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[bioontology-support] Enabling cron job in VA

Pouchard, Line pouchard at
Wed Sep 6 13:53:08 PDT 2017


thank you.  This helps.

Line Pouchard
Computational Science Initiative
Brookhaven National Laboratory
Building 725, room 2-189
PO Box 5000
Upton, New York, 11973-5000
Phone 631 344-4626
Cell 865 405-5120

From: Jennifer Leigh Vendetti <vendetti at>
Date: Wednesday, September 6, 2017 at 1:34 PM
To: "Pouchard, Line" <pouchard at>
Cc: "support at" <support at>, John Graybeal <jgraybeal at>
Subject: Re: [bioontology-support] Enabling cron job in VA

Hello Line,

On Sep 6, 2017, at 7:57 AM, Pouchard, Line <pouchard at<mailto:pouchard at>> wrote:

Dear all:

Can you please send directions on how to enable a cron job for automatic update of ontologies in the Virtual Appliance?

I’m not sure I understand exactly what you’re asking. The BioPortal Virtual Appliance comes with a project called ncbo_cron that contains a background task that checks the ontology parsing queue for new ontologies every 5 minutes. If you add a new ontology submission, the parsing process should begin within 5 minutes. The ncbo_cron background task is automatically launched when you install the Virtual Appliance, so there shouldn’t be any additional steps necessary on your part.

Or, perhaps you’re referring to the desire to enter a URL for an ontology that’s checked nightly for new submissions? If so, this is something you configure yourself when you add a new ontology submission. On any ontology summary page, you can click the "Add submission" link, and enter such a pull URL in the Location section of the resulting form:

[cid:image001.png at 01D32730.9DCABF60]

Choose the “Load from URL” radio button, and enter the URL that points to your ontology source file. Once you’ve filled out this form and click the “Add submission” button, the Virtual Appliance will pull the initial version of your ontology from that URL, and it will also begin checking on a nightly basis for new versions. If a new version is detected, it will automatically get downloaded/processed.

Hope that helps.

Kind regards,

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