getEuropePmcAnnotations

Free

List the genes/proteins, diseases, chemicals, organisms, GO terms, accession numbers and Open Targets gene-disease-drug links that Europe PMC text-mined from up to 5 articles (full text when open access, else abstract), with ontology ids (UniProt, CHEBI, UMLS, NCBITaxon, Ensembl, ChEMBL) and mention counts. Text mining is noisy: trust entities with several mentions, and read genes from mentionedAs (the symbol as written), as the UniProt match is often another species.

Try it

Open in playground

kirha tools run europepmc_getEuropePmcAnnotations \
  --input '{
    "ids": [
      "<ids>"
    ]
  }'

Uses the key saved by kirha auth login.

idsstring[], required, 1 to 5 items
typesstring[], default ["genes","diseases","chemicals"], At least 1 item
One of genes, diseases, chemicals, organisms, gene_ontology, accession_numbers, experimental_methods, gene_disease_links, gene_drug_links, disease_drug_links

Works in any harness

Get your API key, then install with one command