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[bioontology-support] Xrefs hyperlink

Melanie Courtot mcourtot at gmail.com
Fri Jun 24 13:53:49 PDT 2011


Hi Trish,

Thanks for the feedback. I don't know that they follow a specific pattern, I was rather wondering if there would be an option to recognize the prefixes maybe? Or maybe a global mapping file at the BIoPortal level that could be overridden specifically by submitters? For example all people using GeneRIF probably mean the same thing, but for the odd case someone would want to use GeneRIF to point to something else they would be able to as well.

I tried searching BioPortal with some of the IDs referenced from http://purl.bioontology.org/ontology/MCCL/DOID_2841, such as ICD9CM_1993:504 or GeneRIF:11744622, but it doesn't return any result (which could also be a result of the xrefs being wrong) If I look at the full list of ontologies on Bioportal, it looks like ICD9CM is not there, probably as it has been replaced by ICD10CM?

I understand that there is no easy solution, I am just wondering how we could make the situation better for users: right now the DOID I am looking at has no definition, and only that long list of IDs which I really don't know how to browse efficiently, nor if they are exact synonym, related references or else. This is most probably something that would need to be discussed with ontology developers; if BioPortal were willing to support hyperlinking that may be an argument to encourage them to use full URIs for xrefs?  Alternatively, when uploading a file an ontology developer could provide a list of prefixes mapped to full URIs for the xref he has been using? This would allow existing resources to just provide a mapping file without updating all annotations.

What do you think?

Thanks,
Melanie


On 2011-06-24, at 1:20 PM, Trish Whetzel wrote:

> Hi Melanie, 
> 
> I'm not aware that the values of the xref field follow a standard pattern to reconstruct a hyperlink? If so, can you point us to documentation on this? In general, the best way to have the xref content displayed as links would be to include the link in the ontology file itself.  
> 
> Trish 
> 
> 
> On Jun 23, 2011, at 12:51 PM, Melanie Courtot wrote:
> 
>> Hi,
>> 
>> When I am looking at the term DOID:asthma, at http://purl.bioontology.org/ontology/MCCL/DOID_2841, I get a long list of Xrefs that is not very helpful as they are not clickable. Would there be an option to transform them into hyperlinks?
>> Similarly for http://purl.bioontology.org/ontology/ICD10CM/J45, it would be great it the UMLS IDs were hyperlinked.
>> 
>> Thanks,
>> Melanie
>> 
>> ---
>> Mélanie Courtot
>> MSFHR/PCIRN trainee, TFL- BCCRC
>> 675 West 10th Avenue
>> Vancouver, BC
>> V5Z 1L3, Canada
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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