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[bioontology-support] Filtering by semantic types with the Annotator

Clement Jonquet jonquet at lirmm.fr
Thu Jul 10 07:45:15 PDT 2014


Hi all, 

 

This is a bug or feature request depending on the point of views ;)

 

The UMLS Semantic Network (STY in BioPortal) is not parsed completely:

http://bioportal.bioontology.org/ontologies/STY 

Especially the hierarchy as described here: 

http://www.nlm.nih.gov/research/umls/META3_current_semantic_types.html

is not included.

 

Therefore, when filtering annotation with semantic types, the "hierarchy
knowledge " of the Semantic Network cannot be used.

 

For instance: 

When annotating "melanoma" and filtering with T147:"Disease or syndrome" I
should get an annotation with
http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes
<http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=ht
tp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F2092003>
&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F2092003
which is "Malignant melanoma" in SNOMEDCT that actually has T191 (neoplastic
process) which is defined in the UMLS SN has a subtype of T147.

Currently the Annotator does not match anything if filtering with T147 is
on.

 

Of course this should work also with all the parents in the hierarchy.

 

I see 2 bugs to fix: 

-          Parse the UMLS SN completely (has issued at:
https://github.com/ncbo/umls2rdf/issues/9)

-          Change Annotator code to use that hierarchy when filtering

 

 

Hope it helps

Clement

 

PS: as soon as I get a developer in Montpellier, we will do it ;)

 

 

----------------------------------------------------------------------------
-----------------------------------------------

Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor

PI of the  <http://www.lirmm.fr/sifr/> SIFR project: Semantic Indexing of
French Biomedical Data Resources (ANR, UM2, CNRS, IBC)

Organizer of  <http://www.meetup.com/webscience-montpellier/> Web Science
Montpellier Meetup

 

 <mailto:jonquet at lirmm.fr> jonquet at lirmm.fr

 <http://www.lirmm.fr/~jonquet> http://www.lirmm.fr/~jonquet 

 

                University of Montpellier                          Tel:
+33/4 67 14 97 43

                LIRMM
Fax:                     +33/4 67  41 85 00           

                161 rue Ada
Skype:                 clementpro
                34095 Montpellier Cdx 5                            Twitter:
<http://twitter.com/jonquet_lirmm> @jonquet_lirmm

                France
Google:                <mailto:jonquet.lirmm at gmail.com>
jonquet.lirmm at gmail.com

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