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[bioontology-support] [BioPortal] Feedback from misupport

Jennifer Leigh Vendetti vendetti at
Mon Jun 26 11:34:01 PDT 2017

Hello Nazma,

Thank you for the more detailed problem description. See my answers inline below.

On Jun 23, 2017, at 12:27 PM, Nazma Kotcherla <nkotcherla at<mailto:nkotcherla at>> wrote:

Hi Jennifer,

Thank you for your reply.

We are trying to add two more ontologies (CPT and ICD10 CM) to our existing list (ICD 9, ICD 10) in BioPortal. We followed the below navigation path:

BioPortal -> Logged in -> Account Settings -> Custom Ontology Set -> Select Ontologies -> Select from list -> and tried searching in the text box (Search all ontology names)

-          Initially nothing showed up when I typed CPT or ICD 10 CM.
-          Next I tried to check all the names in Groups and Categories( right side of text box) and tried again. I could not find the CPT or ICD 10 CM.
-          Unchecked all the filters from Groups and Categories and then a big list showed up where I found CPT and ICD 10 CM
-          Added them to the list.
-          Clicked on Save Custom Ontologies

OK - now I understand what you mean. This does appear to be a flaw in the user interface. I believe the root of this issue is that the BioPortal application reuses some user interface components across many pages. Once you select a custom ontology set, all other ontologies are hidden from search results - including the search results displayed in the ontology pickers. In other words, once you selected ICD9 and ICD10 for your custom ontology set, all of the ontology picker text boxes in the user interface will only display those two ontologies as options to choose from.

Clearly this should not be the case for the ontology picker on the Account page, because it makes it really difficult to modify the set of custom ontologies you want to work with (as you experienced).

I’ve entered an issue in our GitHub issue tracker to get this fixed [1]. In the mean time, the best workaround I know of would be to:

1). Remove all of the ontologies from your custom ontology set and click the “Save Custom Ontologies" button. This will have the effect of resetting search results in the ontology picker text boxes to include the full list of ontologies in BioPortal.
2). Reenter the list of ontologies you want to use in your custom ontology set, and click the “Save Custom Ontologies” button.

Apologies that this is not particularly convenient, but it will allow you to save the set of ontologies you’re interested in until this issue is addressed in the code base.

It took some time to save the changes but I can see that they have got added to my account. But I am not seeing the new list in the application where we are trying to access these codes using API.

-          Does it take some time to reflect the changes? (or)
-          Is there any additional step that should be done to reflect those changes?

No, I don’t believe either of those should be the case. I’ve created a test account in BioPortal that is limited to the same custom ontology set you’ve specified above. Are you able to send me an example of an API call that doesn’t return the result you expect? I ran a few tests on my end and the functionality seemed to be working as expected.

Kind regards,


From: Jennifer Leigh Vendetti [mailto:vendetti at]
Sent: Thursday, June 22, 2017 5:07 PM
To: NCBO User Support <support at<mailto:support at>>
Cc: Medical Informatics Support <misupport at<mailto:misupport at>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from misupport


It’s unclear to me what you’re asking. Are you working with the Custom Ontology Set functionality on your account page?  Please submit a more detailed problem report.

Kind regards,

On Jun 22, 2017, at 1:38 PM, support at<mailto:support at> wrote:

Name: misupport
Email: misupport at<mailto:misupport at>

I am trying to add CPT ontology to my user account but I am unable to. Could you please help us out with this.

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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