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

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.

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).

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

Figure 3

Graphical representation of section of the PSI-MI XML2.5 schema describing participant with the corresponding lines of XML containing sample data from [26]

Figure 4

Assembly of a mature complex (I2) from two protein components (P1 and P2) that bind to form an intermediate assembly (I1) with which a third protein (P3) interacts. I1 is both the result of an interaction and a subsequent interactor in the PSI-MI2.5 format.

Figure 5

A representative section of the PSI-MI controlled vocabulary displayed in the Ontology Lookup Service.