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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
Graphical representation of the PSI-MI XML2.5 format. Some elements have been collapsed for clarity (indicated by a '+' in a rectangular box).
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Figure 1: Graphical representation of the PSI-MI XML2.5 format. Some elements have been collapsed for clarity (indicated by a '+' in a rectangular box).

Mentions: The root element of PSI-MI XML2.5 is the entrySet. It contains one or more entry elements. An entry is the core element of PSI-MI XML2.5, describing one or more interactions with all associated data as a self-contained unit (Figure 1). Thus, several PSI-MI XML2.5 files can easily be merged by inserting all entry elements into a single entrySet. The entry contains a source element describing the origin of the data in the entry, usually an organisation such as a database provider. The following three elements, availabilityList, experimentList, and interactorList, are container elements for repetitive elements of interactions. The next element, interactionList, contains all interactions described in the entry.


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)

Graphical representation of the PSI-MI XML2.5 format. Some elements have been collapsed for clarity (indicated by a '+' in a rectangular box).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Graphical representation of the PSI-MI XML2.5 format. Some elements have been collapsed for clarity (indicated by a '+' in a rectangular box).
Mentions: The root element of PSI-MI XML2.5 is the entrySet. It contains one or more entry elements. An entry is the core element of PSI-MI XML2.5, describing one or more interactions with all associated data as a self-contained unit (Figure 1). Thus, several PSI-MI XML2.5 files can easily be merged by inserting all entry elements into a single entrySet. The entry contains a source element describing the origin of the data in the entry, usually an organisation such as a database provider. The following three elements, availabilityList, experimentList, and interactorList, are container elements for repetitive elements of interactions. The next element, interactionList, contains all interactions described in the entry.

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