_spike_meristem,eplant,True,True,False,30,30,0,False, +barley_spike_meristem_v3,eplant,True,True,False,30,30,0,False, +brachypodium,efp,True,True,False,30,30,0,False, +brachypodium_Bd21,efp,True,True,False,30,30,0,False, +brachypodium_embryogenesis,legacy_not_in_dropdown,False,True,False,30,30,0,False, +brachypodium_grains,efp,True,True,False,30,30,0,False, +brachypodium_metabolites_map,efp,True,True,True,20,20,0,False, +brachypodium_photo_thermocycle,efp,True,True,False,30,30,0,False, +brassica_rapa,efp,True,True,False,30,30,0,False, +brassica_rapa_developmental_atlas,legacy_not_in_dropdown,False,True,False,30,30,0,False, +cacao_developmental_atlas,efp,True,True,False,30,30,0,False, +cacao_developmental_atlas_sca,efp,True,True,False,30,30,0,False, +cacao_drought_diurnal_atlas,efp,True,True,False,30,30,0,False, +cacao_drought_diurnal_atlas_sca,efp,True,True,False,30,30,0,False, +cacao_infection,efp,True,True,False,30,30,0,False, +cacao_leaf,efp,True,True,False,30,30,0,False, +cacao_meristem_atlas_sca,efp,True,True,False,30,30,0,False, +cacao_seed_atlas_sca,efp,True,True,False,30,30,0,False, +camelina,both,True,True,False,30,30,0,False, +camelina_tpm,efp,True,True,False,30,30,0,False, +cannabis,both,True,True,False,30,30,0,False, +canola,legacy_not_in_dropdown,False,True,False,30,30,0,False, +canola_original,legacy_not_in_dropdown,False,True,False,30,30,0,False, +canola_original_v2,legacy_not_in_dropdown,False,True,False,30,30,0,False, +canola_seed,efp,True,True,True,30,30,0,False, +cassava_atlas,legacy_not_in_dropdown,False,True,False,30,30,0,False, +cassava_cbb,legacy_not_in_dropdown,False,True,False,30,30,0,False, +cassava_eacmv,legacy_not_in_dropdown,False,True,False,30,30,0,False, +circadian_mutants,legacy_not_in_dropdown,False,True,False,30,30,0,False, +cuscuta,legacy_not_in_dropdown,False,True,False,30,30,0,False, +cuscuta_early_haustoriogenesis,legacy_not_in_dropdown,False,True,False,30,30,0,False, +cuscuta_lmd,legacy_not_in_dropdown,False,True,False,30,30,0,False, +dna_damage,both,True,True,False,30,30,0,False, +durum_wheat_abiotic_stress,efp,True,True,False,30,30,0,False, +durum_wheat_biotic_stress,efp,True,True,False,30,30,0,False, +durum_wheat_development,efp,True,True,False,30,30,0,False, +embryo,efp,True,True,False,30,30,0,False, +eucalyptus,eplant,True,True,False,30,30,0,False, +euphorbia,efp,True,True,False,30,30,0,False, +gc_drought,eplant,True,True,False,30,30,0,False, +germination,both,True,True,False,30,30,0,False, +grape_developmental,efp,True,True,False,30,30,0,False, +guard_cell,both,True,True,True,30,30,0,True, +gynoecium,efp,True,True,False,30,30,0,False, +heterodera_schachtii,eplant,True,True,False,30,30,0,False, +hnahal,legacy_not_in_dropdown,False,True,True,30,30,0,True, +human_body_map_2,efp,True,True,False,30,30,0,False, +human_developmental,efp,True,True,True,30,30,0,True, +human_developmental_SpongeLab,legacy_not_in_dropdown,False,True,True,11,11,0,True, +human_diseased,legacy_not_in_dropdown,False,True,True,30,30,0,True, +kalanchoe,efp,True,True,False,30,30,0,False, +kalanchoe_time_course_analysis,legacy_not_in_dropdown,False,True,False,30,30,0,False, +klepikova,both,True,True,False,30,30,0,False, +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/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/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/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()