Releases | Open Source Science

bioregistry - v0.12.37

Commits

1b78df3: Bump version: 0.12.36 → 0.12.37-dev (GitHub Action)
a6a381b: Update minimum Python version to 3.10 (#1668) (Charles Tapley Hoyt) #1668
8baea10: 🫀Health Report (GitHub Action)
e3c44dd: Refactor paper ranking (#1666) (Charles Tapley Hoyt) #1666
58f4a45: Add new prefix snoDB (#1655) (Maaya Manoj) #1655
3cce45c: Add prefix for NFDI KG Registry (#1665) (Charles Tapley Hoyt) #1665
9e5fdd4: Update predictions file with papers between 2025-08-01 and 2025-08-31 (github-actions[bot])
d8d050d: Support processing SWO and add new prefix for OntoDM (#1669) (Charles Tapley Hoyt) #1669
8250ec2: Update BIBO (#1671) (Charles Tapley Hoyt) #1671
fa18a17: Update IANA Media Types (#1672) (Charles Tapley Hoyt) #1672
dcaf91c: Add turtle validation command (#1670) (Charles Tapley Hoyt) #1670
152152e: Bump version: 0.12.37-dev → 0.12.37 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] 10 months ago

bioregistry - v0.12.30

Commits

fae7f23: Bump version: 0.12.29 → 0.12.30-dev (Charles Tapley Hoyt)
4d4a7f6: Expose mailing list (Charles Tapley Hoyt)
e0a53c4: Bump version: 0.12.30-dev → 0.12.30 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] 10 months ago

bioregistry - v0.12.29

Commits

f92d071: Bump version: 0.12.28 → 0.12.29-dev (GitHub Action)
43d0c8a: 🫀Health Report (GitHub Action)
6f02f29: Add CITO owl link (Charles Tapley Hoyt)
700f36a: Add get_logo function (Charles Tapley Hoyt)
05ecb33: Bump version: 0.12.29-dev → 0.12.29 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] 10 months ago

bioregistry - v0.12.27

Commits

2e14028: Bump version: 0.12.26 → 0.12.27-dev (Charles Tapley Hoyt)
cd912bc: Add prefix chembl.mechanism (Charles Tapley Hoyt)
a27f74e: Bump version: 0.12.27-dev → 0.12.27 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] 11 months ago

bioregistry - v0.12.26

Commits

1470c57: Bump version: 0.12.25 → 0.12.26-dev (GitHub Action)
1937d4b: 🫀Health Report (GitHub Action)
33244f8: Require keywords in new prefix requests (#1631) (Charles Tapley Hoyt) #1631
7b65ebe: New prefix: diabetesomic (#1628) (Maaya Manoj) #1628
1374d88: Update URI format for icd10cm (#1630) (Benjamin M. Gyori) #1630
8ddc633: Additional DALIA curations (#1632) (Charles Tapley Hoyt) #1632
c67a119: Update bioregistry.json (Charles Tapley Hoyt)
56aeedb: Bump version: 0.12.26-dev → 0.12.26 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] 11 months ago

bioregistry - v0.12.24

What's Changed

Fix uri_format for infores by @matentzn in https://github.com/biopragmatics/bioregistry/pull/1618
Add new prefix: treehub by @maayamanoj466 in https://github.com/biopragmatics/bioregistry/pull/1619
Exclude ChemSpider provider in MIRIAM's InChI record by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1621

New Contributors

@maayamanoj466 made their first contribution in https://github.com/biopragmatics/bioregistry/pull/1619

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.12.23...v0.12.24

- Python
Published by cthoyt 11 months ago

bioregistry - v0.12.19

Commits

d0d8b12: Bump version: 0.12.18 → 0.12.19-dev (GitHub Action)
993f2ae: Add more DALIA/NFDI-related prefixes (#1603) (Charles Tapley Hoyt) #1603
79986fe: Add prefix: infores (#1602) (github-actions[bot]) #1602
a79f806: Update developer UI (#1605) (Charles Tapley Hoyt) #1605
70a7b95: 🫀Health Report (GitHub Action)
633b45b: New prefix: qualo (Charles Tapley Hoyt)
8dcae61: Bump version: 0.12.19-dev → 0.12.19 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] 12 months ago

bioregistry - v0.12.17

Commits

518588c: Bump version: 0.12.16 → 0.12.17-dev (GitHub Action)
0674da2: 🫀Health Report (GitHub Action)
50c974c: New prefix: spdx.term (#1598) (Charles Tapley Hoyt) #1598
ad8990d: Misc Updates May 21 (#1574) (Charles Tapley Hoyt) #1574
b34bfab: Add prefixes for NFDI/DALIA (#1597) (Charles Tapley Hoyt) #1597
45045d6: Reformat docs (#1599) (Charles Tapley Hoyt) #1599
716a326: Improve usability of derived Pydantic models (#1600) (Charles Tapley Hoyt) #1600
aad47eb: Bump version: 0.12.17-dev → 0.12.17 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] about 1 year ago

bioregistry - v0.12.8

What's Changed

Expand NCIT record with relations by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1483
Fix funderregistry regex by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1485
Add minor curations for SeMRA database build by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1486
Update schema by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1488
Replace mismatch file with more general mappings table by @bgyori in https://github.com/biopragmatics/bioregistry/pull/1458
Add provider: sabdab by @nagutm in https://github.com/biopragmatics/bioregistry/pull/1455
Add prefix: phagedive by @nagutm in https://github.com/biopragmatics/bioregistry/pull/1454
Add prefix: cncb.gwh by @nalikapalayoor in https://github.com/biopragmatics/bioregistry/pull/1452
Add prefix: rdbsb by @nagutm in https://github.com/biopragmatics/bioregistry/pull/1473
Handle empty string predicate modifier and comment when reading mappings by @bgyori in https://github.com/biopragmatics/bioregistry/pull/1491
Update curated mappings with mismatches by @bgyori in https://github.com/biopragmatics/bioregistry/pull/1457
Add prefix: dpbo by @github-actions in https://github.com/biopragmatics/bioregistry/pull/1467
Remove bad URI formats from cellosaurus ingest by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1492
Update ISBN resolver and add examples by @bgyori in https://github.com/biopragmatics/bioregistry/pull/1495

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.12.7...v0.12.8

- Python
Published by cthoyt about 1 year ago

bioregistry - v0.12.14

What's Changed

New prefix: amphiaweb.species by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1552
Add prefixes for several OBO issue trackers by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1553
Add new prefixes from Merck Index by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1554
Add minor curations to support May 2025 PyOBO build by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1555
New prefix: SDDO by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1556
Add uppercase Orphanet synonym by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1557
New prefix: CLM by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1551
New provider for pdb: rnaprodb by @nalikapalayoor in https://github.com/biopragmatics/bioregistry/pull/1547
New prefix: oprlm by @nalikapalayoor in https://github.com/biopragmatics/bioregistry/pull/1558
Add USDA veterinary biological product code number by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1562
Remove CellxGene-based providers that don't exist anymore by @bgyori in https://github.com/biopragmatics/bioregistry/pull/1561
Fix metadata for biocyc by @nalikapalayoor in https://github.com/biopragmatics/bioregistry/pull/1564
New publication: ecocyc by @nalikapalayoor in https://github.com/biopragmatics/bioregistry/pull/1565
Update curated_papers.tsv with irrelevant curations by @nalikapalayoor in https://github.com/biopragmatics/bioregistry/pull/1563
New prefix: hissta by @nalikapalayoor in https://github.com/biopragmatics/bioregistry/pull/1560
New prefix: hubmap by @nalikapalayoor in https://github.com/biopragmatics/bioregistry/pull/1548
Update MedGen by @matentzn in https://github.com/biopragmatics/bioregistry/pull/1567
Curate logo URLs by @nalikapalayoor in https://github.com/biopragmatics/bioregistry/pull/1568
Update ICD9 pattern by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/1569
Add prefixes: icpd.study and icpd.project by @github-actions in https://github.com/biopragmatics/bioregistry/pull/1571

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.12.13...v0.12.14

- Python
Published by github-actions[bot] about 1 year ago

bioregistry - v0.12.7

Commits

fbfe6f5: Bump version: 0.12.6 → 0.12.7-dev (Charles Tapley Hoyt)
26613b2: 🫀Health Report (GitHub Action)
1ed2e50: Update error messages for references (#1482) (Charles Tapley Hoyt) #1482
5d59169: Bump version: 0.12.7-dev → 0.12.7 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] about 1 year ago

bioregistry - v0.12.6

Commits

cc53525: Bump version: 0.12.5 → 0.12.6-dev (GitHub Action)
cd1b3e1: Add strict flag to normalize_prefix (#1481) (Charles Tapley Hoyt) #1481
f92dcae: Bump version: 0.12.6-dev → 0.12.6 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] about 1 year ago

bioregistry - v0.12.3

Commits

0c7a01b: Bump version: 0.12.2 → 0.12.3-dev (GitHub Action)
0f1af8c: Update predictions file with papers between 2025-02-01 and 2025-02-28 (github-actions[bot])
2f8de62: 🫀Health Report (GitHub Action)
bc13cb8: Embeddings-based automated checking of mappings for correctness (#1439) (Benjamin M. Gyori) #1439
087bba5: Remove incorrect HP mappings (#1434) (Benjamin M. Gyori) #1434
8b8560b: Ruff/mypy cleanup (#1442) (Charles Tapley Hoyt) #1442
55ee9f7: Bump version: 0.12.3-dev → 0.12.3 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] over 1 year ago

bioregistry - v0.12.0

Commits

1c69c14: Bump version: 0.11.35 → 0.11.36-dev (Charles Tapley Hoyt)
dc651ee: Add explicit contact and attribution policy (Charles Tapley Hoyt)
39ba3f9: Add prefix: eubopen (#1378) (Nalika Palayoor) #1378
fa48931: Add prefix: deims (#1382) (github-actions[bot]) #1382
57ab5ad: Generate JSON schema with Pydantic 2 (#1210) (Charles Tapley Hoyt) #1210
b5b8274: Apply black 2025 formatting (#1390) (Charles Tapley Hoyt) #1390
fedaae7: Require Pydantic 2 (#1391) (Charles Tapley Hoyt) #1391
f0a1f0f: Start applying ruff (#1371) (Charles Tapley Hoyt) #1371
e315071: Update predictions file with papers between 2025-01-02 and 2025-02-01 (github-actions[bot])
177d904: Override URI format for SIO (#1395) (Benjamin M. Gyori) #1395
9be5cd2: 🫀Health Report (GitHub Action)
ace8b61: Update ECCODE pattern to allow optional dashes (#1396) (Benjamin M. Gyori) #1396
e83e2f4: Adjust the dates for paper_ranking pipeline to be from the first to the last of the previous month (#1402) (Mufaddal Naguthanawala) #1402
89221aa: Add prefix: mibig (#1408) (github-actions[bot]) #1408
a1283c3: New prefix: mirgenedb (#1393) (Nalika Palayoor) #1393
3b9f87d: Update curated_papers.tsv with irrelevant curations (#1380) (Nalika Palayoor) #1380
cf18218: 🫀Health Report (GitHub Action)
60c44c3: Fixing GO entries (#1411) (Chris Mungall) #1411
c0f9641: New schema field - contact page (#1392) (Charles Tapley Hoyt) #1392
7fae7ba: Rename clingene to clingen.allele (#1412) (Mufaddal Naguthanawala) #1412
7005a15: Update URI formats for tair.locus and tair.protein (#1386) (Benjamin M. Gyori) #1386
7b35140: New publication: rgd (#1399) (Nalika Palayoor) #1399
ba174d0: New prefix: psskb (#1398) (Nalika Palayoor) #1398
6fdc2c6: Rename eccode to ec (#1413) (Mufaddal Naguthanawala) #1413
8436c96: New prefix: holofood (#1400) (Nalika Palayoor) #1400
c32768c: Update curated_papers.tsv with irrelevant curations (#1401) (Nalika Palayoor) #1401
9fa6bdf: New schema field - secondary contact list (#1388) (Charles Tapley Hoyt) #1388
d97de9a: New schema field - group email (#1389) (Charles Tapley Hoyt) #1389
8f33ba9: New schema element: secondary reviewers (#1415) (Charles Tapley Hoyt) #1415
79f405f: Add prefix: mite (#1406) (github-actions[bot]) #1406
38f25fe: Show provenance for annotations in web app (#1095) (Charles Tapley Hoyt) #1095
04515e8: Bump version: 0.12.0-dev → 0.12.0 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] over 1 year ago

bioregistry - v0.11.35

Commits

ffd5863: Bump version: 0.11.34 → 0.11.35-dev (GitHub Action)
32b809f: Update prefix: seed --> seed.subsystem (#1365) (Nalika Palayoor) #1365
f70ffa6: Update curated_papers.tsv with irrelevant curations (#1364) (Nalika Palayoor) #1364
e591cfc: 🫀Health Report (GitHub Action)
3bd2d2b: New prefix: PharmGKB Variant (#1368) (Charles Tapley Hoyt) #1368
bfee1d4: Commit Predictions File with Git Hash Link, Remove Artifact Upload (#1350) (Mufaddal Naguthanawala) #1350
fccbfae: Search PubMed Papers In Specific Date Range for Paper Ranking Workflow (#1367) (Mufaddal Naguthanawala) #1367
2e7bcab: Add test for duplicate PubMed in literature curation sheet (#1369) (Charles Tapley Hoyt) #1369
d1d8c00: Avoid returning windows-style line returns (#1370) (Charles Tapley Hoyt) #1370
a97db54: Lint (Charles Tapley Hoyt)
36cad81: Add prefix: seed.role (#1341) (github-actions[bot]) #1341
5439c7a: New prefix: NORD (#1375) (Charles Tapley Hoyt) #1375
8bd8b65: Add prefix: dome (#1374) (Nalika Palayoor) #1374
da38028: Update curated_papers.tsv with irrelevant curations (#1372) (Nalika Palayoor) #1372
4a4d972: Update curated_papers.tsv with irrelevant curations (#1377) (Nalika Palayoor) #1377
de94940: Add data integrity check for bad emails and malformed repositories (#1379) (Charles Tapley Hoyt) #1379
335528b: 🫀Health Report (GitHub Action)
aabc683: Update New Prefix Workflow to Process Specific Issue (#1376) (Mufaddal Naguthanawala) #1376
1a53a3c: Add OWL download for uniprot.core (Charles Tapley Hoyt)
d6c41f4: Add note about prefix pluralization to contribution guidelines (Charles Tapley Hoyt)
0c87a55: Add prefix: silva (#1307) (github-actions[bot]) #1307
c7ad37f: Bump version: 0.11.35-dev → 0.11.35 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] over 1 year ago

bioregistry - 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)

- Python
Published by github-actions[bot] over 1 year ago

bioregistry - 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)

- Python
Published by github-actions[bot] over 1 year ago

bioregistry - v0.11.13

- Python
Published by cthoyt almost 2 years ago

bioregistry - v0.11.0

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

- Python
Published by cthoyt about 2 years ago

bioregistry - v0.10.65

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.10.64...v0.10.65

- Python
Published by cthoyt over 2 years ago

bioregistry - v0.10.64

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.10.63...v0.10.64

- Python
Published by cthoyt over 2 years ago

bioregistry - v0.10.63

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.10.62...v0.10.63

- Python
Published by cthoyt over 2 years ago

bioregistry - 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)

- Python
Published by github-actions[bot] almost 3 years ago

bioregistry - 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)

- Python
Published by github-actions[bot] almost 3 years ago

bioregistry - v0.8.0

What's Changed

Improve CURIE and URI handling by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/791
Update pattern for wikipedia.en by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/795
Export extended prefix maps for contexts by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/793
Add NFDI4chem prefixes and add display of collections to web app by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/782

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

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.7.11...v0.8.0

- Python
Published by cthoyt about 3 years ago

bioregistry - v0.7.1

What's Changed

Update BARTOC by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/785
Use rdflib-endpoint for SPARQL service by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/780

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.7.0...v0.7.1

- Python
Published by cthoyt about 3 years ago

bioregistry - v0.7.0

What's Changed

Mount onto FastAPI by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/779

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.6.108...v0.7.0

- Python
Published by cthoyt about 3 years ago

bioregistry -

- Python
Published by cthoyt over 3 years ago

bioregistry - v0.6.13

Commits

2b9535d: Bump version: 0.6.12 → 0.6.13-dev (GitHub Action)
b882c44: Add additional download links (Charles Tapley Hoyt)
1fd1586: Add top-level converter (#652) (Charles Tapley Hoyt) #652
e278b86: Bump version: 0.6.13-dev → 0.6.13 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] over 3 years ago

bioregistry - v0.6.0

What's Changed

Reimplement prefix map generation by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/642
Add addition prefix map options by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/644
Update project by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/645

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.5.143...v0.6.0

- Python
Published by cthoyt over 3 years ago

bioregistry - v0.5.132 - Manuscript Revision Companion

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.5.131...v0.5.132

- Python
Published by cthoyt over 3 years ago

bioregistry -

- Python
Published by cthoyt over 3 years ago

bioregistry -

- Python
Published by cthoyt over 3 years ago

bioregistry -

- Python
Published by cthoyt over 3 years ago

bioregistry -

- Python
Published by cthoyt over 3 years ago

bioregistry - v0.5.110

What's Changed

Simplify alignment code by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/588
Add new external registry HL7 External Code Sytems by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/587
Update comparison image code by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/589

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.5.109...v0.5.110

- Python
Published by cthoyt over 3 years ago

bioregistry - v0.5.104

Commits

1e763e9: Bump version: 0.5.103 → 0.5.104-dev (GitHub Action)
34c1f35: Revert HGNC and VGNC banana (Charles Tapley Hoyt)
bae54a9: Bump version: 0.5.104-dev → 0.5.104 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] over 3 years ago

bioregistry - v0.5.86

What's Changed

Add twitter and relations highlight pages by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/552
Improve MIRIAM ingest by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/551
Improve URI parsing with tries by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/553
Enable omni-reverse prefix map by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/554

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.5.85...v0.5.86

- Python
Published by cthoyt almost 4 years ago

bioregistry - v0.5.68

What's Changed

Add curations based on KGOBO dump by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/509
Add prefixes: google.book and time by @github-actions in https://github.com/biopragmatics/bioregistry/pull/506
Add script for standardizing attribution by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/514
Add prefixes: hathitrust, langual, and linkml by @github-actions in https://github.com/biopragmatics/bioregistry/pull/513
Add prefix: dbo by @github-actions in https://github.com/biopragmatics/bioregistry/pull/516

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.5.67...v0.5.68

- Python
Published by cthoyt almost 4 years ago

bioregistry - v0.5.64

Commits

6de5b56: Bump version: 0.5.63 → 0.5.64-dev (GitHub Action)
005a836: Add CURIE parse benchmark (#499) (Charles Tapley Hoyt) #499
c7f0bcc: Add CURIE validation benchmark (#500) (Charles Tapley Hoyt) #500
3e6eabc: Collapse configuration files (Charles Tapley Hoyt)
789b2b3: Make getting obo context prefix map easier (#501) (Charles Tapley Hoyt) #501
dbec9fd: Bump version: 0.5.64-dev → 0.5.64 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] almost 4 years ago

bioregistry - v0.5.54

What's Changed

Align with Re3data by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/489

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.5.53...v0.5.54

- Python
Published by cthoyt almost 4 years ago

bioregistry -

- Python
Published by cthoyt almost 4 years ago

bioregistry -

- Python
Published by cthoyt about 4 years ago

bioregistry - v0.5.5

Commits

7d6f389: Bump version: 0.5.4 → 0.5.5-dev (Charles Tapley Hoyt)
4d7a286: Update release.yml (#392) (Adriano Rutz) #392
c4e8ce6: Bump version: 0.5.5-dev → 0.5.5 (Charles Tapley Hoyt)

- Python
Published by github-actions[bot] about 4 years ago

bioregistry - latest

- Python
Published by github-actions[bot] about 4 years ago

bioregistry - v0.5.0

What's Changed

Resolve discrepancy between Prefix Commons and BioContext by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/383
Add additional prefixes by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/384
Update docs by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/385
Update OLS ingestion by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/386
Reorganize aligners and downloaders by @cthoyt in https://github.com/biopragmatics/bioregistry/pull/387

Full Changelog: https://github.com/biopragmatics/bioregistry/compare/v0.4.120...v0.5.0

- Python
Published by cthoyt about 4 years ago

bioregistry - v0.4.0

Add consensus view generation (#235)
Reorganize exports (#235)
Switch schema around (#237)
Change several requirements to optional (#238, #239, #240)

- Python
Published by cthoyt over 4 years ago

bioregistry -

August updates
Switch to bump2version and get automatic tagging ready
Got external curation #154 for wwf.ecoregion (thanks @cmungall)

- Python
Published by cthoyt almost 5 years ago

bioregistry -

Allow custom prefix map in parse_iri function
fix ATCC pattern

- Python
Published by cthoyt almost 5 years ago

bioregistry -

Add selventa resources
Update EC code URL (thanks @bgyori)
Add health check scripts
Implement IRI parsing

- Python
Published by cthoyt almost 5 years ago

bioregistry -

Enforce examples on all non-deprecated/non-proprietary entries and rename ccle.cell to ccle

- Python
Published by cthoyt almost 5 years ago

bioregistry -

More curation updates and added contributors schema/web

- Python
Published by cthoyt almost 5 years ago

bioregistry -

Fix bug in parsing of CURIEs
deprecate bioregistry.get() in favor of bioregistry.get_resource()
Add biogrid.interaction

- Python
Published by cthoyt almost 5 years ago

bioregistry -

fix bug in checking for resources that don't have their own terms, and switch function name to bioregistry.hasnoterms
make normalization of identifiers part of public interface

- Python
Published by cthoyt almost 5 years ago

bioregistry -

blacken code
add some new curated sources

- Python
Published by cthoyt almost 5 years ago

bioregistry -

Add more docs to structs, update JSON schema, and update MeSH URL.

- Python
Published by cthoyt almost 5 years ago

bioregistry -

- Python
Published by cthoyt almost 5 years ago

bioregistry -

Add full schema with Pydantic
Rewrite all downloaders and aligners

- Python
Published by cthoyt about 5 years ago

bioregistry -

Clean up RDF schema and add documentation
Add JSON-LD exports
Fix UniProt metaresource alignment
Add downloads for RDF on individual pages

- Python
Published by cthoyt about 5 years ago

bioregistry -

Add endpoint for ad-hoc generation of context JSON-LD files (#60)
Add RDF, TSV, and YAML exports (#70)
Clean up curated database and add more checks for correctness (#71, #72)

- Python
Published by cthoyt about 5 years ago

bioregistry -

Fix issue where exception isn't caught if git isn't available (I found this when trying to build an alpine docker container with the Bioregistry web application)

- Python
Published by cthoyt about 5 years ago

bioregistry -

Fix logo link

- Python
Published by cthoyt about 5 years ago

bioregistry -

Remove dependence on pandas and unused dataframe-related functions
Add database of mismatches to better automate issues like that with GEO

- Python
Published by cthoyt about 5 years ago

bioregistry -

Add collections
Add FAIRSharing links
Automate comparisons for inclusion of new entries in the metaregistry
Align UniProt registry
Fix OBO Foundry prefix handling
Add autocomplete box to web app (thanks @pagreene)
Add functionality for generating JSON-LD context files

- Python
Published by cthoyt about 5 years ago

bioregistry -

Major improvements to web app and more curation

- Python
Published by cthoyt about 5 years ago

bioregistry -

Add functions for parsing CURIE, getting a homepage for a prefix, and getting a link for a CURIE.

- Python
Published by cthoyt about 5 years ago