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Costanzo, M.C., Arnaud, M.B., Csank, C.J., Hirschman, J.E., Kranz, J.E., Olsen, P., Robertson, L.S., Skrzypek, M.S., Kondu, P., Lengieza, C., Tillberg, M., Garrels, J.I.
Proteome Division, Incyte Genomics, Beverly, MA
Contact mcc@proteome.com
The BioKnowledge® Library is a relational database and website composed of protein-specific information collected from the scientific literature. Each Protein Report on the website summarizes and displays published information about a single protein, including its biochemical function, role in the cell and in the whole organism, localization, mutant phenotype and genetic interactions, regulation, domains and motifs, interactions with other proteins, and other relevant data. The BioKnowledge Library includes species-specific volumes for the model organisms Saccharomyces cerevisiae (YPD*), Schizosaccharomyces pombe (PombePD*), and Caenorhabditis elegans (WormPD*), a volume for the major fungal pathogens of humans including Candida albicans (MycoPathPD*), and a protein survey-level database for human proteins (Public Human PSD'). Protein Reports of each species are unified in format, easily searchable, and extensively cross-referenced between species. YPD, PombePD, MycoPathPD, WormPD, and Public HumanPSD are freely available to academic users at the Proteome website; these and other volumes of the BioKnowledge Library are available to commercial users by subscription.
The protein properties section of each Protein Report has two new fields: domains found by comparison to the Pfam (http://pfam.wustl.edu/) list of domains; and known structural domains as listed in the Protein Data Bank (PDB; http://www.rcsb.org/pdb/index.html). Pfam domains are searchable using the database Full Search forms and can be combined with other search criteria. As of Fall 2001, YPD includes 305 transcription profiles encompassing 509 datasets, which have been organized for more convenient browsing by type of experiment into14 categories. WormPD also includes 5 such profiles encompassing 19 datasets, and new datasets are added to all the databases as they are published. The preliminary set of C. albicans open reading frames from assembly 6 of the genomic sequencing project (http://www-sequence.stanford.edu/group/candida/index.html) has been added to MycoPathPD. The sequences have been analyzed by a proprietary process termed BioKnowledge® Transfer, which involves assessment of family membership and domain structure (from Pfam analysis) and similarity to characterized proteins (from BLAST analysis). For those with sufficient similarity to experimentally characterized proteins, Title Lines have been written and certain properties such as biochemical function and subcellular role have been predicted. Public HumanPSD is a freely available version of HumanPSD, which contains 10,000 human proteins with Title Lines and assigned Gene Ontology classifications. It is a dataset based on annotation provided to the NCBI in December 2000 which appears on the LocusLink website as well as in Public HumanPSD.
Costanzo, M.C., M.E. Crawford, J.E. Hirschman, J.E. Kranz, P. Olsen, L.S. Robertson, M.S. Skrzypek,
B.R. Braun, K.L. Hopkins, P. Kondu, C. Lengieza, J.E. Lew-Smith, M. Tillberg, and J.I. Garrels. (2001)
YPD*, PombePD* and WormPD*: model organism volumes of the BioKnowledge* Library, an
integrated resource for protein information. Nucleic Acids Res. 29: 75-79.
Csank, C., M.C. Costanzo, J.E. Hirschman, P. Hodges, J.E. Kranz, M. Mangan, K.E. O'Neill, L.S.
Robertson, M.S. Skrzypek, J. Brooks, and J. Garrels. 2001. Three Yeast Proteome Databases: YPD,
PombePD, and CalPD (MycoPathPD). In Guide to Yeast Genetics and Molecular and Cell Biology, A
Volume of METHODS IN ENZYMOLOGY. Abelson, J. N., and M. I. Simon, Editors-In-Chief;
Volume editors, Guthrie, C., and G. R. Fink. Academic Press, New York, NY, in press.
Category Genomic Databases
Go to the abstract in the NAR 2001 Database Issue.