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[bioontology-support] [BioPortal] Feedback from RSNA Test

Jennifer Leigh Vendetti vendetti at stanford.edu
Fri Jul 27 12:10:48 PDT 2018


Hi Michael,


On Jul 24, 2018, at 8:13 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

URL: https://bioportal.bioontology.org/ontologies/RAD/?p=classes&conceptid=http%3A%2F%2Fradlex.org%2FRID%2FRID30413&jump_to_nav=true

For some classes the prefixIRI has two values. Like in the url above the value is
RID:RID30413
RID30413

when it should only be RID30413.

So we had a few questions.
1. Do you know why this seems to be only happening on some of the classes and is it something we can fix on our end.



I looked at our source code and the content of the two ontology files that are part of your latest submission. The two values in the prefixIRI property appear to be the result of the use of OWL punning. The class you list above (“wall of left renal pelvis”, with ID http://radlex.org/RID/RID30413) is declared as an entity in RadLex.owl on line 583,219:

<owl:Class rdf:about="http://radlex.org/RID/RID30413">

… and in pun_RadLex.owl on line 145,308:

<owl:NamedIndividual rdf:about="http://radlex.org/RID/RID30413”>

One of the values in the prefixIRI property is prepended with “RID:” because that prefix is declared in pun_RadLex.owl:

<rdf:RDF xmlns="http://radlex.org/RID/"
     xml:base="http://radlex.org/RID/"
     xmlns:RID="http://radlex.org/RID/"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">

… but not in RadLex.owl.

Your ontology files are valid OWL, and it may be the case that we shouldn’t have two values in the prefixIRI property. However, I’m not aware of any issues this is causing with regard to BioPortal’s functionality.


2. Is the prefixIRI slot attached by BioPortal because we don't think it's a field we have.



Yes, this is an annotation property that we attach to classes when we ingest ontologies. We allow end users to submit ontologies in OWL, OBO, and SKOS, all of which have their own formats for knowledge representation. We store class IDs in annotation properties like prefixIRI to facilitate the ability to search for terms across all ontologies in BioPortal, regardless of format.

In the future, if you want to check the source of a property, you can issue a REST call with the “properties” include parameter, e.g.:

http://data.bioontology.org/ontologies/RAD/classes/http%3A%2F%2Fradlex.org%2FRID%2FRID30413?include=prefLabel,properties&display_links=false<http://data.bioontology.org/ontologies/RAD/classes/http://radlex.org/RID/RID30413?include=prefLabel,properties&display_links=false>

In the resulting JSON, the prefixIRI property is visible as part of the data.bioontology.org/metadata<http://data.bioontology.org/metadata> namespace:


[cid:05089E39-9936-4481-B712-2464A0040ECE at stanford.edu]

Best,
Jennifer




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