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[bioontology-support] parsing error

Lian, Zonghui Lian.Zonghui at mayo.edu
Thu Jan 17 12:18:40 PST 2013


Yes, I made an update. I'm looking into it now.

From: Holt, Jonathan [mailto:jonathan.holt at Vanderbilt.Edu]
Sent: Thursday, January 17, 2013 1:33 PM
To: Paul R Alexander
Cc: support at bioontology.org Support; Lian, Zonghui
Subject: Re: [bioontology-support] parsing error

Lian,

Any update?

I have noticed that it happens when I try to import any ontology that is in the RRF format.

Mostly I am trying to import using the import_ontology.rb script.



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 10, 2013, at 1:12 PM, Paul R Alexander <palexander at stanford.edu<mailto:palexander at stanford.edu>> wrote:


Jonathan,

I've CCed our developer at Mayo who is responsible for maintaining the code that processes RRF ontologies to see if he can add some insight. Lian, do we need to do anything to ICD9CM after downloading the zip file containing the RRF files in order to support parsing?

Thanks,
Paul


On Jan 9, 2013, at 3:43 PM, "Holt, Jonathan" <jonathan.holt at Vanderbilt.Edu<mailto:jonathan.holt at Vanderbilt.Edu>> wrote:


I tried to do the ruby import script with my apikey.  That didn't work so I tried downloading it directly from bio portal and uploading the zip folder . Same result .

Jonathan

Sent from my iPhone.

On Jan 9, 2013, at 5:15 PM, "Paul R Alexander" <palexander at stanford.edu<mailto:palexander at stanford.edu>> wrote:
Jonathan,

Can you tell me what file you uploaded for IC9CM? Was it a zip file containing multiple RRF files?

Paul


On Jan 9, 2013, at 3:04 PM, "Holt, Jonathan" <jonathan.holt at Vanderbilt.Edu<mailto:jonathan.holt at Vanderbilt.Edu>> wrote:


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



<Screen Shot 2013-01-09 at 4.59.24 PM.png>

<Screen Shot 2013-01-09 at 2.18.41 PM.png><Screen Shot 2013-01-09 at 4.59.08 PM.png>





.................................
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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