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Remove stale ICBO_PREP.md reference from CLAUDE.md (#362)
* Remove stale ICBO_PREP.md reference from CLAUDE.md The file was deleted but the reference in CLAUDE.md remained. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * Fix broken references to root ICBO_PREP.md throughout repo The root ICBO_PREP.md was deleted but a copy exists at docs/ICBO_PREP.md. Update all references to point to the correct location. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
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‎CLAUDE.md‎

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**Root directory:**
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- ✅ README.md, LICENSE, pyproject.toml, Makefile
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- ✅ CLAUDE.md (this file)
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- ✅ ICBO_PREP.md (temporary for conference prep)
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- ❌ Analysis scripts (.py)
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- ❌ Cleanup planning docs (.md)
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- ❌ Data files (.tsv, .csv)

‎docs/ICBO_CONTENT_VERIFICATION.md‎

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### Created in Option B reorganization:
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1. `ICBO_PREP.md` (487 lines) - Main reference
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1. `docs/ICBO_PREP.md` (487 lines) - Main reference
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2. `docs/icbo_validation_evidence.md` (287 lines) - Validation findings
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3. `docs/icbo_cmm_details.md` (253 lines) - CMM project details
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4. `docs/icbo_open_questions.md` (151 lines) - Questions & issues
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### ✅ Talk Narrative (Slides 1-9)
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**Source:** `docs/icbo_2025_talk_prep.md`
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**Destination:** `ICBO_PREP.md` Section 2
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**Destination:** `docs/ICBO_PREP.md` Section 2
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**Verified:** Complete slide-by-slide speaker notes for all 9 slides preserved
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### ✅ CMM Project Details
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**Source:** `ICBO_PREP_SUMMARY_UPDATED.md`
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**Destination:** `ICBO_PREP.md` Section 1 + `docs/icbo_cmm_details.md`
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**Destination:** `docs/ICBO_PREP.md` Section 1 + `docs/icbo_cmm_details.md`
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**Verified:**
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- Total Budget ($850,000) ✓
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- All 5 Co-PIs with budget breakdowns ✓
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### ✅ Background Context
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**Source:** `docs/icbo_2025_background_summary.md` & `docs/icbo_2025_background_summary_additions.md`
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**Destination:** `ICBO_PREP.md` + `docs/icbo_cmm_details.md`
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**Destination:** `docs/ICBO_PREP.md` + `docs/icbo_cmm_details.md`
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**Verified:**
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- CMM definition (Critical Minerals and Materials) ✓
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- Key people and roles (Marcin, Cici) ✓
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### ✅ Definition Workflow
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**Source:** `ICBO_PREP_SUMMARY_UPDATED.md`
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**Destination:** `ICBO_PREP.md` Section 4
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**Destination:** `docs/ICBO_PREP.md` Section 4
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**Verified:**
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- Current status (255 terms, 46.3% with definitions) ✓
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- Semantic mapping analysis results ✓

‎docs/icbo_2025_prep/CHROMADB_QDRANT_STATUS.md‎

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- Update #258 (non-OLS embeddings completed)
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- Document #256 decision (defer or close)
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6. **Update `../ICBO_PREP.md` with ChromaDB stats**
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- Add ROI improvement numbers
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- Add semantic mapping statistics
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- Reference this document

‎docs/icbo_2025_prep/DOCUMENT_INVENTORY_ICBO_2025.md‎

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### ✅ ICBO Preparation (FOUND)
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**Location:** `/home/mark/gitrepos/metpo/ICBO_PREP.md`
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**Location:** `../ICBO_PREP.md`
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**Size:** Comprehensive guide
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**Content:**
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- CMM project context and budget details
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| File | Purpose | Status |
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|------|---------|--------|
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| `ICBO_PREP.md` | Main preparation document | ✅ Complete |
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| `../ICBO_PREP.md` | Main preparation document | ✅ Complete |
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| `docs/icbo_validation_evidence.md` | ROBOT validation analysis | ✅ Complete |
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| `docs/icbo_cmm_details.md` | CMM project details | ✅ Complete |
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| `docs/icbo_analysis_notes.md` | Technical analysis | ✅ Complete |
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## 8. Undergraduate Assistants' Work
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**From ICBO_PREP.md:**
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**From `../ICBO_PREP.md`:**
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- Marcin has 3 undergraduate assistants
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- Working on LLM-assisted approaches for METPO definitions
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- Trying to satisfy OBO Foundry principles
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## 9. KG-Microbe Status
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**From ICBO_PREP.md:**
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**From `../ICBO_PREP.md`:**
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- Uses METPO CURIEs
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- Powers CMM project (KG-CMREE extension)
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- BioRxiv paper: https://www.biorxiv.org/content/10.1101/2025.02.24.639989v1
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8. Review BioRxiv KG-Microbe paper
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### Evening (1-2 hours)
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9. Update ICBO_PREP.md with progress
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9. Update `../ICBO_PREP.md` with progress
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10. Prepare queries for tomorrow's definition work
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11. Review slide narrative with new examples
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~/LLM_PROVIDER_FUNDING_GUIDE.md # ⭐ NEW
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# METPO repo - ICBO 2025 prep
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~/gitrepos/metpo/ICBO_PREP.md
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~/gitrepos/metpo/docs/ICBO_PREP.md
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~/gitrepos/metpo/docs/icbo_2025_prep/DOCUMENT_INVENTORY_ICBO_2025.md (this file)
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~/gitrepos/metpo/docs/icbo_2025_prep/CHROMADB_QDRANT_STATUS.md
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~/gitrepos/metpo/docs/icbo_2025_prep/madin_et_al_2020_trait_synthesis.pdf

‎docs/presentations/icbo_2025/ICBO_SLIDES_PREP_SESSION.md‎

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**Tasks:**
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1. ⬜ Create `icbo_metpo_slides.md` (Marp format)
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2. ⬜ Write slide content based on ICBO_PREP.md structure:
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- ⬜ Slide 1: Title
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- ⬜ Slide 2: Data Integration Challenge
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- ⬜ Slide 3: Gap in Ontology Landscape
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2. **MicrO has 103 errors, MPO has 155, MCO has 65**
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- Re-run validations on all three
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- Verify from ICBO_PREP.md table
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- Verify from docs/ICBO_PREP.md table
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3. **158 terms mapped to 24 ontologies**
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- Count: `wc -l metpo_cross_references.tsv`
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### Lower Priority (Nice to have)
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10. **CMM project: $850K, FY26**
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- Verify from ICBO_PREP.md (unlikely to change)
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- Verify from docs/ICBO_PREP.md (unlikely to change)
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- "2.4× worse coverage, 14× worse quality"

‎docs/presentations/icbo_2025/archive/CHROMADB_QDRANT_STATUS.md‎

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- Add ROI improvement numbers
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- Add semantic mapping statistics
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- Reference this document

‎docs/presentations/icbo_2025/archive/DOCUMENT_INVENTORY_ICBO_2025.md‎

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### ✅ ICBO Preparation (FOUND)
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**Location:** `/home/mark/gitrepos/metpo/ICBO_PREP.md`
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**Location:** `docs/ICBO_PREP.md`
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**Size:** Comprehensive guide
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**Content:**
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- CMM project context and budget details
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| File | Purpose | Status |
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|------|---------|--------|
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| `ICBO_PREP.md` | Main preparation document | ✅ Complete |
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| `docs/ICBO_PREP.md` | Main preparation document | ✅ Complete |
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| `docs/icbo_validation_evidence.md` | ROBOT validation analysis | ✅ Complete |
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| `docs/icbo_cmm_details.md` | CMM project details | ✅ Complete |
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| `docs/icbo_analysis_notes.md` | Technical analysis | ✅ Complete |
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## 8. Undergraduate Assistants' Work
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**From ICBO_PREP.md:**
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**From `docs/ICBO_PREP.md`:**
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- Marcin has 3 undergraduate assistants
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- Working on LLM-assisted approaches for METPO definitions
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- Trying to satisfy OBO Foundry principles
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## 9. KG-Microbe Status
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**From ICBO_PREP.md:**
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**From `docs/ICBO_PREP.md`:**
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- Uses METPO CURIEs
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- Powers CMM project (KG-CMREE extension)
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- BioRxiv paper: https://www.biorxiv.org/content/10.1101/2025.02.24.639989v1
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### Evening (1-2 hours)
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9. Update ICBO_PREP.md with progress
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9. Update `docs/ICBO_PREP.md` with progress
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10. Prepare queries for tomorrow's definition work
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11. Review slide narrative with new examples
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~/LLM_PROVIDER_FUNDING_GUIDE.md # ⭐ NEW
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# METPO repo - ICBO 2025 prep
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~/gitrepos/metpo/ICBO_PREP.md
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~/gitrepos/metpo/docs/ICBO_PREP.md
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~/gitrepos/metpo/docs/icbo_2025_prep/DOCUMENT_INVENTORY_ICBO_2025.md (this file)
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~/gitrepos/metpo/docs/icbo_2025_prep/CHROMADB_QDRANT_STATUS.md
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~/gitrepos/metpo/docs/icbo_2025_prep/madin_et_al_2020_trait_synthesis.pdf

‎docs/presentations/icbo_2025/archive/ICBO_CONTENT_VERIFICATION.md‎

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### Created in Option B reorganization:
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1. `ICBO_PREP.md` (487 lines) - Main reference
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1. `docs/ICBO_PREP.md` (487 lines) - Main reference
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2. `docs/icbo_validation_evidence.md` (287 lines) - Validation findings
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3. `docs/icbo_cmm_details.md` (253 lines) - CMM project details
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4. `docs/icbo_open_questions.md` (151 lines) - Questions & issues
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### ✅ Talk Narrative (Slides 1-9)
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**Source:** `docs/icbo_2025_talk_prep.md`
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**Destination:** `ICBO_PREP.md` Section 2
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**Destination:** `docs/ICBO_PREP.md` Section 2
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**Verified:** Complete slide-by-slide speaker notes for all 9 slides preserved
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### ✅ CMM Project Details
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**Source:** `ICBO_PREP_SUMMARY_UPDATED.md`
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**Destination:** `ICBO_PREP.md` Section 1 + `docs/icbo_cmm_details.md`
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**Destination:** `docs/ICBO_PREP.md` Section 1 + `docs/icbo_cmm_details.md`
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**Verified:**
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- Total Budget ($850,000) ✓
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- All 5 Co-PIs with budget breakdowns ✓
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### ✅ Background Context
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**Source:** `docs/icbo_2025_background_summary.md` & `docs/icbo_2025_background_summary_additions.md`
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**Destination:** `ICBO_PREP.md` + `docs/icbo_cmm_details.md`
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**Destination:** `docs/ICBO_PREP.md` + `docs/icbo_cmm_details.md`
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**Verified:**
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- CMM definition (Critical Minerals and Materials) ✓
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- Key people and roles (Marcin, Cici) ✓
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### ✅ Definition Workflow
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**Source:** `ICBO_PREP_SUMMARY_UPDATED.md`
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**Destination:** `ICBO_PREP.md` Section 4
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**Destination:** `docs/ICBO_PREP.md` Section 4
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**Verified:**
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- Current status (255 terms, 46.3% with definitions) ✓
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- Semantic mapping analysis results ✓

‎docs/presentations/icbo_2025/archive/ICBO_SLIDES_PREP_SESSION.md‎

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**Tasks:**
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1. ⬜ Create `icbo_metpo_slides.md` (Marp format)
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2. ⬜ Write slide content based on ICBO_PREP.md structure:
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2. ⬜ Write slide content based on docs/ICBO_PREP.md structure:
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- ⬜ Slide 1: Title
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- ⬜ Slide 2: Data Integration Challenge
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- ⬜ Slide 3: Gap in Ontology Landscape
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2. **MicrO has 103 errors, MPO has 155, MCO has 65**
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- Re-run validations on all three
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- Verify from ICBO_PREP.md table
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- Verify from docs/ICBO_PREP.md table
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3. **158 terms mapped to 24 ontologies**
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- Count: `wc -l metpo_cross_references.tsv`
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### Lower Priority (Nice to have)
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10. **CMM project: $850K, FY26**
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- Verify from ICBO_PREP.md (unlikely to change)
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- Verify from docs/ICBO_PREP.md (unlikely to change)
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11. **Expert designation correlation**
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- "2.4× worse coverage, 14× worse quality"

‎literature_mining/README_ICBO_ANALYSIS.md‎

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**Conference:** ICBO 2025
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**Related Documentation:**
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- ICBO preparation: `/home/mark/gitrepos/metpo/ICBO_PREP.md`
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- ICBO preparation: `../docs/ICBO_PREP.md`
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- ChromaDB status: `docs/icbo_2025_prep/CHROMADB_QDRANT_STATUS.md`
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- Document inventory: `docs/icbo_2025_prep/DOCUMENT_INVENTORY_ICBO_2025.md`
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