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[bioontology-support] Annotation GET results

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Apr 29 16:24:53 PDT 2020


Hello Ching-Hua,


On Apr 29, 2020, at 3:37 PM, Ching-Hua Chen <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>> wrote:

I am running the sample code "annotate_txt.py" and experiencing results that I can't understand.

I modified the API call to the following, in order to specifically use the ICD10 ontology:

get_json(REST_URL + "/annotator?ontologies=ICD10&text=" + urllib.parse.quote(text_to_annotate))

When I reference the public bioportal, I get non-zero results for the text_to_annotate provided.


I’m not able to reproduce this on our end. I issued that REST call and public BioPortal returns empty results if you constrain to the ICD10 ontology. This is the specific call that I used:

http://data.bioontology.org/annotator?ontologies=ICD10&text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye.

… and I see an empty result set:

[cid:67099FF0-67F6-41E3-80D6-B12A2DAA72E6 at stanford.edu]



However, when I change the URL to reference my local Virtual Appliance, the annotation results are empty, even though ICD10 is listed as one of the ontologies on my virtual appliance.

This discrepancy only occurs for some ontologies, and not others, that are on my virtual appliance. Any suggestions on why this might be happening?


If you’re not seeing expected Annotator results from a particular ontology, one thing to check is whether that ontology has been fully and successfully processed in your appliance instance. In other words, look at the ontology metadata page and see if there are any error statuses for the last submission of the ontology. You should see a list of statuses for the last submission that include “Parsed, Indexed, Metrics, Annotator”:

[cid:9FCDB055-8868-46ED-B34B-F08CDE085D2F at stanford.edu]


Alternatively, if you have administrative privileges for your appliance instance, you can log in and look at the Admin -> Ontology Administration tab, which will indicate if there are any ontology processing issues.

Kind regards,
Jennifer

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