IntAct: an open source molecular interaction database

Abstract

IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of protein interactions, and allows exploring interaction networks in the context of the GO annotations of the interacting proteins. A web service allows direct computational access to retrieve interaction networks in XML format. IntAct currently contains approximately 2200 binary and complex interactions imported from the literature and curated in collaboration with the Swiss-Prot team, making intensive use of controlled vocabularies to ensure data consistency. All IntAct software, data and controlled vocabularies are available at http://www.ebi.ac.uk/intact.

Figure 1

IntAct search interface, binary view. For each query protein, this view shows all its potential interaction partners, together with a short description. For each interaction partner, a link allows to access the experiment view, displaying all the experiments that provide evidence that these two proteins interact.

Figure 2

IntAct search interface, experiment view. This view provides details on the context in which interactions have been derived, in particular the experimental methods by which the interaction and the interacting proteins have been determined, and a list of relevant interactions that have been determined in this experiment. All controlled vocabulary terms are hyperlinked to their definition, and field descriptors are hyperlinked to their definition in the online user manual. The query used in this example is the GO accession number GO:0000176. Proteins that are annotated with this GO term are shown in the context of their interactions, and are shown in bold italics.

Figure 3

Graphical interaction network viewer. The protein lsm6_yeast (Swiss-Prot Q06406) is shown in the context of its local interaction network. Using the GO browser in the right-hand panel, the GO term ‘mRNA splicing’ has been selected, and all proteins that have this GO term or child terms annotated, are highlighted.