Advertisement

Preparing Molecular Interaction Data for Publication

  • Sandra Orchard
  • Henning Hermjakob
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 694)

Abstract

It is now becoming more usual for journals to request the submission of the data accompanying an article to an appropriate public repository. Such users may access the data in a format appropriate for display and reanalysis. It is commonly accepted that molecular interaction databases will hold all the large-scale interaction datasets and enrich this with lower throughput data. Previously this small-scale interaction data has been archively curated from the literature but, increasingly, deposition of such information is also being seen as an integral part of the publication process. This chapter acts as a brief guide to preparing both large- and small-scale data for publication and gives a range of different submission options.

Key words

Human proteome organisation Proteomics standards initiative International molecular exchange consortium Data standardization 

References

  1. 1.
    Aranda, B., Achuthan, P., Alam-Faruque, Y., Armean, I., Bridge, A., Derow, C., Feuermann, M., Kerrien, S., Khadake, J., Kerssemakers, J., Leroy, C., Menden, M., Michaut, M., Montecchi-Palazzi, L., Neuhauser, S.N., Orchard, S., Perreau, V., Roechert, B., Tashakkori, A., van Eijk, K., Hermjakob, H. (2010) The IntAct molecular interaction database in 2010. Nucleic Acid Res 38, D525–D531.PubMedCrossRefGoogle Scholar
  2. 2.
    Anon. (2005) Proteomics’ new order. Nature 437, 169–170.Google Scholar
  3. 3.
    Orchard, S., Hermjakob, H. (2008) Standardising proteomics data: the work of the HUPO proteomics standards initiative. J Proteomics Bioinform 1, 3–5.CrossRefGoogle Scholar
  4. 4.
    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., 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., Apweiler, R. (2004) The HUPO PSI’s molecular interaction format – a community standard for the representation of protein interaction data. Nat Biotechnol 22, 177–183.PubMedCrossRefGoogle Scholar
  5. 5.
    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., Hermjakob, H. (2007) Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol 5, 44PubMedCrossRefGoogle Scholar
  6. 6.
    Orchard, S., Salwinski, L., Kerrien, S., Montecchi-Palazzi, L., Oesterheld, M., Stümpflen, 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., Priesto, C., Perreau, V.M., Hogue, C., Mewes, H.-W., Apweiler, R., Xenarios, I., Eisenberg, D., Cesareni, C., Hermjakob, H. (2007) The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol 25, 894–898.PubMedCrossRefGoogle Scholar
  7. 7.
    Chiang, T., Li, N., Orchard, S., Kerrien, S., Hermjakob, H., Gentleman, R., Huber, W. (2008) Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. Bioinformatics 24, 1100–1101.PubMedCrossRefGoogle Scholar
  8. 8.
    Chatr-aryamontri, A., Ceol, A., Palazzi, L.M., Nardelli, G., Schneider, M.V., Castagnoli, L., Cesareni, G. (2007) MINT: the Molecular INTeraction database. Nucleic Acids Res 35, D572–D574.PubMedCrossRefGoogle Scholar
  9. 9.
    Xenarios, I., Salwinski, L., Duan, X.J., Higney, P., Kim, S., Eisenberg, D. (2002) DIP: the database of interacting proteins. A research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30, 303–305.PubMedCrossRefGoogle Scholar
  10. 10.
    Chautard, E., Ballut, L., Thierry-Mieg, N., Ricard-Blum, S. (2009) MatrixDB, a database focused on extracellular protein–protein and protein–carbohydrate interactions. Bioinformatics 25, 690–691.PubMedCrossRefGoogle Scholar
  11. 11.
    Goll, J., Rajagopala, S.V., Shiau, S.C., Wu, H., Lamb, B.T., Uetz, P. (2008) MPIDB: the microbial protein interaction database. Bioinformatics 24, 1743–1744.PubMedCrossRefGoogle Scholar
  12. 12.
    Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcantara, R., Darsow, M., Guedj, M., Ashburner, M. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res 36, D344–D350.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Sandra Orchard
    • 1
  • Henning Hermjakob
    • 1
  1. 1.EMBL OutstationEuropean Bioinformatics Institute (EBI)CambridgeUK

Personalised recommendations