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Annota — AI-Powered Paper Annotation Assistant

Turn your PDF library into an intelligent research assistant.

AI reads your papers, highlights key findings, explains formulas, and writes structured notes — all saved back to your reference manager.

License: MIT Python 3.10+ MCP Platform

Features · Quick Start · Usage Examples · Screenshots · Roadmap


What Can It Do?

You say...

AI does...

"高亮摘要中的发现结果" (Highlight findings in the abstract)

Reads the abstract, identifies findings, highlights them in green

"解释第3页的公式" (Explain the formulas on page 3)

Extracts the formula, adds an explanation as a note annotation

"写一份结构化阅读笔记" (Write a structured reading note)

Generates a note with contributions, methods, results, limitations — saved to your library

"以 MICRO 审稿人视角审阅" (Review as a MICRO reviewer)

Produces a structured review with scores and actionable feedback

AI reads the paper → understands content → creates precise annotations

AI generates a structured reading summary with key findings, methods, and conclusions


Related MCP server: Zotero MCP Server

✨ Features

9 MCP Tools

Tool

What it does

search_zotero_items

Search by title / author / key

list_zotero_items

Browse recent items

get_item_metadata

Get authors, year, venue, DOI

get_pdf_text_bulk

Extract full text (no coords, fast)

get_pdf_layout_text

Extract text + precise coordinates

list_annotations

View existing annotations

create_pdf_annotation

Create highlight / underline

batch_annotate

Create multiple annotations at once

add_child_note

Add a note to any item

3 Claude Code Skills (Slash Commands)

Command

Function

/annota-annotate

Smart annotation with semantic color coding

/annota-summarize

Structured reading notes saved to your library

/annota-review

Simulated peer review with scoring rubric

Smart Design

  • Two-phase workflow — Reads full text first (cheap), then only gets coordinates for target sentences (precise). Reduces context usage by 63–80%.

  • Auto-skip references — Detects "References" section and skips it. A 21-page paper extracts only 13 pages.

  • Batch annotations — Creates 10 highlights in 1 API call instead of 10.

  • Friendly errors — Write failures return helpful messages instead of crashing.


🚀 Quick Start (3 Minutes)

Step 1: Clone & Install

git clone https://github.com/dengls24/annota.git
cd annota

python -m venv .venv

# Windows:
.venv\Scripts\activate
# macOS / Linux:
# source .venv/bin/activate

pip install pymupdf mcp

Step 2: Configure Claude Code

Add to ~/.claude.json (or via Claude Code Settings > MCP Servers):

Windows:

{
  "mcpServers": {
    "annota": {
      "command": "C:/path/to/annota/.venv/Scripts/python.exe",
      "args": ["C:/path/to/annota/annota/server.py"],
      "env": {
        "ZOTERO_DATA_DIR": "C:/Users/YourName/Zotero"
      }
    }
  }
}

macOS / Linux:

{
  "mcpServers": {
    "annota": {
      "command": "/path/to/annota/.venv/bin/python",
      "args": ["/path/to/annota/annota/server.py"],
      "env": {
        "ZOTERO_DATA_DIR": "/Users/YourName/Zotero"
      }
    }
  }
}

Finding your Zotero data directory:

  • Windows: Zotero → Edit → Settings → Advanced → Data Directory Location (default: C:\Users\YourName\Zotero)

  • macOS: Zotero → Settings → Advanced → Data Directory Location (default: ~/Zotero)

  • Linux: default ~/Zotero

Step 3: Use It

Just talk to Claude naturally:

# One command to read a full paper:
/annota-read "path/to/paper.pdf"

# Or natural language:
# Highlight the findings in this paper's abstract in green
"/Users/yourname/Zotero/storage/ABCD1234/paper.pdf"

Or use slash commands:

/annota-read "path/to/paper.pdf"
/annota-annotate "path/to/paper.pdf"
/annota-summarize "path/to/paper.pdf"
/annota-review "path/to/paper.pdf" ISCA

macOS path tip: Drag a file from Finder into the terminal to get its full path, or right-click → "Copy as Pathname".

(Optional) Install Skills Globally

# Make skills available in all projects
cp -r .claude/skills/ ~/.claude/skills/

📖 Usage Examples

Example 1: Highlight Key Findings

Input:

把这篇论文摘要中的发现结果用绿色标出来
(Highlight the findings in this paper's abstract in green)
"E:\Zotero\storage\ABCD1234\Song et al. - 2025 - AI washing.pdf"

Result:

AI identifies findings in the abstract and highlights them in green


Example 2: Annotate Hypotheses & Theories

Input:

标注论文中的假设(H1, H2),并用中文解释每个假设的理论基础
(Annotate the hypotheses (H1, H2) and explain the theoretical basis of each in Chinese)

Result:

Hypotheses highlighted in yellow, with Chinese explanation notes for the underlying theory


Example 3: Explain Formulas

Input:

解释论文中的核心公式,添加中文注释
(Explain the key formulas in this paper, add Chinese annotations)

Result:

DID model formula annotated with variable explanations in Chinese


Example 4: Policy Implications & Conclusion Notes

Input:

标注结论部分的政策启示,添加中文总结笔记
(Highlight policy implications in the conclusion, add a Chinese summary note)

Result:

Conclusion highlighted with a structured policy implications note


Example 5: Full Paper Reading Notes

Input:

/annota-summarize "path/to/paper.pdf"

Result:

AI generates a complete reading summary: topic, research question, method, key findings, and implications


Example 6: Detailed Paragraph-by-Paragraph Notes

Input:

逐段阅读这篇论文,为每个重要段落添加中文批注
(Read this paper paragraph by paragraph, add Chinese annotations to each important section)

Result:

Each important paragraph gets a Chinese annotation explaining the content


Example 7: The AI Workflow in Action

Here's what Claude Code looks like when processing a paper:

Claude creates a task list, reads the PDF, and calls MCP tools to create annotations step by step


🎨 Color Convention

Color

Code

Use for

🟡 Yellow

#ffd400

Default / general highlights

🟢 Green

#28CA42

Results, findings, data

🔵 Blue

#2EA8E5

Methods, definitions, algorithms

🔴 Red

#ff6666

Limitations, issues, problems

🟣 Purple

#a28ae5

Contributions, novelty


⚡ How It Handles Large PDFs

For papers >10 pages, a two-phase workflow avoids context overflow:

Phase 1 — Understand (lightweight)
  get_pdf_text_bulk(pdf, skip_refs=True)
  → Full text without coordinates
  → AI identifies which sentences to annotate

Phase 2 — Annotate (precise)
  get_pdf_layout_text(pdf, target_page_only)
  → Coordinates for 1–2 target pages
  batch_annotate(pdf, all_annotations)
  → Write everything in one call

Real-world performance:

Paper

Pages

Old approach

New approach

Savings

Conference paper

2 pages

41 KB coords

15 KB text

63%

Journal article

21 pages

21 pages extracted

13 pages (refs skipped at p.13)

38%

Survey paper

19 pages

19 pages extracted

10 pages (refs skipped at p.10)

47%


📁 Project Structure

annota/
├── annota/                        # MCP Server (Python)
│   ├── server.py                  # 9 tool registrations
│   ├── zotero_db.py               # SQLite read/write layer
│   ├── pdf_tools.py               # PyMuPDF text extraction
│   └── config.py                  # Constants & configuration
├── .claude/skills/                # Claude Code Skills
│   ├── annota-annotate/SKILL.md   # /annota-annotate
│   ├── annota-summarize/SKILL.md  # /annota-summarize
│   └── annota-review/SKILL.md     # /annota-review
├── docs/                          # Design documents
│   ├── annota-guide.md            # Usage guide (CN)
│   ├── large-pdf-design.md        # Large PDF handling design
│   ├── dev-notes.md               # Pitfalls & solutions
│   └── commercial-plan.md         # Commercialization plan
├── assets/                        # Screenshots
└── README.md

⚠️ Known Limitations & Disclaimer

Database Direct Access: Annota writes annotations directly to the Zotero SQLite database, which bypasses Zotero's internal consistency mechanisms. This is a design choice to enable fully offline, local-first annotation workflows without depending on external services. Users are responsible for their own database — please back up your zotero.sqlite before use. We plan to migrate to the official Zotero Web API / Local API in future versions.

Limitation

Workaround

Planned Fix

Direct SQLite write (not officially supported)

Back up your database before use

Migrate to Zotero Local API / Web API

Write ops need Zotero closed

Close Zotero before annotating

Local API bridge

References detection is heuristic

Pass skip_refs=False if needed

Improve heuristics

Tested primarily on Windows

Should work on macOS/Linux — paths auto-detected

Community testing welcome


🗺 Roadmap

  • Zotero Local API / Web API — Migrate from direct SQLite to official API for safer writes

  • More skills/compare-papers, /extract-tables, /literature-map

  • Prompt template marketplace — Share and reuse annotation rules

  • Team features — Shared annotation standards for lab groups

  • Multi-backend — Support Adobe Acrobat, Endnote, and other PDF tools


🤝 Contributing

Issues and PRs are welcome! If you have ideas for new skills or tools, please open an issue.

📄 License

MIT — Use it freely for research and commercial projects.


Built with MCP + Claude Code

If this project helps your research, consider giving it a ⭐

Available Tools

9 tools
add_child_noteA

为 Zotero 文献条目创建子笔记。

支持 HTML 和纯文本。写入后需重启 Zotero 或按 Ctrl+Shift+R 刷新。 注意:写操作需要关闭 Zotero 桌面应用。

Args: parent_item_id: 父文献条目的 itemID(数字字符串) note_content: 笔记内容(HTML 或纯文本,支持 Markdown 风格)

ParametersJSON Schema
NameRequiredDescriptionDefault
parent_item_idYes
note_contentYes

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes

TDQS

A4.4/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Discloses write operation, need to close Zotero, and refresh requirement. No annotations provided, so description bears full burden and does well.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Well-structured with separate sections (description, note, Args). Could be slightly more concise, but every sentence adds value.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Covers purpose, parameters, post-usage steps, and behavioral notes. Output schema is present but description is self-sufficient for a simple 2-param tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Adds meaning beyond schema: describes parent_item_id as numeric string representing item ID, and note_content as HTML/plain text with Markdown support. Schema had 0% coverage, so this is essential.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

Clearly states creating child notes for Zotero items, a specific verb+resource. Distinguishes from sibling tools like batch_annotate or create_pdf_annotation.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Provides explicit post-write refresh requirement and note about needing to close Zotero. Lacks comparison to sibling tools but gives clear context for usage.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

batch_annotateA

一次性创建多条 PDF 标注(减少调用次数)。

每条标注需包含 page_index 和 rects,可选 color/text/comment/type。 写操作需要关闭 Zotero 桌面应用。

Args: item_id: Zotero PDF 附件的 itemID(数字),或 PDF 文件的绝对路径 annotations: 标注列表,每项为: {"page_index": int, "rects": [[x0,y0,x1,y1],...], "color": str, "text": str, "comment": str, "type": str}

ParametersJSON Schema
NameRequiredDescriptionDefault
item_idYes
annotationsYes

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes

TDQS

A4.3/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description must cover behavioral traits. It discloses that it is a write operation and requires closing Zotero. However, it does not mention idempotency, partial failure handling, rate limits, or the format of the return value (though an output schema exists). This leaves gaps in behavioral understanding.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is concise, with no unnecessary words. It front-loads the main purpose in the first line, then provides a prerequisite, followed by a structured argument list that is easy to scan. Every sentence adds value.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The description covers purpose, usage prerequisite, and parameter details adequately. However, it lacks information about the output (e.g., what is returned, success/failure per annotation) and any limitations like maximum batch size or error behavior. While an output schema exists, the description should at least hint at the return structure for completeness.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Despite 0% schema description coverage, the description adds substantial meaning to both parameters. For 'item_id', it explains it can be a Zotero PDF attachment itemID (number) or an absolute PDF path. For 'annotations', it provides a clear template structure with fields like page_index, rects, color, etc., which is far beyond the bare schema type.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's purpose: '一次性创建多条 PDF 标注(减少调用次数)' (create multiple PDF annotations at once to reduce calls). It specifies the verb 'create', the resource 'PDF annotations', and the benefit of batching. This distinguishes it from the sibling tool 'create_pdf_annotation' which presumably creates single annotations.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides a clear prerequisite: '写操作需要关闭 Zotero 桌面应用' (write operation requires closing Zotero desktop app). It implies when to use this tool (when creating multiple annotations to reduce calls) but does not explicitly state when not to use it or suggest alternatives like 'create_pdf_annotation' for single annotations.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

create_pdf_annotationA

在 Zotero PDF 上创建高亮/下划线批注。

坐标使用 get_pdf_layout_text 返回的 rect 值,无需手动转换。 写入后需重启 Zotero 或按 Ctrl+Shift+R 刷新才能看到批注。

注意:写操作需要关闭 Zotero 桌面应用,否则会因数据库锁而失败。

Args: item_id: Zotero PDF 附件的 itemID(数字),或 PDF 文件的绝对路径 page_index: 页码(从 0 开始) rects: 坐标数组,每项为 [x0, y0, x1, y1](来自 get_pdf_layout_text) color: 十六进制颜色,如 "#ffd400"(黄), "#28CA42"(绿), "#2EA8E5"(蓝) comment: 附加在批注上的文字评论(可选) text: 被高亮的原始文本(可选,用于 Zotero 中显示) type: 批注类型: "highlight"(默认) 或 "underline"

ParametersJSON Schema
NameRequiredDescriptionDefault
item_idYes
page_indexYes
rectsYes
colorNo#ffd400
commentNo
textNo
typeNohighlight

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes

TDQS

A4.6/5.0
Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description fully carries the burden. It discloses important behaviors: the operation modifies the PDF, requires a refresh/restart to become visible, and necessitates closing Zotero during write. This goes well beyond basic functionality.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured with a clear purpose first, then usage notes, then parameter list. It is somewhat lengthy due to detailed parameter explanations, but every sentence adds value. A slight trim could improve conciseness.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The description covers the prerequisite (get_pdf_layout_text), the operation, and post-operation steps (restart/refresh). It also warns about the database lock. However, it does not describe the output or error handling, though an output schema exists.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Despite 0% schema coverage, the description explains each parameter in detail, adding meaning: item_id can be ID or path, rects come from get_pdf_layout_text, color with examples, and type default. This provides crucial guidance missing from the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states it creates highlight/underline annotations on Zotero PDFs. The verb 'create' and resource 'annotation' are specific, and it distinguishes from sibling tools like list_annotations or get_pdf_layout_text.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides explicit context: coordinates should come from get_pdf_layout_text, and it warns about needing to restart or refresh after writing. It also advises closing Zotero to avoid database lock. However, it does not compare with batch_annotate or specify when not to use this tool.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

get_item_metadataA

获取 Zotero 条目的完整元数据。

返回标题、作者列表、年份、期刊、DOI 等信息。 支持传入文献条目 ID 或 PDF 附件 ID(自动查找父条目)。

Args: item_id: Zotero 条目或 PDF 附件的 itemID(数字),或 PDF 文件路径

ParametersJSON Schema
NameRequiredDescriptionDefault
item_idYes

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes

TDQS

A3.6/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description must cover behavioral traits. It explains that it accepts item IDs or PDF paths and automatically finds parent items, which is useful. However, it does not disclose error handling, authentication needs, or any side effects of the operation.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is concise with two sentences and an arguments line. It is front-loaded with the main purpose. It could be more structured (e.g., bullet points for args), but the current format is efficient and clear.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given that an output schema exists, the description does not need to explain return values. It covers the input types adequately and mentions key metadata fields. However, it omits information about error scenarios or prerequisites, which would enhance completeness.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The single required parameter item_id has no schema description (0% coverage), but the description adds significant meaning: it specifies that the input can be a numeric itemID or a PDF file path, and that it works for both items and PDF attachments. This compensates well for the lack of schema-level documentation.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states it retrieves complete metadata for a Zotero item, listing returned fields (title, authors, year, journal, DOI). It distinguishes from sibling tools like list_zotero_items and search_zotero_items by focusing on a single item's full metadata, but does not explicitly differentiate.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description indicates it supports item IDs or PDF attachment IDs, but does not provide explicit guidance on when to use this tool versus alternatives (e.g., search_zotero_items for multiple items). No exclusion criteria or context for optimal use are given.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

get_pdf_layout_textA

提取 PDF 指定页面的文本及物理坐标。

返回 JSON,每个文本行包含 text 和 rect [x0, y0, x1, y1](Zotero PDF 坐标系)。 可以直接将 rect 传给 create_pdf_annotation 使用。

Args: item_id: Zotero PDF 附件的 itemID(数字),或 PDF 文件的绝对路径 page_number: 页码(从 0 开始)

ParametersJSON Schema
NameRequiredDescriptionDefault
item_idYes
page_numberYes

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes

TDQS

A4.3/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations provided, so description carries full burden. It discloses return format (JSON with text and rect), coordinate system, and parameter details. Lacks info on error handling or side effects, but overall transparent.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Description is concise but includes an Args section that partly repeats schema info. However, it adds value (type clarifications) and is well-structured in front-loaded style.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's low complexity (2 params, clear output described), the description covers essential aspects: input, output format, and usage hint. No critical gaps.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 0%, so description adds crucial meaning: item_id can be numeric Zotero itemID or file path, page_number is 0-indexed. This fully compensates for schema's lack of description.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

Description clearly states it extracts text and physical coordinates from a specified PDF page, with a specific verb 'extract' and resource 'PDF page'. It distinguishes itself from siblings like get_pdf_text_bulk and create_pdf_annotation.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Mentions that rect can be used with create_pdf_annotation, implying a use case, but does not explicitly state when not to use or compare to alternatives like get_pdf_text_bulk.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

get_pdf_text_bulkA

批量提取多页 PDF 纯文本(无坐标),适合大 PDF 内容理解。

与 get_pdf_layout_text 的区别:不返回坐标,context 占用减少 ~80%。 推荐工作流:

  1. 先用此工具理解全文 → 确定目标页和目标句子

  2. 再用 get_pdf_layout_text 获取目标页的精确坐标

  3. 最后用 create_pdf_annotation 写入标注

Args: item_id: Zotero PDF 附件的 itemID(数字),或 PDF 文件的绝对路径 pages: 要提取的页码列表(0-indexed),不传则提取全文 skip_refs: 是否自动跳过参考文献页(默认 True)

ParametersJSON Schema
NameRequiredDescriptionDefault
item_idYes
pagesNo
skip_refsNo

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes

TDQS

A4.7/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Without annotations, the description covers key behaviors: extraction is pure text without coordinates, context usage is reduced by ~80%, and skip_refs defaults to true. However, it does not mention error handling for invalid item_ids or page ranges.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured with purpose first, then differentiation, then workflow, then args. It is concise but the workflow section is slightly verbose. Overall efficient.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the presence of an output schema, the description does not need to detail return values. It covers purpose, parameters, differentiation from siblings, and usage workflow adequately, making it complete for the agent's decision-making.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 0%, but the description fully explains each parameter: item_id as Zotero itemID (number) or file path, pages as 0-indexed list with default of all pages, skip_refs as boolean to skip references with default true. This adds substantial meaning beyond the bare schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool extracts plain text from PDF pages without coordinates, specifically for large PDF content understanding. It distinguishes from the sibling get_pdf_layout_text by noting the absence of coordinates and reduced context usage.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explicitly specifies when to use this tool (bulk text extraction) and provides a recommended workflow: first use this for full text, then get_pdf_layout_text for coordinates on target pages, then create_pdf_annotation. Also mentions the difference from get_pdf_layout_text.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

list_annotationsA

列出 PDF 附件上已有的所有标注。

用于检查已有标注,避免重复标注。返回每条标注的类型、颜色、文本和评论。

Args: item_id: Zotero PDF 附件的 itemID(数字),或 PDF 文件的绝对路径

ParametersJSON Schema
NameRequiredDescriptionDefault
item_idYes

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes

TDQS

A4.4/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Although no annotations are provided, the description explains what the tool returns (type, color, text, comment) and the acceptable argument format (itemID or file path). It does not mention side effects or permissions, but for a list operation, this level of detail is adequate.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is concise and well-structured, with a clear title line, a usage sentence, a summary of return content, and a precise parameter explanation. Every sentence adds value.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the output schema exists, the description need not detail return values but still does. It covers the tool's purpose, usage, parameter format, and return content, making it complete for an agent to select and invoke correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

With 0% schema description coverage, the description fully compensates by explaining that item_id can be a Zotero PDF attachment itemID (number) or an absolute file path, adding significant meaning beyond the bare schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states it lists all annotations on PDF attachments and provides a use case (checking existing annotations to avoid duplicates). However, it does not differentiate itself from sibling tools like batch_annotate or create_pdf_annotation.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly says it is used to check existing annotations to avoid duplicates, providing clear usage context. It does not mention when not to use or list alternatives, but the implied guidance is sufficient.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

list_zotero_itemsA

列出 Zotero 库中的文献条目。

返回每个条目的 itemID、key、标题,以及 PDF 附件 ID(如有)。 用于发现 item_id 以供其他工具使用。

Args: limit: 最多返回条目数(默认 50)

ParametersJSON Schema
NameRequiredDescriptionDefault
limitNo

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes

TDQS

A3.7/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations provided, so description must disclose behavior. It states the operation (list), return fields, and limit parameter. However, it does not mention pagination, ordering, authentication needs, or potential performance implications for large libraries.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is extremely concise: 4 short sentences in Chinese. It front-loads the main action, lists returns, gives purpose, and explains the parameter. No wasted words.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a simple list tool with one optional parameter and an output schema, the description covers input and basic output. But it omits return format details, sorting, and error handling. Output schema exists but is not shown; description still incomplete on behavior.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

With 0% schema description coverage, the description explains the only parameter 'limit' with default 50 and meaning (max number of items returned). This compensates fully for the schema gap, though no other parameters exist.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states it lists Zotero library entries and specifies returned fields (itemID, key, title, PDF attachment ID). It distinguishes itself from sibling 'search_zotero_items' by implying a full list with limit, not a search filter.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description mentions it is used to discover item_id for other tools, but lacks explicit guidance on when to use it versus alternatives like search_zotero_items. No when-not or exclusion criteria provided.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

search_zotero_itemsA

按标题、作者或 key 搜索 Zotero 条目。

比 list_zotero_items 更高效,可直接定位目标论文。

Args: query: 搜索关键词(标题/作者的部分文字,或 Zotero item key) limit: 最多返回条目数(默认 20)

ParametersJSON Schema
NameRequiredDescriptionDefault
queryYes
limitNo

Output Schema

ParametersJSON Schema
NameRequiredDescription
resultYes

TDQS

A4/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations provided, so description carries full burden. It only describes search capability without disclosing any behavioral traits such as authentication needs, rate limits, or behavior on no results. Minimal additional context beyond purpose.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two-sentence description plus parameter list is compact and front-loaded. Every sentence provides value without redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Parameters are simple, output schema exists (not detailed but present), and the tool is straightforward. Description covers purpose and key parameter meanings adequately for a search tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema has 0% parameter descriptions, but the description explains 'query' as search keyword (partial title/author/Zotero key) and 'limit' as max return count (default 20). This adds meaningful meaning beyond the bare schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

Description clearly states the tool searches Zotero items by title, author, or key, and explicitly contrasts with sibling tool 'list_zotero_items' as more efficient for direct targeting. This provides a specific verb+resource and distinguishes from alternatives.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explicitly states when to use this tool over 'list_zotero_items' (more efficient for direct targeting). However, lacks explicit when-not-to-use or alternative scenarios beyond the sibling.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. 9 tool updatesv1.0.0
    • First observedadd_child_note
    • First observedbatch_annotate
    • First observedcreate_pdf_annotation
    • First observedget_item_metadata
    • First observedget_pdf_layout_text
    • First observedget_pdf_text_bulk
    • First observedlist_annotations
    • First observedlist_zotero_items
    • First observedsearch_zotero_items

TDQS

A4.2/5.0
Disambiguation5/5

Each tool targets a distinct operation: listing vs searching items, extracting text with or without coordinates, creating single vs batch annotations, adding notes, and listing annotations. Descriptions clearly differentiate them, leaving no ambiguity.

Naming Consistency5/5

All tool names follow a consistent verb_noun pattern in snake_case (e.g., 'list_zotero_items', 'create_pdf_annotation'). Even 'batch_annotate' and 'add_child_note' fit the pattern with a verb first. No mixed conventions.

Tool Count5/5

With 9 tools, the server covers the core workflows of Zotero interaction: discovering items, retrieving metadata, extracting PDF text, creating annotations (single/batch), listing annotations, and adding child notes. The count is well-scoped without being too sparse or overwhelming.

Completeness4/5

The tool set covers the main use cases for reading and annotating Zotero items. However, it lacks tools for updating or deleting annotations, modifying item metadata, or managing collections/tags, which are minor gaps that could cause agents to hit dead ends in some workflows.

Maintenance

ActivityInactive
ResponsivenessNo issues

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