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

Melanie Courtot mcourtot at
Tue Mar 22 15:53:25 PDT 2011

Hi Trish,

On 22-Mar-11, at 3:30 PM, Trish Whetzel wrote:

>> I was looking at the AERO page in BioPortal, and I can now see  
>> multiple uploads, which I don't believe reflect any action from me,  
>> including one "UNKNOWN" - see pic below.
>> Can you check what happened?
> We are investigating this.
>> I was also looking at annotations:
>> - I was wondering why the label for the annotation property  
>> IAO_0000115 was "Definitions" instead of "definition" ( 
>> )
> 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".

>> - 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 ( 
) 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.
>> - 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?


> Trish

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M?lanie Courtot
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada

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