The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research
Identifieur interne : 000212 ( Main/Merge ); précédent : 000211; suivant : 000213The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research
Auteurs : Joseline Ratnam [Espagne] ; Barbara Zdrazil [Autriche] ; Daniela Digles [Autriche] ; Emiliano Cuadrado-Rodriguez [Espagne] ; Jean-Marc Neefs [Belgique] ; Hannah Tipney [Royaume-Uni] ; Ronald Siebes [Pays-Bas] ; Andra Waagmeester [Pays-Bas] ; Glyn Bradley [Royaume-Uni] ; Chau Han Chau [Royaume-Uni] ; Lars Richter [Autriche] ; Jose Brea [Espagne] ; Chris T. Evelo [Pays-Bas] ; Edgar Jacoby [Belgique] ; Stefan Senger [Royaume-Uni] ; Maria Isabel Loza [Espagne] ; Gerhard F. Ecker [Autriche] ; Christine Chichester [Suisse]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
English descriptors
- KwdEn :
- MESH :
- methods : Drug Discovery.
- organization & administration : Drug Discovery.
- statistics & numerical data : Drug Discovery.
- Databases as Topic, Software.
Abstract
Integration of open access, curated, high-quality information from multiple disciplines in the Life and Biomedical Sciences provides a holistic understanding of the domain. Additionally, the effective linking of diverse data sources can unearth hidden relationships and guide potential research strategies. However, given the lack of consistency between descriptors and identifiers used in different resources and the absence of a simple mechanism to link them, gathering and combining relevant, comprehensive information from diverse databases remains a challenge. The Open Pharmacological Concepts Triple Store (Open PHACTS) is an Innovative Medicines Initiative project that uses semantic web technology approaches to enable scientists to easily access and process data from multiple sources to solve real-world drug discovery problems. The project draws together sources of publicly-available pharmacological, physicochemical and biomolecular data, represents it in a stable infrastructure and provides well-defined information exploration and retrieval methods. Here, we highlight the utility of this platform in conjunction with workflow tools to solve pharmacological research questions that require interoperability between target, compound, and pathway data. Use cases presented herein cover 1) the comprehensive identification of chemical matter for a dopamine receptor drug discovery program 2) the identification of compounds active against all targets in the Epidermal growth factor receptor (ErbB) signaling pathway that have a relevance to disease and 3) the evaluation of established targets in the Vitamin D metabolism pathway to aid novel Vitamin D analogue design. The example workflows presented illustrate how the Open PHACTS Discovery Platform can be used to exploit existing knowledge and generate new hypotheses in the process of drug discovery.
Url:
DOI: 10.1371/journal.pone.0115460
PubMed: 25522365
PubMed Central: 4270790
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PMC:4270790Le document en format XML
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<author><name sortKey="Loza, Maria Isabel" sort="Loza, Maria Isabel" uniqKey="Loza M" first="Maria Isabel" last="Loza">Maria Isabel Loza</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research</title>
<author><name sortKey="Ratnam, Joseline" sort="Ratnam, Joseline" uniqKey="Ratnam J" first="Joseline" last="Ratnam">Joseline Ratnam</name>
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</nlm:aff>
<country xml:lang="fr">Espagne</country>
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<author><name sortKey="Zdrazil, Barbara" sort="Zdrazil, Barbara" uniqKey="Zdrazil B" first="Barbara" last="Zdrazil">Barbara Zdrazil</name>
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</nlm:aff>
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<author><name sortKey="Digles, Daniela" sort="Digles, Daniela" uniqKey="Digles D" first="Daniela" last="Digles">Daniela Digles</name>
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<author><name sortKey="Cuadrado Rodriguez, Emiliano" sort="Cuadrado Rodriguez, Emiliano" uniqKey="Cuadrado Rodriguez E" first="Emiliano" last="Cuadrado-Rodriguez">Emiliano Cuadrado-Rodriguez</name>
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</nlm:aff>
<country xml:lang="fr">Espagne</country>
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<author><name sortKey="Neefs, Jean Marc" sort="Neefs, Jean Marc" uniqKey="Neefs J" first="Jean-Marc" last="Neefs">Jean-Marc Neefs</name>
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<author><name sortKey="Tipney, Hannah" sort="Tipney, Hannah" uniqKey="Tipney H" first="Hannah" last="Tipney">Hannah Tipney</name>
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<author><name sortKey="Siebes, Ronald" sort="Siebes, Ronald" uniqKey="Siebes R" first="Ronald" last="Siebes">Ronald Siebes</name>
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</nlm:aff>
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<author><name sortKey="Waagmeester, Andra" sort="Waagmeester, Andra" uniqKey="Waagmeester A" first="Andra" last="Waagmeester">Andra Waagmeester</name>
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</nlm:aff>
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<wicri:regionArea>Department of Bioinformatics – BiGCaT, Maastricht University, Maastricht</wicri:regionArea>
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<author><name sortKey="Bradley, Glyn" sort="Bradley, Glyn" uniqKey="Bradley G" first="Glyn" last="Bradley">Glyn Bradley</name>
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</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
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<author><name sortKey="Chau, Chau Han" sort="Chau, Chau Han" uniqKey="Chau C" first="Chau Han" last="Chau">Chau Han Chau</name>
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</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY</wicri:regionArea>
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<author><name sortKey="Richter, Lars" sort="Richter, Lars" uniqKey="Richter L" first="Lars" last="Richter">Lars Richter</name>
<affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria</addr-line>
</nlm:aff>
<country xml:lang="fr">Autriche</country>
<wicri:regionArea>University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna</wicri:regionArea>
<placeName><region type="land" nuts="2">Vienne (Autriche)</region>
<settlement type="city">Vienne (Autriche)</settlement>
</placeName>
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<author><name sortKey="Brea, Jose" sort="Brea, Jose" uniqKey="Brea J" first="Jose" last="Brea">Jose Brea</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Universidade de Santiago de Compostela, Grupo BioFarma-USEF, Departamento de Farmacología, Campus Universitario Sur s/n, 15782 Santiago de Compostela, Spain</addr-line>
</nlm:aff>
<country xml:lang="fr">Espagne</country>
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<placeName><region nuts="2" type="communauté">Galice</region>
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</affiliation>
</author>
<author><name sortKey="Evelo, Chris T" sort="Evelo, Chris T" uniqKey="Evelo C" first="Chris T." last="Evelo">Chris T. Evelo</name>
<affiliation wicri:level="1"><nlm:aff id="aff7"><addr-line>Department of Bioinformatics – BiGCaT, Maastricht University, Maastricht, The Netherlands</addr-line>
</nlm:aff>
<country xml:lang="fr">Pays-Bas</country>
<wicri:regionArea>Department of Bioinformatics – BiGCaT, Maastricht University, Maastricht</wicri:regionArea>
<wicri:noRegion>Maastricht</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Jacoby, Edgar" sort="Jacoby, Edgar" uniqKey="Jacoby E" first="Edgar" last="Jacoby">Edgar Jacoby</name>
<affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Janssen Research & Development, Turnhoutseweg 30, Beerse, Belgium</addr-line>
</nlm:aff>
<country xml:lang="fr">Belgique</country>
<wicri:regionArea>Janssen Research & Development, Turnhoutseweg 30, Beerse</wicri:regionArea>
<wicri:noRegion>Beerse</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Senger, Stefan" sort="Senger, Stefan" uniqKey="Senger S" first="Stefan" last="Senger">Stefan Senger</name>
<affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom</addr-line>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY</wicri:regionArea>
<wicri:noRegion>SG1 2NY</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Loza, Maria Isabel" sort="Loza, Maria Isabel" uniqKey="Loza M" first="Maria Isabel" last="Loza">Maria Isabel Loza</name>
<affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Universidade de Santiago de Compostela, Grupo BioFarma-USEF, Departamento de Farmacología, Campus Universitario Sur s/n, 15782 Santiago de Compostela, Spain</addr-line>
</nlm:aff>
<country xml:lang="fr">Espagne</country>
<wicri:regionArea>Universidade de Santiago de Compostela, Grupo BioFarma-USEF, Departamento de Farmacología, Campus Universitario Sur s/n, 15782 Santiago de Compostela</wicri:regionArea>
<placeName><region nuts="2" type="communauté">Galice</region>
<settlement type="city">Santiago de Compostela</settlement>
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<orgName type="university">Université de Saint-Jacques-de-Compostelle</orgName>
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</author>
<author><name sortKey="Ecker, Gerhard F" sort="Ecker, Gerhard F" uniqKey="Ecker G" first="Gerhard F." last="Ecker">Gerhard F. Ecker</name>
<affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria</addr-line>
</nlm:aff>
<country xml:lang="fr">Autriche</country>
<wicri:regionArea>University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna</wicri:regionArea>
<placeName><region type="land" nuts="2">Vienne (Autriche)</region>
<settlement type="city">Vienne (Autriche)</settlement>
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</affiliation>
</author>
<author><name sortKey="Chichester, Christine" sort="Chichester, Christine" uniqKey="Chichester C" first="Christine" last="Chichester">Christine Chichester</name>
<affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Swiss Institute of Bioinformatics, CALIPHO Group, CMU – Rue Michel-Servet 1, 1211 Geneva 4, Switzerland</addr-line>
</nlm:aff>
<country xml:lang="fr">Suisse</country>
<wicri:regionArea>Swiss Institute of Bioinformatics, CALIPHO Group, CMU – Rue Michel-Servet 1, 1211 Geneva 4</wicri:regionArea>
<wicri:noRegion>1211 Geneva 4</wicri:noRegion>
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<series><title level="j">PLoS ONE</title>
<idno type="eISSN">1932-6203</idno>
<imprint><date when="2014">2014</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases as Topic</term>
<term>Drug Discovery (methods)</term>
<term>Drug Discovery (organization & administration)</term>
<term>Drug Discovery (statistics & numerical data)</term>
<term>Software</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Drug Discovery</term>
</keywords>
<keywords scheme="MESH" qualifier="organization & administration" xml:lang="en"><term>Drug Discovery</term>
</keywords>
<keywords scheme="MESH" qualifier="statistics & numerical data" xml:lang="en"><term>Drug Discovery</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Databases as Topic</term>
<term>Software</term>
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<front><div type="abstract" xml:lang="en"><p>Integration of open access, curated, high-quality information from multiple disciplines in the Life and Biomedical Sciences provides a holistic understanding of the domain. Additionally, the effective linking of diverse data sources can unearth hidden relationships and guide potential research strategies. However, given the lack of consistency between descriptors and identifiers used in different resources and the absence of a simple mechanism to link them, gathering and combining relevant, comprehensive information from diverse databases remains a challenge. The Open Pharmacological Concepts Triple Store (Open PHACTS) is an Innovative Medicines Initiative project that uses semantic web technology approaches to enable scientists to easily access and process data from multiple sources to solve real-world drug discovery problems. The project draws together sources of publicly-available pharmacological, physicochemical and biomolecular data, represents it in a stable infrastructure and provides well-defined information exploration and retrieval methods. Here, we highlight the utility of this platform in conjunction with workflow tools to solve pharmacological research questions that require interoperability between target, compound, and pathway data. Use cases presented herein cover 1) the comprehensive identification of chemical matter for a dopamine receptor drug discovery program 2) the identification of compounds active against all targets in the Epidermal growth factor receptor (ErbB) signaling pathway that have a relevance to disease and 3) the evaluation of established targets in the Vitamin D metabolism pathway to aid novel Vitamin D analogue design. The example workflows presented illustrate how the Open PHACTS Discovery Platform can be used to exploit existing knowledge and generate new hypotheses in the process of drug discovery.</p>
</div>
</front>
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