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[bioontology-support] Issues bringing up the NCBO Virtual Appliance: mgrep does not start

Kyle Reynolds kyle.reynolds at
Fri Mar 8 13:41:49 PST 2013

Got it. Not a factor for us, then.

On Mar 8, 2013, at 4:31 PM, "Paul R Alexander" <palexander at<mailto:palexander at>> wrote:

The mgrep service will fail to start if no dictionary file is found. This isn't critical unless you have already processed some ontologies for use with the Annotator, at which point there should be a dictionary file. The error won't affect other areas of the system.


On Mar 8, 2013, at 9:13 AM, Kyle Reynolds <kyle.reynolds at<mailto:kyle.reynolds at>> wrote:

The database is empty, so if that is a requirement for successful start of the mgrep service, that could be our culprit.

From: Trish Whetzel [mailto:whetzel at<>]
Sent: Friday, March 08, 2013 11:58 AM
To: Stephen Granite; Paul R Alexander
Cc: NCBO User Support; ksr at<mailto:ksr at>
Subject: Re: Issues bringing up the NCBO Virtual Appliance: mgrep does not start

Mgrep is used by the Annotator, however I do not know if having this start successfully is dependent on having ontologies populated in the Annotator database. Have you also populated ontologies in the Annotator database? As for the dependency, Paul can you comment on this?


On Mar 8, 2013, at 5:57 AM, Stephen Granite wrote:

In the CVRG, we are interested in bringing up an instance of the NCBO applicance, to serve as a sandbox for ontologies we develop, to harden them prior to submission to NCBO.  We downloaded a copy of the version 1.0 OVF and were able to get the BioPortal web interface to come up without much effort.  However, in the startup, one service fails to start properly: mgrep.  mgrep is supposed to start from init.d, but when we execute “service mgrep status,” the response says the service is dead and the subsystem is locked.  We don’t see anything showing up in logs about mgrep.  What would you advise that we do?  Thanks.

Stephen J. Granite, MS, MBA
Director of Database and Software Development
Center for Cardiovascular Bioinformatics and Modeling
Institute for Computational Medicine
The Johns Hopkins University
3400 North Charles Street
Hackerman Hall 312
Baltimore, MD 21218-2686
phone: 410-516-8849
fax: 410-516-5294

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