We are pleased to announce the release of PMN 15.5! In this release, twenty-five of our databases have been regenerated using updated genome assemblies. We have also updated our backend to Pathway Tools 26.0 and made minor fixes to several databases (fixed broken links, etc.).
We are pleased to announce the release of PMN 15. This release includes a new species, new features, and fixes to existing species:
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.
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:
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.
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.
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,
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.
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.
