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[bioontology-support] Fwd: IDO, etc. problem with definitions

Lindsay Cowell Lindsay.Cowell at UTSouthwestern.edu
Sun May 6 17:05:14 PDT 2012


Can you please let us know when this gets done.  That way I will know to modify IDO.  I assume doing so now will not work since BioPortal is not yet set up to handle skos:definition with subproperties.

Thanks,

Lindsay
On Apr 11, 2012, at 5:18 PM, Ray Fergerson wrote:

Trish is correct about how this should work. It will not work that way now but we can and should change the system so that it does. The change requires some care and testing but there should be no problem – as Trish points out we have already done this once for synonyms.

To expand a bit, here is what should happen:

Situation:
Ontology A uses property defA to hold definitions
Ontology B uses property defB to hold definitions
Ontology C imports A and B and uses defC to hold definitions
In BioPortal defC is tagged as the definition property for C, while values defA and defB are ignored for the purposes of definition.

Solution:
In BioPortal declare the definition property for C to be skos:definition
In Ontology C
-          declare defA to be a subproperty of skos:definition
-          declare defB to be a subproperty of skos:definition
-          declare defC to be a subproperty of skos:definition

With the addition of these statements, BioPortal will (when fixed) query and get definitions from skos:definition itself and from all of its subproperties.

I will create a tracker item for this so that it will eventually get done.

Ray



From: Trish Whetzel [mailto:whetzel at stanford.edu]
Sent: Wednesday, April 11, 2012 12:28 PM
To: Barry Smith; Ray Fergerson
Cc: Lindsay Cowell; support at bioontology.org<mailto:support at bioontology.org> Support
Subject: Re: [bioontology-support] Fwd: IDO, etc. problem with definitions

Based on the property specified to contain the term definition, the metrics for terms without a definition are correct. The BFO terms are counted as not having a definition since these terms use the "rdfs:comment" property for the definition and there are a few other groups of terms that do not have a definition, e.g. obsolete terms, NCBI Taxon terms.

In past cases of a need to use more than 1 property to represent synonyms, e.g. different types of synonyms (abbreviation, code), the request was to represent these as sub-properties. Ray, would using sub-properties be the suggestion in this case?

Trish


On Apr 11, 2012, at 5:09 PM, Trish Whetzel wrote:


Hi Barry,

The property specified for the definitions in IDO is:
http://purl.obolibrary.org/obo/IAO_0000115
I'll run some additional checks to confirm the definition count.

In the meantime, Lindsay is http://purl.obolibrary.org/obo/IAO_0000115 the property for definitions in IDO?

Trish


On Apr 5, 2012, at 2:01 PM, Barry Smith wrote:


I notice that IDO is said to have 184 terms without definitions. I believe that the reason for this is that Bioportal does not recognize the 'has_definition' label, which is what IDO (and OGMS, and OBI, and BFO ...) uses to link a term to its definition. Can you include this annotation property in your  count of classes with definitions?
BS
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Trish Whetzel, PhD
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Lindsay G. Cowell, PhD
Division of Biomedical Informatics
Department of Clinical Sciences
University of Texas Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX  75390-9066

F4.212b, MC9066

phone: 214-648-2289
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Lindsay.Cowell at utsouthwestern.edu<mailto:Lindsay.Cowell at utsouthwestern.edu>


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