CTO: A community-based clinical trial ontology and its applications in PubChemRDF and SCAIView

Asiyah Yu Lin; Stephan Gebel; Qingliang Leon Li; Sumit Madan; Johannes Darms; Evan Bolton; Barry Smith; Martin Hofmann-Apitius; Yongqun Oliver He; Alpha Tom Kodamullil

CTO: A community-based clinical trial ontology and its applications in PubChemRDF and SCAIView

Asiyah Yu Lin
, Stephan Gebel
, Qingliang Leon Li
, Sumit Madan
, Johannes Darms
, Evan Bolton
, Barry Smith
, Martin Hofmann-Apitius
, Yongqun Oliver He
, Alpha Tom Kodamullil

Philosophy

United States Food and Drug Administration
National Center for Ontological Research
Fraunhofer Institute for Algorithms and Scientific Computing
National Institutes of Health
University of Michigan, Ann Arbor

Research output: Contribution to journal › Conference article › peer-review

4 Scopus citations

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.

Original language	English
Journal	CEUR Workshop Proceedings
Volume	2807
State	Published - 2020
Event	11th International Conference on Biomedical Ontologies, ICBO 2020 - Joint with the 10th Workshop on Ontologies and Data in Life Sciences, ODLS 2020 and Part of the Bolzano Summer of Knowledge, BoSK 2020 - Virtual, Bolzano, Italy Duration: Sep 17 2020 → …

Keywords

BFO
Clinical trial
Clinical trial registry
COVID-19
Ontology

Cite this

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title = "CTO: A community-based clinical trial ontology and its applications in PubChemRDF and SCAIView",

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{\textquoteright}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.",

keywords = "BFO, Clinical trial, Clinical trial registry, COVID-19, Ontology",

author = "Lin, \{Asiyah Yu\} and Stephan Gebel and Li, \{Qingliang Leon\} and Sumit Madan and Johannes Darms and Evan Bolton and Barry Smith and Martin Hofmann-Apitius and He, \{Yongqun Oliver\} and Kodamullil, \{Alpha Tom\}",

note = "Publisher Copyright: Copyright {\textcopyright} 2020 for this paper by its authors.; 11th International Conference on Biomedical Ontologies, ICBO 2020 - Joint with the 10th Workshop on Ontologies and Data in Life Sciences, ODLS 2020 and Part of the Bolzano Summer of Knowledge, BoSK 2020 ; Conference date: 17-09-2020",

year = "2020",

language = "English",

volume = "2807",

journal = "CEUR Workshop Proceedings",

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TY - JOUR

T1 - CTO

T2 - 11th International Conference on Biomedical Ontologies, ICBO 2020 - Joint with the 10th Workshop on Ontologies and Data in Life Sciences, ODLS 2020 and Part of the Bolzano Summer of Knowledge, BoSK 2020

AU - Lin, Asiyah Yu

AU - Gebel, Stephan

AU - Li, Qingliang Leon

AU - Madan, Sumit

AU - Darms, Johannes

AU - Bolton, Evan

AU - Smith, Barry

AU - Hofmann-Apitius, Martin

AU - He, Yongqun Oliver

AU - Kodamullil, Alpha Tom

PY - 2020

Y1 - 2020

N2 - 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.

AB - 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.

KW - BFO

KW - Clinical trial

KW - Clinical trial registry

KW - COVID-19

KW - Ontology

UR - https://www.scopus.com/pages/publications/85101082788

M3 - Conference article

AN - SCOPUS:85101082788

SN - 1613-0073

VL - 2807

JO - CEUR Workshop Proceedings

JF - CEUR Workshop Proceedings

Y2 - 17 September 2020

ER -

CTO: A community-based clinical trial ontology and its applications in PubChemRDF and SCAIView

Abstract

Keywords

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