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[bioontology-support] parsing error

Holt, Jonathan jonathan.holt at Vanderbilt.Edu
Fri Jan 18 14:09:21 PST 2013


Lian,

After trying to up load the zipped file i get,

"we are sorry, but something has gone wrong. We have been notified of this error."  (see below)

[cid:237EA25C-E316-41CB-8924-1951DF8A5224 at dhcp.mc.vanderbilt.edu]


if i try from the import_ontologies.rb script and point to Stanford's server with my apikey,  I get a parsing error as shown below.


[cid:8BAA608B-D931-46C0-BED9-406432C8FD6C at dhcp.mc.vanderbilt.edu]



Of note, this does NOT happen when I import an ontology in a different format, such as OWL or OBO, as shown in my other ontologies that I have successfully imported using the script.


I've tried getting a new build using:

bpdeploy deployui

but that does help things either.



Thanks,

Jonathan


.................................
Jonathan Holt, DO, MS

Assistant Professor of Biomedical Informatics and Medicine
Departments of Biomedical Informatics & Medicine, Division of Genetic Medicine
Vanderbilt University Medical Center
2209 Garland Ave
412 Eskind Biomedical Library
Nashville, TN  37232-8340
Phone:  615-322-8683
Fax: 615-875-1424

jonathan.holt at vanderbilt.edu<mailto:jonathan.holt at vanderbilt.edu>
http://dbmi.mc.vanderbilt.edu/people/holt.html










On Jan 18, 2013, at 10:26 AM, "Lian, Zonghui" <Lian.Zonghui at mayo.edu<mailto:Lian.Zonghui at mayo.edu>>
 wrote:

Hi Dr Holt,

It looks like the rrf files you used may be not correct(in the figure 2, the icd9cm.rrf was incorrect). Can you download the rrf zip from http://bioportal.bioontology.org/ontologies? After that, you can unzip them into the upload folder and overwrite the old one. Please let me know if it works. Thanks.

-Lian



From: Paul R Alexander [mailto:palexander at stanford.edu<http://stanford.edu>]
Sent: Thursday, January 17, 2013 4:11 PM
To: Lian, Zonghui
Subject: Fwd: [bioontology-support] parsing error



Begin forwarded message:


From: "Holt, Jonathan" <jonathan.holt at Vanderbilt.Edu<mailto:jonathan.holt at Vanderbilt.Edu>>
Subject: [bioontology-support] parsing error
Date: January 9, 2013 3:04:05 PM PST
To: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>

I have recently tried to get my ncbo virtual appliance back up and running.

So, I tried to import some ontologies from the bioportal to my own hosted vm, but got a parsing error.

I also tried to manually and still got a java error.


see attached.


Any thoughts?


Jonathan



<image002.jpg>

<image003.png><image005.jpg>





.................................
Jonathan Holt, DO, MS

Assistant Professor of Biomedical Informatics and Medicine
Departments of Biomedical Informatics & Medicine, Division of Genetic Medicine
Vanderbilt University Medical Center
2209 Garland Ave

412 Eskind Biomedical Library
Nashville, TN  37232-8340
Phone:  615-322-8683
Fax: 615-936-1427

jonathan.holt at vanderbilt.edu<mailto:jonathan.holt at vanderbilt.edu>
http://dbmi.mc.vanderbilt.edu/people/holt.html








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