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 17 08:17:48 PDT 2014

Hi Paul, 


The thing is that the REST API offers only what has been parsed by the
umls2rdf tool and the hierarchy is not complete.

For instance:

has for ancestor:

but has empty descendants while the SN defines:


Conceptual Entity 
        Idea or Concept
            Temporal Concept 
            Qualitative Concept 
            Quantitative Concept 
            Functional Concept 
                Body System 
            Spatial Concept 
                Body Space or Junction 
                Body Location or Region 
                Molecular Sequence 
                    Nucleotide Sequence
                    Amino Acid Sequence 
                    Carbohydrate Sequence 
                Geographic Area


The information is only in the files here:




De : Paul R Alexander [mailto:palexander at] 
Envoyé : samedi 12 juillet 2014 00:51
À : Clement Jonquet
Cc : bioportal; Nigam Shah
Objet : Re: [bioontology-support] Filtering by semantic types with the




I’ve added an issue to investigate supporting the use of the Semantic Type
hierarchy when filtering. One easy fix is to use the descendants from the
REST API for a given Semantic Type class as input for the existing filter.





On Jul 10, 2014, at 7:45 AM, Clement Jonquet <jonquet at
<mailto:jonquet at> > wrote:

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


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







bioontology-support mailing list
 <mailto:bioontology-support at>
bioontology-support at


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list