On Mar 26, 2009, at 1:41 PM, Michel_Dumontier wrote:
I found it with the EBI's OLS service
http://www.ebi.ac.uk/ontology-lookup/
oh, I was going to ask - what tool should we use for obo2owl nowadays?
Use the pre-generated OWL files linked from the obofoundry.org webpages
If you want to do a conversion yourself (i.e. on a locally modified
obo file), you can use the REST-ish converter
http://www.berkeleybop.org/obo-conv.cgi
The results should be identical to the pre-generated ones
If you want you run this locally, you can download the xslt.
A few caveats
- this generates purl.org/obo URLs. At some point in the future these
will become weakly deprecated and we will move towards
purl.obofoundry.org URLs. There will be an interim period where we
support both schemes at each URL, and equivalence axioms (possibly as
a separate bridge file).
- XSLT doesn't scale well. If you want to convert ncbi_taxonomy.obo
you'll need a lot of memory. At some point the XSLT will be abandoned
in favour of the java OBO-API, which has a partially implemented
bridge to the OWL API. If you want to be a bleeding edge user you can
try this.
- The current mapping faithfully preserves all terminological metadata
using the n-ary relations pattern. This introduces extra instances
that look odd in some tools and may degrade the performance of some
reasoners. The java converter gives you flexibility regarding whether
you want to preserve or discard this metadata. When OWL2 is
established the official mapping will switch to using axiom
annotations instead of the n-ary relations pattern.
-=Michel=-
-----Original Message-----
From: [email protected] [mailto:public-semweb-
[email protected]] On Behalf Of Chris Mungall
Sent: Thursday, March 26, 2009 4:35 PM
To: Michel_Dumontier
Cc: Kei Cheung; W3C HCLSIG hcls; Matthias Samwald
Subject: Re: blog: semantic dissonance in uniprot
On Mar 26, 2009, at 8:33 AM, Michel_Dumontier wrote:
The Gene Ontology says a Protein (GO:0003675) is a Thing (the entity
was removed, but then later added so the identifier wouldn't be
reused)
More accurately: very early versions of the GO had a term named
"protein", but this was obsoleted because it was out of scope for the
GO. The term was obsoleted, but a historic record is maintained. GO
does not intend to say "protein is_a thing", what you are seeing is
probably an artefact of the translation of obsoletion metadata to
OWL.
