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

Clement Jonquet jonquet at lirmm.fr
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:

 

http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioonto
logy.org%2Fontology%2FSTY%2FT077

has for ancestor:

http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioonto
logy.org%2Fontology%2FSTY%2FT077/ancestors

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:
http://semanticnetwork.nlm.nih.gov/Download/

 

Clement

 

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

 

Clement,

 

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.

 

Paul

 

 

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

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

Especially the hierarchy as described here:

 <http://www.nlm.nih.gov/research/umls/META3_current_semantic_types.html>
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&conceptid=ht
tp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F2092003>
http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=htt
p%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>
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 SIFR project <http://www.lirmm.fr/sifr/> : Semantic Indexing of
French Biomedical Data Resources (ANR, UM2, CNRS, IBC)

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

 

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

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:
@jonquet_lirmm <http://twitter.com/jonquet_lirmm> 

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

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<image001.png>

 

 

 

 

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