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[bioontology-support] MedDRA browsing issues

Melanie Courtot mcourtot at gmail.com
Mon Apr 22 12:11:42 PDT 2013


Hi Trish,

Please see inline.

On 2013-04-18, at 5:00 PM, Trish Whetzel wrote:

> Hi Melanie, 
> 
> Regarding the RO question, I think this might be better suited for Lian who is uploading the UMLS terminologies.
> 
> As for the "?" infobubble, the information displayed is from the ontology itself so if a definition of the property is not provided there will not be any information displayed. There is a bug report on displaying more meaningful property names for UMLS terminologies and hopefully definitions of the properties as listed here (http://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/abbreviations.html) can be displayed in the infobubble.

Thanks for the link towards UMLS properties.

Maybe those could be customized depending on the resource? For example in the case of MedDRA, it probably makes more sense to use the names people are familiar with, such as LLT, PT etc.

> 
> The term "eyes swollen" is not displayed in the tree because it is an orphan term, i.e. it does not have a parent, while the term "eye swelling" does have a parent and therefore can be displayed in the tree. For orphan terms, would it make more sense to display only that term in the tree or do you have another suggestion to clarify the display in these cases?

"eyes swollen" is a Lower Level Term and I think for display it could be attached to the corresponding Preferred Term "eye swelling". So it would display as "Eye swelling" in the hierarchy tree, while opening "Eyes swollen" in the term detail frame. Thanks for the explanation, I know now that at worst I could click on the RQ/PT and get the hierarchy opened.

Cheers,
Melanie

> 
> Trish 
> 
> 
> On Apr 17, 2013, at 6:49 PM, Melanie Courtot wrote:
> 
>> Hi all,
>> 
>> I am looking at the anaphylaxis SMQ at http://bioportal.bioontology.org/ontologies/42280?p=terms&conceptid=20000021, and wondering how you build the RO list? As far as I can understand "RO" represents those terms that should be included in the SMQ? 
>> 
>> Also, while there is a "?" available when hoovering on "RO", the infobubble is not very helpful (see attached screenshot). Could there be a better description of what the various properties are? I have a local version of MedDRA loaded, but couldn't see "RQ" or "PAR" for example (which by looking at terms seem to be LLT and HLT respectively)
>> 
>> Finally, when I search for a term (for example "eyes swollen") it does open in the term details frame, but doesn't indicate its position in the tree - see http://bioportal.bioontology.org/ontologies/42280?p=terms&conceptid=10016014&jump_to_nav=true This does work well for other resources, see for example http://bioportal.bioontology.org/ontologies/50105?p=terms&conceptid=C76431&jump_to_nav=true
>> After testing, it does seem to work if preferred term are used instead, such as "eye swelling" http://bioportal.bioontology.org/ontologies/42280?p=terms&conceptid=10015967&jump_to_nav=true. Would it be possible to have this behaviour for LLTs as well?
>> 
>> Thanks,
>> Melanie
>> 
>> 
>> 
>> 
>> <Screen Shot 2013-04-16 at 3.57.06 PM.png>
>> 
>> 
>> 
>> 
>> 
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> 



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