Literature Sync: Zotero + Obsidian Pipeline

Takes the .bib output of /search-lit (or any user-specified .bib file), synchronizes the references into the Zotero library and Obsidian literature notes, and extracts cross-cutting concept notes once enough literature notes accumulate.

Prerequisites

• Project owner only. Collaborators consume the committed manuscript/_src/refs.bib snapshot

read-only. If the current user is a collaborator (no Zotero access per SSOT.yaml reference_manager.required_for), abort with instructions to flag [@NEW:topic] placeholders in the manuscript and notify the owner.

• Zotero desktop 7.x + Better BibTeX plugin, with Better BibTeX "Keep updated" auto-export

configured to <project>/manuscript/_src/refs.bib.

• Zotero MCP server (if not connected, skip Phase 2; auto-export still refreshes once Zotero is

reopened).

• Obsidian CLI or direct file writing to the vault; vault path from the user's environment

(e.g., $OBSIDIAN_VAULT).

Artifact Contract

/lit-sync is the sole writer of manuscript/_src/refs.bib (via the Better BibTeX auto-export trigger), references/zotero_collection.json, and references/fulltext_retrieval.json (Phase 2.7). NEVER write `refs.bib` directly — not even to compensate for a missing Zotero connection — because only Better BibTeX's export keeps it in step with the library; if auto-export is broken, fix the Zotero setup. Direct hand edits to refs.bib are drift — revert on sight.

Phase 1: Parse BibTeX

Parse the user-specified .bib file, or the references/library.bib just produced by /search-lit, with regex. Extract per entry: citekey, doi, pmid, title, authors (first + last minimum), journal, year, and volume/number/pages if present. Log any parse failures and skip those entries. All bibliographic data in later phases comes from these entries or from API responses.

A parsed citekey is not yet a library key: /search-lit candidate keys (Kim_2024_Validation) are provisional, and Better BibTeX mints the real key when Phase 2 adds the item. Never compose a key; Step 3.2 §Citekey provenance says where the note's key comes from.

Phase 2: Zotero Sync

If the Zotero MCP is not connected, skip this phase (still write the Step 2.3 file with status: "skipped") and proceed to Phase 3.

Step 2.1: Determine project collection

Identify the project from the current working directory or an explicit user override. Reuse a recorded collection key; otherwise check existing Zotero collections for the project and, if none exists, create one with zotero_create_collection. Record the collection key, and report it to the user when a new collection is created.

Step 2.2: Dedupe + add

For each entry:

1. Use zotero_search_items to search by DOI or title — if already present, skip.

This search-first step is what prevents duplicates; zotero_add_by_doi does not dedupe by itself (it fetches CrossRef and creates the item), so never skip the search.

1. Otherwise call zotero_add_by_doi (when a DOI is available) or zotero_add_by_url (the PubMed

URL, when only a PMID is available). An entry with neither DOI nor PMID is not added: count it as failed and ask the user to add it manually.

• zotero_add_by_doi accepts an attach_mode argument that governs the **OA child-PDF

attach attempt at add time (the installed server treats `linked_url` as "bookmark the PDF URL"; other values download/import). Exact accepted values are server-version-specific — verify against the connected server. Do not** use zotero_add_from_file to attach a PDF to an item added here: it has no parent-item argument and would create a duplicate parent item.

1. Use zotero_manage_collections to place the item in the project collection.

Step 2.3: Result report

Zotero Sync:
  Added:     8 papers (new)
  Skipped:   3 papers (already in library)
  Failed:    1 paper (no DOI/PMID)
  Collection: RFA-Meta (TZQEP4NH)

Always write references/zotero_collection.json in the project workspace:

{
  "schema_version": 1,
  "status": "synced",
  "collection": "RFA-Meta",
  "collection_key": "TZQEP4NH",
  "added": 8,
  "skipped": 3,
  "failed": 1
}

If Zotero is unavailable, write the same file with status: "skipped" and a human-readable reason.

Phase 2.5: refs.bib snapshot refresh

Better BibTeX "Keep updated" auto-export normally refreshes manuscript/_src/refs.bib within seconds of a Zotero change. This phase verifies the snapshot actually updated before downstream skills consume it.

Step 2.5.1: Resolve path

Read SSOT.yaml → truth.refs_bib. Default: manuscript/_src/refs.bib. If absent (legacy project), fall back to manuscript/_src/refs.bib and emit a WARN recommending SSOT migration.

Step 2.5.1b: Precondition assertion (early-exit, do NOT poll)

Before entering the 10s polling loop in Step 2.5.2, verify both preconditions. If either fails, abort Phase 2.5 with setup instructions instead of waiting for a timeout that will never resolve.

1. Better BibTeX is answering. Probe the running plugin, not a file on disk:

   curl -s -m 5 -o /dev/null -w "%{http_code}" \
     http://127.0.0.1:23119/better-bibtex/json-rpc    # expect 200

A non-200 means Zotero is closed or BBT has not finished starting. Retry once after Zotero's window is up; BBT registers its endpoint a few seconds after the app does.

⚠️ Do not gate on `~/Zotero/better-bibtex/read-only.json`. Current BBT releases keep auto-export registrations in their own store, so that file is routinely [] on a healthy install; treating it as "not configured" skips this phase on working setups, which is how a stale refs.bib and an invented citekey reach a manuscript.

On failure print:

Phase 2.5 skipped: Better BibTeX did not answer on 127.0.0.1:23119 (HTTP <code>). Open Zotero, wait for it to finish loading, then re-run /lit-sync.

1. Target refs.bib exists. The resolved truth.refs_bib path from Step 2.5.1 must exist on disk (even empty is OK — BBT will overwrite). On failure print:

Phase 2.5 skipped: target snapshot <path> not found. Configure BBT auto-export with "On Change" to the SSOT path, then re-run.

In either early-exit, set refs_bib_refreshed: false + reason: "precondition:<which>" in the Step 2.5.3 JSON, tell the user, and return control to the caller. Nothing downstream enforces this flag, so telling the user is what stands between a stale refs.bib and a manuscript.

Step 2.5.2: Verify refresh

After Phase 2 adds items:

1. Capture stat -f "%m" manuscript/_src/refs.bib before Zotero writes.
2. Wait up to 10s (Better BibTeX debounce). Poll mtime.
3. If mtime unchanged after 10s:

• Prompt user to check Zotero is running and BBT export is "Keep updated".
• If BBT auto-export path is wrong, print the expected path (<project>/manuscript/_src/refs.bib).
• As last resort, offer manual export: File → Export Library → Better BibTeX → target path.

1. Once mtime advances, grep for the newly added citekeys. All must be present; if any is missing, report as failure (do NOT fabricate entries).

Step 2.5.3: Record in zotero_collection.json

Append to the JSON written in Step 2.3:

{
  "refs_bib_path": "manuscript/_src/refs.bib",
  "refs_bib_mtime": "2026-04-24T14:32:11Z",
  "refs_bib_refreshed": true,
  "citekeys_verified": ["smithDeepLearningRadiology2024", "..."]
}

If refresh failed, set refs_bib_refreshed: false and include reason.

Phase 2.7: Fulltext Retrieval (opt-in, owner-only)

Run only when the user asks for full text (e.g. "download the PDFs", "fetch full text", or a worklist supplied with that intent). Default /lit-sync stays metadata-only and network-light — do not auto-run this phase. Runs after items are in Zotero (Phase 2) and the snapshot is verified (Phase 2.5), before Obsidian notes (Phase 3).

Offer both routes below and reconcile them in one report. Retrieve full text only through them: never automate authenticated browser sessions, never bypass paywalls or access controls, and never hard-code institutional proxies, credentials, or hosts into this skill. Route what neither reaches to institutional access, interlibrary loan, or author contact.

Route A — disk OA PDFs (for downstream skills)

Delegate to the /fulltext-retrieval engine (do not re-implement the OA cascade or import its code; invoke it by path):

ENGINE="${CLAUDE_SKILL_DIR}/../fulltext-retrieval/fetch_oa.py"
python3 "$ENGINE" <worklist> -o pdfs/ -e <contact-email> --report pdfs/retrieval_report.json

<worklist> is the DOI/PMID(/Title) list — the Phase-1 .bib DOIs, a worklist supplied in Standalone Modes, or the project collection's DOIs. Output: pdfs/*.pdf for /meta-analysis and pdf_to_md.py, plus pdfs/retrieval_report.json (schema 2: retrieval status/source, source_identity, and file_sha256). Keep the distinction between having a file and assessing its identity.

Route B — in-library PDFs (Zotero-native, higher yield, proxy-aware)

Emit ${CLAUDE_SKILL_DIR}/../fulltext-retrieval/references/find_available_pdf.js for the user to paste into Zotero (Tools → Developer → Run JavaScript) with the project collection selected. It triggers Zotero's own addAvailablePDF/addAvailablePDFs, which reuse the user's OpenURL resolver / institutional proxy — so it typically retrieves more than OA-only, while no credentials or institutional identifiers enter this skill. The no-code equivalent is right-click → "Find Available PDF". Record its {attached, missing} summary from the printed JSON.

Report

Merge Route A's pdfs/retrieval_report.json (and the user-reported Route B summary) into references/fulltext_retrieval.json, and append a short fulltext counts block to references/zotero_collection.json. Read ${CLAUDE_SKILL_DIR}/references/fulltext_report.md before writing them — it has the schema and the identity-evidence rules (a retrieved file is not a verified paper; a consistent status is advisory; unassessed items go to identity_review_needed).

Phase 3: Obsidian Literature Notes

Detect the vault's existing layout before creating notes. If the vault already uses a folder structure (including a Korean one), honor it — never silently rename a user's folders. For a new or unclear vault, default to the English folders Literature/ and Concepts/ with the English templates (Step 3.2, Step 4.3). For a Korean-structured vault, or a user who prefers Korean notes, use the Korean folder layout and Korean-heading templates in ${CLAUDE_SKILL_DIR}/references/locale/ko/note_templates.md (and the vault's own hub-note names).

Step 3.1: Check existing literature notes

# Default English layout; substitute the vault's existing folder if one is present
# (e.g. "02 연구/문헌/" for a Korean-structured vault — see references/locale/ko/note_templates.md).
ls "$VAULT/Literature/" | grep -v "📊" | wc -l

Step 3.2: Create literature notes

For each .bib entry, create Literature/{citekey}.md (or the vault's existing literature folder). Skip if the file already exists — never overwrite, because the user may have added highlights or personal notes.

#### Citekey provenance — the note filename is a claim about the library

A note's filename and citekey: field assert that Zotero has an entry with that key. [@key] in a manuscript, [[key]] between notes, and the Zotero Integration plugin's {{citekey}}.md all depend on it, and a key that resolves to nothing still looks correct. So the key is read, never composed:

1. Take it from the Better BibTeX-exported refs.bib entry, or ask Better BibTeX

(item.search over json-rpc — see ${CLAUDE_SKILL_DIR}/references/bbt_lookup.md).

1. If the paper is not in Zotero, add it first (zotero_add_by_doi) and let BBT mint

the key. Phase 2 owns that step for a reason: a note written ahead of its library entry has no key to be right about.

1. If it cannot be added (no DOI, offline), write the note with citekey: "" and the tag

_needs-citekey. An empty field is recoverable; an invented one is not, because nothing downstream can tell it apart from a real key.

Verify before finishing:

python3 "${CLAUDE_SKILL_DIR}/scripts/check_citekey_provenance.py" --vault "$VAULT" --bib "$REFS_BIB"

INVENTED means the note's key is absent but its DOI resolves to a real key; fix it here. MISMATCH means the key is real but the note's DOI is the library's DOI for another key, so it cites another paper; rename to the suggested key (known limit: a note DOI spelled differently from the library's, e.g. quoted or braced, never raises it). UNPARSED means a literature note's frontmatter never closes, so its key was not read. With --strict these three exit 1, and a scan that finds no literature note exits 2. Match notes to papers by DOI, never by key (AMBIGUOUS, UNUSABLE, NO_IDENTIFIER: see the script's --help), and search the full library (--live) before importing anything it reports missing.

#### Template

---
notetype: literature
citekey: "{citekey}"
title: "{title}"
authors: "{authors}"
journal: "{journal}"
year: {year}
doi: "{doi}"
pmid: "{pmid}"
created: "{today}"
tags:
  - type/literature
  - _unread
---

# {title}

## Bibliographic info
- **Authors**: {authors}
- **Journal**: {journal}{volume_issue_pages}
- **Year**: {year}
- **DOI**: [{doi}](https://doi.org/{doi})
{pmid_line}

## Key points (in my own words)

## My thoughts

## Related notes
- [[Research Hub]]
- [[Papers & Reviews]]
-
-

Rules:

• notetype: literature — compatible with the Zotero Integration template.
• _unread tag — change to _read later after the user reads the PDF in Zotero and adds highlights.
• Leave ## Key points and ## My thoughts blank — the user fills these in personally.
• ## Related notes contains 2 hub links + 2 empty slots (reserved for later concept-note linking).
• If a PMID is available, add a PubMed link.

Step 3.3: Result report

Obsidian Literature Notes:
  Created:   8 notes (new)
  Skipped:   3 notes (already exist)
  Location:  Literature/
  Total in vault: 12 literature notes

Phase 4: Concept Extraction (conditional)

Trigger condition

Run this phase only when there are ≥10 literature notes in the vault. If fewer exist, print a status message like "N literature notes — concept extraction unlocks at ≥10" and stop.

Step 4.1: Cross-cutting concept scan

Read all files under Literature/*.md (or the vault's existing literature folder), extract keywords from each paper's title, journal, and tags and major concepts from the .bib entry titles, and identify concepts that co-occur across ≥3 literature notes.

Step 4.2: Filtering (5 exclusion rules)

Exclude from concept candidates: model names (GPT-4, Claude, etc.), dataset names (MedQA, ImageNet, etc.), journal names, institution names, and generic technique names (too unspecific). Whatever remains becomes a concept-note candidate.

Step 4.3: Draft concept note

Create Concepts/{concept name}.md (or the vault's existing concept-note folder) from the template in ${CLAUDE_SKILL_DIR}/references/concept_note_template.md (Korean-structured vault: the concept template in references/locale/ko/note_templates.md).

Key rules:

• Never auto-fill `## Definition` — keep the > TODO marker; the 2nd-layer note only becomes

meaningful once the user writes the definition in their own words.

• status always starts at 🌱Seedling.
• At least 4 wikilinks under ## Related notes (vault convention).

Step 4.4: Propose to the user

Concept-note candidates (≥3 papers cross-referenced):
  1. {Concept A} (4 papers)
  2. {Concept B} (3 papers)
  3. {Concept C} (5 papers)

Create? (all / selected / skip)

Auto-draft, but create only after user confirmation.

Standalone Modes

This skill can run without a fresh .bib file.

Concept extraction only

On an explicit concept-extraction request, scan existing Literature/*.md (or the vault's existing literature folder) and run only Phase 4.

References tidy

On a "tidy this project's references" request, locate .bib files inside the workspace and run Phase 1–3.

Zotero sync only

On a "sync Zotero" request, diff the Zotero collection against the .bib file and add whatever is missing.

PMID-list ingestion (no .bib)

When the user supplies a list of PMIDs (e.g., from a HANDOFF or a colleague), resolve PMIDs to DOIs via PubMed esummary first, then enter Phase 2 with the DOIs:

PMIDS="12345,67890,..."
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=${PMIDS}&retmode=json" \
  | jq -r '.result | to_entries[] | select(.key != "uids") | "\(.value.uid)\t\(.value.elocationid)\t\(.value.title)"'

For items already in the library (found by the Step 2.2 search), use zotero_manage_collections to attach them to the project collection without re-adding — re-adding by URL/PubMed-URL would bypass the search dedup and create duplicates. Record both added and existing items in references/zotero_collection.json. If a PMID has no DOI in PubMed (older or non-indexed papers), fall back to zotero_add_by_url with the PubMed URL and mark the entry no_doi: true.

Worklist ingestion (DOI/PMID/Title; no .bib)

When the user supplies a worklist file (a .tsv/.csv/.md table with a DOI column, optional PMID/Title, or a plain DOI-per-line list — e.g. an SR include set), enter Phase 2 directly from it: resolve any PMID-only rows to DOIs (esummary above), then run the search-first dedupe + add loop. The same worklist file feeds Phase 2.7 Route A (fetch_oa.py reads .tsv/.csv/.md/plain natively), so no reformatting is needed.