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.
Systematic literature-review workflow for academic, biomedical, technical, and scientific topics, including search planning, source screening, synthesis, citation checks, and evidence logging.
Install Scientific Thinking Literature Review
$ npx skills add affaan-m/ECC --skill scientific-thinking-literature-review -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install affaan-m/ECC scientific-thinking-literature-review --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/affaan-m/ECC.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/scientific-thinking-literature-review .claude/skills/scientific-thinking-literature-review && 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 "scientific-thinking-literature-review" agent skill from https://github.com/affaan-m/ECC/tree/main/skills/scientific-thinking-literature-review into .claude/skills/scientific-thinking-literature-review/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scientific-thinking-literature-review", 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/affaan-m/ECC/tree/main/skills/scientific-thinking-literature-reviewType 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 affaan-m/ECC --skill scientific-thinking-literature-review -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install affaan-m/ECC scientific-thinking-literature-review --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/affaan-m/ECC.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/scientific-thinking-literature-review .agents/skills/scientific-thinking-literature-review && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "scientific-thinking-literature-review" agent skill from https://github.com/affaan-m/ECC/tree/main/skills/scientific-thinking-literature-review into .agents/skills/scientific-thinking-literature-review/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scientific-thinking-literature-review", 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 affaan-m/ECC --skill scientific-thinking-literature-review -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install affaan-m/ECC scientific-thinking-literature-review --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/affaan-m/ECC.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/scientific-thinking-literature-review .cursor/skills/scientific-thinking-literature-review && 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 "scientific-thinking-literature-review" agent skill from https://github.com/affaan-m/ECC/tree/main/skills/scientific-thinking-literature-review into .cursor/skills/scientific-thinking-literature-review/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scientific-thinking-literature-review", 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/affaan-m/ECC.git --path skills/scientific-thinking-literature-review--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 affaan-m/ECC --skill scientific-thinking-literature-review -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install affaan-m/ECC scientific-thinking-literature-review --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/affaan-m/ECC.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/scientific-thinking-literature-review .gemini/skills/scientific-thinking-literature-review && 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 "scientific-thinking-literature-review" agent skill from https://github.com/affaan-m/ECC/tree/main/skills/scientific-thinking-literature-review into .gemini/skills/scientific-thinking-literature-review/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scientific-thinking-literature-review", 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 affaan-m/ECC scientific-thinking-literature-reviewInstalls 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 affaan-m/ECC --skill scientific-thinking-literature-review -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/affaan-m/ECC.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/scientific-thinking-literature-review .github/skills/scientific-thinking-literature-review && 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 "scientific-thinking-literature-review" agent skill from https://github.com/affaan-m/ECC/tree/main/skills/scientific-thinking-literature-review into .github/skills/scientific-thinking-literature-review/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scientific-thinking-literature-review", 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 affaan-m/ECC --skill scientific-thinking-literature-review -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install affaan-m/ECC scientific-thinking-literature-review --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/affaan-m/ECC.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/scientific-thinking-literature-review .opencode/skills/scientific-thinking-literature-review && 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 "scientific-thinking-literature-review" agent skill from https://github.com/affaan-m/ECC/tree/main/skills/scientific-thinking-literature-review into .opencode/skills/scientific-thinking-literature-review/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "scientific-thinking-literature-review", 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
scientific-thinking-literature-review- GitHub stars
- 277k
- Used in
- 1 other repo
- Token cost
- ~1.3k tokens
- SKILL.md length
- 507 words
- Files
- 1
- Skills in repo
- 683
- Repo updated
- First seen
- Licence
- MIT
At a glance
Systematic literature-review workflow for academic, biomedical, technical, and scientific topics, including search planning, source screening, synthesis, citation checks, and evidence logging.
- Works in 8 steps: Define the Question → Plan the Search → Search and Log Evidence → …
- The task is to find
- SKILL.md covers When to Use, Review Types, Workflow and Output Template, plus 1 more section
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Scientific Thinking Literature Review is an agent skill from affaan-m/ECC. Systematic literature-review workflow for academic, biomedical, technical, and scientific topics, including search planning, source screening, synthesis, citation checks, and evidence logging. Use when the task is to find, screen, synthesize, and cite a body of academic or technical literature.
Its SKILL.md is about 1.3k 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 and Citation management. The repository describes itself as: The agent harness performance optimization system. Skills, instincts, memory, security, and research-first development for Claude Code, Codex, Opencode, Cursor and beyond. The licence is MIT.
When your agent uses it
- The task is to find
- Cite a body of academic
- Technical literature
Example prompts
- “/scientific-thinking-literature-review”
Workflow steps
8 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 2d515e4. 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 (its code samples are markdown).
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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
Scientific Thinking Literature Review loads about 1.3k tokens when it runs. Until then it costs about 83 tokens; SKILL.md has 507 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 affaan-m/ECC at commit 2d515e4, republished under its MIT licence (© affaan-m). 507 words, ~1,301 tokens.
Download SKILL.mdSave it as
.claude/skills/scientific-thinking-literature-review/SKILL.md (or your agent's skills folder).- name
- scientific-thinking-literature-review
- description
- Systematic literature-review workflow for academic, biomedical, technical, and scientific topics, including search planning, source screening, synthesis, citation checks, and evidence logging. Use when the task is to find, screen, synthesize, and cite a body of academic or technical literature.
- metadata.origin
- community
Literature Review
Use this skill when the task is to find, screen, synthesize, and cite a body of academic or technical literature.
When to Use
- Building a systematic, scoping, or narrative literature review.
- Synthesizing the state of the art for a research question.
- Finding gaps, contradictions, or future-work directions.
- Preparing citation-backed background sections for papers or reports.
- Comparing evidence across peer-reviewed papers, preprints, patents, and technical reports.
Review Types
- Narrative review: broad synthesis; useful for orientation.
- Scoping review: maps concepts, methods, and evidence gaps.
- Systematic review: predefined protocol, reproducible search, explicit screening and exclusion.
- Meta-analysis: systematic review plus quantitative effect aggregation.
Ask the user which level of rigor is needed. If unspecified, default to a scoping review for exploratory work and a systematic review for publication or clinical claims.
Workflow
1. Define the Question
Convert the prompt into a searchable research question.
For clinical or biomedical work, use PICO:
- Population
- Intervention or exposure
- Comparator
- Outcome
For technical work, use:
- system or domain
- method or intervention
- comparison baseline
- evaluation metric
2. Plan the Search
Create a search protocol before collecting sources:
- databases to search
- date range
- languages
- publication types
- inclusion criteria
- exclusion criteria
- exact search strings
Minimum useful database set:
- PubMed for biomedical and life-sciences literature.
- arXiv for CS, math, physics, quantitative biology, and preprints.
- Semantic Scholar or Crossref for broad academic discovery.
- Domain-specific sources when relevant, such as clinical-trial registries, patent databases, standards bodies, or official technical docs.
3. Search and Log Evidence
Keep a search log that makes the review reproducible:
| Database | Date searched | Query | Filters | Results | Export |
| --- | --- | --- | --- | ---: | --- |
| PubMed | 2026-05-11 | `("CRISPR"[tiab] OR "Cas9"[tiab]) AND "sickle cell"[tiab]` | 2020:2026, English | 86 | PMID list |
| arXiv | 2026-05-11 | `CRISPR sickle cell gene editing` | q-bio, 2020:2026 | 9 | BibTeX |Save raw IDs, URLs, DOIs, abstracts, and notes separately from the final prose.
4. Deduplicate
Deduplicate in this order:
- DOI
- PMID or arXiv ID
- exact title
- normalized title plus first author and year
Record how many duplicates were removed.
Show full SKILL.md (212 more words)Show less
5. Screen Sources
Screen in stages:
- title
- abstract
- full text
For systematic work, record exclusion reasons:
- wrong population
- wrong intervention
- wrong outcome
- not primary research
- duplicate
- unavailable full text
- outside date range
6. Extract Data
Use a structured extraction table:
| Study | Design | Population/Data | Method | Comparator | Outcome | Key finding | Limitations |
| --- | --- | --- | --- | --- | --- | --- | --- |
| Author Year | RCT/cohort/review/etc. | sample or corpus | method | baseline | measured outcome | result | caveat |For technical papers, include dataset, benchmark, metric, baseline, and reproducibility notes.
7. Synthesize
Group evidence by theme rather than summarizing papers one by one.
Useful synthesis lenses:
- strongest evidence
- conflicting evidence
- methodological weaknesses
- population or dataset limits
- recency and replication
- practical implications
- unanswered questions
Separate claims by confidence:
- High confidence: replicated, high-quality evidence across sources.
- Medium confidence: plausible but limited by sample, method, or recency.
- Low confidence: early, speculative, single-source, or weakly measured.
8. Verify Citations
Before finalizing:
- verify DOI, PMID, arXiv ID, or official URL
- check author names and publication year
- do not cite a paper for a claim it does not make
- mark preprints as preprints
- distinguish reviews from primary evidence
Output Template
# Literature Review: <Topic>
Generated: <date>
Review type: <narrative | scoping | systematic | meta-analysis>
Search window: <dates>
Databases: <list>
## Research Question
## Search Strategy
## Inclusion and Exclusion Criteria
## Evidence Summary
## Thematic Synthesis
## Gaps and Limitations
## References
## Search LogPitfalls
- Do not treat search snippets as evidence.
- Do not mix preprints, reviews, and primary studies without labeling them.
- Do not omit negative or conflicting findings.
- Do not claim systematic-review rigor without a reproducible protocol.
- Do not use a single database for a broad claim unless the scope is explicitly limited to that database.
© affaan-m, 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/scientific-thinking-literature-review of affaan-m/ECC.
Open the folder on GitHubat commit 2d515e4
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 affaan-m/ECC, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Scientific Thinking Literature Review 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 |
|---|---|---|---|---|---|---|
| Scientific Thinking Literature Review this skillaffaan-m/ECC | 277k | 1 repos | ~1.3k | Automated safety check: Pass | MIT | |
| 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 | |
| Deep Research WorkflowTokenRhythm/opensquilla | 7.1k | — | ~1.3k | Automated safety check: Pass | Apache-2.0 |
Similar skills
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.
Academic Research Suite for Codex
Imbad0202/academic-research-skills-codex
A router skill that sends academic work such as literature reviews, drafting, citation checks, peer review and revision to the right workflow in the ARS suite.
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Related
Categories
Questions about Scientific Thinking Literature Review
What does Scientific Thinking Literature Review do?
Systematic literature-review workflow for academic, biomedical, technical, and scientific topics, including search planning, source screening, synthesis, citation checks, and evidence logging. Scientific Thinking Literature Review is an agent skill from affaan-m/ECC. Systematic literature-review workflow for academic, biomedical, technical, and scientific topics, including search planning, source screening, synthesis, citation checks, and evidence logging.
When should I use Scientific Thinking Literature Review?
Scientific Thinking Literature Review fits situations like: the task is to find; cite a body of academic; technical literature.
How do I install Scientific Thinking Literature Review in Claude Code?
Run `npx skills add affaan-m/ECC --skill scientific-thinking-literature-review -a claude-code`. Or copy the skill folder (skills/scientific-thinking-literature-review in affaan-m/ECC) into .claude/skills/scientific-thinking-literature-review in your project. Claude Code loads it when a task matches its description.
How do I install Scientific Thinking Literature Review in Codex?
Run `npx skills add affaan-m/ECC --skill scientific-thinking-literature-review -a codex`. Or copy the skill folder (skills/scientific-thinking-literature-review in affaan-m/ECC) into .agents/skills/scientific-thinking-literature-review in your project. Codex loads it when a task matches its description.
Can I use Scientific Thinking Literature Review 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 affaan-m/ECC --skill scientific-thinking-literature-review -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/scientific-thinking-literature-review, .gemini/skills/scientific-thinking-literature-review, .github/skills/scientific-thinking-literature-review and .opencode/skills/scientific-thinking-literature-review in your project.
What does Scientific Thinking Literature Review need to run?
SKILL.md names no scripts, command-line tools or credentials: Scientific Thinking Literature Review is instructions for the agent only.
Does Scientific Thinking Literature Review access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Scientific Thinking Literature Review 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 Scientific Thinking Literature Review use?
Scientific Thinking Literature Review 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 Scientific Thinking Literature Review use?
About 1.3k tokens (SKILL.md is roughly 5.2k 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 Scientific Thinking Literature Review?
Skills that share tags, products or a category with Scientific Thinking Literature Review: Systematic Review Screener (Imbad0202/academic-research-skills, 51k stars), Literature Review (neflibata-feng/MyArxiv-Agent, 126 stars), Preprint Search on bioRxiv (LigphiDonk/Oh-my--paper, 739 stars) and Academic Paper Writing Pipeline (Imbad0202/academic-research-skills, 51k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Scientific Thinking Literature Review?
affaan-m (a GitHub user) maintains it in affaan-m/ECC, which has 276,673 GitHub stars. The repository holds 683 skills in this directory. The repository was last updated on October 11, 2026.
Source: affaan-m/ECC on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.