Issues

• Include more specific association types in edge RDF output

  enhancement
  biolink/kgx#564 · Filter by author ptgolden opened on Sep 11, 2026

• Catch-all namespace in prefix_maps shadows specific mappings in the fallback maps (OBO:DDPHENO_0000001 instead of DDPHENO:0000001)

  biolink/kgx#558 · Filter by author kevinschaper opened on Aug 12, 2026

• Use "xrefs" field with curies rather than "val" field for names when getting exactSynonyms from json files

  enhancement
  biolink/kgx#530 · Filter by author bsantansb opened on Dec 12, 2025

• HTTP Error 404 for biolink-model.yaml v4.2.2 on startup/import

  bug
  biolink/kgx#527 · Filter by author bsantansb opened on Nov 18, 2025
  2

• Memory leak in neo4j-upload

  bug
  biolink/kgx#526 · Filter by author Schmoho opened on Nov 3, 2025
  3

• Update to linkml-map required

  biolink/kgx#525 · Filter by author daithi-walker opened on Oct 8, 2025

• Bad link in README.md to kgx-format.md

  bug
  biolink/kgx#518 · Filter by author chrisroederucdenver opened on Jun 27, 2025

• installation error in python 3.13

  bug
  biolink/kgx#517 · Filter by author saramsey opened on Jun 25, 2025
  1

• Make JSON Lines sink support ".tar.gz" formatting.

  enhancement
  biolink/kgx#505 · Filter by author DnlRKorn opened on Apr 8, 2025

• Parallel processing of single transform

  enhancement
  biolink/kgx#501 · Filter by author ptgolden opened on Oct 17, 2024

• Update KGX code to process new merge.yaml design

  biolink/kgx#500 · Filter by author hrshdhgd opened on Aug 6, 2024

• Make more distinction between source and sink options when parsing CLI input

  bug
  biolink/kgx#491 · Filter by author caufieldjh opened on Apr 15, 2024

• Support duckdb as alternate sink/source...or more

  enhancement
  biolink/kgx#482 · Filter by author caufieldjh opened on Apr 1, 2024
  4

• KGX support for additional formats

  enhancement
  biolink/kgx#481 · Filter by author realmarcin opened on Mar 27, 2024

• Undocumented requirements for input nodes/edges file names?

  bug
  biolink/kgx#471 · Filter by author amykglen opened on Oct 25, 2023

• KGX merge overwrites "provided_by" property

  biolink/kgx#463 · Filter by author stimon opened on Jul 12, 2023

• update KGX to optionally provide "retrieval_source_ids" attribute to collect information retrieval properties

  enhancement
  biolink/kgx#458 · Filter by author sierra-moxon opened on Jun 22, 2023

• log_error in validation scales poorly

  bug
  biolink/kgx#440 · Filter by author kevinschaper opened on Mar 21, 2023
  1

• kgx validate -o option writes an empty file, output goes to stderr rather than stdout

  bug
  biolink/kgx#435 · Filter by author kevinschaper opened on Mar 15, 2023

• Automate mapping of infores in primary_knowledge_source

  enhancement
  biolink/kgx#430 · Filter by author caufieldjh opened on Mar 10, 2023
  1

• Option to add un-prefixed labels in neo4j labels

  enhancement
  biolink/kgx#428 · Filter by author kevinschaper opened on Feb 16, 2023

• neo_sink.py constraints not created in neo4j v5+

  bug
  biolink/kgx#419 · Filter by author frdougal opened on Nov 30, 2022

• Knowledge Graph Exchange (KGE) Archive Download

  bug
  biolink/kgx#417 · Filter by author codewarrior2000 opened on Nov 9, 2022

• Dynamic configuration of Biolink Model semantics in KGX validation

  enhancement
  biolink/kgx#416 · Filter by author RichardBruskiewich opened on Nov 2, 2022

• add documentation to the kgx merge doc that shows when to use cat-merge as well as a set of steps to use merge config

  documentationenhancementgood first issue
  biolink/kgx#414 · Filter by author sierra-moxon opened on Oct 24, 2022