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[bioontology-support] MeSH on Bioportal

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Dec 9 18:14:30 PST 2019


OK, thank you for the report Samson. I’ve entered a ticket in our GitHub repository so that we can hopefully find some time to look into this:

https://github.com/ncbo/umls2rdf/issues/31

Best,
Jennifer


On Dec 6, 2019, at 9:00 AM, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

Hi,

Someone on the Protege mailing list pointed out that the MeSH hierarchy in Bioportal and the TreeView of MESH at the NLM site look very different. The MeSH “Anatomy” concept on Bioportal refers to the discipline of anatomy while the MESH “Anatomy” refers to body structures and systems. (In Bioportal’s MESH, there is a “Anatomy (MeSH Category)” but it doesn’t appear in the hierarchy and can only be found in a search.) “Bacteria” in both has the same definition, but on Bioportal, Bacterium is a subclass of Organism (which is a subclass of Physical Object), but “Bacterium” is not in NLM’s MeSH or in NLM’s UMLS Metathesaurus Browser.

One clue is that Bioportal’s MeSH Physical Object/Organism/Bacterium hierarchy is the same as the one in the UMLS Semantic Type hierarchy.

Perhaps I am just confused. Nevertheless, given that Bioportal derives its MESH vocabulary from UMLS, you may want to check the script to find out the source of the discrepancies.

With best regards,
Samson





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