[Arabidopsis] Plant Metabolic Network News Announcement

Peifen Zhang via arab-gen%40net.bio.net (by peifenz from acoma.stanford.edu)
Thu Jun 19 17:10:04 EST 2008


Dear Plant Researchers,


The Plant Metabolic Network (PMN) is pleased to announce the initial 
launch of its official web site (http://plantcyc.org) and the first 
release of PlantCyc, a comprehensive biochemical pathway reference 
database dedicated to the plant kingdom.

The PMN is an NSF-funded collaborative project among databases and 
biochemists with a common goal to build a broad network of plant 
metabolic pathway databases. The central database of PMN, PlantCyc 
(version 1.0), has over 500 pathways and about 3000 enzymes involved in 
primary and secondary metabolism, consolidated from over 290 plant 
species. The majority of these pathways come from AraCyc (version 4.5, 
http://www.arabidopsis.org/biocyc/index.jsp) and MetaCyc (version 12.0, 
http://metacyc.org). Many pathway diagrams were manually extracted from 
the plant literature. They are either supported by experimental evidence 
or are based on expert hypotheses. A small portion of the pathways were 
computationally predicted but validated by curators with supporting 
evidence in the literature. Evidence codes are attached to pathways and 
to enzymes to indicate data quality.

In addition to PlantCyc, the PMN will develop and host a collection of 
single-species databases like that of AraCyc (Arabidopsis).  We are 
currently developing databases for several agronomically important 
plants including poplar, soybean, wheat and maize. PMN will also host 
databases developed elsewhere such as RiceCyc (rice), MedicCyc 
(medicago) and LycoCyc (tomato). These single-species pathway databases 
place the sequenced and annotated genomes or ESTs in a biochemical 
context to facilitate the discovery of enzymes and the engineering of 
metabolic pathways. They also provide a platform for users to display 
and analyze functional genomics data, such as those generated from 
microarray and metabolomic experiments.

Nearly 30 plant biochemists serve on the PMN editorial board to provide 
overall vision and guidance to the PMN project and they play an active 
role in ensuring the high quality of the information present in the PMN. 
The enhancement of the PMN databases is an ongoing effort. All users are 
encouraged to send corrections, feedback, and new data. Please contact 
us at curator from plantcyc.org.


The PMN Team



More information about the Arab-gen mailing list