Mapping between the OBO and OWL ontology languagesSyed Hamid Tirmizi
Department of Computer Science, The University of Texas at Austin, Austin, Texas 78701, USA
J Biomed Semantics 2:S3. 2011
..In addition, it provides a roadmap for bridging the gap between the two ontology languages in order to enable the use of ontology content in a language independent manner...
- Improving ontologies by automatic reasoning and evaluation of logical definitions
Sebastian Kohler
Institute for Medical Genetics and Human Genetics, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
BMC Bioinformatics 12:418. 2011
..A recent approach of defining terms using logical definitions is now increasingly being adopted as a method for quality control as well as for facilitating interoperability and data integration...
- Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development
Jennifer I Deegan née Clark
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
BMC Bioinformatics 11:530. 2010
..The lack of an explicit formalization of these constraints can lead to errors and inconsistencies in automated and manual annotation...
- An improved ontological representation of dendritic cells as a paradigm for all cell types
Anna Maria Masci
Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
BMC Bioinformatics 10:70. 2009
..This approach limits the CL's utility for computation and for cross-species data integration...
- Logical development of the cell ontology
Terrence F Meehan
Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, USA
BMC Bioinformatics 12:6. 2011
..By making the information in the ontology computable, we can use automated reasoners to detect errors and assist with classification. Here we report on the generation of computable definitions for the hematopoietic cell types in the CL...
- Integrating phenotype ontologies across multiple species
Christopher J Mungall
Genome Dynamics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Genome Biol 11:R2. 2010
..We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology...
- JBrowse: a next-generation genome browser
Mitchell E Skinner
Department of Bioengineering, University of California at Berkeley, Berkeley, California 94720, USA
Genome Res 19:1630-8. 2009
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- Uberon, an integrative multi-species anatomy ontology
Christopher J Mungall
Genomics Division, Lawrence Berkeley National Laboratory, 1 Cycltotron Road MS 64 121, Berkeley, CA 94720, USA
Genome Biol 13:R5. 2012
..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...
- AmiGO: online access to ontology and annotation data
Seth Carbon
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Bioinformatics 25:288-9. 2009
..AmiGO is free open source software developed and maintained by the GO Consortium...
- Linking human diseases to animal models using ontology-based phenotype annotation
Nicole L Washington
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
PLoS Biol 7:e1000247. 2009
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A Chado case study: an ontology-based modular schema for representing genome-associated biological informationChristopher J Mungall
Lawrence Berkeley National Laboratory, Lawrence Berkeley National Lab, Mail Stop 64R0121, Berkeley, CA 94720, USA
Bioinformatics 23:i337-46. 2007
..Our question was whether we could create a relational database schema that would be successfully reused...
- The Sequence Ontology: a tool for the unification of genome annotations
Karen Eilbeck
Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729 3200, USA
Genome Biol 6:R44. 2005
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- Cross-product extensions of the Gene Ontology
Christopher J Mungall
Lawrence Berkeley National Laboratory, Mail Stop 64R0121, Berkeley, CA 94720, USA
J Biomed Inform 44:80-6. 2011
..These definitions also enhance the GO by weaving it into the fabric of a wider collection of interoperating ontologies, increasing opportunities for data integration and enhancing genomic analyses...
- Evolution of the Sequence Ontology terms and relationships
Christopher J Mungall
Lawrence Berkeley National Laboratory, Mail Stop 64R0121, Berkeley, CA 94720, USA
J Biomed Inform 44:87-93. 2011
..Here, we report changes and improvements made to SO including new relationships to better define the mereological, spatial and temporal aspects of biological sequence...
- Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
Sima Misra
Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720 3200, USA
Genome Biol 3:RESEARCH0083. 2002
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