Overview

My research focuses on functional and comparative genome informatics. I work on the development of systems to integrate and analyze genetic, genomic and phenotypic information. I am one of the principal investigators of the Gene Ontology (GO) Consortium, an international effort to provide controlled structured vocabularies for molecular biology that serve as terminologies, classifications and ontologies to further data integration, analysis and reasoning. My interest in bio-ontologies stems as well from the work I do as a principal investigator with the Mouse Genome Informatics (MGI) project at The Jackson Laboratory. The MGI system is a model organism community database resource that provides integrated information about the genetics, genomics and phenotypes of the laboratory mouse. My current research projects combine bio-ontologies and database knowledge systems to analyze disease processes with the objective of discovering new molecular elements and pathways that contribute to particular pathologies such as respiratory diseases.

Scientific report

Functional and Comparative Genome Informatics

My research focuses on functional and comparative genome informatics. I work on the development of systems to integrate and interrogate genetic, genomic and phenotypic information. I am one of the leaders of the Gene Ontology (GO) project and I have been deeply involved with the work of the GO Consortium since its inception. The Gene Ontology project is an international effort to provide controlled structured vocabularies for molecular biology that serve as terminologies, classifications and ontologies to further data integration, analysis and reasoning. My interest in bio-ontologies stems as well from the work I do as a principal investigator with the Mouse Genome Informatics (MGI) project at The Jackson Laboratory. The MGI system is a model organism community database resource that provides integrated information about the genetics, genomics and phenotypes of the laboratory mouse. My current research projects combine bio-ontologies and database knowledge systems to represent disease processes with the objective of discovering molecular elements that contribute to particular pathologies such as respiratory diseases.

The Gene Ontology Consortium
Widespread use of the GO system for functional annotation of genomes enables comparative analysis of genome-size data sets. Understanding and supporting the GO annotation process and bringing new groups into the GO community is essential to the continued development of a broad, integrated network of biological information that can be transparently shared to enable and advance knowledge discovery. The GO Consortium group now consists of 19 model organism databases and genome-annotation groups who work cooperatively to construct the GO bio-ontologies, to provide functional annotations for a wide variety of organisms, and to support a GO information resource. GO participants located at The Jackson Laboratory lead ontology development projects, develop new software applications for the GO project, and provide GO annotations for mouse gene products. Other core groups of the GO project include an ontology development group based at the European Bioinformatics Institute in the United Kingdom, a software and resource development group based at Lawrence Berkeley National Laboratory, and a production database group based at Stanford University.

The Mouse Genome Informatics Project
MGI supports scientific research that uses the laboratory mouse as a model for the study of human biology and disease. MGI data are curated both from the biomedical literature and from co-curated data loads from other major bioinformatics resources. My research group is responsible for the functional and comparative annotation of mouse genes in the MGI resource. This work includes defining the mouse gene set (in co-curation with other informatics resource providers), indexing the biomedical literature for functional annotation, providing official gene nomenclature along with a robust set of synonyms, and extending the representation of relationships between mouse, human and rat genes and genomes. We work closely with the MGI Sequences and Sequence Maps group to resolve sequence-based inconsistencies in the representations of the mouse genome and the sequence and mapping data integrated in MGI and between MGI and other informatics resource centers such as the NCBI, Ensembl and the UniProt groups. We also work closely with the MGI Phenotypes group to support the development of standards for the representation of phenotype/genotype data in MGI.

MGI-GO Scientific Curators are using a combination of algorithmic and manual approaches to update annotations of mouse gene products to the GO vocabularies. Currently, more than 17,500 mouse genes have at least preliminary GO annotations and over 9,700 have annotations based on experimental assays in mouse. We use data-mining and other strategies to semi-automate gene annotation to the GO. The highest quality annotations, however, depend on skilled scientific curators who review published literature for information that provides experimental verification for the GO attributions.

Lab staff

Principal Investigator:
Judith A. Blake, Ph.D.

Multi-Principal Investigators and Subcontract Principal Investigators:
Rolf Apweiler, Ph.D., European Molecular Biological Laboratory
Carol J. Bult, Ph.D.,  The Jackson Laboratory
J. Michael Cherry, Ph.D., Stanford University
Rex Chisholm, Ph.D., Northwestern University
Mindy Dwinell, Ph.D., Medical College of Wisconsin
Janan T. Eppig, PhD., The Jackson Laboratory
Eva Huang, Ph.D., Carnegie Institution of Washington
James A. Kadin, Ph.D., The Jackson Laboratory
Suzanna Lewis, M.S., Lawrence Berkeley National Laboratory
Paula MayBee, Ph.D., University of South Dakota
Joel E. Richardson, Ph.D., The Jackson Laboratory
Barry Smith, Ph.D., SUNY, Buffalo
Paul W. Sternberg, Ph.D., California Institute of Technology
Paul Thomas, Ph.D. University of Southern California
Cathy Wu, Ph.D. University of Delaware

Research Scientists:
David P. Hill, Ph.D.
Mary Dolan, Ph.D.

Senior Scientific Curators:
Harold J. Drabkin,  Ph.D.
Li Ni, Ph.D.

Scientific Curators:

Karen Christie, Ph.D.
Karen Rassmusen, Ph.D.
Dmitry Sitnikov, Ph.D

Assistant Scientific Curator:
Monica McAndrews, B.S.

Information Specialist II:
Nancy E. Butler

Research Administrative Assistant:
Glenn Smallidge


 

Publication listings

 

2013

 

Blake JA, 2013. Ten Quick Tips for Using the Gene Ontology. PLoS Comput Biol 9(11): e1003343. Doi. PMCID: PMC3828149

Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Laegreid A.  Gen Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. Database (Oxford) Aug 27 doi: 10.1093/database/bat062.  PMC3753819 

Bult CJ, Eppig JT, Blake JA, Kadin JA, Richardson JE, Mouse Genome Database Group. 2013.  The mouse genome database: genotypes, phenotypes, and models of human disease. Nucleic Acids Res. Jan;41(Database issue)D885-91. doi: 10. 1093/nar/gks1115.

Gene Ontology Consortium. 2013.  Gene Ontology annotations and resources.   Nucleic Acids Res. Jan;41(Database issue):D530-5. doi: 10.1093/nar/gks1050.

2012

 

Drabkin HJ and Blake JA. 2012. Manual Gene Ontology Annotation Workflow at the Mouse Genome Informatics Database. Database: doi:10.1083/database/bas045 PMCID: PMC3483533

Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Cherry MJ, D'Eustachio P, Finn R, Giglio M, Hirschman L, Kania R, Klimke W, Martin MJ, Karsch-Mizrachi I, Munoz-Torres M, Natale D, O'Donovan C, Ouellette F, Pruitt KD, Robinson-Rechavi M, Sansone SA, Schofield P, Sutton G, Van Auken K, Vasudevan S, Wu C, Young J, Mazumder R.  2012. Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference.  Database (Oxford) 2012 Oct 29; 2012:bas036. Gene Ontology Consortium 2013 NAR (database issue) PMCID:PMC3483532

Bada M, Ecker M, Evans D, Garcia K, Shipley K, Sitnikov D, Baumgartner WA, Cohen KB, Verspoor K, Blake JA, Hunter LE. 2012. Concept Annotation in the CRAFT Corpus. BMC Bioinformatics. Jul 9;13(1):161. PMCID:PMC3476437

Bello SM, Richardson JE, Davis AP, Wiegers TC, Mattingly CJ, Dolan ME, Smith CL, Blake JA, Eppig, JT. 2012.  Disease Model Curation Improvements at Mouse Genome Informatics. Database doi:10.1093/database/bar063.

Mattingly, CJ, McKone, TE, Callahan, MA, Blake JA, Cohen Hubel, EA. 2012. Providing the Missing Link: the Exposure Science Ontology ExO. Environ Sci Technol 2012 March 12 [Epub ahead of print]

Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA; on behalf of the Gene Ontology Consortium. 2012. On the Use of gene Ontology Annotations to Assess Functional Similarity amoung Orthologs and Paralogs: A Short Report. PLoS Comput Biol. 2012 Feb;8(2):e1002386. Epub 2012 Feb 16. PMCID:PMC3280971

Taşan M, Drabkin HJ, Beaver JE, Chua HN, Dunham J, Tian W, Blake JA, Roth FP. 2012. A Resource of Quantitative Functional Annotation for Homo sapiens Genes. G3 (Bethesda). 2012 Feb;2(2):223-33. Epub 2012 Feb 1. PMCID:PMC3284330

The Gene Ontology Consortium. The Gene Ontology: enhancements for 2012. Nucleic Acids Res Jan;40(Database issue):D559-64. Epub 2011 Nov 18. PMCID: PMC3245151

Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE; the Mouse Genome Database Group. 2012. The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. Nucleic Acids Res. 2012 Jan;40(Database issue):D881-6. Epub 2011 Nov 10. PMCID: PMC3245042

2011

 

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cocharane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hacock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamsaki C; BioDBCore Working Group. Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford) Jan 4 PMC3017395.  

Bult CJ, Drabkin HJ, Eviskov A, Natale D, Arighi C, Roberts, N, Ruttenberg, A D'Eustachio P, Smith B, Blake J, Wu C. 2011. The Representation of Protein Complexes in the Protein Ontology (PRO). BMC Bioinformatics Sep 19;12:371.

Meehan TF, Carr CJ, Bult CJ, Chesler EJ, Blake JA. 2011. Autism Candidate Genes via Mouse Phenomics. J Biomed Inform. Mar 21 [Epub ahead of print].  

Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD. Logical Development of the Cell Ontology. 2011.  BMC Bioinformatics 12:6. PMCID: PMC3024222

Bult CJ, Drabkin HJ, Eviskov A, Natale D, Arighi C, Roberts, N, Ruttenberg, A D'Eustachio P, Smith B, Blake J, Wu C. 2011. The Representation of Protein Complexes in the Protein Ontology (PRO). BMC Bioinformatics Sep 19;12:371. PMCID: PMC3189193

Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, GondrŽ-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. 2011. Hematopoietic cell types: Prototype for a revised cell ontology. J Biomed Inform. 44: 75-79. PMCID: PMC2892030

Blake JA, Bult CJ, Kadin JA, Richardson JE, Eppig JT; the Mouse Genome Database Group. 2011. The mouse genome database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res. Jan;39 (Database issue):D842-8. Epub 2010 Nov 3.

2010

 

Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D'Eustachio P, Evsikov AV, Huang H, Nchoutmboube J, Roberts NV, Smith B, Zhang J, Wu CH. 2010. The Protein Ontology: a structured representation of protein forms and complexes. Nucleic Acids Res. 2010 Oct 8. [Epub ahead of print] PMCID: PMC3013777

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; on behalf of the BioDBCore working group. 2010.  Towards BioDBcore: A community-defined information specification for biological databases. Nucleic Acids Res Jan;39(Database issue):D7-10. Epub 2010 Nov 18. PMCID: PMC3013734

Bult CJ, Kadin JA, Richardson JE, Blake JA, Eppig JT, Mouse Genome Database Group. 2010. The Mouse Genome Database: Enhancements and Updates. Nucleic Acids Res D586 Ð 592.PMCID: PMC2808942

Gene Ontology Consortium. 2010.  The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010 January; 38(Database issue): D331ÐD335. PMCID: PMC2808930

2009

 

Dowell KG, McAndrews-Hill M, Hill DP, Drabkin HJ, Blake JA. 2009.  Integrating text the MGI biocuration workflow. Database(Oxford) 2009 bap019. doi:101.1093/database/base. Epub 2009 Nov 21. PMC2797454

Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. 2010. Ontology Engineering. Nature Biotech. Feb;28(2):128-30. 

Bult CJ, Kadin JA, Richardson JE, Blake JA, Eppig JT; the Mouse Genome Database Group. 2010.  The Mouse Genome Database: enhancements and updates.  Nucleic Acids Res.Jan;38(Database issue):D586-92  Epub Oct 27. PMCID: PMC2808942

Reference Genome Group of the Gene Ontology Consortium.  2009.  The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.   PLoS Comput Biol. Jul;5(7):e1000431. Epub 2009 Jul 3. PMCID: PMC2699109 

Arighi CN, Liu H, Natale DA, Barker WC, Drabkin H, Blake JA, Smith B, Wu CH. 2009. TGF-beta signaling proteins and the Protein Ontology. BMC Bioinformatics 10(Suppl 5):S3. PMCID:PMC2679403

Blake JA, Bult CJ, Eppig JT, Kadin JA, Richardson JE; Mouse Genome Database Group. 2009. The Mouse Genome Database genotypes::phenotypes. Nucleic Acids Res 37(Database):D712-D719.

Dolan ME, Blake JA. 2009. Using ontology visualization to facilitate access to knowledge about human disease genes. Applied Ontology 4(1):35-49.

Sam LT, Mendonca EA, Li J, Blake J, Friedman C, Lussier YA. 2009. PhenoGO: an integrated resource for the multiscale mining of clinical and biological data. BMC Bioinformatics 10(Suppl 2):S8. PMCID:PMC2646241

Joslyn C, Baddeley B, Blake J, Bult C, Dolan M, Riensche R, Rodland K, Sanfilippo A, White A. 2009. Automated Annotation-Based Bio-Ontology Alignment with Structural Validation. Proceedings of ICBO:http://dx.doi.org/10.1038/npre.2009.3518.1. (2009)

The Reference Genome Group of the Gene Ontology Consortium. 2009. The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species. PLoS Comput Biol Jul;5(7):e1000431.

 

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