Exactly, Matthias.
This is why I say there should be some vetting of what's there and
decisions made as to what would be the most useful without causing
unwanted problems.
As I mention (and as Chris has in fact already made clear), most of
what is here can be fairly easily addressed (in the URI/URL sense)
via algorithmic means.
Both you and Chris point out - not all of what is here would be
sensible to "mix in" to the growing, high-value NeuroCommons (NC [1])
repository.
My point in bringing it up is this is a rich source of OWL (possibly
not of RDF, as Chris points out) of immediate relevance to
bioinformatics - and some of it very specific relevance to the goals
we've had in HCLS.
It would be silly to not give it a thorough vetting, at this stage.
One thing I would add is, as I assume the OWL versions of OBO
ontologies are derived from the OBO2OWL translater(s), we should take
a look at some of the details of what that produces. We may be able
to provide some advice on how to make to results more useful - or
find out from the OBO folks how its intended to be used, when that is
not obvious. One of the things I'm having trouble with right now is
the form that OBO ontology entity definitions are provided in these
OWL translations [2]
Cheers,
Bill
[1] sorry for the unannouced acronym, Chris
[2] For instance, definitions in the PATO OWL file (quality.owl) are
not visible in Protege. The OWL version of PATO has an
AnnotationProperty called "oboInOwl:hasDefintion" that has the value
"@_:A4843". Looking in the quality.owl file directly, I see "heart
shaped" contains the following oboInOwl:hasDefinition XML entity:
<oboInOwl:hasDefinition>
<oboInOwl:Definition>
<rdfs:label xml:lang="en">Having the shape of heart.</
rdfs:label>
<oboInOwl:hasDbXref>
<oboInOwl:DbXref>
<rdfs:label>PATOC:GVG</rdfs:label>
<oboInOwl:hasURI rdf:datatype="http://www.w3.org/2001/
XMLSchema#anyURI">http://purl.org/obo/owl/PATOC#PATOC_GVG</
oboInOwl:hasURI>
</oboInOwl:DbXref>
</oboInOwl:hasDbXref>
</oboInOwl:Definition>
</oboInOwl:hasDefinition>
oboInOwl:Definition and oboInOwl:DbXref are defined as owl:Class
types. oboInOwl:hasDefinition and oboInOwl:hasDbXref are defined as
an OWL AnnotationProperty types. But Protege-OWL v3.x (and probably
the Jena library calls being used in Protege to parse the content in
these instances of the oboInOwl:hasDefinition AnnotationProperty)
have no idea how to parse such complex content contained within an
AnnotationProperty. For OWL 1.0, you CAN stuff whatever you like
inside an AnnotationProperty, but it's going to by and large be
interpreted as being unstructured text, unless core rdfs or owl types
are used to provide more structure inside the AnnotationProperty. Of
course, if you create AnnotationProperty instances like that, then
you are no longer in OWL-DL.
For this complex construction:
AnnotationProperty (oboInOwl:hasDefinition)
Class (oboInOwl:Definition)
rdfs:label
AnnotationProperty (oboInOwl:hasDbXref)
Class (oboInOwl:DbXref)
rdfs:label
AnnotationProperty (oboInOwl:hasURI)
Protege-OWL 3.x (and Jena, I assume) doesn't have the slightest idea
how to represent this information, hence the opaque and meaningless:
< oboInOwl:hasDefinition>@_:A4843</oboInOwl:hasDefinition>
The entity icons being displayed indicate Protege thinks this is some
manner of OWL instance.
I should add I do have all the required namespaces declared, and the
file itself when checked in Pellet 1.4 comes out as OWL-DL species
and "consistent".
On May 24, 2007, at 3:11 PM, [EMAIL PROTECTED] wrote:
Rather than going through and copy & pasting ALL the OWL & RDF links
into a text file, I thought I just send this reminder and cc to
Chris, as he may have other ideas about how to get these into the NC
repository that don't include error-prone copy & pasting or require
someone to write a scraper for this page.
I think that we probably do not want to use (and even import) all
of the ontologies in the current OBO collection. We should probably
focus on the OBO Foundry ontologies and some of the more consistent
OBO Foundry candidates. Some of the ontologies would need some
remodelling before they can be integrated into a consistent demo
scenario in a really useful way.
For example, the evidence code ontology could better be represented
as an ontology of processes of biomedical experiments and techniques.
-- Matthias
--
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Bill Bug
Senior Research Analyst/Ontological Engineer
Laboratory for Bioimaging & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA 19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)
Please Note: I now have a new email - [EMAIL PROTECTED]
