From 4145a621f22f472d8cf42af63924b8d7c9295d3e Mon Sep 17 00:00:00 2001 From: Vahid Kiani Date: Mon, 23 Jan 2023 16:12:01 +0000 Subject: [PATCH] introduce source_types --- .../default_data/source_types/isa_test.json | 756 ++++++++++++++++++ 1 file changed, 756 insertions(+) create mode 100644 config/default_data/source_types/isa_test.json diff --git a/config/default_data/source_types/isa_test.json b/config/default_data/source_types/isa_test.json new file mode 100644 index 0000000000..3b6a88fa1f --- /dev/null +++ b/config/default_data/source_types/isa_test.json @@ -0,0 +1,756 @@ +{ + "data": [ + { + "metadata": { + "name": "ISA Source", + "group": "ISA Test", + "group_order": 1, + "temporary_name": "1_ISA_Test_Source", + "template_version": "1.0.0", + "isa_config": null, + "isa_measurement_type": null, + "isa_technology_type": null, + "isa_protocol_type": null, + "repo_schema_id": null, + "organism": "any", + "level": "study" + }, + "data": [ + { + "iri": null, + "name": "Source Name", + "description": "Sources are considered as the starting biological material used in a study.", + "dataType": "String", + "title": true, + "required": true, + "isaTag": "source" + }, + { + "iri": null, + "name": "Source Characteristic 1", + "description": "A characteristic of the source", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "source_characteristic" + }, + { + "iri": null, + "name": "Source Characteristic 2", + "description": "A characteristic of the source. With a controlled vocabulary of Yes and No.", + "dataType": "Controlled Vocabulary", + "required": false, + "ontology": null, + "CVList": ["Yes", "No"], + "isaTag": "source_characteristic" + }, + { + "iri": null, + "name": "Source Characteristic 3", + "description": "A characteristic of the source. With terms from an Ontology as accepted values", + "dataType": "Ontology", + "required": false, + "ontology": { + "name": "ENVO", + "version": "", + "description": "Environment Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/ENVO_00005803" + }, + "CVList": null, + "isaTag": "source_characteristic" + } + ] + }, + { + "metadata": { + "name": "ISA sample collection", + "group": "ISA Test", + "group_order": 2, + "temporary_name": "2_ISA_Test_sample_collection", + "template_version": "1.0.0", + "isa_config": null, + "isa_measurement_type": null, + "isa_technology_type": null, + "isa_protocol_type": null, + "repo_schema_id": null, + "organism": "any", + "level": "study" + }, + "data": [ + { + "iri": null, + "name": "Input", + "description": "Existing Samples in DataHub that represent input for this protocol.", + "dataType": "Registered Sample (multiple)", + "required": true, + "isaTag": null + }, + { + "iri": null, + "name": "sample collection", + "description": "type of assay or experimental step performed.", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "protocol" + }, + { + "iri": null, + "name": "sample collection parameter value 1", + "description": "Parameter value 1 for sample collection", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "sample collection parameter value 2", + "description": "Parameter value 2 for sample collection", + "dataType": "Controlled Vocabulary", + "required": false, + "ontology": null, + "CVList": ["a", "b", "c"], + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "sample collection parameter value 3", + "description": "Parameter value 3 for sample collection", + "dataType": "Ontology", + "required": false, + "ontology": { + "name": "PATO", + "version": "", + "description": "Phenotype And Trait Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/PATO_0002317" + }, + "CVList": null, + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "Sample Name", + "description": "Name of the major output resulting from the application of the protocol.", + "dataType": "String", + "title": true, + "required": true, + "isaTag": "sample" + }, + { + "iri": null, + "name": "sample characteristic 1", + "description": "sample characteristic 1", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "sample_characteristic" + }, + { + "iri": null, + "name": "sample characteristic 2", + "description": "sample characteristic 2", + "dataType": "Controlled Vocabulary", + "required": false, + "ontology": null, + "CVList": ["d", "e", "f"], + "isaTag": "sample_characteristic" + }, + { + "iri": null, + "name": "sample characteristic 3", + "description": "sample characteristic 3", + "dataType": "Ontology", + "required": false, + "ontology": { + "name": "FOODON", + "version": "", + "description": "Food Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/FOODON_00001800" + }, + "CVList": null, + "isaTag": "sample_characteristic" + } + ] + }, + { + "metadata": { + "name": "ISA Assay 1", + "group": "ISA Test", + "group_order": 3, + "temporary_name": "3_ISA_Test_Assay_1", + "template_version": "1.0.0", + "isa_config": null, + "isa_measurement_type": null, + "isa_technology_type": null, + "isa_protocol_type": null, + "repo_schema_id": null, + "organism": "any", + "level": "assay" + }, + "data": [ + { + "iri": null, + "name": "Input", + "description": "Existing Samples in DataHub that represent input for this protocol.", + "dataType": "Registered Sample (multiple)", + "required": true, + "isaTag": null + }, + { + "iri": null, + "name": "Protocol Assay 1", + "description": "type of assay or experimental step performed.", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "protocol" + }, + { + "iri": null, + "name": "Assay 1 parameter value 1", + "description": "Parameter value 1 for Assay 1", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "Assay 1 parameter value 2", + "description": "Parameter value 2 for Assay 1", + "dataType": "Controlled Vocabulary", + "required": false, + "ontology": null, + "CVList": ["1", "2", "3"], + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "Assay 1 parameter value 3", + "description": "Parameter value 3 for Assay 1", + "dataType": "Ontology", + "required": false, + "ontology": { + "name": "BAO", + "version": "", + "description": "BioAssay Ontology", + "rootTermURI": "http://www.bioassayontology.org/bao#BAO_0002099" + }, + "CVList": null, + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "other material 1", + "description": "Name of the major output resulting from the application of the protocol.", + "dataType": "String", + "title": true, + "required": true, + "isaTag": "other_material" + }, + { + "iri": null, + "name": "other material characteristic 1", + "description": "other material characteristic 1", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "other_material_characteristic" + }, + { + "iri": null, + "name": "other material characteristic 2", + "description": "other material characteristic 2", + "dataType": "Controlled Vocabulary", + "required": false, + "ontology": null, + "CVList": ["4", "5", "6"], + "isaTag": "other_material_characteristic" + }, + { + "iri": null, + "name": "other material characteristic 3", + "description": "other material characteristic 3", + "dataType": "Ontology", + "required": false, + "ontology": { + "name": "FOODON", + "version": "", + "description": "Food Ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/FOODON_00001800" + }, + "CVList": null, + "isaTag": "other_material_characteristic" + } + ] + }, + { + "metadata": { + "name": "ISA Assay 2", + "group": "ISA Test", + "group_order": 4, + "temporary_name": "4_ISA_Test_Assay_2", + "template_version": "1.0.0", + "isa_config": null, + "isa_measurement_type": null, + "isa_technology_type": null, + "isa_protocol_type": null, + "repo_schema_id": null, + "organism": "any", + "level": "assay" + }, + "data": [ + { + "iri": null, + "name": "Input", + "description": "Existing Samples in DataHub that represent input for this protocol.", + "dataType": "Registered Sample (multiple)", + "required": true, + "isaTag": null + }, + { + "iri": null, + "name": "Protocol Assay 2", + "description": "type of assay or experimental step performed.", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "protocol" + }, + { + "iri": null, + "name": "Assay 2 parameter value 1", + "description": "Parameter value 1 for Assay 2", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "Assay 2 parameter value 2", + "description": "Parameter value 2 for Assay 2", + "dataType": "Controlled Vocabulary", + "required": false, + "ontology": null, + "CVList": ["7", "8", "9"], + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "Assay 2 parameter value 3", + "description": "Parameter value 3 for Assay 2", + "dataType": "Ontology", + "required": false, + "ontology": { + "name": "OMIT", + "version": "", + "description": "Ontology for MIRNA Target", + "rootTermURI": "http://purl.obolibrary.org/obo/OMIT_0004895" + }, + "CVList": null, + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "other material 2", + "description": "Name of the major output resulting from the application of the protocol.", + "dataType": "String", + "title": true, + "required": true, + "isaTag": "other_material" + }, + { + "iri": null, + "name": "other material 2 characteristic 1", + "description": "other material characteristic 2", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "other_material_characteristic" + }, + { + "iri": null, + "name": "other material 2 characteristic 2", + "description": "other material characteristic 2", + "dataType": "Controlled Vocabulary", + "required": false, + "ontology": null, + "CVList": ["10", "11", "12"], + "isaTag": "other_material_characteristic" + }, + { + "iri": null, + "name": "other material 2 characteristic 3", + "description": "other material characteristic 3", + "dataType": "Ontology", + "required": false, + "ontology": { + "name": "SNOMED", + "version": "", + "description": "SNOMED CT (International Edition)", + "rootTermURI": "http://snomed.info/id/226818000" + }, + "CVList": null, + "isaTag": "other_material_characteristic" + } + ] + }, + { + "metadata": { + "name": "ISA Assay 3", + "group": "ISA Test", + "group_order": 5, + "temporary_name": "5_ISA_Test_Assay_3", + "template_version": "1.0.0", + "isa_config": null, + "isa_measurement_type": null, + "isa_technology_type": null, + "isa_protocol_type": null, + "repo_schema_id": null, + "organism": "any", + "level": "assay" + }, + "data": [ + { + "iri": null, + "name": "Input", + "description": "Existing Samples in DataHub that represent input for this protocol.", + "dataType": "Registered Sample (multiple)", + "required": true, + "isaTag": null + }, + { + "iri": null, + "name": "Protocol Assay 3", + "description": "type of assay or experimental step performed.", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "protocol" + }, + { + "iri": null, + "name": "Assay 3 parameter value 1", + "description": "Parameter value 1 for Assay 3", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "Assay 3 parameter value 2", + "description": "Parameter value 2 for Assay 3", + "dataType": "Controlled Vocabulary", + "required": false, + "ontology": null, + "CVList": ["13", "14", "15"], + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "Assay 3 parameter value 3", + "description": "Parameter value 3 for Assay 3", + "dataType": "Ontology", + "required": false, + "ontology": { + "name": "AFO", + "version": "", + "description": "Allotrope Merged Ontology Suite", + "rootTermURI": "http://purl.allotrope.org/ontologies/equipment#AFE_0002157" + }, + "CVList": null, + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "other material 3", + "description": "Name of the major output resulting from the application of the protocol.", + "dataType": "String", + "title": true, + "required": true, + "isaTag": "other_material" + }, + { + "iri": null, + "name": "other material 3 characteristic 1", + "description": "other material characteristic 2", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "other_material_characteristic" + }, + { + "iri": null, + "name": "other material 3 characteristic 2", + "description": "other material characteristic 2", + "dataType": "Controlled Vocabulary", + "required": false, + "ontology": null, + "CVList": ["16", "17", "18"], + "isaTag": "other_material_characteristic" + }, + { + "iri": null, + "name": "other material 3 characteristic 3", + "description": "other material characteristic 3", + "dataType": "Ontology", + "required": false, + "ontology": { + "name": "SNOMED", + "version": "", + "description": "SNOMED CT (International Edition)", + "rootTermURI": "http://snomed.info/id/226863004" + }, + "CVList": null, + "isaTag": "other_material_characteristic" + } + ] + }, + { + "metadata": { + "name": "ISA Assay 4", + "group": "ISA Test", + "group_order": 6, + "temporary_name": "6_ISA_Test_Assay_4", + "template_version": "1.0.0", + "isa_config": null, + "isa_measurement_type": null, + "isa_technology_type": null, + "isa_protocol_type": null, + "repo_schema_id": null, + "organism": "any", + "level": "assay" + }, + "data": [ + { + "iri": null, + "name": "Input", + "description": "Existing Samples in DataHub that represent input for this protocol.", + "dataType": "Registered Sample (multiple)", + "required": true, + "isaTag": null + }, + { + "iri": null, + "name": "Protocol Assay 4", + "description": "type of assay or experimental step performed.", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "protocol" + }, + { + "iri": null, + "name": "Assay 4 parameter value 1", + "description": "Parameter value 1 for Assay 4", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "Assay 4 parameter value 2", + "description": "Parameter value 2 for Assay 4", + "dataType": "Controlled Vocabulary", + "required": false, + "ontology": null, + "CVList": ["19", "20", "21"], + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "Assay 4 parameter value 3", + "description": "Parameter value 3 for Assay 4", + "dataType": "Ontology", + "required": false, + "ontology": { + "name": "ERO", + "version": "", + "description": "eagle-i resource ontology", + "rootTermURI": "http://purl.obolibrary.org/obo/ERO_0000071" + }, + "CVList": null, + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "data file 1", + "description": "Name of the major output resulting from the application of the protocol.", + "dataType": "String", + "title": true, + "required": true, + "isaTag": "data_file" + }, + { + "iri": null, + "name": "comment 1", + "description": "data file comment 1", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "data_file_comment" + }, + { + "iri": null, + "name": "comment 2", + "description": "data file comment 2", + "dataType": "Controlled Vocabulary", + "required": false, + "ontology": null, + "CVList": ["22", "23", "24"], + "isaTag": "data_file_comment" + }, + { + "iri": null, + "name": "comment 3", + "description": "data file comment 3", + "dataType": "Ontology", + "required": false, + "ontology": { + "name": "MS", + "version": "", + "description": "Mass spectrometry ontology)", + "rootTermURI": "http://purl.obolibrary.org/obo/MS_1001459" + }, + "CVList": null, + "isaTag": "data_file_comment" + } + ] + }, + { + "metadata": { + "name": "ISA Assay 5", + "group": "ISA Test", + "group_order": 7, + "temporary_name": "7_ISA_Test_Assay_4", + "template_version": "1.0.0", + "isa_config": null, + "isa_measurement_type": null, + "isa_technology_type": null, + "isa_protocol_type": null, + "repo_schema_id": null, + "organism": "any", + "level": "assay" + }, + "data": [ + { + "iri": null, + "name": "Input", + "description": "Existing Samples in DataHub that represent input for this protocol.", + "dataType": "Registered Sample (multiple)", + "required": true, + "isaTag": null + }, + { + "iri": null, + "name": "Protocol Assay 5", + "description": "type of assay or experimental step performed.", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "protocol" + }, + { + "iri": null, + "name": "Assay 5 parameter value 1", + "description": "Parameter value 1 for Assay 5", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "Assay 5 parameter value 2", + "description": "Parameter value 2 for Assay 5", + "dataType": "Controlled Vocabulary", + "required": false, + "ontology": null, + "CVList": ["25", "26", "27"], + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "Assay 5 parameter value 3", + "description": "Parameter value 3 for Assay 5", + "dataType": "Ontology", + "required": false, + "ontology": { + "name": "EDAM", + "version": "", + "description": "Bioinformatics operations, data types, formats, identifiers and topics", + "rootTermURI": "http://edamontology.org/operation_2409" + }, + "CVList": null, + "isaTag": "parameter_value" + }, + { + "iri": null, + "name": "data file 2", + "description": "Name of the major output resulting from the application of the protocol.", + "dataType": "String", + "title": true, + "required": true, + "isaTag": "data_file" + }, + { + "iri": null, + "name": "comment 1", + "description": "data file 2 comment 1", + "dataType": "String", + "required": true, + "ontology": null, + "CVList": null, + "isaTag": "data_file_comment" + }, + { + "iri": null, + "name": "comment 2", + "description": "data file 2 comment 2", + "dataType": "Controlled Vocabulary", + "required": false, + "ontology": null, + "CVList": ["28", "29", "30"], + "isaTag": "data_file_comment" + }, + { + "iri": null, + "name": "comment 3", + "description": "data file 2 comment 3", + "dataType": "Ontology", + "required": false, + "ontology": { + "name": "NCIT", + "version": "", + "description": "NCI Thesaurus OBO Edition)", + "rootTermURI": "http://purl.obolibrary.org/obo/NCIT_C171252" + }, + "CVList": null, + "isaTag": "data_file_comment" + } + ] + } + ] +}