[Bioperl-l] GO categories and load_ontology.pl
Annie.Law at nrc-cnrc.gc.ca
Wed Mar 17 11:50:07 EST 2004
I have used the load_ontology.pl script and bioperl-db to load GO
information into a database.
The input for this script includes the GO.defs file and each of the files
representing each of the ontologies ie.
Molecular function, biological process, and cellular component.
All of this information is loaded into the table called 'term' in the
It seems that most of the Entries in the term table are of Ontoloy Id = 1
(Gene ontology) and only around 200 entries molecular function, biological
process, and cellular component put together when there are about 16000
entries in the term table.
This is only true if I load locuslink into the database. If I don't load
locuslink into the database then all of the entries
In the database are of Ontology Id 1.
When the data is being entered into the database it is already known which
GO category the GO identifer fits into.
I need to know which category the GO id belongs to. I would appreciate
some ideas on how I can get this information.
Is there an option in the script that I can use maybe theres another table
somewhere that has this information??
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