Key Project Background Papers

BeeSpace Project Proposal:

Bruce Schatz (PI), Gene Robinson, ChengXiang Zhai, Sandra Rodriguez-Zas, Bertram Bruce, Susan Fahrbach [2004] BeeSpace – An Interactive Environment for Analyzing Nature and Nurture in Societal Roles, NSF FIBR Frontiers in Integrative Biological Research, Biological Sciences Directorate-wide competition, Grant 0425852 awarded $4,987,688 for period Sep 1, 2004 to Aug 31, 2009.

One-page summary - PDF
Project Proposal text - PDF

These Press Releases appeared in September 2004:

National Science Foundation Press Release

UIUC Press Release

These sources relate to key informatics aims of the project:

Schatz, B.R. (2002). "Building Analysis Environments: Beyond the Genome and the Web," invited essay for Trends and Controversies section about Mining Information for Functional Genomics, IEEE Intelligent Systems 17: 70-73 (May/June 2002). PDF

Schatz, B.R. (2002). "The Interspace: Concept Navigation across Distributed Communities," Information Infrastructure article for annual issue on Technology Trends, IEEE Computer 35: 54-62 (January 2002). PDF

These sources relate to key biology aims of the project:

Robinson, Gene E. (2004). Beyond Nature and Nurture, invited essay for Perspectives section about Genomics, Science 304: 397-399 (April 16). PDF

Whitfield, C., Cziko, A-M., & Robinson. G. (2003). Gene Expression Profiles in the Brain Predict Behavior in Individual Honey Bees, Science 302: 296-299 (Oct. 10). PDF

These sources offer additional background information relevant to aspects of the project:

Biology Sources

BeeSpace data sources [HTML] [MS Word] - by Bruce Schatz. Links to genome databases, genome classifications, and model organisms. Prepared October 2004.

BeeSpace information sources [HTML] [MS Word] - by Bruce Schatz. Links to bibliographic databases, natural history books, and database samples. Prepared October 2004.

Drysdale, R.A., Crosby, M.A., & The FlyBase Consortium. (2005). "FlyBase: genes and gene models." [PDF] Nucleid Acids Research, 33: D390-D395.

Gene Ontology Consortium. (2001). "Creating the Gene Ontology Resource: Design and Implementation" [PDF]. Genome Research, 11: 1425-1433.

Ogata, H., Goto, S., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999). "KEGG: Kyoto Encyclopedia of Genes and Genomes" [PDF]. Nucleic Acids Research, 27(1):1, 29-34.

Pennisi, E. (2005). "A Genomic View of Animal Behavior." [PDF] Science Magazine, 307:5706 (Jan. 7), 30-32.

Biology examples

Schatz, B., Robinson, G., Zhai. C.X., Doan, A.H., &  Roth, D. (2005.) "Interactive systems for information integration of bioinformatics sources." [MS Word] Proposal to NSF SEIII Scientific Informatics program.

Bioinformatics technologies

Hu, Y., Hines, L.M., Weng, H., Zuo, D., Rivera, M., Richardson, A., & LaBaer, J. (2003)."Analysis of Genomic and Proteomic Data Using Advanced Literature Mining." [PDF]. Journal of Proteome Research, 2003(2), 405-412.

Leroy, G., and Chen, H. (Undated.) "An Ontology-enhanced Integration of Top-down and Bottom-up Created Biomedical Knowledge." [PDF]

Schatz, B., Robinson, G., Roth, D., Doan, A.H., & Zhai, C.X.. (2004). "Information integration using entity-relations across bioinformatics sources." [PDF]

Wilkinson, D.M., & Huberman, B.A. (2004). "A method of finding communities of related genes." [PDF] PNAS 101.