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

Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H - BMC Biol. (2007)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. skerrien@ebi.ac.uk

ABSTRACT

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.

Show MeSH
A representative section of the PSI-MI controlled vocabulary displayed in the Ontology Lookup Service.
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Figure 5: A representative section of the PSI-MI controlled vocabulary displayed in the Ontology Lookup Service.

Mentions: Controlled vocabularies (CVs) are used throughout the PSI-MI schema to standardize the meaning of data objects. Their use ensures that the same term used throughout a description by a data producer, instead of a synonym or alternative spelling, and also that the interpretation of the meaning of that term remains consistent between multiple data producers and data users. In order to achieve this, all terms have definitions and, where appropriate, are supported by a literature reference. The controlled vocabularies have a hierarchical structure, higher level terms being more general than lower level descriptors, allowing annotation to be performed to an appropriate level of granularity whilst also enabling search tools to return all mapped objects to both parent and child terms, if required (Figure 5).


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

Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H - BMC Biol. (2007)

A representative section of the PSI-MI controlled vocabulary displayed in the Ontology Lookup Service.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2189715&req=5

Figure 5: A representative section of the PSI-MI controlled vocabulary displayed in the Ontology Lookup Service.
Mentions: Controlled vocabularies (CVs) are used throughout the PSI-MI schema to standardize the meaning of data objects. Their use ensures that the same term used throughout a description by a data producer, instead of a synonym or alternative spelling, and also that the interpretation of the meaning of that term remains consistent between multiple data producers and data users. In order to achieve this, all terms have definitions and, where appropriate, are supported by a literature reference. The controlled vocabularies have a hierarchical structure, higher level terms being more general than lower level descriptors, allowing annotation to be performed to an appropriate level of granularity whilst also enabling search tools to return all mapped objects to both parent and child terms, if required (Figure 5).

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. skerrien@ebi.ac.uk

ABSTRACT

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.

Show MeSH