Biology Reference
In-Depth Information
easy access for computational analyses. We have chosen the Genomics
Unified Schema (GUS) database architecture (http://www.gusdb.org)
to address our information storage needs. GUS offers a schema and
user interface that integrates genomic, transcriptomic and proteomic
data of multiple organisms, along with information on their metabolic
and regulatory networks. It also has provisions to store ontologies
and controlled vocabularies, gene expression data, and comparative
genomic data. GUS is an open-source, relational database schema that
has been developed by the Computational Biology and Informatics
Laboratory at the University of Pennsylvania. It has been successfully
implemented by other biological web-resources. GUS currently uses
the Oracle database management system, and there are plans to port
it to other DBMSs.
Genomic Analysis Tools
PATRIC's software systems will play three primary roles: support the
in-house genomic annotation/curation efforts; provide the scientific
community with access to the curated information, together with an
evolving suite of analysis tools aimed at helping researchers develop
vaccines, therapeutics, and diagnostics; and enable consumers of this
information to provide the project curators with both general and
specific feedback. Users will be able to browse the archived genome
annotations via powerful query and navigation capabilities. The various
levels of biological information will be seamlessly interconnected so
that a user may move, for example, from viewing gene annotations to
querying metabolic pathways to viewing results of high-throughput
experiments and a summary of published literature. The analysis tools
will support both whole-genome and gene-level comparisons.
The Scientific Community — Outreach and Feedback
In addition to providing information, PATRIC will engage the scien-
tific communities it serves through a series of outreach activities.
These activities include establishing and maintaining contact with
genome providers (sequencing centers), participating in scientific meet-
ings relevant to the organisms we curate, and seeking and accepting
