Jul
08
2020
Downtime - July 8th
By Administrator
PMN Databases will be offline on July 8th due to datacenter maintenance
PMN Databases will be offline on July 8th due to datacenter maintenance
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.
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).
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).
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.
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:
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.
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.
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:
We are pleased to announce PlantCyc 9.5, which fixes a bug in PlantCyc (version 9.0), which was released in September 5, 2014. This bug was caused by internal ID conflict affected only P. patens and C. papaya enzyme annotations in PlantCyc (9.0). Overall, the incorrect annotations accounted for about 2% of total enzyme annotations in PlantCyc (9.0). We have now fixed the problem in PlantCyc 9.5. Also released is an updated PapayaCyc 3.5 with new internal IDs.
PlantCyc 9.5 and PapayaCyc 3.5 will be available for download on our ftp site shortly (on Nov 7th).
We improved enzyme and reaction prediction using our new version Ensemble Enzyme Prediction Pipeline (E2P2 v2.1) and update all the 17 species-specific databases.
