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

Trish Whetzel whetzel at stanford.edu
Tue Mar 15 11:48:47 PDT 2011


The program is in Java and uses standard Java imports and imports from the Protege 3.4.5 (download available at: http://protege.stanford.edu/download/protege/3.4/installanywhere/Web_Installers/). I'll add additional documentation to include the link for the Protege download.  I run this in Eclipse. 

Trish 


On Mar 15, 2011, at 6:46 AM, Ma, Guozhong (NIH/NHLBI) [C] wrote:

> Hi Dr. Whetzel,
> 
> I was pulled away to do a different project and just came back for a
> little.
> 
> I visited the page using the link from you and browsed this page (screen
> capture attached):
> /trunk/NCItProcessor
> 
> Question: what is the API used to generate the source files, please? I am
> guessing it is Eclipse?
> 
> I programmed in Java using JBuilder years and years, ago. I need to start
> with the right API so that project progress faster...
> 
> Thanks and have a great day!
> 
> 
> -- 
> Guozhong Ma, PhD
> Senior Engineer (Contractor)
> Software Engineering Branch
> Center for Biomedical Informatics (CBI)
> National Heart Lung and Blood Institute, NIH
> Telephone: 301-435-0425 | Email: guozhong.ma at nih.gov
> 
> 
> 
> 
> 
> 
> On 2/17/11 3:09 PM, "Natasha Noy" <noy at stanford.edu> wrote:
> 
>> The way we usually do this "backdoor" upload is as follows:
>> 
>> - Create the cleaned up version of NCIT using the code that Trish pointed
>> you to
>> - Open this OWL file in Protege 3 and save it as a OWL/RDF database (use
>> "Convert project to format..")
>> - Create an entry for NCIT in BioPortal, uploading a dummy OWL file
>> instead of the real one -- it needs to be a valid OWL file, but can
>> contain a single class
>> - Note the table in the database that is created for this file:
>> bioportal_protege/tbl_{versio_id}
>> - replace the content of this table (keeping the name) with the table
>> that you generated in Protege (for example, by deleting the tbl_...
>> table, copying the table from the Protege database to bioportal_protege
>> and then renaming it to tbl_{versio_id}
>> - use the Admin tool to kick off the indexing for this ontology.
>> 
>> It is easier than it sounds. Good luck :)
>> 
>> Natasha
>> 
>> PS. To others on the support list: please feel free to correct or clarify
>> if I missed something
>> 
>> On Feb 17, 2011, at 8:49 AM, Trish Whetzel wrote:
>> 
>>> 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/?actio
>>> n=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: guozhong.ma at nih.gov
>>>> 
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>> 
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 
> 
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