Abstract
BackgroundMolecular 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.ResultsThe 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.ConclusionThe 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.
Highlights
Molecular interaction Information is a key resource in modern biomedical research
We have developed version 2.5 of the PSI-molecule or ChEBI (MI) XML schema for molecular interactions, extended the associated controlled vocabularies and updated the tools supporting the format
The PSI-MI XML1.0 format provided the molecular interaction community with a common mechanism for data exchange that enabled data to be shared between multiple sources, integrated, analysed and visualised by a range of software tools
Summary
We have developed version 2.5 of the PSI-MI XML schema for molecular interactions, extended the associated controlled vocabularies and updated the tools supporting the format. 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). All tools are freely available and can be accessed and downloaded from the PSI-MI web pages These include applications to view and validate the use of the schema, to enable graphical representation of interaction network, to convert between data formats and to facilitate the use of controlled vocabularies. The full data set can be viewed as supplementary materials in both PSIMI 2.5 XML or MITAB2.5 formats or can be viewed as a fully curated dataset in the IntAct database (EBI-914159, EBI-914232, EBI-914360)
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