Reference Manager

Overview

Parse academic paper requirements document, extract references by section, and fetch fulltext content from Zotero library.

Supports two Zotero MCP providers:

•zotero-mcp (Python version) - see hyperbolic-c/zotero-mcp
•zotero-mcp-plugin (TypeScript/Zotero Plugin version) - see cookjohn/zotero-mcp

Configuration:

•Run /academic-write-setup to select your preferred MCP provider
•Config stored in ~/.config/auto-writing/config.json

When to Use

•Need to parse requirements document for section structure
•Need to extract references listed under each section
•Need to fetch fulltext content for referenced papers
•Need semantic matching between section content and reference paragraphs

Input Format

markdown

{
  "requirements_doc": "完整的需求文档内容（Markdown格式）"
}

支持的需求文档格式

格式1：固定模板（结构化）

markdown

论文题目：p-MQWs-n型AlGaN日盲紫外探测器研究

# 第1章 绪论
## 1.1 研究背景与意义
- 研究背景描述
- 研究意义

### 参考文献
- "Reference Title 1"
- "Reference Title 2"

# 第2章 器件研究
## 2.1 引言
- 内容要点1
- 内容要点2

### 参考文献
- "Reference Title 3"

格式2：自由格式（行内标注）

markdown

论文题目：AlGaN日盲紫外探测器研究

# 第2章 器件研究
## 2.1 引言
日盲紫外探测器在导弹尾焰探测中具有重要应用。参考文献：ZnO基日盲紫外探测器研究进展。当前技术面临的主要挑战包括噪声控制问题。
- 材料生长工艺复杂

参考文献识别规则

格式	识别方式	示例
模板格式	`### 参考文献` + `- "标题"`	`### 参考文献\n- "Title1"`
行内格式	`参考文献：...。` 或 `参考文献：...`	`参考文献：ZnO日盲探测器研究进展。`

Processing Steps

•Parse requirements document - Extract paper title, section structure (H1 → H2 → content points)
•Extract references by section - Identify references under each section
•Search references in Zotero - Match reference titles with Zotero items
•Fetch fulltext for all references - REQUIRED: Call zotero_get_item_fulltext or get_content for each referenced paper
•Analyze reference content - Split fulltext into paragraphs, ignoring headings
•Return structured output - Sections with content points + fulltext content

Tool Mapping (Based on Configuration)

zotero-mcp (Python Version)

Function	Description
`zotero_search_items`	Keyword/title search
`zotero_semantic_search`	AI-powered semantic search
`zotero_get_item_metadata`	Get item details
`zotero_get_item_fulltext`	REQUIRED - Get PDF fulltext as markdown
`zotero_search_by_tag`	Search by tags

zotero-mcp-plugin (TypeScript Version)

Function	Description
`search_library`	Keyword/title search
`semantic_search`	AI-powered semantic search
`get_item_details`	Get item details
`get_content`	REQUIRED - Get PDF fulltext content
`search_fulltext`	Fulltext search

Output Format

markdown

**需求文档解析结果:**

- **论文题目:** {title}
- **章节数量:** {n} 个

---

## 全文获取日志:

[FETCH_FULLTEXT] Section 2.1: "High-performance AlGaN UV detector" → zotero_get_item_fulltext ✓ [FETCH_FULLTEXT] Section 2.1: "ZnO-based photodetector..." → zotero_get_item_fulltext ✓ [FETCH_FULLTEXT] Section 2.2: "MQWs structure design..." → zotero_get_item_fulltext ✓

code


---

## 章节结构与引用:

### 第1章 绪论

#### 1.1 研究背景与意义

**内容要点:**
- 研究背景描述
- 研究意义

**参考文献:**
| # | 标题 | Key |
|---|------|-----|
| 1 | "Reference Title 1" | ABC123 |
| 2 | "Reference Title 2" | DEF456 |

---

### 第2章 器件研究

#### 2.1 引言

**内容要点:**
- 日盲紫外探测器的重要性
- 研究进展与存在的问题

**参考文献:**
| # | 标题 | Key |
|---|------|-----|
| 1 | "High-performance AlGaN UV detector" | GHI789 |
| 2 | "ZnO-based photodetector..." | JKL012 |

---

## 章节写作输入:

```json
{
  "paper_title": "{title}",
  "sections": [
    {
      "title": "第1章 绪论",
      "subsections": [
        {
          "title": "1.1 研究背景与意义",
          "content_points": ["研究背景描述", "研究意义"],
          "references": [
            {"title": "Reference Title 1", "key": "ABC123"},
            {"title": "Reference Title 2", "key": "DEF456"}
          ]
        }
      ]
    }
  ],
  "citation_style": "APA"
}

Error Handling

•No items found: Report zero results for each reference
•Missing PDF attachment: Report error for that specific reference, continue with others
•PDF conversion failed: Report error, continue with abstract
•Network/API errors: Report and suggest retry
•Configuration missing: Prompt user to run /academic-write-setup
•No references found in section: Report section has no references

Example

Input:

markdown

论文题目：AlGaN日盲紫外探测器研究

# 第2章 器件研究
## 2.1 引言
- 日盲紫外探测器的重要性
- 研究进展与存在的问题

### 参考文献
- "High-performance AlGaN UV detector"

Output:

code

**需求文档解析结果:**

- **论文题目:** AlGaN日盲紫外探测器研究
- **章节数量:** 1 个

---

## 全文获取日志:

[FETCH_FULLTEXT] Section 2.1: "High-performance AlGaN UV detector" → zotero_get_item_fulltext ✓

---

## 章节结构与引用:

### 第2章 器件研究

#### 2.1 引言

**内容要点:**
- 日盲紫外探测器的重要性
- 研究进展与存在的问题

**参考文献:**
| # | 标题 | Key |
|---|------|-----|
| 1 | "High-performance AlGaN UV detector" | ABC123 |

---

## 章节写作输入:

```json
{
  "paper_title": "AlGaN日盲紫外探测器研究",
  "sections": [
    {
      "title": "第2章 器件研究",
      "subsections": [
        {
          "title": "2.1 引言",
          "content_points": ["日盲紫外探测器的重要性", "研究进展与存在的问题"],
          "references": [
            {"title": "High-performance AlGaN UV detector", "key": "ABC123"}
          ]
        }
      ]
    }
  ],
  "citation_style": "APA"
}

code


## Limitations by Provider

### zotero-mcp (Python Version)

- ✅ Full PDF text extraction via `zotero_get_item_fulltext` (**REQUIRED** for all references)
- ✅ Tag-based expansion via `zotero_search_by_tag`
- ✅ Rich metadata and annotations

### zotero-mcp-plugin (TypeScript Version)

- ✅ Full PDF text extraction via `get_content` (**REQUIRED** for all references)
- ⚠️ Limited tag-based expansion
- ✅ Semantic search with embedding vectors
- ✅ Streamable HTTP for real-time communication