Open Bio Ontologies

There is a newer version of the record available.

Published September 22, 2023 | Version v0.5.20
Software Open

INCATools/ontology-access-kit: v0.5.20

Authors/Creators

  • 1. Lawrence Berkeley National Laboratory
  • 2. Northeastern University
  • 3. @jhu-bids
  • 4. Leibniz-Institut für Katalyse e.V. (LIKAT)
  • 5. Lawrence Berkeley National Lab
  • 6. LBNL
  • 7. Uni of Cambridge / @PomBase
  • 8. semanticly Ltd
  • 9. SIB Swiss Institute of Bioinformatics
  • 10. @det-lab @tis-lab @monarch-initiative
  • 11. Queen Mary University of London
  • 12. University College London
  • 13. University of São Paulo

Description

Highlights Optional extra: LLM for Named Entity Recognition (Annotation)

Optional extra, https://llm.datasette.io/

pip install 'oaklib[llm]'

This provides a lightweight version of OntoGPT. Currently only the annotate endpoint is implemented.

Create a file conf.yaml

categories: [PhenotypicFeature, Disease]
sources: [human-phenotype-ontology]

The conf file is optional - this affects the prompt

Note the conf file format for LLM is experimental and liable to change:

Run:

runoak -i llm:sqlite:obo:hp annotate -C conf.yaml "the patient has bowed and shortened tibia, as well as absent ears and no lungs"

The output is in the standard OAK text annotation format

TODO:

  • experiment with different prompt settings
  • stabilize format
  • further documentation
Attaching metadata to relationships

See:

Example code:

        >>> from oaklib import get_adapter
        >>> adapter = get_adapter("sqlite:obo:mondo")
        >>> rels = list(adapter.relationships(["MONDO:0009831"]))
        >>> for rel, metadatas in adapter.relationships_metadata(rels):
        ...     for p, v in metadatas:
        ...         print(rel, p, v)
        <BLANKLINE>
        ...
        ('MONDO:0009831', 'rdfs:subClassOf', 'MONDO:0002516') oio:source NCIT:C9005
        ...

Or on the command line:

runoak -i sqlite:obo:mondo relationships MONDO:0009831 --include-metadata -p i
What's Changed

Full Changelog: https://github.com/INCATools/ontology-access-kit/compare/v0.5.19...v0.5.20

Files

INCATools/ontology-access-kit-v0.5.20.zip

Files (16.4 MB)

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Additional details

Related works

Is supplement to
https://github.com/INCATools/ontology-access-kit/tree/v0.5.20 (URL)