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[bioontology-support] concept definitions in API?

Ray Fergerson ray.fergerson at stanford.edu
Mon Mar 23 14:34:52 PDT 2015


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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