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[protege-dev] [Protege 3.4] Developing a plugin to visualize the FMA. Have a few question

Tania Tudorache tudorache at stanford.edu
Tue Sep 16 15:16:07 PDT 2014


The pprj files can only be opened by the Protege 3.x series (and 
earlier). Protege 3 is not under development anymore, it is in 
maintenance mode.

Rather than using the pprj/pont/pins files, I would recommend using the 
OWL file 
(http://sig.biostr.washington.edu/share/downloads/fma/FMA_Release/alt/v3.2/owl_file/fma_3.2_owl_file.zip) 
and develop a plugin for Protege 4 or 5. Here are some instructions:
http://protegewiki.stanford.edu/wiki/Protege4DevDocs

BioPortal also offers some nice dynamic visualizations of the 
ontologies, including FMA, e.g.:
http://bioportal.bioontology.org/ontologies/FMA/?p=classes&conceptid=http%3A%2F%2Fsig.uw.edu%2Ffma%23Heart&jump_to_nav=true#visualization

that you can embed in your application, if it fits the purpose.

Cheers,
Tania


On 09/16/2014 03:06 PM, Luchen wrote:
> So as the title says, i'm trying to develop a plugin the visualizes a fairly
> simple visualization model for the Foundational model of anatomy (
> http://sig.biostr.washington.edu/projects/fm/AboutFM.html
> <http://sig.biostr.washington.edu/projects/fm/AboutFM.html>   ) which has
> been kind of problematic. I've tried searching and couldn't find an answer.
>
> My problem began trying to set up the FMA  following this guide:
> http://sig.biostr.washington.edu/projects/fma/release/v3.2/setup-protege.html
> <http://sig.biostr.washington.edu/projects/fma/release/v3.2/setup-protege.html>
> found here:
> http://sig.biostr.washington.edu/projects/fma/release/versions.html
> <http://sig.biostr.washington.edu/projects/fma/release/versions.html>
>
> The first problem i encountered is that i couldn't open the .pprj file and
> after being unable to find a way to do it i switched to Protegé 3.4. Now
> comes my next problem. I cant seem to find plugin development documentation
> for that version of protege and even though there are some projects out
> there, it's easy to get overwhlemed by the source and i'm not too kin on
> reusing large portions of code that i don't really understand.
>
> If there's any documentation out there that could help me it'd be greatly
> appreciated.
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Protege-3-4-Developing-a-plugin-to-visualize-the-FMA-Have-a-few-question-tp4661449.html
> Sent from the Protege Developer mailing list archive at Nabble.com.
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