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Ontologies

Cortellis APIs are back online

Dear Life Sciences Data Products users,

As of 2:30pm EDT, Wed, June 19th, the Cortellis APIs are back online! Our sincere apologies for the inconvenience!

The Ontologies API provides access to the 22 Life Sciences controlled vocabularies from Clarivate Analytics for use in your own applications.

Controlled vocabularies may be represented as either as a flat list or in a hierarchical tree structure where a relationship exists between primary and ancillary terms e.g. parent and subsidiary companies.

  • Use the 4 taxonomy functions to:
    • Fetch the top level entries for a given taxonomy
    • Retrieve direct children of a particular term or descendants within the tree from a particular point
    • Identify the immediate ancestors of a taxonomy term
    • Search for synonyms for a given term
  • Use the idMappings function to map terms from different ontologies:
    • Map drug identifiers between CI (Investigational Drug API) and SI (Drug Design API) content sets
    • Map company identifiers between CI and Thomson Reuters permanent identifier (organizationId)
    • Map disease identifiers between MeSH, ICD10, ICD9, MedDRA, Orphanet, ciIndication, siCondition, omicsDisease
    • Map target identifiers between CI targets, SI targets, Omics Network Objects and SwissProt
    • Map action identifiers between CI actions and SI mechanisms
  • Conduct Named Entity Recognition (NER) where users may submit passages of plain text to the API to be screened for synonyms matching controlled vocabulary terms (drug, biomarker, company, target, action, development status phase, indication, technology), returning the identifier and the position of the synonym in the initial text
  • Apply the NER on your own information allowing you to mash it up with Clarivate Analytics and/or public one (for indication and target data thanks to the indexed external data bank identifiers) to get a comprehensive understanding of the studied concept
  • Use a set of summaries functions (drug, company, patent, journal, meeting, action, indication, deal, regulatory, disease briefing, trial, source, patent family, event transcript) in association with the NER entities tagging

Ontologies API can help you to

  • Deploy proven ontologies, saving time and resources in creating your own ontologies
  • Access a “dictionary” of names and synonyms from Clarivate Analytics, making it easier and faster to get to the information needed
  • Auto-index free text to Cortellis ontologies to provide context from other Cortellis APIs

Content

  • Controlled vocabulary terms owned and maintained by Clarivate Analytics – Actions, Indications, Technologies, Companies, Conditions, Target Classification, Tissues, Processes, Organisms, Fluids, Localizations, Cell Lines, Molecular Functions, Patient Segment, Trial Endpoints, Development Status, Country, Exclusion Criteria, Inclusion Criteria and Literature
  • Drug synonyms and mappings
  • Mappings of disease identifiers to standard ontologies (MeSH, ICD9/10, MedDRA, and Orphanet) and target identifiers to SwissProt
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