Adding expression input schema definition to repo #3368
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For helping communication with expression data providers (eg. PRIDE) the expected input schema should be added to JSON schema repo.
Adding the following schemas:
gs://atlas_baseline_expression/rel_40_2024-05-08/aggregated_data/E-CURD-25/E-CURD-25-expression-data-tpms.jsonl.bz2) [1].gs://atlas_baseline_expression/rel_40_2024-05-08/metadata/E-CURD-25/E-CURD-25.metadata.json) [2].gs://atlas_baseline_expression/rel_40_2024-05-08/unaggregated_data/E-CURD-25/E-CURD-25-unaggregated-expression-data-fpkms.jsonl.bz2) [3].These schemas will serve as a common ground, also a way to get feedback and maybe adjusting.
[1] Aggregated data:
{ "geneProductId": "ENSRNA049436185", "expression": [ { "assayGroupId": "g1", "min": 0.0, "q1": 0.0, "q2": 0.0, "q3": 0.0, "max": 0.0 }, { "assayGroupId": "g2", "min": 0.0, "q1": 0.0, "q2": 0.0, "q3": 0.0, "max": 0.0 }, { "assayGroupId": "g3", "min": 0.0, "q1": 0.0, "q2": 0.0, "q3": 0.0, "max": 0.0 }, { "assayGroupId": "g4", "min": 0.0, "q1": 0.0, "q2": 0.0, "q3": 0.0, "max": 0.0 } ], "unit": "tpms" }[2] Study metadata:
{ "experimentId": "E-CURD-25", "experimentType": "rnaseq_mrna_baseline", "species": "Sorghum bicolor", "speciesOntURI": "http://purl.obolibrary.org/obo/NCBITaxon_4558", "pubmedIds": [ "28186631" ], "provider": "Gina; Turco; Kaisa; Kajala; Govindarajan; Kunde-Ramamoorthy; Chew-Yee; Ngan; Andrew; Olson; Shweta; Deshphande; Barbara; Waring; Scott; Stelpflug; Patricia; Klein; Shawn; Kaeppler; Doreen; Ware; Chia-Lin; Wei; J; Etchells; Siobhan; Brady", "experimentalDesigns": [ { "assayGroupId": "g1", "assayId": "SRR2102337", "assayGroup": "nonvascular system", "age": "3 day", "cultivar": "BTx623", "genotype": "wild type genotype", "organismPart": "nonvascular system" }, { "assayGroupId": "g1", "assayId": "SRR2102338", "assayGroup": "nonvascular system", "age": "3 day", "cultivar": "BTx623", "genotype": "wild type genotype", "organismPart": "nonvascular system" }, { "assayGroupId": "g1", "assayId": "SRR2102336", "assayGroup": "nonvascular system", "age": "3 day", "cultivar": "BTx623", "genotype": "wild type genotype", "organismPart": "nonvascular system" }, { "assayGroupId": "g2", "assayId": "SRR2102328", "assayGroup": "root", "age": "3 day", "cultivar": "BTx623", "genotype": "wild type genotype", "organismPart": "root", "organismPartOntURI": "http://purl.obolibrary.org/obo/PO_0009005" }, { "assayGroupId": "g2", "assayId": "SRR2102327", "assayGroup": "root", "age": "3 day", "cultivar": "BTx623", "genotype": "wild type genotype", "organismPart": "root", "organismPartOntURI": "http://purl.obolibrary.org/obo/PO_0009005" }, { "assayGroupId": "g2", "assayId": "SRR2102329", "assayGroup": "root", "age": "3 day", "cultivar": "BTx623", "genotype": "wild type genotype", "organismPart": "root", "organismPartOntURI": "http://purl.obolibrary.org/obo/PO_0009005" }, { "assayGroupId": "g3", "assayId": "SRR2102330", "assayGroup": "shoot", "age": "3 day", "cultivar": "BTx623", "genotype": "wild type genotype", "organismPart": "shoot", "organismPartOntURI": "http://purl.obolibrary.org/obo/PO_0009006" }, { "assayGroupId": "g3", "assayId": "SRR2102331", "assayGroup": "shoot", "age": "3 day", "cultivar": "BTx623", "genotype": "wild type genotype", "organismPart": "shoot", "organismPartOntURI": "http://purl.obolibrary.org/obo/PO_0009006" }, { "assayGroupId": "g3", "assayId": "SRR2102332", "assayGroup": "shoot", "age": "3 day", "cultivar": "BTx623", "genotype": "wild type genotype", "organismPart": "shoot", "organismPartOntURI": "http://purl.obolibrary.org/obo/PO_0009006" }, { "assayGroupId": "g4", "assayId": "SRR2102335", "assayGroup": "vascular system", "age": "3 day", "cultivar": "BTx623", "genotype": "wild type genotype", "organismPart": "vascular system", "organismPartOntURI": "http://purl.obolibrary.org/obo/PO_0000034" }, { "assayGroupId": "g4", "assayId": "SRR2102334", "assayGroup": "vascular system", "age": "3 day", "cultivar": "BTx623", "genotype": "wild type genotype", "organismPart": "vascular system", "organismPartOntURI": "http://purl.obolibrary.org/obo/PO_0000034" }, { "assayGroupId": "g4", "assayId": "SRR2102333", "assayGroup": "vascular system", "age": "3 day", "cultivar": "BTx623", "genotype": "wild type genotype", "organismPart": "vascular system", "organismPartOntURI": "http://purl.obolibrary.org/obo/PO_0000034" } ] }[3] Unaggregated data:
{ "geneProductId": "ENSRNA049436185", "unit": "fpkms", "expression": [ { "assayId": "SRR2102331", "value": 0.0 }, { "assayId": "SRR2102328", "value": 0.0 }, { "assayId": "SRR2102329", "value": 0.0 }, { "assayId": "SRR2102332", "value": 0.0 }, { "assayId": "SRR2102336", "value": 0.0 }, { "assayId": "SRR2102338", "value": 0.0 }, { "assayId": "SRR2102335", "value": 0.0 }, { "assayId": "SRR2102337", "value": 0.0 }, { "assayId": "SRR2102330", "value": 0.0 }, { "assayId": "SRR2102333", "value": 0.0 }, { "assayId": "SRR2102334", "value": 0.0 }, { "assayId": "SRR2102327", "value": 0.0 } ] }The text was updated successfully, but these errors were encountered: