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

Melanie Courtot mcourtot at gmail.com
Tue Mar 15 13:40:33 PDT 2011


Hi Trish,

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?

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 
)
- as you can see in the second picture, the other iIAO annotation  
properties don't show their labels, but their IDs. Any idea why?
- 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?

Thanks,
Melanie


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On 23-Feb-11, at 11:26 AM, Melanie Courtot wrote:

> Hi Trish,
>
> On 23-Feb-11, at 11:08 AM, Trish Whetzel wrote:
>
>> Hi Melanie,
>>
>> There appears to be a bug upon first submission of the ontology.  
>> The developers are working on this.   Subsequent versions should  
>> extract the version info field, as I've seen this with GO and my  
>> own test files.
>
> Thanks!
>
>>
>>> label display, would it be possible to have that being a manual  
>>> choice from the user
>>
>> I'm not sure what "that" refers to. Can you clarify?
>
> You could have a defautLanguage field upon submission of the  
> ontology (such as the ones for synonym property etc) which could be  
> defaulted to "en" maybe (such as for rdfs:label for label display)  
> and allow the user to override that value if desired.
>
> Cheers,
> Melanie
>
>
>>
>> Thanks,
>> Trish
>>
>>
>> On Feb 23, 2011, at 11:03 AM, Melanie Courtot <mcourtot at gmail.com>  
>> wrote:
>>
>>> Hi Trish,
>>>
>>> Thanks for the reply. I just checked and the file has been updated.
>>>
>>> I did notice however that the version info I had supplied manually  
>>> disappeared at the same time to be replaced by "unknown" - I  
>>> gather this is in relation to your email about how this will get  
>>> parsed directly from the file. May I suggest to remove the manual  
>>> entry field then? It is a bit mean to ask the user for the info  
>>> and not take it into account :) I will make sure to add the  
>>> version info property into my file.
>>>
>>> Regarding the label display, would it be possible to have that  
>>> being a manual choice from the user upon submitting the project? I  
>>> think it would make it clearer/easier; my P4 install doesn't  
>>> require me to set that property to display labels, so it is a bit  
>>> strange to have to add a Protege annotation to load the file in  
>>> BioPortal. An other option could be to use the language requested  
>>> in the browser's header.
>>>
>>> Best,
>>> Melanie
>>>
>>>
>>>
>>>
>>> On 22-Feb-11, at 11:42 AM, Trish Whetzel wrote:
>>>
>>>> Hi Melanie,
>>>>
>>>> To resolve the label display issue, on the Protege Metadata tab  
>>>> add the property "protege:defaultLanguage" with value "en".
>>>>
>>>> The issue with the automatic update has been resolved.
>>>>
>>>> Trish
>>>>
>>>>
>>>> On Feb 22, 2011, at 9:23 AM, Melanie Courtot wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I recently submitted the AERO ontology to the BioPortal, with  
>>>>> instruction to "use default" for label display, which is  
>>>>> rdfs:label. See the screenshot AEROsettings.png attached.
>>>>>
>>>>> When browsing the ontology however, URIs are used. See the  
>>>>> screenshot AEROdisplay.png attached. As you can see on the  
>>>>> right, there is a property label for the class.
>>>>>
>>>>> Could you let me know how to get the interface to use the  
>>>>> rdfs:label instead, in the hierarchy but also in the details  
>>>>> panel; for example I would prefer the equivalent classes to be  
>>>>> displayed using their labels as well.
>>>>>
>>>>> Also, when entering the URL for file download, it was mentioned  
>>>>> that an automatic update would be done every day. I updated the  
>>>>> file on Sunday (almost 48h ago, http://bit.ly/eop2KQ) but the  
>>>>> changes are not reflected yet on the BioPortal. Is there  
>>>>> anything I should be doing to force the update, or should that  
>>>>> be going through automatically?
>>>>>
>>>>> Thanks,
>>>>> Melanie
>>>>>
>>>>>
>>>>> <AEROdisplay.png><AEROsettings.png>
>>>>> ---
>>>>> M?lanie Courtot
>>>>> MSFHR trainee, TFL- BCCRC
>>>>> 675 West 10th Avenue
>>>>> Vancouver, BC
>>>>> V5Z 1L3, Canada
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> bioontology-support mailing list
>>>>> bioontology-support at lists.stanford.edu
>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>
>>>
>

---
M?lanie Courtot
MSFHR trainee, TFL- BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada








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