Extend MeSH-PubMed and NCBI Taxonomy connection

sorgerlab / indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

http://indra.bio

BSD 2-Clause "Simplified" License

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Extend MeSH-PubMed and NCBI Taxonomy connection #1457

Closed bgyori closed 2 months ago

bgyori commented 3 months ago

This PR adds better search functions by MeSH terms in the PubMed client. It also extends the MeSH resource file to include NCBI taxonomy mappings and makes these available via the MeSH client.

bgyori commented 2 months ago

Further useful features in a future PR could be:

Put these mappings into the BioOntology to be used during ID normalization
Add dedicated functions in the mesh_client for retrieving these mappings (currently they are still available from a module-level data structure)