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      The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

      research-article
      1 , * , 2 , 1 , 3 , 4 , 5 , 6 , 1 , 7 , 1 , 1 , 1 , 4 , 3 , 4 , 8 , 1 , 1 , 9 , 4 , 6 , 1 , 6 , 1 , 10 , 4 , 1 , 11 , 12 , 3 , 3 , 3 , 13 , 4 , 10 , * , 1 , *
      Nucleic Acids Research
      Oxford University Press

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          Abstract

          IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium ( http://www.imexconsortium.org).

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          Most cited references27

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          DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.

          I Xenarios (2002)
          The Database of Interacting Proteins (DIP: http://dip.doe-mbi.ucla.edu) is a database that documents experimentally determined protein-protein interactions. It provides the scientific community with an integrated set of tools for browsing and extracting information about protein interaction networks. As of September 2001, the DIP catalogs approximately 11 000 unique interactions among 5900 proteins from >80 organisms; the vast majority from yeast, Helicobacter pylori and human. Tools have been developed that allow users to analyze, visualize and integrate their own experimental data with the information about protein-protein interactions available in the DIP database.
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            Cytoscape Web: an interactive web-based network browser

            Summary: Cytoscape Web is a web-based network visualization tool–modeled after Cytoscape–which is open source, interactive, customizable and easily integrated into web sites. Multiple file exchange formats can be used to load data into Cytoscape Web, including GraphML, XGMML and SIF. Availability and Implementation: Cytoscape Web is implemented in Flex/ActionScript with a JavaScript API and is freely available at http://cytoscapeweb.cytoscape.org/ Contact: gary.bader@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online.
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              InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

              InnateDB (http://www.innatedb.com) is an integrated analysis platform that has been specifically designed to facilitate systems-level analyses of mammalian innate immunity networks, pathways and genes. In this article, we provide details of recent updates and improvements to the database. InnateDB now contains >196 000 human, mouse and bovine experimentally validated molecular interactions and 3000 pathway annotations of relevance to all mammalian cellular systems (i.e. not just immune relevant pathways and interactions). In addition, the InnateDB team has, to date, manually curated in excess of 18 000 molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks, pathways and their component molecules. More recently, InnateDB has also initiated the curation of allergy- and asthma-related interactions. Furthermore, we report a range of improvements to our integrated bioinformatics solutions including web service access to InnateDB interaction data using Proteomics Standards Initiative Common Query Interface, enhanced Gene Ontology analysis for innate immunity, and the availability of new network visualizations tools. Finally, the recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                January 2014
                13 November 2013
                13 November 2013
                : 42
                : D1 , Database issue
                : D358-D363
                Affiliations
                1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, 2School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ 85721-0036, USA, 3Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 Rue Michel-Servet, CH-1211 Geneva 4, Switzerland, 4Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy, 5Ontario Cancer Institute, the Campbell Family Institute for Cancer Research, and Techna Institute, University Health Network, Toronto, Ontario M5G 0A3, Canada, 6Cardiovascular Gene Annotation Initiative, Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London WC1E 6BT, UK, 7Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada, 8Mechanobiology Institute, National University of Singapore, T-Lab #05-01, 5A Engineering Drive 1, Singapore 117411, Singapore, 9Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7489 Trondheim, Norway, 10Research Institute IRCSS “Fondazione Santa Lucia”, Rome 00179, Italy, 11Molecular Connections Pvt. Ltd., Bangalore 560 004, India, 12Institut de Biologie et Chimie des Protéines, Unité Mixte de Recherche 5086, Centre National de la Recherche Scientifique, Université Lyon 1, Lyon, France and 13Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany
                Author notes
                *To whom correspondence should be addressed. Tel: +44 1223 494 675; Fax: +44 1223 494 468; Email: orchard@ 123456ebi.ac.uk
                Correspondence may also be addressed to Henning Hermjakob. Tel: +44 1223 494 671; Fax: +44 1223 494 468; Email: hhe@ 123456ebi.ac.uk
                Correspondence may also be addressed to Gianni Cesareni. Tel: +39 0672 594315; Fax: +39 0620 23500; Email: cesareni@ 123456uniroma2.it
                Article
                gkt1115
                10.1093/nar/gkt1115
                3965093
                24234451
                e0d21efc-a2b7-4431-8ece-f84ceb713795
                © The Author(s) 2013. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 14 October 2013
                : 22 October 2013
                Page count
                Pages: 6
                Categories
                II. Protein sequence and structure, motifs and domains
                Custom metadata
                1 January 2014

                Genetics
                Genetics

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