Program of the 2001 International Worm Meeting - Sternberg Lab ...

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233. WorfDB: The C. elegans
ORFeome database
Philippe Vaglio, Jerome Reboul,
Philippe E. Lamesch, Jean-Francois
Rual, David D. Hill, Marc Vidal
Dana-Farber Cancer Institute and Harvard
Medical School
WorfDB, (http://worfdb.dfci.harvard.edu) the
database of the C. elegans ORFeome cloning
project, was created to integrate and
disseminate the data from our attempt to
clone the 19,000 predicted open reading
frames (ORFs).
WorfDB serves as a central data repository
enabling the scientific community to search
for available clones and find information
about their quality. The database contains all
available ORF sequence with the data
pertinent to the cloning process. This
information includes: the names and
sequences of the primers used to amplify the
ORFs, the success of the PCR amplification,
photographs of the resulting PCR products
separated on agarose gels and ORF sequence
tags (OSTs) when available. The database is
searchable by gene name, prediction name or
blast searches. A list of ORFs can also be
searched for availability and amplification.
The database currently contains PCR
amplification data for about 10,000 ORFs.
234. The BioKnowledge Library TM :
an Integrated Collection of
Databases for Model Organism and
Human Proteomes
Philip Olsen, Marek Skrzypek, Jodi
Hirschman, Martha Arnaud, Maria
Costanzo, Laura Robertson, Janice
Kranz, James I. Garrels
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PROTEOME, Division of Incyte Genomics, 100
Cummings Center, Beverly, MA 01915
The BioKnowledge Library TM is a database of
protein information designed to integrate
biological knowledge from the scientific
literature with genomic information. The
BioKnowledge Library contains several
interconnected species-specific volumes
maintained in a relational database format and
presented through a Web-based platform, and is
updated weekly with new information. Versions
of the BioKnowledge Library are available to
industry researchers through subscription, and a
Web-based version is available free to academic
scientists at http://www.proteome.com,
including: PombePD TM (S. pombe),
WormPD TM (C. elegans), YPD TM (S.
cerevisiae), and soon to be added,
MycoPathPD TM - a volume of information
regarding Candida albicans and 16 other fungal
pathogens of humans. In addition, the
BioKnowledge Library contains Public
HumanPSD TM , the Human Proteome Survey
Database of over 10,000 human proteins that
encompasses Title Lines, biochemical functions,
cellular and organismal roles and subcellular
localization, as well as Gene Ontology
classification terms. New features are being
introduced into WormPD. First, the coverage of
functional genomic literature has been
incorporated, including major enhancements in
the presentation of transcription profiles,
allowing users to browse all published
microarray results in one Web platform.
Conclusions from transcription profiling and
other high-throughput, functional genomic
experiments are included in individual protein
reports, making them easily accessible and fully
integrated with other curated literature
information. Second, information collected for
uncloned genetic loci,never before available in
WormPD, will be displayed. Third, Gene
Ontology terms will be applied to the proteins in