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[bioontology-support] parsing error

Erick Antezana erick.antezana at gmail.com
Fri Feb 1 08:47:09 PST 2013


Hi Trish,

I managed to load my ontology by playing a bit with the ontology
version IDs: I was using number such as 1, 2, 3, ...which didn't
work... but later it worked with numbers such as 10002, 10003, ...

The problem I am facing now is to actually visualise it...After
clicking on the "Visualization" tab, the only thing I can see is a
progress bar that is still running since 2 hours ago...

I have no other issues (the tree view works fine, etc)...

I am working with the sequence ontology.

cheers,
Erick


On 1 February 2013 17:08, Trish Whetzel <whetzel at stanford.edu> wrote:
> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>>
>>
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