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[bioontology-support] SNOMED circular parent

Ray Fergerson ray.fergerson at stanford.edu
Thu Feb 20 11:56:46 PST 2014


We are looking into rolling this version back. Will try to have this done
later today.

 

Ray

 

From: Ted Bashor [mailto:ted at wonderlakesoftware.com] 
Sent: Thursday, February 20, 2014 9:14 AM
To: Ray Fergerson
Cc: support at bioontology.org
Subject: Re: [bioontology-support] SNOMED circular parent

 

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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