The PMN is eager to work with scientists who want to do metabolic-pathway-based analyses.
PlantMetabolomics.org is a data repository for a series of metabolomic experiments performed in Arabidopis thaliana
You can read about efforts to incorporate their experimentally identified compounds into AraCyc in Bais et al 2010

The Plant Metabolic Network is pleased to announce new releases of the metabolic pathway databases AraCyc 6.0 and PlantCyc 3.0, plus the inaugural release of PoplarCyc 1.0

This PMN release includes many updates to AraCyc enzyme/reaction assignments based on a new PMN enzyme annotation pipeline, plus, 34 additional pathways have been added to AraCyc 6.0.

PoplarCyc 1.0 was created by applying the PMN enzyme annotation pipeline to the Populus trichocarpa 1.1 genome release sequences provided by JGI, and then using the Pathologic software from SRI International. The new computationally predicted database was then validated by PMN curators. 321 pathways and 3434 predicted poplar enzymes are now available in PoplarCyc 1.0. The data have also been incorporated into PlantCyc 3.0. In addition, 75 new pathways have been added to the new version of PlantCyc.

The PMN also now provides a BLAST tool and two customized enzyme sets for PMN users.

Please come watch an amazing and enormous Amorphophallus titanum flower bloom . . . and be thankful that you can't smell it.

You can use the PMN to get more information about the stinky metabolites (putrescine and cadaverine) that "Trudy" the "corpse flower" produces to attract insects as she flowers in the University of California Botanical Garden in Berkeley.

Many researchers and students from around the world had a chance to see PMN presentations and posters at conferences and universities during the summer of 2009.

• CIGRAS / UCR
  July 27-31 San Pedro, Costa Rica

• American Society of Plant Biologists
  July 18 - 22, Honolulu, HI
  

• 20th International Conference on Arabidopsis Research
  June 30 - July 4, Edinburgh, Scotland

Please see our presentations page for more details.

These releases contain many new pathways, enzymes, reactions, and compounds!

A few highlights . . .

• PlantCyc 2.0 has a whole new set of predicted enzymes from Medicago, tomato, and rice mapped onto the metabolic pathways and more . . .


• AraCyc 5.0 has new compounds identified through the NSF 2010 Metabolomics Project and from the KNApSAcK database and more . .


• You can read about all the new data and features in the PlantCyc and AraCyc release notes.


• New downloads of the database files are available for registered users. Please sign-up today if you would like to access these valuable resources.


• We are grateful for help from our contributors in the scientific community.

Have you ever wondered what information PlantCyc has about apples, bluebells, or carrots? To find out more, please come visit the newly created PlantCyc species page found on the "Databases" submenu.

• Quickly link to all of the pathways with curated information for your favorite species


• Browse through the list of over 250 species, from Abies grandis to Zingiber officinale


• Help the PMN expand its species coverage by contributing pathway, reaction, or enzyme information for even more plants

An important part of the PMN mandate is to encourage interactions and data exchange within the metabolic research community. So, please come meet the PMN staff, give us feedback, and learn about how PMN can help your research at the following conferences in the summer of 2008:

• American Society of Plant Biologists Conference. June 22-25, 2008. Merida, Mexico


• 5th International Conference on Plant Metabolomics . July 15-18, 2008. Yokohama, Japan


• 19th International Conference on Arabidopsis Research . July 23-27, 2008. Montreal, Canada


• Banff Conference on Plant Metabolism . July 30-August 3, 2008. Banff, Canada


• Presentations can now be accessed from the presentations page.

• Come see new links to metabolite identification resources and data analysis tools from PRIMe on our Metabolomics Resources page.
• While you're there, explore the array of helpful websites you can access through these pages.

On June 17, 2008, PlantCyc made its web debut, containing biochemical pathways from over 250 plant species. The multi-organism database brings together more than 2000 reactions, and includes a total of over 500 pathways.

Members of the PMN welcomed collaborators from the University of Calgary (David Liscombe, Jeorg Ziegler, Peter Facchini), the Canadian National Research Council - Plant Biotechnology Institute (Dustin Cram, Jonathan Page (via WebX)), and Cornell University (Anuradha Pujar) to an organizational meeting and curatorial jamboree. The Carnegie Canada cross-border cooperative effort will seek to improve our understanding of the metabolism of two plants with great pharmcalogical value: Papaver somniferum (opium poppy) and Cannabis sativa (marijuana, hemp). The meeting generated a roadmap of immediate and long-term goals for the BIACyc (Benzylisoquinoline alkaloid Cyc) and CannaCyc (Cannabaceae Cyc) projects and included a pathway update party where experts in the field of alkaloid metabolism helped curators to improve existing pathways and suggested new pathways for inclusion in PlantCyc and MetaCyc.