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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