PMN: Plant Metabolic Network
The central goal of the Plant Metabolic Network (PMN) is to bring together biochemical pathway databases and research communities focused on plant metabolism.
PMN, first made public in June 2008, draws upon the work of many individuals with expertise in annotating genomes, generating metabolic pathway databases, curating biochemical information from the literature, and forming extensive network of collaborations with biological databases and biochemistry researchers.
Global Vision and Mission
As the worldwide demand for production of food, animal feed, biofuels, industrial inputs, and new medicines continues to grow, there is an increasingly urgent need to develop new technologies using plants. The long-term goal of developing these technologies has prompted the sequencing of plant genomes and gene complements. There is a growing need to place the sequenced and annotated genomes in a biochemical context in order to facilitate discovery of enzymes and engineering of metabolism. PMN will generate an infrastructure for drawing together diverse sources of plant metabolism information.
At the center of the PMN is PlantCyc, a database containing pathways and their catalytic enzymes and genes, as well as compounds from many plant species. The majority of pathway diagrams in PlantCyc 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. These pathways are known to exist in other non-plant organisms, but have not been found in plants. However, some hints indicate that plants may utilize the same pathway or similar routes. Both experimentally-verified and computationally-predicted enzymes and genes are assigned to pathways. Evidence codes are attached to pathways and to the assignments of genes/enzymes to provide information about data quality.
In addition to new pathways curated in-house, PlantCyc also contains all pathways from AraCyc and the 16 other species-specific databases, all plant pathways from MetaCyc, and a number of curated pathways from other plant pathway databases including RiceCyc and MedicCyc. We also integrated computational assignments of enzymes and genes from all 17 PMN databases, such as AraCyc, BarleyCyc, and CornCyc, as well as from the externally generated MedicCyc and SolCyc pathway databases. Thus, PlantCyc brings together information about over 900 pathways in more than 300 plant species (See Database Statistics). The content of PlantCyc is expected to grow rapidly as more plant genomes are sequenced and annotated and new biochemical data are published. Curated plant pathway data from MetaCyc and other resources will be continuously added to augment the in-house data. Semi-annual releases will be made to provide the most up-to-date information to the public.
Species-specific Metabolic Pathway Databases
PMN will generate metabolic pathway databases for a number of other plant organisms. Our choices were based on criteria including the available number of genome/EST sequences, the utility and agronomical value of the individual species, as well as taxonomic interest. The new databases will include, but are not limited to, wheat, sugarcane, moss, and papaya. To build each database, putative enzyme sequences will first be identified for each organism using our in-house-developed annotation methods. The Pathway Tools software will then be used in the initial pathway prediction using PlantCyc and MetaCyc as reference databases. The predicted pathways and enzymes will be further curated with literature information. It is a daunting task. We thus ask for contributions from the plant research community. An entire new database may be adopted for curation and maintenance. Please contact us if your group is interested.
Curation and Community Collaboration
The Plant Metabolic Network aims to foster cooperation and sharing of resources and expertise among many different members of the research community. PMN will rely heavily on the work of curators at the PMN, but will also depend upon contributions from the curation teams at other databases interested in different species. Currently we are collaborating with MetaCyc, MaizeGDB, SolCyc, and GoFORSYS for data exchange. Biochemistry experts on the PMN Editorial Board will review the pathways related to their field of expertise. Moreover, all other researchers who are interested in specific domains of metabolism are encouraged to provide new data, feedback, suggestions, and corrections to improve the content of PlantCyc and the other species-specific databases. Plus, scientists can contribute information directly to curators at major scientific meetings and during fun-filled curatorial jamborees. In addition, PMN members work closely with the Bioinformatics Research Group at SRI International. This group provides the Pathway Tools software that is used to predict, display, and search the PMN databases and other related metabolic pathway databases.
Enhancing Metabolic Research Efforts
Metabolic databases built from this project will address the need of the scientific community to analyze and display the growing body of data that is emerging from both conventional biochemistry and high-throughput/large-scale data experiments. The proposed network of databases will facilitate the discovery of new enzymes and pathways, and the engineering of metabolic pathways. In addition, researchers studying individual genes and mutants will be able to put their findings in the context of overall metabolic scheme of an organism, thereby deepening their understanding of the roles played by their genes of interest.
PMN and Education
The Plant Metabolic Network of databases will not only facilitate research, but also provide an up-to-date, easily accessible set of teaching and educational resources for students. In addition to providing biochemical reaction diagrams, organism-specific metabolic maps, detailed descriptions of enzymes and pathways, and links to other resources, the PMN website will house tutorials to help guide teachers and students as they learn more about the valuable bioinformatic data and analysis tools that are crucial elements of modern biological research.
The PMN is supported by the National Science Foundation (Grant #: 1026003 and 0640769), as well as by the Department of Energy (BER Grant #: ER65472 ). The PMN is based at the Department of Plant Biology at the Carnegie Institution for Science