Many molecular interaction databases have chosen the PSI-MI format for providing data to their users.
For example, BioGRID (Breitkreutz et al., 2008) and IntAct (Aranda et al., 2009) are major molecular interaction databases of PPIs.
MImerge and MIscore were used to calculate the score distribution across several molecular interaction databases (Table 3).
It is able to fetch data from I) molecular interaction databases, II) Biomart, and III) different ontologies out of the box.
Molecular interaction databases have made searching for interactions between interesting genes easier, and have thus brought countless new hypotheses to the work of researchers around the globe.
The human PPI network was constructed by integrating human PPIs from several molecular interaction databases, both public (BIND, BioGRID, HPRD, MINT, Reactome, DIP, and IntAct) and commercial (Ingenuity, Proteome, MetaBase, and NetPro).
The Y2H data were isolated from downloads of the BioGRID Interaction Database, Database for Interacting Proteins (DIP), IntAct database, and Molecular INTeraction Database (MINT) [ 52- 59], yielding 29096 unique interactions from 1680 publications.
The protein-protein interaction data were obtained from five PPI databases, the Human Protein Reference Database (HPRD) [ 43], IntAct [ 44], the Database of Interacting Proteins (DIP) [ 45], the Molecular INTeraction Database (MINT) [ 46] and the Biomolecular Interaction Network Database (BIND) [ 47].
Despite the importance of cooperative interactions in regulating biological molecular systems, they are currently not adequately captured in bioinformatics resources, for instance, interaction databases such as IntAct (26), the Database of Interacting Proteins (DIP) (27) and the Molecular Interaction database (MINT) (28), but also pathway databases like Reactome (29).
We gathered 78,804 PPIs between human proteins from seven databases: the Biomolecular Interaction Network Database [7], the Database of Interacting Proteins [12], the Human Protein Reference Database [11], IntAct [9], the Molecular INTeraction database [13], the Munich Information Center for Protein Sequences [8], and Reactome [10].
Several databases have now been established as repositories for molecular interaction data including the Molecular Interaction database (MINT) [ 23]; the IntAct database [ 24]; the Database of Interacting Proteins (DIP) [ 25]; the General Repository for Interaction Datasets (BioGRID) [ 26] and the Biomolecular Interaction Network Database (BIND) [ 27].
