Claude Task: Create Missing Concept Nodes and Promote Foundational Graph Edges

You are Claude running through the claude-reviewer Hermes profile. Hermes is the orchestrator and verifier. Work only inside:

/Users/bylee/Documents/Research_Knowledge/ECC_Research_Atlas/

Goal

Continue the ECC Research Atlas system build by creating missing concept nodes referenced by the foundational paper graph plan, promoting safe candidate graph edges to confirmed, and preparing the graph for the next claim-evidence matrix pass.

Context

Foundational paper system status:

• 13/13 PDFs preserved.
• 13/13 full text extracted.
• 13/13 source notes created.
• 13/13 paper cards created.

Important existing files:

• 07_visualization/foundational_paper_graph_edge_promotion_plan.md
• 07_visualization/full_graph_candidate_edges.csv
• 07_visualization/concept_graph_expanded.json
• 07_visualization/cross_link_map.md
• 03_papers/foundational_paper_cards_index.md

The promotion plan identifies missing concept nodes:

• interface_properties
• surface_treatment
• matrix_micro_spalling
• cook_gordon_effect
• two_way_debonding

Non-negotiable constraints

1. Do not fabricate facts, DOI, exact page numbers, figure numbers, or table numbers. Mark uncertain items as needs verification.
2. Do not edit raw PDFs or raw extracted text.
3. Do not edit 06_lab_position/.
4. Keep professor/lab-specific integration deferred.
5. Prefer additive files and careful CSV edits.
6. Preserve existing graph files; if creating a full graph, make a new file rather than overwriting concept_graph_expanded.json.

Source files to inspect

• 07_visualization/foundational_paper_graph_edge_promotion_plan.md
• 07_visualization/full_graph_candidate_edges.csv
• 03_papers/lin_li_1997_crack_bridging_slip_hardening.md
• 03_papers/redon_etal_2001_pva_interface_properties.md
• 03_papers/li_wang_wu_2001_pva_ecc_tensile_strain_hardening.md
• 03_papers/li_wu_wang_etal_2002_interface_tailoring_pva_ecc.md
• 03_papers/yang_etal_2008_fiber_bridging_constitutive_law.md
• 03_papers/li_wang_2006_microstructure_variability.md
• 03_papers/li_li_2012_rheology_fiber_dispersion.md
• 03_papers/zhou_etal_2012_mixing_sequence_fiber_distribution.md
• 02_concepts/fiber_bridging_law.md
• 02_concepts/strain_hardening_criteria.md
• 02_concepts/micromechanics_based_design.md
• 02_concepts/fiber_dispersion.md
• 02_concepts/processing_rheology.md

Deliverables

A. Missing concept nodes

Create these files under 02_concepts/:

1. interface_properties.md
2. surface_treatment.md
3. matrix_micro_spalling.md
4. cook_gordon_effect.md
5. two_way_debonding.md

Each node must include:

• Source basis: paper cards and source notes it is based on.
• Core idea.
• Role in ECC micromechanics.
• Key parameters if applicable.
• Linked nodes.
• Evidence status, with uncertain details marked needs verification.

B. Update cross-link map

Update 07_visualization/cross_link_map.md to include the five new concept nodes under the appropriate groups:

• interface_properties and surface_treatment: Micromechanics core / Interface tailoring.
• matrix_micro_spalling, cook_gordon_effect, two_way_debonding: Fiber-bridging constitutive law subnodes.

C. Promote safe graph edges

Read 07_visualization/foundational_paper_graph_edge_promotion_plan.md.

If the exact rows exist in 07_visualization/full_graph_candidate_edges.csv, safely change status from candidate to confirmed for the 9 edges listed in section A of the plan.

Rules:

• Do not restructure the CSV.
• Preserve header and columns.
• If a row cannot be found exactly, leave it unchanged and report it in the validation report.
• Add evidence card filename to notes only if the notes field already exists and editing will not break CSV. Otherwise leave notes unchanged and record evidence in the validation report.

D. Append deferred edges now enabled by new concept nodes

If safe, append new rows to full_graph_candidate_edges.csv for the 7 group B edges in the promotion plan, now that concept nodes exist.

Use columns already present in the CSV. Status should be confirmed if directly supported by the paper cards; otherwise candidate.

E. Create updated graph files

Create new files, do not overwrite old graph:

• 07_visualization/full_graph_foundational.json
• 07_visualization/full_graph_foundational.md

These should include:

• existing high-level graph concepts where possible;
• new concept nodes;
• confirmed/promoted foundational edges;
• candidate edges not yet verified, clearly marked.

F. Validation report

Create:

07_visualization/graph_promotion_validation_report.md

Include:

• concept nodes created
• edges promoted
• deferred edges appended
• rows not found or not promoted
• files modified
• blockers and recommended next task

Verification before finishing

Verify:

1. five new concept node files exist;
2. cross_link_map references the five new node names;
3. full_graph_candidate_edges.csv remains parseable as CSV;
4. validation report exists;
5. full_graph_foundational.json and .md exist;
6. no file under originals/, extracted_text/, or 06_lab_position/ was modified.

Return concise completion summary.