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

Alison Victoria Callahan acallaha at stanford.edu
Wed Jan 11 11:36:02 PST 2017


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-c0cfc439b16e&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_synonyms=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

[cid:568B89ED-B05E-4329-8816-4A321281967D at stanford.edu]

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