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[bioontology-support] Fwd: [BioPortal] Feedback from Jean

John Graybeal jgraybeal at
Wed Apr 15 09:53:25 PDT 2020

Reforwarding to list after deleting API key information...

Begin forwarded message:

From: Jean Travassos-EXT <Jean.Travassos-EXT at<mailto:Jean.Travassos-EXT at>>
Subject: RE: [bioontology-support] [BioPortal] Feedback from Jean
Date: April 15, 2020 at 6:11:46 AM PDT
To: John Graybeal <jgraybeal at<mailto:jgraybeal at>>, "support at<mailto:support at>" <support at<mailto:support at>>

Hello John,

Thank you for replying me.
I don’t actually know why but I could get this working in NiFi by passing parameters twice:<DELETED>&include=all&include=all&display_context=false&display_context=false<>

Params include=all and display_context=false was only read after duplicate them. But it is working.

I checked with our infrastructure team and we only have one instance of BP.

Another strange behaviour is exclusive of BP:
We have this Ontology with 3 submissions. When we open the Ontology, its tree is outdated.
After we click in any node, the tree updates itself for the latest and correct version.
Do you know if this may be caused by the lack of any property when submitting a new version?
There’s nothing to do with we trying to consume data, it’s something exclusive from BioPortal…

In attachment there’s examples:
-          AAT38 is our Ontology, contains 3 submissions.
-          Submission3-WhenEnters is the tree in the moment when we first see the Ontology. There’s ‘Reference Compound UoM’ node, which is outdated.
-          Submission3-AfterSelection show the reloaded tree after we select any valid node.
-          Submission3-SelectingUnexisting is the error page if we select the node that shouldn’t be shown anymore, since it existed only in the first submission.

Thank you very much for your attention and time.

If you prefer, I can arrange a quick call.

Best Regards,
Jean Travassos

From: John Graybeal <jgraybeal at<mailto:jgraybeal at>>
Sent: 11 April 2020 01:09
To: support at<mailto:support at>
Cc: Jean Travassos-EXT <Jean.Travassos-EXT at<mailto:Jean.Travassos-EXT at>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Jean

*** CAUTION : External e-mail ***


I confess I am uncertain about what might is causing this, but I can ask some useful questions that will help our team troubleshoot more next week.

The clearest picture would be to see the logs corresponding to those requests, ideally from the Apache or similar logs. The requests from your NiFi flow almost certainly will look different in some way.

Is it possible there are two ontologies that look almost the same, and the flow is asking for the second ontology which only has one submission?  Or alternatively, there are two Bioportal instances and the Apache flow is accessing an instance with only one submission for that ontology?

The more concrete details you can provide, the better our chance of coming up with useful suggestions.


On Apr 10, 2020, at 8:53 AM, support at<mailto:support at> wrote:

Name: Jean
Email: jean.travassos-ext at<mailto:jean.travassos-ext at>

Hello, I'm facing a problem while using BioPortal API and was wondering if you can get me some clarification.
I have BP installed in one server for dev purposes and while I use the URL to GET all children of the master node of our Ontology, it works well (testing in Postman or Firefox or curl).
However, our Ontology has 3 submissions. When another application (an Apache NiFi flow) makes the http GET request with exactly the same URL, in returns only data from the FIRST submission. It should return the data of the latest submission, of course.
Can you get any direction? Is there any parameter or something like that I should configure to prevent this to happen?
Thank you for your attention.
Best regards

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

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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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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