The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).
Hermjakob
Henning
H
European Bioinformatics Institute, EBI-Hinxton, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. hhe@ebi.ac.uk
Montecchi-Palazzi
Luisa
L
Bader
Gary
G
Wojcik
Jérôme
J
Salwinski
Lukasz
L
Ceol
Arnaud
A
Moore
Susan
S
Orchard
Sandra
S
Sarkans
Ugis
U
von Mering
Christian
C
Roechert
Bernd
B
Poux
Sylvain
S
Jung
Eva
E
Mersch
Henning
H
Kersey
Paul
P
Lappe
Michael
M
Li
Yixue
Y
Zeng
Rong
R
Rana
Debashis
D
Nikolski
Macha
M
Husi
Holger
H
Brun
Christine
C
Shanker
K
K
Grant
Seth G N
SG
Sander
Chris
C
Bork
Peer
P
Zhu
Weimin
W
Pandey
Akhilesh
A
Brazma
Alvis
A
Jacq
Bernard
B
Vidal
Marc
M
Sherman
David
D
Legrain
Pierre
P
Cesareni
Gianni
G
Xenarios
Ioannis
I
Eisenberg
David
D
Steipe
Boris
B
Hogue
Chris
C
Apweiler
Rolf
R
D003628:Database Management Systems / Q000592:standards*; D030562:Databases, Protein / Q000592:standards*; D017408:Guidelines as Topic; D016247:Information Storage and Retrieval / Q000379:methods / Q000592:standards*; D038622:Internationality; D009323:Natural Language Processing; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods / Q000592:standards*; D011506:Proteins / Q000737:chemistry / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods / Q000592:standards*; D012015:Reference Standards; D012984:Software; D014584:User-Computer Interface
D011506:Proteins