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

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 P...

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Autores principales: Kerrien, Samuel, Orchard, Sandra, Montecchi-Palazzi, Luisa, Aranda, Bruno, Quinn, Antony F, Vinod, Nisha, Bader, Gary D, Xenarios, Ioannis, Wojcik, Jérôme, Sherman, David, Tyers, Mike, Salama, John J, Moore, Susan, Ceol, Arnaud, Chatr-aryamontri, Andrew, Oesterheld, Matthias, Stümpflen, Volker, Salwinski, Lukasz, Nerothin, Jason, Cerami, Ethan, Cusick, Michael E, Vidal, Marc, Gilson, Michael, Armstrong, John, Woollard, Peter, Hogue, Christopher, Eisenberg, David, Cesareni, Gianni, Apweiler, Rolf, Hermjakob, Henning
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2189715/
https://www.ncbi.nlm.nih.gov/pubmed/17925023
http://dx.doi.org/10.1186/1741-7007-5-44
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author Kerrien, Samuel
Orchard, Sandra
Montecchi-Palazzi, Luisa
Aranda, Bruno
Quinn, Antony F
Vinod, Nisha
Bader, Gary D
Xenarios, Ioannis
Wojcik, Jérôme
Sherman, David
Tyers, Mike
Salama, John J
Moore, Susan
Ceol, Arnaud
Chatr-aryamontri, Andrew
Oesterheld, Matthias
Stümpflen, Volker
Salwinski, Lukasz
Nerothin, Jason
Cerami, Ethan
Cusick, Michael E
Vidal, Marc
Gilson, Michael
Armstrong, John
Woollard, Peter
Hogue, Christopher
Eisenberg, David
Cesareni, Gianni
Apweiler, Rolf
Hermjakob, Henning
author_facet Kerrien, Samuel
Orchard, Sandra
Montecchi-Palazzi, Luisa
Aranda, Bruno
Quinn, Antony F
Vinod, Nisha
Bader, Gary D
Xenarios, Ioannis
Wojcik, Jérôme
Sherman, David
Tyers, Mike
Salama, John J
Moore, Susan
Ceol, Arnaud
Chatr-aryamontri, Andrew
Oesterheld, Matthias
Stümpflen, Volker
Salwinski, Lukasz
Nerothin, Jason
Cerami, Ethan
Cusick, Michael E
Vidal, Marc
Gilson, Michael
Armstrong, John
Woollard, Peter
Hogue, Christopher
Eisenberg, David
Cesareni, Gianni
Apweiler, Rolf
Hermjakob, Henning
author_sort Kerrien, Samuel
collection PubMed
description 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.
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spelling pubmed-21897152008-01-11 Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions Kerrien, Samuel Orchard, Sandra Montecchi-Palazzi, Luisa Aranda, Bruno Quinn, Antony F Vinod, Nisha Bader, Gary D Xenarios, Ioannis Wojcik, Jérôme Sherman, David Tyers, Mike Salama, John J Moore, Susan Ceol, Arnaud Chatr-aryamontri, Andrew Oesterheld, Matthias Stümpflen, Volker Salwinski, Lukasz Nerothin, Jason Cerami, Ethan Cusick, Michael E Vidal, Marc Gilson, Michael Armstrong, John Woollard, Peter Hogue, Christopher Eisenberg, David Cesareni, Gianni Apweiler, Rolf Hermjakob, Henning BMC Biol Software 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. BioMed Central 2007-10-09 /pmc/articles/PMC2189715/ /pubmed/17925023 http://dx.doi.org/10.1186/1741-7007-5-44 Text en Copyright © 2007 Kerrien et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Kerrien, Samuel
Orchard, Sandra
Montecchi-Palazzi, Luisa
Aranda, Bruno
Quinn, Antony F
Vinod, Nisha
Bader, Gary D
Xenarios, Ioannis
Wojcik, Jérôme
Sherman, David
Tyers, Mike
Salama, John J
Moore, Susan
Ceol, Arnaud
Chatr-aryamontri, Andrew
Oesterheld, Matthias
Stümpflen, Volker
Salwinski, Lukasz
Nerothin, Jason
Cerami, Ethan
Cusick, Michael E
Vidal, Marc
Gilson, Michael
Armstrong, John
Woollard, Peter
Hogue, Christopher
Eisenberg, David
Cesareni, Gianni
Apweiler, Rolf
Hermjakob, Henning
Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
title Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
title_full Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
title_fullStr Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
title_full_unstemmed Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
title_short Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
title_sort broadening the horizon – level 2.5 of the hupo-psi format for molecular interactions
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2189715/
https://www.ncbi.nlm.nih.gov/pubmed/17925023
http://dx.doi.org/10.1186/1741-7007-5-44
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