Nature Paper Card
Yuan1z0825/nature-skills
Builds a structured deep-reading card for one scientific paper, covering methods, how experiments support claims, limitations and research ideas, with a script to prepare the source.
Multi-source exhaustive literature search across academic databases
Install Deep Literature Search
$ npx skills add wentorai/research-plugins --skill deep-literature-search -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install wentorai/research-plugins deep-literature-search --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/literature/search/deep-literature-search .claude/skills/deep-literature-search && 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 "deep-literature-search" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/deep-literature-search into .claude/skills/deep-literature-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-literature-search", 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/literature/search/deep-literature-searchType 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 deep-literature-search -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install wentorai/research-plugins deep-literature-search --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/literature/search/deep-literature-search .agents/skills/deep-literature-search && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "deep-literature-search" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/deep-literature-search into .agents/skills/deep-literature-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-literature-search", 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 deep-literature-search -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install wentorai/research-plugins deep-literature-search --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/literature/search/deep-literature-search .cursor/skills/deep-literature-search && 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 "deep-literature-search" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/deep-literature-search into .cursor/skills/deep-literature-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-literature-search", 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/literature/search/deep-literature-search--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 deep-literature-search -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install wentorai/research-plugins deep-literature-search --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/literature/search/deep-literature-search .gemini/skills/deep-literature-search && 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 "deep-literature-search" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/deep-literature-search into .gemini/skills/deep-literature-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-literature-search", 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 deep-literature-searchInstalls 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 deep-literature-search -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/literature/search/deep-literature-search .github/skills/deep-literature-search && 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 "deep-literature-search" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/deep-literature-search into .github/skills/deep-literature-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-literature-search", 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 deep-literature-search -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 deep-literature-search --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/literature/search/deep-literature-search .opencode/skills/deep-literature-search && 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 "deep-literature-search" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/literature/search/deep-literature-search into .opencode/skills/deep-literature-search/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-literature-search", 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
deep-literature-search- GitHub stars
- 298
- Used in
- 1 other repo
- Token cost
- ~1.7k tokens
- SKILL.md length
- 735 words
- Files
- 1
- Skills in repo
- 405
- Repo updated
- First seen
- Licence
- MIT
At a glance
Multi-source exhaustive literature search across academic databases
- Works in 4 steps: Define the Research Question → Identify Key Concepts and Synonyms → Build the Search String → …
- Tasks that involve Literature review
- SKILL.md covers Overview, Search Strategy Design, Multi-Database Execution and Deduplication and Screening, plus 2 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Deep Literature Search is an agent skill from wentorai/research-plugins. Multi-source exhaustive literature search across academic databases
Its SKILL.md is about 1.7k 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 Literature review. 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 Literature review
Example prompts
- “/deep-literature-search”
Workflow steps
4 steps, taken from the step headings in SKILL.md.
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
No scripts in the folder and no shell commands in SKILL.md.
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):
prisma-statement.orgtraining.cochrane.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
Deep Literature Search loads about 1.7k tokens when it runs. Until then it costs about 23 tokens; SKILL.md has 735 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 passed
The automated check found no risky patterns in SKILL.md.
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). 735 words, ~1,726 tokens.
Download SKILL.mdSave it as
.claude/skills/deep-literature-search/SKILL.md (or your agent's skills folder).- name
- deep-literature-search
- description
- Multi-source exhaustive literature search across academic databases
Deep Literature Search
Overview
A deep literature search goes beyond a quick Google Scholar query. It is a methodical, multi-source search process designed to identify all relevant publications on a topic with minimal omissions. This level of thoroughness is required for systematic reviews, meta-analyses, grant applications, and dissertation literature reviews where comprehensiveness is not optional—it is a methodological requirement.
This skill provides a structured framework for planning, executing, and documenting exhaustive literature searches across multiple academic databases. It covers query formulation using controlled vocabularies, database selection strategy, deduplication, screening workflows, and PRISMA-compliant documentation of the search process.
The framework is database-agnostic and can be applied across disciplines, from biomedical sciences (PubMed, Cochrane) to social sciences (PsycINFO, ERIC), engineering (IEEE Xplore, Compendex), and multidisciplinary databases (Web of Science, Scopus, OpenAlex).
Search Strategy Design
Step 1: Define the Research Question
Use the PICO/PEO/SPIDER framework appropriate to your field:
- PICO (clinical/biomedical): Population, Intervention, Comparison, Outcome
- PEO (qualitative): Population, Exposure, Outcome
- SPIDER (mixed methods): Sample, Phenomenon of Interest, Design, Evaluation, Research type
Example: "What is the effect of mindfulness-based interventions (I) on academic stress (O) in graduate students (P) compared to no intervention (C)?"
Step 2: Identify Key Concepts and Synonyms
Break your research question into 2-4 key concepts. For each concept, list all synonyms, related terms, abbreviations, and controlled vocabulary terms:
| Concept | Synonyms and Related Terms |
|---|---|
| Mindfulness | mindfulness-based stress reduction, MBSR, meditation, mindful awareness |
| Academic stress | study stress, exam anxiety, academic burnout, student distress |
| Graduate students | postgraduate, doctoral students, PhD candidates, master's students |
Step 3: Build the Search String
Combine concepts using Boolean logic:
("mindfulness" OR "MBSR" OR "mindfulness-based stress reduction" OR "meditation")
AND
("academic stress" OR "study stress" OR "exam anxiety" OR "academic burnout")
AND
("graduate student*" OR "postgraduate*" OR "doctoral student*" OR "PhD candidate*")Key syntax rules:
- Use
ORwithin concept groups (broadens) - Use
ANDbetween concept groups (narrows) - Use
*for truncation (e.g.,student*matches students, student's) - Use
""for exact phrases - Use
NOTsparingly and document its use
Step 4: Adapt for Each Database
Each database has its own syntax and controlled vocabulary. You must translate your master search string for each target:
- PubMed: Use MeSH terms alongside free-text; syntax uses
[MeSH]tags - Scopus: Uses
TITLE-ABS-KEY()field codes - Web of Science: Uses
TS=(Topic) andTI=(Title) field tags - IEEE Xplore: Uses "Command Search" with field codes
- OpenAlex: Uses concept IDs and filter parameters in the API
Multi-Database Execution
Recommended Database Selection by Discipline
| Discipline | Primary Databases | Supplementary |
|---|---|---|
| Biomedical | PubMed, Cochrane, Embase | CINAHL, PsycINFO |
| Computer Science | IEEE Xplore, ACM DL, DBLP | Scopus, arXiv |
| Social Sciences | PsycINFO, ERIC, Sociological Abstracts | Web of Science |
| Engineering | Compendex, IEEE Xplore | Scopus, Web of Science |
| Multidisciplinary | Web of Science, Scopus, OpenAlex | Google Scholar (supplementary) |
Show full SKILL.md (319 more words)Show less
Execution Checklist
For each database:
- Translate the master search string to the database's syntax
- Run the search and record the date, exact query string, and result count
- Export all results in a structured format (RIS, BibTeX, or CSV)
- Save a screenshot or copy of the search interface showing the query and results count
Grey Literature and Supplementary Sources
A truly exhaustive search also covers non-indexed sources:
- Preprint servers: arXiv, bioRxiv, medRxiv, SSRN
- Dissertations: ProQuest Dissertations, EThOS, institutional repositories
- Conference proceedings: Check major conferences in your field
- Citation chaining: Forward (who cited this?) and backward (what did this cite?) from key papers
- Expert consultation: Contact domain experts for unpublished or in-press work
- Trial registries: ClinicalTrials.gov, WHO ICTRP (for clinical topics)
Deduplication and Screening
Deduplication Process
After collecting results from multiple databases, expect 20-40% overlap. Use reference management software to deduplicate:
- Import all exported results into a single library (Zotero, EndNote, or Rayyan)
- Run automatic deduplication using DOI matching first, then title+author matching
- Manually review flagged potential duplicates—automated tools miss ~5-10%
- Record the count: total imported, duplicates removed, unique records remaining
Screening Workflow
Apply a two-stage screening process:
- Title/Abstract screening: Review each unique record against your inclusion/exclusion criteria. Mark as Include, Exclude, or Maybe.
- Full-text screening: Retrieve full texts for all Include and Maybe records. Apply detailed eligibility criteria.
Use screening tools like Rayyan, Covidence, or ASReview to manage this process, especially for large result sets (500+ records).
PRISMA Documentation
Document your entire search process using the PRISMA 2020 flow diagram:
Records identified (N = ?)
├── Database 1 (n = ?)
├── Database 2 (n = ?)
└── Other sources (n = ?)
Duplicates removed (n = ?)
Records screened (n = ?)
Records excluded (n = ?)
Full-text assessed (n = ?)
Full-text excluded with reasons (n = ?)
Studies included (n = ?)Save your complete search strategies (exact query strings, dates, result counts per database) as supplementary material for your publication. This transparency is essential for reproducibility and is increasingly required by journals.
References
- PRISMA 2020 Statement: https://www.prisma-statement.org
- Cochrane Handbook, Ch. 4 (Searching for studies): https://training.cochrane.org/handbook
- Literature Search tool: wentor-research-plugins
- Bramer, W.M. et al. (2017). "De-duplication of database search results." BMC Medical Research Methodology.
© 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/literature/search/deep-literature-search 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
Deep Literature Search 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 |
|---|---|---|---|---|---|---|
| Deep Literature Search this skillwentorai/research-plugins | 298 | 1 repos | ~1.7k | Automated safety check: Pass | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 47k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Systematic Review ScreenerImbad0202/academic-research-skills | 51k | — | ~8.4k | Automated safety check: Pass | Custom licence | |
| Literature Reviewneflibata-feng/MyArxiv-Agent | 126 | 20 repos | ~5.9k | Automated safety check: Notes | MIT | |
| Preprint Search on bioRxivLigphiDonk/Oh-my--paper | 739 | 12 repos | ~3.7k | Automated safety check: Pass | MIT | |
| Academic Paper Writing PipelineImbad0202/academic-research-skills | 51k | — | ~16k | Automated safety check: Pass | Custom licence |
Similar skills
Systematic Review Screener
Imbad0202/academic-research-skills
Screens records for systematic, scoping and rapid reviews against fixed eligibility rules, using two blinded AI reviewers and a third adjudicator, with traceable PRISMA counts.
Literature Review
neflibata-feng/MyArxiv-Agent
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.).
Preprint Search on bioRxiv
LigphiDonk/Oh-my--paper
Searches bioRxiv life sciences preprints by keyword, author, date range or category with a Python script, returning JSON metadata and optional PDF downloads.
Academic Paper Writing Pipeline
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.
Deep Research Workflow
TokenRhythm/opensquilla
Runs multi-round research in three stages with a persisted state file, evidence tracking and a long-form report with per-claim citations.
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Academic Paper Summarizer
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Related
Categories
Questions about Deep Literature Search
What does Deep Literature Search do?
Multi-source exhaustive literature search across academic databases. Deep Literature Search is an agent skill from wentorai/research-plugins.
When should I use Deep Literature Search?
Deep Literature Search fits situations like: tasks that involve Literature review.
How do I install Deep Literature Search in Claude Code?
Run `npx skills add wentorai/research-plugins --skill deep-literature-search -a claude-code`. Or copy the skill folder (skills/literature/search/deep-literature-search in wentorai/research-plugins) into .claude/skills/deep-literature-search in your project. Claude Code loads it when a task matches its description.
How do I install Deep Literature Search in Codex?
Run `npx skills add wentorai/research-plugins --skill deep-literature-search -a codex`. Or copy the skill folder (skills/literature/search/deep-literature-search in wentorai/research-plugins) into .agents/skills/deep-literature-search in your project. Codex loads it when a task matches its description.
Can I use Deep Literature Search 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 deep-literature-search -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/deep-literature-search, .gemini/skills/deep-literature-search, .github/skills/deep-literature-search and .opencode/skills/deep-literature-search in your project.
What does Deep Literature Search need to run?
SKILL.md names no scripts, command-line tools or credentials: Deep Literature Search is instructions for the agent only.
Does Deep Literature Search access the network?
SKILL.md names 2 domains. As links in the text: prisma-statement.org and training.cochrane.org. This is read from the text; nothing was executed.
Is Deep Literature Search safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Deep Literature Search use?
Deep Literature Search 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 Deep Literature Search use?
About 1.7k tokens (SKILL.md is roughly 6.9k 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 Deep Literature Search?
Skills that share tags, products or a category with Deep Literature Search: Nature Paper Card (Yuan1z0825/nature-skills, 47k stars), Systematic Review Screener (Imbad0202/academic-research-skills, 51k stars), Literature Review (neflibata-feng/MyArxiv-Agent, 126 stars) and Preprint Search on bioRxiv (LigphiDonk/Oh-my--paper, 739 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Deep Literature Search?
wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 405 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.