[DO NOT MERGE] eval #3521 i:1: Add reference dataset and NS-Forest marker for human bipolar neuron types (opencode/openai/gpt-5.4, .)

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#3521: Add reference dataset and NS-Forest marker for human bipolar neuron types

Original PR (human solution)

#3583: Add reference transcriptomic dataset see_also link for 13 human bipolar neuron cell types

Agent Commits

• Add CAP dataset links for human bipolar neuron types

Note: This PR diff shows ONLY the agent's changes. The baseline is eval_base_branch.

Agent Response - PR Comments

Implemented the CL-side part of issue #3521 by adding the imported Cell Annotation Platform reference transcriptomic dataset link to the requested human retinal bipolar neuron classes.

Changed file:

• src/ontology/cl-edit.owl

What changed:

• Added rdfs:seeAlso annotations with the URL https://celltype.info/project/544/dataset/1157 to these classes:
• CL_0000748 retinal bipolar neuron
• CL_0000751 rod bipolar cell
• CL_4033019 ON-blue cone bipolar cell
• CL_4033027 diffuse bipolar 1 cell
• CL_4033028 diffuse bipolar 2 cell
• CL_4033029 diffuse bipolar 3a cell
• CL_4033030 diffuse bipolar 3b cell
• CL_4033031 diffuse bipolar 4 cell
• CL_4033032 diffuse bipolar 6 cell
• CL_4033033 flat midget bipolar cell
• CL_4033034 invaginating midget bipolar cell
• CL_4033035 giant bipolar cell
• CL_4033036 OFFx cell

Rationale:

• The issue comments explicitly supplied a database_cross_reference URL and the annotation label reference transcriptomic data on Cell Annotation Platform for these terms.
• In this checkout, the actionable change was in cl-edit.owl, and rdfs:seeAlso is already an established annotation property in the ontology for external follow-up links.
• I kept the change minimal and localized rather than rewriting textual definitions without a clearer in-file pattern for dataset-location wording.

Background research and review performed:

• Read __issue_context__.json for the imported issue title, body, and comments.
• Checked the target term stanzas in src/ontology/cl-edit.owl.
• Reviewed the referenced CAP dataset page to confirm it is the human retina bipolar-cell reference dataset.
• Reviewed the referenced CellMark PR to understand the NS-Forest-marker request.

Scope decision:

• The NS-Forest marker part mentioned in the issue appears to refer to upstream CellMark work that was already completed there.
• Per repository guidance for this checkout, I edited only src/ontology/cl-edit.owl and did not attempt unrelated marker-file changes outside the local CL ontology task.

Validation performed:

• Ran robot convert --input src/ontology/cl-edit.owl --output /tmp/opencode/cl-edit.ofn to confirm the edited ontology file parses successfully.

Checklist completed:

• Read imported issue context
• Verified the 13 requested CL terms in cl-edit.owl
• Confirmed the external dataset target
• Added the dataset annotations to all requested classes
• Validated ontology syntax with robot convert
• Committed only the ontology file change

---

🤖 Generated by opencode agent

• Runtime: opencode
• Model: openai/gpt-5.4
• Agent config: ai4curation/cl-agent-config@v3:.
• Iteration: 1
• Run: View workflow run

Agent Response - Issue Comments

Addressed in PR #.

Added the Cell Annotation Platform reference transcriptomic dataset link (https://celltype.info/project/544/dataset/1157) to the 13 requested human retinal bipolar neuron classes in CL.

The NS-Forest marker portion referenced in the issue appears to have been handled upstream in CellMark; there were no corresponding local marker-input files to update in this checkout.

---

🤖 Generated by opencode agent

• Runtime: opencode
• Model: openai/gpt-5.4
• Agent config: ai4curation/cl-agent-config@v3:.
• Iteration: 1
• Run: View workflow run

Experiment Config

Parameter	Value
Model	openai/gpt-5.4
Agent config	ai4curation/cl-agent-config@v3:.
Iteration	1
URL prefix	https://href.li/?
Base branch	eval-base-issue-3521

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25977540094