The Publication and Database Deposition of Molecular Interaction Data

Sandra Orchard1, Bruno Aranda1, Henning Hermjakob1

1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 25.3
DOI:  10.1002/0471140864.ps2503s60
Online Posting Date:  April, 2010
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Abstract

Depositing data to a public domain interaction database not only improves the quality and quantity of interactions available to the user community, but also increases the visibility of the data, with members of the International Molecular Exchange (IMEx) databases making the information available in all participating resources. Datasets submitted prior to publication will be issued an accession number that may be included in a publication and which increases user accessibility to the data. No dataset is too small for submission, and the database curators will provide assistance in ensuring the information is correctly represented. This unit provides several alternative protocols to assist the author in preparing and submitting data as an integral part of the manuscript‐preparation process. Which method the author selects is largely dictated by the amount of data to be deposited. In addition, two support protocols describe assignment of unambiguous accession numbers and use of controlled vocabulary terms. Curr. Protoc. Protein Sci. 60:25.3.1‐25.3.13. © 2010 by John Wiley & Sons, Inc.

Keywords: molecular interaction; data deposition; IMEx; data standardization

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Submission of Small‐Scale Amounts of Data to Molecular Interaction Databases
  • Basic Protocol 2: Submission of Medium‐Scale Amounts of Data to Molecular Interaction Databases
  • Alternate Protocol 1: Submission of Medium‐Scale Amounts of Data to Molecular Interaction Databases Using a Preformatted Excel Sheet
  • Basic Protocol 3: Submission of Large‐Scale Amounts of Data to Molecular Interaction Databases
  • Support Protocol 1: Assigning Accession Numbers to Molecules
  • Support Protocol 2: Accessing and Using Controlled Vocabulary Terms
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

   Chatr‐aryamontri, A., Ceol, A., Palazzi, L.M., Nardelli, G., Schneider, M.V., Castagnoli, L., and Cesareni, G. 2007. MINT: The Molecular INTeraction database. Nucl. Acids Res. 35:572‐574.
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Internet Resources
   http://www.ebi.ac.uk/intact
  IMEx Consortium Member Databases currently accepting Direct Submissions.
   http://matrixdb.ibcp.fr/
  The IMEx Consortium.
   http://mint.bio.uniroma2.it/mint
  The PSI‐MI XML schema and related resources.
   http://dip.doe‐mbi.ucla.edu
  Interactor Databases.
   http://imex.sf.net
  The Ontology‐Lookup Service.
   http://psidev.sourceforge.net/mi/rel25/src/MIF25.xsd
   http://www.ebi.ac.uk/intact/validator/start.xhtml
   http://www.uniprot.org
   http://www.ensembl.org
   http://www.ensemblgenomes.org/
   http://www.ncbi.nlm.nih.gov/sites/entrez
   http://www.ebi.ac.uk/chebi
   http://www.ebi.ac.uk/ontology‐lookup/browse.do?ontName=MI
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