Literature Sync: Zotero + Obsidian Pipeline

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

Communication Rules

• Communicate with the user in their preferred language.
• Vault layout — honor what exists, default to English. Before creating notes, detect the vault's existing layout: if the vault already uses a particular folder structure (including a Korean one such as 02 연구/문헌/ and 02 연구/개념노트/), 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 note templates below.
• A Korean opt-in variant (Korean folder layout + Korean-heading templates) lives in references/locale/ko/note_templates.md — use it when the vault is Korean-structured or the user prefers Korean notes.

When to Use

• After /search-lit completes — sync the produced .bib into Zotero + Obsidian.
• Bulk-register references from an existing .bib into Zotero + Obsidian.
• Tidy the references/ folder inside a project workspace.
• On explicit concept-extraction request → extract cross-cutting concepts from existing literature notes.

Prerequisites

• Project owner only — /lit-sync is an owner-scoped operation per docs/zotero_policy.md. Collaborators consume the committed manuscript/_src/refs.bib snapshot read-only.
• Zotero desktop 7.x + Better BibTeX plugin installed.
• Better BibTeX "Keep updated" auto-export configured to <project>/manuscript/_src/refs.bib (owner setup checklist in docs/zotero_policy.md §Setup).
• Zotero MCP server available (skip the Zotero phase if not connected; auto-export refresh still fires once Zotero is reopened).
• Obsidian CLI or direct file writing to the Obsidian vault.
• Obsidian vault path: configured in user's environment (e.g., $OBSIDIAN_VAULT).

Artifact Contract

Per docs/artifact_contract.md, /lit-sync is the sole writer of:

Artifact	Writer	Readers
manuscript/_src/refs.bib	/lit-sync (via Better BibTeX auto-export trigger)	/write-paper, /verify-refs, /manage-refs
references/zotero_collection.json	/lit-sync	/verify-refs, /sync-submission

Direct hand edits to refs.bib are drift — revert on sight.

Pipeline Overview

.bib file (or /search-lit output)
    │
    ▼ Phase 1: Parse
    Extract DOI, PMID, title, authors, journal, year
    │
    ▼ Phase 2: Zotero Sync (owner)
    Dedupe → zotero_add_by_doi → place in collection → pin citekey
    │
    ▼ Phase 2.5: refs.bib snapshot refresh
    Trigger Better BibTeX auto-export → verify manuscript/_src/refs.bib mtime updated
    │
    ▼ Phase 2.7: Fulltext Retrieval (opt-in)
    Disk OA PDFs via /fulltext-retrieval + in-library via find_available_pdf.js → reconcile report
    │
    ▼ Phase 3: Obsidian Literature Notes
    Create Literature/{citekey}.md (empty note OK — fill later with highlights)
    │
    ▼ Phase 4: Concept Extraction (conditional)
    ≥10 literature notes → scan for cross-cutting concepts → propose concept notes

---

Phase 1: Parse BibTeX

Input

The user-specified .bib file path, or the .bib just produced by /search-lit.

Process

# Parse .bib entries with regex.
# Extract per entry:
#   - citekey — read it from the entry, never compose one.
#     Better BibTeX keys look like `smithDeepLearningRadiology2024`
#     (author + title words + year). A key shaped like `Smith_2024_Validation`
#     or `smith2024validation` was almost certainly invented rather than read,
#     and will not resolve against the library. See Step 3.2 §Citekey provenance.
#   - doi
#   - pmid
#   - title
#   - authors (first + last minimum)
#   - journal
#   - year
#   - volume, number, pages (if present)

Log any parse failures and skip those entries.

---

Phase 2: Zotero Sync

Step 2.1: Determine project collection

Identify the project from the current working directory or from an explicit user override. Reuse an existing collection key if one is recorded; otherwise create a new collection.

Collection mapping: Check existing Zotero collections for the current project. If no collection exists, create one with zotero_create_collection. Record the collection key for future use.

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.
2. Otherwise call zotero_add_by_doi (when a DOI is available) or zotero_add_by_url (falling back to the PubMed URL when no DOI is available).
   • 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). Set it when you want a PDF attached during the add. 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.
3. 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)

If the Zotero MCP is not connected, skip this entire phase and proceed to Phase 3.

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 perfectly healthy install. Treating an empty list as "not configured" skips this phase on working setups — and a skipped Phase 2.5 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.

2. 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 and return control to the caller. Record it and tell the user; nothing downstream enforces it. verify_refs.py has never read this flag, and the sentence that said it did was the only thing standing 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) and refer to docs/zotero_policy.md §Setup.
   • As last resort, offer manual export: File → Export Library → Better BibTeX → target path.
4. 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. The flag records whether the export ran. It is a note to the reader, not a gate.

---

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).

There are two complementary retrieval routes; offer both and reconcile them in one report:

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). Resolve the engine as:

ENGINE="${MEDSCI_SKILLS_ROOT:-$HOME/workspace/medsci-skills}/skills/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, the worklist supplied in the standalone mode below, or the project collection's DOIs. Output: pdfs/*.pdf for /meta-analysis and pdf_to_md.py, plus pdfs/retrieval_report.json (per-DOI status/source/title_match).

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

Emit ${MEDSCI_SKILLS_ROOT:-$HOME/workspace/medsci-skills}/skills/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". This route is user-initiated and session-dependent; 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 (owner of this file is /lit-sync):

{
  "schema_version": 1,
  "retrieved_oa_disk": [{"doi": "...", "source": "unpaywall", "file": "...", "title_match": "match"}],
  "retrieved_zotero_native": [{"doi": "...", "via": "addAvailablePDF"}],
  "not_retrieved": [{"doi": "...", "journal": "..."}],
  "institutional_fallback": ["<DOIs needing institutional access / ILL / author contact>"],
  "title_mismatch_flagged": ["<DOIs whose downloaded PDF title did not match>"]
}

Also append a short fulltext block (counts) to references/zotero_collection.json. not_retrieved DOIs are candidates for institutional access, interlibrary loan, or author contact — never bypass paywalls or access controls from this skill.

---

Phase 3: Obsidian Literature Notes

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).

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

A literature note's filename and its citekey: field assert that an entry with that key exists in Zotero. Every downstream use depends on it: [@key] in a manuscript, [[key]] between notes, the Zotero Integration plugin writing {{citekey}}.md into the same folder. A key that resolves to nothing turns all three into dead ends at once — and the note still looks correct, which is why this goes unnoticed for months.

So the key is read, never composed:

1. Take it from the .bib entry, or ask Better BibTeX (item.search over json-rpc — see references/bbt_lookup.md).
2. 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.
3. 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 scripts/check_citekey_provenance.py --vault "$VAULT" --bib "$REFS_BIB"

Every reported INVENTED is a note whose key exists nowhere — fix it here rather than letting it reach a manuscript.

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]]
-
-

(For a Korean-structured vault, use the Korean-heading template in references/locale/ko/note_templates.md and the vault's own hub-note names.)

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):

1. Extract keywords from each paper's title, journal, and tags.
2. Extract major concepts from the .bib entry titles.
3. 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.
• 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):

---
title: "{concept name}"
type: concept
tags:
  - concept
  - {domain tag}
aliases:
  - {alternative name}
related_papers:
  - "[[{lit-note-1}]]"
  - "[[{lit-note-2}]]"
  - "[[{lit-note-3}]]"
status: 🌱Seedling
---

# {concept name}

## Definition (My Understanding)
> TODO: write in your own words

## Why it matters
{why the concept matters in this domain — AI supplies a draft}

## Per-paper perspectives
- **[[{lit-note-1}]]**: {this paper's angle}
- **[[{lit-note-2}]]**: {a different angle}
- **[[{lit-note-3}]]**: {comparison / complement}

## Related concepts
- [[{another concept}]]

## Open questions
- {open question 1}
- {open question 2}

## Related notes
- [[Research Hub]]
- [[{related project hub}]]
- [[{lit-note-1}]]
- [[{lit-note-2}]]

(For a Korean-structured vault, use the Korean-heading concept template in references/locale/ko/note_templates.md.)

Key rules:

• Keep the ## Definition section as a > 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)

Create only after user confirmation. Auto-draft but always confirm.

---

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 each resolved DOI, search-first with zotero_search_items, then call zotero_add_by_doi — the search is what dedupes (add-by-doi alone does not). For items already in the library (detected via zotero_search_items by DOI), 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 (rare; older papers, non-indexed), fall back to zotero_add_by_url with the PubMed URL and mark the entry as 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.

---

Safety Rules

1. Never overwrite literature notes — the user may have added highlights or personal notes.
2. Never auto-fill ## Definition of a concept note — keep the TODO marker; the essence of the 2nd-layer note is the user's own wording.
3. Skip Zotero for entries without a DOI — ask the user to add those manually.
4. Gracefully skip Zotero when the MCP is not connected — Obsidian notes are created independently; but do NOT hand-edit refs.bib to compensate (violates artifact contract).
5. Always record the collection key — report the key to the user when a new collection is created.
6. Never write refs.bib directly. Only Better BibTeX auto-export may write that file. If auto-export is broken, fix the Zotero setup rather than writing the file from this skill.
7. Owner-only execution. 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.
8. Fulltext boundary (Phase 2.7). Retrieve full text only via OA APIs (the /fulltext-retrieval engine) and the user-run Zotero "Find Available PDF" snippet (which uses the user's own proxy config). Never automate authenticated browser sessions, never bypass paywalls/access controls, and never hard-code institutional proxies, credentials, or hosts into this skill. not_retrieved items are routed to institutional access / ILL / author contact, not worked around.

Anti-Hallucination

• Never fabricate DOIs, PMIDs, or citation metadata. All bibliographic data must come from the .bib file or API responses.
• Never auto-fill the "Definition (My Understanding)" section of concept notes. This must be written by the user.
• Never overwrite existing literature notes. User highlights and annotations may be present.
• If a DOI lookup fails, report the failure rather than guessing the metadata.