v1.4.0

1.4.0 - 2023-12-01

Features

• Added new curation_report.py to assist in upgrading ontologies between versions
• New disambiguation strategy to prefer mappings that have a default label that matches an entity.
• The OpenTargetsDiseaseOntologyParser has been heavily reworked, so that it uses the therapeutic_area concept to decide what records should be included. This has in turn yielded the subsets: measurement, medical_procedure, biological_process and phenotype. The measurement configuration is currently disabled as it requires heavy curation of the underlying strings. In addition, the OpenTargetsDiseaseOntologyParser now supports a custom ID grouping method, to make use of cross references.

Bugfixes

• MemoryEfficientStringMatchingStep now only produces a single entity per class where multiple curations exist with different cases.
• Previously, the tested_dependencies.txt file in the model packs included an editable install of kazu, which wasn't intended.
  We now exclude kazu from that output.
• Speed up model pack builds for model packs using ExplosionStringMatchingStep, by fixing a bug that caused the parsers to be populated twice in this case.

Deprecations and Removals

• Removed pytorch-lightning as a dependency. The signatures of SapbertStringSimilarityScorer and TransformersModelForTokenClassificationNerStep have changed
• Renamed create_phrasematchers_using_curations method of OntologyMatcher to create_phrasematchers. The old name will continue to work until kazu 1.6, but using it will produce a DeprecationWarning.
• MetadataDatabase.add_parser now requires an entity_class.
  This enables correct string normalisation in the MappingStep for the new disambiguation strategy.