Recent News

Mar
15
2022

PMN Downtime March 15

By Charles Hawkins

Update 2: The PMN databases are now back up. We thank you for your patience during the move.

Update: Due to unexpected difficulties with the server move, PMN downtime has been extended into March 16th. We expect to have PMN back up later today. We again apologize for the inconvenience.

Original Post: Due to a server move, pmn.plantcyc.org (the part of the site that contains the databases), will be down for part or all of March 15th. We apologize for the inconvenience.

Jan
12
2021

PMN 15.0 Released!

By Administrator

We are pleased to announce the release of PMN 15. This release includes a new species, new features, and fixes to existing species:

  • We have released a new pathway genome database, StoraCyc, for the legume Senna tora
  • PMN now uses Pathway Tools 24.0, with new features that include:
    • All pathways that include transport between subcellular compartments are now shown with the compounds moving across the membranes. For example, the glutamate-glutamine shuttle in AraCyc
    • You can now pull up a SmartTable of all pathways, reactions, etc. for an organism right from the organism info page (e.g. this page for AraCyc) by clicking the orange SmartTable buttons next to the database statistics
  • The previous release of OryzaCyc erroneously included old enzyme data alongside the current data. The old data has now been removed
Jul
08
2020

Downtime - July 8th

By Administrator

PMN Databases will be offline on July 8th due to datacenter maintenance

Apr
07
2020

New feature: Metabolic Cluster Viewer

By Administrator

We are pleased to announce the launch of a new website feature, the Metabolic Cluster Viewer. We have run our PlantClusterFinder software on nine of the PMN species' genomes, and the Cluster Viewer allows you to search and view the results without having to download and run the cluster finder yourself. The species currently available are Arabidopsis thaliana, Glycine max (soybean), Medicago truncatula (wild relative of alfalfa), Oryza sativa (rice), Populus trichocarpa (poplar), Senna tora (a wild legume), Solanum lycopersicum (tomato), Vitis vinifera (grape), and Zea mays (maize).

The tool will show a gene diagram of the cluster and a list of genes, with EC numbers and Metacyc IDs of catalyzed reactions and GO terms for each gene. It will also show co-expression data of the genes from the ATTED-II database if available.

The Cluster Viewer can be accessed from the PMN Data menu under PMN Tools, where BLAST has also been moved.

Feb
05
2020

PMN 14.0 released!

By Administrator

We are pleased to announce the PMN14 release. In this release we introduce 25 new organism-specific metabolic pathway databases, which brings the total number of organism pathway databases to 125!  New species include ten crops, six wild crop-relatives, three ornamentals, two oak trees, a model plant, our first gymnosperm, our first parasitic plant, and a green alga.

Arabidopsis thaliana Landsberg, Cajanus cajan (pigeon pea),  Camellia sinensis (tea), Chlorella variabilis (a green alga), Citrullus lanatus (watermelon), Cucumis melo (Cantaloupe, Honeydew, and related melons),  Cuscuta campestris (a parasitic plant), Elaeis guineensis (African oil palm), Ginkgo biloba, Hevea brasiliensis (rubber tree), Lactuca sativa (lettuce), Musa balbisiana (a wild banana), Nelumbo nuficera (sacred lotus), Oryza barthii (African wild rice), Oryza longistaminanta (another wild rice), Oryza meridionalis (Australian wild rice), Oryza nivara (still another wild rice), Phoenix dactylifera (date palm), Phyllostachys edulis (Moso bamboo), Prunis avium (cherry), Pyrus communis (European pear), Quercus lobata (valley oak), Quercus suber (cork oak), Saccharum spontanaeum (wild sugar cane), and Tarenaya hassleriana (Spider flower).

The full list of 125 species and details of the database constructions can be found here.

We have also updated the pan-plant pathway database PlantCyc (version 14.0). The PlantCyc database includes only literature-curated enzymes and pathways, including from species that do not have a full genome database in PMN.  

Please note that the following 8 databases were constructed or updated from genome releases which are under prepublication data usage restrictions:

AhalleriCyc (Arabidopsis halleri), CashewCyc (Anacardium occidentale), CommonbeanCyc (Phaseolus vulgaris), MsinensisCyc (Miscanthus sinensis), PhalliiCyc (Panicum hallii), SfallaxCyc (Sphagnum fallax), SviridisCyc (Setaria viridis), SwitchgrassCyc (Panicum virgatum). Please see detailed data policy at the corresponding species pages from Phytozome (v12.1).

Jul
12
2018

PMN13.0 released!

By Administrator

We are pleased to announce the PMN13 release. In this release we introduce 24 new organism-specific metabolic pathway databases, which brings the total number of organism pathway databases to 100!  New species include nine crops, two medicinal plants, four ornamental plants, two wild relatives of domesticated crops, two grasses, a succulent, a basal eudicot, two lower plants and a green alga:

Anacardium occidentale (cashew); Asparagus officinalis (asparagus); Capsicum annuum (pepper); Chenopodium quinoa (quinoa); Corchorus capsularis (white jute); Dioscorea rotundata (white yam); Helianthus annuus (sun flower); Humulus lupulus (hop); Solanum melongena (eggplant); Calotropis gigantea (a medicinal plant); Camptotheca acuminata (a medicinal plant); Dianthus caryophyllus (carnation); Petunia axillaris (white petunia); Rosa chinensis (rose); Rosa multiflora (rose); Olea europaea (a wild olive); Solanum pennellii (a wild tomato); Miscanthus sinensis (Chinese silver grass); Panicum hallii (Hall's panicgrass); Kalanchoe fedtschenkoi (a succulent); Aquilegia coerulea (a basal eudicot); Sphagnum fallax (a moss); Marchantia polymorpha (a liverwort) and Chromochloris zofingiensis (a unicellular green alga).

 

The full list of 100 species and details of the database constructions can be found here.

We also updated the pan-plant pathway database PlantCyc (version 13.0). PlantCyc database now includes only literature-curated enzymes and pathways. Using the new virtual data integration feature (provided by Pathway Tools software version 21.5 and up), users can select up to 10 organism pathway databases from which their predicted enzymes will be displayed onto PlantCyc pathway diagrams.

 

Please note that the following 11 databases were constructed or updated from genome releases which are under prepublication data usage restrictions:

AcoeruleaCyc (Aquilegia coerulea), AhalleriCyc (Arabidopsis halleri), AhypochondriacusCyc (Amaranthus hypochondriacus), CashewCyc (Anacardium occidentale), CommonbeanCyc (Phaseolus vulgaris), MsinensisCyc (Miscanthus sinensis), PhalliiCyc (Panicum hallii), SfallaxCyc (Sphagnum fallax), SorghumbicolorCyc (Sorghum bicolor), SviridisCyc (Setaria viridis), SwitchgrassCyc (Panicum virgatum). Please see detailed data policy at the corresponding species pages from Phytozome (v12).

Apr
12
2018

PMN12.5 released

By Administrator

We are pleased to announce PMN12.5 release. In this release we added locus IDs to genes in all PMN databases. The locus IDs were extracted from public genome releases that were used in constructing the PMN metabolic pathway databases. Protein sequence IDs from the genome releases are associated with proteins. The locus IDs, along with protein sequence IDs, should greatly facilitate data query and usage. Additional data cleaning was done to several databases, most noticeably in AraCyc where we removed more than 140 redundant gene entries.

May
11
2017

PMN 12.0 released!

By Administrator

We are pleased to announce the PMN12 release. In this release we introduce 54 new species-specific metabolic pathway databases, which brings the total number of species-specific databases to 76.  The 76 species cover the green plant lineage widely, including green algae, a moss, a club moss, a basal flowering plant, and higher plants of monocots and eudicots. They include major crops from grains to vegetables and fruits. Several medicinal plants are also added to this release, such as Madagascar periwinkle (Catharanthus roseus), red sage (Salvia miltiorrhiza) and flax (Linum usitatissimum). The new release also expands the number of species in three plant families: 17 species in Poaceae, 13 in Brassicaceae and 6 in Fabaceae.

Examples of new species-specific metabolic pathway databases:

Bread wheat

Carrot

Spinach

Sweet orange

Sugar beet

Madagascar periwinkle

Please find complete list of databases here.

 

An important note about downloading complete PMN databases:

The following five databases were constructed from genome releases which are under prepublication data usage restrictions and thus can only be accessed by online searching and browsing at the PMN web site: AhalleriCyc (version 1.0) (Arabidopsis halleri), LperrieriCyc (1.0) (Leersia perrieri), ObrachyanthaCyc (1.0) (Oryza brachyantha), OpunctataCyc (1.0) (Oryza punctate), OrufipogonCyc (1.0) (Oryza rufipogon). Please see detailed data policy at the corresponding species page from Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html) or EnsemblPlants (http://plants.ensembl.org/index.html).

CornCyc (version 8.0) was constructed from the maize B73 RefGen_V4 genome release, which is also under prepublication data usage restrictions. We communicated with the genome release provider and was allowed to provide the PMN users full access to the CornCyc database, online browsing and complete download. However we ask that you respect the data usage restrictions posted on http://plants.ensembl.org/Zea_mays/Info/Index. The preprint of the maize B73 RefGen_V4 genome paper can be found at http://biorxiv.org/content/early/2016/12/19/079004.

 

Jun
02
2016

PMN 11.0 released!

By Administrator

We are pleased to announce the PMN11 release. Highlights include the addition of curated information of rate-limiting steps in over 50 pathways. To see an example, follow this link,

http://pmn.plantcyc.org/PLANT/NEW-IMAGE?type=PATHWAY&object=PWY-695

To see a complete list of pathways with rate-limiting info, follow this link,

http://pmn.plantcyc.org/group?id=pmn-prod.dpb.carnegiescience.edu-1-3673...

Clicking on any pathway from the SmartTable, you will see a pathway diagram where the rate-limiting reaction is indicated with an icon of hourglass. Mouse over the icon to see the literature source of the curated rate-limiting data. We will continue curating and adding available rate-limiting data from the literature.

In this release we removed additional data of macro-molecule metabolism from the PMN databases, including enzymes, reactions and pathways that metabolize or modify proteins, DNAs, and RNAs.

The PMN databases are now updated to the Pathway Tools 19.5 data schema.

Jun
05
2015

PMN 10.0 released!

By Administrator

We are pleased to announce the PMN10 release. In this release, we introduce 5 new metabolic pathway databases for species including tomato, potato, two diploid progenitors of the bread wheat, Aegilops tauschii  (D-genome) and Triticum Urartu (A-genome), and the great duckweed (Spirodela polyrhiza). We substantially updated the 17 existing species-specific databases and the multi-species database PlantCyc. PMN now hosts 23 databases in total.

The computational predictions of enzyme functions in PMN 10 are based on an enhanced Ensemble Enzyme Prediction Pipeline (E2P2 v3.0), with increased precision and a 62% increase of enzyme function space. We also made the following major changes to the scope and rules used in PMNs databases:

  1. To reinforce the PMNs focus on small molecule metabolism, enzymes that metabolize macromolecules such as serine protein kinase are excluded from the pathway databases.
  2. In our enzyme to reaction association, EC number-based enzyme predictions are transferred to distinct MetaCyc reaction IDs. To reduce false-positive associations, when multiple MetaCyc reactions exist for the same EC number, only the MetaCyc reaction corresponding to the official EC reaction is used for annotation.
  3. When multiple splice variants of a gene locus exist in a genome, only the protein sequence that represents the longest coding sequence is included in the pathway database.

Pages

  

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.