Load Gene Annotation

The gene annotations information can be downloaded from Ensembl Plant.

The download link can be found at Ensembl Plant Wheat or Barley under "Gene anotation" heading.

For May 2018 the file can be found at Wheat Release 39 or Barley Release 39.

1. The first step is to create an entry in the assemblies table.

   INSERT INTO assemblies (assembly_name, description, data_public_flag) values ("TGACv1", "IWGSC.39", "Triticum aestivum", 1)

2. The upload script (get_gene_annotation_wheat.php or get_gene_annotation_barley.php) generates a file which is loaded with the MySQL command.

   LOAD DATA INFILE '/var/lib/mysql-files/Triticum_aestivum.TGACv1.39.gff3.load' into table gene_annotations (type, bin, start, stop, gene_id, gene_name, assembly_name, gene_reference, description, uniprot);

Ensembl Plant has releases every 2-4 months.

The release intentions for July 2018 can be found at Release 40.