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[bioontology-support] Quick follow-up on the semantic types

Clement Jonquet jonquet at lirmm.fr
Mon Nov 21 10:10:51 PST 2016


Hi Misha, all,

 

Flushing the REDIS cache of the Annotator was the issue for the STY property that was ignored:

See details here:

https://github.com/sifrproject/ncbo_annotator/issues/7

 

For the expansion over the semantic type hierarchy, the transitive bug is described here:

https://github.com/sifrproject/annotators/issues/13

Still ongoing open.

 

Clement

 

De : Michael Dorf [mailto:mdorf at stanford.edu] 
Envoyé : jeudi 17 novembre 2016 16:00
À : Clement Jonquet <jonquet at lirmm.fr>
Cc : support at bioontology.org
Objet : Re: Quick follow-up on the semantic types

 

Hi Clement,

 

Per the NCBO API docs as well as having verified this in the code, there are two parameters that need to be set in the Annotator call that determine how it uses semantic types:

 

http://data.bioontology.org/documentation#nav_annotator

 

*  semantic_types={semType1,semType2..,semTypeN} 

*  expand_semantic_types_hierarchy={true|false} // default = false. true means to use the semantic types passed in the "semantic_types" parameter as well as all their immediate children. false means to use ONLY the semantic types passed in the "semantic_types" parameter. 

 

Let me know if after setting these you get results that are unexpected.

 

Thanks!

 

Misha

 

 

 

On Nov 17, 2016, at 14:08, Clement Jonquet <jonquet at lirmm.fr <mailto:jonquet at lirmm.fr> > wrote:

 

As discussed in the hall ;)

 

I have explicitly added to an ontology in OWL some cui, tui and hasty properties to see if the Annotator will then after consider them… and it does not work.

 

For instance: 

 <http://stageportal.lirmm.fr/ontologies/MEDLINEPLUS/?p=classes&conceptid=http%3A%2F%2Fchu-rouen.fr%2Fcismef%2FMedlinePlus%239&jump_to_nav=true> http://stageportal.lirmm.fr/ontologies/MEDLINEPLUS/?p=classes&conceptid=http%3A%2F%2Fchu-rouen.fr%2Fcismef%2FMedlinePlus%239&jump_to_nav=true

has been enriched with 

<umls:cui xml:datatype="string">C0150933</umls:cui>

<umls:tui xml:datatype="string">T023</umls:tui>

<umls:hasSTY rdf:resource=" <http://purl.lirmm.fr/ontology/STY/T023> http://purl.lirmm.fr/ontology/STY/T023"/>

 

In the OWL file. This (modulo the syntax) exactly how the UMLS2RDF tool represent the semantic type information.

 

And the Annotator does not got it:

 <http://services.stageportal.lirmm.fr/annotator?text=yeux> http://services.stageportal.lirmm.fr/annotator?text=yeux et vision&ontologies=MEDLINEPLUS&longest_only=false&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false&expand_mappings=false&semantic_types=T023

  

So this is official, I don’t understand how the filtering by semantic type occurs.

If you have any information, I am interested.

This would be cool for someone who decide to enrich his/her ontology with semantic types to get them parsed by the Annotator.

 

Clement

 

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