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Changelog for reference_file.json

Minor changes since schema version 15

  • Extend collections enum list to include IGVF_catalog_beta_v0.5.
  • Add checkfiles_version.
  • Extend upload_status enum list to include validation exempted.
  • Extend status enum list to include preview.
  • Update calculation of summary.
  • Extend transcriptome_annotation enum list to include GENCODE 32.

Schema version 15

  • Remove external_id.
  • Update dbxrefs regex to add ENCODE as a namespace.

Minor changes since schema version 14

  • Extend assembly enum list to include custom.
  • Add derived_manually.
  • Extend collections enum list to include VarChAMP.
  • Extend assembly enum list to include Cast - GRCm39.
  • Extend transcriptome_annotation enum list to include GENCODE Cast - M32.
  • Adjust content_type enum list to allow usage of transcriptome reference for all users.
  • Add calculated property assay_titles.
  • Adjust content_type enum list to restrict usage of biological_context to admin users.
  • Adjust content_type enum list to restrict usage of coding_variants to admin users.
  • Adjust content_type enum list to restrict usage of complexes to admin users.
  • Adjust content_type enum list to restrict usage of complexes_complexes to admin users.
  • Adjust content_type enum list to restrict usage of complexes_proteins to admin users.
  • Adjust content_type enum list to restrict usage of complexes_terms to admin users.
  • Adjust content_type enum list to restrict usage of diseases_genes to admin users.
  • Adjust content_type enum list to restrict usage of documentation (readme) to admin users.
  • Adjust content_type enum list to restrict usage of drugs to admin users.
  • Adjust content_type enum list to restrict usage of elements_genes to admin users.
  • Adjust content_type enum list to restrict usage of genes to admin users.
  • Adjust content_type enum list to restrict usage of genes_genes to admin users.
  • Adjust content_type enum list to restrict usage of genes_pathways to admin users.
  • Adjust content_type enum list to restrict usage of genes_terms to admin users.
  • Adjust content_type enum list to restrict usage of genes_transcripts to admin users.
  • Adjust content_type enum list to restrict usage of go_terms_proteins to admin users.
  • Adjust content_type enum list to restrict usage of motifs to admin users.
  • Adjust content_type enum list to restrict usage of motifs_proteins to admin users.
  • Adjust content_type enum list to restrict usage of ontology_terms to admin users.
  • Adjust content_type enum list to restrict usage of ontology_terms_ontology_terms to admin users.
  • Adjust content_type enum list to restrict usage of pathways to admin users.
  • Adjust content_type enum list to restrict usage of pathways_pathways to admin users.
  • Adjust content_type enum list to restrict usage of proteins to admin users.
  • Adjust content_type enum list to restrict usage of proteins_proteins to admin users.
  • Adjust content_type enum list to restrict usage of regulatory_regions to admin users.
  • Adjust content_type enum list to restrict usage of regulatory_regions_genes to admin users.
  • Adjust content_type enum list to restrict usage of regulatory_regions_genes_biosamples to admin users.
  • Adjust content_type enum list to restrict usage of regulatory_regions_genes_biosamples_donors to admin users.
  • Adjust content_type enum list to restrict usage of regulatory_regions_genes_biosamples_treatments_chebi to admin users.
  • Adjust content_type enum list to restrict usage of regulatory_regions_genes_biosamples_treatments_proteins to admin users.
  • Adjust content_type enum list to restrict usage of regulatory_regions_regulatory_regions to admin users.
  • Adjust content_type enum list to restrict usage of studies to admin users.
  • Adjust content_type enum list to restrict usage of studies_variants to admin users.
  • Adjust content_type enum list to restrict usage of studies_variants_phenotypes to admin users.
  • Adjust content_type enum list to restrict usage of transcriptome reference to admin users.
  • Adjust content_type enum list to restrict usage of transcripts to admin users.
  • Adjust content_type enum list to restrict usage of transcripts_proteins to admin users.
  • Adjust content_type enum list to restrict usage of variants to admin users.
  • Adjust content_type enum list to restrict usage of variants_coding_variants to admin users.
  • Adjust content_type enum list to restrict usage of variants_diseases to admin users.
  • Adjust content_type enum list to restrict usage of variants_diseases_genes to admin users.
  • Adjust content_type enum list to restrict usage of variants_drugs to admin users.
  • Adjust content_type enum list to restrict usage of variants_drugs_genes to admin users.
  • Adjust content_type enum list to restrict usage of variants_genes to admin users.
  • Adjust content_type enum list to restrict usage of variants_genes_terms to admin users.
  • Adjust content_type enum list to restrict usage of variants_phenotypes to admin users.
  • Adjust content_type enum list to restrict usage of variants_phenotypes_studies to admin users.
  • Adjust content_type enum list to restrict usage of variants_proteins to admin users.
  • Adjust content_type enum list to restrict usage of variants_proteins_terms to admin users.
  • Adjust content_type enum list to restrict usage of variants_proteins_biosamples to admin users.
  • Adjust content_type enum list to restrict usage of variants_proteins_phenotypes to admin users.
  • Adjust content_type enum list to restrict usage of variants_regulatory_regions to admin users.
  • Extend content_type enum list to include coding_variants.
  • Extend content_type enum list to include documentation (readme).
  • Extend content_type enum list to include variants_coding_variants.
  • Extend content_type enum list to include variants_diseases.
  • Extend content_type enum list to include variants_diseases_genes.
  • Extend content_type enum list to include variants_phenotypes.
  • Extend content_type enum list to include variants_phenotypes_studies.
  • Update calculation of summary.
  • Add analysis_step_version.
  • Add calculated property input_file_for.

Schema version 14

  • Reduce upload_status enum list to exclude deposited.
  • Remove anvil_source_url.
  • Add anvil_url.
  • Require controlled_access.

Minor changes since schema version 13

  • Extend content_type enum list to include regulatory_regions_regulatory_regions.
  • Extend file_format_type enum list to include mpra_starr.
  • Extend collections enum list to include Vista.
  • Extend collections enum list to include IGVF_catalog_beta_v0.2.
  • Extend collections enum list to include IGVF_catalog_beta_v0.3.
  • Extend collections enum list to include IGVF_catalog_beta_v0.4.

Schema version 13

  • Extend upload_status enum list to include deposited.
  • Add controlled_access.
  • Add anvil_source_url.
  • Add calculated property anvil_destination_url.

Schema version 12

  • Require derived_from to contain at least one value.
  • Require file_format_specifications to contain at least one value.

Minor changes since schema version 11

  • Add calculated property integrated_in.

Schema version 11

  • Require release_timestamp for any objects with released, archived, or revoked status.

Minor changes since schema version 10

  • Update aliases regex to add buenrostro-bernstein as a namespace.
  • Add elements reference to content_type.
  • Add GENCODE 44, GENCODE 45, GENCODE M33, and GENCODE M34 to transcriptome_annotation.
  • Add release_timestamp.
  • Add MPRAbase to collections.
  • Add proteins_proteins, regulatory_regions_genes, regulatory_regions_genes_biosamples, regulatory_regions_genes_biosamples_donors, regulatory_regions_genes_biosamples_treatments_chebi, regulatory_regions_genes_biosamples_treatments_proteins, and variants_genes_terms to content_type.
  • Adjust content_type enum list to restrict usage of guide RNA sequences, sequence barcodes, vector sequences to admin users.

Schema version 10

  • Require assembly if file_format is one of bam, bed, bedpe, bigWig, bigBed, bigInteract, tabix, or vcf.

Schema version 9

  • Require publicly released files to have upload_status of validated or invalidated.

Schema version 8

  • Disallow empty strings in description.

Schema version 7

  • Add a default value for external.

Minor changes since schema version 6

  • Add tsv to file_format.
  • Add variants_proteins_biosamples and variants_proteins_phenotypes to content_type.
  • Add sources.
  • Add external.
  • Add external_id.

Schema version 6

  • Enable submission of GENCODE, ENSEMBL, and GRC database references to dbxrefs.
  • Require a minimum of 1 item for dbxrefs.

Schema version 5

  • Add file_format_type.

Minor changes since schema version 4

  • Add vcf to file_format.
  • Add variants to content_type.
  • Add bed, csv, dat, gaf, gds, obo, owl, PWM and xml to file_format.
  • Add biological_context, complexes, complexes_complexes, complexes_proteins, complexes_terms, diseases_genes, drugs, elements_genes, genes, genes_genes, genes_pathways, genes_terms, genes_transcripts, go_terms_proteins, motifs, motifs_proteins, ontology_terms, ontology_terms_ontology_terms, pathways, pathways_pathways, proteins, regulatory_regions, studies, studies_variants, studies_variants_phenotypes, transcriptome reference, transcripts, transcripts_proteins, variants, variants_drugs, variants_drugs_genes, variants_genes, variants_proteins, variants_proteins_terms, variants_regulatory_regions, variants_variants to content_type.
  • Expand collections enum list to include ClinGen, GREGoR, IGVF_catalog_beta_v0.1, and MaveDB.

Schema version 4

  • Update enums in transcriptome_annotation to include GENCODE prefix.

Schema version 3

  • Rename source to source_url.
  • Add format to source_url.