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      PomBase: a comprehensive online resource for fission yeast

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          Abstract

          PomBase (www.pombase.org) is a new model organism database established to provide access to comprehensive, accurate, and up-to-date molecular data and biological information for the fission yeast Schizosaccharomyces pombe to effectively support both exploratory and hypothesis-driven research. PomBase encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets, and supports sophisticated user-defined queries. The implementation of PomBase integrates a Chado relational database that houses manually curated data with Ensembl software that supports sequence-based annotation and web access. PomBase will provide user-friendly tools to promote curation by experts within the fission yeast community. This will make a key contribution to shaping its content and ensuring its comprehensiveness and long-term relevance.

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          Ensembl BioMarts: a hub for data retrieval across taxonomic space

          Rhoda J. Kinsella, Andreas Kähäri, Syed Haider … (2011)
          For a number of years the BioMart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data provided by the Ensembl project. The launch of the Ensembl Genomes project in 2009 complemented the Ensembl project by utilizing the same visualization, interactive and programming tools to provide users with a means for accessing genome data from a further five domains: protists, bacteria, metazoa, plants and fungi. The Ensembl and Ensembl Genomes BioMarts provide a point of access to the high-quality gene annotation, variation data, functional and regulatory annotation and evolutionary relationships from genomes spanning the taxonomic space. This article aims to give a comprehensive overview of the Ensembl and Ensembl Genomes BioMarts as well as some useful examples and a description of current data content and future objectives. Database URLs: http://www.ensembl.org/biomart/martview/; http://metazoa.ensembl.org/biomart/martview/; http://plants.ensembl.org/biomart/martview/; http://protists.ensembl.org/biomart/martview/; http://fungi.ensembl.org/biomart/martview/; http://bacteria.ensembl.org/biomart/martview/
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            Artemis: sequence visualization and annotation

            K Rutherford, J. Parkhill, Robyn Crook … (2000)
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              BioGRID: a general repository for interaction datasets

              Chris Stark, Bobby-Joe Breitkreutz, Teresa Reguly … (2005)
              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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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: January 2012
                Publication date (Print): January 2012
                Publication date (Electronic): 28 October 2011
                Publication date PMC-release: 28 October 2011
                Volume: 40
                Issue: D1 , Database issue
                Pages: D695-D699
                Affiliations
                1Cambridge Systems Biology Centre, 2Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, 3Cell Cycle Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London UK WC2A 3LY, 4European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, 5Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA and 6Department of Genetics, Evolution and Environment, and UCL Cancer Institute, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
                Author notes
                *To whom correspondence should be addressed. Tel: +44 1223 746961; Fax: +44 1223 766002; Email: vw253@ 123456cam.ac.uk
                Correspondence may also be addressed to Midori A. Harris. Tel: +44 1223 761211; Fax: +44 1223 766002; Email: mah79@ 123456cam.ac.uk
                Correspondence may also be addressed to Stephen G. Oliver. Tel: +44 1223 333667; Fax: +44 1223 766002; Email: sgo24@ 123456cam.ac.uk
                Article
                Publisher ID: gkr853
                DOI: 10.1093/nar/gkr853
                PMC ID: 3245111
                PubMed ID: 22039153
                SO-VID: 29cf7d3a-304c-4225-91b9-ccae611631c5
                Copyright © © The Author(s) 2011. Published by Oxford University Press.
                License:

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

                History
                Date received : 7 September 2011
                Date accepted : 24 September 2011
                Page count
                Pages: 5
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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