biolink/kgx

Issues

• Update KGX code to process new `merge.yaml` design

  #500 opened 3 months ago by hrshdhgd
  0

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

  #491 opened 7 months ago by caufieldjh
  0

• Provide source or sink as Parquet

  #484 opened 7 months ago by caufieldjh
  0

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

  #482 opened 7 months ago by caufieldjh
  2

• KGX support for additional formats

  #481 opened 7 months ago by realmarcin
  0

• Obsolete/Deprecated property is not populated when converting from obojson

  #470 opened a year ago by kevinschaper
  15

• Undocumented requirements for input nodes/edges file names?

  #471 opened a year ago by amykglen
  0

• KGX merge overwrites "provided_by" property

  #463 opened a year ago by stimon
  0

• Relax KGX's `pandas` version dependency.

  #461 opened a year ago by hrshdhgd
  0

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

  #458 opened a year ago by sierra-moxon
  0

• When translating kgx tsvs to ntriples, type assertions are wrong

  #445 opened 2 years ago by matentzn
  0

• add SQL sink

  #443 opened 2 years ago by sierra-moxon
  0

• log_error in validation scales poorly

  #440 opened 2 years ago by kevinschaper
  1

• run kgx validate from inside the project - need scripts defined in pyproject.toml

  #432 opened 2 years ago by sierra-moxon
  2

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

  #435 opened 2 years ago by kevinschaper
  0

• Automate mapping of infores in primary_knowledge_source

  #430 opened 2 years ago by caufieldjh
  1

• Fetching biolink-model for validate is confused by `v` in biolink version

  #431 opened 2 years ago by kevinschaper
  1

• Option to add un-prefixed labels in neo4j labels

  #428 opened 2 years ago by kevinschaper
  0

• migrate KGX to poetry

  #403 opened 2 years ago by sierra-moxon
  1

• Error occurs when specifying a version starting with "v" in get_biolink_model_schema method

  #421 opened 2 years ago by daikiad
  1

• remove pinning of docutils==0.16.0 so that downstream users can also use sphinx

  #423 opened 2 years ago by sierra-moxon
  0

• Perhaps KGX files should be somewhat self documenting with respect to key parameters like their Biolink Model version

  #392 opened 2 years ago by RichardBruskiewich
  1

• Do the KGX serialization formats support representation of Biolink qualifiers?

  #420 opened 2 years ago by bill-baumgartner
  2

• neo_sink.py constraints not created in neo4j v5+

  #419 opened 2 years ago by frdougal
  0

• Knowledge Graph Exchange (KGE) Archive Download

  #417 opened 2 years ago by codewarrior2000
  0

• Duplication of identifiers in pipe-delimited slot value lists

  #373 opened 2 years ago by RichardBruskiewich
  3

• add ability to walk up ontologies to find Biolink-Model mappings

  #378 opened 3 years ago by sierra-moxon
  2

• Remove legacy Biolink Model fields like 'relation'

  #363 opened 3 years ago by RichardBruskiewich
  1

• Dynamic configuration of Biolink Model semantics in KGX validation

  #416 opened 2 years ago by RichardBruskiewich
  0

• 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

  #414 opened 2 years ago by sierra-moxon
  0

• KGX edge merge does not take into account enough attributes on the edge

  #413 opened 2 years ago by sierra-moxon
  1

• Add ability to "turn off" KGX's prefix mapping functionality

  #412 opened 2 years ago by sierra-moxon
  0

• command line option to drop "not" edges

  #393 opened 2 years ago by sierra-moxon
  0

• Description of affect of clique_merge on node properties

  #394 opened 2 years ago by frdougal
  1

• Set the `provided_by` of nodes.tsv as an option

  #400 opened 2 years ago by 0m1n0
  3

• TSV->TSV transform ignores transform-level metadata about knowledge sources

  #407 opened 2 years ago by sierra-moxon
  0

• Clean up tests, code around provided_by.

  #383 opened 2 years ago by sierra-moxon
  0

• Create citable archive on Zenodo

  #401 opened 2 years ago by cthoyt
  2

• remove knowledge source parameters from node files (instead rely on provided_by for nodes)

  #404 opened 2 years ago by sierra-moxon
  4

• Edge attribute JSON is stringified

  #399 opened 2 years ago by maximusunc
  0

• Neo4j 4.x empty after loading with kgx transform

  #402 opened 2 years ago by kevinschaper
  1

• kgx_validate sometimes hangs

  #379 opened 2 years ago by sierra-moxon
  1

• Does Sphinx need to be anchored between versions (sphinx<5,>=3.1)

  #395 opened 2 years ago by hrshdhgd
  0

• The neo4j docker image doesn't work on M1 macs as described in doc

  #389 opened 2 years ago by goodb
  1

• Questions about clique_merge

  #391 opened 2 years ago by frdougal
  3

• Make stream processing the default mode for validation and graph summaries; possibly transform in general; maybe remove --stream option for these commands

  #384 opened 3 years ago by RichardBruskiewich
  1

• Capture ensmallen graph topologies in KGX

  #366 opened 3 years ago by sierra-moxon
  2

• pip dependency conflict?

  #371 opened 3 years ago by RichardBruskiewich
  3

• Allow user-provided SSSOM maps to be used for prefix prioritization

  #369 opened 3 years ago by caufieldjh
  1

• !!set markup seen in KGX yaml output

  #360 opened 3 years ago by RichardBruskiewich
  2