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      Integrating phenotype ontologies across multiple species

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          Abstract

          A phenotypic ontology that can be used for the analysis of phenotype-genotype data across multiple species, paving the way for truly cross species translational research.

          Abstract

          Phenotype ontologies are typically constructed to serve the needs of a particular community, such as annotation of genotype-phenotype associations in mouse or human. Here we demonstrate how these ontologies can be improved through assignment of logical definitions using a core ontology of phenotypic qualities and multiple additional ontologies from the Open Biological Ontologies library. We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology.

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          Gene Ontology: tool for the unification of biology

          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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            ChEBI: a database and ontology for chemical entities of biological interest

            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/
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              The Human Genome Project: lessons from large-scale biology.

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                Author and article information

                Journal
                Genome Biol
                Genome Biology
                BioMed Central
                1465-6906
                1465-6914
                2010
                8 January 2010
                : 11
                : 1
                : R2
                Affiliations
                [1 ]Genome Dynamics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
                [2 ]Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
                [3 ]The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
                [4 ]Zebrafish Information Network, University of Oregon, Eugene, OR 97403-5291, USA
                Article
                gb-2010-11-1-r2
                10.1186/gb-2010-11-1-r2
                2847714
                20064205
                9ac37e2c-78dd-4c7d-87eb-fe3df3e5b62e
                Copyright ©2010 Mungall et al.; licensee BioMed Central Ltd.

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 26 August 2009
                : 19 November 2009
                : 8 January 2010
                Categories
                Method

                Genetics
                Genetics

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