Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions
Abstract 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 stan...
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2018-04-01
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Series: | BMC Bioinformatics |
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Online Access: | http://link.springer.com/article/10.1186/s12859-018-2118-1 |
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language |
English |
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Article |
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DOAJ |
author |
M. Sivade (Dumousseau) D. Alonso-López M. Ammari G. Bradley N. H. Campbell A. Ceol G. Cesareni C. Combe J. De Las Rivas N. del-Toro J. Heimbach H. Hermjakob I. Jurisica M. Koch L. Licata R. C. Lovering D. J. Lynn B. H. M. Meldal G. Micklem S. Panni P. Porras S. Ricard-Blum B. Roechert L. Salwinski A. Shrivastava J. Sullivan N. Thierry-Mieg Y. Yehudi K. Van Roey S. Orchard |
spellingShingle |
M. Sivade (Dumousseau) D. Alonso-López M. Ammari G. Bradley N. H. Campbell A. Ceol G. Cesareni C. Combe J. De Las Rivas N. del-Toro J. Heimbach H. Hermjakob I. Jurisica M. Koch L. Licata R. C. Lovering D. J. Lynn B. H. M. Meldal G. Micklem S. Panni P. Porras S. Ricard-Blum B. Roechert L. Salwinski A. Shrivastava J. Sullivan N. Thierry-Mieg Y. Yehudi K. Van Roey S. Orchard Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions BMC Bioinformatics Molecular interactions Protein-protein interaction Protein complexes Data standards XML HUPO-PSI |
author_facet |
M. Sivade (Dumousseau) D. Alonso-López M. Ammari G. Bradley N. H. Campbell A. Ceol G. Cesareni C. Combe J. De Las Rivas N. del-Toro J. Heimbach H. Hermjakob I. Jurisica M. Koch L. Licata R. C. Lovering D. J. Lynn B. H. M. Meldal G. Micklem S. Panni P. Porras S. Ricard-Blum B. Roechert L. Salwinski A. Shrivastava J. Sullivan N. Thierry-Mieg Y. Yehudi K. Van Roey S. Orchard |
author_sort |
M. Sivade (Dumousseau) |
title |
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions |
title_short |
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions |
title_full |
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions |
title_fullStr |
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions |
title_full_unstemmed |
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions |
title_sort |
encompassing new use cases - level 3.0 of the hupo-psi format for molecular interactions |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2018-04-01 |
description |
Abstract 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. |
topic |
Molecular interactions Protein-protein interaction Protein complexes Data standards XML HUPO-PSI |
url |
http://link.springer.com/article/10.1186/s12859-018-2118-1 |
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doaj-9fd01102da0f43b2a9c9ea2fd780c54c2020-11-25T00:14:20ZengBMCBMC Bioinformatics1471-21052018-04-011911810.1186/s12859-018-2118-1Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactionsM. Sivade (Dumousseau)0D. Alonso-López1M. Ammari2G. Bradley3N. H. Campbell4A. Ceol5G. Cesareni6C. Combe7J. De Las Rivas8N. del-Toro9J. Heimbach10H. Hermjakob11I. Jurisica12M. Koch13L. Licata14R. C. Lovering15D. J. Lynn16B. H. M. Meldal17G. Micklem18S. Panni19P. Porras20S. Ricard-Blum21B. Roechert22L. Salwinski23A. Shrivastava24J. Sullivan25N. Thierry-Mieg26Y. Yehudi27K. Van Roey28S. Orchard29European Bioinformatics Institute (EMBL-EBI), European Molecular Biology LaboratoryCancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL)School of Animal and Comparative Biomedical Sciences, University of ArizonaTarget Sciences, GSKInstitute of Cardiovascular Science, University College LondonCenter for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT)Department of Biology, University of Rome Tor VergataWellcome Trust Centre for Cell Biology, School of Biological Sciences, University of EdinburghCancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL)European Bioinformatics Institute (EMBL-EBI), European Molecular Biology LaboratoryCambridge Systems Biology Centre, University of CambridgeEuropean Bioinformatics Institute (EMBL-EBI), European Molecular Biology LaboratoryKrembil Research Institute, University Health NetworkEuropean Bioinformatics Institute (EMBL-EBI), European Molecular Biology LaboratoryDepartment of Biology, University of Rome Tor VergataInstitute of Cardiovascular Science, University College LondonEMBL Australia Group, South Australian Health and Medical Research InstituteEuropean Bioinformatics Institute (EMBL-EBI), European Molecular Biology LaboratoryCambridge Systems Biology Centre, University of CambridgeDepartment of Biology, Ecology and Earth Sciences, Università della CalabriaEuropean Bioinformatics Institute (EMBL-EBI), European Molecular Biology LaboratoryUniv Lyon, University Claude Bernard Lyon 1, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS)SIB Swiss Institute of Bioinformatics, Centre Medical UniversitaireUCLA-DOE Institute for Genomics and ProteomicsEuropean Bioinformatics Institute (EMBL-EBI), European Molecular Biology LaboratoryCambridge Systems Biology Centre, University of CambridgeTIMC-IMAG, CNRS, Univ. Grenoble AlpesCambridge Systems Biology Centre, University of CambridgeStructural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EMBL-EBI), European Molecular Biology LaboratoryAbstract 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.http://link.springer.com/article/10.1186/s12859-018-2118-1Molecular interactionsProtein-protein interactionProtein complexesData standardsXMLHUPO-PSI |