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Showing papers by "Peter Buneman published in 2016"

Journal Article•DOI•
The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands

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Christopher Southan, Joanna L. Sharman, Helen E. Benson1, Elena Faccenda1, Adam J. Pawson1, Stephen P.H. Alexander2, Peter Buneman, Anthony P. Davenport3, John C. McGrath4, John C. McGrath5, John A. Peters6, Michael Spedding, William A. Catterall7, Doriano Fabbro, Jamie A. Davies •
University of Edinburgh1, University of Nottingham2, University of Cambridge3, Glasgow Caledonian University4, University of Glasgow5, University of Dundee6, University of Washington7
04 Jan 2016-Nucleic Acids Research
TL;DR: The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) database provides expert-curated molecular interactions between successful and potential drugs and their targets in the human genome, and provides an expanded substrate for the biennially published compendium, the Concise Guide topharmacology.
Abstract: The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, http://www.guidetopharmacology.org) provides expert-curated molecular interactions between successful and potential drugs and their targets in the human genome. Developed by the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS), this resource, and its earlier incarnation as IUPHAR-DB, is described in our 2014 publication. This update incorporates changes over the intervening seven database releases. The unique model of content capture is based on established and new target class subcommittees collaborating with in-house curators. Most information comes from journal articles, but we now also index kinase cross-screening panels. Targets are specified by UniProtKB IDs. Small molecules are defined by PubChem Compound Identifiers (CIDs); ligand capture also includes peptides and clinical antibodies. We have extended the capture of ligands and targets linked via published quantitative binding data (e.g. Ki, IC50 or Kd). The resulting pharmacological relationship network now defines a data-supported druggable genome encompassing 7% of human proteins. The database also provides an expanded substrate for the biennially published compendium, the Concise Guide to PHARMACOLOGY. This article covers content increase, entity analysis, revised curation strategies, new website features and expanded download options.

1,030 citations

Proceedings Article•DOI•
2016 ACM PODS Alberto O. Mendelzon Test-of-Time Award

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Marcelo Arenas, Peter Buneman1, Jan Van den Bussche2•
University of Edinburgh1, University of Hasselt2
15 Jun 2016
TL;DR: It is shown that satisfiability for two-variable first-order logic is decidable if the tree structure can be accessed only through the child and the next sibling predicates and the access to data values is restricted to equality tests.
Abstract: Motivated by reasoning tasks in the context of XML languages, the satisfiability problem of logics on data trees is investigated. The nodes of a data tree have a label from a finite set and a data value from a possibly infinite set. It is shown that satisfiability for two-variable first-order logic is decidable if the tree structure can be accessed only through the child and the next sibling predicates and the access to data values is restricted to equality tests. From this main result decidability of satisfiability and containment for a dataaware fragment of XPath and of the implication problem for unary key and inclusion constraints is concluded.

4 citations