Retire metpo/presentations/ analysis scripts (#433 scope-narrowing)

README.md

@@ -148,7 +148,7 @@ make -C literature_mining icbo-analyze
 
 Example inputs, templates, and outputs are in `literature_mining/abstracts/icbo_examples/` and `literature_mining/outputs/icbo_examples/`.
 
-**Presentation materials**: See `docs/presentations/icbo_2025/` for slides and analysis from ICBO 2025.
+**Presentation materials**: See `docs/presentations/icbo_2025/` for slides and analysis from ICBO 2025. The Python scripts that generated the figures for that talk (formerly in `metpo/presentations/`) are preserved at the release tag `2025-11-17`. Recover them with `git checkout 2025-11-17 -- metpo/presentations/`.
 
 ### 4. Database Reconciliation (`metpo/scripts/`)
 

docs/CLI_STANDARDIZATION_PLAN.md

@@ -90,28 +90,9 @@
 
 ---
 
-### **Category 4: Presentation Scripts (9 scripts) - OPTIONAL**
+### **Category 4: Presentation Scripts - RETIRED**
 
-**Location**: `metpo/presentations/` (ICBO 2025)
-
-| Script | Lines | Effort | Priority | Notes |
-|--------|-------|--------|----------|-------|
-| analyze_bactotraits.py | 153 | Low | Optional | One-time figure generation |
-| analyze_kg_microbe_metpo.py | 178 | Low | Optional | One-time figure generation |
-| analyze_madin_etal.py | 187 | Low | Optional | One-time figure generation |
-| analyze_ontogpt_grounding.py | 134 | Low | Optional | One-time figure generation |
-| analyze_ontology_landscape.py | 209 | Low | Optional | One-time figure generation |
-| analyze_primary_sources.py | 165 | Low | Optional | One-time figure generation |
-| analyze_sssom_mappings.py | 71 | Low | Optional | One-time figure generation |
-| calculate_minimum_import_set.py | 161 | Low | Optional | One-time figure generation |
-| generate_feedback_loop.py | 213 | Low | Optional | One-time figure generation |
-
-**Recommendation**: Leave as-is unless they need to be rerun frequently
-- These are research output scripts for a specific presentation
-- Already executed and generated figures
-- Low value in CLI standardization unless reusability is important
-
-**Total for Category 4**: 9-18 hours if standardized (not recommended)
+The 9 scripts that previously lived under `metpo/presentations/` were one-shot code for the ICBO 2025 talk. They have been removed from `main` and are preserved at the release tag `2025-11-17`. Recover with `git checkout 2025-11-17 -- metpo/presentations/`. No CLI standardization work is planned for these scripts.
 
 ---
 

docs/METPO_CAPABILITIES.md

@@ -536,22 +536,15 @@ Stubs contain only ID, LABEL, and TYPE columns, allowing templates to reference
 
 ---
 
-## 18. KG-Microbe Integration Analysis
+## 18. KG-Microbe Integration Analysis (retired)
 
-Scripts to analyze how METPO terms are used across the KG-Microbe knowledge graph datasets.
+A set of analysis scripts that examined METPO usage across the KG-Microbe knowledge graph datasets (BactoTraits, Madin et al., BacDive) and produced figures for the ICBO 2025 talk. The scripts were one-shot and were not maintained as ongoing CLI tools.
 
-Located in `metpo/presentations/`:
+The scripts have been removed from `main` to keep the repository focused on ontology maintenance. They are preserved at the release tag `2025-11-17` and can be recovered with:
 
-| Script | Purpose |
-|--------|---------|
-| `analyze_kg_microbe_metpo.py` | METPO usage across all KG-Microbe datasets |
-| `analyze_bactotraits.py` | BactoTraits-specific analysis |
-| `analyze_madin_etal.py` | Madin et al. dataset analysis |
-| `analyze_primary_sources.py` | Primary source comparison |
-| `analyze_ontogpt_grounding.py` | OntoGPT grounding quality |
-| `analyze_ontology_landscape.py` | Related ontology comparison |
-| `calculate_minimum_import_set.py` | Compute minimal import closure |
-| `generate_feedback_loop.py` | Generate feedback for improvements |
+```bash
+git checkout 2025-11-17 -- metpo/presentations/
+```
 
 ---