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[bioontology-support] getting UMLS Semantic Type when using the NCBO Annotator

Clement Jonquet jonquet at lirmm.fr
Thu Jan 12 17:29:11 PST 2017


Dear Alison, 

 

The semantic type information is in the class information, which means that
for each annotatedClass you need to follow the annotatedClass.links.self
field and access the .semanticType field in the resulting JSON.

For instance (first annotation of your example): 

http://data.bioontology.org/ontologies/OMIM/classes/http%3A%2F%2Fpurl.bioont
ology.org%2Fontology%2FOMIM%2F158343 

 

Another alternative for you if you don’t want to do this and you’re setting
a routine with multiple call to the annotator is to call the Annotator only
with one semanticType restrictions, then you will now that each returned
annotatedClass will have either that semanticType or a semantic Type that is
a direct descendent in the SNN hierarchy
 

(attention: NCBO is currently fixing a bug to make this transitive to all
the descendants of a given semantic type)

 

Best regards

Clement

 

Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
University of Montpellier

Coordinator of the SIFR <http://www.lirmm.fr/sifr/>  and AgroPortal
<http://agroportal.lirmm.fr/>  projects

Visiting scholar, Stanford University (EU Marie Curie fellow)

 

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

http://www.lirmm.fr/~jonquet 

 

@Montpellier : +33/4 67 14 97 43

@Stanford       : +1 650 723 6725

 

 

 

De : bioontology-support
[mailto:bioontology-support-bounces at lists.stanford.edu] De la part de Alison
Victoria Callahan
Envoyé : mercredi 11 janvier 2017 11:36
À : support at bioontology.org
Objet : [bioontology-support] getting UMLS Semantic Type when using the NCBO
Annotator

 

Hi team! 

 

I have question about using the NCBO Annotator and restricting annotations
to specific UMLS semantic types: is it possible to return the semantic type
of each annotation? When I try out an example annotation at
https://bioportal.bioontology.org/annotator, the result set has a column for
semantic type, but it is empty (see attached screenshot).

 

The corresponding REST service call for this example is:

 

http://data.bioontology.org/annotator?apikey=ee724711-0705-4c6c-82f6-c0cfc43
9b16e
<http://data.bioontology.org/annotator?apikey=ee724711-0705-4c6c-82f6-c0cfc4
39b16e&text=Multidrug> &text=Multidrug resistance-associated protein 1
(MRP-1) is a ubiquitously expressed member of the ATP-binding cassette
transporter family. MRP-1 is one of the primary transporters of glutathione
and glutathione conjugates. This protein also transports antiretroviral
therapeutics, such as HIV-1 protease inhibitors (PI). We hypothesized that
inflammatory mediators that activate macrophages would modify the expression
and activity of MRP-1 in macrophages. Real-time PCR assays, western blots,
and calcein efflux assays were used to show that exposure of macrophage cell
line RAW 264.7 to lipopolysaccharide (LPS) increased expression of MRP-1 at
the levels of mRNA, protein, and functional activity. Treatment of
macrophages with LPS resulted in 2-fold increases of MRP-1 expression or
functional activity. LPS-mediated increases in calcein efflux were repressed
by the MRP-specific inhibitor MK-571. These results suggest that the
effectiveness of HIV-1 PI therapy may be compromised by the presence of
opportunistic infections.
&longest_only=true&exclude_numbers=true&whole_word_only=true&exclude_synonym
s=false&mappings=all&semantic_types=T017,T008,T038,T043,T047,T028,T001 

 

Thanks!

Alison

 

--

Alison Callahan, PhD

Research scientist - Shah Lab

Stanford Center for Biomedical Informatics Research

Stanford University

 



 

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