Linked Data Modeling Language (LinkML)

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Published October 6, 2025 | Version v4.3.0
Software Open

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Authors/Creators

Description

What's Changed

  • Added "guanyl_nucleotide_exchange" as a molecular interaction aspect … by @beasleyjonm in https://github.com/biolink/biolink-model/pull/1538
  • moves specialization qualifiers & disease context qualifier up to disease or phenotypic feature association by @kevinschaper in https://github.com/biolink/biolink-model/pull/1536
  • add icd11 and icd11.foundation as prefixes to biolink for disease by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1540
  • Add UMLS to biological process by @cbizon in https://github.com/biolink/biolink-model/pull/1541
  • regenerate files by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1544
  • fix link to https://github.com/biolink/biolink-model/blob/master/src/… by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1547
  • add object_specialization_qualifier to gene to expression site association by @kevinschaper in https://github.com/biolink/biolink-model/pull/1548
  • Copy prefixmaps json to src to access from importlib by @kevinschaper in https://github.com/biolink/biolink-model/pull/1551
  • Add FMA by @cbizon in https://github.com/biolink/biolink-model/pull/1554
  • Bump jinja2 from 3.1.4 to 3.1.6 by @dependabot[bot] in https://github.com/biolink/biolink-model/pull/1553
  • Release candidate v4.2.6 rc5 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1556
  • Add ontology class mixin to disease/phenotype/anatomy etc by @kevinschaper in https://github.com/biolink/biolink-model/pull/1564
  • update linkml to 1.9.1, keep click below 8.2.0 by @kevinschaper in https://github.com/biolink/biolink-model/pull/1565
  • Add additional case associations to represent phenopackets by @kevinschaper in https://github.com/biolink/biolink-model/pull/1558
  • Bump setuptools from 70.0.0 to 78.1.1 by @dependabot[bot] in https://github.com/biolink/biolink-model/pull/1568
  • modeling chemical/protein affinities by @cbizon in https://github.com/biolink/biolink-model/pull/1566
  • Add sources and source record urls to align with TRAPI by @colleenXu in https://github.com/biolink/biolink-model/pull/1569
  • Add z score edge property (from STATO) by @colleenXu in https://github.com/biolink/biolink-model/pull/1570
  • Update gene variant qualifiers by @colleenXu in https://github.com/biolink/biolink-model/pull/1575
  • Add HGVS Expression by @cbizon in https://github.com/biolink/biolink-model/pull/1582
  • Add has confidence score edge property (from SEPIO) by @colleenXu in https://github.com/biolink/biolink-model/pull/1571
  • Bump urllib3 from 2.2.2 to 2.5.0 by @dependabot[bot] in https://github.com/biolink/biolink-model/pull/1580
  • Bump protobuf from 4.25.1 to 4.25.8 by @dependabot[bot] in https://github.com/biolink/biolink-model/pull/1578
  • Bump requests from 2.32.3 to 2.32.4 by @dependabot[bot] in https://github.com/biolink/biolink-model/pull/1573
  • Update clinical trial node properties by @kevinschaper in https://github.com/biolink/biolink-model/pull/1562
  • response to predicate additions by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1525
  • Make sources an inlined list on Association by @kevinschaper in https://github.com/biolink/biolink-model/pull/1586
  • Add allelic requirement property by @colleenXu in https://github.com/biolink/biolink-model/pull/1576
  • Node property added for Genetic Inheritance (to complement an edge assertion model for same) by @RichardBruskiewich in https://github.com/biolink/biolink-model/pull/1588
  • Add slots to associations by @colleenXu in https://github.com/biolink/biolink-model/pull/1591
  • Tmkp classes to support TMKP pull through ingest by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1593
  • Bump lycheeverse/lychee-action from 1.9.0 to 2.0.2 in /.github/workflows by @dependabot[bot] in https://github.com/biolink/biolink-model/pull/1590
  • Bump pypa/gh-action-pypi-publish from 1.2.2 to 1.13.0 in /.github/workflows by @dependabot[bot] in https://github.com/biolink/biolink-model/pull/1592
  • Add slots to Associations for DISEASES ingest by @colleenXu in https://github.com/biolink/biolink-model/pull/1595
  • Clarifying correlated_with predicate description and note by @mbrush in https://github.com/biolink/biolink-model/pull/1603
  • Adding AI integrations by @cmungall in https://github.com/biolink/biolink-model/pull/1608
  • Add kg nodes edges to support KGX in Biolink JSONSchema serialization by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1597

Full Changelog: https://github.com/biolink/biolink-model/compare/v4.2.5...v4.3.0

Notes

Please cite the following works when using this software.

Files

biolink/biolink-model-v4.3.0.zip

Files (3.4 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/biolink/biolink-model/tree/v4.3.0 (URL)

Software

Repository URL
https://github.com/biolink/biolink-model