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From vijay garla <vnga...@gmail.com>
Subject Re: YTEX semantic similarity concept graph questions
Date Thu, 16 Oct 2014 10:29:13 GMT
I don't know what the difference between PAR/CHD (parent/child) and RB/RN
(broader/narrower) is supposed to be.  some umls source vocabularies use
PAR/CHD only/predominantly (e.g. SNOMED-CT), others use RB/RN (e.g.
RXNORM).  You can use and experiment with whatever relationships you want
(I think there might be part of/contains relationships too).

the concept graph is a directed acyclic graph, and the query should return
parent-child edges (or maybe the other way around, not sure).  If your
query uses e.g. rel in ('PAR', 'CHD'), you will return edges going both
directions.  This shouldn't cause any problems, as we discard edges that
induce cycles, but it will create a bunch of overhead for no gain.

If you look at other concept graph configs, e.g.
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.template.xml,
you will see that we use both PAR & RB relationships.

HTH,

VJ





On Thu, Oct 16, 2014 at 2:58 AM, John Green <john.travis.green@gmail.com>
wrote:

> Hope this finds everyone well.
>
> It is not immediately clear to me why
>
>         select distinct cui1, cui2
>         from umls.MRREL
>         where sab in ('SNOMEDCT')
>         and rel in ('PAR')
>         order by cui1, cui2
>
> would only be selecting the relationship (REL) of PAR. Im not sure the
> selection criteria. This is honestly probably directed mostly at Vijay, but
> anyone else with experience in this domain would be a welcome voice. In the
> paper on YTEX, for instance, PAR and RB are chosen for UMLS. Why? Does this
> have to do with the "flattening" or "orphaning" that UMLS does to the
> vocabularies it includes? Why not PAR, RB, and RN? Why not more? Was this a
> computational (speed/memory) consideration, or a functional one that my
> lack of familiarity to the domain is keeping me from seeing.
>
> Im posting this fairly specific question to the Dev because it directly
> relates to building YTEX concept graphs, which is a functionality of our
> distro here.
>
> Best!
> JG
>

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