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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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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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.
   Chautard, E., Ballut, L., Thierry‐Mieg, N., and Ricard‐Blum, S. 2009. MatrixDB, a database focused on extracellular protein‐protein and protein‐carbohydrate interactions. Bioinformatics 25:690‐691.
   Cote, R.G., Jones, P., Martens, L., Apweiler, R., and Hermjakob, H. 2008. The Ontology Lookup Service: More data and better tools for controlled vocabulary queries. Nucl. Acids Res. 36:w372‐376.
   Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcantara, R., Darsow, M., Guedj, M., and Ashburner, M. 2008. ChEBI: A database and ontology for chemical entities of biological interest. Nucl. Acids Res. 36:d344‐350.
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   Kerrien, S., Alam‐Faruque. Y., Aranda, B., Bancarz, I., Bridge, A., Derow, C., Dimmer, E., Feuermann, M., Friedrichsen, A., Huntley, R., Kohler, C., Khadake, J., Leroy, C., Liban, A., Lieftink, C., Montecchi‐Palazzi, L., Orchard, S., Risse, J., Robbe, K., Roechert, B., Thorneycroft, D., Zhang, Y., Apweiler, R. and Hermjakob, H. 2007a. IntAct: Open source resource for molecular interaction data. Nucl. Acids Res. 35:561‐565.
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   Koegl, M. and Uetz, P. 2007. Improving yeast two‐hybrid screening systems. Briefings in Functional Genomics & Proteomics 6:302‐312
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   Orchard, S., Salwinski, L., Kerrien, S., Montecchi‐Palazzi, L., Oesterheld, M., Stumpflen, V., Ceol, A., Chatr‐aryamontri, A., Armstrong, J., Woollard, P., Salama, J.J., Moore, S., Wojcik, J., Bader, G.D., Vidal, M., Cusick, M.E., Gerstein, M., Gavin, A‐C., Superti‐Furga, G., Greenblatt, J., Bader, J., Uetz, P., Tyers, M., Legrain, P., Fields, S., Mulder, N., Gilson, M., Niepmann, M., Burgoon, L., De Las Rivas, J., Prieto, C., Perreau, V.M., Hogue, C., Mewes, H‐W., Apweiler, R., Xenarios, I., Eisenberg, D., Cesareni, G. and Hermjakob, H. 2007a. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat. Biotech. 25:894‐898.
   Orchard, S., Kerrien, S., Jones, P., Ceol, A., Chatr‐Aryamontri, A., Salwinski, L., Nerothin, J., and Hermjakob, H. 2007b. Submit your interaction data the IMEx way: A step by step guide to trouble‐free deposition. Proteomics 7:28‐34.
   Xenarios, I., Salwinski, L., Duan, X.J., Higney, P., Kim, S.M., and Eisenberg, D. 2002. DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions. Nucl. Acids Res. 30:303‐305.
Internet Resources
  IMEx Consortium Member Databases currently accepting Direct Submissions.
  The IMEx Consortium.
  The PSI‐MI XML schema and related resources.
  Interactor Databases.
  The Ontology‐Lookup Service.‐lookup/
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