v4.1.1

What's Changed

• Add RO mapping for gene/condition relations by @cbizon in #1443
• fix whitespace issues by @gprice1129 in #1441
• Adding 'phenotypic feature to disease association' plus related mixins by @RichardBruskiewich in #1444
• Documentation bug fixes and adding more examples and visualizations to help with the treats migration by @sierra-moxon in #1445

New Contributors

• @gprice1129 made their first contribution in #1441

Full Changelog: v4.1.0...v4.1.1

v4.1.0

What's Changed

• ubergraph and sri-reference-kg/monarchinitiative updates by @EvanDietzMorris in #1428
• Add infores validation checks to PRs and makefile target by @sierra-moxon in #1434
• add canonical flag to superclass of by @sierra-moxon in #1433
• make subclass of an inverse of superclass of by @sierra-moxon in #1435
• make changes according to https://docs.google.com/spreadsheets/d/12SP… by @sierra-moxon in #1436
• Adds infores:aop-cam (Adverse Outcome Pathways Casual Activity Models) by @gaurav in #1437
• Treats viz test by @sierra-moxon in #1439
• "max predicate approach" for refactoring "treats" by @sierra-moxon in #1328
• Dec 2023 infores updates for Service Provider/BTE by @colleenXu in #1429
• add context at beginning, fix some awkward wording by @nlharris in #1438
• ready for release 4.1.0 by @sierra-moxon in #1440

Full Changelog: v4.0.0...v4.1.0

v4.0.0

What's Changed

• Documentation and repo hierarchy refactoring by @sierra-moxon in #1418

Summary: 4.0.0 is a major release that includes many changes to the documentation for Biolink Model as well
as the reorganization of the repository to support the new documentation structure and comply with LinkML best
practices. The model itself has not changed significantly, but the documentation has been updated to reflect
the current state of the model, and includes new visualizations of the model, additional text-based documentation,
and a new gh-pages documentation layout.

Full Changelog: v3.6.0...v4.0.0

v3.6.0

What's Changed

• adding aspect qualifier enums by @EvanDietzMorris in #1380
• update name for gtrx infores source to match BTE's name. by @sierra-moxon in #1384
• reorder id_prefixes for small molecule, fixes #1375 by @sierra-moxon in #1376
• Update infores_catalog.yaml by @beasleyjonm in #1389
• PFCOR->PFOCR by @sierra-moxon in #1385
• Bump certifi from 2023.5.7 to 2023.7.22 by @dependabot in #1382
• Created new class GeneAffectsChemicalAssociation with qualifiers by @RichardBruskiewich in #1388
• Cx infores edits by @colleenXu in #1391
• Update understanding-the-model.md by @pabloDumas in #1394
• Fix answer appraiser infores by @maximusunc in #1396
• Chemical prefixes - propagate id_prefixes down the chemical entity hierarchy by @sierra-moxon in #1398
• Bump urllib3 from 2.0.2 to 2.0.6 by @dependabot in #1397
• Fix foodb prefixes by @cbizon in #1399
• Update xref URL for infores:arax in infores_catalog.yaml by @saramsey in #1403
• add pydantic-v2 model by @glass-ships in #1404
• Bump urllib3 from 2.0.2 to 2.0.7 by @dependabot in #1400
• add semantic map to STY:T167, fixes #1370 by @sierra-moxon in #1406
• Add qualifier to Association by @kevinschaper in #1407
• Bump urllib3 from 2.0.2 to 2.0.7 by @dependabot in #1409
• Adds deprecated as a node property slot added to biolink:Entity by @kevinschaper in #1421
• Update infores_catalog.yaml by @karafecho in #1422
• Update infores_catalog.yaml by @karafecho in #1423
• bump release to pre-doc change, 3.6.0 release, regenerate pydantic models by @sierra-moxon in #1427

New Contributors

• @pabloDumas made their first contribution in #1394
• @maximusunc made their first contribution in #1396
• @saramsey made their first contribution in #1403
• @glass-ships made their first contribution in #1404

Full Changelog: v3.5.4...v3.6.0

v3.5.4

What's Changed

• adding infores for MolePro new data source. by @sierra-moxon in #1377
• many URL updates in the infores catalog to conform with Translator wiki requirements.

Full Changelog: v3.5.3...v3.5.4

v3.5.3

What's Changed

• fix: chemical-affects-gene-association aspect qualifier range by @colleenXu in #1362
• add association slot annotation to support graphs slot, add 'semmed agreement count' as an association slot by @sierra-moxon in #1364
• Adds synonym to named thing, removes it from gene by @kevinschaper in #1369
• Update domain and range of gene condition association by @nicholsn in #1367
• Bump certifi from 2023.5.7 to 2023.7.22 by @dependabot in #1365

Full Changelog: v3.5.2...v3.5.3

v3.5.2

What's Changed

• refactor exclusion list code to remove predicate 'humn', fix t-codes by @sierra-moxon in #1358
• Exlusion list by @sierra-moxon in #1359
• more infores updates by @sierra-moxon in #1360

Full Changelog: v3.5.1...v3.5.2

v3.5.1

What's Changed

• a few new entries for the infores catalog by @EvanDietzMorris in #1350
• fix duplicated 'deprecated' syntax by @sierra-moxon in #1349
• Semmed exclusion yaml by @sierra-moxon in #1356
• Information resource updates - per TAQA curation by @sierra-moxon in #1357

Full Changelog: v3.5.0...v3.5.1

v3.5.0

What's Changed

• Adding xref for Text Mining KP by @edgargaticaCU in #1332
• Update MolePro xref in infores catalog by @vdancik in #1334
• Fix broken link in guidelines/README.md by @Daniel-Mietchen in #1336
• update BTE link in infores catalog by @andrewsu in #1337
• Add "full name" slot to the "named thing" slot list by @kevinschaper in #1335
• log odds ratio 95 ci by @CaseyTa in #1340
• Update dataset iri mappings by @nicholsn in #1338
• Stop gap changes to infores_catalog.yaml including knowledge_level and agent_type fields by @sierra-moxon in #1331
• Update BTE link to point to Translator wiki page by @andrewsu in #1342
• add simple script to extract infores resources without URLs or with g… by @sierra-moxon in #1343
• Updated infores catalog according to spreadsheet curation by @sierra-moxon in #1345
• fix : in url by @sierra-moxon in #1346
• Update infores_catalog.yaml by @karafecho in #1347

New Contributors

• @Daniel-Mietchen made their first contribution in #1336
• @nicholsn made their first contribution in #1338

Full Changelog: v3.4.3...v3.5.0

v3.4.3

What's Changed

• add 'in taxon label' as a slot on 'thing with taxon' by @kevinschaper in #1329

Full Changelog: v3.4.2...v3.4.3