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

Ma, Guozhong (NIH/NHLBI) [C] mag at nhlbi.nih.gov
Tue Mar 15 06:46:11 PDT 2011


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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