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[bioontology-support] New bioportal install at ORNL - issues

Pouchard, Line Catherine pouchardlc at ornl.gov
Fri Jan 20 10:11:17 PST 2012


Dear all:

Here are some issues that we encountered at ORNL while installing the latest release (below are mail exchanges with Trish):

1)  After deleting an ontology using the admin login, classes were deleted.  However, the ontology was still listed in the browser tab.

2) I have not been able to access the visualization of the classes from my home.  I can access them from inside the lab, and have no performance problems otherwise.  Here is the URL of our implementation:

http://mercury-ncbo.ornl.gov

The Bioporal VM is hosted on our VMWare cluster, running vSphere 4.5.
The underlying hardware are multiple Dell R710 servers.

Line

Line C. Pouchard
Staff Scientist
Extreme Scale Systems Center
Computer Science and Mathematics
DataONE Integration and Semantics WG
Oak Ridge National Laboratory
1 Bethel Valley Road
Oak Ridge, TN 37831-6367
865-574-6125
linepouchard at gmail.com<mailto:linepouchard at gmail.com>

Begin forwarded message:

From: Trish Whetzel <whetzel at stanford.edu<mailto:whetzel at stanford.edu>>
Date: January 20, 2012 3:34:11 AM EST
To: "Pouchard, Line Catherine" <pouchardlc at ornl.gov<mailto:pouchardlc at ornl.gov>>, Paul R Alexander <palexander at stanford.edu<mailto:palexander at stanford.edu>>
Cc: "Eby, Pete I." <ebypi at ornl.gov<mailto:ebypi at ornl.gov>>, "Palanisamy, Giri" <palanisamyg at ornl.gov<mailto:palanisamyg at ornl.gov>>, Natasha Noy <noy at stanford.edu<mailto:noy at stanford.edu>>
Subject: Re: New bioportal install at ORNL - issues

Hi Line,

If possible, it would be best to email our user support mailing list at support at bioontology.org<mailto:support at bioontology.org> which is our public, archived mailing list. Otherwise, individual emails are ok. I have looped in Paul who can help troubleshoot issues with the latest VM Appliance (0.4).

A few comments/questions,
1 - Are you able to load the SWEET ontology in Protege 3.4.7? Are you loading this as an OWL file?

2 - After deleting an ontology, in addition to clearing your browser cache you may also need to clear the BioPortal cache. There is an Admin page at: http://YourDomainName/admin. On this admin page there is a button to "Flush the Memcache" and "Reset the Memcache connection". I believe this cache is periodically refreshed by BioPortal so these ontology entries may have been cleared.

3 - Our instance also has "Re-assign Ontology owner", "Update Ontology metadata", and "User Administration" grayed out. The "user" items can be acted on using the Protege client to access the BioPortal Ontology Metadata and the "Reload Metadata Ontology" link used to refresh the data. Are there user actions that you need to perform? If so, we can set-up a WebEx or I can do a quick demo movie on how to do the tasks you need.

As a note, I will be out of the office next Monday for a meeting and then Tuesday onwards for 1-2 weeks following foot surgery.

Best,
Trish


On Jan 19, 2012, at 1:04 PM, Pouchard, Line Catherine wrote:

Hi Trish and Natasha:

We are having some difficulties that I did not encounter with the previous version of bioportal:

1)The SWEET ontology did not parse.  I am using the same file I did for the last install.

2)I deleted it.  The terms and classes are deleted, but the name is still visible in the browse list.
I also just deleted the Quantities and Units ontology, cleared my browser cache, and it's still visible in the Browse page.

3)In the bioportal admin, Re-assign Ontology owner and Update Ontology metadata are shaded links.  So is User Admin.

I have a demo for the Woods Hole Institute in 2 weeks, and need to make sure the ORNL software we had on top of bioportal has not changed.    I am getting very uncomfortable.

On the positive side, it's now installed outside the ORNL firewall so you can see it at:
http://mercury-ncbo.ornl.gov/ontologies

Please help!
Line

Line C. Pouchard
Staff Scientist
Extreme Scale Systems Center
Computer Science and Mathematics
DataONE Integration and Semantics WG
Oak Ridge National Laboratory
1 Bethel Valley Road
Oak Ridge, TN 37831-6367
865-574-6125
linepouchard at gmail.com<mailto:linepouchard at gmail.com>







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