Update README.adoc

[ypriverol]

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⚡ Recommended focus areas for review Documentation Update The PR adds Mondo Disease Ontology (MONDO) to the list of supported ontologies/controlled vocabularies. Reviewer should verify if this addition is correct and if any related documentation or code changes are needed.

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PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Enhancement	✅ Add a brief description of the newly added ontology to provide context Consider adding a brief description or explanation of the Mondo Disease Ontology (MONDO) to provide context for users who may not be familiar with it. This can help readers understand its relevance and importance in the list of supported ontologies. sdrf-proteomics/README.adoc [118] -+- Mondo Disease Ontology (MONDO) ++- Mondo Disease Ontology (MONDO): A unified disease ontology integrating multiple disease resources [Suggestion has been applied] Suggestion importance[1-10]: 7 Why:	7
Best practice	✅ Adjust the formatting to maintain consistency with the existing list style To maintain consistency with the existing list format, consider adding a hyphen (-) at the beginning of the new line for the Mondo Disease Ontology. This will ensure that the new entry matches the style of the other items in the list. sdrf-proteomics/README.adoc [118] -+- Mondo Disease Ontology (MONDO) ++ - Mondo Disease Ontology (MONDO) [Suggestion has been applied] Suggestion importance[1-10]: 7 Why:	7

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Walkthrough

The changes involve updates to multiple documentation files within the SDRF-Proteomics project. The README.adoc file has been enhanced by adding the Mondo Disease Ontology (MONDO) to the supported ontologies section and introducing a new section on technology type. Additionally, the README.adoc in the templates directory has been modified to clarify sample metadata templates and experiment types. The .gitignore file has also been updated to include new patterns for ignored files and directories.

Changes

File Path	Change Summary
sdrf-proteomics/README.adoc	Added Mondo Disease Ontology (MONDO) and new "Technology type" section.
.gitignore	Added .vscode/ and new_path/ to ignored files and directories.
templates/README.adoc	Expanded sample metadata templates section and clarified experiment types.

Poem

In the garden of science, we grow,
With MONDO now added, our knowledge will flow.
Ontologies flourish, like flowers in bloom,
Enhancing our research, dispelling the gloom.
With each little change, our data takes flight,
A hop towards clarity, in the soft moonlight. 🐇✨

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📥 Commits

Files that changed from the base of the PR and between cfa8be3673d3f63dd42e018e4199fecac8296909 and 5b5f5e2a0dd4657888d444468a4a03943958b10f.

📒 Files selected for processing (1)

• sdrf-proteomics/README.adoc (3 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• sdrf-proteomics/README.adoc

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[ypriverol]

My main question is about the MONDO ontology. It's not immediately clear to me, does it include all of the EFO terms about disease? Can there be conflicts because of this change? What do we need to do in the validator to support it?

The other comment is about technology type terms, I suggest to directly list the ones we should use in proteomics.

• For the validator, this only means that we will look for diseases now in MONGO and EFO.
• The URL of the technology type is not available yet because it needs to be indexed in OLS. I will also update the terms as you suggested in the specification because it will not be a long list.

[ypriverol]

This looks good except for a small typo. Also about the term: I found it in the PRIDE ontology here. but in the current annotations there are also occurrences of "proteomic profiling by mass spectrometry", which sounds even more natural. I don't see any synonyms in the ontology, so I guess "mass spectrometry" is now technically incorrect? Do you want to add these synonyms to the ontology? (maybe also "proteomics profiling", that would be 4 options though)

• The terms were added last night, but still need to be indexed in OLS.
• The term added is:

[Term]
id: PRIDE:0000664
name: proteomic profiling by mass spectrometry
def: "An assay where proteins in a sample are detected, quantified or otherwise analysed using mass spectrometry" [EFO:EFO_0002766]
is_a: PRIDE:0000663 ! technology type

Which is also in EFO and other ontologies but now we are controlling in PRIDE. I will update the term in my side to proteomic profiling by mass spectrometry

[levitsky]

Should we also change it to "mass spectrometry" in all annotations then?

[ypriverol]

Should we also change it to "mass spectrometry" in all annotations then?

I will after we agree on this PR ;)