Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

Sivade Dumousseau M; Alonso-López D; Ammari M; Bradley G; Campbell NH; Ceol A; Cesareni G; Combe C; De Las Rivas J; Del-Toro N; Heimbach J; Hermjakob H; Jurisica I; Koch M; Licata L; Lovering RC; Lynn DJ; Meldal BHM; Micklem G; Panni S; Porras P; Ricard-Blum S; Roechert B; Salwinski L; Shrivastava A; Sullivan J; Thierry-Mieg N; Yehudi Y; Van Roey K; Orchard S

doi:10.1186/s12859-018-2118-1

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Journal article

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

Sivade Dumousseau M European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
Alonso-López D Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007, Salamanca, Spain.
Ammari M School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, USA.
Bradley G Target Sciences, GSK, Stevenage, UK.
Campbell NH Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London, WC1E 6JF, UK.
Ceol A Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, I-20139, Milan, Italy.
Cesareni G Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy.
Combe C Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
De Las Rivas J Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), 37007, Salamanca, Spain.
Del-Toro N European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
Heimbach J Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
Hermjakob H European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
Jurisica I Krembil Research Institute, University Health Network, Toronto, ON, M5T 2S8, Canada.
Koch M European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
Licata L Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy.
Lovering RC Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London, WC1E 6JF, UK.
Lynn DJ EMBL Australia Group, South Australian Health and Medical Research Institute, Adelaide, Australia.
Meldal BHM European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
Micklem G Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
Panni S Department of Biology, Ecology and Earth Sciences, Università della Calabria, Rende, Italy.
Porras P European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
Ricard-Blum S Univ Lyon, University Claude Bernard Lyon 1, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, F-69622, Villeurbanne, France.
Roechert B SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211, Geneva 4, Switzerland.
Salwinski L UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, USA.
Shrivastava A European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
Sullivan J Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
Thierry-Mieg N TIMC-IMAG, CNRS, Univ. Grenoble Alpes, F-38000, Grenoble, France.
Yehudi Y Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
Van Roey K Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117, Heidelberg, Germany.
Orchard S European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK. orchard@ebi.ac.uk.

2018-04-13

Published in:

BMC bioinformatics. - 2018

English 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.

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