Citation Management
neflibata-feng/MyArxiv-Agent
Comprehensive citation management for academic research. An agent skill from neflibata-feng/MyArxiv-Agent.
Guide to JabRef open-source BibTeX and BibLaTeX reference manager
Install Jabref Reference Guide
$ npx skills add wentorai/research-plugins --skill jabref-reference-guide -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install wentorai/research-plugins jabref-reference-guide --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/writing/citation/jabref-reference-guide .claude/skills/jabref-reference-guide && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "jabref-reference-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/writing/citation/jabref-reference-guide into .claude/skills/jabref-reference-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jabref-reference-guide", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/wentorai/research-plugins/tree/main/skills/writing/citation/jabref-reference-guideType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add wentorai/research-plugins --skill jabref-reference-guide -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install wentorai/research-plugins jabref-reference-guide --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/writing/citation/jabref-reference-guide .agents/skills/jabref-reference-guide && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "jabref-reference-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/writing/citation/jabref-reference-guide into .agents/skills/jabref-reference-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jabref-reference-guide", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add wentorai/research-plugins --skill jabref-reference-guide -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install wentorai/research-plugins jabref-reference-guide --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/writing/citation/jabref-reference-guide .cursor/skills/jabref-reference-guide && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "jabref-reference-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/writing/citation/jabref-reference-guide into .cursor/skills/jabref-reference-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jabref-reference-guide", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/wentorai/research-plugins.git --path skills/writing/citation/jabref-reference-guide--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add wentorai/research-plugins --skill jabref-reference-guide -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install wentorai/research-plugins jabref-reference-guide --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/writing/citation/jabref-reference-guide .gemini/skills/jabref-reference-guide && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "jabref-reference-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/writing/citation/jabref-reference-guide into .gemini/skills/jabref-reference-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jabref-reference-guide", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install wentorai/research-plugins jabref-reference-guideInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add wentorai/research-plugins --skill jabref-reference-guide -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/writing/citation/jabref-reference-guide .github/skills/jabref-reference-guide && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "jabref-reference-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/writing/citation/jabref-reference-guide into .github/skills/jabref-reference-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jabref-reference-guide", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add wentorai/research-plugins --skill jabref-reference-guide -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install wentorai/research-plugins jabref-reference-guide --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/writing/citation/jabref-reference-guide .opencode/skills/jabref-reference-guide && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "jabref-reference-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/writing/citation/jabref-reference-guide into .opencode/skills/jabref-reference-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jabref-reference-guide", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
jabref-reference-guide- GitHub stars
- 298
- Used in
- 1 other repo
- Token cost
- ~1.8k tokens
- SKILL.md length
- 867 words
- Files
- 1
- Skills in repo
- 428
- Repo updated
- First seen
- Licence
- MIT
At a glance
Guide to JabRef open-source BibTeX and BibLaTeX reference manager
- Works in 3 steps: Visit https://www.jabref.org and… → Run the installer and follow the setup… → Launch JabRef and create a new BibTeX or…
- Tasks that involve Citation management
- SKILL.md covers Overview, Installation and Setup, Core Features and LaTeX Writing Workflow, plus 2 more sections
- Calls brew and winget
What it does
Jabref Reference Guide is an agent skill from wentorai/research-plugins. Guide to JabRef open-source BibTeX and BibLaTeX reference manager
Its SKILL.md is about 1.8k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Citation management. It works with LaTeX and Linux. The repository describes itself as: 350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents. The licence is MIT.
When your agent uses it
- Tasks that involve Citation management
Example prompts
- “/jabref-reference-guide”
Workflow steps
3 steps, taken from the first numbered list in SKILL.md.
- Visit https://www.jabref.org and download the installer for your platform
- Run the installer and follow the setup wizard
- Launch JabRef and create a new BibTeX or BibLaTeX database
What it can do on your machine
Read from SKILL.md and the folder at commit bf44b3c. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
brewwinget
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
jabref.orggithub.comdocs.jabref.orgblog.jabref.orgctan.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Jabref Reference Guide loads about 1.8k tokens when it runs. Until then it costs about 22 tokens; SKILL.md has 867 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check: notes
The automated check noted patterns worth knowing about, such as sudo or a known installer.
- NoteRuns commands with sudoSKILL.md:34
- Linux (Snap): `sudo snap install jabref`
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from wentorai/research-plugins at commit bf44b3c, republished under its MIT licence (© wentorai). 867 words, ~1,758 tokens.
Download SKILL.mdSave it as
.claude/skills/jabref-reference-guide/SKILL.md (or your agent's skills folder).- name
- jabref-reference-guide
- description
- Guide to JabRef open-source BibTeX and BibLaTeX reference manager
JabRef Reference Manager Guide
Overview
JabRef is an open-source, cross-platform reference manager with over 4,000 GitHub stars, specifically designed for researchers who work with BibTeX and BibLaTeX bibliographies. Written in Java, it runs on Windows, macOS, and Linux, providing a graphical interface for managing bibliographic databases that integrates seamlessly with LaTeX-based writing workflows.
Unlike general-purpose reference managers that treat BibTeX export as an afterthought, JabRef is built from the ground up around the BibTeX format. Every feature, from the entry editor to the search system, understands BibTeX entry types and field semantics natively. This means researchers who write primarily in LaTeX get a tool that speaks their language without the impedance mismatch of converting between proprietary formats.
JabRef supports both BibTeX and BibLaTeX formats, handles cross-references, string constants, and preambles, and provides powerful tools for maintaining bibliography quality. It can fetch metadata from online databases, check entries for completeness, detect duplicates, and generate citation keys following customizable patterns. For researchers who prefer to keep their bibliographic data in plain-text BibTeX files under version control, JabRef is the reference manager of choice.
Installation and Setup
JabRef can be installed through multiple methods:
Direct Download:
- Visit https://www.jabref.org and download the installer for your platform
- Run the installer and follow the setup wizard
- Launch JabRef and create a new BibTeX or BibLaTeX database
Package Managers:
- macOS:
brew install --cask jabref - Linux (Snap):
sudo snap install jabref - Linux (Flatpak):
flatpak install org.jabref.jabref - Windows:
winget install JabRef.JabRef
Initial Configuration:
- Go to Options > Preferences > General
- Set your default bibliography mode (BibTeX or BibLaTeX)
- Configure the default encoding (UTF-8 recommended)
- Set up the citation key generator pattern under Preferences > Citation Key Generator:
- Default:
[auth][year]produces keys likeSmith2024 - Custom example:
[auth:lower][year][veryshorttitle:lower]producessmith2024deep
- Default:
- Configure external tool integration:
- Set your LaTeX editor path for push-to-editor functionality
- Configure your PDF viewer for opening attachments
- Set up the external file directory for organizing linked PDFs
Core Features
Entry Management: JabRef provides a table view and an entry editor for managing bibliography entries. The entry editor shows all fields relevant to the selected entry type (article, book, inproceedings, etc.) and validates field content against BibTeX specifications.
Online Database Search: Search and import references from multiple academic databases directly within JabRef:
- CrossRef for DOI-based metadata
- Google Scholar for broad academic search
- IEEE Xplore for engineering and computer science
- arXiv for preprints
- DBLP for computer science bibliography
- Springer and other publisher databases
- ISBN lookup for books
- INSPIRE-HEP for high-energy physics
Duplicate Detection: JabRef identifies potential duplicate entries using configurable similarity algorithms that compare titles, authors, years, and other fields. The merge dialog allows you to combine duplicates while preserving the most complete metadata from each entry.
Group Management: Organize entries into hierarchical groups based on:
- Manual assignment (drag and drop)
- Keyword matching (automatic based on BibTeX keywords field)
- Search expressions (dynamic groups based on field content)
- Referenced entries (cross-reference chains)
Quality Checks: Run integrity checks on your database to identify:
- Missing required fields for each entry type
- Inconsistent formatting (e.g., mixed abbreviation styles for journal names)
- Broken file links to PDFs or other attachments
- Invalid DOIs, ISBNs, or other identifiers
- Entries without citation keys
Push to Editor: Send citation commands directly to your LaTeX editor. JabRef supports integration with:
- TeXstudio, TeXmaker, and other LaTeX editors
- Vim and Emacs with LaTeX plugins
- VS Code with LaTeX Workshop extension
- LyX document processor
Show full SKILL.md (307 more words)Show less
LaTeX Writing Workflow
Setting Up a Project Bibliography:
- Create a new
.bibfile in your LaTeX project directory - Open it in JabRef as your working database
- Add references through online search, DOI import, or manual entry
- JabRef automatically saves changes to the
.bibfile - Reference the file in your LaTeX document with
\bibliography{references}or\addbibresource{references.bib}
Collaborative Writing:
- Store your
.bibfile in a Git repository alongside your LaTeX source - JabRef's plain-text BibTeX format is diff-friendly and merge-friendly
- Use consistent citation key patterns across collaborators to avoid conflicts
- JabRef's cleanup tools help normalize entries contributed by different team members
Integration with Overleaf:
- Export your JabRef database as a
.bibfile - Upload to your Overleaf project or link via Git
- Use JabRef locally for curation and Overleaf for collaborative editing
Journal Submission Preparation:
- Run JabRef's integrity checks to ensure all entries are complete
- Use the "Find unlinked files" feature to attach any missing PDFs
- Verify journal name abbreviations match the target journal's requirements
- Export the final bibliography in the format required by the submission system
Advanced Features
Custom Entry Types: Define custom BibTeX entry types for specialized references not covered by the standard types. This is useful for datasets, software, standards documents, and other non-traditional academic sources.
Journal Abbreviation Management: JabRef includes a comprehensive database of journal name abbreviations. Configure automatic abbreviation or expansion of journal names to match specific publisher requirements.
String Constants: Use BibTeX string constants to define frequently used values (journal names, publisher details, conference series names) once and reference them throughout your database. This ensures consistency and simplifies bulk updates.
Web Search Customization: Configure custom web search providers or API endpoints for specialized databases relevant to your field.
References
- Official Website: https://www.jabref.org
- GitHub Repository: https://github.com/JabRef/jabref
- JabRef User Documentation: https://docs.jabref.org
- JabRef Blog: https://blog.jabref.org
- CTAN BibTeX Documentation: https://ctan.org/pkg/bibtex
© wentorai, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/writing/citation/jabref-reference-guide of wentorai/research-plugins.
Open the folder on GitHubat commit bf44b3c
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in wentorai/research-plugins, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Jabref Reference Guide next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Jabref Reference Guide this skillwentorai/research-plugins | 298 | 1 repos | ~1.8k | Automated safety check: Notes | MIT | |
| Citation Managementneflibata-feng/MyArxiv-Agent | 126 | 20 repos | ~8.1k | Automated safety check: Notes | MIT | |
| Academic Paper Writing PipelineImbad0202/academic-research-skills | 51k | — | ~16k | Automated safety check: Pass | Custom licence | |
| Literature Review AgentAr9av/PaperOrchestra | 676 | 2 repos | ~5.2k | Automated safety check: Pass | Custom licence | |
| Academic Searchustc-ai4science/academic-search | 665 | — | ~1.1k | Automated safety check: Pass | MIT | |
| Collaborating With Claudeappautomaton/latex-arxiv-SKILL | 457 | 1 repos | ~1.5k | Automated safety check: Pass | MIT |
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Imbad0202/academic-research-skills
Runs a 12-agent pipeline that plans, drafts, cites, reviews and formats academic papers, with modes for revision, rebuttals, abstracts and citation checks.
Literature Review Agent
Ar9av/PaperOrchestra
Step 3 of the PaperOrchestra pipeline (arXiv:2604.05018). An agent skill from Ar9av/PaperOrchestra.
Academic Search
ustc-ai4science/academic-search
A skill your agent uses when the user asks to search or review academic papers, retrieve scholarly metadata or citation counts, validate or deduplicate scholarly records, find an author's…
Collaborating With Claude
appautomaton/latex-arxiv-SKILL
Use the Claude Code CLI to consult Claude and delegate coding tasks for prototyping, debugging, and code review.
Arxiv MCP Server
blazickjp/arxiv-mcp-server
A skill your agent uses when finding, comparing, reading, or monitoring arXiv papers, including requests for abstracts, citation graphs, original LaTeX, section-level technical details, or…
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Related
Categories
Questions about Jabref Reference Guide
What does Jabref Reference Guide do?
Guide to JabRef open-source BibTeX and BibLaTeX reference manager. Jabref Reference Guide is an agent skill from wentorai/research-plugins.
When should I use Jabref Reference Guide?
Jabref Reference Guide fits situations like: tasks that involve Citation management.
How do I install Jabref Reference Guide in Claude Code?
Run `npx skills add wentorai/research-plugins --skill jabref-reference-guide -a claude-code`. Or copy the skill folder (skills/writing/citation/jabref-reference-guide in wentorai/research-plugins) into .claude/skills/jabref-reference-guide in your project. Claude Code loads it when a task matches its description.
How do I install Jabref Reference Guide in Codex?
Run `npx skills add wentorai/research-plugins --skill jabref-reference-guide -a codex`. Or copy the skill folder (skills/writing/citation/jabref-reference-guide in wentorai/research-plugins) into .agents/skills/jabref-reference-guide in your project. Codex loads it when a task matches its description.
Can I use Jabref Reference Guide in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add wentorai/research-plugins --skill jabref-reference-guide -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/jabref-reference-guide, .gemini/skills/jabref-reference-guide, .github/skills/jabref-reference-guide and .opencode/skills/jabref-reference-guide in your project.
What does Jabref Reference Guide need to run?
Going by SKILL.md and its folder, Jabref Reference Guide needs the command-line tools its instructions call (brew and winget).
Does Jabref Reference Guide access the network?
SKILL.md names 5 domains. As links in the text: jabref.org, github.com, docs.jabref.org, blog.jabref.org and ctan.org. This is read from the text; nothing was executed.
Is Jabref Reference Guide safe to install?
Our automated static check of SKILL.md found notes only (runs commands with sudo), nothing it rates as a warning. It is not a guarantee. Review the folder before installing.
What licence does Jabref Reference Guide use?
Jabref Reference Guide is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Jabref Reference Guide use?
About 1.8k tokens (SKILL.md is roughly 7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Jabref Reference Guide?
Skills that share tags, products or a category with Jabref Reference Guide: Citation Management (neflibata-feng/MyArxiv-Agent, 126 stars), Academic Paper Writing Pipeline (Imbad0202/academic-research-skills, 51k stars), Literature Review Agent (Ar9av/PaperOrchestra, 676 stars) and Academic Search (ustc-ai4science/academic-search, 665 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Jabref Reference Guide?
wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 428 skills in this directory. The repository was last updated on June 19, 2026.
Source: wentorai/research-plugins on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.