Dataset Information

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.

SUBMITTER: Kerrien S

PROVIDER: S-EPMC2189715 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature

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Publications

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

Kerrien Samuel S Orchard Sandra S Montecchi-Palazzi Luisa L Aranda Bruno B Quinn Antony F AF Vinod Nisha N Bader Gary D GD Xenarios Ioannis I Wojcik Jérôme J Sherman David D Tyers Mike M Salama John J JJ Moore Susan S Ceol Arnaud A Chatr-Aryamontri Andrew A Oesterheld Matthias M Stümpflen Volker V Salwinski Lukasz L Nerothin Jason J Cerami Ethan E Cusick Michael E ME Vidal Marc M Gilson Michael M Armstrong John J Woollard Peter P Hogue Christopher C Eisenberg David D Cesareni Gianni G Apweiler Rolf R Hermjakob Henning H

BMC biology 20071009

<h4>Background</h4>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 ...[more]

PMID: 17925023

Similar Datasets

Project description:BACKGROUND:Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes. RESULTS:The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal. CONCLUSIONS:PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.

Dataset Information

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

Background

Results

Conclusion

Publications

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

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