Biocuration in the structure-function linkage database: the anatomy of a superfamily.

Journal: Database : the journal of biological databases and curation
Published Date: Jan 1, 2017

Abstract

UNLABELLED: With ever-increasing amounts of sequence data available in both the primary literature and sequence repositories, there is a bottleneck in annotating molecular function to a sequence. This article describes the biocuration process and methods used in the structure-function linkage database (SFLD) to help address some of the challenges. We discuss how the hierarchy within the SFLD allows us to infer detailed functional properties for functionally diverse enzyme superfamilies in which all members are homologous, conserve an aspect of their chemical function and have associated conserved structural features that enable the chemistry. Also presented is the Enzyme Structure-Function Ontology (ESFO), which has been designed to capture the relationships between enzyme sequence, structure and function that underlie the SFLD and is used to guide the biocuration processes within the SFLD.

Authors

  • Gemma L Holliday
    Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland, Department of Medicine and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA, School of Information, University of South Florida, Tampa, FL, 33647, USA, Genomics Division, Lawrence Berkeley National Lab, 1 Cyclotron Rd., Berkeley, 94720 CA USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland, ETH Zurich, Department of Computer Science, Universitätstr. 19, 8092 Zürich, Switzerland, SIB Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zürich, Switzerland and University College London, Gower St, London WC1E 6BT, UK.
  • Shoshana D Brown
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.
  • Eyal Akiva
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.
  • David Mischel
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.
  • Michael A Hicks
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.
  • John H Morris
    Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.
  • Conrad C Huang
    Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.
  • Elaine C Meng
    Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.
  • Scott C-H Pegg
    Gladstone Institutes, San Francisco, CA 94158, USA.
  • Thomas E Ferrin
    Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.
  • Patricia C Babbitt
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.

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