Recent News

PMN 11.0 released!

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.

PMN 10.0 released!

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.

PlantCyc 9.5 and PapayaCyc 3.5 release

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). 

PMN 9.0 provides enhanced predictions of enzymes, reactions and pathways!

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.

PlantCyc 8.0 joins 17 species-specific databases at the PMN: Grasses galore and much more!

Grasses galore and much more! 

We continue to roll out our PMN 8 release that started in June: 

New additions:

Released in June 2013:
Seven new databases:

Seven updated databases:

Plus explore new software features for data display and analysis at the PMN website.

PMN 8.0 provides 17 species: Grasses galore and much more!

Grasses galore and much more! 

Seven new databases:

Ten updated databases:

Plus explore new software features for data display and analysis at the PMN website.

Get your data groove going with Groups!

Get the data you want in the format you need using the Groups functions at the PMN. 

* Got a list of up-regulated genes?

* Want to know all of the compounds present in the pathways they act in?

* Need to get their structures in SMILES or InChi format?

Then get going with PMN Groups

Simply register for free and then watch for opportunities to turn your search results into data-rich Groups.

Come see the PMN at PAG in January

The PMN invites you to come to our workshop at the Plant and Animals Genome Conference (PAG XXI) on Sunday, January 13 in San Diego. 

The PMN, the Sol Genomics Network (SolCyc), and PMN users will present an overview of our databases and examples of their applications to ongoing research.

Early registration ends on November 1.

We hope to see you there! 
Or you can download the presentation to view on your computer. 

Finding your favorite gene in AraCyc just got easier!

Now you're doubly likely to find Arabidopsis genes using

  • AGI locus codes (e.g. AT4G33030)

AND

  • Gene symbols (e.g. SQD1)

because the PMN has loaded the latest set of gene "symbols" from TAIR into AraCyc

Now over 4600 symbols are linked to over 3100 genes!

We hope this will make it easier than ever to find your favorite metabolic genes in AraCyc!

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