title: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. skerrien@ebi.ac.uk
authors.forename: Samuel
authors.initials: S
authors.lastname: Kerrien
authors.forename: Sandra
authors.initials: S
authors.lastname: Orchard
authors.forename: Luisa
authors.initials: L
authors.lastname: Montecchi-Palazzi
authors.forename: Bruno
authors.initials: B
authors.lastname: Aranda
authors.forename: Antony F
authors.initials: AF
authors.lastname: Quinn
authors.forename: Nisha
authors.initials: N
authors.lastname: Vinod
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bader
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.forename: Jérôme
authors.initials: J
authors.lastname: Wojcik
authors.forename: David
authors.initials: D
authors.lastname: Sherman
authors.forename: Mike
authors.initials: M
authors.lastname: Tyers
authors.forename: John J
authors.initials: JJ
authors.lastname: Salama
authors.forename: Susan
authors.initials: S
authors.lastname: Moore
authors.forename: Arnaud
authors.initials: A
authors.lastname: Ceol
authors.forename: Andrew
authors.initials: A
authors.lastname: Chatr-Aryamontri
authors.forename: Matthias
authors.initials: M
authors.lastname: Oesterheld
authors.forename: Volker
authors.initials: V
authors.lastname: Stümpflen
authors.forename: Lukasz
authors.initials: L
authors.lastname: Salwinski
authors.forename: Jason
authors.initials: J
authors.lastname: Nerothin
authors.forename: Ethan
authors.initials: E
authors.lastname: Cerami
authors.forename: Michael E
authors.initials: ME
authors.lastname: Cusick
authors.forename: Marc
authors.initials: M
authors.lastname: Vidal
authors.forename: Michael
authors.initials: M
authors.lastname: Gilson
authors.forename: John
authors.initials: J
authors.lastname: Armstrong
authors.forename: Peter
authors.initials: P
authors.lastname: Woollard
authors.forename: Christopher
authors.initials: C
authors.lastname: Hogue
authors.forename: David
authors.initials: D
authors.lastname: Eisenberg
authors.forename: Gianni
authors.initials: G
authors.lastname: Cesareni
authors.forename: Rolf
authors.initials: R
authors.lastname: Apweiler
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
mesh_terms: D019295:Computational Biology; D003196:Computer Graphics; D003628:Database Management Systems; D030562:Databases, Protein / Q000592:standards*; D009323:Natural Language Processing; D025941:Protein Interaction Mapping / Q000379:methods*; D040901:Proteomics / Q000379:methods* / Q000592:standards; D014584:User-Computer Interface