biolink/biolink-model issues and pull requests

#1443 - Add RO mapping for gene/condition relations

Pull Request - State: closed - Opened by cbizon 11 months ago - 2 comments

#1442 - fIx definition of support_graphs association slot

Issue - State: closed - Opened by mbrush 11 months ago
Labels: bug

#1441 - fix whitespace issues

Pull Request - State: closed - Opened by gprice1129 11 months ago

#1440 - ready for release 4.1.0

Pull Request - State: closed - Opened by sierra-moxon 11 months ago

#1439 - Treats viz test

Pull Request - State: closed - Opened by sierra-moxon 11 months ago

#1438 - add context at beginning, fix some awkward wording

Pull Request - State: closed - Opened by nlharris 11 months ago

#1437 - Adds infores:aop-cam (Adverse Outcome Pathways Casual Activity Models)

Pull Request - State: closed - Opened by gaurav 11 months ago - 1 comment

#1436 - make changes according to https://docs.google.com/spreadsheets/d/12SP…

Pull Request - State: closed - Opened by sierra-moxon 11 months ago - 1 comment

#1435 - make subclass of an inverse of superclass of

Pull Request - State: closed - Opened by sierra-moxon 11 months ago

#1434 - Add infores validation checks to PRs and makefile target

Pull Request - State: closed - Opened by sierra-moxon 11 months ago

#1433 - add canonical flag to superclass of

Pull Request - State: closed - Opened by sierra-moxon 11 months ago

#1432 - Reconfigure OWL export

Issue - State: closed - Opened by cmungall 11 months ago

#1431 - Some confusion about the URL to be used for NCBIGene in the prefix map

Issue - State: closed - Opened by gaurav 12 months ago - 3 comments
Labels: identifiers, next release candidate

#1430 - https://biolink.github.io/ returns 404

Issue - State: open - Opened by nlharris 12 months ago
Labels: bug, documentation, next release candidate

#1429 - Dec 2023 infores updates for Service Provider/BTE

Pull Request - State: closed - Opened by colleenXu 12 months ago - 11 comments

#1428 - ubergraph and sri-reference-kg/monarchinitiative updates

Pull Request - State: closed - Opened by EvanDietzMorris 12 months ago - 1 comment

#1427 - bump release to pre-doc change, 3.6.0 release, regenerate pydantic models

Pull Request - State: closed - Opened by sierra-moxon 12 months ago

#1426 - Dependency updates

Pull Request - State: closed - Opened by glass-ships 12 months ago

#1425 - NCIT prefix should be defined in the biolink-model.yaml `prefixes` section

Issue - State: closed - Opened by gaurav 12 months ago - 3 comments
Labels: identifiers

#1424 - a few more trivial fixes of typos

Pull Request - State: closed - Opened by nlharris about 1 year ago - 1 comment

#1423 - Update infores_catalog.yaml

Pull Request - State: closed - Opened by karafecho about 1 year ago

#1422 - Update infores_catalog.yaml

Pull Request - State: closed - Opened by karafecho about 1 year ago

#1421 - Adds `deprecated` as a node property slot added to `biolink:Entity`

Pull Request - State: closed - Opened by kevinschaper about 1 year ago - 1 comment

#1420 - schema fails linkml validation

Issue - State: closed - Opened by glass-ships about 1 year ago - 2 comments
Labels: bug, LinkML

#1419 - Should `OrganismTaxon` be a child of `OrganismalEntity` ?

Issue - State: closed - Opened by hrshdhgd about 1 year ago - 2 comments
Labels: question

#1418 - initial documentation and repo hierarchy refactoring

Pull Request - State: closed - Opened by sierra-moxon about 1 year ago - 1 comment

#1417 - Improve formulation of PMC in prefix map

Issue - State: closed - Opened by cthoyt about 1 year ago - 1 comment

#1416 - representing components that can be present in complex mixture

Issue - State: open - Opened by vdancik about 1 year ago
Labels: question, working-group/chemical

#1415 - additional aspect qualifiers

Issue - State: closed - Opened by vdancik about 1 year ago - 2 comments
Labels: enhancement, working-group/MolePro, next release candidate

#1414 - representing active metabolites

Issue - State: open - Opened by vdancik about 1 year ago - 2 comments
Labels: enhancement, working-group/chemical, working-group/MolePro, next release candidate

#1413 - representing strains/variants

Issue - State: open - Opened by vdancik about 1 year ago
Labels: enhancement, working-group/predicates, working-group/MolePro

#1412 - Biolink Model "Cookbook" or ...

Issue - State: closed - Opened by RichardBruskiewich about 1 year ago - 1 comment
Labels: documentation

#1411 - Add a public visibility tag to mixins

Issue - State: open - Opened by RichardBruskiewich about 1 year ago - 2 comments

#1410 - Add biolink model purl to top level README

Issue - State: closed - Opened by kevinschaper about 1 year ago - 3 comments
Labels: documentation

#1409 - Bump urllib3 from 2.0.2 to 2.0.7

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#1408 - Docs refactor

Pull Request - State: closed - Opened by sierra-moxon about 1 year ago

#1407 - Add qualifier to Association

Pull Request - State: closed - Opened by kevinschaper about 1 year ago

#1406 - add semantic map to STY:T167, fixes #1370

Pull Request - State: closed - Opened by sierra-moxon about 1 year ago

#1405 - Promote GenomicEntity to be a concrete class instead of a mixin

Issue - State: open - Opened by gaurav about 1 year ago - 5 comments
Labels: enhancement, working-group/NodeNormalizer

#1404 - add pydantic-v2 model

Pull Request - State: closed - Opened by glass-ships about 1 year ago - 1 comment

#1403 - Update xref URL for infores:arax in infores_catalog.yaml

Pull Request - State: closed - Opened by saramsey about 1 year ago

#1402 - Update biolink-model-prefix-map.json to fix PMCID prefix expansion

Pull Request - State: open - Opened by mbrush about 1 year ago

#1401 - New predicate request for micro-organisms <=> media

Issue - State: open - Opened by hrshdhgd about 1 year ago - 4 comments
Labels: working-group/predicates, kg-hub, next release candidate

#1400 - Bump urllib3 from 2.0.2 to 2.0.7

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#1399 - Fix foodb prefixes

Pull Request - State: closed - Opened by cbizon about 1 year ago

#1398 - Chemical prefixes - propagate id_prefixes down the chemical entity hierarchy

Pull Request - State: closed - Opened by sierra-moxon about 1 year ago

#1397 - Bump urllib3 from 2.0.2 to 2.0.6

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#1396 - Fix answer appraiser infores

Pull Request - State: closed - Opened by maximusunc about 1 year ago

#1395 - Update biolink-model.yaml

Pull Request - State: closed - Opened by mbrush about 1 year ago

#1394 - Update understanding-the-model.md

Pull Request - State: closed - Opened by pabloDumas about 1 year ago

#1393 - BioLink documentation website style broken for some months now (missing the sidebar that was critical for navigation)

Issue - State: closed - Opened by vemonet about 1 year ago - 4 comments
Labels: bug, documentation

#1392 - Updating infores catalog guidelines?

Issue - State: open - Opened by colleenXu about 1 year ago
Labels: question, documentation

#1391 - Cx infores edits

Pull Request - State: closed - Opened by colleenXu about 1 year ago - 2 comments

#1390 - Undeprecate RWE predicate

Issue - State: closed - Opened by karafecho about 1 year ago
Labels: working-group/clinical, working-group/predicates, next release candidate

#1389 - Update infores_catalog.yaml

Pull Request - State: closed - Opened by beasleyjonm about 1 year ago

#1388 - Created new class GeneAffectsChemicalAssociation with qualifiers

Pull Request - State: closed - Opened by RichardBruskiewich about 1 year ago - 2 comments

#1387 - GeneAffectsChemicalAssociation with qualifiers

Issue - State: closed - Opened by RichardBruskiewich about 1 year ago - 1 comment

#1387 - GeneAffectsChemicalAssociation with qualifiers

Issue - State: closed - Opened by RichardBruskiewich about 1 year ago - 1 comment

#1386 - Duplicate `id_prefixes` for all ChemicalEntities, including all possible chemical namespaces on each class

Issue - State: closed - Opened by sierra-moxon about 1 year ago - 5 comments
Labels: working-group/chemical

#1386 - Duplicate `id_prefixes` for all ChemicalEntities, including all possible chemical namespaces on each class

Issue - State: open - Opened by sierra-moxon about 1 year ago
Labels: working-group/chemical

#1385 - PFCOR->PFOCR

Pull Request - State: closed - Opened by sierra-moxon about 1 year ago

#1385 - PFCOR->PFOCR

Pull Request - State: open - Opened by sierra-moxon about 1 year ago

#1384 - update name for gtrx infores source to match BTE's name.

Pull Request - State: closed - Opened by sierra-moxon about 1 year ago

#1384 - update name for gtrx infores source to match BTE's name.

Pull Request - State: closed - Opened by sierra-moxon about 1 year ago

#1383 - Representing references to methodology documentation

Issue - State: open - Opened by mbrush over 1 year ago
Labels: working-group/EPC

#1383 - Representing references to methodology documentation

Issue - State: open - Opened by mbrush over 1 year ago
Labels: working-group/EPC, working-group/MolePro

#1382 - Bump certifi from 2023.5.7 to 2023.7.22

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#1382 - Bump certifi from 2023.5.7 to 2023.7.22

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#1381 - Use rules constraints in LinkML to further constrain association models

Issue - State: open - Opened by sierra-moxon over 1 year ago
Labels: LinkML

#1381 - Use rules constraints in LinkML to further constrain association models

Issue - State: open - Opened by sierra-moxon over 1 year ago
Labels: LinkML

#1380 - adding aspect qualifier enums

Pull Request - State: closed - Opened by EvanDietzMorris over 1 year ago

#1380 - adding aspect qualifier enums

Pull Request - State: closed - Opened by EvanDietzMorris over 1 year ago

#1379 - Fix missing biolink:Association subclass and related slot_usage for qualifier validation (driven by specific use case)

Issue - State: open - Opened by RichardBruskiewich over 1 year ago
Labels: enhancement

#1379 - Fix missing biolink:Association subclass and related slot_usage for qualifier validation (driven by specific use case)

Issue - State: closed - Opened by RichardBruskiewich over 1 year ago - 1 comment
Labels: enhancement

GitHub / biolink/biolink-model issues and pull requests