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[bioontology-support] SNOMED circular parent

Paul R Alexander palexander at stanford.edu
Mon Feb 24 10:14:57 PST 2014


Ted,

This issue should be corrected. The 2013AB distribution of UMLS contained a combined US/International version of SNOMEDCT that added some relations we weren’t handling properly. I believe we’ve corrected this problem and we’ll be looking into other things as they arise.

Thanks for reporting the issue.

Paul


On Feb 20, 2014, at 9:14 AM, Ted Bashor <ted at wonderlakesoftware.com> wrote:

> Thanks for the update.  Looks like it isn’t just one or two cases — it’s bad in a lot of places like the one below.  Too many to work around.  Any chance you can revert to the previous SNOMED index while this is being sorted out?
> 
> Disorder of upper digestive tract : 50410009
>   Disorder of digestive tract : 84410009
>     Disorder of digestive organ : 76712006
>       Disorder of digestive tract : 84410009
>         Disorder of digestive organ : 76712006
>           ...
> 
> The version says it is 2013AA.  Would be great if the more recent UMLS 2013AB release were available.   (There’s actually a 2014 SNOMED release, but sounds like you only use the UMLS distributions)
> 
> Thanks, Ted
> 
> On Feb 19, 2014, at 5:13 PM, Ray Fergerson <ray.fergerson at stanford.edu> wrote:
> 
>> Yes, this does appear to be wrong. The best that I can tell is that “Disorder of connective tissue” really has a single parent “Disorder by body site”.  I don’t know why this loop with “Musculoskeletal ….” is getting created.
>>  
>> Unfortunately the expert on these sorts of bizarre problems just went on vacation. It will probably be late next week before this gets sorted out. Sorry.
>>  
>> Ray
>>  
>> From: bioontology-support-bounces at lists.stanford.edu [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Ted Bashor
>> Sent: Wednesday, February 19, 2014 4:04 PM
>> To: support at bioontology.org
>> Subject: [bioontology-support] SNOMED circular parent
>>  
>> Looks like the version of SNOMED was updated yesterday.  I’ve run into a few funky things with new inferred relationships, but the one that is most serious is a circular parent/subClassOf.  Walking up the parent hierarchy from Soft tissue lesion, you find "Musculoskeletal and connective tissue disorder” has a parent of "Disorder of connective tissue” which has a parent "Musculoskeletal and connective tissue disorder” etc.
>>  
>> Soft tissue lesion : 239953001
>>   Rheumatism : 29913006
>>     Arthropathies and related disorders : 201433006
>>       Musculoskeletal and connective tissue disorder : 312225001
>>         Disorder of connective tissue : 105969002
>>           Musculoskeletal and connective tissue disorder : 312225001
>>             Disorder of connective tissue : 105969002
>>               ...
>>  
>> I haven’t dug into the UMLS source for this release yet, any idea if this could be a bug in bioportal’s indexing.
>> Thanks, Ted
> 
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