PMN Release 8.0 Update

November 2013
Release Information: 

Following our initial release in June 2013, we were pleased to add PlantCyc 8.0 to the complete release in July 2013. It includes data from the 17 species-specific databases, plus information on enzymes and pathways from over 300 additional plant species.

Also in July of 2013, we released updated versions of AraCyc (11.5), ChlamyCyc (3.5), and CornCyc (3.5). We removed proteins from previous releases that were no longer associated to any reactions, to complete the process of annotation updates.
In November 2013, we are releasing an updated version of CornCyc (v.4.0). We identified and fixed a technical data-processing error and added missing components to CornCyc, including 24 new pathways, 839 new enzymes, and 173 new reactions.

The data content of all eighteen databases are described on our Content Statistics page while the data sources and methods for each database's contruction are listed on the Databases Overview page

Past releases are described in the Release Notes Archives and Databases Overview Archives


Overall Highlights: 

The PMN 8.0 release includes seven NEWLY created databases for several important monocots, including rice, barley, sorghum, switchgrass (Panicum virgatum), Setaria italica, Brachypodium distachyon, as well as another member of the Brassicaceae family, Brassica rapa ssp. pekinensis, also known as Chinese cabbage. 

We also have completely rebuilt databases for seven phylogenetically diverse species including moss, Selaginella, grape, cassava, and poplar and we have significantly revised and updated AraCyc, CornCyc, and ChlamyCyc

Our computational predictions of enzyme functions in PMN 8.0 are based on an enhanced Ensemble Enzyme Prediction Pipeline (E2P2 v.2.0) that can cover a significantly greater reaction space. And our final database construction relies upon a pathway-level Semi-Automated Validation and Integration (SAVI) refinement process. 

We also moved from using loci (e.g. At2g44990) in AraCyc 10.0 to using gene models (splice variants) (e.g.At2g44990.1) in AraCyc 11.0. For all cases in which a locus in AraCyc 10.0 only had one corresponding splice variant in AraCyc 11.0, all of the previous experimental annotations of enzyme function were transferred to the single splice variant. For loci with more than one splice variant in AraCyc 11.0, the experimental data were transferred to the "representative" gene model (splice variant). Representative gene models are selected by TAIR and typically have the longest coding region. 

PlantCyc 8.0 currently houses over 180,000 proteins and over 1000 metabolic pathways.
PlantCyc 8.0 now contains all of the enzymes present in each of the 17 species-specific databases. Earlier versions of PlantCyc only included enzymes associated with pathways from the species-specific databases. 

All of the PMN databases can now be explored using the updated 16.5 version of the Pathway Tools software.

We hope that these enhanced resources will be useful to researchers, educators, and students who want to learn more about plant metabolism!

Noteworthy new manually curated pathways: 
  • Three types of C4 photosynthesis are present among our many species including NAD-ME in switchgrass, NADP-ME in sorghum, and PEPCK in corn.

Enzymes required to produce (+)-5-deoxystrigol, a branching-promoting strigolactone are described for rice and arabidopsis

The synthesis of gramine, a simple indole alkaloid, can help barley protect itself from pests.

Betulinic acid, a hydroxyl pentacyclic triterpenoic acid with anti-tumor activity and other medicinal activities is produced in grape.

Noteworthy new software features: 
  • Examine your transcriptomic, proteomic, or metabolomic data directly on a pathway page by choosing the Pathway --> Customize Pathway Diagram option.
  • Get a data report table when you overlay your Omics data on the Metabolic Overview using the Show Data selector.
  • Track your favorite oxygen, sulfur, or other part of a chemical compound through many reactions using the new atom mapping feature.
Collaborator Release Notes: 

You can find more information on the releases provided by our collaborators at MetaCyc, the multi-species, multi-kingdom database, in their Release Notes