To download complete copies of ALL of the plant metabolic pathway databases hosted by the PMN, including AraCyc, please fill out and submit the license agreement form.

Please note that this license is freely available to everyone, including commercial users.

The complete download, together with the Pathway Tools software, will allow a user to install and have a local copy of AraCyc/PlantCyc, just like the one visible from the PMN web site. In addition, all of the BioCyc format flat files and a complete biopax.owl file are available as part of this download. You can get more details about the format of all the file types from BioCyc.

Additional custom flat files containing data extracted for ALL of the databases in the latest PMN release can be freely downloaded without a license:

• "nnn"Cyc pathways ("nnn"cyc_dump.yyyy.mm.dd)


• "nnn"Cyc compounds ("nnn"cyc_compounds.yyyy.mm.dd)
  (Note:This file ONLY contains compounds used in the "nnn"Cyc pathways)

The current BLAST sets provided by the PMN can also be downloaded without registration:

• Reference Enzymes (2.0) (from June 2012)
• PlantCyc Enzymes (from PlantCyc release 6.0)
• AraCyc Enzymes (from AraCyc release 9.0)
• CassavaCyc Enzymes (from CassavaCyc release 1.0)
• CornCyc Enzymes (from CornCyc release 1.0)
• Grape Enzymes (from GrapeCyc release 1.0)
• PoplarCyc Enzymes (from PoplarCyc release 4.0)
• SoyCyc Enzymes (from SoyCyc release 2.0)
• Reference Enzymes (1.0) (from October 2009)

The PMN has also generated three lists of pathways that are used to help expedite the validation process when generating new single-species databases. These lists are updated during the preparation of each new PMN release

• The Non-plant Pathway (NPP) list contains pathways that are present in the multi-kingdom MetaCyc pathway database but that are not expected to exist in any plant species. It also includes pathways that PMN curators wish to exclude from PMN databases for discretionary reasons such as redundancy with existing pathways
  (The NPP list can be used to quickly and accurately prune false positive predictions from new single-species databases)


• PMN 7.0 validated using: NPP 3.0


• The Universal Plant Pathway (UPP) list contains pathways that are expected to be present in all land plants**. This list is not yet comprehensive and will grow over time.
  (The UPP list can be used to quickly and accurately add missing pathways that should have been predicted for new land plant pathway databases)


• PMN 7.0 land plant databases validated using: UPP 3.0


• **NEW** While many UPP pathways found in all land plants, such as glycolysis, may also be present in all algae, some "UPP" pathways, such as auxin biosynthesis, may not exist in all algae or may be entirely absent from this group of species. Therefore we have begun to develop a new list of Common Viridiplantae Pathways (CVP 1.0 - (a limited version of UPP 3.0)).
  (These pathways can be safely imported into new databases created for algal or other "lower" plant species if they are not predicted by the Pathologic program.)



• PMN 7.0 algal database (ChlamyCyc 2.0) validated using: CVP 1.0