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[bioontology-support] concept definitions in API?

Ben Leinfelder leinfelder at nceas.ucsb.edu
Mon Mar 23 15:05:41 PDT 2015


Exactly, I wasn't seeing it _returned_. I haven't even begun to evaluate the efficacy of search terms against values in the ontology…. :)
-ben

On Mar 23, 2015, at 2:55 PM, Ray Fergerson <ray.fergerson at stanford.edu> wrote:

> This is a bit confusing. The generic "include" parameter on all commands
> says what fields get returned in the response for that command. It does
> not determine what fields are searched by the search command.
> 
> Ray 
> 
> -----Original Message-----
> From: Ben Leinfelder [mailto:leinfelder at nceas.ucsb.edu] 
> Sent: Monday, March 23, 2015 2:47 PM
> To: Ray Fergerson
> Cc: support at bioontology.org
> Subject: Re: [bioontology-support] concept definitions in API?
> 
> 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#O
>> WLCl 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
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 
> 
> 



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