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[bioontology-support] Getting CUI and TUI in annotations

Leyla Jael García Castro leylajael at
Mon Mar 11 10:44:26 PDT 2019

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 = ''
    #requestURL = ''
    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 =, 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.


On Wed, Mar 6, 2019 at 8:32 PM Clement Jonquet <jonquet.lirmm at>

> Hello Leyla
> See
> 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
> Clement Jonquet
> Asst. Prof., Univ.  of Montpellier, LIRMM
> Le 6 mars 2019 à 21:25, Leyla Jael García Castro <leylajael at> a
> écrit :
> Dear all,
> Is there any how to get CUI and TUI from the annotation service?
> I am using your example
> .
> 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
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at
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