PMN Databases Overview

There are two types of databases developed and maintained by the PMN project: a reference database called PlantCyc and single species/taxon databases, such as AraCyc.

  • Additional external metabolic pathway databases listed in this overview are affiliated with the PMN. These databases remain under the autonomous control of the PMN collaborators who provide them.

PMN databases (created and/or maintained at PMN)

PlantCyc [Search]

PlantCyc is a metabolic pathway reference database containing more than 500 pathways and their catalytic enzymes and genes, as well as compounds from over 250 plant species (See Database Statistics).

  • The majority of the pathways have been curated from experimental literature by curators at the PMN and collaborators' sites. In addition, PlantCyc includes hypothetical pathways that are published in peer-reviewed journals based on the educated conjectures of experts, and cmputationally predicted pathways that have been manually validated by PMN curtors.

  • Similarly, enzymes in PlantCyc may have experimental support or may be based solely on computational predictions.

  • For both pathways and enzymes, evidence codes are assigned to clearly indicate the type of support associated with these database items.

AraCyc - Arabidopsis thaliana [Search]

AraCyc, a single species database maintained in collaboration with TAIR (The Arabidopsis Information Resource), houses a large set of curated metabolic pathways.

  • The majority of the pathways found in AraCyc have some measure of experimental support, but additional computationally-predicted pathways are included to maximize the hypothesis-generating power of the database. These pathways are known to exist in other species or in non-plant organisms, but have not been reported in Arabidopsis. However, some hints indicate that Arabidopsis may utilize the same pathway or similar routes. All predicted pathways are manually reviewed by curators who add comments concerning their potential validity.

  • As in PlantCyc, enzymes present in AraCyc may have experimental support or may be based solely on computational predictions. And, an identical set of evidence codes is used to clearly identify the source of the information.

  • The structures for the genes included in AraCyc are based on TAIR genome annotations. Additional Gene Ontology and Plant Ontology functional annotations derived from experimental data and computational predictions may be listed at the TAIR gene pages. These are categorized using a different set of evidence codes.

PoplarCyc - Populus trichocarpa (and other Populus species and hybrids) [Search]

PoplarCyc, a genus-level database was developed largely computationally using:

  1. A newly developed enzyme annotation pipeline from the PMN
  2. The Populus trichocarpa 1.1 genome release provided by JGI
  3. The Pathologic pathway prediction software from SRI International


  • The majority of the pathways found in PoplarCyc are based on computational predictions, however, these pathways have been reviewed by curators. Comments and references have often been added to try to explain the specific criteria used to establish their potential validity.

  • A few manually curated pathways have been added if there is experimental support for their existence in Populus species or hybrids. The associated enzymes have been included in the database even if they were not isolated from or studied in Populus trichocarpa. In these cases, comments were added on the enzyme page to indicate the species or hybrid of origin (see isoprene synthase). When no species is indicated in the enzyme comments, the enzyme sequence has been taken from Populus trichocarpa.

  • As in the case for all PMN databases, evidence codes on both the pathway and enzyme pages can be used to determine the experimental or computational support for the information in PoplarCyc.

External Databases

Plant metabolic databases from collaborators

Although several external single species databases are affiliated with the PMN, these databases are developed and maintained exclusively by the collaborators. Some of the data from these databases has been incorporated into PlantCyc, as described in our release notes. We provide collaborator contact information and direct links to their homepages below.

Gramene databases


Noble Foundation database


SGN (Solanaceae Genomics Network) databases

Additional metabolic databases

SRI International databases

SRI International plays a special role as a collaborator.

Through the MetaCyc database, SRI provides some of the data content for PlantCyc. Prior to the creation of PlantCyc, any plant metabolic pathways with experimental or literature support were entered into MetaCyc by curators from the PMN or collaborating groups. More information about the inclusion of MetaCyc data in PlantCyc is described in our release notes.

  • MetaCyc (one database / many organisms)

SRI also provides access to a number of externally generated species-specific databases from outside the plant kingdom through the BioCyc website. They are not part of the PMN, but they may prove useful for comparative studies.

  • BioCyc (multiple databases / many organisms)

The Pathway Tools software used for displaying existing PMN databases and for predicting new databases is also generated and supported by the Bioinformatics Research Group at SRI International.



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