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After install chado schema:

Load the yeast sample data

Per instructions: get the yeast file from ftp://ftp.yeastgenome.org/pub/yeast/data_download/chromosomal_feature/saccharomyces_cerevisiae.gff. cd to my downloads directory and do

gmod_bulk_load_gff3.pl —organism yeast —gfffile saccharomyces_cerevisiae.gff

gmod_bulk_load_gff3.pl was installed in /usr/bin, so it can be run from anywhere. Messages during load (with comments/questions):

(Re)creating the uniquename cache in the database…
Creating table…

What table is being created? Chado installation already created a zillion tables.

Populating table…
Creating indexes…Done.
Preparing data for inserting into the chado_trial database
(This may take a while …)

This GFF file has CDS and/or UTR features that do not belong to a
‘central dogma’ gene (ie, gene/transcript/CDS). The features of
this type are being stored in the database as is.

Should be interesting to look at these.

Loading data into feature table …
Loading data into featureloc table …
Loading data into feature_relationship table …
Loading data into featureprop table …
Loading data into feature_cvterm table …
Loading data into synonym table …
Loading data into feature_synonym table …
Loading data into dbxref table …
Loading data into feature_dbxref table …
Skipping analysisfeature table since the load file is empty…

TestChado.png