ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

Rice DB can search and display Gene Ontology plant slim terms (GO Slim) as annotated by MSU for Oryza sativa, based on TAIR annotations of orthologous genes in Gramene.

Rice DB downloads these assignments from the latest version of Michigan State University’s Rice Genome Annotation Project (MSU RGAP http://rice.plantbiology.msu.edu/) based on Gramene http://www.gramene.org/plant_ontology/. The slimmed ontology terms come from the Gene Ontology Consortium (GO http://www.geneontology.org/), as do the evidence codes.

Usage When Searching Rice DB Usage Viewing Rice DB Results
  • Searching for one or more GO:xxx IDs will return a list of all annotated TIGR IDs.
  • Full text searches will match GO Plant Slim terms and return a list of all annotated TIGR IDs.
  • TIGR IDs can be resolved to GO IDs.
  • GO terms can be shown for any TIGR ID.
Example: get GOSlim annotations for LOC_Os07g18120.1
Example: get GO IDs for LOC_Os07g18120.1

Imported Vocabulary Stats

Information about the meaning of these data can be found at the Gene Ontology website:

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System Information

Transcript of last update

Opened FTP connection ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/
Entering local passive mode for FTP
Official version is version_7.0
Loading MSU GO Slim assignments version_7.0
Using existing file /var/folders/75/983jwhw537q11ck7b_b0zwf80000gn/T/RiceDB/GOSlim_/all.GOSlim_assignment