Evolving BioAssay Ontology (BAO): modularization, integration and applications
Saminda Abeyruwan,Uma D. Vempati,Hande Küçük-McGinty,Ubbo Visser,Amar Koleti,Ahsan Mir,Kunie Sakurai,Caty Chung,Joshua A. Bittker,Paul A. Clemons,Steve Brudz,Anosha Siripala,Arturo J. Morales,Martin Romacker,David Twomey,Svetlana Bureeva,Vance Lemmon,Vance Lemmon,Stephan C. Schürer +18 more
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TLDR
The evolution of BAO related to its formal structures, engineering approaches, and content is described to enable modeling of complex assays and integration with other ontologies and datasets to enable effective integration, aggregation, retrieval, and analyses of drug screening data.Abstract:
The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary drug screening data to their maximum potential. We have created the BioAssay Ontology (BAO) project (http://bioassayontology.org) to develop common reference metadata terms and definitions required for describing relevant information of low-and high-throughput drug and probe screening assays and results. The main objectives of BAO are to enable effective integration, aggregation, retrieval, and analyses of drug screening data. Since we first released BAO on the BioPortal in 2010 we have considerably expanded and enhanced BAO and we have applied the ontology in several internal and external collaborative projects, for example the BioAssay Research Database (BARD). We describe the evolution of BAO with a design that enables modeling complex assays including profile and panel assays such as those in the Library of Integrated Network-based Cellular Signatures (LINCS). One of the critical questions in evolving BAO is the following: how can we provide a way to efficiently reuse and share among various research projects specific parts of our ontologies without violating the integrity of the ontology and without creating redundancies. This paper provides a comprehensive answer to this question with a description of a methodology for ontology modularization using a layered architecture. Our modularization approach defines several distinct BAO components and separates internal from external modules and domain-level from structural components. This approach facilitates the generation/extraction of derived ontologies (or perspectives) that can suit particular use cases or software applications. We describe the evolution of BAO related to its formal structures, engineering approaches, and content to enable modeling of complex assays and integration with other ontologies and datasets.read more
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Journal ArticleDOI
The ChEMBL database in 2017.
Anna Gaulton,Anne Hersey,Michal Nowotka,A. Patrícia Bento,Jon Chambers,David Mendez,Prudence Mutowo,Francis Atkinson,Louisa J. Bellis,Elena Cibrian-Uhalte,Mark Davies,Nathan Dedman,Anneli Karlsson,María Paula Magariños,John P. Overington,George Papadatos,Ines Smit,Andrew R. Leach +17 more
TL;DR: ChEMBL is an open large-scale bioactivity database that includes the annotation of assays and targets using ontologies, the inclusion of targets and indications for clinical candidates, addition of metabolic pathways for drugs and calculation of structural alerts.
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The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY
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TL;DR: This update describes content expansion, new features and interoperability improvements introduced in the 10 releases since August 2015, and introduces the newly funded project for the Guide to IMMUNOPHARMACOLOGY (GtoImmuPdb, www.guidetoimmunopharmacology.org).
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ChEMBL: towards direct deposition of bioassay data
David Mendez,Anna Gaulton,A. Patrícia Bento,Jon Chambers,Marleen De Veij,Eloy Felix,María Paula Magariños,Juan F Mosquera,Prudence Mutowo,Michal Nowotka,María Gordillo-Marañón,Fiona M. I. Hunter,Laura Junco,Grace Mugumbate,Milagros Rodríguez-López,Francis Atkinson,Nicolas Bosc,Chris J Radoux,Aldo Segura-Cabrera,Anne Hersey,Andrew R. Leach +20 more
TL;DR: Several important improvements have been made to ChEMBL in the last two years, including more robust capture and representation of assay details; a new data deposition system, allowing updating of data sets and deposition of supplementary data; and a completely redesigned web interface, with enhanced search and filtering capabilities.
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