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[bioontology-support] Trying to troubleshoot annotate_text output

John Graybeal jgraybeal at stanford.edu
Thu Apr 16 09:06:01 PDT 2020


I'm glad the issue is resolved.

One thing you can check if it comes back is whether the same annotation request from the UI works. If it does, then the delay may be coming from your application. (You can also try running the request from a browser, or from curl, to see how fast it comes back, and to make sure your API command is working as you expect.)

If the UI request doesn't work, then there may be a problem with processing the ontology. If the UI works but the API doesn't, there is likely a problem with the API request format, and you could send it to the support list (along with the behaviors that result) if you can't figure out what it should be.

John

On Apr 16, 2020, at 7:48 AM, Ching-Hua Chen <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>> wrote:

This issue is resolved. Not sure why... but I am getting outputs. I think there was a really long lag in print to screen for some reason. Thanks.

Ching-Hua Chen

Computational Health Behavior & Decision Science
IBM, T.J. Watson Research Center
1101 Kitchawan Road, Yorktown Heights, NY 10598

chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>
(914) 945-2061 (o); (845) 519-7582 (m)

"Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson


----- Original message -----
From: Ching-Hua Chen/Watson/IBM
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc:
Subject: Trying to troubleshoot annotate_text output
Date: Thu, Apr 16, 2020 7:06 AM

Hi,

I have used the ruby script (bioportal_ontologies_import.rb) provided to import the OCHV ontology to my virtual appliance. When I run "list_ontologies.py" I see that it is listed, after the ontology "STY". I only have these two ontologies on my appliance at the moment.

When I ran "annotate_text.py", as is, using the data.bioontology.org<http://data.bioontology.org> URL, the script returned results from OCHV (I only have OCHV in my bioportal account).

However, when I edited "annotate_text.py" to reference my virtual appliance URL (I didn't not edit anything else in the script), the script returned nothing. It ran to completion without error.

I'm wondering why I'm not getting any results when I run "annotate_text" on my virtual appliance, compared to when I ran the same thing on the bioontology.org<http://bioontology.org>.

Best,

Ching-Hua Chen

Computational Health Behavior & Decision Science
IBM, T.J. Watson Research Center
1101 Kitchawan Road, Yorktown Heights, NY 10598

chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>
(914) 945-2061 (o); (845) 519-7582 (m)

"Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson


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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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