Table of Contents

• Website
• Genome Release Notes
• Pathways Release Notes
• Infrastructure

#Website

In this release we have moved the gramene homepage to our integrated search interface. Blog content and other static pages have been moved to news.gramene.org so they can be displayed within the new interface.

See also legacy data in Gramene's Archive.

#Genomes Release Notes

• Updated genomes
  • New genome and genebuild for Sorghum bicolor (sorghum V2)
• New data
  • New variation data for Triticum aestivum (wheat)
  • New Oryza sativa Japonica (rice) QTL data from the Q-TARO database
• Updated data
  • Updated genebuild (including new gene descriptions) for Zea mays (B73 maize RefGen_V4)
  • Reincorporated Japonica rice SSR/RFLP and QTLs from Gramene's archives remapped to IRGSPv1
  • Updated protein features from InterPro
  • Updated peptide comparative genomics
  • Updated gene and variation BioMarts
• Updated software
  • Updated to Ensembl 88 software

Genomes

Genetic and Structural Variation

New and updated genetic variation data for Japonica rice was incorporated to the Oryza sativa Japonica genome browser. Legacy rice SSR/RFLP markers and QTLs from Gramene's archives, as well as QTLs from the Q-TARO database were remapped to IRGSPv1 coordinates by the KeyGene coorporation.

Compara

Gene Trees

• The EnsemblCompara GeneTree database was updated to include updated barley, sorghum, corn and wheat. A total of 61,696 GeneTree families were constructed comprising 1,457,923 individual genes (1,618,436 input proteins) from 44 plant genomes (and 5 non-plant outgroups).

Putative Split Genes

• Split gene predictions were updated in this release and are available from Gramene's FTP site.

Synteny

• No updates in this release. Last update done in release 52 (November 2016).

WGA and other nucleotide alignments

• No updates in this release. Last update done in release 52 (November 2016).

Protein Annotation, Go, Xref Protein domain information was updated based on the latest InterProScan analysis.

Mart

• New Plant Gene and Plant Variation Marts

# Pathways

Plant Reactome software platform

The Plant Reactome underwent a major software, user interface and functionality upgrade: 

• Upgraded to the Reactome v3.3 platform, which includes a new Neo4j graph database and a new Fireworks hierarchical graph display of pathways
• Improved visualization of uploaded Omics data, capabilities to import gene-gene interaction data from external resources for overlaying on pathway diagram and including them in analysis, and comparative pathway analysis between the reference and projected species.
• Supports display of gene expression profiles in the context of pathways accessed remotely from the EMBL-EBI gene expression ATLAS.
• Added ContentService and AnalysisService data APIs that allow direct RESTful access to Plant Reactome data.
• Implemented DiagramJs and FireworksJs graphical widget APIs for users to embed interactive pathway navigation in their web sites.
• Implemented a revised Solr Search data index and search results layout.
• All data objects carry stable IDs for cross-referencing.
• Plant Reactome data and diagrams are now integrated with Gramene’s new search interface mentioned above.

The Plant Reactome database was built in collaboration with the Human Reactome project.

Pathway Curation

• Revision made to set the top-level pathways as Cellular Processes, Circadian Rhythm, Metabolism & Regulation, Response to Stress, and Inflorescence Development (for Fireworks utility).

Pathway Projection Statistics and Status

• Last update release 52 (November 2016). See release 52 notes for a table of pathway projection counts, data source and methods.

"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 offer 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 53_88 is set as version 35_88.

Gramene currently a legacy public, read-only MySQL server for release 40 of our databases. You can connect to the host "gramenedb.gramene.org" with the password "gramene," e.g.:

mysql -hgramenedb.gramene.org -pgramene