Christopher J Mungall

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc The Release 5.1 annotation of Drosophila melanogaster heterochromatin
    Christopher D Smith
    Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
    Science 316:1586-91. 2007
  2. 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
  3. pmc Relations in biomedical ontologies
    Barry Smith
    Institute for Formal Ontology and Medical Information Science, Saarland University, D 66041 Saarbrucken, Germany
    Genome Biol 6:R46. 2005
  4. pmc Survey-based naming conventions for use in OBO Foundry ontology development
    Daniel Schober
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 10:125. 2009
  5. pmc An integrated computational pipeline and database to support whole-genome sequence annotation
    C J Mungall
    Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Genome Biol 3:RESEARCH0081. 2002
  6. 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
  7. 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
  8. 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
  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 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

Collaborators

Detail Information

Publications19

  1. pmc The Release 5.1 annotation of Drosophila melanogaster heterochromatin
    Christopher D Smith
    Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
    Science 316:1586-91. 2007
    ..Drosophila heterochromatin contains "islands" of highly conserved genes embedded in these "oceans" of complex repeats, which may require special expression and splicing mechanisms...
  2. 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...
  3. pmc Relations in biomedical ontologies
    Barry Smith
    Institute for Formal Ontology and Medical Information Science, Saarland University, D 66041 Saarbrucken, Germany
    Genome Biol 6:R46. 2005
    ..The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena...
  4. pmc Survey-based naming conventions for use in OBO Foundry ontology development
    Daniel Schober
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 10:125. 2009
    ....
  5. pmc An integrated computational pipeline and database to support whole-genome sequence annotation
    C J Mungall
    Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Genome Biol 3:RESEARCH0081. 2002
    ..The key contributions to overall annotation quality are the marshalling of high-quality sequences for alignments and the design of a system with an adaptable and expandable flexible architecture...
  6. 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...
  7. 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...
  8. 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
    ....
  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 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...
  11. pmc Apollo: a sequence annotation editor
    S E Lewis
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94720 3200, USA
    Genome Biol 3:RESEARCH0082. 2002
    ..FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects...
  12. pmc A method for increasing expressivity of Gene Ontology annotations using a compositional approach
    Rachael P Huntley
    Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, CA 94720, USA
    BMC Bioinformatics 15:155. 2014
    ..This has limited the specificity of knowledge that can be expressed by GO annotations...
  13. pmc The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
    Sebastian Kohler
    Institute for Medical Genetics and Human Genetics, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Lawrence Berkeley National Laboratory, Mail Stop 84R0171, Berkeley, CA 94720, USA, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Department of Medical Genetics, Cambridge University Addenbrooke s Hospital, Cambridge CB2 2QQ, UK, Universite Paul Sabatier, Faculte de Chirurgie Dentaire, CHU Toulouse, France, Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre MAHSC, Manchester, UK, Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, MAHSC, Manchester M13 9WL, UK, Institute of Genetic Medicine Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK, Department of Computer Science, University of Toronto, Ontario, Canada
    Nucleic Acids Res 42:D966-74. 2014
    ..We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online. ..
  14. 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
    ....
  15. 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...
  16. 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
    ....
  17. 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
    ....
  18. pmc The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
    Barry Smith
    Department of Philosophy and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York 14203, USA
    Nat Biotechnol 25:1251-5. 2007
    ..We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved...