OMyPaper Skills is a local literature-management and knowledge-base workflow for researchers who read papers in Zotero, sync literature notes into Obsidian through ZotLit, and then use an LLM Agent to continuously organize, refine, retrieve, review, summarize, and project-manage the accumulated knowledge.
Instead of treating an LLM as a temporary question-answering tool that re-reads raw documents from scratch every time, this project treats the Agent as a persistent local knowledge-base maintainer.
The core workflow is:
- Zotero for reading, annotating, and reference management
- ZotLit for exporting literature notes into Obsidian
- Obsidian for the local markdown-based knowledge container
- Agent / Skills for turning raw notes into structured wiki pages, project structures, session traces, reviews, reports, and retrieval paths
This repository is Agent-agnostic. Any agent that can read and write local files can adapt these Skills.
This Skills set is developed and organized around the following environment:
- Zotero:
7.0.32 - Obsidian:
1.6.7 - ZotLit plugin: used as the bridge between Zotero and Obsidian
These versions are the recommended baseline for this repository.
Other versions may also work, but the current structure and workflow are designed and tested around the versions listed above.
To use this Skills system correctly:
- Copy the folder
OMyPaperinto your Obsidian vault. - Install and enable the ZotLit plugin in Obsidian.
- In ZotLit settings, set:
Default location for new literature notes = OMyPaper/LiteratureNotes
This setting matters because the Skills assume that all raw literature notes imported from Zotero will be stored under:
OMyPaper/LiteratureNotes
If this path is changed, the Agent-side workflows, note matching logic, and knowledge-base maintenance routines may fail or require manual modification.
For ZotLit installation and configuration details, please refer to the official documentation:
OMyPaper follows a layered design:
- Raw layer:
LiteratureNotes/stores raw reading traces imported from Zotero via ZotLit. - Global knowledge layer:
Notes/stores durable paper, concept, method, comparison, and topic pages. - Project layer:
projects/organizes literature into project-specific structures. - Control layer:
Management/stores rules, templates, indices, logs, reports, queues, and Skill specifications.
In other words:
- the raw literature note is the source layer
- the Agent-maintained wiki is the knowledge layer
- the project tree is the research-organization layer
The long-term goal is to turn scattered reading traces into a continuously evolving, locally stored, and cross-linked personal paper wiki + project workspace.
0.1.0 established the first working version of the OMyPaper Skills system.
- paper-centric local knowledge-base workflow
LiteratureNotes/as the raw note layerNotes/as the global wiki layerManagement/as the control and reporting layer- core Skills focused on:
- structure check
- single-paper ingestion
- whole-wiki cleanup
- weekly report generation
- paper recall
- local knowledge retrieval
- turning raw Zotero reading notes into structured wiki pages
- maintaining a local paper knowledge base
- organizing concepts, methods, datasets, and comparisons across papers
- generating weekly reading summaries
- recalling a paper efficiently
- answering topic-based questions from the local knowledge base first
0.1.0 was still primarily paper-centric.
It did not yet fully support:
- project-aware workflows
- project-level review and navigation
- project-level session capture
- hierarchical parent/child project structures
- conservative paper-to-project assignment queues
0.2.0 upgrades OMyPaper from a paper-centric wiki workflow into a paper + hierarchical project tree workflow.
projects/layer for project organizationManagement/ProjectIndex.mdManagement/ProjectTree.mdManagement/ProjectAssignmentQueue.mdManagement/ProjectSessionNotes/- project-aware templates such as:
ProjectManifest.template.ymlProjectLiteratureMap.template.mdProjectOutline.template.mdProjectReview.template.mdProjectSessionNote.template.mdProjectTree.template.mdProjectIndex.template.mdProjectAssignmentQueue.template.md
0.2.0 introduces a project tree with:
- parent projects
- child projects
- standalone projects
Project hierarchy is now represented through project metadata such as project_type and parent_project.
All seven Skills were upgraded from paper-only behavior into paper + project-aware behavior.
Skill 1 is no longer just a single-paper summarizer. It now follows three mandatory phases:
- ingest into the global wiki
- generate project-placement suggestions from the saved global result
- write suggestions into
Management/ProjectAssignmentQueue.mdand wait for user confirmation
This means paper placement into projects is now:
- conservative
- reviewable
- user-confirmed
Whole-vault maintenance now includes:
- project-tree health
- project manifest consistency
- parent-child coherence
- sibling overlap checks
- drift between
文献地图.mdand论文大纲.md
Weekly reports are no longer only paper logs. They now summarize:
- weekly paper reading progress
- global wiki progress
- parent-project progress
- child-project progress
- next project priorities
Review is no longer limited to one paper.
0.2.0 adds support for:
- paper review
- child-project review
- parent-project review
- quick familiarization paths for projects
Local retrieval now supports:
- paper retrieval
- project-tree listing
- parent/child project explanation
- sibling-project comparison
- fast familiarization routes for one project
High-value discussions can now be captured as:
- paper session
- child-project session
- parent-project session
- hybrid session
These sessions can later support S1, S3, S4, and S5.
| Dimension | v0.1.0 | v0.2.0 |
|---|---|---|
| Main paradigm | paper-centric | paper + hierarchical project tree |
| Global paper wiki | yes | yes |
| Project organization | very limited / not fully supported | fully introduced as a first-class layer |
| Parent-child projects | no | yes |
| Project assignment queue | no | yes |
| Project session capture | no | yes |
| S1 flow | ingest one paper | ingest → project suggestion → confirmation |
| S2 scope | Notes/ mainly |
Notes/ + projects/ |
| S3 scope | weekly paper summary | weekly paper + project summary |
| S4 targets | one paper | paper / child project / parent project |
| S5 retrieval | paper/topic retrieval | paper + project-tree navigation |
| S6 capture | paper-centric | paper / project / hybrid |
| Templates | paper/wiki oriented | paper + project + queue + tree templates |
A recommended folder layout is now:
OMyPaper/
├─ LiteratureNotes/ # Raw notes imported from Zotero via ZotLit
├─ Notes/
│ ├─ Papers/ # Per-paper wiki pages
│ ├─ Concepts/ # Concept pages
│ ├─ Methods/ # Method pages
│ ├─ Datasets/ # Dataset pages
│ ├─ Comparisons/ # Cross-paper comparison pages
│ ├─ Topics/ # Thematic pages
│ └─ Syntheses/ # Higher-level synthesis pages
├─ Management/
│ ├─ AGENTS.md # Agent instructions / schema
│ ├─ CurrentQuestions.md # Current research questions
│ ├─ index.md # Global wiki index
│ ├─ log.md # Append-only operation log
│ ├─ PaperRegistry.md # Paper mapping registry
│ ├─ SessionIndex.md # Session index
│ ├─ ProjectIndex.md # Project summary index
│ ├─ ProjectTree.md # Parent-child project tree index
│ ├─ ProjectAssignmentQueue.md # Pending project-placement suggestions
│ ├─ WeeklyReports/ # Weekly reports
│ ├─ ReviewNotes/ # Review / recall notes
│ ├─ LintReports/ # Vault health reports
│ ├─ SessionNotes/ # Paper sessions
│ ├─ ProjectSessionNotes/ # Project sessions / hybrid sessions
│ ├─ Templates/ # Shared templates
│ └─ Skills/ # Skill specifications
├─ projects/ # Hierarchical project layer
└─ Attachments/ # Optional local attachments
| Skill | Name | What It Does | Key Upgrade in 0.2.0 |
|---|---|---|---|
S0 |
Bootstrap / Consistency Check | checks whether the global vault, project tree, and session layers are complete and consistent | now checks projects/, tree cycles, manifest validity, and project-session readiness |
S1 |
Paper Ingest | compiles one paper into the global wiki and generates project-placement suggestions | now has mandatory three phases and writes suggestions into ProjectAssignmentQueue.md |
S2 |
Whole-Vault Lint | maintains the structural health of Notes/ and projects/ |
now checks parent-child project coherence, sibling overlap, and map/outline drift |
S3 |
Weekly Report | generates a weekly report across papers and projects | now includes parent-project and child-project progress |
S4 |
Review / Recall | helps you recall one paper, one child project, or one parent project | now supports project-level review and quick familiarization paths |
S5 |
Local Retrieval / Navigation | answers with local evidence and gives re-read paths | now supports project-tree listing, project explanation, and sibling comparison |
S6 |
Session Capture / Matching | turns valuable discussion into paper sessions, project sessions, or hybrid sessions | now supports project-aware and hybrid session capture |
- Read and annotate papers in Zotero.
- Sync/import literature notes into Obsidian via ZotLit.
- If a discussion becomes worth preserving, run S6 first.
- Run S1 to compile the paper into the global wiki.
- Review the placement suggestions written into
Management/ProjectAssignmentQueue.md. - After confirmation, write the final project placement into
project.yml. - Use S4 for recall.
- Use S5 for answer + path + re-read order.
- Run S2 for whole-vault lint.
- Review the lint report.
- Run S3 to generate the weekly report.
- Keep paper knowledge unique in
Notes/. - Keep project grouping and hierarchy inside
projects/. - Use
project.ymlas the only project-membership interface. - Use S4 and S5 to revisit or navigate one project quickly.
OMyPaper is designed for:
- academic paper reading
- literature management
- research note organization
- local personal knowledge-base building
- concept/method comparison across papers
- project-oriented research organization
- long-term research memory support
It is especially suitable for users who prefer:
- local-first workflows
- markdown-based knowledge systems
- Obsidian-based note taking
- reproducible and inspectable file structures
- Agent-assisted but user-controlled knowledge management
- This repository is Agent-agnostic.
- The system assumes a local file-based workflow.
LiteratureNotes/should still be treated as the raw source layer.- Agent-maintained content should mainly live in
Notes/,projects/, andManagement/. - If you customize the folder structure, you should also update the corresponding Skill prompts and Agent instructions.
OMyPaper Skills 是一套面向本地论文知识库与项目组织工作流的 Skills 设计方案，适用于这样的阅读流程：你在 Zotero 中阅读和批注文献，通过 ZotLit 将文献笔记导入 Obsidian，再由 LLM Agent 持续完成笔记整理、知识沉淀、结构维护、主题检索、论文复盘、项目导航与周报生成。
它的核心思想不是把 LLM 当作一个“临时读 PDF、临时回答问题”的工具，而是把它当作一个持续维护本地知识库与项目结构的助手。
核心链路是：
- Zotero 负责阅读、批注与参考文献管理
- ZotLit 负责将阅读痕迹导入 Obsidian
- Obsidian 负责承载本地 Markdown 知识库
- Agent / Skills 负责将原始笔记转化为结构化 wiki、项目结构、session 沉淀、复盘、周报与导航路径
本仓库中的 Skills 设计为适用于任意 Agent 工具。只要 Agent 具备本地文件读写能力，就可以将本 Skills 体系应用到自己的论文管理流程中。
本 Skills 体系基于以下版本进行开发与组织：
- Zotero：
7.0.32 - Obsidian：
1.6.7 - ZotLit 插件：作为 Zotero 与 Obsidian 之间的桥接工具
上述版本是本仓库推荐的基准环境。
其他版本未必不能使用，但当前目录结构、工作流约定与相关 Skills 均围绕这些版本进行设计。
要正确使用本 Skills，请先完成以下设置：
- 将仓库中的
OMyPaper文件夹复制到你的 Obsidian 仓库中。 - 在 Obsidian 中安装并启用 ZotLit 插件。
- 在 ZotLit 设置中，将以下项设置为：
Default location for new literature notes = OMyPaper/LiteratureNotes
这一设置非常关键，因为本 Skills 默认假设所有从 Zotero 导入的原始文献笔记都保存在：
OMyPaper/LiteratureNotes
如果这个路径被修改，那么 Agent 在执行笔记匹配、单篇整理、知识库维护和项目导航时，可能无法正确找到原始笔记，或者需要你手动调整相应的提示词与规则。
关于 ZotLit 的安装与详细配置，请参考官方文档：
OMyPaper 采用分层设计：
- 原始层：
LiteratureNotes/保存 Zotero / ZotLit 导入的原始阅读痕迹 - 全局知识层：
Notes/保存稳定的论文页、概念页、方法页、比较页和主题页 - 项目层：
projects/保存项目组织、项目文献地图与论文大纲 - 控制层：
Management/保存规则、模板、索引、日志、报告、队列与 Skill 规范
换句话说：
- 原始文献笔记是来源层
- Agent 维护的 wiki 是知识层
- 项目树是研究组织层
长期目标，是把零散的阅读痕迹转化成一个不断演化的、本地存储的、可交叉链接的个人论文 wiki + 项目工作区。
0.1.0 是 OMyPaper Skills 的第一版可用版本。
- 以单篇论文和全局知识库为中心
LiteratureNotes/作为原始笔记层Notes/作为全局 wiki 层Management/作为管理与报告层- 核心 Skills 主要覆盖：
- 结构检查
- 单篇论文整理
- 全库整理
- 周报生成
- 论文复盘
- 本地检索导航
- 将 Zotero 的原始阅读痕迹转为结构化 wiki 页面
- 持续维护本地论文知识库
- 组织跨论文的概念、方法、数据集与比较关系
- 生成周报
- 支持单篇论文复盘
- 优先从本地知识库中回答主题问题
0.1.0 仍然主要是paper-centric：
- 还没有完整的 project-aware 工作流
- 还不支持项目级复盘与导航
- 还不支持项目级 session 沉淀
- 还不支持父项目 / 子项目层级结构
- 还没有“项目归属建议 + 待确认队列”的保守机制
0.2.0 将 OMyPaper 从“论文中心的 wiki 工作流”升级为论文 + 层级项目树的工作流。
projects/项目层Management/ProjectIndex.mdManagement/ProjectTree.mdManagement/ProjectAssignmentQueue.mdManagement/ProjectSessionNotes/- 一组 project-aware 模板，例如：
ProjectManifest.template.ymlProjectLiteratureMap.template.mdProjectOutline.template.mdProjectReview.template.mdProjectSessionNote.template.mdProjectTree.template.mdProjectIndex.template.mdProjectAssignmentQueue.template.md
0.2.0 新增了项目树结构，支持：
- 父项目
- 子项目
- 独立项目
项目层级关系通过 project_type 与 parent_project 等元数据表达。
7 个 Skills 不再只是面向论文，而是升级为 论文 + 项目 双层能力。
Skill 1 不再只是“单篇论文整理器”，而变成：
- 先整理进全局 wiki
- 再根据全局整理结果生成项目归属建议
- 把建议写入
Management/ProjectAssignmentQueue.md，等待用户确认
这样，论文进入项目的过程变成了：
- 保守的
- 可审核的
- 由用户最终确认的
全库整理现在会同时检查：
- 项目树健康度
- 项目清单一致性
- 父子项目逻辑
- 兄弟项目重叠
文献地图.md与论文大纲.md的漂移
周报不再只是论文阅读流水，而会同时总结：
- 本周论文阅读进展
- 全局 wiki 更新
- 父项目推进
- 子项目推进
- 下周优先推进的项目
复盘不再只针对单篇论文，还支持：
- 单篇论文复盘
- 子项目复盘
- 父项目复盘
- 项目快速熟悉路径输出
本地检索现在支持：
- 论文检索
- 项目树列出
- 父项目 / 子项目说明
- 兄弟项目比较
- 项目快速熟悉路径
高价值讨论现在可以保存为：
- paper session
- child-project session
- parent-project session
- hybrid session
这些 session 后续可以被 S1、S3、S4、S5 复用。
| 维度 | v0.1.0 | v0.2.0 |
|---|---|---|
| 主要范式 | paper-centric | paper + hierarchical project tree |
| 全局论文 wiki | 有 | 有 |
| 项目组织层 | 很弱 / 未完整支持 | 成为正式一层 |
| 父项目 / 子项目 | 无 | 有 |
| 项目归属待确认队列 | 无 | 有 |
| 项目级 session | 无 | 有 |
| S1 流程 | 整理一篇论文 | 整理 → 建议 → 确认 |
| S2 范围 | 主要是 Notes/ |
Notes/ + projects/ |
| S3 范围 | 论文周报 | 论文 + 项目周报 |
| S4 复盘对象 | 单篇论文 | 论文 / 子项目 / 父项目 |
| S5 检索对象 | 论文 / 主题 | 论文 + 项目树 |
| S6 沉淀对象 | 论文为主 | 论文 / 项目 / hybrid |
| 模板体系 | 偏论文 / wiki | 扩展到项目 / 队列 / 项目树 |
推荐目录结构现在是：
OMyPaper/
├─ LiteratureNotes/ # 由 ZotLit 从 Zotero 导入的原始文献笔记
├─ Notes/
│ ├─ Papers/ # 单篇论文 wiki 页面
│ ├─ Concepts/ # 概念页
│ ├─ Methods/ # 方法页
│ ├─ Datasets/ # 数据集页
│ ├─ Comparisons/ # 跨论文比较页
│ ├─ Topics/ # 主题页
│ └─ Syntheses/ # 高层综合页
├─ Management/
│ ├─ AGENTS.md # Agent 说明 / schema
│ ├─ CurrentQuestions.md # 当前重点问题
│ ├─ index.md # 全局索引
│ ├─ log.md # 追加式日志
│ ├─ PaperRegistry.md # 论文映射登记表
│ ├─ SessionIndex.md # Session 索引
│ ├─ ProjectIndex.md # 项目索引
│ ├─ ProjectTree.md # 项目树
│ ├─ ProjectAssignmentQueue.md # 项目归属待确认队列
│ ├─ WeeklyReports/ # 周报
│ ├─ ReviewNotes/ # 复盘记录
│ ├─ LintReports/ # 整理报告
│ ├─ SessionNotes/ # 论文级 session
│ ├─ ProjectSessionNotes/ # 项目级 / hybrid session
│ ├─ Templates/ # 模板集合
│ └─ Skills/ # Skills 规范
├─ projects/ # 层级项目层
└─ Attachments/ # 可选的本地附件目录
| Skill | 名称 | 它做什么 | 0.2.0 中的关键升级 |
|---|---|---|---|
S0 |
规范检查 / 初始化 | 检查全局库、项目树和会话层是否齐全且一致 | 现在会检查 projects/、树关系成环、manifest 合法性、project-session 就绪情况 |
S1 |
单篇论文整理 | 把一篇论文编译进全局 wiki，并生成项目归属建议 | 现在有强制三阶段流程，并写入 ProjectAssignmentQueue.md |
S2 |
全库整理 | 维护 Notes/ 和 projects/ 的结构健康 |
现在检查父子项目一致性、兄弟项目重叠以及地图/大纲漂移 |
S3 |
周报生成 | 生成覆盖论文与项目的周报 | 现在同时总结父项目与子项目推进 |
S4 |
复盘 | 帮你复盘单篇论文、子项目或父项目 | 现在支持项目复盘与快速熟悉路径 |
S5 |
本地检索 / 导航 | 基于本地证据回答问题并给出重读路径 | 现在支持项目树列出、项目结构说明和兄弟项目比较 |
S6 |
会话沉淀 / 匹配 | 把高价值讨论沉淀为 paper / project / hybrid session | 现在支持项目感知与 hybrid session |
- 在 Zotero 中阅读并批注文献。
- 通过 ZotLit 将文献笔记导入 Obsidian。
- 如果讨论中出现值得保留的内容，先运行 S6。
- 运行 S1，把论文编译进全局 wiki。
- 查看
Management/ProjectAssignmentQueue.md中的项目建议。 - 确认后，再把最终项目归属写入
project.yml。 - 需要快速回顾时用 S4。
- 需要“答案 + 路径 + 重读顺序”时用 S5。
- 运行 S2 进行全库整理。
- 查看 lint 报告。
- 运行 S3 生成周报。
- 让论文知识保持唯一地写在
Notes/中。 - 让项目归类和层级关系保持在
projects/中。 - 始终把
project.yml当作唯一项目归属接口。 - 需要快速熟悉项目时，优先使用 S4 与 S5。
本项目适用于：
- 学术论文阅读
- 文献管理
- 研究笔记整理
- 本地个人知识库建设
- 跨论文概念与方法比较
- 以项目为导向的研究组织
- 长期研究记忆支持
尤其适合偏好以下工作流的用户：
- 本地优先
- Markdown 文件化管理
- 基于 Obsidian 的笔记系统
- 结构清晰、可追踪、可检查的文件组织
- Agent 辅助但仍由用户掌控的知识管理方式
- 本仓库是 Agent 无关（Agent-agnostic） 的。
- 本系统默认采用 本地文件工作流。
LiteratureNotes/中的内容应尽量作为原始来源层保留。- Agent 维护的整理性内容应主要写入
Notes/、projects/与Management/。 - 如果你自行修改目录结构，请同步修改对应的 Skill 提示词与 Agent 说明文件。