v0.11.23

Commits

• ffa3211: Bump version: 0.11.22 → 0.11.23-dev (GitHub Action)
• 6374569: Add prefix: gtdb (#1242) (Benjamin M. Gyori) #1242
• f2ccb57: Add missing gtdb license (Charles Tapley Hoyt)
• d9a9df5: Add prefix: dpvocab (#1240) (github-actions[bot]) #1240
• 84581d5: Add new provider for hgnc.symbol: cbgda (#1225) (Mufaddal Naguthanawala) #1225
• bca56b1: Remove incorrect fairsharing mapping from seed (#1245) (Charles Tapley Hoyt) #1245
• 2fac64e: 🫀Health Report (GitHub Action)
• 15bc130: New prefix: humap (#1249) (Charles Tapley Hoyt) #1249
• 75be565: Update dpvocab license info (#1250) (Arthit Suriyawongkul) #1250
• 9573b48: Data updates for obo-db-ingest (#1252) (Charles Tapley Hoyt) #1252
• 400a417: Bump version: 0.11.23-dev → 0.11.23 (Charles Tapley Hoyt)

v0.11.19

Commits

• cd2c8c4: Bump version: 0.11.17 → 0.11.18-dev (GitHub Action)
• 8e9108c: 🫀Health Report (GitHub Action)
• 932b18a: Update ncbigene record (#1184) (Benjamin M. Gyori) #1184
• 8378dce: Add prefix: ncbiortholog (#1182) (github-actions[bot]) #1182
• 553a5b2: 🫀Health Report (GitHub Action)
• 41b0d13: Update wormbase pattern (#1187) (Mufaddal Naguthanawala) #1187
• 4134c17: 🫀Health Report (GitHub Action)
• 9d72627: 🫀Health Report (GitHub Action)
• c583dcc: MolMeDB homepage and repository update (#1188) (DominikMartinat) #1188
• 025b409: Update HBA and DHBA URI formats (#1192) (Benjamin M. Gyori) #1192
• be42d27: 🫀Health Report (GitHub Action)
• d3fb451: Fall cleanup (#1197) (Charles Tapley Hoyt) #1197
• fe2a685: Update minimum Python to 3.9 (#1198) (Charles Tapley Hoyt) #1198
• c09eb5d: Add meta guide (Charles Tapley Hoyt)
• 3a09989: Manual update and resolution of BioDeep issue (#1200) (Charles Tapley Hoyt) #1200
• 29ade6e: Add curation docs (Charles Tapley Hoyt)
• 5ef643d: 🫀Health Report (GitHub Action)
• 8d07ce2: Add curation guide for publications and improve testing (Charles Tapley Hoyt)
• 22f53b4: Update documentation build and CI configuration (#1205) (Charles Tapley Hoyt) #1205
• 519e867: Add publications field to providers (#1208) (Benjamin M. Gyori) #1208
• 957d28e: Update pyproject.toml and use bump-my-version (#1211) (Charles Tapley Hoyt) #1211
• 8de89f0: Address deprecation warnings (#1213) (Charles Tapley Hoyt) #1213
• 9fbd4e6: Update tox.ini (Charles Tapley Hoyt)
• e8c52cb: Update tox command in update CI configuration (Charles Tapley Hoyt)
• b6dc94e: Bump version: 0.11.18-dev → 0.11.19-dev (Charles Tapley Hoyt)
• 6d0902d: Update curated papers and add new PDB provider (FURNA) (#1193) (Mufaddal Naguthanawala) #1193
• 4cc1090: Add aipd as a provider for uniprot (#1202) (Mufaddal Naguthanawala) #1202
• 772b11a: 🫀Health Report (GitHub Action)
• 4ca5c71: Bump version: 0.11.19-dev → 0.11.19 (Charles Tapley Hoyt)

v0.11.13

Bump version: 0.11.13-dev → 0.11.13

v0.11.0

What's Changed

• Add PubMed and PMC contact and update PMC information by @cthoyt in #968
• Externalize prefix map export implementation by @cthoyt in #972
• Refactor converter generation code by @cthoyt in #974
• Reimplement CURIE prefix reconciliation for prescriptive contexts by @cthoyt in #975
• Implement rewiring by @cthoyt in #977
• Add NIST CODATA by @cthoyt in #980
• Add DOAP to semantic web collection, remove "integration status" label, and remove bulk prefix form generation by @cthoyt in #981
• Add prefix: m4i by @github-actions in #971
• Update NMDC pattern and URI format by @cthoyt in #982
• Update OBO in OWL by @cthoyt in #973
• Add NCBIGene synonym by @cthoyt in #988
• Remove unused hierarchical annotation and add additional mismatches by @cthoyt in #994
• Add field for annotating unresolvable ontologies, update OLS processing, and better annotate HPATH by @cthoyt in #993
• Add prefix: mvx by @github-actions in #987
• Add prefix: devtox by @cthoyt in #995
• Update lab and funding text by @cthoyt in #996
• Add prefix: oecd.template by @github-actions in #998
• Improve new prefix form by @cthoyt in #1000
• Add cellguide providers for CL and UBERON by @github-actions in #1002
• New prefix: openWEMI by @cthoyt in #1004
• Add Bioregistry canonical prefixes as synonyms in OBO export by @cthoyt in #1005
• New prefixes: cc and rdfa by @cthoyt in #1006
• Update shex by @cthoyt in #1007
• Add prefix: metacyc.pathway by @github-actions in #1013
• Update glygen by @jeet-vora in #1015
• Add Dewey Decimal Classification, AFTOL Categories, and improve BARTOC import by @cthoyt in #1017
• Improve FAIRsharing import by @cthoyt in #1018
• Align with Linked Open Vocabularies (LOV) by @cthoyt in #1019
• Add Zazuko Prefix Registry by @cthoyt in #1020
• Align with TogoID by @cthoyt in #1021
• Update prefix: m4i by @Zack-83 in #1022
• Add VectorBase contact by @cthoyt in #1023
• Improve ORCID validation by @cthoyt in #1024
• Align Integbio by @cthoyt in #1025
• Align with Pathguide by @cthoyt in #1026
• Add some synonyms for prefixes by @bgyori in #1027
• Updates to the WikiPathways record by @egonw in #1028
• Added the ERM Identifier Database as provider by @egonw in #1029
• Hide RDFLib import in togoid by @cthoyt in #1030
• Fix Integbio downloader by @cthoyt in #1031
• Fix new prefix action code, add missing publications key by @bgyori in #1033
• Add SID as synonym for pubchem.substance by @cthoyt in #1036
• Improve redirection by @cthoyt in #1037
• Add prefix: hgvs by @cthoyt in #1035
• Fix UniProt alignment by @cthoyt in #1038
• Update mass spec records by @cthoyt in #1040
• Mark three Bgee resources as deprecated by @cthoyt in #1041
• Add WB uppercase prefix to bioregistry by @matentzn in #1042
• Add prefix: mavedb by @github-actions in #1046
• Add missing pandas dependency for alignment by @cthoyt in #1047
• Update IDO pattern by @cthoyt in #1049
• Add NCBITaxon contact by @cthoyt in #1055
• New prefix: biocompute by @cthoyt in #1053
• Add prefix: OncoMX by @cthoyt in #1054
• Proactively update Prefix.cc by @cthoyt in #1056
• Add prefix: osti by @github-actions in #1051
• Fix Pydantic models for health report by @cthoyt in #1057
• Add license for ORDO and update OBO Foundry patterns/examples by @cthoyt in #1059
• Prepare training materials for monday by @cthoyt in #1060
• Add new providers and logo to MeSH by @rombaum in #1066
• Update contributors page by @cthoyt in #1069
• Add stylization of MeSH prefix to OBO Foundry Community Context by @kevinschaper in #1062
• Remove incorrect mapping for ICDO by @cthoyt in #1071
• Update URL for Cellosaurus OBO file by @cthoyt in #1072
• Add contact and publications for GARD by @cthoyt in #1073
• Add UMLS resource licenses by @cthoyt in #1068
• Add URI parsing endpoint by @cthoyt in #1070
• Update reference handling by @cthoyt in #1076
• License curations for gene resources by @cthoyt in #1078
• Add documentation about PURLs by @cthoyt in #1080
• More curations by @cthoyt in #1081
• Fix broken links by @cthoyt in #1082
• Add nztcs record with wikidata mapping by @cthoyt in #1083
• Don't display Twitter handles by @cthoyt in #1088
• Improve Pydantic handling of private attribute by @cthoyt in #1089
• Add new provider to Reactome record for Pathway Viewer by @github-actions in #1086
• Add lowercase preferred prefix for semweb resources, update rdf example by @bgyori in #1091
• Update GO providers and enable overriding Identifiers.org by @cthoyt in #1093
• Improve provider section of resource page on web app by @cthoyt in #1094
• Improve contribution docs by @cthoyt in #1097
• Reorganize repository structure by @cthoyt in #1103
• Change update schedule to weekly by @cthoyt in #1101
• Add new contact people by @cthoyt in #1102

New Contributors

• @jeet-vora made their first contribution in #1015
• @Zack-83 made their first contribution in #1022
• @rombaum made their first contribution in #1066
• @kevinschaper made their first contribution in #1062

Full Changelog: v0.10.65...v0.11.0

v0.10.65

Full Changelog: v0.10.64...v0.10.65

v0.10.64

Full Changelog: v0.10.63...v0.10.64

v0.10.63

Full Changelog: v0.10.62...v0.10.63

v0.9.64

Commits

• fad8d63: Bump version: 0.9.63 → 0.9.64-dev (GitHub Action)
• e82a658: Get mappings between external registries (#902) (Charles Tapley Hoyt) #902
• 2dec881: Bump version: 0.9.64-dev → 0.9.64 (Charles Tapley Hoyt)

v0.9.62

Warning
This is the last version of the Bioregistry that will support Pydantic 1.X.Y. Bioregistry v0.10.Y will require Pydantic 2.0

Commits

• e87512b: Bump version: 0.9.61 → 0.9.62-dev (GitHub Action)
• 451c878: Pin pydantic below 2.0 (Charles Tapley Hoyt)
• a48d8ad: Bump version: 0.9.62-dev → 0.9.62 (Charles Tapley Hoyt)

v0.8.0

What's Changed

• Improve CURIE and URI handling by @cthoyt in #791
• Update pattern for wikipedia.en by @cthoyt in #795
• Export extended prefix maps for contexts by @cthoyt in #793
• Add NFDI4chem prefixes and add display of collections to web app by @cthoyt in #782

Note, this release removes the ability to pass a custom prefix_map for IRI parsing. Use the curies package instead.

Full Changelog: v0.7.11...v0.8.0