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Thanks to Mark & calling all perl programmers

Chris Mungall cjm at fruitfly.bdgp.berkeley.edu
Thu Oct 5 21:17:54 PDT 2000


Three cheers for Mark Waugh for producing a schema diagram for the go
database, something we should have done ages ago (our schema diagrams are
all of the ephemeral whiteboard variety). John will put this up on the web
site and check it into the repository. Mark - would it be ok for you to
send the sybase-specific sql table/index creation commands, so we can
check these into the cvs repository?

Just to let everyone on gofriends know, the perl API for GO is an easy way
to write perl scripts for getting information from the GO database. the
API is currently at 'beta' stage, and is stable enough for you to write
programs against it. The 1.0 release will be on Oct27th, with the first
major tool, an ontology editor, following soon after.

have a look at 
ftp://ftp.geneontology.org/go/software/README
for instructions on how to install the perl interface.

*new* *new* *new*
there are now online docs for the API, see:
www.fruitfly.org/annot/go/database/modules/GO::AppHandle.html
(John - could you add this to the main db page?)

for examples on how to write scripts that use the perl interface see
ftp://ftp.geneontology.org/go/software/scripts/
[more to follow here]

all these scripts should run remotely, though they will be a little slow
just now, until the corba server is ready. if you find it's too slow you
can always install the database yourself; the API has been tested on both
MySQL and informix and should work on oracle/sybase no bother.

If anyone has programs or plans to write programs that use the go database
let us know and we can include them in the cvs repository or grant you an
account to play with the code already in there. A lot of us here have been
coding GO stuff on the side, we can't afford to spend as much time on this
as we'd like to. I know there's some good programmers out there so I'd
like to encourage you all to get in there and play with the code, any
improvements/comments/criticism welcome.

--
Chris


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