Unifying the Identification of Biomedical Entities with the Bioregistry

What's Changed

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

New Contributors

• @jeet-vora made their first contribution in https://github.com/biopragmatics/bioregistry/pull/1015
• @Zack-83 made their first contribution in https://github.com/biopragmatics/bioregistry/pull/1022
• @rombaum made their first contribution in https://github.com/biopragmatics/bioregistry/pull/1066
• @kevinschaper made their first contribution in https://github.com/biopragmatics/bioregistry/pull/1062

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.10.65...v0.11.0