PathDB is a biochemical pathways database that is currently focused on plant
metabolic data from Arabidopsis and Soybean (thanks to Soybase). We are in
the process on making significant modifications to the schema and tools and
would appreciate your feedback. The next generation PathDB (which we hope
to release this fall) will include
- A data model encompassing all cellular interactions (not just metabolic).
- Information on protein modifications and whether they are linked to an
- The ability to visualize and manipulate complex pathways (i.e. with
- The ability to view and analyze gene, protein and metabolite expression
data in the context of
- Be capable of estimating the effect of a gene knockout on a network.
- New statistical and network analysis tools.
We have recently submitted several collaborative grant proposals using the
new schema and tools as a basis for proteomic and metabolic profiling
facilities and are interested in additional collaborations. We have a
PathDB Research database with a test version of the new schema that we have
parsed in data from other public available sources including data from other
pathways databases and information from yeast and Arabidopsis sequencing
projects. Our goal in the coming year is to create a system that will allow
researchers to create model cells from genomic data in conjunction with the
published literature, then test the robustness of their models using tools
for analyzing cellular networks.
To download the software and for additional information please see
http://www.ncgr.org/software/PathDB or drop me a line.
PS If your are at a company with a stringent firewall. Please contact me
directly. We have a new version available for download that replaces the
RMI communication layer with our homegrown ServerBroker. This solution only
requires the http port be open (thus you do not have to the SA open new
holes in the firewall). If you a developer interested in the ServerBroker
let us know...it is available for free.
Jeffrey L. Blanchard
National Center for Genome Resources
2935 Rodeo Park Dr.
Santa Fe, NM 87505