zotero-obsidian-bridge

name	zotero-obsidian-bridge
description	Use this skill when papers are collected in Zotero but the user wants detailed reading notes, project-linked literature synthesis, collection-wide paper-note coverage checks, and a connected knowledge map inside the bound Obsidian project knowledge base.
version	0.2.0

Zotero Obsidian Bridge

Bridge Zotero as the literature source of truth with Obsidian as the durable project knowledge base.

Use this skill when the user wants to:

• collect and organize papers in Zotero,
• read papers from Zotero MCP,
• create or update one detailed paper note per paper under Obsidian Papers/,
• synthesize those notes into Knowledge/ notes,
• verify that a whole Zotero collection has complete canonical note coverage,
• visualize the literature structure as a default Obsidian canvas.

Core stance

• Zotero owns collection, metadata, attachments, PDF full text, annotations.
• Obsidian owns durable reading notes, project-facing literature knowledge, cross-note links, synthesis.
• Prefer one canonical paper note per paper.
• Prefer filesystem-first Obsidian notes; do not require Obsidian MCP.
• Use this as an explicit, agent-first skill for Zotero ingestion.
• Prefer Papers/ + Knowledge/ as the default bridge targets.
• Prefer Maps/literature.canvas as the default graph artifact.
• Prefer a strong review schema inside each canonical paper note:
  • Claim
  • Method
  • Evidence
  • Limitation
  • Direct relevance to repo
  • Relation to other papers
• Treat some Zotero webpage items as valid literature sources when they still expose useful metadata, attachment text, or fulltext.

Default workflow

1. Resolve the current project via $obsidian-project-memory.
   • If the repo is already bound, use the existing vault.
   • If it looks like a research repo but is not bound, bootstrap it first.
2. Read Zotero items from the target collection/query.
   • If the user asked for a full collection pass, prefer full coverage over a small representative subset.
   • If the transport path through MCP is failing but a local zotero-mcp source checkout or Python environment is available, use that local fallback to read metadata/fulltext instead of stopping the workflow.
3. For each paper:
   • get metadata,
   • get full text when available,
   • get annotations/notes when helpful,
   • create or update the canonical paper note in Papers/.
4. Add project-facing structure to each paper note:
   • claim,
   • research question,
   • method,
   • evidence,
   • strengths,
   • limitation,
   • direct relevance to repo,
   • relation to other papers,
   • links to related papers and the best matching Knowledge/ notes.
5. Synthesize the batch into durable Knowledge/ notes such as:
   • Knowledge/Literature-Overview.md
   • Knowledge/Method-Families.md
   • Knowledge/Research-Gaps.md only when the synthesis is stable enough to deserve a canonical note.
6. If the request is collection-scoped, update a durable inventory note that records:
   • collection size,
   • item triage,
   • item -> canonical note mapping,
   • current coverage count such as 16 / 16.
   • use the canonical inventory path Knowledge/Zotero-Collection-{collection-slug}-Inventory.md.
7. Refresh Maps/literature.canvas.
   • Prefer semantic filtering and edge thinning.
   • Prefer argument-map structure (paper + claim + method + gap) over dense all-to-all paper links.
   • If needed, keep a second lightweight display canvas such as Maps/literature-main.canvas.
8. If the user also wants writing deliverables, update:
   • Writing/literature-review.md

Default outputs

• Papers/*.md - one detailed reading note per paper
• Knowledge/*.md - durable literature synthesis notes when the batch yields stable knowledge
• Knowledge/Zotero-Collection-{collection-slug}-Inventory.md - when the source is a concrete Zotero collection and coverage tracking matters
• Maps/literature.canvas - default visual literature graph
• Maps/literature-main.canvas - optional lightweight presentation graph after semantic filtering
• Writing/literature-review.md - when the user asks for synthesis
• Writing/comparison-matrix.md - when cross-paper comparison is useful

Safety rules

• Do not dump raw full text into Obsidian.
• Do not create a new note if the canonical paper note already exists.
• Do not create Concepts/ or Datasets/ trees by default.
• Do not treat Experiments/, Results/, or Writing/ as the default bridge target during Zotero ingestion.
• Do not force every relationship into a new note; use frontmatter fields, sections, wikilinks, and linked_knowledge first.
• If a relationship is uncertain, record it in the note body or Daily/ instead of manufacturing durable structure.
• Do not stop at a representative subset if the user explicitly asked to check all papers in a collection.
• Do not leave schema drift unresolved across notes in the same collection after a batch pass.

References

Load only what is needed:

• references/WORKFLOW.md - end-to-end Zotero -> Obsidian procedure
• references/PAPER-NOTE-SCHEMA.md - detailed paper note fields and sections
• references/COLLECTION-INVENTORY-SCHEMA.md - canonical inventory note naming and mapping contract
• references/LOCAL-ZOTERO-FALLBACK.md - local fallback runbook when MCP transport fails
• examples/example-collection-inventory.md - example inventory note
• scripts/verify_paper_notes.py - deterministic schema, zotero-key, and inventory consistency check
• ../obsidian-literature-workflow/references/PAPER-NOTE-SCHEMA.md - shared note schema
• ../obsidian-literature-workflow/references/CANVAS-WORKFLOW.md - default literature canvas refresh rules