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[bioontology-support] Getting CUI and TUI in annotations

Clement Jonquet jonquet.lirmm at gmail.com
Tue Mar 12 01:52:17 PDT 2019


Hi Leyla, 

This is a working call generated by the UI: 

http://services.bioportal.lirmm.fr/ncbo_annotatorplus/?text=this%20is%20coming%20from%20a%20json%20variable&longest_only=false&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false&expand_mappings=false&negation=false&experiencer=false&temporality=false&score_threshold=0&confidence_threshold=0&lemmatize=false&display_links=false&disp lay_context=false&apikey=4a5011ea-75fa-4be6-8e89-f45c8c84844e

And another one with your parameters: 
http://services.bioportal.lirmm.fr/ncbo_annotatorplus/?text=this%20is%20coming%20from%20a%20json%20variable&stop_words=toujours,rien&minimum_match_length=3&ontologies=OGG,NCBITAXON,NCIT&apikey=4a5011ea-75fa-4be6-8e89-f45c8c84844e&format=json

Seems to work. 
Please provide such a link for you failing. 

Clement

> Le 11 mars 2019 à 18:44, Leyla Jael García Castro <leylajael at gmail.com> a écrit :
> 
> Hi Clement, 
> 
> That is what I am looking for, thanks for the links. I have not played enough with the service but it looks like, programmatically, options could be different from those supported by the NCBO annotator.
> 
> I tried, in Python
>     requestURL = 'http://data.bioontology.org/annotator <http://data.bioontology.org/annotator>'
>     #requestURL = 'http://services.bioportal.lirmm.fr/ncbo_annotatorplus <http://services.bioportal.lirmm.fr/ncbo_annotatorplus>'
>     payload = {
>         'apikey': 'a valid api key here', 
>         'stop_words': stop, @this comes from a text variable
>         'minimum_match_length': 3, 
>         'ontologies': ontos, #list of ontology ids
>         'text': data['text'], #this is coming from a json variable
>         'format': 'json'
>     }
>     resp = requests.post(requestURL, data=payload)
> 
>     if resp.ok:
>         annData = resp.json()
>         with open('PMC5833734_annotations.json', 'w') as outfile:
>             json.dump(annData, outfile)
> 
> With the regular NCBO annotator I get the response, but with the Annotator+ I get an error 
> [{"error": "Mandatory parameter 'text' missing"}]
> 
> Any suggestions on what I am doing wrong here? I will go again to the documentation you shared to try and figure out what I am missing.
> 
> Regards,
> 
> On Wed, Mar 6, 2019 at 8:32 PM Clement Jonquet <jonquet.lirmm at gmail.com <mailto:jonquet.lirmm at gmail.com>> wrote:
> Hello Leyla
> 
> See 
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5972606/ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5972606/>
> To use  the NCBO Annotator +
> This is currently another server but Stanford is working on offering this directly on their box. 
> 
> We have a format that return tabbed results with CUIs. 
> See also 
> https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2429-2 <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2429-2>
> 
> Clement Jonquet
> Asst. Prof., Univ.  of Montpellier, LIRMM
> 
> 
> Le 6 mars 2019 à 21:25, Leyla Jael García Castro <leylajael at gmail.com <mailto:leylajael at gmail.com>> a écrit :
> 
>> Dear all, 
>> 
>> Is there any how to get CUI and TUI from the annotation service?
>> 
>> I am using your example http://data.bioontology.org/annotator?text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye <http://data.bioontology.org/annotator?text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye>.
>> 
>> Melanoma is annotated with OMIM which includes CUI  C0025202  and TUI T191. Is it possible to get that information form the annotation service? I tried  expand_mappings =true but did not work.
>> 
>> Kind regards,
>> lj 
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