v0.5.21

What's Changed

• Fix for #662 - Update address for node normalizer endpoint by @caufieldjh in #663
• Use passthrough from curies v0.6.6 by @cthoyt in #669

Full Changelog: v0.5.20...v0.5.21

v0.5.21-rc2

Full Changelog: v0.5.19-rc1...v0.5.21-rc2

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

As requested by @joeflack4

See:

• #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)
        <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

• Adding llm as an extra, adding llm implementation for annotation by @cmungall in #658
• Additional documentation by @cmungall in #655
• Adding ability to retrieve axiom annotations on relationships (axiom annotations) by @cmungall in #656 @joeflack4
• minor obographviz config change: new color disambiguating chebi by @cmungall in #657

Full Changelog: v0.5.19...v0.5.20

v0.5.19

Highlights

The release adds a command validate-mappings:

Given an ontology, it will fetch all mappings, and check them for

• cardinality problems
• links to obsolete classes

The output is an SSSOM file containing only problematic lines, with the problem injected into the comment file

Example notebook:

https://github.com/INCATools/ontology-access-kit/blob/main/notebooks/Commands/ValidateMappings.ipynb

can be used in python like this

    >>> from oaklib import get_adapter
    >>> from oaklib.utilities.mapping.mapping_validation import validate_mappings
    >>> adapter = get_adapter("sqlite:obo:xao")
    >>> mappings = list(adapter.sssom_mappings())
    >>> for errors, m in validate_mappings(mappings):
    ...     print(errors, m.subject_id, m.object_id)
    <BLANKLINE>
    ...

What's Changed

• examples for working with disjoints by @cmungall in #651
• Adding validate-mappings command. by @cmungall in #652

Full Changelog: v0.5.18...v0.5.19

v0.5.19-rc1

What's Changed

• New notebook that runs examples showcased in Mondo paper by @hrshdhgd in #584
• Allow diffs to be filtered by change type (kgcl) by @cmungall in #647
• First pass at interface for association search by @cmungall in #646

Full Changelog: v0.5.18-rc2...v0.5.19-rc1

v0.5.18

Highlights

Query and Generate disjointness constraints in the ontology

This release adds the disjoints and generate-disjoints for querying and generating candidate disjointness axioms, along with corresponding python API.

This tool is intended primarily for ontology developers, to better explore axioms in there ontology, and to suggest new ones. See the example notebook:

https://github.com/INCATools/ontology-access-kit/blob/main/notebooks/Commands/Disjoints.ipynb

What's Changed

• New notebook that runs examples showcased in Mondo paper by @hrshdhgd in #584
• Allow diffs to be filtered by change type (kgcl) by @cmungall in #647
• Interface for association search by @cmungall in #646
• Adding utilities for working with disjoint classes. by @cmungall in #650

Full Changelog: v0.5.17...v0.5.18

v0.5.18-rc2

Full Changelog: v0.5.18-rc1...v0.5.18-rc2

v0.5.18-rc1

Full Changelog: v0.5.17...v0.5.18-rc1

v0.5.17

What's Changed

• initial notebook example for omop by @cmungall in #640
• Output for semsimian's termset_pairwise_similarity formatted correctly by @hrshdhgd in #643

Full Changelog: v0.5.16...v0.5.17

v0.5.16

What's Changed

• Adding more notebook examples of associations by @cmungall in #636
• Create Semsimian object with concerned predicates only. by @hrshdhgd in #631

Full Changelog: v0.5.15...v0.5.16