[Plant-biology] Plant Metabolic Network News Announcement
(by peifenz from acoma.stanford.edu)
Thu Jun 19 17:14:48 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 Plantbio