All notable changes to the HCA metadata schema will be documented in this file. Starting with v5.0.0, the schema will be versioned independently. Therefore, this changelog will contain notes for independent updates/releases per schema.
Starting after v5.0.0 release, updates will be declared for schemas independently in the form [<schema_name>.json vX.Y.Z] - Release-date
. Changes will be organized across six categories: Added, Changed, Removed, Fixed, Deprecated, and Security. The format is based on Keep a Changelog
and (starting with v4.0.0) this project adheres to Semantic Versioning. Unreleased changes may be indicated under the Unreleased
heading.
Changed user_friendly name of reagent field
Added optional digestion_time field
Added optional digestion_time_unit field
Added optional digestion_temperature field
Added optional digestion_solution field
Changed enum value in hca_bionetwork.name. Fix #1600
Changed enum value in hca_bionetwork.name. Fix #1600
Added non-required gender identity field.
Added ontology module for gender identity.
Changed medication field type Fix#1589
Added medication ontology module Fix#1589
Changed medication field type Fix#1589
Added comorbidities field in the donor_organism Fix#1569
Added atlas names in hca_bionetwork
Added atlas names in hca_bionetwork
Added new disease profile module with COPD fields. Fixes#1572
Added an optional disease profile field in the donor_organism. Fixes#1572
Added 'drs_uri' property to file_descriptor
Added optional smoking related fields in medical_history module. Fix #1565
Removed smoking_history in medical_history module. Fix #1565
Added optional smoking related fields in medical_history module. Fix #1565
Fixed class from data:0006 to EDAM:0006. Fixes #1571
Fixed class from data:0006 to EDAM:0006. Fixes #1571
Fixed class from data:0006 to EDAM:0006. Fixes #1571
Fixed class from data:0006 to EDAM:0006. Fixes #1571
Fixed class from data:0006 to EDAM:0006. Fixes #1571
Fixed class from data:0006 to EDAM:0006. Fixes #1571
Fixed class from data:0006 to EDAM:0006. Fixes #1571
Added medical_tests module
Added optional medical_tests module in donor_organism. Fixes #1562
Added sequencing_run_batch field in the sequencing_file - Fixes#1557
Added intron_inclusion field in analysis_protocol Fixes#1554
Added transplant_organ field in specimen_from_organism Fixes#1547"
Added DUOS id field. Fixes #1550
Added data_use_restriction field
Added gene_annotation_version field in analysis_protocol Fixes#1543
Added alignment_software & alignment_software_version field in analysis_protocol Fixes#1533
Added timecourse module. Fixes #1511
Removed timecourse module.
Removed timecourse module.
Removed timecourse module.
Added timecourse module. Fixes #1511
Added timecourse module. Fixes #1511
Added timecourse module. Fixes #1511
Added new values to hca_atlas field
Added new values to hca_atlas field
Added the hca_bionetwork module with four fields for recording bionetwork and atlas information
Added the hca_bionetwork module to be loaded in project
Added new optional field adjacent_diseases. Fixes #1512
Added genome assembly and patch version. Fixes #1508.
Fixed typo in apostrophe. Fixes #1410
Fixed typo in apostrophe. Fixes #1410
Fixed typo in gestational age description
Added value to enum for file source. Fixes #1487.
Added value to enum for file source. Fixes #1487.
Added value to enum for file source. Fixes #1487.
Added value to enum for file source. Fixes #1487.
Added value to enum for file source. Fixes #1487.
Added value to enum for file source. Fixes #1487.
Added treatment protocol to protocol_type. Fixes #1488.
Changed class to BFO:0000023 to match ontology changes.
Changed class to BFO:0000023 to match ontology changes.
Changed class to BFO:0000023 to match ontology changes.
Added permeabilisation time field with time units. Fixes #1471
Changed class to BFO:0000023 to match ontology changes.
Changed class to BFO:0000023 to match ontology changes.
Changed class to BFO:0000023 to match ontology changes.
Added Treatment protocol entity. Fixes #1428
Added Treatment protocol method ontology to be used to annotate the Treatment protocol method. Fixes #1428
Added Treatment protocol target pathway ontology which will be used to describe the target pathway that is targeted by a treatment method. Fixes #1428
Added the phenotype branch to graphRestrictions. Fixes #1460
Added the phenotype branch to graphRestrictions. Fixes #1460
Added the phenotype branch to graphRestrictions. Fixes #1460
Added the phenotype branch to graphRestrictions. Fixes #1460
Added information entity branch to graphRestrictions. Fixes #1450
Changed overlapping_tiles, numerical_aperture and pixel_size non-required. Fixes #1441
Removed channel and probe from required fields. #Fixes 1420
Added anchors to ega_accessions and dbgap_accessions. Fixes #1425
Added read3, read4 to read index enum. Fixes #1401
Added Read 3, Read 4 to barcode read enum. Fixes #1401
Added Read 3, Read 4 to barcode read enum. Fixes #1401
Added spatial barcode field loading barcodes module
Added required official_hca_publication field. Fixes #1345
Added required official_hca_publication field. Fixes #1345
Added required official_hca_publication field. Fixes #1345
Added project-level cell count. Fixes #1337.
Added matrix module
Changed 'computational_method' field to optional, added matrix module field
Added optional 'matrix_cell_count' field.
Added optional file_source field.
Added optional file_source field.
Added optional file_source field.
Added optional file_source field.
Added optional file_source field.
Added ega_accessions and dbgap_accessions. Fixes #1336.
Changed protocol_type from string to enum of strings. Fixes #1333
Removed schema major minor versions.
Added file_descriptor schema
Fixed incomplete refs urls Fixes#1303
Changed reference_bundle properties to reference_files and removed input_bundles. Fixes #1275
Added supplementary_links. Fixes #1285.
Changed properties for links to capture entire processes. Fixes #1278
Changed pattern match in fields 'insdc_sample_accession' and 'schema_version'. Fixes #1090
Changed pattern match in fields 'insdc_sample_accession' and 'schema_version'. Fixes #1090
Changed pattern match in fields 'insdc_sample_accession' and 'schema_version'. Fixes #1090
Changed pattern match in fields 'insdc_sample_accession' and 'schema_version'. Fixes #1090
Changed pattern match in fields 'insdc_sample_accession' and 'schema_version'. Fixes #1090
Changed pattern match in fields 'insdc_sample_accession' and 'schema_version'. Fixes #1090
Changed pattern match in fields 'insdc_sample_accession' and 'schema_version'. Fixes #1090
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Added two optional fields to represent schema major and minor versions. Fixes #1076.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed description of schema. Fixes #1035.
Fixed identifiers to be lower-cased in ontology classes and example. Fixes #1037
Fixed identifiers to be lower-cased in ontology classes and example. Fixes #1037
Fixed identifiers to be lower-cased in ontology classes and example. Fixes #1037
Fixed identifiers to be lower-cased in ontology classes and example. Fixes #1037
Fixed identifiers to be lower-cased in ontology classes and example. Fixes #1037
Fixed identifiers to be lower-cased in ontology classes and example. Fixes #1037
Fixed identifiers to be lower-cased in ontology classes and example. Fixes #1037
Added new ontology module. Partially fixes #812
Added content_description field. Fixes #542.
Added new file_content_ontology schema. Fixes #542.
Added content_description field. Fixes #542.
Added content_description field. Fixes #542.
Added content_description field. Fixes #542.
Added content_description field. Fixes #542.
Added content_description field. Fixes #542.
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Added user friendly names to fields submission_date, update_date, accession, submitter_id, document_id, updater_id. Fixes #989
Changed multiplexed property friendly name. Fixes #963
Changed corresponding_contributor property friendly name. Fixes #963
Changed normothermic_regional_perfusion and cold_perfused friendly names. Fixes #963
Changed paired_end property friendly name. Fixes #963
Changed pluripotency_vector_removed property friendly name. Fixes #963
Changed overlapping_tiles property friendly name. Fixes #963
Changed is_living property friendly name. Fixes #963
Changed embedded_in_matrigel property friendly name. Fixes #963
Changed corresponding_contributor property friendly name. Fixes #963
Fixed probe field where relevant in the imaging_protocol. Fixes #980.
Added start_time and end_time to process.json. Fixes #742.
Changed format for date_established property. Fixes #966
Changed format for time_of_death property. Fixes #966
Changed format for collection_time property. Fixes #966
Changed format for expiry_date property. Fixes #966
Changed format for time_of_death property. Fixes #966
Changed format for expiry_date property. Fixes #966
Changed format for expiry_date property. Fixes #966
Changed format for expiry_date property. Fixes #966
Changed format for expiry_date property. Fixes #966
Changed format for expiry_date property. Fixes #966
Changed format for expiry_date property. Fixes #966
Changed format for expiry_date property. Fixes #966
Changed format for expiry_date property. Fixes #966
Added description, example, user-friendly name, and guidelines to all definition fields. Fixes #955.
Added not applicable to is_living. Fixes #921
Changed process_type to type. Fixes #931
Changed process_type to type. Fixes #931
Changed protocol_type to type. Fixes #931
Changed protocol_type to type. Fixes #931
Changed contact_name to name. Fixes #927.
Changed contact_name to name. Fixes #927.
Changed file_format to format. Fixes #375.
Changed file_format to format. Fixes #375.
Changed file_format to format. Fixes #375.
Changed file_format to format. Fixes #375.
Changed file_format to format. Fixes #375.
Changed file_format to format. Fixes #375.
Changed description, guidelines and example for gestational_age. Fixes #911.
Added HDBR_accession to biomaterial_core. Fixes #945.
Added HDBR_accession to biomaterial_core. Fixes #945.
Added HDBR_accession to biomaterial_core. Fixes #945.
Added HDBR_accession to biomaterial_core. Fixes #945.
Added HDBR_accession to biomaterial_core. Fixes #945.
Added HDBR_accession to biomaterial_core. Fixes #945.
Added HDBR_accession to biomaterial_core. Fixes #945.
Changed selected_cell_type to selected_cell_types. Fixes #923.
Added optional timecourse field. Fixes #917.
Changed ipsc_induction_method to method, ipsc_induction_factors to reprogramming_factors, protocol_reagents to reagents. Removed ipsc_induction_produced_in_house. Fixes #926.
Added new probe.json module. Fixes #813
Changed process_location to location and operator to operators. Fixes #930.
Changed process_location to location and operator to operators. Fixes #930.
Changed process_location to location and operator to operators. Fixes #930.
Changed 'enrichment_method' to 'method', 'min_size_selected' to 'minimum_size' and 'max_size_selected' to 'maximum_size'. Fixes #925.
Changed differentiation_method to method. Fixes #924.
Changed biosd_biomaterial to biosamples_accession and insdc_biomaterial to insdc_sample_accession. Fixes #929
Changed biosd_biomaterial to biosamples_accession and insdc_biomaterial to insdc_sample_accession. Fixes #929
Changed biosd_biomaterial to biosamples_accession and insdc_biomaterial to insdc_sample_accession. Fixes #929
Changed biosd_biomaterial to biosamples_accession and insdc_biomaterial to insdc_sample_accession. Fixes #929
Changed biosd_biomaterial to biosamples_accession and insdc_biomaterial to insdc_sample_accession. Fixes #929
Changed biosd_biomaterial to biosamples_accession and insdc_biomaterial to insdc_sample_accession. Fixes #929
Changed biosd_biomaterial to biosamples_accession and insdc_biomaterial to insdc_sample_accession. Fixes #929
Changed publication_title to title and publication_url to url. Fixes #928.
Changed publication_title to title and publication_url to url. Fixes #928.
Changed publication_title to title and publication_url to url. Fixes #928.
Changed cell_line_type to type. Fixes #935.
Changed project_role from enum to ontology. Fixes #894
Changed project_role from enum to ontology. Fixes #894
Added 'frozen at -80C' to storage_method field. Fixes #916.
Added 'frozen at -80C' to storage_method field. Fixes #916.
Added 'frozen at -80C' to storage_method field. Fixes #916.
Added new contributor_role_ontology schema. Fixes #893.
Changed example and guidelines in filter_range. Fixes#878.
Changed example and guidelines in filter_range. Fixes#878.
Added optional biostudies_accesssion field. Fixes #852.
Changed well and plate ID to label. Fixes #837.
Changed well and plate ID to label. Fixes #837.
Added second example to test_results. Fixes #846.
Added second example to test_results. Fixes #846.
Changed organ_part to organ_parts since it is an array. Fixes #648.
Changed nucleic_acid_source field to be required. Fixes #824.
Removed required outputs fields. Fixes #664.
Fixed insdc_experiment_accession field to adhere to Style Guide. Fixes #809.
Fixed well_quality field. Fixes #809.
Fixed insdc_experiment_accession field to adhere to Style Guide. Fixes #809.
Fixed well_quality field. Fixes #809.
Added administrator value to project role enum. Fixes #845.
Added administrator value to project role enum. Fixes #845.
Fixed array field names to be plural to adhere to Style Guide. Fixes #792.
Fixed array field names to be plural to adhere to Style Guide. Fixes #792.
Changed examples in molecule_id and assay_type. Fixes #830.
Changed examples in molecule_id and assay_type. Fixes #830.
Added enum value to preservation_storage. Fixes #831.
Added enum value to preservation_storage. Fixes #831.
Added enum value to preservation_storage. Fixes #831.
Fixed array field names to be plural to adhere to Style Guide. Fixes #805.
Changed date_established from date-time to date format. Fixes #821.
Changed u-f, examples, and description for some fields. Fixes #816.
Changed u-f, examples, and description for some fields. Fixes #816.
Added examples. Fixes #816.
Changed u-f, examples, and description for some fields. Fixes #816.
Added examples. Fixes #816.
Changed hancestro example from underscore to colon
Changed hancestro example from underscore to colon
Changed hancestro example from underscore to colon
Changed guidelines, descriptions, and user-friendly names. Fixes #796.
Changed guidelines, descriptions, and user-friendly names. Fixes #797.
Changed guidelines, descriptions, and user-friendly names. Fixes #797.
Fixed reagent and method field names to remove redundancy to adhere to Style Guide. Fixes #807.
Fixed reagent and method field names to remove redundancy to adhere to Style Guide. Fixes #807.
Fixed method field name to be consistent with other protocols. Fixes #807.
Fixed method field name to be consistent with other protocols. Fixes #807.
Added user_friendly name to file_core in image_file. Fixes #798
Changed total_estimated_cells to estimated_cell_count. Fixes #649.
Fixed inconsistencies with Style Guide as caught by linter. Fixes #789
Fixed inconsistencies with Style Guide as caught by linter. Fixes #789
Fixed inconsistencies with Style Guide as caught by linter. Fixes #789
Fixed inconsistencies with Style Guide as caught by linter. Fixes #789
Fixed inconsistencies with Style Guide as caught by linter. Fixes #789
Fixed inconsistencies with Style Guide as caught by linter. Fixes #789
Fixed inconsistencies with Style Guide as caught by linter. Fixes #789
Fixed inconsistencies with Style Guide as caught by linter. Fixes #789
Fixed inconsistencies with Style Guide as caught by linter. Fixes #789
Fixed inconsistencies with Style Guide as caught by linter. Fixes #789
Fixed inconsistencies with Style Guide as caught by linter. Fixes #789
Fixed inconsistencies with Style Guide as caught by linter. Fixes #789
Fixed channel_id field which was declared as an array but missing items{} block Fixes #777
Fixed channel_id field which was declared as an array but missing items{} block Fixes #777
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed descriptions to end in full stops. Fixes #785
Fixed examples that were separated by comma instead of semi-colon. Fixes #784
Fixed examples that were separated by comma instead of semi-colon. Fixes #784
Fixed examples that were separated by comma instead of semi-colon. Fixes #784
Fixed examples that were separated by comma instead of semi-colon. Fixes #784
Fixed examples that were separated by comma instead of semi-colon. Fixes #784
Fixed examples that were separated by comma instead of semi-colon. Fixes #784
Fixed examples that were separated by comma instead of semi-colon. Fixes #784
Fixed examples that were separated by comma instead of semi-colon. Fixes #784
Fixed incorrect name field value identified by linter. Fixes #776
Fixed incorrect describedBy field pattern identified by linter. Fixes #776
Fixed incorrect describedBy field pattern identified by linter. Fixes #776
Fixed missing description field in describedBy property. Fixes #780
Fixed missing description field in describedBy property. Fixes #780
Fixed missing description field in describedBy property. Fixes #780
Fixed missing description field in describedBy property. Fixes #780
Fixed missing description field in describedBy property. Fixes #780
Fixed missing description field in describedBy property. Fixes #780
Fixed missing description field in describedBy property. Fixes #780
Fixed missing description field in describedBy property. Fixes #780
Fixed missing description field in describedBy property. Fixes #780
Fixed missing description field in describedBy property. Fixes #780
Fixed missing description field in describedBy property. Fixes #780
Fixed missing description field in describedBy property. Fixes #780
Fixed missing description field in describedBy property. Fixes #780
Fixed missing description field in describedBy property. Fixes #780
Fixed missing user_friendly field in file_core. Fixes #778.
Fixed missing user_friendly field in protocol_core. Fixes 778
Fixed missing user_friendly field in file_core. Fixes #778.
Added timecourse field to schema. Fixes #755.
Changed familial_relationship to be plural. Fixes #768.
Change accession fields to arrays. Changed field names to adhere to Style Guide. Fixes #324.
Added required model_organ field to cell line schema. Fixes #606.
Removed organoid_type field. Fixes #736.
Update field names/descriptions. Fixes #746.
Change enum list to remove commas from values. Fixes #743.
Change enum list to remove commas from values. Fixes #743.
Change enum list to remove commas from values. Fixes #743.
Changed grant_id and funder_name to be required. Fixes #731.
Changed funders to be required. Fixes #731.
Changed fields to remove timecourse_. Fixes #745.
Changed fields to remove timecourse_. Fixes #745.
Updated field names to remove organoid_ prefix. Fixes #480.
Added second example for fastq creation method and fastq creation method version.Fixes #723
Added second example for fastq creation method and fastq creation method version.Fixes #723
Update examples to be separated by semicolon instead of comma. Fixes #728.
Update field examples/descriptions for grammar. Fixes #729.
Update field examples/descriptions for grammar. Fixes #729.
Fixed typo in field user_friendly in property organoid_morphology. Fixes #726
Fixed typo in field user_friendly in property protocol_core. Fixes #726
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Update examples, description, user-friendly names, and guideslines. Fixes #690.
Fixed bug in spelling of user_friendly field in timecourse module. Fixes #710
Fixed bug in spelling of user_friendly field in timecourse module. Fixes #710
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #703.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #685.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Add examples and user-friendly names. Fixes #613.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #674.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #697.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #699.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #706.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #679.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #680.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #678.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #701.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #701.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #701.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #701.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #683.
Added user-friendly name, examples, and guidelines to adhere to Style Guide
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #687.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #687.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #687.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #687.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #687.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #687.
Changed donor_organism to make development_stage required. Fixes #607
Removed normothermic_regional_perfusion. Fixes #590.
Added normothermic_regional_perfusion. Fixes #590.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #672.
Added system entity to capture license under which data are released. Fixes #338.
Changed molecule_ID to lower case in target.json Fixes #666
Changed molecule_ID to lower case in target.json Fixes #666
Removed extra example and fixed field name to match Style Guide. Fixes #668
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #650.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #662.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #662.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #653.
Changed description, user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #652.
Added user-friendly name for biomaterial_core. Fixes #656
Added new schema target.json to replace deprecated imaging_target.json. Fixes #641
Added new schema target.json to replace deprecated imaging_target.json. Fixes #641
Added new optional fields nominal_length and nominal_sdev. Fixes #594.
Changed technical_replicate_group_id to library_preparation_id. Fixes #262.
Changed user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #620.
Changed user-friendly, example, and guidelines attributes to adhere to Style Guide. Fixes #612.
Changed field names and updated examples in imaged_specimen to match the Style Guide
Changed channel_id from string to array
Changed channel_id from string to array
Changed name of the required field channel_name to channel_id
Changed name of the required field channel_name to channel_id
Added optional field timecourse.
Fixed a bug in the links schema still referencing core instead of system
Changed channel field type to array
Changed channel field type to array
Changed channel field to optional
Changed channel field to optional
Changed description for paired_end. Fixes #592.
Removed required field protocol_type
from imaging_protocol (not actually in the schema). Fixes #572.
Fixed issue with organ ontology assignment by using less stringent term restriction. Fixes #567.
Fixed issue with organ ontology assignment by using less stringent term restriction. Fixes #567.
Fixed issue with organ ontology assignment by using less stringent term restriction. Fixes #567.
Updated user-friendly term for is_living.
Added 'not provided' to enum for strand field. Fixes #544.
Made publication a single object instead of an array of objects. Fixes #557
Fixed missing required field project_core
Fixed organ validation issue by including embryo and children as allowed values
Fixed organ validation issue by including embryo and children as allowed values
Fixed organ validation issue by including embryo and children as allowed values
Added missing provenance field
Fixed name/title mix-up bug
Fixed name/title mix-up bug
Fixed name/title mix-up bug
Fixed name/title mix-up bug
Fixed name/title mix-up bug
Updated schema to json-schema draft-07
Updated schema to json-schema draft-07
Updated schema to json-schema draft-07
Updated schema to json-schema draft-07
Updated schema to json-schema draft-07
Updated schema to json-schema draft-07
Updated schema to json-schema draft-07
Added new schema
Added new schema
Added new schema
Added new schema
Added new schema
Added new schema
Added new schema
Added several new fields including new required fields to address imaging use cases
Removed differentiation from 7 fields. Fixes #517
Added user-friendly name to some properties
Added user-friendly name to some properties
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Added schema name. Updated schema title. Fixes #501
Changed optional field disease to diseases
Changed optional field disease to diseases
Fixed schema validation by setting include_self to true
Fixed schema validation by setting include_self to true
Fixed schema validation by setting include_self to true
Fixed schema validation by correcting a casing issue
Fixed schema validation by setting include_self to true
Fixed schema validation by setting include_self to true
Fixed schema validation by setting include_self to true
Fixed schema validation by setting include_self to true
Fixed schema validation by setting include_self to true
Fixed schema validation by correcting a casing issue
Changed several field names from induced_pluripotent_cell_* to ipsc_*
Added new culture_environment field. Fixes #234.
Added new culture_environment field. Fixes #234.
Added new culture_environment field. Fixes #234.
Added stem cell to cell line type enum. Fixes #498.
Fixed the ontology reference to work with the new hancestro
Fixed the ontology reference to work with the new hancestro
Fixed the ontology reference to work with the new hancestro
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed from json-schema draft-4 to draft-07
Changed supplementary_files to supplementary_links.
Removed deprecated smartseq2 field that was accidentally re-added.
Added optional field technical_replicate_group
fixes #421
Changed paired_ends to paired_end. Fixes #467.
Changed sequencing_approach friendly name to Sequencing approach. Fixes #469.
Changed biological_sex to sex. Fixes #384.
Changed operator_identity to operator. Fixes #377.
Changed operator_identity to operator. Fixes #377.
Changed operator_identity to operator. Fixes #377.
Changed is_parent_of to child, is_child_of to parent, and is_sibling_of to sibling.
Changed is_parent_of to child, is_child_of to parent, and is_sibling_of to sibling.
Fixes 10x url bug
Fixes 10x url bug
Removed requirement for non-existent field.
Added optional nucleic_acid_source field. Fixes #385.
Removed nucleic_acid_source field. Fixes #385.
Changed descriptions, user-friendly names, and examples.
Changed example.
Changed example.
Added a new field - feeder_layer_type
- to capture the type of feeder layer cells biomaterial is grown on as this may have different effects on biomaterial growth/proliferation.
Added a new field - feeder_layer_type
- to capture the type of feeder layer cells biomaterial is grown on as this may have different effects on biomaterial growth/proliferation.
Added a new field - feeder_layer_type
- to capture the type of feeder layer cells biomaterial is grown on as this may have different effects on biomaterial growth/proliferation.
Added schema for analysis_process as required by the analysis team
Removed a number of fields from analysis protocol as they are more appropriate in analysis_process
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Changed descriptions.
Added module with 10x-specific fields.
Added reference to optional 10x module.
Added module with 10x-specific fields.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Changed descriptions, user-friendly names, and examples.
Added module plate_based_sequencing. Fixes Issue #397
Deprecated module smartseq2 in favour of a more generic plate_based_sequncing module. Fixes Issue #397
Added field plate_based_sequencing
importing the module of the same name. Fixes Issue #397.
Removed field smartseq2
as the module has been deprecated. Fixes Issue #397.
Added new optional field corresponding_contributor
to contact schema. Fixes #409.
Added new optional field corresponding_contributor
to contact schema. Fixes #409.
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Added optional provenance field
Changed email to be optional. Changed institution to be required. Fixes #411.
Changed email to be optional. Changed institution to be required. Fixes #411.
Added optional iPSC induction factors field to iPSC induction protocol.
Added optional iPSC induction factors field to iPSC induction protocol.
A new file type entity for supplemental files. Fixes #422.
Changed project_shortname
to project_short_name
. Fixes #378.
Changed project_shortname
to project_short_name
. Fixes #378.
Changed project_shortname
to project_short_name
. Fixes #378.
Added two new optional fields - project_role
and orcid_id
. Fixes #352.
Added two new optional fields - project_role
and orcid_id
. Fixes #352.
Added two new optional fields - project_role
and orcid_id
. Fixes #352.
Changed descriptions and examples for fields in the project_core and project_type schemas.
Added some examples to fields in the project_core and project_type schemas.
Changed descriptions and examples for fields in the project_core and project_type schemas.
Added some examples to fields in the project_core and project_type schemas.
Changed descriptions and examples for fields in the project_core and project_type schemas.
Added some examples to fields in the project_core and project_type schemas.
Changed descriptions, examples, and user friendly names in the contact module.
Changed descriptions, examples, and user friendly names in the contact module.
Changed descriptions, examples, and user friendly names in the contact module.
Added model_organ_part
, organoid_size
, organoid_size_unit
, organoid_morphology
, embedded_in_matrigel
, organoid_growth_environment
, input_aggregate_cell_count
and organoid_stored_oxygen_levels
optional fields. Fixes #344. Fixes #347.
Changed organoid_age
description
Added model_organ_part
, organoid_size
, organoid_size_unit
, organoid_morphology
, embedded_in_matrigel
, organoid_growth_environment
, input_aggregate_cell_count
and organoid_stored_oxygen_levels
optional fields. Fixes #344. Fixes #347.
Changed organoid_age
description
Added optional field normothermic_regional_perfusion
to donor_organism. Fixes #362.
Added optional field normothermic_regional_perfusion
to donor_organism. Fixes #362.
Renamed field mus_musculus_specific
to mouse_specific
and updated relevant refs. Fixes #387
Renamed field mus_musculus_specific
to mouse_specific
and updated relevant refs. Fixes #387
Added module human_specific
to replace deprecated homo_sapiens_specific
. Fixes #387
Added module mouse_specific
to replace deprecated mus_musculus _specific
. Fixes #387
Deprecated module homo_sapiens_specific
in favour of common name module human_specific
. Fixes #387
Deprecated module mus_musculus_specific
in favour of common name module mouse_specific
. Fixes #387
Added optional fields length_of_time
and length_of_time_unit
to process. Fixes #400
Added optional fields length_of_time
and length_of_time_unit
to process. Fixes #400
Removed length_of_time
and length_of_time_unit
from process_core. Fixes #400
Removed length_of_time
and length_of_time_unit
from process_core. Fixes #400
Removed length_of_time
and length_of_time_unit
from process_core. Fixes #400
Fixed a typo in the curie for the enrichment ontology root class.
Fixed typo in is_living
enum from "unkown" to "unknown"
Fixed typo in is_living
enum from "unkown" to "unknown"
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field ontology_label
to all ontology modules.
Fixes Issue #383
Added optional field organ_donation_death_type
to module death.
Fixes Issue #361.
Added optional field organ_donation_death_type
to module death.
Fixes Issue #361.
Added optional field organ_donation_death_type
to module death.
Fixes Issue #361.
Changed the type of is_living to a string and added an enum to accommodate "unknown" as well as yes/no. Fixes Issue #371.
Changed the type of is_living to a string and added an enum to accommodate "unknown" as well as yes/no. Fixes Issue #371.
Added new aggregate_generation_protocol.json schema. Fixes Issue #345.
Added new aggregate_generation_protocol.json schema. Fixes Issue #345.
Added optionals small_molecules and differentiation_media fields.
Added optionals small_molecules and differentiation_media fields.
Updated the schema URL pattern to cell_line.
Updated the schema URL pattern to cell_line.
Renamed start_time
to length_of_time
with updated description and added a number-only patterns.
Added length_of_time_unit
referencing the time unit ontology module to provide a time unit for the duration in the length_of_time
field.
Renamed start_time
to length_of_time
with updated description and added a number-only patterns.
Added length_of_time_unit
referencing the time unit ontology module to provide a time unit for the duration in the length_of_time
field.
Renamed start_time
to length_of_time
with updated description and added a number-only patterns.
Added length_of_time_unit
referencing the time unit ontology module to provide a time unit for the duration in the length_of_time
field.
Added optional field confluency
to cell_line
Added optional field confluency
to cell_line
Removed field karyotype
from biomaterial_core as it does not apply to all biomaterials.
Removed field karyotype
from biomaterial_core as it does not apply to all biomaterials.
Removed field karyotype
from biomaterial_core as it does not apply to all biomaterials.
Removed field karyotype
from biomaterial_core as it does not apply to all biomaterials.
Removed field karyotype
from biomaterial_core as it does not apply to all biomaterials.
Removed field karyotype
from biomaterial_core as it does not apply to all biomaterials.
Added optional field karyotype
to cell_line
Removed field karyotype
from biomaterial_core as it does not apply to all biomaterials.
Removed fields growth_conditions
and cell_morphology
from organoid.
Removed fields growth_conditions
and cell_morphology
from organoid.
Added the field purchased_specimen
referencing the purchased_reagents module, to capture purchasing of specimens such as blood samples.
Added the field purchased_specimen
referencing the purchased_reagents module, to capture purchasing of specimens such as blood samples.
Added the field tissue
referencing the organ part ontology module, to capture the tissue the cell line was derived from.
Added the field tissue
referencing the organ part ontology module, to capture the tissue the cell line was derived from.
Made project_description a required field.
Made project_description a required field.
Made project_description a required field.
Updated definition of ischemic_time
to address confusion from users.
Updated definition of ischemic_time
to address confusion from users.
Updated definition of ischemic_time
to address confusion from users.
Added a pointer to new module with three optional fields to track project funders.
A new module with three optional fields to track project funders.
Updated descriptions and examples.
Added new protocol types to the oneOf list for protocol bundle.
Added new module to capture timecourse information.
Added new protocol for IPSC induction.
Added new protocol for cell differentiation.
Made fields ncbi_taxon_id
, genus_species
, assembly_type
, reference_type
and reference_version
required.
Made field protocol_type
required.
Made field nucleic_acid_source
required.
Made field protocol_type
required.
Made field cell_line_type
required.
Updated the description for the schema.
Dependency update for specimen_from_organism
Dependency update for preserveration_storage
Fixed (patch) incorrect user-friendly name.
Updated protocol types.
Added the field sequencing_approach
referencing the new sequencing ontology module and made it required.
Removed the field protocol_type
as it duplicates the information in sequencing_approach
.
Removed the field protocol_type
as it duplicates the information in library_preparation_approach
.
Changed the type of field enrichment_method
to use a different ontology module.
Removed the field protocol_type
as it duplicates the information in enrichment_method
.
Changed the type of field dissociation_method
from string-enums to ontology object references.
Removed the field protocol_type
as it duplicates the information in dissociation_method
.
Changed the type of field collection_method
from string-enums to ontology object references and made it required.
Removed the field protocol_type
as it duplicates the information in collection_method
.
Added a new ontology module for sequencing approach.
Updated regex for all 66 schemas to match a range of schema.{}.humancellatlas domains and accept both version numbers in standard major.minor.patch format and "latest". Patch version increment to all schema versions.
Updated regex for all 66 schemas to match http or https and schema.data or schema.dev.data.
Updated enrichment_protocol.
Changed the type of field enrichment_approach
from string-enums to ontology object references.
Added a new ontology module for enrichment approach.
Updated all protocol type references.
Changed protocol_type ontology reference for all protocol schemas to reference process_type_ontology module for ontology modelling reasons.
Changed protocol_type ontology reference for all protocol schemas to reference process_type_ontology module for ontology modelling reasons.
Changed protocol_type ontology reference for all protocol schemas to reference process_type_ontology module for ontology modelling reasons.
Changed protocol_type ontology reference for all protocol schemas to reference process_type_ontology module for ontology modelling reasons.
Changed protocol_type ontology reference for all protocol schemas to reference process_type_ontology module for ontology modelling reasons.
Changed protocol_type ontology reference for all protocol schemas to reference process_type_ontology module for ontology modelling reasons.
Changed protocol_type ontology reference for all protocol schemas to reference process_type_ontology module for ontology modelling reasons.
Changed protocol_type ontology reference for all protocol schemas to reference process_type_ontology module for ontology modelling reasons.
Changed the type of fields library_construction_approach
, library_preamplification_method
and cdna_library_amplification_method
from string-enums to ontology object references.
Added a new ontology module for library amplification approach.
Added a new ontology module for library construction approach.
Field batch_number changed to lot_number.
Removed the has_input_biomaterial
property as the purpose is misleading and no longer required by the spreadsheet importer
Added supplier
field to capture supplier of purchased cell line.
Added lot_number
field to capture lot number of purchased cell line.
Added induced pluripotent
to enum of cell line type.
Changed name of cell_viability field to percent_cell_viability to accurately reflect the value of this field.
Added a new field - cell_viability_result - to capture whether the cell_viability_method assay passed or failed.
This update is a major change due to the changing of the cell_viability field name.
Changed the field target_cell_type
to selected_cell_type
.
Added a new field - kit_titer
- to record the appropriate titer and volume recommendations found in a kit's Certificate of Analysis.
Bug fix to make ontology validation work - root species ontology node changed from "NCBITaxon:131567" to ["OBI:0100026","NCBITaxon:2759"] to reflect usage in HCAO. Patch update to referencing biomaterials and bundles.
This change is to make the fields mycoplasma_testing_method and mycoplasma_testing_results enums. This is a major change.
Bug fix to make reference bundle schema reference its own definition with correct version
Bug fix to make reference bundle schema use the correct dependent version numbers
Bug fix to make reference_file schema use the correct dependent version numbers
Added reference bundle entity to address the analysis pipeline use case for reference bundles
Added reference_file entity to address the analysis pipeline use case for reference bundles
A links entity was added to allow linking of entites in bundles.
The new generic process type was added to the list of processes that can be imported into a process bundle
A new generic process type was created to allow the creation of processes for which no metadata is available.
The field describedBy
was removed from the list of required fields as it was redundant. Only type entites and bundle entities need to explicitly declare a schema in data instances. As a result, all referencing types and bundles were also updated.
The field organ_part
was removed from the list of required fields as it was causing issues for datasets where a sub-organ sampling site is not known.
The incorrect field title
in the list of required field was fixed to be the correct field publication_title
.
Reference to patch version update of module/project/publication.json
was updated.
Reference to patch version update of module/project/publication.json
was updated.
Reference to patch version update of type/project/project.json
was updated.
Reference to patch version update of type/biomaterial/cell_line.json
was updated.
5.0.0 - 2018-02-19
- New fields based on feedback from extensive user evaluation sessions
- New modules which now capture domain-specific fields
- New field attributes (e.g. example, user_friendly) to improve schema clarity
- New example v5.0.0 JSON files and template spreadsheets
- New markdown-formatted table of current metadata fields for easy browsing
- Structural changes to the hierarchy of schema entities
- Updated field names and descriptions based on user feedback
- Expanded use ontologies to validate relevant fields
- Improved automatic Travis CI testing (new passing and failing example JSON)
- Improved documentation for schema updates (changelog.md, Metadata_schema_lifecycle_doc.md)
- Removal of fields that were deemed unnecessary
v4.6.1 - 2017-12-15
- Remove controlled vocabulary for
file.file_format
- Remove regex for
file.filename
v4.6.0 - 2017-12-14
- Add
name
field tofile
definition inanalysis_bundle.json
- Change
checksum
from required to optional inanalysis_bundle.json
- Remove undefined property
log
fromtask
definition inanalysis_bundle.json
v4.5.0 - 2017-12-13
- Add
analysis_bundle.json
as a core type
- Update
assay_bundle.json
to includehas_input
andhas_output
references - Update
analysis.json
to be fully compliant with JSON schema format - Update enums on multiple fields to based on example test datasets
- Convert
contact.country
andcontact.country_division
free text string fields
v4.4.0 - 2017-12-08
- Add
core
field toassay_bundle.json
,project_bundle.json
, andsample_bundle.json
- Add bundle schemas to list of accepted core types
- Add description to
derived_from
field insample_bundle.json
- Made
sample_bundle.json
,assay_bundle.json
, andproject_bundle.json
objects instead of arrays
v4.3.0 - 2017-12-06
- Add "10X" and "10x" as options to
seq.library_construction
,rna.library_construction
, andsingle_cell.cell_handling
- Add "Cambridgeshire" as options to
contact.country_division
- Increase maximum
state_of_specimen.ischemic_time
andstate_of_specimen.postmortem_interval
value to 1000000
- Fix
sample.biosd_sample
regex insample.json
v4.2.0 - 2017-12-05
- Change
donor.json
' fieldsheight
,weight
, andage
from number type to string type with a regex to allow entering a number range - Extend enums for
donor.age_unit
to allow plural forms - Change
death.time_of_death
from required to optional
v4.1.0 - 2017-12-05
- Update ontologies for
body_part_ontology.json
andcell_type_ontology.json
- Add ontology restrictions for
disease_ontology.json
- Update example JSON used for testing for above ontologies
- Fix
sample.biosd_sample
regex insample.json
v4.0.0 - 2017-11-21
- Schema for entities (cell_suspension, immortalized_cell_line, ingest, organoid, file, primary_cell_line, specimen_from_organism, imaging)
- Schema for ontologies (ontology_meta, body_part_ontology, cell_type_ontology, disease_ontology)
- Schema for bundles (assay_bundle, project_bundle, sample_bundle)
- Fields for all entities (name, description, core, id)
- Specific fields (contact.phone, donor.alcohol_history, donor.nutritional_state, donor.smoking_history, ncbi_taxon_id, genus_species, derived_from, sample_acessions, )
- Schema
cell_line
split intoimmortalized_cell_line
andprimary_cell_line
schema - Schema
preservation.json
tostate_of_specimen.json
- Field
sample.donor
to owndonor.json
- Field
id
to<entity>_id
- Fields moved to core schema (
id
,species
,name
,description
) - Fields
project.ddjb_trace
andproject.sra_project
toproject.insdc_project
- Field
project.ncbi_bioproject
toproject.insdc_study
- Fields
sra_experiment
andena_experiment
toinsdc_experiment
- Fields
ena_run
andsra_run
toinsdc_run
- Fields
sample.ena_sample
andsample.ncbi_biosample
tosample.insdc_sample
- Field
organ
fromsample.json
tospecimen_from_organism.json
- Field
preservation
fromsample.json
tostate_of_specimen.json
- Fields
enrichment
,total_estimated_cells
,well
fromsample.json
tocell_suspension.json
- Field
cell_type
fromwell.json
tocell_suspension.json
- Field
core
from non-core entities - Field
culture_type
fromsample.json
- Field
sample.geo_sample
- Field
sample.title
v3.0 - 2017-09-19
- First official release.