An automated tool for obtaining QSAR-ready series of compounds using semantic web technologies

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• dc.contributor.author López-Massaguer, Oriolca
• dc.contributor.author Sanz, Ferranca
• dc.contributor.author Pastor Maeso, Manuelca
• dc.date.accessioned 2018-03-14T10:17:29Z
• dc.date.available 2018-03-14T10:17:29Z
• dc.date.issued 2018
• dc.description.abstract SUMMARY: We describe an application (Collector) for obtaining series of compounds annotated with bioactivity data, ready to be used for the development of quantitative structure-activity relationships (QSAR) models. The tool extracts data from the 'Open Pharmacological Space' (OPS) developed by the Open PHACTS project, using as input a valid name of the biological target. Collector uses the OPS ontologies for expanding the query using all known target synonyms and extracts compounds with bioactivity data against the target from multiple sources. The extracted data can be filtered to retain only drug-like compounds and the bioactivities can be automatically summarised to assign a single value per compound, yielding data ready to be used for QSAR modeling. The data obtained is locally stored facilitating the traceability and auditability of the process. Collector was used successfully for the development of models for toxicity endpoints within the eTOX project. AVAILABILITY AND IMPLEMENTATION: The software is available at http://phi.upf.edu/collector. The source code is located at https://github.com/phi-grib/Collector and is free for use under the GPL3 license. The web version is hosted at http://collector.upf.edu/. CONTACT: manuel.pastor@upf.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
• dc.description.sponsorship This project was developed under the Innovative Medicines Initiative Joint Undertaking Open PHACTS Project, grant agreement number 115191 and eTOX project, grant agreement n° 115002, resources of which are composed of financial contribution from the European Union’s Seventh Framework Programme (FP7/2007–2013) and EFPIA companies’ in kind contributions
• dc.format.mimetype application/pdf
• dc.identifier.citation López-Massaguer O, Sanz F, Pastor M. An automated tool for obtaining QSAR-ready series of compounds using semantic web technologies. Bioinformatics. 2018 Jan 1;34(1):131-3. DOI: 10.1093/bioinformatics/btx566
• dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btx566
• dc.identifier.issn 1367-4803
• dc.identifier.uri http://hdl.handle.net/10230/34098
• dc.language.iso eng
• dc.publisher Oxford University Pressca
• dc.relation.ispartof Bioinformatics. 2018 Jan 1;34(1):131-3
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/115191
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/115002
• dc.rights © Oxford University Press. This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version López-Massaguer O, Sanz F, Pastor M. An automated tool for obtaining QSAR-ready series of compounds using semantic web technologies. Bioinformatics. 2018 Jan 1; 34(1): 131-133 is available online at: http://dx.doi.org/10.1093/bioinformatics
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.subject.other Medicina--Informàtica
• dc.title An automated tool for obtaining QSAR-ready series of compounds using semantic web technologiesca
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/acceptedVersion