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[bioontology-support] concept definitions in API?

Ben Leinfelder leinfelder at nceas.ucsb.edu
Mon Mar 23 14:47:27 PDT 2015


Hi Ray,
Those are fantastic explanations - my apologies for overlooking the definition field in the ontology submission form - you shouldn't have to guess when I can just tell you!

What I was meaning to express with my example queries was that I requested the definition field (whatever that meant) returned in the results.
From your api docs:
> Parameter: include
> Possible values: :all {comma-separated list of attributes, EX: attr1,attr2}
> Description: By default, the API will show a subset of the available attributes for a given media type. This behavior can be overridden by providing include=all to show all attributes or include=attribute1,attribute2 to include a specific list. 

So I thought using this parameter would explicitly include the fields listed: include=prefLabel,definition

It is perplexing I sometimes get a definition field returned in my results for certain classes, even though I have no skos:definition properties on those classes.

At any rate, I'll update the submission and carry on. 

Thanks for the help,
-ben


On Mar 23, 2015, at 2:34 PM, Ray Fergerson <ray.fergerson at stanford.edu> wrote:

> This behavior is a bit confusing. The short answer to your question is
> that if you use the "also_seach_properties=true" parameter you will get
> the behavior you want.
> 
> Before going into the long answer, you state below that you explicitly
> included definitions in the search. I don't think that this is possible.
> We do have a "require definitions" property but this just requires that
> the class have a definition. It does not require that the search find a
> match in the definition. You should get matches on definitions by default
> (however, see below).
> 
> And now for the longer answer, if you care. BioPortal uses as a default
> the skos:definition property as the property containing a definition. If
> you do not use skos:definition in your ontology, when you submit the
> ontology you need to specify which property contains the definition. The
> private D1-CARBON-FLUX ontology does not do this so BioPortal finds no
> definition. The fact that this ontology has another property named
> "definition" is irrelevant (for BioPortal).
> 
> Having said all this, it would be more user friendly if we could "guess"
> the definition property. This question has come up before. I will look
> into doing this. Also you could edit the submission to define the
> definition property properly. (Say that three times fast.) The system
> should the reparse the ontology and create a BioPortal definition which
> will be searched automatically.
> 
> Ray
> 
> -----Original Message-----
> From: bioontology-support
> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Ben
> Leinfelder
> Sent: Monday, March 23, 2015 12:58 PM
> To: support at bioontology.org
> Subject: [bioontology-support] concept definitions in API?
> 
> Hi folks,
> I'm looking into some unexpected results when querying classes with the
> BioPortal API. 
> 
> Take this class in the D1_CARBON_FLUX ontology:
> 	
> https://purl.org/dataone/ontologies/observation/D1_carbon_flux_1.owl#OWLCl
> ass_1a9b59a0_d424_41c6_afe0_0a1f46378d5f
> 
> This query  for "plankton" returns the concept...
> 	
> https://data.bioontology.org/search?ontologies=D1-CARBON-FLUX&suggest=true
> &include=prefLabel,definition&q=plankton&apikey=XXXX
> 
> .but does not include the "definition" field even when explicitly
> requested in the query string. I only get these:
> 	"prefLabel": "Plankton_Carbon_Pool",
> 	"@id":
> "https://purl.org/dataone/ontologies/observation/D1_carbon_flux_1.owl#OWLC
> lass_1a9b59a0_d424_41c6_afe0_0a1f46378d5f",
> 	"@type": "http://www.w3.org/2002/07/owl#Class",
> 
> But I can see the definition in the BioPortal web interface and, of
> course, in the OWL file directly.
> 	
> http://bioportal.bioontology.org/ontologies/D1-CARBON-FLUX/?p=classes&conc
> eptid=https%3A%2F%2Fpurl.org%2Fdataone%2Fontologies%2Fobservation%2FD1_car
> bon_flux_1.owl%23OWLClass_1a9b59a0_d424_41c6_afe0_0a1f46378d5f&jump_to_nav
> =true
> 
> What's odd, is that I can retrieve definition for some other classes
> (e.g., "carbon_flux"):
> 	
> https://data.bioontology.org/search?ontologies=D1-CARBON-FLUX&suggest=true
> &include=prefLabel,definition&q=carbon_pool&apikey=XXXX
> 
> Am I doing something wrong with the API? 
> 
> Thank you!
> -ben
> 
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