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

Ray Fergerson ray.fergerson at stanford.edu
Wed Apr 11 15:18:21 PDT 2012


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 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

Outreach Coordinator

The National Center for Biomedical Ontology

Ph: 650-721-2378

http://www.bioontology.org

 

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