[InterMine Dev] gene_ontology_edit.obo
hitz at stanford.edu
Wed Feb 22 21:11:59 GMT 2012
> We load the ontology file from here..
> 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"
> 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.
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** hitz at stanford.edu
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