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[bioontology-support] [BioPortal] Feedback from Joachim Geeraert
redcap at uzgent.be
Fri Mar 9 02:08:49 PST 2018
* If you want to provide production-level services based on BioPortal…
We use Bioportal in combination with REDCap which we use for electronic data capture for academic studies.
* 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.To obtain the VMWare Virtual Appliance, contact NCBO Support<mailto:support at bioontology.org> to initiate your request.
I would like to initiate a request for a virtual machine.
Do you also have installation instructions? We can setup most popular Linux distributions in our institution datacenter but importing virtual machines is not allowed/supported. They suggest installing it the ‘classic way’.
Thanks in advance,
Project advisor Big Data
Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent
T +32 9 332 08 00
lieven.vaneeckhaute at uzgent.be<mailto:lieven.vaneeckhaute at uzgent.be>
Ingang 81 | Route 812 | uzgent.be<http://www.uzgent.be> | [Facebook UZ Gent] <https://www.facebook.com/uzgent> | [Twitter UZ Gent] <https://twitter.com/UZGent>
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From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: woensdag 7 maart 2018 17:01
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Joachim Geeraert <Joachim.Geeraert at UGent.be<mailto:Joachim.Geeraert at UGent.be>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Joachim Geeraert
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 bioontology.org<mailto:support at bioontology.org> wrote:
Name: Joachim Geeraert
Email: joachim.geeraert at ugent.be<mailto:joachim.geeraert at ugent.be>
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?
+32 9 332 05 33
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
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