PMN Release 9.0

September 2014
Release Information: 

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 9.0 release completely rebuilt databases for twelve phylogenetically diverse species including moss, Selaginella, barley, Brachypodium, grape, cassava, Chinese cabbage, papaya, poplar, setaria, sorghum and switchgrass. We have significantly revised and updated AraCyc, CornCyc, ChlamyCyc, OryzaCyc and SoyCyc

Our computational predictions of enzyme functions in PMN 9.0 are based on an enhanced Ensemble Enzyme Prediction Pipeline (E2P2 v2.1) that can cover a significantly greater reaction space and reduce false positive enzyme predictions. Our final database construction relies upon a pathway-level Semi-Automated Validation and Integration (SAVI v3.02) refinement process. 

PlantCyc 9.0 currently houses over 180,000 proteins and over 1000 metabolic pathways.

All of the PMN databases can now be explored using the updated 17.5 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 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