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      Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over

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          Most cited references 48

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          BioGRID: a general repository for interaction datasets

          Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at . BioGRID release version 2.0 includes >116 000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. Over 30 000 interactions have recently been added from 5778 sources through exhaustive curation of the Saccharomyces cerevisiae primary literature. An internally hyper-linked web interface allows for rapid search and retrieval of interaction data. Full or user-defined datasets are freely downloadable as tab-delimited text files and PSI-MI XML. Pre-computed graphical layouts of interactions are available in a variety of file formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID.
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            IntAct: an open source molecular interaction database.

            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.
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              DIP: the database of interacting proteins.

              The Database of Interacting Proteins (DIP; http://dip.doe-mbi.ucla.edu) is a database that documents experimentally determined protein-protein interactions. This database is intended to provide the scientific community with a comprehensive and integrated tool for browsing and efficiently extracting information about protein interactions and interaction networks in biological processes. Beyond cataloging details of protein-protein interactions, the DIP is useful for understanding protein function and protein-protein relationships, studying the properties of networks of interacting proteins, benchmarking predictions of protein-protein interactions, and studying the evolution of protein-protein interactions.
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                Author and article information

                Affiliations
                Computational Biology Lab, National Agri-Food Biotechnology Institute Mohali, India
                Author notes

                Edited by: Alessandro Laganà, Icahn School of Medicine at Mount Sinai, USA

                Reviewed by: Yongqun “Oliver” He, University of Michigan, USA

                *Correspondence: Shrikant S. Mantri shrikant@ 123456nabi.res.in ; bioinfoman3@ 123456gmail.com

                This article was submitted to Bioinformatics and Computational Biology, a section of the journal Frontiers in Genetics

                Contributors
                Journal
                Front Genet
                Front Genet
                Front. Genet.
                Frontiers in Genetics
                Frontiers Media S.A.
                1664-8021
                31 March 2016
                2016
                : 7
                27066067 4814459 10.3389/fgene.2016.00046
                Copyright © 2016 Gupta and Mantri.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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                Figures: 0, Tables: 1, Equations: 0, References: 53, Pages: 6, Words: 4527
                Categories
                Genetics
                Opinion

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