Open Bio Ontologies

There is a newer version of the record available.

Published November 29, 2022 | Version v0.1.56
Software Open

INCATools/ontology-access-kit: v0.1.56

Creators

  • 1. Lawrence Berkeley National Laboratory
  • 2. Harvard Medical School
  • 3. @TB-Modeling
  • 4. SIB Swiss Institute of Bioinformatics
  • 5. LBNL
  • 6. Leibniz-Institut für Katalyse e.V.
  • 7. Queen Mary University of London
  • 8. Lawrence Berkeley National Lab
  • 9. semanticly Ltd

Description

Enhanced Diff Functionality

This release includes additional functionality in the diff command, and underlying python library

Supported KGCL types

Diff will recognize the following types

  • ClassCreation: new class was created
  • NewSynonym: new synonym was created
  • RemoveSynonym: a synonym was removed
  • SynonymPredicateChange: synonym scope change (e.g exact to related)
  • NodeDeletion: a node (class or other) was deleted
  • NodeObsoletion: an obsoletion of a node
    • NodeObsoletionWithDirectReplacement: as above, with a replaced-by
    • NodeDirectMerge: a merge obsoletion (resulting in alt_id)
  • NodeMove: a move from one parent to another
  • NodeRename: a label changes
  • PredicateChange: an edge label changes (e.g. isa to partof)

Output can be

  • YAML
  • JSON
  • KGCL syntax
Diff statistics

The --statistics option can be added to the diff command.

this can also be grouped by obo namespace, prefix, or any annotation property

runoak -i go-2020.obo diff -X go-2022.obo --group-by-obo-namespace --statistics

__RESIDUAL__:
  NodeCreation: 1
  NodeDeletion: 52
biological_process:
  ClassCreation: 217
  NewSynonym: 1433
  NodeDeletion: 5
  NodeDirectMerge: 219
  NodeMove: 6637
  NodeObsoletion: 782
  NodeObsoletionWithDirectReplacement: 35
  NodeRename: 1606
  PredicateChange: 27
  RemoveSynonym: 1011
  SynonymPredicateChange: 90
cellular_component:
  ClassCreation: 34
  NewSynonym: 110
  NodeDirectMerge: 30
  NodeMove: 906
  NodeObsoletion: 19
  NodeObsoletionWithDirectReplacement: 132
  NodeRename: 197
  PredicateChange: 1
  RemoveSynonym: 58
  SynonymPredicateChange: 13
external:
  NodeRename: 2
molecular_function:
  ClassCreation: 315
  NewSynonym: 906
  NodeDirectMerge: 133
  NodeMove: 1695
  NodeObsoletion: 65
  NodeObsoletionWithDirectReplacement: 10
  NodeRename: 568
  NodeUnobsoletion: 3
  PredicateChange: 7
  RemoveSynonym: 806
  SynonymPredicateChange: 277
What's Changed

Full Changelog: https://github.com/INCATools/ontology-access-kit/compare/v0.1.55...v0.1.56

Files

INCATools/ontology-access-kit-v0.1.56.zip

Files (9.8 MB)

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Additional details

Related works

Is supplement to
https://github.com/INCATools/ontology-access-kit/tree/v0.1.56 (URL)