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

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

Luchen
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 ) 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 
found here: 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.
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Re: [Protege 3.4] Developing a plugin to visualize the FMA. Have a few question

Tania Tudorache
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.
> _______________________________________________
> protege-dev mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-dev


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Re: [Protege 3.4] Developing a plugin to visualize the FMA. Have a few question

Luchen
Hi Tania!

I've tried using the OWL file in Protegé 5 but performance took a noticeable hit when dealing with the FMA this way while Protegé 3.4 ran smoothly. Though i have no actual knowledge of how either software actually works i'd guess that it has something to do with response time of queing a local database instance in the case of protege 3.4 (which one of the steps in the setup) vs. loading and parsing the .owl file.

Is there anyway i can get around this? I'm checking the Protege 5 documentation as we speak just be ready, but would you personally recommend developing this plugin for Protegé 4 or 5?
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Re: [Protege 3.4] Developing a plugin to visualize the FMA. Have a few question

Tania Tudorache
You probably need to increase the heap size for Protege 5. Edit the run.sh or run.bat and change the argument -Xmx500M.

I tried it with 4000M, and it loads the FMA owl file in 50 seconds.

You are right, that with the Protege 3 database backend, you would have a faster load time, but then all operations that would follow (read/writes) would be slower as they happen in the database. Protege 5 will read the ontology in memory (so you have a longer load time), but then all following operations would be very fast as they happen in memory. There is always this trade-off.

I suggested to implement a plugin for Protege 4/5 because this is the current version. Protege 3 is not under development anymore.

The OWL-API underlying Protege 4/5 is also very well documented and supported:
http://owlapi.sourceforge.net/

Good luck!
Tania



On 09/16/2014 04:27 PM, Luchen wrote:
Hi Tania!

I've tried using the OWL file in Protegé 5 but performance took a noticeable
hit when dealing with the FMA this way while Protegé 3.4 ran smoothly.
Though i have no actual knowledge of how either software actually works i'd
guess that it has something to do with response time of queing a local
database instance in the case of protege 3.4 (which one of the steps in the
setup) vs. loading and parsing the .owl file.

Is there anyway i can get around this? I'm checking the Protege 5
documentation as we speak just be ready, but would you personally recommend
developing this plugin for Protegé 4 or 5?



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Sent from the Protege Developer mailing list archive at Nabble.com.
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Re: [Protege 3.4] Developing a plugin to visualize the FMA. Have a few question

Luchen
Well. After having some conversations with my professor it seems that i'm stuck with Protege 3.4 and there's no way around it. The plugin I intend to develop in the following weeks, as I've said before, will look like the following:
(Thanks to Tania pointing me towards Bioportal which i used for the crude mock up)

Which leads me to a bunch of different questions, the main one being. Is it possible? I've been trying to get around the documentation in the Wiki but i've failed to find how to:
"Embed" the class viewer into my plugin.
Access information related to the highlighted/selected class.
Draw the graph itself.

What i've accomplished so far:
Display a new tab (following the tutorial on the wiki which pretty much lays it out for me). I'm playing around with what i can do with the tab but so far i'm gotten little to no progress with my goal.

As you've may have noticed, i'm pretty much clueless here and while i'm indeed asking for too much, just a nudge in the right direction would help me a lot.
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Re: [Protege 3.4] Developing a plugin to visualize the FMA. Have a few question

Luchen
Just an update on the situation. Since what i'm trying to do is pretty much a stripped (and a bit more adaptable) version of jambalaya's Class Tree i've been trying to check that out. Since there's no source code aviable i've been trying to check out Ontograph's code but it's a bit way over my head but at least i've got options to explore now.