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add knowledge_engineering_methodology file v1 - #34

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txellext wants to merge 12 commits into
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33-add-methodology-file-for-ontology-engineering
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txellext wants to merge 12 commits into
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33-add-methodology-file-for-ontology-engineering

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@txellext

@txellext txellext commented Aug 19, 2026 •

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First draft of the knowledge engineering methodology
It is a WIP guideline, but first version here.
Before merging to main I will test it with Lea and Alberto and add their respective feedback.
Shawn feedback will come later.

See the preview for the last modified PR:

@txellext txellext linked an issue Aug 19, 2026 that may be closed by this pull request
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@txellext txellext self-assigned this Aug 19, 2026
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txellext requested a review from leamms August 19, 2026 12:16
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# Knowledge Engineering Methodology

## Table of Contents

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I would just delete it. there is a TOC added using sphinx on the right. But in principle this link is correct. You will just need to tag the headers with the respective target:
https://mystmd.org/guide/cross-references

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txellext requested a review from enryH August 19, 2026 13:28
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enryH marked this pull request as ready for review September 2, 2026 05:41

@enryH enryH left a comment

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I would have a look at the rendered website and remove all <br>. See the other small details and suggestions.

https://biosustain.github.io/dsp_notes/dev/ontologies/knowledge_engineering_methodology.html


(step-1-determine-the-domain-and-scope-of-the-ontology)=
### Step 1. Determine the Domain and Scope of the Ontology
<br>

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I would leave the manuel spacing out and let it the template decide how much space should be after headings...

So I would remove all <br>

### Step 2. Ontology Development

<br>
> Main idea: **Iterative design** — Ontology development is an iterative process.

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Here the <br> even breaks the rendering of the quote (block quote):

https://biosustain.github.io/dsp_notes/dev/ontologies/knowledge_engineering_methodology.html

Comment thread ontologies/knowledge_engineering_methodology.md Outdated
Comment thread ontologies/knowledge_engineering_methodology.md Outdated
@@ -0,0 +1,92 @@
# Knowledge Engineering Methodology

(engineering-workflow)=

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These links are not needed for sphinx to build the references, but if you want to use it in other places, they do not hurt. Other documents in the dsp_notes do not have these link tags.

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txellext requested a review from enryH September 2, 2026 07:31
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txellext marked this pull request as draft September 3, 2026 11:05
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txellext commented Sep 3, 2026 •

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this is a WIP guide, I will update step 3 tomorrow. I had to move it back to draft as it took so long to merge that I have changes already... ^^´ (folded hands)

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enryH commented Sep 4, 2026

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Well. Looks good now as it is. I will approve the PR so you can merge it once you are ready !

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Add methodology file for ontology engineering

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