ASassyro
PubTator3

Search PubTator3

Search PubTator3 (NCBI), relations text-mined from every PubMed abstract and PMC full-text article, from Assyro's monthly copy: find which genes, chemicals, diseases and variants articles relate to each other, by entity names (e.g. "metformin breast cancer") or concept ids (a MeSH id such as "MESH:D008687", an NCBI Gene id such as "5468", a dbSNP id such as "rs4986172"), and narrow by relation type (treat, cause, associate, inhibit, stimulate, positive_correlate, negative_correlate, interact, drug_interact, cotreat, prevent, compare), by the kind of entity on the other side, or by how many articles state it. Each result gives the relation, both entities with their ids, the number of articles and the newest PMIDs; the relations most articles state come first. Relations are machine readings of article text, not curated findings. Call read_pubtator_relation for up to 50 PMIDs with their PubMed pages.

get/v1/sources/pubtator/search

Request

  • Base URL
    https://api.assyro.com
  • Auth
    none declared

Query parameters

querystring

Names of the entities, every word required, e.g. "metformin breast cancer" or "BRCA1".

entitystring

A concept id on either side: "MESH:D008687" (chemical or disease), "5468" (NCBI Gene), "rs4986172" (variant).

otherEntitystring

A second concept id: keep only relations between entity and this one.

relationType'associate' | 'cause' | 'compare' | 'cotreat' | 'drug_interact' | 'inhibit' | 'interact' | 'negative_correlate' | 'positive_correlate' | 'prevent' | 'stimulate' | 'treat'

Keep relations of this type.

entityType'gene' | 'chemical' | 'disease' | 'variant'

Keep relations with a gene, chemical, disease or variant on one side, e.g. "gene" for the genes related to a drug.

minArticlesinteger

Keep relations stated in at least this many articles.

limitinteger

Relations to return, default 10.

offsetinteger

Skip this many results (for paging), default 0.

Response

Matching records.

versionunknown required
totalinteger nullable required

Total matches the source reports, when it says.

notestring
summarystring[]

Changes

No recorded changes to this operation across all 1 revision of this API.