Hi Luis,
I think I understand what you are doing with the properties. You have
(in abstract syntax)
Class(Subiculum_ventral_part_stratum_radiatum partial)
ObjectProperty(Subiculum_ventral_part_stratum_radiatum-has
range(unionOf(alpha2_subunit_nicotinic_receptor
sulfhydryl_oxidase
alpha4-2_subunit_nicotinic_receptor
alpha4-1_subunit_nicotinic_receptor))
domain(Subiculum_ventral_part_stratum_radiatum))
What this says, is that if you have X
Subiculum_ventral_part_stratum_radiatum-has Y, then X must be a
Subiculum_ventral_part_stratum_radiatum
and Y can be either a alpha2_subunit_nicotinic_receptor or a
alpha4-2_subunit_nicotinic_receptor or a ...
A more common idiom would be:
ObjectProperty(has domain(Brain_Parts) range(Brain_Parts)) // is
this right? or is the range protein/receptor?
The following says for any X where
Subiculum_ventral_part_stratum_radiatum has X, X must be
either a alpha2_subunit_nicotinic_receptor, or a sulfhydryl_oxidase
or a....
It doesn't say is actually has any Xs, though (neither does the the
current version)
Class(Subiculum_ventral_part_stratum_radiatum
restriction(has allValuesFrom
unionOf(alpha2_subunit_nicotinic_receptor
sulfhydryl_oxidase
alpha4-2_subunit_nicotinic_receptor
alpha4-1_subunit_nicotinic_receptor)))
The following says that every Subiculum_ventral_part_stratum_radiatum
has at least one
alpha2_subunit_nicotinic_receptor and at least one sulfhydryl_oxidase
and at least one ...
Class(Subiculum_ventral_part_stratum_radiatum partial
intersectionOf(restriction(has someValuesFrom
(alpha2_subunit_nicotinic_receptor))
restriction(has someValuesFrom(sulfhydryl_oxidase))
restriction(has someValuesFrom
(alpha4-2_subunit_nicotinic_receptor))
restriction(has someValuesFrom
(alpha4-1_subunit_nicotinic_receptor))))
Do either of these capture what the "has" relationship is supposed to
mean? Is the object of a "has" relationship always a some sort of
protein/receptor?
-Alan
On Mar 15, 2007, at 4:26 PM, Alan Ruttenberg wrote:
Hi Luis,
Thanks for this! I'm starting to have a look...
In the following, owl:range should be owl:Class, I think.
<owl:ObjectProperty rdf:ID="Subiculum_ventral_part_stratum_radiatum-
has">
<rdfs:domain
rdf:resource="#Subiculum_ventral_part_stratum_radiatum"/>
<rdfs:range>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<owl:range rdf:about="#alpha2_subunit_nicotinic_receptor"/>
<owl:range rdf:about="#sulfhydryl_oxidase"/>
<owl:range rdf:about="#alpha4-2_subunit_nicotinic_receptor"/>
<owl:range rdf:about="#alpha4-1_subunit_nicotinic_receptor"/>
</owl:unionOf>
</owl:Class>
</rdfs:range>
</owl:ObjectProperty>
The class named "_" isn't defined - was this intended?
<owl:Class rdf:about="#BAMS-Atlases">
<rdfs:subClassOf rdf:resource="#_" />
</owl:Class>
Also, BAMS-Atlases is class without subclasses or instances - was
that your intention?
What's the idea behind making all the object properties, rather
than, for instance a single has, has-target, etc?
-Alan
On Mar 15, 2007, at 2:50 PM, Luis Marenco wrote:
Hi All,
I helped Mihai Bota design the prototype BAMS xml protocol (for
anatomical data)
for the purpose of facilitating export of its contents into
Ontology servers.
(e.g.: QIS system. In very alpha version: http://os-
qis.med.yale.edu ), There
some vocabularies and simple ontologies can be automatically
imported, mapped,
and allowed to be exported in several experimental protocols.
For Bams, an Owl dump can be accessed at
http://os-qis.med.yale.edu/site/tools/export/owl_export2.aspx?sid=22
You can import this ontology directly into Protege following the
next steps
. Select -> File\New Project
. Check the box "[ ]Create from Existing sources"
. Select Project type "OWL/RDF Files"
. Click [next] button
. Copy and paste
"http://os-qis.med.yale.edu/site/tools/export/owl_export2.aspx?
sid=22"
. Click [Next >] button
. Select "OWL DL"
. Click [Next >] button
. Select "Logic View"
. Click [Finish] button
Use the same stpes to import an old ontology version of NeuronDB
http://os-qis.med.yale.edu/site/tools/export/owl_export2.aspx?sid=9
ModelDB
http://os-qis.med.yale.edu/site/tools/export/owl_export2.aspx?sid=19
and others ...
Thanks,
________________________
Luis Marenco
Yale Center for Medical Informatics
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of John
Barkley
Sent: Thursday, March 15, 2007 2:22 PM
To: public-semweb-lifesci@w3.org
Subject: updated bams instance style model
I put the updated bams instance style model on the wiki page
http://esw.w3.org/topic/HCLS/HCLSIG_DemoHomePage_HCLSIG_Demo
The new version modifies the old version according to Alan's
suggestions from tuesday's f2f.
jb
