[bioontology-support] FW: NCBO Appliance: problem submitting large ontology

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[bioontology-support] FW: NCBO Appliance: problem submitting large ontology

Ma, Guozhong (NIH/NHLBI) [C]
Hi,

Please see what I just sent to Trish below. Please get back to me if you are familiar with Trish's development work.
Thanks,
GM

-----Original Message-----
From: Ma, Guozhong (NIH/NHLBI) [C]
Sent: Tuesday, April 05, 2011 12:38 PM
To: 'Trish Whetzel'
Subject: RE: [bioontology-support] NCBO Appliance: problem submitting large ontology

Hi Trish,

I checked out your code and downloaded the latest version of NCIt (3/15/2011).

Below is the exception from running "NCITVeryfy" in Eclipse. Could you adivise?

Thanks,

Start conversion at Tue Apr 05 12:33:38 EDT 2011
SEVERE: Error loading instances -- edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
Was expecting one of:
    <EOF>
    "(" ...
    ";+" ...
    ";+" ...
   
        at edu.stanford.smi.protege.storage.clips.Parser.generateParseException(Unknown Source)
        at edu.stanford.smi.protege.storage.clips.Parser.jj_consume_token(Unknown Source)
        at edu.stanford.smi.protege.storage.clips.Parser.parseKnowledgeBase(Unknown Source)
        at edu.stanford.smi.protege.storage.clips.Parser.loadInstances(Unknown Source)
        at edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.loadKnowledgeBase(Unknown Source)
        at edu.stanford.smi.protege.model.Project.loadProjectKB(Unknown Source)
        at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
        at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
        at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
        at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
        at NCITVerify.main(NCITVerify.java:23)

SEVERE: no project instance -- Project.getProjectInstance()
Error: edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
Was expecting one of:
    <EOF>
    "(" ...
    ";+" ...
    ";+" ...

-----Original Message-----
From: Trish Whetzel [mailto:[hidden email]]
Sent: Thursday, February 17, 2011 11:49 AM
To: Ma, Guozhong (NIH/NHLBI) [C]
Cc: support; Paul R Alexander; Galvez, Jose (NIH/NHLBI) [C]; Kadalli, Shiv (NIH/NHLBI) [C]
Subject: Re: [bioontology-support] NCBO Appliance: problem submitting large ontology
Importance: High

Loading the NCI Thesaurus requires a few steps due to the size of the file and since it is developed with a modified version of Protege. If you plan to use the NCI Thesaurus in the Annotator workflow, then the additional XML tags added into the synonym property values need to be removed. Code to pre-process NCIt is located at:
https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F
and can be checked out via anonymous SVN. This information is now also in the VM Appliance documentation.

After the file is processed, due to the size of the file the NCIt is usually not loaded via the BioPortal Submit New Ontology form via the Web UI. Others on the support mailing list can expand on the loading process.

Trish


On Feb 17, 2011, at 3:51 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:

> Hi Paul,
>
> I downloaded NCI Thesaurus from BioPortal. Tried to upload to our local NCBO Appliance. Got an error message:
>
> "Errors On Form
> File is too large"
>
> Question: Did this ontology go through web form upload at BioPortal? Or, it was simply saved onto your server by admin?
>
> I am trying to see if this is resulted from our end due to memory, timeout setting, etc.
>
> Thanks,
>
> --
> Guozhong Ma, PhD
> Senior Engineer (Contractor)
> Software Engineering Branch (SEB)
> Center for Biomedical Informatics (CBI)
> National Heart Lung and Blood Institute, NIH
> Telephone: 301-435-0425 | Email: [hidden email]
>
> _______________________________________________
> bioontology-support mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology

Natasha Noy
What are you passing in as your argument to the Java program?

Natasha



On Apr 5, 2011, at 9:41 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:

> Hi,
>
> Please see what I just sent to Trish below. Please get back to me if you are familiar with Trish's development work.
> Thanks,
> GM
>
> -----Original Message-----
> From: Ma, Guozhong (NIH/NHLBI) [C]
> Sent: Tuesday, April 05, 2011 12:38 PM
> To: 'Trish Whetzel'
> Subject: RE: [bioontology-support] NCBO Appliance: problem submitting large ontology
>
> Hi Trish,
>
> I checked out your code and downloaded the latest version of NCIt (3/15/2011).
>
> Below is the exception from running "NCITVeryfy" in Eclipse. Could you adivise?
>
> Thanks,
>
> Start conversion at Tue Apr 05 12:33:38 EDT 2011
> SEVERE: Error loading instances -- edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
> Was expecting one of:
>    <EOF>
>    "(" ...
>    ";+" ...
>    ";+" ...
>
> at edu.stanford.smi.protege.storage.clips.Parser.generateParseException(Unknown Source)
> at edu.stanford.smi.protege.storage.clips.Parser.jj_consume_token(Unknown Source)
> at edu.stanford.smi.protege.storage.clips.Parser.parseKnowledgeBase(Unknown Source)
> at edu.stanford.smi.protege.storage.clips.Parser.loadInstances(Unknown Source)
> at edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.loadKnowledgeBase(Unknown Source)
> at edu.stanford.smi.protege.model.Project.loadProjectKB(Unknown Source)
> at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> at NCITVerify.main(NCITVerify.java:23)
>
> SEVERE: no project instance -- Project.getProjectInstance()
> Error: edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
> Was expecting one of:
>    <EOF>
>    "(" ...
>    ";+" ...
>    ";+" ...
>
> -----Original Message-----
> From: Trish Whetzel [mailto:[hidden email]]
> Sent: Thursday, February 17, 2011 11:49 AM
> To: Ma, Guozhong (NIH/NHLBI) [C]
> Cc: support; Paul R Alexander; Galvez, Jose (NIH/NHLBI) [C]; Kadalli, Shiv (NIH/NHLBI) [C]
> Subject: Re: [bioontology-support] NCBO Appliance: problem submitting large ontology
> Importance: High
>
> Loading the NCI Thesaurus requires a few steps due to the size of the file and since it is developed with a modified version of Protege. If you plan to use the NCI Thesaurus in the Annotator workflow, then the additional XML tags added into the synonym property values need to be removed. Code to pre-process NCIt is located at:
> https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F
> and can be checked out via anonymous SVN. This information is now also in the VM Appliance documentation.
>
> After the file is processed, due to the size of the file the NCIt is usually not loaded via the BioPortal Submit New Ontology form via the Web UI. Others on the support mailing list can expand on the loading process.
>
> Trish
>
>
> On Feb 17, 2011, at 3:51 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>
>> Hi Paul,
>>
>> I downloaded NCI Thesaurus from BioPortal. Tried to upload to our local NCBO Appliance. Got an error message:
>>
>> "Errors On Form
>> File is too large"
>>
>> Question: Did this ontology go through web form upload at BioPortal? Or, it was simply saved onto your server by admin?
>>
>> I am trying to see if this is resulted from our end due to memory, timeout setting, etc.
>>
>> Thanks,
>>
>> --
>> Guozhong Ma, PhD
>> Senior Engineer (Contractor)
>> Software Engineering Branch (SEB)
>> Center for Biomedical Informatics (CBI)
>> National Heart Lung and Blood Institute, NIH
>> Telephone: 301-435-0425 | Email: [hidden email]
>>
>> _______________________________________________
>> bioontology-support mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
> _______________________________________________
> bioontology-support mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology

Ma, Guozhong (NIH/NHLBI) [C]
The file downloaded: Thesaurus.owl

GM

-----Original Message-----
From: Natasha Noy [mailto:[hidden email]]
Sent: Tuesday, April 05, 2011 12:54 PM
To: Ma, Guozhong (NIH/NHLBI) [C]
Cc: NCBO support
Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology

What are you passing in as your argument to the Java program?

Natasha



On Apr 5, 2011, at 9:41 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:

> Hi,
>
> Please see what I just sent to Trish below. Please get back to me if you are familiar with Trish's development work.
> Thanks,
> GM
>
> -----Original Message-----
> From: Ma, Guozhong (NIH/NHLBI) [C]
> Sent: Tuesday, April 05, 2011 12:38 PM
> To: 'Trish Whetzel'
> Subject: RE: [bioontology-support] NCBO Appliance: problem submitting large ontology
>
> Hi Trish,
>
> I checked out your code and downloaded the latest version of NCIt (3/15/2011).
>
> Below is the exception from running "NCITVeryfy" in Eclipse. Could you adivise?
>
> Thanks,
>
> Start conversion at Tue Apr 05 12:33:38 EDT 2011
> SEVERE: Error loading instances -- edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
> Was expecting one of:
>    <EOF>
>    "(" ...
>    ";+" ...
>    ";+" ...
>
> at edu.stanford.smi.protege.storage.clips.Parser.generateParseException(Unknown Source)
> at edu.stanford.smi.protege.storage.clips.Parser.jj_consume_token(Unknown Source)
> at edu.stanford.smi.protege.storage.clips.Parser.parseKnowledgeBase(Unknown Source)
> at edu.stanford.smi.protege.storage.clips.Parser.loadInstances(Unknown Source)
> at edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.loadKnowledgeBase(Unknown Source)
> at edu.stanford.smi.protege.model.Project.loadProjectKB(Unknown Source)
> at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> at NCITVerify.main(NCITVerify.java:23)
>
> SEVERE: no project instance -- Project.getProjectInstance()
> Error: edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
> Was expecting one of:
>    <EOF>
>    "(" ...
>    ";+" ...
>    ";+" ...
>
> -----Original Message-----
> From: Trish Whetzel [mailto:[hidden email]]
> Sent: Thursday, February 17, 2011 11:49 AM
> To: Ma, Guozhong (NIH/NHLBI) [C]
> Cc: support; Paul R Alexander; Galvez, Jose (NIH/NHLBI) [C]; Kadalli, Shiv (NIH/NHLBI) [C]
> Subject: Re: [bioontology-support] NCBO Appliance: problem submitting large ontology
> Importance: High
>
> Loading the NCI Thesaurus requires a few steps due to the size of the file and since it is developed with a modified version of Protege. If you plan to use the NCI Thesaurus in the Annotator workflow, then the additional XML tags added into the synonym property values need to be removed. Code to pre-process NCIt is located at:
> https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F
> and can be checked out via anonymous SVN. This information is now also in the VM Appliance documentation.
>
> After the file is processed, due to the size of the file the NCIt is usually not loaded via the BioPortal Submit New Ontology form via the Web UI. Others on the support mailing list can expand on the loading process.
>
> Trish
>
>
> On Feb 17, 2011, at 3:51 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>
>> Hi Paul,
>>
>> I downloaded NCI Thesaurus from BioPortal. Tried to upload to our local NCBO Appliance. Got an error message:
>>
>> "Errors On Form
>> File is too large"
>>
>> Question: Did this ontology go through web form upload at BioPortal? Or, it was simply saved onto your server by admin?
>>
>> I am trying to see if this is resulted from our end due to memory, timeout setting, etc.
>>
>> Thanks,
>>
>> --
>> Guozhong Ma, PhD
>> Senior Engineer (Contractor)
>> Software Engineering Branch (SEB)
>> Center for Biomedical Informatics (CBI)
>> National Heart Lung and Blood Institute, NIH
>> Telephone: 301-435-0425 | Email: [hidden email]
>>
>> _______________________________________________
>> bioontology-support mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
> _______________________________________________
> bioontology-support mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology

Natasha Noy
I just looked at the code, and it takes the .pprj file, not the owl file.

So you need to open this Thesaurus.owl file in Protege and then save it -- the saving will create an additional file, Thesaurus.pprj -- that's the one you pass to the Java code.

Natasha



On Apr 5, 2011, at 9:57 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:

> The file downloaded: Thesaurus.owl
>
> GM
>
> -----Original Message-----
> From: Natasha Noy [mailto:[hidden email]]
> Sent: Tuesday, April 05, 2011 12:54 PM
> To: Ma, Guozhong (NIH/NHLBI) [C]
> Cc: NCBO support
> Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology
>
> What are you passing in as your argument to the Java program?
>
> Natasha
>
>
>
> On Apr 5, 2011, at 9:41 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>
>> Hi,
>>
>> Please see what I just sent to Trish below. Please get back to me if you are familiar with Trish's development work.
>> Thanks,
>> GM
>>
>> -----Original Message-----
>> From: Ma, Guozhong (NIH/NHLBI) [C]
>> Sent: Tuesday, April 05, 2011 12:38 PM
>> To: 'Trish Whetzel'
>> Subject: RE: [bioontology-support] NCBO Appliance: problem submitting large ontology
>>
>> Hi Trish,
>>
>> I checked out your code and downloaded the latest version of NCIt (3/15/2011).
>>
>> Below is the exception from running "NCITVeryfy" in Eclipse. Could you adivise?
>>
>> Thanks,
>>
>> Start conversion at Tue Apr 05 12:33:38 EDT 2011
>> SEVERE: Error loading instances -- edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
>> Was expecting one of:
>>   <EOF>
>>   "(" ...
>>   ";+" ...
>>   ";+" ...
>>
>> at edu.stanford.smi.protege.storage.clips.Parser.generateParseException(Unknown Source)
>> at edu.stanford.smi.protege.storage.clips.Parser.jj_consume_token(Unknown Source)
>> at edu.stanford.smi.protege.storage.clips.Parser.parseKnowledgeBase(Unknown Source)
>> at edu.stanford.smi.protege.storage.clips.Parser.loadInstances(Unknown Source)
>> at edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.loadKnowledgeBase(Unknown Source)
>> at edu.stanford.smi.protege.model.Project.loadProjectKB(Unknown Source)
>> at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>> at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>> at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>> at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>> at NCITVerify.main(NCITVerify.java:23)
>>
>> SEVERE: no project instance -- Project.getProjectInstance()
>> Error: edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
>> Was expecting one of:
>>   <EOF>
>>   "(" ...
>>   ";+" ...
>>   ";+" ...
>>
>> -----Original Message-----
>> From: Trish Whetzel [mailto:[hidden email]]
>> Sent: Thursday, February 17, 2011 11:49 AM
>> To: Ma, Guozhong (NIH/NHLBI) [C]
>> Cc: support; Paul R Alexander; Galvez, Jose (NIH/NHLBI) [C]; Kadalli, Shiv (NIH/NHLBI) [C]
>> Subject: Re: [bioontology-support] NCBO Appliance: problem submitting large ontology
>> Importance: High
>>
>> Loading the NCI Thesaurus requires a few steps due to the size of the file and since it is developed with a modified version of Protege. If you plan to use the NCI Thesaurus in the Annotator workflow, then the additional XML tags added into the synonym property values need to be removed. Code to pre-process NCIt is located at:
>> https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F
>> and can be checked out via anonymous SVN. This information is now also in the VM Appliance documentation.
>>
>> After the file is processed, due to the size of the file the NCIt is usually not loaded via the BioPortal Submit New Ontology form via the Web UI. Others on the support mailing list can expand on the loading process.
>>
>> Trish
>>
>>
>> On Feb 17, 2011, at 3:51 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>>
>>> Hi Paul,
>>>
>>> I downloaded NCI Thesaurus from BioPortal. Tried to upload to our local NCBO Appliance. Got an error message:
>>>
>>> "Errors On Form
>>> File is too large"
>>>
>>> Question: Did this ontology go through web form upload at BioPortal? Or, it was simply saved onto your server by admin?
>>>
>>> I am trying to see if this is resulted from our end due to memory, timeout setting, etc.
>>>
>>> Thanks,
>>>
>>> --
>>> Guozhong Ma, PhD
>>> Senior Engineer (Contractor)
>>> Software Engineering Branch (SEB)
>>> Center for Biomedical Informatics (CBI)
>>> National Heart Lung and Blood Institute, NIH
>>> Telephone: 301-435-0425 | Email: [hidden email]
>>>
>>> _______________________________________________
>>> bioontology-support mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>> _______________________________________________
>> bioontology-support mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology

Ma, Guozhong (NIH/NHLBI) [C]

I followed what the instruction said.

 

Anyways, I tried to open it using Protégé 3.4.5. Here is what I got: (just so you know. I’ll keep trying.)

 

 

-----Original Message-----
From: Natasha Noy [mailto:[hidden email]]
Sent: Tuesday, April 05, 2011 1:00 PM
To: Ma, Guozhong (NIH/NHLBI) [C]
Cc: NCBO support
Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology

 

I just looked at the code, and it takes the .pprj file, not the owl file.

 

So you need to open this Thesaurus.owl file in Protege and then save it -- the saving will create an additional file, Thesaurus.pprj -- that's the one you pass to the Java code.

 

Natasha

 

 

 

On Apr 5, 2011, at 9:57 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:

 

> The file downloaded: Thesaurus.owl

>

> GM

>

> -----Original Message-----

> From: Natasha Noy [mailto:[hidden email]]

> Sent: Tuesday, April 05, 2011 12:54 PM

> To: Ma, Guozhong (NIH/NHLBI) [C]

> Cc: NCBO support

> Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology

>

> What are you passing in as your argument to the Java program?

>

> Natasha

>

>

>

> On Apr 5, 2011, at 9:41 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:

>

>> Hi,

>>

>> Please see what I just sent to Trish below. Please get back to me if you are familiar with Trish's development work.

>> Thanks,

>> GM

>>

>> -----Original Message-----

>> From: Ma, Guozhong (NIH/NHLBI) [C]

>> Sent: Tuesday, April 05, 2011 12:38 PM

>> To: 'Trish Whetzel'

>> Subject: RE: [bioontology-support] NCBO Appliance: problem submitting large ontology

>>

>> Hi Trish,

>>

>> I checked out your code and downloaded the latest version of NCIt (3/15/2011).

>>

>> Below is the exception from running "NCITVeryfy" in Eclipse. Could you adivise?

>>

>> Thanks,

>>

>> Start conversion at Tue Apr 05 12:33:38 EDT 2011

>> SEVERE: Error loading instances -- edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.

>> Was expecting one of:

>>   <EOF>

>>   "(" ...

>>   ";+" ...

>>   ";+" ...

>>

>>    at edu.stanford.smi.protege.storage.clips.Parser.generateParseException(Unknown Source)

>>    at edu.stanford.smi.protege.storage.clips.Parser.jj_consume_token(Unknown Source)

>>    at edu.stanford.smi.protege.storage.clips.Parser.parseKnowledgeBase(Unknown Source)

>>    at edu.stanford.smi.protege.storage.clips.Parser.loadInstances(Unknown Source)

>>    at edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.loadKnowledgeBase(Unknown Source)

>>    at edu.stanford.smi.protege.model.Project.loadProjectKB(Unknown Source)

>>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)

>>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)

>>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)

>>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)

>>    at NCITVerify.main(NCITVerify.java:23)

>>

>> SEVERE: no project instance -- Project.getProjectInstance()

>> Error: edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.

>> Was expecting one of:

>>   <EOF>

>>   "(" ...

>>   ";+" ...

>>   ";+" ...

>>

>> -----Original Message-----

>> From: Trish Whetzel [mailto:[hidden email]]

>> Sent: Thursday, February 17, 2011 11:49 AM

>> To: Ma, Guozhong (NIH/NHLBI) [C]

>> Cc: support; Paul R Alexander; Galvez, Jose (NIH/NHLBI) [C]; Kadalli, Shiv (NIH/NHLBI) [C]

>> Subject: Re: [bioontology-support] NCBO Appliance: problem submitting large ontology

>> Importance: High

>>

>> Loading the NCI Thesaurus requires a few steps due to the size of the file and since it is developed with a modified version of Protege. If you plan to use the NCI Thesaurus in the Annotator workflow, then the additional XML tags added into the synonym property values need to be removed. Code to pre-process NCIt is located at:

>> https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F

>> and can be checked out via anonymous SVN. This information is now also in the VM Appliance documentation.

>>

>> After the file is processed, due to the size of the file the NCIt is usually not loaded via the BioPortal Submit New Ontology form via the Web UI. Others on the support mailing list can expand on the loading process.

>>

>> Trish

>>

>>

>> On Feb 17, 2011, at 3:51 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:

>>

>>> Hi Paul,

>>>

>>> I downloaded NCI Thesaurus from BioPortal. Tried to upload to our local NCBO Appliance. Got an error message:

>>>

>>> "Errors On Form

>>> File is too large"

>>>

>>> Question: Did this ontology go through web form upload at BioPortal? Or, it was simply saved onto your server by admin?

>>>

>>> I am trying to see if this is resulted from our end due to memory, timeout setting, etc.

>>>

>>> Thanks,

>>>

>>> --

>>> Guozhong Ma, PhD

>>> Senior Engineer (Contractor)

>>> Software Engineering Branch (SEB)

>>> Center for Biomedical Informatics (CBI)

>>> National Heart Lung and Blood Institute, NIH

>>> Telephone: 301-435-0425 | Email: [hidden email]

>>>

>>> _______________________________________________

>>> bioontology-support mailing list

>>> [hidden email]

>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

>>

>> _______________________________________________

>> bioontology-support mailing list

>> [hidden email]

>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

>

 


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Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology

Natasha Noy
Actually, true -- it might have worked with the .owl file as well. My bad.

However, the fact that you cannot open it in Protege means that your OWL file is somehow corrupt. Maybe it wasn't downloaded properly? Your screenshot doesn't show the complete error message, so it is hard to tell. But you need to be able to open the file in Protege before you can run Trish's script.

Natasha



On Apr 5, 2011, at 10:06 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:

> I followed what the instruction said.
>  
> Anyways, I tried to open it using Protégé 3.4.5. Here is what I got: (just so you know. I’ll keep trying.)
>  
> <image001.png>
>  
> -----Original Message-----
> From: Natasha Noy [mailto:[hidden email]]
> Sent: Tuesday, April 05, 2011 1:00 PM
> To: Ma, Guozhong (NIH/NHLBI) [C]
> Cc: NCBO support
> Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology
>  
> I just looked at the code, and it takes the .pprj file, not the owl file.
>  
> So you need to open this Thesaurus.owl file in Protege and then save it -- the saving will create an additional file, Thesaurus.pprj -- that's the one you pass to the Java code.
>  
> Natasha
>  
>  
>  
> On Apr 5, 2011, at 9:57 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>  
> > The file downloaded: Thesaurus.owl
> >
> > GM
> >
> > -----Original Message-----
> > From: Natasha Noy [mailto:[hidden email]]
> > Sent: Tuesday, April 05, 2011 12:54 PM
> > To: Ma, Guozhong (NIH/NHLBI) [C]
> > Cc: NCBO support
> > Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology
> >
> > What are you passing in as your argument to the Java program?
> >
> > Natasha
> >
> >
> >
> > On Apr 5, 2011, at 9:41 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
> >
> >> Hi,
> >>
> >> Please see what I just sent to Trish below. Please get back to me if you are familiar with Trish's development work.
> >> Thanks,
> >> GM
> >>
> >> -----Original Message-----
> >> From: Ma, Guozhong (NIH/NHLBI) [C]
> >> Sent: Tuesday, April 05, 2011 12:38 PM
> >> To: 'Trish Whetzel'
> >> Subject: RE: [bioontology-support] NCBO Appliance: problem submitting large ontology
> >>
> >> Hi Trish,
> >>
> >> I checked out your code and downloaded the latest version of NCIt (3/15/2011).
> >>
> >> Below is the exception from running "NCITVeryfy" in Eclipse. Could you adivise?
> >>
> >> Thanks,
> >>
> >> Start conversion at Tue Apr 05 12:33:38 EDT 2011
> >> SEVERE: Error loading instances -- edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
> >> Was expecting one of:
> >>   <EOF>
> >>   "(" ...
> >>   ";+" ...
> >>   ";+" ...
> >>
> >>    at edu.stanford.smi.protege.storage.clips.Parser.generateParseException(Unknown Source)
> >>    at edu.stanford.smi.protege.storage.clips.Parser.jj_consume_token(Unknown Source)
> >>    at edu.stanford.smi.protege.storage.clips.Parser.parseKnowledgeBase(Unknown Source)
> >>    at edu.stanford.smi.protege.storage.clips.Parser.loadInstances(Unknown Source)
> >>    at edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.loadKnowledgeBase(Unknown Source)
> >>    at edu.stanford.smi.protege.model.Project.loadProjectKB(Unknown Source)
> >>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> >>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> >>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> >>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> >>    at NCITVerify.main(NCITVerify.java:23)
> >>
> >> SEVERE: no project instance -- Project.getProjectInstance()
> >> Error: edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
> >> Was expecting one of:
> >>   <EOF>
> >>   "(" ...
> >>   ";+" ...
> >>   ";+" ...
> >>
> >> -----Original Message-----
> >> From: Trish Whetzel [mailto:[hidden email]]
> >> Sent: Thursday, February 17, 2011 11:49 AM
> >> To: Ma, Guozhong (NIH/NHLBI) [C]
> >> Cc: support; Paul R Alexander; Galvez, Jose (NIH/NHLBI) [C]; Kadalli, Shiv (NIH/NHLBI) [C]
> >> Subject: Re: [bioontology-support] NCBO Appliance: problem submitting large ontology
> >> Importance: High
> >>
> >> Loading the NCI Thesaurus requires a few steps due to the size of the file and since it is developed with a modified version of Protege. If you plan to use the NCI Thesaurus in the Annotator workflow, then the additional XML tags added into the synonym property values need to be removed. Code to pre-process NCIt is located at:
> >> https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F
> >> and can be checked out via anonymous SVN. This information is now also in the VM Appliance documentation.
> >>
> >> After the file is processed, due to the size of the file the NCIt is usually not loaded via the BioPortal Submit New Ontology form via the Web UI. Others on the support mailing list can expand on the loading process.
> >>
> >> Trish
> >>
> >>
> >> On Feb 17, 2011, at 3:51 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
> >>
> >>> Hi Paul,
> >>>
> >>> I downloaded NCI Thesaurus from BioPortal. Tried to upload to our local NCBO Appliance. Got an error message:
> >>>
> >>> "Errors On Form
> >>> File is too large"
> >>>
> >>> Question: Did this ontology go through web form upload at BioPortal? Or, it was simply saved onto your server by admin?
> >>>
> >>> I am trying to see if this is resulted from our end due to memory, timeout setting, etc.
> >>>
> >>> Thanks,
> >>>
> >>> --
> >>> Guozhong Ma, PhD
> >>> Senior Engineer (Contractor)
> >>> Software Engineering Branch (SEB)
> >>> Center for Biomedical Informatics (CBI)
> >>> National Heart Lung and Blood Institute, NIH
> >>> Telephone: 301-435-0425 | Email: [hidden email]
> >>>
> >>> _______________________________________________
> >>> bioontology-support mailing list
> >>> [hidden email]
> >>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> >>
> >> _______________________________________________
> >> bioontology-support mailing list
> >> [hidden email]
> >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> >
>  

_______________________________________________
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Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology

Ma, Guozhong (NIH/NHLBI) [C]
I'll keep trying. Thanks for your advise...
GM

-----Original Message-----
From: Natasha Noy [mailto:[hidden email]]
Sent: Tuesday, April 05, 2011 1:10 PM
To: Ma, Guozhong (NIH/NHLBI) [C]
Cc: NCBO support; Galvez, Jose (NIH/NHLBI) [C]; Kadalli, Shiv (NIH/NHLBI) [C]; Butler, Lee (NIH/NHLBI) [C]; Martin, Norman (NIH/NHLBI) [C]
Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology

Actually, true -- it might have worked with the .owl file as well. My bad.

However, the fact that you cannot open it in Protege means that your OWL file is somehow corrupt. Maybe it wasn't downloaded properly? Your screenshot doesn't show the complete error message, so it is hard to tell. But you need to be able to open the file in Protege before you can run Trish's script.

Natasha



On Apr 5, 2011, at 10:06 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:

> I followed what the instruction said.
>  
> Anyways, I tried to open it using Protégé 3.4.5. Here is what I got: (just so you know. I'll keep trying.)
>  
> <image001.png>
>  
> -----Original Message-----
> From: Natasha Noy [mailto:[hidden email]]
> Sent: Tuesday, April 05, 2011 1:00 PM
> To: Ma, Guozhong (NIH/NHLBI) [C]
> Cc: NCBO support
> Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology
>  
> I just looked at the code, and it takes the .pprj file, not the owl file.
>  
> So you need to open this Thesaurus.owl file in Protege and then save it -- the saving will create an additional file, Thesaurus.pprj -- that's the one you pass to the Java code.
>  
> Natasha
>  
>  
>  
> On Apr 5, 2011, at 9:57 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>  
> > The file downloaded: Thesaurus.owl
> >
> > GM
> >
> > -----Original Message-----
> > From: Natasha Noy [mailto:[hidden email]]
> > Sent: Tuesday, April 05, 2011 12:54 PM
> > To: Ma, Guozhong (NIH/NHLBI) [C]
> > Cc: NCBO support
> > Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology
> >
> > What are you passing in as your argument to the Java program?
> >
> > Natasha
> >
> >
> >
> > On Apr 5, 2011, at 9:41 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
> >
> >> Hi,
> >>
> >> Please see what I just sent to Trish below. Please get back to me if you are familiar with Trish's development work.
> >> Thanks,
> >> GM
> >>
> >> -----Original Message-----
> >> From: Ma, Guozhong (NIH/NHLBI) [C]
> >> Sent: Tuesday, April 05, 2011 12:38 PM
> >> To: 'Trish Whetzel'
> >> Subject: RE: [bioontology-support] NCBO Appliance: problem submitting large ontology
> >>
> >> Hi Trish,
> >>
> >> I checked out your code and downloaded the latest version of NCIt (3/15/2011).
> >>
> >> Below is the exception from running "NCITVeryfy" in Eclipse. Could you adivise?
> >>
> >> Thanks,
> >>
> >> Start conversion at Tue Apr 05 12:33:38 EDT 2011
> >> SEVERE: Error loading instances -- edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
> >> Was expecting one of:
> >>   <EOF>
> >>   "(" ...
> >>   ";+" ...
> >>   ";+" ...
> >>
> >>    at edu.stanford.smi.protege.storage.clips.Parser.generateParseException(Unknown Source)
> >>    at edu.stanford.smi.protege.storage.clips.Parser.jj_consume_token(Unknown Source)
> >>    at edu.stanford.smi.protege.storage.clips.Parser.parseKnowledgeBase(Unknown Source)
> >>    at edu.stanford.smi.protege.storage.clips.Parser.loadInstances(Unknown Source)
> >>    at edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.loadKnowledgeBase(Unknown Source)
> >>    at edu.stanford.smi.protege.model.Project.loadProjectKB(Unknown Source)
> >>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> >>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> >>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> >>    at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
> >>    at NCITVerify.main(NCITVerify.java:23)
> >>
> >> SEVERE: no project instance -- Project.getProjectInstance()
> >> Error: edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
> >> Was expecting one of:
> >>   <EOF>
> >>   "(" ...
> >>   ";+" ...
> >>   ";+" ...
> >>
> >> -----Original Message-----
> >> From: Trish Whetzel [mailto:[hidden email]]
> >> Sent: Thursday, February 17, 2011 11:49 AM
> >> To: Ma, Guozhong (NIH/NHLBI) [C]
> >> Cc: support; Paul R Alexander; Galvez, Jose (NIH/NHLBI) [C]; Kadalli, Shiv (NIH/NHLBI) [C]
> >> Subject: Re: [bioontology-support] NCBO Appliance: problem submitting large ontology
> >> Importance: High
> >>
> >> Loading the NCI Thesaurus requires a few steps due to the size of the file and since it is developed with a modified version of Protege. If you plan to use the NCI Thesaurus in the Annotator workflow, then the additional XML tags added into the synonym property values need to be removed. Code to pre-process NCIt is located at:
> >> https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F
> >> and can be checked out via anonymous SVN. This information is now also in the VM Appliance documentation.
> >>
> >> After the file is processed, due to the size of the file the NCIt is usually not loaded via the BioPortal Submit New Ontology form via the Web UI. Others on the support mailing list can expand on the loading process.
> >>
> >> Trish
> >>
> >>
> >> On Feb 17, 2011, at 3:51 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
> >>
> >>> Hi Paul,
> >>>
> >>> I downloaded NCI Thesaurus from BioPortal. Tried to upload to our local NCBO Appliance. Got an error message:
> >>>
> >>> "Errors On Form
> >>> File is too large"
> >>>
> >>> Question: Did this ontology go through web form upload at BioPortal? Or, it was simply saved onto your server by admin?
> >>>
> >>> I am trying to see if this is resulted from our end due to memory, timeout setting, etc.
> >>>
> >>> Thanks,
> >>>
> >>> --
> >>> Guozhong Ma, PhD
> >>> Senior Engineer (Contractor)
> >>> Software Engineering Branch (SEB)
> >>> Center for Biomedical Informatics (CBI)
> >>> National Heart Lung and Blood Institute, NIH
> >>> Telephone: 301-435-0425 | Email: [hidden email]
> >>>
> >>> _______________________________________________
> >>> bioontology-support mailing list
> >>> [hidden email]
> >>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> >>
> >> _______________________________________________
> >> bioontology-support mailing list
> >> [hidden email]
> >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> >
>  

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Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology

Trish Whetzel
Administrator
What version of the NCIt are you trying to process?

Trish


On Apr 5, 2011, at 6:11 PM, Ma, Guozhong (NIH/NHLBI) [C] wrote:

> I'll keep trying. Thanks for your advise...
> GM
>
> -----Original Message-----
> From: Natasha Noy [mailto:[hidden email]]
> Sent: Tuesday, April 05, 2011 1:10 PM
> To: Ma, Guozhong (NIH/NHLBI) [C]
> Cc: NCBO support; Galvez, Jose (NIH/NHLBI) [C]; Kadalli, Shiv (NIH/NHLBI) [C]; Butler, Lee (NIH/NHLBI) [C]; Martin, Norman (NIH/NHLBI) [C]
> Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology
>
> Actually, true -- it might have worked with the .owl file as well. My bad.
>
> However, the fact that you cannot open it in Protege means that your OWL file is somehow corrupt. Maybe it wasn't downloaded properly? Your screenshot doesn't show the complete error message, so it is hard to tell. But you need to be able to open the file in Protege before you can run Trish's script.
>
> Natasha
>
>
>
> On Apr 5, 2011, at 10:06 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>
>> I followed what the instruction said.
>>
>> Anyways, I tried to open it using Protégé 3.4.5. Here is what I got: (just so you know. I'll keep trying.)
>>
>> <image001.png>
>>
>> -----Original Message-----
>> From: Natasha Noy [mailto:[hidden email]]
>> Sent: Tuesday, April 05, 2011 1:00 PM
>> To: Ma, Guozhong (NIH/NHLBI) [C]
>> Cc: NCBO support
>> Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology
>>
>> I just looked at the code, and it takes the .pprj file, not the owl file.
>>
>> So you need to open this Thesaurus.owl file in Protege and then save it -- the saving will create an additional file, Thesaurus.pprj -- that's the one you pass to the Java code.
>>
>> Natasha
>>
>>
>>
>> On Apr 5, 2011, at 9:57 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>>
>>> The file downloaded: Thesaurus.owl
>>>
>>> GM
>>>
>>> -----Original Message-----
>>> From: Natasha Noy [mailto:[hidden email]]
>>> Sent: Tuesday, April 05, 2011 12:54 PM
>>> To: Ma, Guozhong (NIH/NHLBI) [C]
>>> Cc: NCBO support
>>> Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology
>>>
>>> What are you passing in as your argument to the Java program?
>>>
>>> Natasha
>>>
>>>
>>>
>>> On Apr 5, 2011, at 9:41 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>>>
>>>> Hi,
>>>>
>>>> Please see what I just sent to Trish below. Please get back to me if you are familiar with Trish's development work.
>>>> Thanks,
>>>> GM
>>>>
>>>> -----Original Message-----
>>>> From: Ma, Guozhong (NIH/NHLBI) [C]
>>>> Sent: Tuesday, April 05, 2011 12:38 PM
>>>> To: 'Trish Whetzel'
>>>> Subject: RE: [bioontology-support] NCBO Appliance: problem submitting large ontology
>>>>
>>>> Hi Trish,
>>>>
>>>> I checked out your code and downloaded the latest version of NCIt (3/15/2011).
>>>>
>>>> Below is the exception from running "NCITVeryfy" in Eclipse. Could you adivise?
>>>>
>>>> Thanks,
>>>>
>>>> Start conversion at Tue Apr 05 12:33:38 EDT 2011
>>>> SEVERE: Error loading instances -- edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
>>>> Was expecting one of:
>>>>  <EOF>
>>>>  "(" ...
>>>>  ";+" ...
>>>>  ";+" ...
>>>>
>>>>   at edu.stanford.smi.protege.storage.clips.Parser.generateParseException(Unknown Source)
>>>>   at edu.stanford.smi.protege.storage.clips.Parser.jj_consume_token(Unknown Source)
>>>>   at edu.stanford.smi.protege.storage.clips.Parser.parseKnowledgeBase(Unknown Source)
>>>>   at edu.stanford.smi.protege.storage.clips.Parser.loadInstances(Unknown Source)
>>>>   at edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.loadKnowledgeBase(Unknown Source)
>>>>   at edu.stanford.smi.protege.model.Project.loadProjectKB(Unknown Source)
>>>>   at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>>>>   at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>>>>   at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>>>>   at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>>>>   at NCITVerify.main(NCITVerify.java:23)
>>>>
>>>> SEVERE: no project instance -- Project.getProjectInstance()
>>>> Error: edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
>>>> Was expecting one of:
>>>>  <EOF>
>>>>  "(" ...
>>>>  ";+" ...
>>>>  ";+" ...
>>>>
>>>> -----Original Message-----
>>>> From: Trish Whetzel [mailto:[hidden email]]
>>>> Sent: Thursday, February 17, 2011 11:49 AM
>>>> To: Ma, Guozhong (NIH/NHLBI) [C]
>>>> Cc: support; Paul R Alexander; Galvez, Jose (NIH/NHLBI) [C]; Kadalli, Shiv (NIH/NHLBI) [C]
>>>> Subject: Re: [bioontology-support] NCBO Appliance: problem submitting large ontology
>>>> Importance: High
>>>>
>>>> Loading the NCI Thesaurus requires a few steps due to the size of the file and since it is developed with a modified version of Protege. If you plan to use the NCI Thesaurus in the Annotator workflow, then the additional XML tags added into the synonym property values need to be removed. Code to pre-process NCIt is located at:
>>>> https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F
>>>> and can be checked out via anonymous SVN. This information is now also in the VM Appliance documentation.
>>>>
>>>> After the file is processed, due to the size of the file the NCIt is usually not loaded via the BioPortal Submit New Ontology form via the Web UI. Others on the support mailing list can expand on the loading process.
>>>>
>>>> Trish
>>>>
>>>>
>>>> On Feb 17, 2011, at 3:51 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>>>>
>>>>> Hi Paul,
>>>>>
>>>>> I downloaded NCI Thesaurus from BioPortal. Tried to upload to our local NCBO Appliance. Got an error message:
>>>>>
>>>>> "Errors On Form
>>>>> File is too large"
>>>>>
>>>>> Question: Did this ontology go through web form upload at BioPortal? Or, it was simply saved onto your server by admin?
>>>>>
>>>>> I am trying to see if this is resulted from our end due to memory, timeout setting, etc.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> --
>>>>> Guozhong Ma, PhD
>>>>> Senior Engineer (Contractor)
>>>>> Software Engineering Branch (SEB)
>>>>> Center for Biomedical Informatics (CBI)
>>>>> National Heart Lung and Blood Institute, NIH
>>>>> Telephone: 301-435-0425 | Email: [hidden email]
>>>>>
>>>>> _______________________________________________
>>>>> bioontology-support mailing list
>>>>> [hidden email]
>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> [hidden email]
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>
>>
>
> _______________________________________________
> bioontology-support mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology

Ma, Guozhong (NIH/NHLBI) [C]
Hi Trish,

It's 11.01

Thanks,

Guozhong Ma, PhD
Senior Engineer (Contractor)
Software Engineering Branch (SEB)
Center for Biomedical Informatics (CBI)
National Heart Lung and Blood Institute, NIH
Telephone: 301-435-0425 | Email: [hidden email]



-----Original Message-----
From: Trish Whetzel [mailto:[hidden email]]
Sent: Tuesday, April 05, 2011 8:34 PM
To: Ma, Guozhong (NIH/NHLBI) [C]
Cc: Natasha Noy; Martin, Norman (NIH/NHLBI) [C]; Galvez, Jose (NIH/NHLBI) [C]; Kadalli, Shiv (NIH/NHLBI) [C]; Butler, Lee (NIH/NHLBI) [C]; NCBO support
Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology

What version of the NCIt are you trying to process?

Trish


On Apr 5, 2011, at 6:11 PM, Ma, Guozhong (NIH/NHLBI) [C] wrote:

> I'll keep trying. Thanks for your advise...
> GM
>
> -----Original Message-----
> From: Natasha Noy [mailto:[hidden email]]
> Sent: Tuesday, April 05, 2011 1:10 PM
> To: Ma, Guozhong (NIH/NHLBI) [C]
> Cc: NCBO support; Galvez, Jose (NIH/NHLBI) [C]; Kadalli, Shiv (NIH/NHLBI) [C]; Butler, Lee (NIH/NHLBI) [C]; Martin, Norman (NIH/NHLBI) [C]
> Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology
>
> Actually, true -- it might have worked with the .owl file as well. My bad.
>
> However, the fact that you cannot open it in Protege means that your OWL file is somehow corrupt. Maybe it wasn't downloaded properly? Your screenshot doesn't show the complete error message, so it is hard to tell. But you need to be able to open the file in Protege before you can run Trish's script.
>
> Natasha
>
>
>
> On Apr 5, 2011, at 10:06 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>
>> I followed what the instruction said.
>>
>> Anyways, I tried to open it using Protégé 3.4.5. Here is what I got: (just so you know. I'll keep trying.)
>>
>> <image001.png>
>>
>> -----Original Message-----
>> From: Natasha Noy [mailto:[hidden email]]
>> Sent: Tuesday, April 05, 2011 1:00 PM
>> To: Ma, Guozhong (NIH/NHLBI) [C]
>> Cc: NCBO support
>> Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology
>>
>> I just looked at the code, and it takes the .pprj file, not the owl file.
>>
>> So you need to open this Thesaurus.owl file in Protege and then save it -- the saving will create an additional file, Thesaurus.pprj -- that's the one you pass to the Java code.
>>
>> Natasha
>>
>>
>>
>> On Apr 5, 2011, at 9:57 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>>
>>> The file downloaded: Thesaurus.owl
>>>
>>> GM
>>>
>>> -----Original Message-----
>>> From: Natasha Noy [mailto:[hidden email]]
>>> Sent: Tuesday, April 05, 2011 12:54 PM
>>> To: Ma, Guozhong (NIH/NHLBI) [C]
>>> Cc: NCBO support
>>> Subject: Re: [bioontology-support] FW: NCBO Appliance: problem submitting large ontology
>>>
>>> What are you passing in as your argument to the Java program?
>>>
>>> Natasha
>>>
>>>
>>>
>>> On Apr 5, 2011, at 9:41 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>>>
>>>> Hi,
>>>>
>>>> Please see what I just sent to Trish below. Please get back to me if you are familiar with Trish's development work.
>>>> Thanks,
>>>> GM
>>>>
>>>> -----Original Message-----
>>>> From: Ma, Guozhong (NIH/NHLBI) [C]
>>>> Sent: Tuesday, April 05, 2011 12:38 PM
>>>> To: 'Trish Whetzel'
>>>> Subject: RE: [bioontology-support] NCBO Appliance: problem submitting large ontology
>>>>
>>>> Hi Trish,
>>>>
>>>> I checked out your code and downloaded the latest version of NCIt (3/15/2011).
>>>>
>>>> Below is the exception from running "NCITVeryfy" in Eclipse. Could you adivise?
>>>>
>>>> Thanks,
>>>>
>>>> Start conversion at Tue Apr 05 12:33:38 EDT 2011
>>>> SEVERE: Error loading instances -- edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
>>>> Was expecting one of:
>>>>  <EOF>
>>>>  "(" ...
>>>>  ";+" ...
>>>>  ";+" ...
>>>>
>>>>   at edu.stanford.smi.protege.storage.clips.Parser.generateParseException(Unknown Source)
>>>>   at edu.stanford.smi.protege.storage.clips.Parser.jj_consume_token(Unknown Source)
>>>>   at edu.stanford.smi.protege.storage.clips.Parser.parseKnowledgeBase(Unknown Source)
>>>>   at edu.stanford.smi.protege.storage.clips.Parser.loadInstances(Unknown Source)
>>>>   at edu.stanford.smi.protege.storage.clips.ClipsKnowledgeBaseFactory.loadKnowledgeBase(Unknown Source)
>>>>   at edu.stanford.smi.protege.model.Project.loadProjectKB(Unknown Source)
>>>>   at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>>>>   at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>>>>   at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>>>>   at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
>>>>   at NCITVerify.main(NCITVerify.java:23)
>>>>
>>>> SEVERE: no project instance -- Project.getProjectInstance()
>>>> Error: edu.stanford.smi.protege.storage.clips.ParseException: Encountered " <SYMBOL_LITERAL> "<?xml "" at line 1, column 1.
>>>> Was expecting one of:
>>>>  <EOF>
>>>>  "(" ...
>>>>  ";+" ...
>>>>  ";+" ...
>>>>
>>>> -----Original Message-----
>>>> From: Trish Whetzel [mailto:[hidden email]]
>>>> Sent: Thursday, February 17, 2011 11:49 AM
>>>> To: Ma, Guozhong (NIH/NHLBI) [C]
>>>> Cc: support; Paul R Alexander; Galvez, Jose (NIH/NHLBI) [C]; Kadalli, Shiv (NIH/NHLBI) [C]
>>>> Subject: Re: [bioontology-support] NCBO Appliance: problem submitting large ontology
>>>> Importance: High
>>>>
>>>> Loading the NCI Thesaurus requires a few steps due to the size of the file and since it is developed with a modified version of Protege. If you plan to use the NCI Thesaurus in the Annotator workflow, then the additional XML tags added into the synonym property values need to be removed. Code to pre-process NCIt is located at:
>>>> https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F
>>>> and can be checked out via anonymous SVN. This information is now also in the VM Appliance documentation.
>>>>
>>>> After the file is processed, due to the size of the file the NCIt is usually not loaded via the BioPortal Submit New Ontology form via the Web UI. Others on the support mailing list can expand on the loading process.
>>>>
>>>> Trish
>>>>
>>>>
>>>> On Feb 17, 2011, at 3:51 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:
>>>>
>>>>> Hi Paul,
>>>>>
>>>>> I downloaded NCI Thesaurus from BioPortal. Tried to upload to our local NCBO Appliance. Got an error message:
>>>>>
>>>>> "Errors On Form
>>>>> File is too large"
>>>>>
>>>>> Question: Did this ontology go through web form upload at BioPortal? Or, it was simply saved onto your server by admin?
>>>>>
>>>>> I am trying to see if this is resulted from our end due to memory, timeout setting, etc.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> --
>>>>> Guozhong Ma, PhD
>>>>> Senior Engineer (Contractor)
>>>>> Software Engineering Branch (SEB)
>>>>> Center for Biomedical Informatics (CBI)
>>>>> National Heart Lung and Blood Institute, NIH
>>>>> Telephone: 301-435-0425 | Email: [hidden email]
>>>>>
>>>>> _______________________________________________
>>>>> bioontology-support mailing list
>>>>> [hidden email]
>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>
>>>> _______________________________________________
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>>>> [hidden email]
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>
>>
>
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