/zotero-review - Zotero Collection Literature Analysis

Read and analyze papers in the Zotero collection "$collection", with analysis depth "$depth".

Default target

Preferred target: the bound Obsidian project knowledge base
Fallback target: related-work-draft.md in the current working directory

Workflow

Step 0: Resolve the project context

If the current repo is already bound to an Obsidian project KB, use that project root.
If the repo looks like a research project but is not bound yet, bootstrap it first.
If there is no project binding, generate the review in the working directory.

Step 1: Locate and read the Zotero collection

Call mcp__zotero__zotero_get_collections to find the matching collection.
Call mcp__zotero__zotero_get_collection_items to get all papers.
For each paper:
- call mcp__zotero__zotero_get_item_metadata with include_abstract: true
- call mcp__zotero__zotero_get_item_fulltext when available
- use abstract metadata as fallback when PDF full text is unavailable
If MCP transport fails but a local zotero-mcp checkout is available, use the local Python fallback instead of aborting.
Treat Zotero webpage items as weak-source entries unless they clearly expose full paper metadata and useful full text. Abstract-only or placeholder pages can appear in coverage summaries, but cannot support Knowledge, Writing, manuscript, or rebuttal claims.

Step 2: Ensure detailed paper notes exist

Before high-level synthesis, ensure the collection has durable paper notes.

If the project is Obsidian-bound:

create or update Sources/Papers/*.md canonical notes first
keep one canonical paper note per paper whenever possible
align notes to the canonical schema (Claim / Method / Evidence / Limitation / Direct relevance to repo / Relation to other papers)
update the best matching Knowledge/ literature synthesis notes
refresh Maps/literature.canvas
update a collection inventory note with item -> note mapping and coverage summary

If not Obsidian-bound:

create intermediate paper-notes/*.md files in the working directory when depth=deep

Step 3: Synthesize across paper notes

Create or update:

Knowledge/Literature Overview.md
Knowledge/Method Taxonomy.md when useful
Knowledge/Research Gaps.md when useful
Writing/related-work-draft.md only when the user wants writing-facing synthesis and the promoted claims pass the evidence gate
Writing/comparison-matrix.md when useful and promoted claims pass the evidence gate

The synthesis should include:

thematic grouping
method families
key findings and tensions
research gaps
direct relevance to the current project
explicit links across Sources/Papers/ and Knowledge/
Evidence Record IDs, source type, claim strength, allowed wording, and forbidden stronger wording for claims that may later enter writing or rebuttal

If core papers lack full text or Evidence Records, stop at a collection audit / claim map and state what is missing. Do not generate a polished related-work draft from weak notes.

Step 4: Push downstream only when justified

keep the default review surface in Sources/Papers/, Knowledge/, and Maps/literature.canvas
update Writing/ only when the user wants a manuscript-facing review or comparison narrative and promoted claims pass the evidence gate
only update Experiments/ or Results/ in a later project workflow when the user explicitly wants that handoff

Step 5: Minimal write-back

Always update:

today's Daily/YYYY-MM-DD.md
repo-local binding summary when project state changes

Step 6: Final response

Include:

collection size and coverage summary
updated note paths
optional obsidian://open links
optional obsidian open ... suggestions when CLI is available

Notes

Prefer the Obsidian-bound project workflow over loose markdown files when available.
Keep Sources/Papers/ first-class; the review should be grounded in canonical paper notes rather than only one-shot synthesis.
The default graph artifact is Maps/literature.canvas.

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