CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView

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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2020
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9389640/
https://www.ncbi.nlm.nih.gov/pubmed/35992013
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author 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
author_facet 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
author_sort LIN, Asiyah Yu
collection PubMed
description 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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spelling pubmed-93896402022-08-19 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 CEUR Workshop Proc Article 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. 2020-09 /pmc/articles/PMC9389640/ /pubmed/35992013 Text en https://creativecommons.org/licenses/by/4.0/Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).
spellingShingle Article
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
CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView
title CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView
title_full CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView
title_fullStr CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView
title_full_unstemmed CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView
title_short CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView
title_sort cto: a community-based clinical trial ontology and its applications in pubchemrdf and scaiview
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9389640/
https://www.ncbi.nlm.nih.gov/pubmed/35992013
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