Judith A Blake

Summary

Affiliation: The Jackson Laboratory
Country: USA

Publications

  1. pmc Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse
    Judith A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 45:D723-D729. 2017
  2. 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
  3. pmc DFLAT: functional annotation for human development
    Heather C Wick
    Department of Computer Science, Tufts University, 155 College Ave, Medford, MA 02155, USA
    BMC Bioinformatics 15:45. 2014
  4. pmc Ontology based molecular signatures for immune cell types via gene expression analysis
    Terrence F Meehan
    Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, 100 High Street, Buffalo, NY 14203, USA
    BMC Bioinformatics 14:263. 2013
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications51

  1. pmc Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse
    Judith A Blake
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 45:D723-D729. 2017
    ..Here, we report on recent enhancements made to the resource and new features...
  2. 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...
  3. pmc DFLAT: functional annotation for human development
    Heather C Wick
    Department of Computer Science, Tufts University, 155 College Ave, Medford, MA 02155, USA
    BMC Bioinformatics 15:45. 2014
    ....
  4. pmc Ontology based molecular signatures for immune cell types via gene expression analysis
    Terrence F Meehan
    Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, 100 High Street, Buffalo, NY 14203, USA
    BMC Bioinformatics 14:263. 2013
    ....
  5. 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...
  6. 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...
  7. 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...
  8. 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
    ....
  9. 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
    ....
  10. 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
    ....
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  15. 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
    ....
  16. 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...
  17. 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
  18. pmc 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. ..
  19. 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
    ....
  20. 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...
  21. pmc Mouse genome database 2016
    Carol J Bult
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 44:D840-7. 2016
    ....
  22. pmc Orthology for comparative genomics in the mouse genome database
    Mary E Dolan
    The Jackson Laboratory, Bar Harbor, ME, 04609, USA
    Mamm Genome 26:305-13. 2015
    ..Here, we describe current comparative data in MGD and review the history and refinement of orthology representation in this resource. ..
  23. 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...
  24. 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
    ....
  25. 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...
  26. 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
    ....
  27. 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...
  28. ncbi request reprint Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research
    Janan T Eppig
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
    Methods Mol Biol 1488:47-73. 2017
    ..Here we present an overview of the current data content of MGI, describe its general organization, and provide examples using simple and complex searches, and tools for mining and retrieving sets of data...
  29. pmc 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. 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/..
  31. 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
    ....
  32. 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
    ....
  33. 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...
  34. pmc Mouse Genome Informatics (MGI): reflecting on 25 years
    Janan T Eppig
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, 04609, USA
    Mamm Genome 26:272-84. 2015
    ..Here, we review some of the major changes in research approaches over that last quarter century, how these changes are reflected in the MGI resource you use today, and what may be around the next corner. ..
  35. pmc Mouse Genome Database: From sequence to phenotypes and disease models
    Janan T Eppig
    The Jackson Laboratory, Bar Harbor, Maine
    Genesis 53:458-73. 2015
    ..Here, we describe the data acquisition process, specifics about MGD's key data areas, methods to access and query MGD data, and outreach and user help facilities...
  36. pmc Application of comparative biology in GO functional annotation: the mouse model
    Harold J Drabkin
    The Jackson Laboratory, Bar Harbor, ME, 04609, USA
    Mamm Genome 26:574-83. 2015
    ..Here the application of comparative approaches to capturing functional data in the mouse system is described. ..
  37. 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...
  38. 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...
  39. 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...
  40. 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
    ....
  41. pmc The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease
    Janan T Eppig
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Nucleic Acids Res 43:D726-36. 2015
    ..MGD resources are freely available to the scientific community. ..
  42. pmc Modeling biochemical pathways in the gene ontology
    David P Hill
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Database (Oxford) 2016:. 2016
    ..With carbohydrate metabolic pathways as a use case, we discuss how our representation supports the integration of variant pathway classes into a unified ontological structure that can be used for data comparison and analysis. ..
  43. 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
  44. 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...
  45. 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...
  46. 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
    ....
  47. 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...
  48. pmc Standardized description of scientific evidence using the Evidence Ontology (ECO)
    Marcus C Chibucos
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Saccharomyces Genome Database, Department of Genetics, Stanford University, Stanford, CA 94305, USA, Computational Biology and Bioinformatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA, European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK, Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA and Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USAInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Saccharomyces Genome Database, School of Medicine
    Database (Oxford) 2014:. 2014
    ..ECO remains under active development in response to user-requested terms and in collaborations with other ontologies and database resources. Database URL: Evidence Ontology Web site: http://evidenceontology.org. ..
  49. pmc Methodology for the inference of gene function from phenotype data
    Joao A Ascensao
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
    BMC Bioinformatics 15:405. 2014
    ..This work is in contrast to previous studies that have focused on inferring gene function from phenotype primarily through lexical or semantic similarity measures...
  50. 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