Download

Complete Databases

To download complete copies of all of the plant metabolic pathway databases hosted by the PMN, including AraCyc, PlantCyc, CornCyc, etc., 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.

 Tab-delimited text files 

  • Pathways ("nnn"cyc_pathways.yyyy.mm.dd)
  • 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:

  • ZmarinaCyc Enzymes
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  • VcarteriCyc Enzymes
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  • TparvulaCyc Enzymes
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  • SweetorangeCyc Enzymes
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  • SviridisCyc Enzymes
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  • SugarbeetCyc Enzymes
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  • SoleraceaCyc Enzymes
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  • RedsageCyc Enzymes
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  • RedcloverCyc Enzymes
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  • PpersicaCyc Enzymes
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  • PineappleCyc Enzymes
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  • OthomaeumCyc Enzymes
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  • OrufipogonCyc Enzymes
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  • OpunctataCyc Enzymes
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  • OlucimarinusCyc Enzymes
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  • OilseedrapeCyc Enzymes
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  • OglaberrimaCyc Enzymes
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  • ObrachyanthaCyc Enzymes
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  • Ntabacum_Tn90Cyc Enzymes
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  • MtruncatulaCyc Enzymes
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  • MpusillaCyc Enzymes
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  • MguttatusCyc Enzymes
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  • MdomesticaCyc Enzymes
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  • McommodaCyc Enzymes
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  • LperrieriCyc Enzymes
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  • LjaponicusCyc Enzymes
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  • KlaxifloraCyc Enzymes
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  • GraimondiiCyc Enzymes
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  • Fvesca_VescaCyc Enzymes
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  • FlaxCyc Enzymes
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  • EsalsugineumCyc Enzymes
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  • EgrandisCyc Enzymes
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  • CucumberCyc Enzymes
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  • CsubellipsoideaCyc Enzymes
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  • Csativa_PkCyc Enzymes
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  • CrubellaCyc Enzymes
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  • CroseusCyc Enzymes
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  • CommonbeanCyc Enzymes
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  • CocoaCyc Enzymes
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  • ClementineCyc Enzymes
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  • CgrandifloraCyc Enzymes
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  • CastorbeanCyc Enzymes
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  • CarrotCyc Enzymes
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  • Carietinum_Icc4958Cyc Enzymes
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  • BstrictaCyc Enzymes
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  • BreadwheatCyc Enzymes
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  • Brapa_FpscCyc Enzymes
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  • Boleracea_OleraceaCyc Enzymes
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  • Boleracea_CapitataCyc Enzymes
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  • BananaCyc Enzymes
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  • AmborellaCyc Enzymes
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  • AlyrataCyc Enzymes
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  • AhypochondriacusCyc Enzymes
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  • AhalleriCyc Enzymes
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  • WheatDCyc Enzymes
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  • WheatACyc Enzymes
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  • TomatoCyc Enzymes
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  • SwitchgrassCyc Enzymes
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  • SpirodelaCyc Enzymes
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  • SoyCyc Enzymes
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  • SorghumBicolorCyc Enzymes
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  • SetariaCyc Enzymes
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  • SelaginellaCyc Enzymes
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  • PotatoCyc Enzymes
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  • PoplarCyc Enzymes
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  • PapayaCyc Enzymes
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  • OryzaCyc Enzymes
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  • MossCyc Enzymes
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  • Grape Enzymes
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  • CornCyc Enzymes
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  • ChlamyCyc Enzymes
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  • ChineseCabbageCyc Enzymes
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  • CassavaCyc Enzymes
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  • BrachypodiumCyc Enzymes
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  • BarleyCyc Enzymes
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  • AraCyc Enzymes
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  • PlantCyc Enzymes
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  • Reference Enzymes (3.1)
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    Archived PMN BLAST datasets are also available.

     

    The PMN has also generated several lists of pathways that are used to help expedite the validation process when generating new single-species databases. These Semi-Automated Validation and Integration (SAVI) lists are updated during the preparation of each new PMN release.

    Current and archived SAVI pathway lists are available to download including:

    The original NPP and UPP SAVI lists were reviewed by members of the PMN Editorial Board. The remainder of the lists are still awaiting external validation.

    Additional feedback from users is very welcome.


    E2P2 enzyme function annotation software

    Ensemble-based Enzyme Prediction Program (E2P2) predicts metabolic enzymes in a sequenced genome.

    README
    Download Software

    SAVI pathway validation software

    Semi-Automated Validation Infrastructure (SAVI) processes predicted metabolic pathways using pathway meta data such as taxonomic distribution and key reactions and makes decisions about which pathways to keep, remove, or subject to manual validation. More info

    README
    Download Software

    PlantClusterFinder

    A pipeline to predict metabolic gene clusters from plant genomes

    README
    Download Software

    API

    PerlCyc and JavaCyc can be used to access internal Pathway Tools functions by Perl and Java scripts. The two packages were originally developed by TAIR, and are currently maintained by the SGN (Sol Genomics Network). Please contact Lukas Mueller (lam87_at_cornell.edu) at the SGN with any questions.

    JavaCyc

    Javacyc is a java class for accessing internal Pathway-Tools functions.

    Download javacyc
    PerlCyc

    Perlcyc.pm is a Perl module for accessing internal Pathway-Tools functions.

    Download perlcyc

    The PMN is funded by the National Science Foundation (Grant #: 1546838, 1026003 and 0640769) and the Department of Energy (BER Grant #:  ER65472 ), governed by an Editorial Board composed of internationally renowned scientists, and executed at the Carnegie Institution for Science, Department of Plant Biology.