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      Brain: biomedical knowledge manipulation

      research-article
      Author(s): * ,   ,
      Publication date (Electronic):
      Journal: Bioinformatics
      Publisher: Oxford University Press

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Summary: Brain is a Java software library facilitating the manipulation and creation of ontologies and knowledge bases represented with the Web Ontology Language (OWL).

          Availability and implementation: The Java source code and the library are freely available at https://github.com/loopasam/Brain and on the Maven Central repository (GroupId: uk.ac.ebi.brain). The documentation is available at https://github.com/loopasam/Brain/wiki.

          Contact: croset@ 123456ebi.ac.uk

          Supplementary information: Supplementary data are available at Bioinformatics online.

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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.
          Article 0 comments Cited 15277 times – based on 0 reviews     Review now
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            Chemical Entities of Biological Interest: an update

            Paula de Matos, Rafael Alcántara, Adriano Dekker … (2010)
            Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. Genome-encoded macromolecules (nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities. ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac.uk/chebi/. This article reports on new features in ChEBI since the last NAR report in 2007, including substructure and similarity searching, a submission tool for authoring of ChEBI datasets by the community and a 30-fold increase in the number of chemical structures stored in ChEBI.
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              Concurrent Classification of $\mathcal{EL}$ Ontologies

              Yevgeny Kazakov, Markus Krötzsch, Frantisek Simancík (2011)
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                Author and article information

                Journal
                Journal ID (nlm-ta): Bioinformatics
                Journal ID (iso-abbrev): Bioinformatics
                Journal ID (publisher-id): bioinformatics
                Journal ID (hwp): bioinfo
                Title: Bioinformatics
                Publisher: Oxford University Press
                ISSN (Print): 1367-4803
                ISSN (Electronic): 1367-4811
                Publication date (Print): 1 May 2013
                Publication date (Electronic): 16 March 2013
                Publication date PMC-release: 16 March 2013
                Volume: 29
                Issue: 9
                Pages: 1238-1239
                Affiliations
                EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
                Author notes
                *To whom correspondence should be addressed.

                Associate Editor: Janet Kelso

                Article
                Publisher ID: btt109
                DOI: 10.1093/bioinformatics/btt109
                PMC ID: 3634181
                PubMed ID: 23505292
                SO-VID: 44537c31-660d-49ad-b524-67817e36e5a7
                Copyright © © The Author 2013. Published by Oxford University Press.
                License:

                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
                Date received : 7 November 2012
                Date revision received : 15 January 2013
                Date accepted : 28 February 2013
                Page count
                Pages: 2
                Categories
                Subject: Applications Notes
                Subject: Databases and Ontologies

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology

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