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GtoPdb ELIXIR-All Hands 2018


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Poster presented at the ELIXIR All-Hands 2018, Berlin on status of the Guide to PHARMACOLOGY

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GtoPdb ELIXIR-All Hands 2018

  1. 1. Contact IUPHAR/BPS Guide to PHARMACOLOGY Title Title Simon D. Harding1 , Jane Armstrong1 , Elena Faccenda1 , Adam J. Pawson1 , Joanna L. Sharman1 , Christopher Southan1 , Stephen P.H. Alexander2 , Anthony P. Davenport3 , Michael Spedding4 , Jamie A. Davies1 and NC-IUPHAR* 1 Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK. 2 School of Life Sciences, University of Notngham Medical School, Notngham, UK. 3 Experimental Medicine and Immunotherapeutcs, University of Cambridge, Cambridge. 4 Spedding Research Solutons SAS, Paris, France. * The Internatonal Union of Basic and Clinical Pharmacology Commitee on Receptor Nomenclature and Drug Classifcaton. 1. Introducton The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) is an open, expert-driven database of pharmacological targets and the substances that act on them [1]. It is a joint initatve between the Britsh Pharmacological Society (BPS) and the Internatonal Union of Basic and Clinical Pharmacology (IUPHAR), which aims to cover the human targets of licensed drugs and other likely targets of future therapeutcs. The informaton is presented at two levels: 1. Overviews of the key propertes, selectve ligands and further reading for a wide range of human biological targets, which form the basis for the Concise Guide to PHARMACOLOGY (CGTP) [2]. 2. Detailed pharmacological, functonal and clinical informaton for a subset of important targets. All data are manually curated from the primary literature and reviewed by an internatonal network of >500 experts in 96 subcommitees of the IUPHAR Commitee on Receptor Nomenclature and Drug Classifcaton (NC-IUPHAR). 2. Current database content ~ 1,700 established or potental data-supported drug targets ~ 1,100 additonal related proteins > 9,000 ligands, over 5,500 with quanttatve interacton data > 1,300 approved drugs, >800 with quanttatve informaton Title 3. New search tools Various search tools are available to fnd targets and ligands by name, ID, reference, chemical structure similarity, or BLAST sequence search. A new Pharmacology Search Tool (Fig. 1) allows users to upload lists of protein IDs and fnd ligands that modulate them, from both the GtoPdb and ChEMBL [3] databases. Title Title 4. Disease informaton A list of diseases associated to targets and ligands in GtoPdb is now available. (A) Disease list (B) A disease summary for ALL A B (A) Pharmacology Search Tool with searching restricted to 3 interactons per target. (B) Results show actvity data summarised from GtoPdb and ChEMBL Results from searches can be downloaded as a CSV fle Tip B A Title 5. Navigatng target and ligand families Targets are organised by class, which can be browsed as a tree with families and subfamilies (A). Ligands have recently been organised into related families and groups (B). Each family/group page lists summary informaton for the ligands, with links to more detailed pages (C). B A C Title 6. Comparing ligand afnity across species Ligand actvity graphs provide a quick way to visualise afntty at diferent targets and across species. Box plots (A) summaries standardised actvity data from GtoPdb and ChEMBL. Individual data points, assay details and references are provided in an accompanying table (B). B A Chart and table showing palosuran actvity at human and rat UT receptors Title 7. Interoperability, RDF and data access As part of our contnuing efort to increase interoperability of GtoPdb we have:  Created an RDF version of GtoPdb  Submited ligands to WikiPathways  Worked with Bioschemas to implement mark-up  Set up a new subcommitee of Data Interoperability (Chaired by Dr. Alasdair Gray) GtoPdb RDF provided in N3 format with metadata generate in accordance with W3C HCLS Profle to ensure FAIR compliance. Development of SPARQL end-point is planned. Data access GtoPdb data are available to download in various formats:  Lists of targets, ligands and interactons in CSV format  REST web services for computatonal access to data in JSON format  SQL database dump fles  Interacton data are now available in RDF format for semantc integraton 8. References 1. Harding SD, et al. (2018). Nucl. Acids Res. 46 (Issue D1): D1091-D1106. 2. Alexander SPH, et al. (2017). Br J Pharmacol. 174 (Suppl 1): S1-S446. 3. Bento AP, et al. (2014). Nucl. Acids Res. 42 (Database Issue): D1083-D1090. In additon, for a “how-to” guide on using GtoPdb see: Sharman JL, et al. (2018) Accessing Expert Curated Pharmacological Data in the IUPHAR/BPS Guide to PHARMACOLOGY.‐ Curr Protoc Bioinformatcs. 61: 1.34.1-1.34.46. @GuidetoPHARM