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      The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

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          Abstract

          The Protein Data Bank (PDB) is the central worldwide repository for three-dimensional (3D) structure data of biological macromolecules. The Research Collaboratory for Structural Bioinformatics (RCSB) has completely redesigned its resource for the distribution and query of 3D structure data. The re-engineered site is currently in public beta test at http://pdbbeta.rcsb.org. The new site expands the functionality of the existing site by providing structure data in greater detail and uniformity, improved query and enhanced analysis tools. A new key feature is the integration and searchability of data from over 20 other sources covering genomic, proteomic and disease relationships. The current capabilities of the re-engineered site, which will become the RCSB production site at http://www.pdb.org in late 2005, are described.

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Is Open Access

            Bioinformatics

            Silvia Regina Cavani Jorge Santos, John Osborne, Rainer Breitling … (2011)
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              A database for post-genome analysis.

              Minoru Kanehisa (1997)
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 1 January 2005
                Publication date (Electronic): 17 December 2004
                Volume: 33
                Issue: Database Issue
                Pages: D233-D237
                Affiliations
                [1 ]San Diego Supercomputer Center and [2 ]Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA and [3 ]Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
                Author notes
                [*]

                To whom correspondence should be addressed. Tel: +1 858 534 8301; Fax: +1 858 822 0873; Email: bourne@ 123456sdsc.edu

                [a]

                The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions@ 123456oupjournals.org .

                [a]

                © 2005, the authors

                Article
                Publisher ID: gki057
                DOI: 10.1093/nar/gki057
                PMC ID: 540011
                PubMed ID: 15608185
                SO-VID: c571c86c-40ab-45ba-98f9-4be54a15dfe7
                Copyright © Copyright © 2005 Oxford University Press
                History
                Date received : 15 September 2004
                Date revision received : 1 October 2004
                Date accepted : 1 October 2004
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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