MetaCyc is a database representing knowledge about biochemical pathways in over 500 different organisms (Caspi et al., 2006). It is used to predict biochemical pathways of a given organism (using the PathoLogic software) based on the annotation of its genome. The Pathway Tools software developed by SRI International allows users to create new Pathway/Genome Databases (PGDBs), in which genes can be associated with biochemical pathways.

If GDR is renewed (current funding runs out August 31, 2008) we plan to implement the proven framework of MetaCyc to implement GDR plant family-specific databases with pathway visualization capabilities. Using the available EST information for Rosaceae the Pathway Tools software will be employed to generate the RosaCyc databases which will be made accessible to users via this website. Users will be able to query and browse these databases, upload pathways (which are generated dynamically from the database) that feature hyperlinks with various kinds of relevant information (e.g., gene function, reactions, metabolites, and links to other databases such as SwissProt and PubMed).

This will include:

• Evaluating and transferring appropriate biochemical pathways from Arabidopsis to Rosaceae:
• Arguably, the Arabidopsis community has achieved the best annotation of any plant genome. AraCyc, which is the database for pathway-based gene annotation,      contains annotation and maps covering more than 200 pathways (containing roughly 1,800 genes) in Arabidopsis. These Arabidopsis pathways will be reviewed      for their presence/absence in the available Rosaceae ESTs and manually curated by biochemical pathway annotators at WSU.



• Develop maps for new pathways in Rosaceae:
  
• Pathways occurring in Rosaceae for which no public maps exist will be drawn from scratch. These maps will be, besides being made available to users as      RosaCyc, integrated into the MetaCyc database for across-species comparisons. Many pathways can be annotated in RosaCyc based on high sequence      homology of the associated genes in Rosaceae to their putative orthologs in Arabidopsis (B.M. Lange and M. Ghassemian, unpublished results). For another 60      pathways represented in AraCyc, manual curation will play an important role in generating RosaCyc, whereas sequence similarity appears to be insufficient to      build RosaCyc using the remaining AraCyc pathways. In addition, we will draw and annotate 20 pathways that are not represented in AraCyc or are substantially      different in Arabidopsis and the Rosaceae. Among these pathways are those responsible for the metabolism of monoterpenes, sesquiterpenes, diterpenes,      flavonoids, green leaf volatiles, aliphatic and aromatic esters, coumarins, furanones, and aliphatic acids. The maps and the annotation of genes involved in the      represented pathways will be evaluated by external curators.