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IntAct


NAR Molecular Biology Database Collection entry number 507
Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, Del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H.
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ 85721-0036, USA, Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 Rue Michel-Servet, CH-1211 Geneva 4, Switzerland, Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy, Ontario Cancer Institute, the Campbell Family Institute for Cancer Research, and Techna Institute, University Health Network, Toronto, Ontario M5G 0A3, Canada, Cardiovascular Gene Annotation Initiative, Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London WC1E 6BT, UK, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada, Mechanobiology Institute, National University of Singapore, T-Lab #05-01, 5A Engineering Drive 1, Singapore 117411, Singapore, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7489 Trondheim, Norway, Research Institute IRCSS "Fondazione Santa Lucia", Rome 00179, Italy, Molecular Connections Pvt. Ltd., Bangalore 560 004, India, Institut de Biologie et Chimie des Protéines, Unité Mixte de Recherche 5086, Centre National de la Recherche Scientifique, Université Lyon 1, Lyon, France and Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
Contact hhe@ebi.ac.uk

Database Description

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 annotation or InterPro domains of the interacting proteins. A web service allows direct computational access to retrieve interaction networks in XML format. IntAct currently contains >170,000 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 the URL provided.

Recent Developments

IntAct has grown in size to >170,000 binary interactions over the last year, and includes nucleic acid and ligand interactions as well as protein. Different molecule types are described by a generalized 'interactor' datatype, which is further specified by a hierarchical controlled vocabulary of the PSI-MI ontology. Interacting molecules are systematically mapped to stable identifiers from public databases such as UniProtKB for proteins, ChEBI for small molecules and DDBJ/EMBL/GenBank nucleotide databases and/or Ensembl for nucleic acids.
The entire database source code has been updated, but the database remains completely open-source and available for local installation. The search facility has been considerably improved and updated to cope with the ever-increasing amount of data present in the database. Data downloads are available in both PSI-MI XML2.5 and PSI MITAB2.5.
Data are taken both from direct submissions or from detail-rich, "deep", high quality manual curation of molecular interactions from the literature. The curation manual is publicly available via the website, to ensure maximum transparency for the user. IntAct is an active member of the IMEx consortium.

Acknowledgements

The IntAct project is funded by the FELICS grant contract number 021902 (RII3) within the Research Infrastructure Action of the FP6 "Structuring the European Research Area" Programme

References

Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., Mudali, S., Kerrien, S., Orchard, S., Vingron, M., Roechert, B., Roepstorff, P., Valencia, A., Margalit, H., Armstrong, J., Bairoch, A., Cesareni, G., Sherman, D., Apweiler, R. (2004) IntAct: an open source molecular interaction database. Nucleic Acids Research 32(1), D452-D455.


Go to the abstract in the NAR 2014 Database Issue.
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