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[bioontology-support] <External> RE: Squamous cell carcinoma child relationships

Ray Fergerson rayferg at stanford.edu
Fri Oct 2 11:17:25 PDT 2015


I’m not the expert on the UMLS broader and narrower concepts. It could just be that these have weaker semantics than is-a and thus is-a should automatically be considered to be “narrorwer than”, even without an explicit statement to that effect. My guess would be that ontologies with stronger semantics are modeled in UMLS with is-a and those with less well defined semantics get “narrower” but that both relations are not used in the same ontology. This is really just my guess though.

I don’t know how the UMLS browser decides what to put in the report view. I generally use the basic view because it tells me what I want to know…

Ray

From: Brian Cajes [mailto:brian.cajes at regeneron.com]
Sent: Friday, October 2, 2015 5:48 AM
To: Ray Fergerson; support at bioontology.org
Subject: Re: <External> RE: Squamous cell carcinoma child relationships

Great, thank you Ray, I see it now in the "raw view”.  I find it odd that these "isa" relationships are not reflected as broader (RB) and narrower (RN) relationships in MTH and in the Report View of the UMLS browser.  Do you have any insight as to why this is the case?

Thanks,
Brian


From: Ray Fergerson <rayferg at stanford.edu<mailto:rayferg at stanford.edu>>
Date: Thursday, October 1, 2015 at 7:18 PM
To: Brian Cajes <brian.cajes at regeneron.com<mailto:brian.cajes at regeneron.com>>, "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: <External> RE: Squamous cell carcinoma child relationships

Brian,

When I go to the UMLS browser, and look up the “skin of face” class in SNOMED US in the “basic view” and then expand the “relations” section, the very first one I see is:

CHD | isa | SNOMEDCT_US | Squamous cell carcinoma of skin |

C0553723<javascript:;>



This is where we got the relation that we display.

Ray


From: bioontology-support [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Brian Cajes
Sent: Thursday, October 1, 2015 3:44 PM
To: support at bioontology.org<mailto:support at bioontology.org>
Subject: [bioontology-support] Squamous cell carcinoma child relationships

Hello, attached is a screenshot of the hierarchy for Squamous cell carcinoma.  We can see from this hierarchy that "Squamous cell carcinoma of skin of face" is a child of "Squamous cell carcinoma”.  When we inspect the relationship from the UMLS dataset we do not see this hierarchy present in any of the ontologies.  Can you inform as as to how this relationship was derived and from what data sources?

Thanks,
Brian
Data Architect, Regeneron Genetics Center
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