Web Services

Public Read-only MySQL Database 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 48_82 is set as version 29_82.

Gramene offers 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

Programmatic access over http

We have deployed an API using swagger to support searching Gramene's gene annotations at data.gramene.org.

In addition to the automatic documentation here are some example queries:

Search for the "NAC001" gene by keyword

http://data.gramene.org/genes?q=NAC001&fl=_id,name,biotype,species,location

Search for GO terms containing the keyword "NADP"

http://data.gramene.org/GO?q=NADP

Retrieve gene structure annotation from the Ensembl API

http://data.gramene.org/ensembl/lookup/id/AT3G52430?content-type=application/json;expand=1

Explore the Plant Reactome pathway hierarchy for Oryza sativa (XML)

http://data.gramene.org/reactome/pathwayHierarchy/oryza+sativa