Claude Task: Foundational Papers Figure/Page/DOI Verification Pass

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

Resolve the first batch of verification gaps in the 13-paper foundational claim-evidence matrix:

1. 3 rows with needs_page_verification.
2. 5 rows with needs_figure_table_verification.
3. Open DOI / bibliographic verification for key papers.
4. Promote rows to verified_from_full_text where evidence is directly verified from extracted full text.

Non-negotiable constraints

1. Do not fabricate exact page numbers, figure numbers, table numbers, equations, DOI, or numerical values.
2. Only change matrix status if you can directly verify from extracted full text, source note, or reliable bibliographic metadata already present in files.
3. If uncertain, leave status as-is and explain why.
4. Do not edit raw PDFs, raw extracted text, source notes, or 06_lab_position/.
5. Use UTF-8-sig for CSV output.
6. Keep this pass focused on verification; do not edit concept nodes.

Source files to inspect

• 07_visualization/foundational_papers_claim_evidence_matrix.csv
• 07_visualization/concept_evidence_coverage_report.md
• 03_papers/foundational_paper_evidence_ledger.md
• 07_visualization/foundational_paper_integration_report.md
• extracted texts under 00_sources/foundational_papers/extracted_text/
• paper cards under 03_papers/
• source notes under 00_sources/foundational_papers/source_notes/

Verification targets

A. Rows tagged needs_page_verification

Find rows in the matrix with status = needs_page_verification. For each:

• search the relevant extracted full text for key terms / equation names / figure titles / numeric values;
• if evidence can be located, update the row status to verified_from_full_text, and add extracted full-text page/section evidence to the notes column;
• if not, leave the status and record in the verification report.

B. Rows tagged needs_figure_table_verification

Find rows in the matrix with status = needs_figure_table_verification. For each:

• search the relevant extracted full text for figure/table/equation tokens and numeric constants;
• if the row can be verified sufficiently, update to verified_from_full_text and add the evidence location in notes;
• if only the claim but not the figure/table number is verifiable, use verified_from_full_text only if the evidence summary no longer depends on the exact figure/table number. Otherwise leave status unchanged.

Known tokens to search, from the reports:

• Kanda & Li 2006: 1.3, 2.7, J’b/Jtip, sigma, Fig. 16, Fig. 17, saturated PSH.
• Li & Wang 2006: Fig. 12, 7 vol, expanded shale, plastic beads, artificial flaws.
• Zhou et al. 2012: alpha, R² = 0.98, mixing sequence, tensile strain capacity.
• Li & Li 2012/2013: 24-33, Marsh cone, R = 0.95, Fig. 12, Table 3.
• Li & Leung 1992: steady-state, failure mechanism, delta, crack opening.
• Lin & Li 1997: fracture energy, post-debonding, beta Lf, 2df.

C. DOI / bibliographic verification

Create a DOI/bibliographic ledger. Use only information already in source notes, paper cards, or extracted text unless you can verify via reliable bibliographic metadata with a simple web/DOI lookup available to the Hermes profile. Do not invent DOI.

Targets:

• Lin & Li 1997
• Redon et al. 2001
• Li et al. 2002
• Kanda & Li 2006
• Yang et al. 2008
• Li, Wang & Wu 2001 DOI 10.14359/10724 independent check if possible

Deliverables

1. Updated matrix

Update in place if safe:

07_visualization/foundational_papers_claim_evidence_matrix.csv

Rules:

• preserve all columns;
• preserve all rows;
• only status and notes should change for verified rows;
• do not delete rows;
• keep UTF-8-sig.

2. Verification report

Create:

07_visualization/foundational_matrix_verification_report.md

Include:

• initial counts by status;
• final counts by status;
• rows promoted to verified_from_full_text;
• rows still unresolved;
• DOI / bibliographic ledger summary;
• exact files searched;
• recommended next task.

3. DOI / bibliographic ledger

Create:

03_papers/foundational_bibliographic_verification_ledger.md

Include one block per target paper:

• current citation in paper card/source note;
• DOI status: verified / not found / needs external check;
• journal, volume, issue, pages status;
• notes.

4. Verification summary JSON

Create:

07_visualization/foundational_matrix_verification_summary.json

Include machine-readable counts and lists:

• initial_status_counts
• final_status_counts
• promoted_rows
• unresolved_rows
• doi_status

Verification before finishing

Verify:

1. matrix CSV remains parseable and has same row count as before;
2. verification report exists;
3. bibliographic ledger exists;
4. summary JSON exists and parses;
5. no file under originals/, extracted_text/, source_notes/, or 06_lab_position/ was modified.

Return concise completion summary.