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[bioontology-support] parsing error

Holt, Jonathan jonathan.holt at Vanderbilt.Edu
Fri Jan 25 12:38:17 PST 2013


any update?

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 21, 2013, at 11:01 AM, "Jonathan Holt, DO, MS" <jonathan.holt at vanderbilt.edu<mailto:jonathan.holt at vanderbilt.edu>> wrote:

sure,

mine is in a slightly different place.

for ICD-9 is is located in: /srv/ncbo/bioportal_resources/uploads/1101/1

see below:

root at ncbo 1]# pwd
/srv/ncbo/bioportal_resources/uploads/1101/1
[root at ncbo 1]# ls -hal
total 25M
drwxr-xr-x 2 tomcat tomcat 4.0K Jan 18 13:30 .
drwxr-xr-x 3 tomcat tomcat 4.0K Jan 18 13:30 ..
-rw-r--r-- 1 tomcat tomcat  25M Jan 18 13:30 icd9cm.rrf



<Screen Shot 2013-01-21 at 11.01.05 AM.png>



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 21, 2013, at 10:35 AM, "Lian, Zonghui" <Lian.Zonghui at mayo.edu<mailto:Lian.Zonghui at mayo.edu>>
 wrote:

Dr Holt,

The error may be caused by the file uploader. Can you check if the file was uploaded correctly? For example, for the below ontology, its ontology id is (1290).

<image001.png>

In the linux box, you can find its uploaded files are under
<image006.png>

Please use this method to check the file for your case. As what I know, the file uploader is not stable when the file size is big. Once you find this file you can manually replace them with the right one.  (For rrf format, you need to unzip the zipped file) .

Thanks,
-Lian




From: Holt, Jonathan [mailto:jonathan.holt at Vanderbilt.Edu<http://vanderbilt.edu/>]
Sent: Friday, January 18, 2013 4:09 PM
To: Lian, Zonghui
Cc: support at bioontology.org<mailto:support at bioontology.org> Support
Subject: Re: [bioontology-support] parsing error

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)

<image003.jpg>


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.


<image005.jpg>



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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