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[bioontology-support] Support request for the Cardiovascular Research Grid project

Paul R Alexander palexander at stanford.edu
Mon May 7 16:11:28 PDT 2012


Sanjay,

There was a bug in some versions of the Virtual Appliance that may have 
made metrics calculation break from the BioPortal Admin UI. 
Unfortunately there's no easy fix for that. Metrics are not necessary to 
utilize the ontology via the REST service or UI, however, so the only 
thing you'll be missing are class count and related information on the 
summary page.

Paul R Alexander
Web / UI Developer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research


On 5/7/12 2:19 PM, Agravat, Sanjay wrote:
> Re: [bioontology-support] Support request for the Cardiovascular 
> Research Grid project Hi Paul,
>
> So I tried doing this and was able to at least get some of the classes 
> loaded, but when I go to Calculate Metrics, I get this error: 
> “BioPortal returned an error: The method specified in the request is 
> not allowed for the resource identified by the request URI”.
>
> Do you know how to resolve this issue?
>
> Thanks,
>
> Sanjay
>
>
> On 5/7/12 2:44 PM, "Paul R Alexander" <palexander at stanford.edu> wrote:
>
>      Unfortunately, we don't support loading ontologies from a Protege
>     database. You can attempt to swap a Protege database back-end
>     table with the one used in BioPortal, but it's not a
>     straightforward process. However, if you want to give it a shot,
>     you would need to:
>
>      1. Submit a dummy ontology file with all of the information for
>         the real ontology. This file should be something small that
>         will parse properly
>      2. Parse the dummy ontology
>     3.
>
>      4. Find the version number for the dummy ontology
>      5. Go to the database on the Virtual Appliance and find the table
>         that corresponds to the dummy version in the
>         'bioportal_protege' database
>      6. Note the table name (should be something like 'tbl_10000') and
>         delete the table
>      7. Import your parsed version of the real ontology and rename the
>         imported table to match the old dummy table name (ex:
>         'tbl_10000')
>     8.
>
>      9. Using the BioPortal Admin tool: 1) calculate metrics and 2)
>         index the ontology
>
>
>
>     Give that a shot and let me know if you run into problems.
>
>
>
>     Paul R Alexander
>      Web / UI Developer
>      NCBO BioPortal
>      Stanford Center for Biomedical Informatics Research
>
>
>
>     On 5/7/12 10:35 AM, Trish Whetzel wrote:
>
>
>
>         Hi Sanjay,
>
>
>
>
>         I believe there is a mechanism to swap in the Protege database
>         table into the Protege backend for BioPortal.
>
>
>
>
>         Paul, is this what you would recommend and/or can help Sanjay
>         with this item?
>
>
>
>
>         Trish
>
>
>
>
>
>
>
>
>
>         On May 7, 2012, at 9:09 AM, Agravat, Sanjay wrote:
>
>
>
>              Hi,
>
>              I have a local instance of bioportal running  and I’m
>             having a problem loading my ontology into bioportal.   The
>             ontology is stored in the protégé database so I tried
>             uploading the .pprj file with the database located on the
>             same server as bioportal and that didn’t work.  I also
>             tried converting the .pprj to use .pins and .ponts but
>             that didn’t work because the upload form doesn’t take the
>             classes or instances file as input.
>
>              I am not able to export the ontology to .owl since the
>             ontology is  very large and protégé doesn’t seem to be
>             able to do it.  Do you have any suggestions?
>
>              Thanks,
>
>              Sanjay
>
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