Christopher J Mungall

Summary

Publications

  1. pmc Mapping between the OBO and OWL ontology languages
    Syed Hamid Tirmizi
    Department of Computer Science, The University of Texas at Austin, Austin, Texas 78701, USA
    J Biomed Semantics 2:S3. 2011
  2. pmc 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
  3. pmc 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
  4. pmc 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
  5. pmc Logical development of the cell ontology
    Terrence F Meehan
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, USA
    BMC Bioinformatics 12:6. 2011
  6. pmc 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
  7. pmc 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
  8. pmc 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
  9. pmc AmiGO: online access to ontology and annotation data
    Seth Carbon
    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Bioinformatics 25:288-9. 2009
  10. pmc 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

Collaborators

Detail Information

Publications15

  1. pmc Mapping between the OBO and OWL ontology languages
    Syed 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...
  2. pmc 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...
  3. pmc 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...
  4. pmc 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...
  5. pmc 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...
  6. pmc 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...
  7. pmc 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
    ....
  8. pmc 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...
  9. pmc 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...
  10. pmc 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
    ....
  11. ncbi request reprint A Chado case study: an ontology-based modular schema for representing genome-associated biological information
    Christopher 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...
  12. pmc 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
    ....
  13. pmc 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...
  14. pmc 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...
  15. pmc 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
    ....