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

Paul R Alexander palexander at stanford.edu
Thu Jul 17 12:04:43 PDT 2014


We have it on our todo list to fix the hierarchy and to support hierarchy expansion in semantic type filtering, so both of these will get addressed soon.

Paul


On Jul 17, 2014, at 8:17 AM, Clement Jonquet <jonquet at lirmm.fr> wrote:

> 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.bioontology.org%2Fontology%2FSTY%2FT077
> has for ancestor:
> http://data.bioontology.org/ontologies/STY/classes/http%3A%2F%2Fpurl.bioontology.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> 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
> 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 withhttp://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&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 SIFR project: Semantic Indexing of French Biomedical Data Resources (ANR, UM2, CNRS, IBC)
> Organizer of Web Science Montpellier Meetup
>  
> 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
>                 France                                                            Google:               jonquet.lirmm at gmail.com
> ----------------------------------------------------------------------------------------------------------------------
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>  
>  
>  
>  
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