Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Clement Jonquet jonquet at
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: 

Especially the hierarchy as described here:

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
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


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:

-          Change Annotator code to use that hierarchy when filtering



Hope it helps



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  <> SIFR project: Semantic Indexing of
French Biomedical Data Resources (ANR, UM2, CNRS, IBC)

Organizer of  <> Web Science
Montpellier Meetup


 <mailto:jonquet at> jonquet at



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

Fax:                     +33/4 67  41 85 00           

                161 rue Ada
Skype:                 clementpro
                34095 Montpellier Cdx 5                            Twitter:
<> @jonquet_lirmm

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






-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 204 bytes
Desc: not available
URL: <>

More information about the bioontology-support mailing list