Request for Recommendations: Online Documentation Tools for a WebProtégé Ontology

[Marcelo Xavier Guterres]

Dear community,

I would like to kindly request suggestions on the best way to create online documentation for an ontology currently being developed in WebProtégé.

We are looking for tools or approaches that enable us to share the progress and structural details of the ontology in a clear and accessible manner for all stakeholders involved.

Thank you very much in advance for your help and recommendations.

Sincerely,
Marcelo Xavier

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Prof. Marcelo Xavier Guterres

Instituto Tecnológico de Aeronáutica (ITA) 

Divisão de Engenharia civilGabinete: 2133
Telefone: 12-39476817
https://marceloguterres.github.io/



Pesquisador do Laboratório de Gerenciamento de Tráfego Aéreo 
http://www.labgeta.ita.br/

https://orcid.org/0000-0002-7414-3157 

[Alex Shkotin]

Dear Marcelo,

I am personally for self documented code, then we need one or another rendering engine. Did you ask OBO Foundry and [protege-user] list?

I asked Gemini, have a look https://gemini.google.com/share/6e091b60d275

Best,

Alex

вт, 13 янв. 2026 г. в 15:34, Marcelo Xavier Guterres <m.gut...@gmail.com>:

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[Nico Matentzoglu]

Dear Marcelo,

Unfortunately I cannot answer your question for WebProtege specifically; Note that independently of your issue (and despite this: https://github.com/protegeproject/webprotege/issues/284), I would urge anyone developing an ontology regardless of where it is curated/edited to use a standard version control system like GitHub or GitLab for community engagement and "open science best practice" (standard workflows, etc).

A lot of OBO ontologies use the Ontology Development Kit (ODK) which comes with some built-in functions to generate an mkdocs (material-themed) documentation scaffolding which can then be extended by the ontology team. This is usually deployed on github.io (which you seem to have some personal experience with as well). Some of our docs pages are very detailed, others vanilla, see for example:

• https://obophenotype.github.io/uberon/
• https://obophenotype.github.io/human-phenotype-ontology/
• https://oborel.github.io/obo-relations/

We mostly curate our documentation manually, but claude code or similar can, with some guidance and careful review, generate quite reasonable pages as well. 

On a more personal note: 

- I like the clarity of the diataxis framework (https://diataxis.fr/) for organising docs, which we more or less try to follow in OBO Academy (https://oboacademy.github.io/obook/). 

- I really like it if modelling patterns in the ontology are documented explicitly using something like DOSDP: https://github.com/monarch-initiative/mondo/blob/master/src/patterns/dosdp-patterns/autoimmune.yaml. It is trivially possible to generate documentation pages from these to have something like this: https://mondo.readthedocs.io/en/latest/editors-guide/patterns/ (I find this is, if I may be so bold, the most important part of ontology documentation - even though hardly anyone does it).

Good luck!

Nico

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[Mike Peters]

Hi Marcelo, Alex and Nico

Marcel,
How to create online documentation is an important question.

Alex,
Thanks for discovering a way to generate online documentation via Gemini. I'm going to try it.

Nico,
Your example of using diataxis at OBO Academy with OBOOK is excellent. Adding pathways is a real insight. I found it inspiring.

Pipi 9
At Ajabbi, the same problem persists: how to automatically generate Pipi 9's self-documentation using 20,000 web pages.

We are using a combination of Diataxis, Read the Docs, and IEEE Learning Objects. And now Pathways (inspired by Salesforce Education Data Model)

I wrote up this discussion, including all your comments, and Gemini here. I hope that is OK.

https://www.blog.ajabbi.com/2026/01/ontology-documentation-tools-and.html

​Thank you

Mike Peters
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[Alex Shkotin]

Hi Mike, and welcome. I found it's useful to ask AI before asking people. 

And just for me, could you please put my url https://www.linkedin.com/in/ashkotin/ under my name in your blog?

Thank you,

Alex 🏋️

пт, 16 янв. 2026 г. в 21:44, Mike Peters <mi...@redworks.co.nz>:

To view this discussion visit https://groups.google.com/d/msgid/ontolog-forum/e016d449-e080-43c8-af54-ffa04354c8c4n%40googlegroups.com.

[Mike Peters]

Hi Alex

Done :)

Mike

[Michael DeBellis]

I'm not sure I understand the question. There isn't anything special about an ontology developed in WebProtege. Well except that (at least IMO) developing an ontology and ONLY using WebProtege is a really bad idea. WebProtege doesn't support reasoners so you can't define axioms on classes, SWRL rules, etc. If you aren't going to use the cool stuff from OWL why use OWL at all? Go with something like just RDF or Neo4J. It's like asking "are there any tools for documenting code written using PyCharm?" The IDE shouldn't dictate how you document your code and the tool you use to develop your ontology shouldn't dictate how you document it. 

But IMO, the clear answer... at least a very good answer is Widoco which is the same tool that many people use already to document ontologies: https://github.com/dgarijo/Widoco You can export your ontology from WebProtege and use Widoco. One thing to look out for, at least this confused me for a long time, is if your ontology is just on your local file system (although it sounds like that isn't an issue for you) and you use Widoco the results will be virtually empty documentation. This isn't because of a limitation of Widoco, actually I guess in some ways it is, it is because Widoco is designed for ontologies that are hosted on the Internet and if you don't currently host on the Internet but on your local file system Widoco will generate your documentation but when you try to look at it your Operating System will block it and it will look mostly  empty. One way around that is to host Widoco documentation on GitHub. Which IMO is a much better solution in the long term than leaving it in WebProtege. WebProtege is a great collaboration tool but doesn't have the support for real software development like branching, merging, issues, etc. that GitHub does. Here's an example where I did that for an ontology I developed last year on the social science research called Climate Obstruction: https://mdebellis.github.io/Climate_Obstruction/ 

Also, in my revision of the Pizza Tutorial: https://www.michaeldebellis.com/post/new-protege-pizza-tutorial I added a chapter (chapter 11) that talks about Web Protege and how you can go back and forth between WebProtege and Desktop Protege which is what I recommend. That way you get the collaboration features of WebProtege but you can write axioms and get other features only available on the Desktop version of Protege. The nice thing is that WebProtege was designed to do what we used to call in the CASE world "round trip engineering" I.e., you can export the ontology, make changes in Desktop Protege (and/or other tools) then re-import the ontology into WebProtege and the changes are a part of the WebProtege history as if you made them in WebProtege. Also, WebProtege does some odd things to IRIs that I talk about in the tutorial.

Cheers,

Michael

https://www.michaeldebellis.com/blog