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[software-group] Admin group update

Benjamin Hitz hitz at genome.Stanford.EDU
Wed Jan 30 16:19:09 PST 2008

So, I just thought I would give everyone an update on what the  
Stanford GO admin group (me) is up to.
With Stan leaving the group and a big SGD schema upgrade due to start  
soon, I will probably try to tie up these ends and drop back to pure  
maintenance for the go-loading and other admin tasks.

This is in rough order of (my) priority.  I would hope to wrap all  
this up in Februrary.

1) Waiting for Amigo release to be blessed so I can put it on the dev  
server, then production

2) Testing a new sequence loading script for go-full which loads all  
Uniprot, and has a smaller memory footprint.  Maybe a little faster too.

3) Final testing of bulk loading of associations

4) Making some modifications to output ref-genome specific fasta files

5) An idea Mike had recently to all "partial" IEAs to golite.  We  
looked at the numbers and if we skip loading IEAs for every file  
EXCEPT goa_uniprot and goa_pdb (i.e., the "mixed species" files) we  
will only double the number of associations in golite, and get all  
the ref genomes + human, + other "MOD" IEAs.  If Amigo can handle  
this database size effeciently, we are going to float this to the GOC.

Any thoughts from the software group on 5?


Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Stanford University ** hitz at

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