Uberon, an integrative multi-species anatomy ontology

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org

[1]  Martin F. Porter,et al.  An algorithm for suffix stripping , 1997, Program.

[2]  A L Rector,et al.  Goals for concept representation in the GALEN project. , 1993, Proceedings. Symposium on Computer Applications in Medical Care.

[3]  S. Carroll,et al.  The origin and evolution of animal appendages. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[4]  M. Ashburner,et al.  Systematic determination of patterns of gene expression during Drosophila embryogenesis , 2002, Genome Biology.

[5]  Alan L. Rector,et al.  Modularisation of domain ontologies implemented in description logics and related formalisms including OWL , 2003, K-CAP '03.

[6]  José L. V. Mejino,et al.  A reference ontology for biomedical informatics: the Foundational Model of Anatomy , 2003, J. Biomed. Informatics.

[7]  Winston Hide,et al.  FRAGS: estimation of coding sequence substitution rates from fragmentary data , 2004, BMC Bioinformatics.

[8]  M. Ashburner,et al.  An ontology for cell types , 2005, Genome Biology.

[9]  Mary E. Mangan,et al.  The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data , 2005, Genome Biology.

[10]  Christopher J. Mungall,et al.  Obol: Integrating Language and Meaning in Bio-Ontologies , 2004, Comparative and functional genomics.

[11]  Cynthia L. Smith,et al.  The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information , 2004, Genome Biology.

[12]  John M. Hancock,et al.  Building Mouse Phenotype Ontologies , 2003, Pacific Symposium on Biocomputing.

[13]  A. Rector,et al.  Relations in biomedical ontologies , 2005, Genome Biology.

[14]  Jonathan B L Bard,et al.  Anatomics: the intersection of anatomy and bioinformatics , 2005, Journal of anatomy.

[15]  M. Eisen All motifs are NOT created equal: structural properties of transcription factor-DNA interactions and the inference of sequence specificity , 2005, Genome Biology.

[16]  Cathy H. Wu,et al.  Framework for a Protein Ontology , 2006, TMBIO '06.

[17]  Robert Stevens,et al.  The Manchester OWL Syntax , 2006, OWLED.

[18]  Ian Horrocks,et al.  FaCT++ Description Logic Reasoner: System Description , 2006, IJCAR.

[19]  L. Stein,et al.  The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant1[W][OA] , 2006, Plant Physiology.

[20]  Victor B. Strelets,et al.  FlyBase: anatomical data, images and queries , 2005, Nucleic Acids Res..

[21]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[22]  Olivier Bodenreider,et al.  Experience in Aligning Anatomical Ontologies , 2007, Int. J. Semantic Web Inf. Syst..

[23]  Oliver Hofmann,et al.  Simplified ontologies allowing comparison of developmental mammalian gene expression , 2007, Genome Biology.

[24]  Midori A. Harris,et al.  OBO-Edit - an ontology editor for biologists , 2007, Bioinform..

[25]  Jennifer L. Leopold,et al.  An Anatomical Ontology for Amphibians , 2006, Pacific Symposium on Biocomputing.

[26]  Olivier Bodenreider,et al.  Lessons Learned from Cross-Validating Alignments between Large Anatomical Ontologies , 2007, MedInfo.

[27]  Ceri E. Van Slyke,et al.  The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes , 2007, Nucleic Acids Res..

[28]  José L. V. Mejino,et al.  CARO - The Common Anatomy Reference Ontology , 2008, Anatomy Ontologies for Bioinformatics.

[29]  S. Saule,et al.  Relationship of Pax6 Activity Levels to the Extent of Eye Development in the Mouse, Mus musculus , 2008, Genetics.

[30]  S. Saule,et al.  Relationship of Pax 6 activity levels to the extent of eye development in the mouse , Mus musculus , 2008 .

[31]  P. Robinson,et al.  The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. , 2008, American journal of human genetics.

[32]  Giorgio Valle,et al.  The Gene Ontology project in 2008 , 2007, Nucleic Acids Res..

[33]  Jessica A. Turner,et al.  The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience , 2008, Neuroinformatics.

[34]  Erik Segerdell,et al.  An ontology for Xenopus anatomy and development , 2008, BMC Developmental Biology.

[35]  Philippe Gautier,et al.  Subfunctionalization of Duplicated Zebrafish pax6 Genes by cis-Regulatory Divergence , 2008, PLoS genetics.

[36]  Michael Darsow,et al.  ChEBI: a database and ontology for chemical entities of biological interest , 2007, Nucleic Acids Res..

[37]  Cynthia L. Smith,et al.  Integrating phenotype ontologies across multiple species , 2010, Genome Biology.

[38]  Jens Lehmann,et al.  DBpedia - A crystallization point for the Web of Data , 2009, J. Web Semant..

[39]  Antje Chang,et al.  BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009 , 2008, Nucleic Acids Res..

[40]  Gilberto Fragoso,et al.  The NCI Thesaurus quality assurance life cycle , 2009, J. Biomed. Informatics.

[41]  Chris Mungall,et al.  Experiences Using Logic Programming in Bioinformatics , 2009, ICLP.

[42]  Monte Westerfield,et al.  Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation , 2009, PLoS biology.

[43]  Paul W. Sternberg,et al.  Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community , 2011, BMC Bioinformatics.

[44]  Dietrich Rebholz-Schuhmann,et al.  Interoperability between phenotype and anatomy ontologies , 2010, Bioinform..

[45]  Jessica A. Turner,et al.  Modeling biomedical experimental processes with OBI , 2010, J. Biomed. Semant..

[46]  Hilmar Lapp,et al.  The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age , 2010, Systematic biology.

[47]  Carlo Torniai,et al.  eagle-i: An Ontology-Driven Framework For Biomedical Resource Curation And Discovery , 2010 .

[48]  Brian L. Nelms,et al.  Transcriptional Control Of Neural Crest Development , 2010 .

[49]  Alexander D. Diehl,et al.  Logical Development of the Cell Ontology , 2011, BMC Bioinformatics.

[50]  Emily Dimmer,et al.  Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development , 2010, BMC Bioinformatics.

[51]  Frederic B. Bastian,et al.  Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy , 2010, Bioinform..

[52]  Anna Zhukova,et al.  Modeling sample variables with an Experimental Factor Ontology , 2010, Bioinform..

[53]  R. Scotland,et al.  Deep homology: A view from systematics , 2010, BioEssays : news and reviews in molecular, cellular and developmental biology.

[54]  Smith Barry,et al.  Proceedings of the 2nd International Conference on Biomedical Ontology , 2011 .

[55]  G. Allan Johnson,et al.  Digital Atlasing and Standardization in the Mouse Brain , 2011, PLoS Comput. Biol..

[56]  Harry Hochheiser,et al.  The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. , 2011, Developmental biology.

[57]  Erhard Rahm,et al.  Mapping Composition for Matching Large Life Science Ontologies , 2011, ICBO.

[58]  John M. Hancock,et al.  The Vertebrate Bridging Ontology (VBO) , 2011, ICBO.

[59]  Carlo Torniai,et al.  Developing an Application Ontology for Biomedical Resource Annotation and Retrieval: Challenges and Lessons Learned , 2011, ICBO.

[60]  Tanya Z. Berardini,et al.  Cross-product extensions of the Gene Ontology , 2009, J. Biomed. Informatics.

[61]  Linda G. Shapiro,et al.  An ontology-based comparative anatomy information system , 2011, Artif. Intell. Medicine.

[62]  David Osumi-Sutherland,et al.  FUNCARO: A Functional Extension to CARO , 2011, ICBO.

[63]  David Osumi-Sutherland,et al.  Caro 2.0 , 2011, ICBO.

[64]  Alan Ruttenberg,et al.  MIREOT: The minimum information to reference an external ontology term , 2009, Appl. Ontology.

[65]  Michel Dumontier,et al.  A common layer of interoperability for biomedical ontologies based on OWL EL , 2011, Bioinform..

[66]  Anne Niknejad,et al.  vHOG, a multispecies vertebrate ontology of homologous organs groups , 2012, Bioinform..

[67]  Chris Mungall,et al.  A knowledge based approach to matching human neurodegenerative disease and animal models , 2013, Front. Neuroinform..