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[bioontology-support] SNOMED circular parent

Ted Bashor ted at wonderlakesoftware.com
Thu Feb 20 09:14:10 PST 2014


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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