Frequently Asked Questions

General FAQs

  1. How can I report an error or make a suggestion?

    Please use our feedback form. If you need to contact us over the phone or by mail, please see our contact information page. We have also provided specific contact information for our PMN staff members and collaborators

  2. What is the difference between the PMN and PlantCyc?

    The PMN (Plant Metabolic Network) is a network that involves both information, and the individuals who generate it and curate it. Its core data repository is a series of databases that focus on the pathways, enzymes, reactions, compounds, and genes that are relevant to metabolism in plants.  PlantCyc is the comprehensive multi-species database hosted by the PMN that brings together accumulated biochemical information from many plants.

  3. What is the difference between PlantCyc and MetaCyc?

    Both PlantCyc and MetaCyc are multi-organism metabolic pathway databases. MetaCyc contains pathways from many kingdoms, but the pathways in PlantCyc have all been identified in plants. In addition, although MetaCyc requires experimental evidence to support all of their pathways, PlantCyc allows the inclusion of pathways that are proposed in published, peer-reviewed literature based on expert opinion that lack experimental validation. These pathways are clearly marked with the evidence code: EV-AS-HYPO (Evidence-Author Statement-Hypothesis). The inclusion of these pathways broadens the scope of PlantCyc and provides testable hypotheses for further research. There is more detailed information available at the evidence codes tutorial.

  4. What do you mean by a "single species" or "species-specific" database? How about a "single taxon" or "taxon-specific" database?

    In the context of the PMN, a single species or species-specific database contains all of the predicted and experimentally verified pathways for a single organism. Some of these pathways might be unique to the species, but many pathways, for example, those involved in primary metabolism, are likely to be shared with many other organisms. Nevertheless, these shared pathways will appear in each species-specific database accompanied by the enzymes associated with that pathway from the single organism. In other words, species-specific does not imply that the pathways present in the database are unique to the particular organism.

    To provide a more concrete example, the pathway for cellulose biosynthesis is present in AraCyc because Arabidopsis synthesizes cellulose. The pathway for cellulose biosynthesis is also present in RiceCyc because rice also synthesizes cellulose. But, the AraCyc cellulose biosynthesis page only shows information about Arabidopsis enzymes and the RiceCyc page only shows information about rice enzymes.

    It is important to note that pathways with the same name in two different species-specific databases will not always be identical. If they are exactly the same in terms of intermediate compounds, number of steps, co-factors involved, etc., then they are likely to share the same frame ID (a unique identifier assigned by the Pathway Tools software at the time of the initial computational build). However, there can easily be small variations between pathways in different species. For instance, NADH may be used in one species while NADPH is used in another species. Or, one species may first deaminate a compound and then decarboxylate it while a second species may first decarboxylate and then deaminate even though both pathways have the same starting product and final reactant. These pathways may have the same name, but should have different frame IDs.

    Similar to a single species or species-specific database, a single taxon or taxon-specific database contains metabolic pathway data for a small number of closely related species that fall within a relatively small taxonomic unit, such as a family. These databases can prove particularly useful for examining secondary metabolic pathways that are shared among members of the defined taxon. The BIACyc and CannaCyc databases proposed as part of the Carnegie-Canada project will be single taxon databases focusing on specific classes of secondary metabolites.

  5. How can I make a database for my favorite plant and get it into the PMN and PlantCyc?

    We would love to help you with this process. Please contact us if you are interesting in pursuing this project.
    The main steps required are:
    • Download the Pathway Tools software
    • Create an input file based on the annotated genome of your organism
    • Generate a new species-specific database using the Pathologic program with PlantCyc as the reference database
    • Validate the Pathologic predictions
    • Curate the pathways and add comments and references for the enzymes
    • Contact us to determine how we can make this information available through the PMN

  6. How can I find out what specific terms in the database mean?

    Biocyc provides a helpful glossary to explain some of the terms used in the PMN pathways.

If you have any additional questions or comments, please contact us
- We will add your question to the FAQs if we think it can help other users.