Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.

Détails

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Etat: Public
Version: Final published version
ID Serval
serval:BIB_90CF4FDC2CED
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
Périodique
BMC Biology
Auteur(s)
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.
ISSN
1741-7007 (Electronic)
ISSN-L
1741-7007
Statut éditorial
Publié
Date de publication
2007
Volume
5
Pages
44
Langue
anglais
Résumé
BACKGROUND: Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions.
RESULTS: The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration.
CONCLUSION: The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel.
Mots-clé
Computational Biology, Computer Graphics, Database Management Systems, Databases, Protein/standards, Natural Language Processing, Protein Interaction Mapping/methods, Proteomics/methods, Proteomics/standards, User-Computer Interface
Pubmed
Web of science
Open Access
Oui
Création de la notice
17/10/2012 10:56
Dernière modification de la notice
20/08/2019 14:54
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