Judith Blake

Summary

Affiliation: The Jackson Laboratory
Country: USA

Publications

  1. pmc The mouse genome database (MGD): new features facilitating a model system
    Janan T Eppig
    The Jackson Laboratory 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 35:D630-7. 2007
  2. pmc Ontological visualization of protein-protein interactions
    Harold J Drabkin
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, USA
    BMC Bioinformatics 6:29. 2005
  3. pmc Framework for a protein ontology
    Darren A Natale
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven St, NW, Washington, DC 20007, USA
    BMC Bioinformatics 8:S1. 2007
  4. pmc Gene Ontology annotations: what they mean and where they come from
    David P Hill
    The Jackson Laboratory, Bar Harbor, ME, USA
    BMC Bioinformatics 9:S2. 2008
  5. ncbi request reprint Beyond the data deluge: data integration and bio-ontologies
    Judith A Blake
    The Jackson Laboratory, Bar Harbor, ME, USA
    J Biomed Inform 39:314-20. 2006
  6. pmc The Mouse Genome Database (MGD): updates and enhancements
    Judith A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 34:D562-7. 2006
  7. ncbi request reprint Bio-ontologies-fast and furious
    Judith Blake
    The Jackson Laboratory, Maine 04609, USA
    Nat Biotechnol 22:773-4. 2004
  8. pmc The Mouse Genome Database (MGD). A comprehensive public resource of genetic, phenotypic and genomic data. The Mouse Genome Informatics Group
    J A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 25:85-91. 1997
  9. pmc MGD: the Mouse Genome Database
    Judith A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 31:193-5. 2003
  10. pmc The Mouse Genome Database genotypes::phenotypes
    Judith A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 37:D712-9. 2009

Collaborators

Detail Information

Publications34

  1. pmc The mouse genome database (MGD): new features facilitating a model system
    Janan T Eppig
    The Jackson Laboratory 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 35:D630-7. 2007
    ....
  2. pmc Ontological visualization of protein-protein interactions
    Harold J Drabkin
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, USA
    BMC Bioinformatics 6:29. 2005
    ..The work reported here presents a methodology for integrating and visualizing information on protein-protein interactions...
  3. pmc Framework for a protein ontology
    Darren A Natale
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven St, NW, Washington, DC 20007, USA
    BMC Bioinformatics 8:S1. 2007
    ..Here we describe the initial development of PRO, illustrated using human and mouse proteins involved in the transforming growth factor-beta and bone morphogenetic protein signaling pathways...
  4. pmc Gene Ontology annotations: what they mean and where they come from
    David P Hill
    The Jackson Laboratory, Bar Harbor, ME, USA
    BMC Bioinformatics 9:S2. 2008
    ....
  5. ncbi request reprint Beyond the data deluge: data integration and bio-ontologies
    Judith A Blake
    The Jackson Laboratory, Bar Harbor, ME, USA
    J Biomed Inform 39:314-20. 2006
    ....
  6. pmc The Mouse Genome Database (MGD): updates and enhancements
    Judith A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 34:D562-7. 2006
    ..informatics.jax.org. Recent improvements in MGD described here include the incorporation of an interactive genome browser, the enhancement of phenotype resources and the further development of functional annotation resources...
  7. ncbi request reprint Bio-ontologies-fast and furious
    Judith Blake
    The Jackson Laboratory, Maine 04609, USA
    Nat Biotechnol 22:773-4. 2004
  8. pmc The Mouse Genome Database (MGD). A comprehensive public resource of genetic, phenotypic and genomic data. The Mouse Genome Informatics Group
    J A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 25:85-91. 1997
    ..User support is provided through dedicated staff providing documentation, training, and response to individual user queries. MGD is accessible over the Internet at URL http://www.informatics.jax.org...
  9. pmc MGD: the Mouse Genome Database
    Judith A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 31:193-5. 2003
    ..Recent developments include a general implementation of database structures for controlled vocabularies and the integration of a phenotype classification system...
  10. pmc The Mouse Genome Database genotypes::phenotypes
    Judith A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 37:D712-9. 2009
    ..Recent improvements in MGD described here include the unified mouse gene catalog for NCBI Build 37 of the reference genome assembly, and improved representation of mouse mutants and phenotypes...
  11. pmc The Mouse Genome Database (MGD): a community resource. Status and enhancements. The Mouse Genome Informatics Group
    J A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 26:130-7. 1998
    ..Interactive graphical displays of cytogenetic, genetic and physical maps are available. User support is provided through dedicated staff, bulletin boards, and user documentation. MGD can be accessed at http://www.informatics.jax.org..
  12. pmc The Mouse Genome Database (MGD): the model organism database for the laboratory mouse
    Judith A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 30:113-5. 2002
    ....
  13. pmc The Mouse Genome Database (MGD): genetic and genomic information about the laboratory mouse. The Mouse Genome Database Group
    J A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 27:95-8. 1999
    ..MGD is accessible at http://www.informatics.jax.org..
  14. pmc The Mouse Genome Database (MGD): integration nexus for the laboratory mouse
    J A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
    Nucleic Acids Res 29:91-4. 2001
    ..This link between the genome and the biology of the mouse is especially important as phenotype information grows from large mutagenesis projects and genotype information grows from large-scale sequencing projects...
  15. pmc The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse. The Mouse Genome Database Group
    J A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 28:108-11. 2000
    ..Recent improvements focus on the representation of phenotypic information and the enhancement of gene and allele descriptions...
  16. pmc The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology
    Janan T Eppig
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 33:D471-5. 2005
    ....
  17. pmc The Mouse Genome Database (MGD): integrating biology with the genome
    Carol J Bult
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 32:D476-81. 2004
    ..Recent developments in MGD discussed here include an extensive integration of the mouse sequence data and substantial revisions in the presentation, query and visualization of sequence data...
  18. doi request reprint The Gene Ontology (GO) project: structured vocabularies for molecular biology and their application to genome and expression analysis
    Judith A Blake
    The Jackson Laboratory, Bar Harbor, Maine, USA
    Curr Protoc Bioinformatics . 2008
    ..It addresses the issue of how GO vocabularies are constructed and related to genes and gene products. It concludes with a discussion of how researchers can access, browse, and utilize the GO project in the course of their own research...
  19. pmc The Mouse Genome Database: enhancements and updates
    Carol J Bult
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
    Nucleic Acids Res 38:D586-92. 2010
    ....
  20. pmc The Mouse Genome Database (MGD): mouse biology and model systems
    Carol J Bult
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 36:D724-8. 2008
    ..Recent improvements in MGD described here include the association of gene trap data with mouse genes and a new batch query capability for customized data access and retrieval...
  21. pmc The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics
    Judith A Blake
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 39:D842-8. 2011
    ....
  22. ncbi request reprint Mouse genome informatics (MGI) resources for pathology and toxicology
    Janan T Eppig
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Toxicol Pathol 35:456-7. 2007
  23. ncbi request reprint Ontology development for biological systems: immunology
    Alexander D Diehl
    Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04605, USA
    Bioinformatics 23:913-5. 2007
    ..AVAILABILITY: http://www.geneontology.org...
  24. ncbi request reprint Corralling conditional mutations: a unified resource for mouse phenotypes
    Janan T Eppig
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
    Genesis 32:63-5. 2002
  25. ncbi request reprint Rules and guidelines for mouse gene, allele, and mutation nomenclature: a condensed version
    Lois J Maltais
    The Jackson Laboratory, 600 Main St, Bar Harbor, Maine 04609, USA
    Genomics 79:471-4. 2002
  26. pmc Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies
    David P Hill
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Genome Res 12:1982-91. 2002
    ..The combination of concepts from orthogonal vocabularies provides a robust representation of relevant terms and an opportunity for evaluation of hypothetical concepts...
  27. 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...
  28. pmc Connecting sequence and biology in the laboratory mouse
    Richard M Baldarelli
    Mouse Genome Informatics Group, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
    Genome Res 13:1505-19. 2003
    ..In particular, we describe the methods and results of integration of 60,770 FANTOM2 mouse cDNAs with gene records in the databases of MGI and LocusLink...
  29. pmc The mouse Gene Expression Database (GXD): updates and enhancements
    David P Hill
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 32:D568-71. 2004
    ..GXD is accessible through the MGI website at http://www.informatics.jax.org/ or directly at http://www. informatics.jax.org/menus/expression_menu.shtml...
  30. ncbi request reprint A procedure for assessing GO annotation consistency
    Mary E Dolan
    Mouse Genome Informatics MGI, The Jackson Laboratory 600 Main Street, Bar Harbor, ME 04609, USA
    Bioinformatics 21:i136-43. 2005
    ..The development of methodologies that are broadly applicable for the assessment of GO annotation consistency is an important issue for the comparative genomics community...
  31. doi request reprint The Gene Ontology (GO) project: structured vocabularies for molecular biology and their application to genome and expression analysis
    Judith A Blake
    The Jackson Laboratory, Bar Harbor, Maine, USA
    Curr Protoc Bioinformatics . 2002
    ..It addresses the issue of how GO vocabularies are constructed and related to genes and gene products. It concludes with a discussion of how researchers can access, browse, and utilize the GO project in the course of their own research...
  32. pmc Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set
    Lynn M Schriml
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 13:1496-500. 2003
    ..Allelic variant and gene functional information available in MGI provides additional information relative to these mouse models, whereas computed sequence-based connections at NCBI support facile navigation through multiple genomes...
  33. pmc An en masse phenotype and function prediction system for Mus musculus
    Murat Tasan
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Longwood Avenue, Boston, Massachusetts 02115, USA
    Genome Biol 9:S8. 2008
    ..Integration of accumulated evidence should permit researchers to form fewer - and more accurate - hypotheses for further study through experimentation...
  34. pmc A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
    Lourdes Pena-Castillo
    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S3E1, Canada
    Genome Biol 9:S2. 2008
    ..Several algorithms using diverse genomic data have been applied to this task in model organisms; however, the performance of such approaches in mammals has not yet been evaluated...