biosynonyms 0.0.1

A decentralized database of synonyms for biomedical concepts and entities.

Biosynonyms

A decentralized database of synonyms for biomedical entities and concepts. This resource is meant to be complementary to ontologies, databases, and other controlled vocabularies that provide synonyms. It's released under a permissive license (CC0), so they can be easily adopted by/contributed back to upstream resources.

Here's how to get the data:

import biosynonyms

# Uses an internal data structure
positive_synonyms = biosynonyms.get_positive_synonyms()
negative_synonyms = biosynonyms.get_negative_synonyms()

# Get ready for use in NER with Gilda, only using positive synonyms
gilda_terms = biosynonyms.get_gilda_terms()

Synonyms

The data are also accessible directly through TSV such that anyone can consume them from any programming language.

The positives.tsv has the following columns:

1. text the synonym text itself
2. curie the compact uniform resource identifier (CURIE) for a biomedical entity or concept, standardized using the Bioregistry
3. name the standard name for the concept
4. scope the match type, written as a CURIE from the OBO in OWL (oio) controlled vocabulary, i.e., one of:
   • oboInOwl:hasExactSynonym
   • oboInOwl:hasNarrowSynonym
   • oboInOwl:hasBroadSynonym
   • oboInOwl:hasRelatedSynonym
   • oboInOwl:hasSynonym (use this if the scope is unknown)
5. type the synonym property type, written as a CURIE from the OBO Metadata Ontology (omo) controlled vocabulary, e.g., one of:
   • OMO:0003000 (abbreviation)
   • OMO:0003001 (ambiguous synonym)
   • OMO:0003002 (dubious synonym)
   • OMO:0003003 (layperson synonym)
   • OMO:0003004 (plural form)
   • ...
6. references a comma-delimited list of CURIEs corresponding to publications that use the given synonym (ideally using highly actionable identifiers from semantic spaces like pubmed, pmc, doi)
7. contributor the ORCID identifier of the contributor

Here's an example of some rows in the synonyms table (with linkified CURIEs):

text	curie	scope	references	contributor
PI(3,4,5)P3	CHEBI:16618	oio:hasExactSynonym	pubmed:29623928, pubmed:20817957	0000-0003-4423-4370
phosphatidylinositol (3,4,5) P3	CHEBI:16618	oio:hasExactSynonym	pubmed:29695532	0000-0003-4423-4370

Incorrect Synonyms

The negatives.tsv has the following columns for non-trivial examples of text strings that aren't synonyms. This document doesn't address the same issues as context-based disambiguation, but rather helps dscribe issues like incorrect sub-string matching:

1. text the non-synonym text itself
2. curie the compact uniform resource identifier (CURIE) for a biomedical entity or concept that does not match the following text, standardized using the Bioregistry
3. references same as for positives.tsv, illustrating documents where this string appears
4. contributor the ORCID identifier of the contributor

Here's an example of some rows in the negative synonyms table (with linkified CURIEs):

text	curie	references	contributor
PI(3,4,5)P3	hgnc:22979	pubmed:29623928, pubmed:20817957	0000-0003-4423-4370

Known Limitations

It's hard to know which exact matches between different vocabularies could be used to deduplicate synonyms. Right now, this isn't covered but some partial solutions already exist that could be adopted.

License

All data are available under CC0 license. All code is available under MIT license.