Implement the semantic type expansion

[jonquet]

When using the Annotator and filtering the result by smeantic types, the hiearchy of the semantic network must be used to include all the sub classes (transitive) of the selected semantic types.

For instance, if I select T057 http://bioportal.lirmm.fr/ontologies/STY/?p=classes&conceptid=http%3A%2F%2Fpurl.lirmm.fr%2Fontology%2FSTY%2FT058

then it is equivalent to select:T058, T060, T061, T059

This must be implemented in the Java proxy (i.e. this project) by automatically expanding the parameter &semantic_types=T058 to &semantic_types=T058,T060,T061,T059

[jonquet]

Once implemented (@twktheainur looks into this), assign to @vemonet to add the following sentence: "Selected semantic types are non exclusives (like a OR) and expanded to include their sub types as described by the hierarchy of the UMLS Semantic Network (http://bioportal.lirmm.fr/ontologies/STY)"

[jonquet]

After checking with @mdorf from NCBO this is actually partially implemented with the &expand_semantic_types_hierarchy=true option.

For instance: http://services.bioportal.lirmm.fr/annotator/?text=yeux&ontologies=MSHFRE&longest_only=false&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false&semantic_types=T021&expand_mappings=false&apikey=c34b7653-0639-4946-81af-8ac76fe809dd&&expand_semantic_types_hierarchy=true

returns D005123 that has semantic type 023

[jonquet]

However, there the current implementation is not transitive... i.e., all the childrena are not inclulded.

For instances: http://services.bioportal.lirmm.fr/annotator/?text=yeux&ontologies=MSHFRE&longest_only=false&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false&semantic_types=T017&expand_mappings=false&apikey=c34b7653-0639-4946-81af-8ac76fe809dd&&expand_semantic_types_hierarchy=true

Does not return anything where as it should...as the hierarchy is T017 -----T021 ---------T023

Will create an issue on NCBO tracker for this.

[jonquet]

See https://jira.bmir.stanford.edu/browse/NCBO-1838 for fix

[jonquet]

@mdorf Any news on this ?

[mdorf]

I haven't worked on this yet. The priority at this point is a) Re-designed BP Homepage, b) AllegroGraph, c) CEDAR Enhancements. NCBO-1838 is marked as "Low" priority. Let me know if this needs to be elevated (I'll need to coordinate with John).

[syphax-bouazzouni]

is it done @jonquet ?

[jonquet]

We can address this with @Bilelkihal