Judith A Blake

Summary

Affiliation: The Jackson Laboratory
Country: USA

Publications

  1. pmc Concept annotation in the CRAFT corpus
    Michael Bada
    Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
    BMC Bioinformatics 13:161. 2012
  2. pmc PhenoGO: an integrated resource for the multiscale mining of clinical and biological data
    Lee T Sam
    Center for Biomedical Informatics, Department of Medicine, The University of Chicago, Chicago, IL, USA
    BMC Bioinformatics 10:S8. 2009
  3. pmc TGF-beta signaling proteins and the Protein Ontology
    Cecilia N Arighi
    Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
    BMC Bioinformatics 10:S3. 2009
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications36

  1. pmc Concept annotation in the CRAFT corpus
    Michael Bada
    Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
    BMC Bioinformatics 13:161. 2012
    ..Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text...
  2. pmc PhenoGO: an integrated resource for the multiscale mining of clinical and biological data
    Lee T Sam
    Center for Biomedical Informatics, Department of Medicine, The University of Chicago, Chicago, IL, USA
    BMC Bioinformatics 10:S8. 2009
    ..A web portal has also been developed, allowing for advanced filtering and querying of the database as well as download of the entire dataset http://www.phenogo.org...
  3. pmc TGF-beta signaling proteins and the Protein Ontology
    Cecilia N Arighi
    Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
    BMC Bioinformatics 10:S3. 2009
    ..Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO...
  4. 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
    ....
  5. 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
    ....
  6. 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
    ....
  7. 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...
  8. 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...
  9. 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...
  10. 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...
  11. 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...
  12. 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
    ....
  13. 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
  14. pmc The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse
    Janan T Eppig
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 40:D881-6. 2012
    ....
  15. 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...
  16. 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...
  17. pmc The mouse genome database: genotypes, phenotypes, and models of human disease
    Carol J Bult
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
    Nucleic Acids Res 41:D885-91. 2013
    ....
  18. 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...
  19. 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
    ....
  20. 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...
  21. pmc Disease model curation improvements at Mouse Genome Informatics
    Susan M Bello
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Database (Oxford) 2012:bar063. 2012
    ..Here we describe our evaluation of the CTD application, the extensions made by MGI and discuss the strengths and weaknesses of this approach. DATABASE URL: http://www.informatics.jax.org/..
  22. pmc The representation of protein complexes in the Protein Ontology (PRO)
    Carol J Bult
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    BMC Bioinformatics 12:371. 2011
    ....
  23. 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
    ....
  24. pmc Hematopoietic cell types: prototype for a revised cell ontology
    Alexander D Diehl
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    J Biomed Inform 44:75-9. 2011
    ..The methods and improvements to the CL in this area represent a paradigm for improvement of the entire ontology over time...
  25. pmc Autism candidate genes via mouse phenomics
    Terrence F Meehan
    The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
    J Biomed Inform 44:S5-11. 2011
    ..2010). Prediction and characterization of autistic mutant mouse alleles assists researchers in studying the complex nature of ASD and provides a generalizable approach to candidate gene prioritization...
  26. 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...
  27. 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
    ....
  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. doi request reprint Protein Ontology: a controlled structured network of protein entities
    Darren A Natale
    Protein Information Resource, Georgetown University Medical Center, WA 20007, USA, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Bioinformatics and Computational Biology, The Jackson Laboratory, Bar Harbor, ME 04609, USA, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, NY 10016, USA, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA, Department of Immunology, Duke University Medical Center, Durham, NC 27705, USA and Department of Oral Diagnostic Sciences, University at Buffalo School of Dental Medicine, Buffalo, NY 14214, USA
    Nucleic Acids Res 42:D415-21. 2014
    ..The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. ..
  30. doi request reprint The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse
    Judith A Blake
    Bioinformatics and Computational Biology, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 42:D810-7. 2014
    ..All MGD resources are freely available to the research community. ..
  31. pmc Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database
    Harold J Drabkin
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Database (Oxford) 2012:bas045. 2012
    ..These vocabularies range from pick-lists to structured vocabularies such as the GO. All data associations are supported with statements of evidence as well as access to source publications...
  32. 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...
  33. 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
    ....
  34. 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...
  35. 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
  36. 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