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[bioontology-support] parsing error

Paul R Alexander palexander at stanford.edu
Thu Jan 10 11:12:57 PST 2013


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> 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> 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> 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
>>> http://dbmi.mc.vanderbilt.edu/people/holt.html
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 

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