[InterMine Dev] gene_ontology_edit.obo

Benjamin Hitz hitz at stanford.edu
Wed Feb 22 21:11:59 GMT 2012

> We load the ontology file from here..
> http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/ontology/gene_ontology_edit.obo
> It takes about 7 minutes to load it on our production server..
> setenv ANT_OPTS "-server -XX:MaxPermSize=256m -Xmx10000m -XX:+UseParallelGC -Xms1800m -XX:SoftRefLRUPoli
> cyMSPerMB=1 -XX:MaxHeapFreeRatio=99"

And JD:
> A follow up on that problem I've been having about > 40 min loading times for the GO source.  It was because I was loading a version with part_of and intersection_of relationships.  Choosing a version without these features pushed that down to around 6 minutes.

The file in CVS Kalpana posted is identical to the one on the GO.downloads.ontology.shtml page: http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo
I believe the GOC decided to not use the "edit" file format syntax for "external users" to prevent confusion.

The "ext" version that JD loaded has ALL the relationships.  As a practical matter, most MOD dbs don't bother with the full EXT version, although I think GO mine probably should.


Ben Hitz 
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** hitz at stanford.edu

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