Set up AI agent #393

ar-ibrahim · 2025-09-02T14:45:30Z

No description provided.

.github/copilot-instructions.md

matentzn · 2025-09-02T15:17:56Z

.github/copilot-instructions.md

+#### Overview
+- IMPORTANT: Do not edit the edit file directly, it's large
+- OBA terms are compositional, check DOSDP design patterns: `src/patterns/dosdp-patterns/*.yaml`
+- Desgin pattern templates are found in `src/patterns/data/default`


Suggested change

- Desgin pattern templates are found in `src/patterns/data/default`

- Design pattern templates are found in `src/patterns/data/default`

matentzn · 2025-09-02T15:18:53Z

.github/copilot-instructions.md

+            ```
+            ```
+
+    2- Check whether design pattern components have been imported to OBA. Search `src/ontology/imports/merged_import.owl`


Suggested change

2- Check whether design pattern components have been imported to OBA. Search `src/ontology/imports/merged_import.owl`

2- Check whether design pattern filler terms have been imported to OBA. Search `src/ontology/imports/merged_import.owl`

matentzn · 2025-09-02T15:21:03Z

.github/copilot-instructions.md

+            sh run.sh make IMP=false MIR=false ../patterns/definitions.owl 
+
+    5- Refresh OBA imports by running
+            sh run.sh make refresh-merged 


i hope this will work but it might.. run out memory?

matentzn · 2025-09-02T15:23:02Z

.github/copilot-instructions.md

+
+    6 - Run sh run.sh make IMP=false MIR=false ../patterns/definitions.owl again.
+
+    7- When creating new OBA terms using DOSDP patterns, it may be necessary to import terms from other ontologies like ChEBI, the Chemical Entities of Biological Interest or PRO, the PRotein Ontology. However, they are too large to be managed as standard imports so are managed as slims. When a new term you are using in a DOSDP pattern is not yet in a slim you will have to refresh the slim first. They are located here:


If a term does not exist in pro_obo_slim, ncbitaxon or chebi_obo_slim, make a comment in the issue asking these terms to be added manually.

matentzn · 2025-09-02T15:23:39Z

.github/copilot-instructions.md

+
+## Handling GitHub issues and requests
+- Use `gh` to read and write issues/PRs
+- Sign all commits and PRs as `@dragon-ai-agent`


Suggested change

- Sign all commits and PRs as `@dragon-ai-agent`

matentzn · 2025-09-02T15:26:32Z

.github/workflows/copilot-setup-steps.yml

+      uses: actions/cache@v4
+      with:
+        path: ~/.jar-cache
+        key: ${{ runner.os }}-robot-v1.9.7


this is not the latest robot;

your instruction above use ODK, so I dont know if you need to install ROBOT here.. maybe do

matentzn · 2025-09-02T15:27:31Z

.github/copilot-instructions.md

+
+    cd PATH-TO/bio-attribute-ontology/src/ontology
+    sh run.sh make ../patterns/definitions.owl
+    sh run.sh make components/obsoletes.owl


Suggested change

sh run.sh make components/obsoletes.owl

make components/obsoletes.owl

Remove run.sh and see if ROBOT alone works for this (the robot instealled in the setup steps). Ask me if any problems.

- update AI agent signature

aleixpuigb · 2025-09-30T17:35:57Z

.github/workflows/copilot-setup-steps.yml

+      uses: actions/cache@v4
+      with:
+        path: ~/.jar-cache
+        key: ${{ runner.os }}-robot-v1.9.7


Suggested change

key: ${{ runner.os }}-robot-v1.9.7

key: ${{ runner.os }}-robot-v1.9.8

aleixpuigb · 2025-09-30T17:36:15Z

.github/workflows/copilot-setup-steps.yml

+      run: |
+        mkdir -p ~/.jar-cache
+        if [ ! -f ~/.jar-cache/robot.jar ]; then
+          curl -L https://github.com/ontodev/robot/releases/download/v1.9.7/robot.jar -o ~/.jar-cache/robot.jar


Suggested change

curl -L https://github.com/ontodev/robot/releases/download/v1.9.7/robot.jar -o ~/.jar-cache/robot.jar

curl -L https://github.com/ontodev/robot/releases/download/v1.9.8/robot.jar -o ~/.jar-cache/robot.jar

aleixpuigb · 2025-09-30T17:36:42Z

.github/workflows/copilot-setup-steps.yml

+    - name: Setup ROBOT tools
+      run: |
+        cp ~/.jar-cache/robot.jar ${{ github.workspace }}/tools/robot.jar
+        curl -L https://raw.githubusercontent.com/ontodev/robot/v1.9.7/bin/robot -o ${{ github.workspace }}/tools/robot


Suggested change

curl -L https://raw.githubusercontent.com/ontodev/robot/v1.9.7/bin/robot -o ${{ github.workspace }}/tools/robot

curl -L https://raw.githubusercontent.com/ontodev/robot/v1.9.8/bin/robot -o ${{ github.workspace }}/tools/robot

.github/workflows/copilot-setup-steps.yml

- Updated to latest version of robot.

aleixpuigb · 2025-10-06T13:05:11Z

.github/copilot-instructions.md

+    - `obo-grep.pl -r 'OBA_2040177' src/patterns/definitions.owl`
+- Note that `obo-grep.pl` is in your PATH, no need to search for it    
+- Only search over `src/patterns/definitions.owl`
+- DO NOT bother doing your own greps over the file, or looking for other files, unless otherwise asked, you will just waste time.


OBA has a different system than other ontologies, so it might be useful that copilot looks at other files, such as as the DOSDP yaml files or tsv tables, specially if the idea is to provide only a label and it recognizes which pattern should it use. However, it doesn't need grep for it.

aleixpuigb · 2025-10-06T13:08:09Z

.github/copilot-instructions.md

+
+        Example 3: A trait that affects the response to prednisolone. Use the design pattern template `response_to_chemical_stimulus_trait.tsv` and the filler term: prednisolone.
+
+    2- Check whether design pattern fillers have been imported to OBA. Search `src/ontology/imports/merged_import.owl`


Since this is a large file, maybe here it needs grep?

aleixpuigb · 2025-10-06T13:10:44Z

.github/copilot-instructions.md

+    3- If they have been imported, please proceed to creating the new OBA term using the appropriate DOSDP pattern template.
+
+    4- Add the term to the template, then run 
+            make IMP=false MIR=false ../patterns/definitions.owl 


It can be added as a command format (use ` before and after the code, or ```)

Same comment for points 5 and 6

aleixpuigb · 2025-10-06T13:13:13Z

.github/copilot-instructions.md

+- Each term requires: id, name, definition with references
+- Never guess OBA IDs, or ontology term IDs, use search tools above to determine actual term
+- Never guess PMIDs for references, do a web search if needed
+- Use standard relationship types: is_a, part_of, has_part, etc.


you can add usual OBA relations

.github/copilot-instructions.md

aleixpuigb · 2025-10-06T13:16:19Z

.github/copilot-instructions.md

+## Obsoleting terms originating from DOS-DP templates
+
+- Delete the row with the targeted term from the appropriate data table (tsv file) in folder: src/patterns/data/default/
+- Fill in the IRI of the term to be obsoleted in src/templates/obsoletes.tsv along with other relevant information. It is useful add a comment with an explanation for the obsoletion. Start the comment with 'Reason for obsoletion: '.


It might need an example or some more information

aleixpuigb · 2025-10-06T13:17:34Z

.github/copilot-instructions.md

+
+## Other metadata
+
+- Link back to the issue you are dealing with using the `term_tracker_item`


Does OBA include this?

.github/copilot-instructions.md

aleixpuigb · 2025-10-06T13:18:48Z

.github/copilot-instructions.md

+
+- Link back to the issue you are dealing with using the `term_tracker_item`
+- All terms should have definitions, with at least one definition xref, ideally a PMID
+- You can sign terms as `created_by: AI agent`


I believe this should be in a column of the DOSDP

Removed troubleshooting instructions

ar-ibrahim added 3 commits September 2, 2025 18:36

Create copilot-setup-steps.yml

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Assign ID range for AI agent

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Create copilot-instructions.md

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ar-ibrahim self-assigned this Sep 2, 2025

matentzn reviewed Sep 2, 2025

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ar-ibrahim added 3 commits September 24, 2025 11:54

Merge branch 'master' into set_up_AI_agent

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Merge branch 'master' into set_up_AI_agent

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Update copilot-instructions.md

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ar-ibrahim requested review from aleixpuigb and jamesamcl September 30, 2025 14:03

ar-ibrahim marked this pull request as ready for review September 30, 2025 14:04

Update copilot-instructions.md

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- update AI agent signature

aleixpuigb reviewed Oct 6, 2025

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Update copilot-setup-steps.yml

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- Updated to latest version of robot.

aleixpuigb reviewed Oct 6, 2025

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ar-ibrahim requested a review from zoependlington October 6, 2025 13:27

ar-ibrahim added 2 commits October 22, 2025 10:36

Update oba-idranges.owl

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Update copilot-instructions.md

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ar-ibrahim requested a review from aleixpuigb October 22, 2025 09:40

Update copilot-instructions.md

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Removed troubleshooting instructions

jamesamcl approved these changes Oct 22, 2025

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jamesamcl merged commit f21aacd into master Oct 22, 2025
2 checks passed

	- Desgin pattern templates are found in `src/patterns/data/default`
	- Design pattern templates are found in `src/patterns/data/default`

	2- Check whether design pattern components have been imported to OBA. Search `src/ontology/imports/merged_import.owl`
	2- Check whether design pattern filler terms have been imported to OBA. Search `src/ontology/imports/merged_import.owl`


		6 - Run sh run.sh make IMP=false MIR=false ../patterns/definitions.owl again.

		7- When creating new OBA terms using DOSDP patterns, it may be necessary to import terms from other ontologies like ChEBI, the Chemical Entities of Biological Interest or PRO, the PRotein Ontology. However, they are too large to be managed as standard imports so are managed as slims. When a new term you are using in a DOSDP pattern is not yet in a slim you will have to refresh the slim first. They are located here:

	sh run.sh make components/obsoletes.owl
	make components/obsoletes.owl

	key: ${{ runner.os }}-robot-v1.9.7
	key: ${{ runner.os }}-robot-v1.9.8

	curl -L https://github.com/ontodev/robot/releases/download/v1.9.7/robot.jar -o ~/.jar-cache/robot.jar
	curl -L https://github.com/ontodev/robot/releases/download/v1.9.8/robot.jar -o ~/.jar-cache/robot.jar

	curl -L https://raw.githubusercontent.com/ontodev/robot/v1.9.7/bin/robot -o ${{ github.workspace }}/tools/robot
	curl -L https://raw.githubusercontent.com/ontodev/robot/v1.9.8/bin/robot -o ${{ github.workspace }}/tools/robot


		Example 3: A trait that affects the response to prednisolone. Use the design pattern template `response_to_chemical_stimulus_trait.tsv` and the filler term: prednisolone.

		2- Check whether design pattern fillers have been imported to OBA. Search `src/ontology/imports/merged_import.owl`


		## Other metadata

		- Link back to the issue you are dealing with using the `term_tracker_item`

Set up AI agent #393

Set up AI agent #393

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ar-ibrahim commented Sep 2, 2025

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