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[bioontology-support] AERO - rdfs:label display and file update

Trish Whetzel whetzel at stanford.edu
Tue Mar 22 18:10:52 PDT 2011


>>> I was also looking at annotations:
>>> - I was wondering why the label for the annotation property IAO_0000115 was "Definitions" instead of "definition" (http://purl.obolibrary.org/obo/iao/ontology-metadata.owl)
>> 
>> Properties that are specified on the ontology submission form in the "Ontology Format" block are displayed with a consistent label across all ontologies in BioPortal and is why the text "Definitions" is displayed vs. the label of the specified definition property. There is a feature request to make this more understandable when viewing your ontology via the BioPortal Web interface.
> 
> I didn't understand that, sorry. I attach a picture of the ontology information I submitted below. As you can see from the definition property I did ask to use IAO_0000115 (even though it doesn't show here because the input text is too short) Could you tell me where else are those properties specified?
> If I look at other ontologies using IAO_000015 for their definition property (IAO, OGMS) they correctly display the label as "Definition".

IAO and OGMS do not specify a Definition property for display in BioPortal, therefore the text displayed is the property name. For example, if you review the output of the Get latest version of an ontology by ontology id Web service ( http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_latest_version_of_an_ontology_id ), for BRO [1] the XML output includes the element <documentationSlot> with value "http://bioontology.org/ontologies/biositemap.owl#definition". However, for IAO [2] the output does not include the element <documentationSlot> since the definition property was not specified. 

[1] http://rest.bioontology.org/bioportal/virtual/ontology/1104?email=example@example.org 
[2] http://rest.bioontology.org/bioportal/virtual/ontology/1393?email=example@example.org 


>>> - as you can see in the second picture, the other IAO annotation properties don't show their labels, but their IDs. Any idea why?
>> 
>> The property "protege:defaultLanguage" with value "en" needs to be set on the Metadata tab in order to have these properties be displayed with their label.  I believe this is a "development artifact" based on the process we (i.e. me, you, OBI, etc.) used when adding IDs instead of labels in the URI and following the Protege documentation on "Hiding IDs with Labels" that stated that the terms should have the language property specified. I'll check into this further to see if there are updates to this documentation and if Protege 4 still requires this same process.
> 
> I am not sure I am following you either, sorry :( If I browse IAO on BioPortal (http://bioportal.bioontology.org/visualize/40642/?conceptid=obo%3AIAO_0000030) I get the correct labels display. However in my file which imports IAO I don't get them. Shouldn't that indicate that IAO is ok with respect to enabling label display?
> 
> Regarding the defaultLanguage property this is, as far as I know, specific to P3. I am now using P4 for development and didn't need to set this.

BioPortal uses Protege 3.4.x in the backend and Protege 3.4.x does look for a language value while Protege 4 does not.  After talking to folks here, I'll put in a feature request to have BioPortal take english to be the default language value while preserving correct display of ontologies developed in other languages as well. The version of IAO on BioPortal does have the protege:defaultLanguage set. 


>>> - finally, I was browsing MedDRA, and I was wondering if it would be possible to add a link towards a definition of the annotation properties. See last picture. I am not sure what "Par" means (parent?) nor "Rq", or semantic type, or Synonym Lt. I suspect Tui is a term unique identifier? I think adding link to annotation properties definitions (if they are available) would be very helpful. I know that IAO properties have such a definition, do you think that could be implemented easily?
>> 
>> There is a feature request to display more meaningful property names for MedDRA, SNOMED, and other ontologies loaded from the RRF representation format.
> 
> Thanks, that would be very useful. Are you planning to make those property links clickable, and available for all metadata scheme? For example, if I click on "Editor note" I would get the definition etc of that IAO property too?

I know that the request includes displaying the full property name. I'm checking to see if display of the property definition has also been requested/discussed and if not can request this to see if it is feasible.

Trish 









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