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[bioontology-support] parsing error

Trish Whetzel whetzel at stanford.edu
Fri Feb 1 08:08:57 PST 2013


Erick, 

What ontology were you trying to load?

Trish 


On Feb 1, 2013, at 2:59 AM, Erick Antezana wrote:

> Hi,
> 
> I got similar error messages:
> 
>    BioPortal returned an error: Error Parsing Ontologies: [(Id: 1004) - Ontology version with the given id does not exist]
> 
> any suggestions where to check?  log files or so?
> 
> cheers,
> erick
> 
> On 25 January 2013 22:29, Holt, Jonathan <jonathan.holt at vanderbilt.edu> wrote:
> When I tried to upload the ontology manually, I got the error, 
> 
> 
> "we are sorry, but something has gone wrong. We have been notified of this error." 
> 
> 
> 
> <image003.jpg>
>  
> 
> 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
> http://dbmi.mc.vanderbilt.edu/people/holt.html
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On Jan 25, 2013, at 3:02 PM, "Lian, Zonghui" <Lian.Zonghui at mayo.edu>
>  wrote:
> 
>> One you uploaded the files, you can run the parser through this page: http://rest.bioontology.org/bioportal_admin/parseontologies.jsf
>>  
>> From: Holt, Jonathan [mailto:jonathan.holt at Vanderbilt.Edu] 
>> Sent: Friday, January 25, 2013 2:38 PM
>> To: Lian, Zonghui
>> Cc: Paul R Alexander (palexander at stanford.edu); support at bioontology.org Support
>> Subject: Re: [bioontology-support] parsing error
>>  
>> 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
>> 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> 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
>> http://dbmi.mc.vanderbilt.edu/people/holt.html
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>> 
>>  
>> On Jan 21, 2013, at 10:35 AM, "Lian, Zonghui" <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] 
>> Sent: Friday, January 18, 2013 4:09 PM
>> To: Lian, Zonghui
>> Cc: 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
>> http://dbmi.mc.vanderbilt.edu/people/holt.html
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>> 
>>  
>> On Jan 18, 2013, at 10:26 AM, "Lian, Zonghui" <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] 
>> 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>
>> Subject: [bioontology-support] parsing error
>> Date: January 9, 2013 3:04:05 PM PST
>> To: "support at bioontology.org" <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
>> 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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