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[bioontology-support] Possible cycling problems in MeSH

Ray Fergerson ray.fergerson at stanford.edu
Fri Apr 8 17:50:43 PDT 2011


Tanja,

 

This is pretty confusing. First, we should not even be displaying the MeSH
hierarchy. After investigating this thoroughly some time ago we decided
that we could not support an accurate display of the hierarchy so, rather
than support the wrong display, we would not show any hierarchy. The MeSH
terms themselves should be available in BioPortal but the hierarchy should
not. That you seen something is actually a bug.

 

The problem that we discovered with our support of MeSH is that the
"hierarchical" relationship between nodes in MeSH is not transitive. The
effect of this is that the children of a term depend upon the path that
you used to reach that term. This is not consistent with usual ontology
is-a relationships which BioPortal was designed around. Addressing this
correctly for MeSH would require a redo of the UI, backends, and of all of
our REST services.  This is just not feasible. BioPortal is really
designed to explore transitive is-a and part-of relations and we have to
limit ourselves to this domain. Fortunately this domain covers the
overwhelming number of terminologies. Unfortunately it does not cover
MeSH.

 

Ray

 

 

From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Bekhuis, Tanja
Sent: Thursday, April 07, 2011 1:59 PM
To: support at bioontology.org
Cc: Bekhuis, Tanja; Rebecca Crowley
Subject: [bioontology-support] Possible cycling problems in MeSH

 

Hello, 

 

For the last few weeks I have been exploring the structure of several
terminologies available via the NCBO BioPortal. As a consequence, I have
become familiar with displays of trees in the left pane. So I was rather
perplexed by the tree for MeSH as it appears in the portal. 

 

I attached a brief document with 4 images: 2 from the NCBO BioPortal and 2
from the NLM online browser for comparison. 

 

Notably, only 4 of the 16 categories display in the initial screen for
MeSH in the portal. If I try to add a category that should be there, e.g.
the Humanities category, topmost concepts repeat as one traverses the tree
and the system 'hangs' when I try to explore further. 

 

If you read through the attached document and compare the two sources, you
will see odd discrepancies that suggest internal cycles in the NCBO
version. 

 

I would very much appreciate guidance regarding how to interpret your
version of MeSH, as I had intended to use it in a research project
underway. 

 

Sincerely, 

Tanja

Tanja Bekhuis, PhD, MS, MLIS

 

Postdoctoral Associate

Department of Biomedical Informatics / School of Medicine

University of Pittsburgh

Pittsburgh, Pennsylvania 15232, USA

E-mail: tcb24 at pitt.edu 

Phone at UPMC Shadyside:  +1 412-647-6705

 

 

 

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