Protogé Documentation for developer (broken links)

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Protogé Documentation for developer (broken links)

yk.tru
This post was updated on .
Can someone explain to me why it is so hard to find support/*working*
documentation from the Protégé community/main developers for people trying
to make 3rd party plugin?


1- After searching for hours an unambigous answer from different
posts/forums, I asked what I think is a basic, legitimate question like: "Is the latest
JavaFX *fully* works with Protégé, or will I waste countless hours in case some parts of its architecture are not fully compatible"

no one answered. Other answers for the same question in this forum don't
look convincing, since embedding from Swing doesn't appear to me like a good
solution sincerely

---

2- And look at this link:
https://protege.stanford.edu/protege/4.1/docs/api/

It's broken! How can I easily refer to or learn about the
architecture/classes/methods/implementations etc. otherwise?

--

3- this one date back from 2016, though the new Protege 5 is out since over
a year:
https://protegewiki.stanford.edu/wiki/Protege4DevDocs

Again, no API documentation for Protégé 5

--


It's really frustrating...

So please, can we have (or where to find) access to *a proper documentation* and an
up-to-date *developer guide* for plugin implentation?

Otherwise I - and I suppose I'm not the only one - have to wander everywhere
from sometimes really outdated documentation (in the like of 2008, 2010, 2014) to broken
links. How to not totally give up?

I see from other posts/forums that I'm
not the only one struggling to find what I consider to be the basics: an api documentation, and more concrete implementation examples.

Thank you, I hope to find answer to this perpetual state of wandering.



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Re: Protogé Documentation for developer (

John Graybeal
Hello,

I'm John Graybeal, I've started to help out in the Protege group with some of the Protege documentation. 

I wanted to let you know we welcomed your email (fair questions!) and are composing a reply, but due to conflicting schedules couldn't get it out the door today. Please be patient with us and we'll provide more thoughtful answers tomorrow. 

John

On May 23, 2020, at 1:51 PM, yk.tru <[hidden email]> wrote:

Can someone explain to me why is there SO LITTLE support/*working*
documentation from the Protégé community/main developers for people trying
to make 3rd party plugin?


1- After searching for hours an unambigous answer from different
posts/forums, I asked a basic legitimate question like: "Is the latest
JavaFX *fully* works with Protégé, or will I waste countless hours in the
case some parts of its architecture are not compatible"

and no one answered. Other answers for the same question in this forum don't
look convincing, and embedding from Swing doesn't appear to me like a good
solution sincerely

---

2- And look at this link:
https://protege.stanford.edu/protege/4.1/docs/api/

It's broken! How can I easily refer to or learn about the
architecture/classes/methods/implementations etc. otherwise?

--

3- this one date back from 2016, though the new Protege 5 is out since over
a year:
https://protegewiki.stanford.edu/wiki/Protege4DevDocs

Again, no API documentation for Protégé 5

--


It's really frustrating...

So can we have (or where to find) access to *a proper documentation* and an
up-to-date *developer guide* for plugin implentation?

Otherwise I - and I suppose I'm not the only one - have to wander everywhere
from outdated documentation (in the like of 2008, 2010, 2014) to broken
link. How not to totally give up?

I'm sorry about this message tone, but I see from other post/forum that I'm
not the only one struggling to find what I consider to be the basics.

Thank you, I hope to get precise answers



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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360




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Re: Protogé Documentation for developer (

yk.tru
Thanks alot I really hope to be able (and other in my situation) to
contribute enventually!



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Re: Protogé Documentation for developer (

John Graybeal
Hello again,

Hello, 

We received your comment on the developer’s list (thank you) and would like to reply in part today, and further when we have more information to report.  

I volunteered to reply on behalf of the Protege team, because I have just recently started to work on improving Protege documentation, and so many fixes will involve me.

First, sorry for the troubles, I have been in your shoes and I know it is extremely frustrating. We will do what we can to help, as soon as we can.

I think you raised 4 categories of concern: (a) responsiveness on the list, (b) technical concerns about whether JavaFX will be suitable for creating a plug-in, (c) missing documentation for Protege 5, and (d) documentation organization. Let me respond to each with what we can say today.

(a) Responsiveness: We do respond to the lists when we have unique expertise in Protege questions; in this case, we had no experience or knowledge to help with your specific issue. As you know, we rely on others to help the community learn about Protege, and the hope here is that someone in the community can offer that experience. Given there are relatively few developers compared to general users, we won’t be surprised if there are no responses

(b) Technical concerns: Mostly addressed in (a). One knowledgeable colleague said he would strongly recommend Java because it’s known to have a path to success, but he is not experienced with JavaFX. Another path from here could be to visit the GitHub repos for other plugins to see if any of them are using JavaFX. We’ll beat the bushes on our end to see if anyone else can provide input. My own suspicion is that the best and fastest way to find out may be to try it; as it seems to be a future path, we'd really appreciate getting your feedback.

(c) Missing documentation: You are absolutely correct that there is no viable documentation for the API, nor for the plug-in development. We will discuss fixing both of these issues; some of them may be fixed as I work to transition much of the Protege 4 and 5 documentation on the Protege Wiki to the Protege 5 GitHub site. I can’t say what the delivery timing will be, everyone on the team is pretty fully committed (or more!), but we’ll get back to you with an estimate. 

(d) The existing documentation has some dead-end links (thank you for pointing those out), which we’ll fix, and may be organizable in better ways. The team will review that as well.

I hope this is a reasonable start, recognizing that there are many challenges on the Protege plug-in road and we won’t be able to make all of them go away.  I am sure the answer in part is “not enough time to do everything”, but we know this is important.

Please let us know if you have further requests, information, or contributions as we move forward.

John


On May 26, 2020, at 10:17 PM, yk.tru <[hidden email]> wrote:

Thanks alot I really hope to be able (and other in my situation) to
contribute enventually!



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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360




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Re: Protogé Documentation for developer (

yk.tru
Excellent!

I can't wait to see the new wiki/Protege 5 api/implentation documentation!

Thanks for your answer and the team devotion, I'll check weekly for update
on this post.



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