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[bioontology-support] [BioPortal] Feedback from Joachim Geeraert

John Graybeal jgraybeal at
Wed Mar 7 08:01:29 PST 2018

Hi Joachim, Zjamed, other users,

We are aware of the recent frequent failures of BioPortal, typically late at night Pacific Time and lasting through much of the night.

As near as we can tell so far, these failures have been caused by extremely heavy and consistent load to our Recommender service. We are evaluating today how to respond to the situation.

In addition to attempting to find the source of the load, and contacting (or failing that, restricting) that source, we will evaluate transferring the Recommender service to a separate machine, or restricting the number of calls allowed to it. Obviously, if you have recently been making a lot of automated calls to BioPortal's API, we would appreciate hearing from you.

With regard to using BioPortal for production services, we have always provided BIoPortal as a research service. We do not have resources—neither computing nor funding—to provide production-level operations. All of our BioPortal staff are filling multiple roles for the Center in a regular day job, so 24x7 monitoring is simply not feasible.

If you want to provide production-level services based on BioPortal, we invite you to contact us to discuss a contracting arrangement that would allow us to offer you that service with a negotiated Service Level Agreement. Alternatively, Bioportal is available as a stand-alone service (the Virtual Appliance) that you can install yourself, or arrange for us to install and maintain as a dedicated service for your needs.

We will be responding to this list with further information as soon as we have further addressed these concerns.


On Mar 7, 2018, at 4:58 AM, support at<mailto:support at> wrote:

Name: Joachim Geeraert

Email: joachim.geeraert at<mailto:joachim.geeraert at>




We're very happy Bioportal exists and advice all our REDCap user to explore the ontologies you offer and use the ontologies in their REDCap projects.
However lately bioportal is often unavailable "We're sorry but something has gone wrong. We have been notified of this error."; not just the webpage, but also the feature in REDCap projects.

The problem is that some of these projects are in production status and have continuous active inclusions of patients which becomes impossible if ontology fields can't be used.
Are you aware of the downtime of bioportal? Are we doing something wrong? Are you aware of solutions in use by other institutions to avoid downtime in projects using the ontologies?

Joachim Geeraert
+32 9 332 05 33

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

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