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CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView.
Lin, Asiyah Yu; Gebel, Stephan; Li, Qingliang Leon; Madan, Sumit; Darms, Johannes; Bolton, Evan; Smith, Barry; Hofmann-Apitius, Martin; He, Yongqun Oliver; Kodamullil, Alpha Tom.
Afiliação
  • Lin AY; Center for Devices and Radiological Health, FDA, Silver Spring, MD, USA.
  • Gebel S; National Center for Ontological Research, Buffalo, NY, USA.
  • Li QL; Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany.
  • Madan S; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
  • Darms J; Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany.
  • Bolton E; Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany.
  • Smith B; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
  • Hofmann-Apitius M; National Center for Ontological Research, Buffalo, NY, USA.
  • He YO; University at Buffa1o, Buffalo, NY, USA.
  • Kodamullil AT; Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany.
CEUR Workshop Proc ; 28072020 Sep.
Article em En | MEDLINE | ID: mdl-35992013
ABSTRACT
Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple clinical trials investigating Gleevec's related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Ano de publicação: 2020 Tipo de documento: Article
Texto completo
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Ano de publicação: 2020 Tipo de documento: Article