The Publication and Database Deposition of Molecular Interaction Data
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- Abstract
- Table of Contents
- Figures
- Literature Cited
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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PDF or HTML at Wiley Online LibraryTable 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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Figure 25.3.1 The International Molecular Exchange (IMEx) Web site. View Image -
Figure 25.3.2 The preformatted IMEx Excel sheet, suitable for medium‐scale depositions. View Image -
Figure 25.3.3 Performing a BLAST against the human data held in the UniProtKB database to access an accession number. View Image -
Figure 25.3.4 Using the Ontology‐Lookup Service to find a term in the PSI‐MI controlled vocabulary. View Image
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. | |
| 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. | |
| Hermjakob, H., Montecchi‐Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., Roechert, B., Poux, S., Jung, E., Mersch, H., Kersey, P., Lappe, M., Li, Y., Zeng, R., Rana, D., Nikolski, M., Husi, H., Brun, C., Shanker, K., Grant, S.G.N., Sander, C., Bork, P., Zhu, W., Pandey, A., Brazma, A., Jacq, B., Vidal, M., Sherman, D., Legrain, P., Cesareni, G., Xenarios, I., Eisenberg, D., Steipe, B., Hogue, C., and Apweiler, R. 2004. The HUPO PSI's molecular interaction format: A community standard for the representation of protein interaction data. Nat. Biotech. 22:177‐183. | |
| 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. | |
| Kerrien, S., Orchard, S., Montecchi‐Palazzi, L., Aranda, B., Quinn, A.F., Vinod, N., Bader, G.D., Xenarios, I., Wojcik, J., Sherman, D., Tyers, M., Salama, J.J., Moore, S., Ceol, A., Chatr‐Aryamontri, A., Oesterheld, M., Stümpflen, V., Salwinski, L., Nerothin, J., Cerami, E., Cusick, M.E., Vidal, M., Gilson, M., Armstrong, J., Woollard, P., Hogue, C., Eisenberg, D., Cesareni, G., Apweiler, R., and Hermjakob, H. 2007b. Broadening the horizon: Level 2.5 of the HUPO‐PSI format for molecular interactions. BMC Biol. 5:44. | |
| Koegl, M. and Uetz, P. 2007. Improving yeast two‐hybrid screening systems. Briefings in Functional Genomics & Proteomics 6:302‐312 | |
| Montecchi‐Palazzi, L., Kerrien, S., Reisinger, F., Aranda, B., Jones, A.R., Martens, L., and Hermjakob, H. 2009. The PSI semantic validator: A framework to check MIAPE compliance of proteomics data Proteomics 9:5112‐5119. | |
| 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 | |
| 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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