INCATools/ontology-access-kit: v0.5.20

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: https://github.com/INCATools/ontology-access-kit/pull/656 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) ... ('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 Adding llm as an extra, adding llm implementation for annotation by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/658 Additional documentation by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/655 Adding ability to retrieve axiom annotations on relationships (axiom annotations) by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/656 minor obographviz config change: new color disambiguating chebi by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/657 Full Changelog: https://github.com/INCATools/ontology-access-kit/compare/v0.5.19...v0.5.2