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[gofriends] GO ontology in OWL format

markov at mpiz-koeln.mpg.de markov at mpiz-koeln.mpg.de
Wed Sep 12 08:16:38 PDT 2007


Hi list,

I'm new here and hope this is the appropriate list for this question. If
you know of a better list for it, please tell me.

I am trying to load the GO ontology, including annotations (synonyms,
etc.) as well as is_a and part_of relationships, into a Sesame 2.0
repository. Seems that it should be a common enough task to have an easy
solution -- perhaps somebody has done this successfully? Anyway, here's
what I've tried.

To get the data into the Sesame repository, I am using the
(RDFFormat.)RDF-XML format choice, since the other options are N3, Turtle,
TRIG, TRIX, N Triples (which I'm not too familiar with myself but assume
GO comes in none of these).

If I use the GO .rdf-xml files from their download page, ironically, I get
errors that disappear when using the .owl files. Namely, I get "<rdf:RDF>
is not allowed as a property element", and if I replace this tag in the
data file with the OWL equivalent, <owl:OWL> or whatever, I get further
problems.

The .owl termdb file on the ftp download
(ftp://ftp.geneontology.org/pub/go/godatabase/archive/) works (or rather
worked; the archive put up on Sept 11 2007 gives unzip errors, something
like "can't find end of file"). However, this file does not contain any
is_a or part_of, just the annotations. There is no other relevant .owl
file.

The .obo termdb file, as well as the .rdf-xml termdb file, include the
is_a and part_of. Therefore I tried to use the obo2owl perl thingy to
conert the .obo into an owl file. However I get "format problem detected"
about 62353 lines into the file, on some very long GO term name.

Finally I downloaded OBO-Edit and tried to use the OWL plugin (mentioned
here:
http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page#OboEdit_OWL_plugin)
to convert obo to owl. However, putting the plugin files into the
extensions directory (as per the instructions) resulted in a series of
NullPointerErrors that prevented OBO-Edit from starting up. Without the
plugin, OBO-Edit works fine.

Cheers,

Maria Markov



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