Version 0.2.5

New Features 🥇

New Models

• Models compatible with Spacy 2.3.0 🥳

Entity Linkers

#246, #233

• Updated the UMLS KB to use the 2020AA release, categories 0,1,2,9.

• umls: Links to the Unified Medical Language System, levels 0,1,2 and 9. This has ~3M concepts.

• mesh: Links to the Medical Subject Headings. This contains a smaller set of higher quality entities, which are used for indexing in Pubmed. MeSH contains ~30k entities. NOTE: The MeSH KB is derrived directly from MeSH itself, and as such uses different unique identifiers than the other KBs.

• rxnorm: Links to the RxNorm ontology. RxNorm contains ~100k concepts focused on normalized names for clinical drugs. It is comprised of several other drug vocabularies commonly used in pharmacy management and drug interaction, including First Databank, Micromedex, and the Gold Standard Drug Database.

• go: Links to the Gene Ontology. The Gene Ontology contains ~67k concepts focused on the functions of genes.

• hpo: Links to the Human Phenotype Ontology. The Human Phenotype Ontology contains 16k concepts focused on phenotypic abnormalities encountered in human disease.

Bug Fixes 🐛

#217 - Fixes a bug in the Abbreviation detector

API Changes

• Entity Linkers now modify the Span._.kb_ents rather than the Span._.umls_ents to reflect the fact that we now have more than one entity linker. Span._.umls_ents will be deprecated in v1.0.