Table of Contents

• Website
• Genome Release Notes
• Pathways Release Notes
  • Pathway Projections Summary Table
• Infrastructure

#Genomes Release Notes

See full details in release notes for build 56. New data in release 56b is limited to Pathways.

# Pathways

Release 56b contains 22 newly curated and 3 revised pathways from reference species rice (O. sativa). The hierarchical list of pathways has been updated accordingly.

Newly curated pathways:

• Reproductive structure development
• Anther and pollen Development
• Vegetative structure development
• Primary root development
• Response to submergence
• Underwater shoot and internode elongation
• Response to phosphate deficiency
• Photorespiration
• Ureide biosynthesis
• Beta-alanine betaine biosynthesis
• Proline biosynthesis V from arginine
• Phospholipid biosynthesis I
• Sphingolipid metabolism
• Response to iron deficiency
• Mugineic acid biosynthesis
• Iron uptake and transport in root vascular system
• Proline degradation
• Glutamate degradation
• Phenylalanine degradation III
• Lysine degradation II
• Threonine degradation

Revised pathways:

• Cardiolipin biosynthesis
• Ent-kaurene biosynthesis
• Responses to stimuli

Pathway Projections (8 new species included)

The Plant Reactome has expanded gene homology-based pathway projections to 74 plant species. Newly projected species include garden cucumber (Cucumis sativus), white yam (Dioscorea rotundata), sunflower (Helianthus annuus), white jute (Corchorus capsularis), blue lupin (Lupinus angustifolius), coyote tobacco (Nicotiana attenuata), Irish moss (Chondrus crispus), and an extremophilic unicellular species of red algae Galdieria sulphuraria (capable of photosynthesis as well as heterotrophic growth by utilizing ~50 different extracellular carbon sources).

In addition, we have revised pathway projections (converted from Inparanoid to Compara orthology) for three species: a wild South American cotton (Gossypium raimondii), cassava (Manihot esculenta), and common bean (Phaseolus vulgaris). Notable updated Compara orthology data has been kindly provided by Ensembl for updated species.

Pathway Projection Statistics and Status (new/updated)

• *data from sequenced transcriptomes
• ^ projections currently exclude cell-cycle pathways and annotations
• Planteome Inparanoid data was kindly provided by the Planteome project
• When available the outgoing links from gene product IDs mapped to reactions are always hyperlinked to respective entries in collaborator databases/online resources

NOTE: The pathway counts for both reference and projected species include a few organizational “container” names, such as “Hormone biosyntheses” and “Metabolism”. Additionally, the bulk of the projected pathways occur in the areas of metabolic and regulatory function, whereas the rice reference data set has additional pathways related to cell cycle functions. We are not currently using these additional pathways as a source for orthology projection. Visit the Download page to access the updated data files associated with pathways, reactions, gene products, metabolites and external reference sources such as ChEBI, Ensembl, and UniProt.

New Functionalities: 

Expanded Reference Species Gene Name listings

Additional and alternate O. sativa gene names are now visible under the Molecules tab when viewing rice pathways.

Interactor Overlays

Users can display gene-gene interaction data on Plant Reactome pathways either by choosing a publicly-available dataset under “Interactor Overlay”, or by uploading a dataset of their choice. This feature can aid researchers by extending the network of known complexes and pathways with candidate proteins. The Plant Reactome team has specifically provided locally-hosted interaction data for A. thaliana (courtesy of the Planteome project). This data can be viewed by selecting “Plant Interactome” on the Interactor Overlay panel and A. thaliana on the species selector.

* "Cyc" Pathways

• BioCyc-based pathway databases on Pathway Tools ver. 19.0 are available from a virtual server hosted at CyVerse. Summary tables for the Cyc pathway databases created by Gramene is available in release 46 notes.

* Ontologies Release Notes

• No updates in this release. Last update done in release 31 (May 2010). A summary of ontologies data was last provided in release 46.

# Infrastructure

Web Services: Gramene's web services page documents many ways to directly connect to and analyze our databases.

Public MySQL Server

Our partner Ensembl Genomes offers a public, read-only MySQL server with copies of the species-specific and comparative genomic databases that we use. To use this with the mysql command-line client:

$ mysql -hmysql-eg-publicsql.ebi.ac.uk -P4157 -uanonymous

Please note that the versioning scheme used at this public database differs from ours; Gramene's release 56_91 is set as version 38_91 at Ensembl.