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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
Use of interactorType within the PSI-MI XML2.5 schema to describe the molecular class of two participating molecules – a small molecule interactor and a RNA – using the appropriate controlled vocabulary term
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Figure 2: Use of interactorType within the PSI-MI XML2.5 schema to describe the molecular class of two participating molecules – a small molecule interactor and a RNA – using the appropriate controlled vocabulary term

Mentions: An interactor element describes a molecule participating in an interaction. In version 1.0, the corresponding element was named proteinInteractor, as version 1.0 was only intended to represent protein interactions. The original plan was to add additional interactor types, e.g. rnaInteractor, as separate elements in future versions of the schema, however, it quickly became apparent that a full modelling of all relevant interactor types, for example mRNA, tRNA, rRNA and so on, would make the schema unnecessarily repetitive and complex. Thus, version 2.5 contains a lightweight representation of an interacting molecule, with the key element interactorType, which qualifies an interactor with a term from the PSI-MI controlled vocabulary, for example 'protein' (MI:0326; see Availability and requirements for instructions on how to access this and other entries) or 'small nucleolar rna' (MI:0607) (Figure 2). This allows a compact, yet very expressive representation of an interactor. The schema does not attempt to provide a detailed representation of interacting molecules – interactor elements will usually contain only basic information and refer to external databases for detailed descriptions. The controlled vocabulary for interactorType currently comprises >25 terms and can be easily expanded should a user wish to describe an additional interactor type, for example phospholipids, without any change to the XML schema. Additional cross-references to external resources allow for a more detailed description of the interactor, for example to UniProtKB (MI:0018) [17] to further describe a protein molecule or ChEBI (MI:0474) [18] for a chemical entity (Figure 3). The schema also now supports the hierarchical build-up of complexes from component sub-complexes, in that a sub-complex can be recycled as an interactor using the appropriate controlled vocabulary term and internal referencing (Figure 4). This allows the visualisation of a series of consecutive events, for example in the case where a receptor must form from two or more subunits before its agonist can bind.


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)

Use of interactorType within the PSI-MI XML2.5 schema to describe the molecular class of two participating molecules – a small molecule interactor and a RNA – using the appropriate controlled vocabulary term
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Use of interactorType within the PSI-MI XML2.5 schema to describe the molecular class of two participating molecules – a small molecule interactor and a RNA – using the appropriate controlled vocabulary term
Mentions: An interactor element describes a molecule participating in an interaction. In version 1.0, the corresponding element was named proteinInteractor, as version 1.0 was only intended to represent protein interactions. The original plan was to add additional interactor types, e.g. rnaInteractor, as separate elements in future versions of the schema, however, it quickly became apparent that a full modelling of all relevant interactor types, for example mRNA, tRNA, rRNA and so on, would make the schema unnecessarily repetitive and complex. Thus, version 2.5 contains a lightweight representation of an interacting molecule, with the key element interactorType, which qualifies an interactor with a term from the PSI-MI controlled vocabulary, for example 'protein' (MI:0326; see Availability and requirements for instructions on how to access this and other entries) or 'small nucleolar rna' (MI:0607) (Figure 2). This allows a compact, yet very expressive representation of an interactor. The schema does not attempt to provide a detailed representation of interacting molecules – interactor elements will usually contain only basic information and refer to external databases for detailed descriptions. The controlled vocabulary for interactorType currently comprises >25 terms and can be easily expanded should a user wish to describe an additional interactor type, for example phospholipids, without any change to the XML schema. Additional cross-references to external resources allow for a more detailed description of the interactor, for example to UniProtKB (MI:0018) [17] to further describe a protein molecule or ChEBI (MI:0474) [18] for a chemical entity (Figure 3). The schema also now supports the hierarchical build-up of complexes from component sub-complexes, in that a sub-complex can be recycled as an interactor using the appropriate controlled vocabulary term and internal referencing (Figure 4). This allows the visualisation of a series of consecutive events, for example in the case where a receptor must form from two or more subunits before its agonist can bind.

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