What is literature-search?

A skill for searching scholarly literature, including papers in biomedical fields. It uses SearchPaper to find records and resolve identifiers such as DOI, PMID, and PMCID.

Finding papers, checking known identifiers, expanding searches from a seed paper, retrieving biomedical literature signals, and exporting literature records.

It keeps paper metadata, source information, and citation links organised when searching or combining literature, while leaving scientific interpretation to the user or another workflow.

How FreddieWho/SearchPaper configures Claude Code and Codex

Reuse

Borrowing it

Nothing to install: this file belongs to FreddieWho/SearchPaper. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/FreddieWho/SearchPaper/main/.agents/skills/literature-search/SKILL.md

Clone the repo

git clone --depth 1 https://github.com/FreddieWho/SearchPaper

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/freddiewho/searchpaper/literature-search/github.svg)](https://agentmods.dev/skills/freddiewho/searchpaper/literature-search)

Your own site

<a href="https://agentmods.dev/skills/freddiewho/searchpaper/literature-search"><img src="https://agentmods.dev/badge/skills/freddiewho/searchpaper/literature-search/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/freddiewho/searchpaper/literature-search"><img src="https://agentmods.dev/badge/skills/freddiewho/searchpaper/literature-search.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 42 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 541 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00042	$0.00541
Opus 5.5	$0.00017	$0.00216
Sonnet 5.5	$0.00008	$0.00108
Haiku 4.5	$0.00004	$0.00054

Measured 2mo ago against content hash df0ee93425ad, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

literature-search scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.agents/skills/literature-search/SKILL.md · 57 lines

How it starts

The opening of the file, as written. The whole thing — 57 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Literature Search with SearchPaper

Use SearchPaper when a task requires scholarly literature search, paper metadata, DOI/PMID/PMCID resolution, citation/context expansion, biomedical literature signals, or exportable literature records.

SearchPaper is not a research agent and does not evaluate scientific truth. It returns literature records, provenance, identifiers, and signals that must be interpreted by the user or a downstream research workflow.

Preferred Workflow

Start with searchpaper search "<query>" --json or MCP search_literature. Use searchpaper plan "<query>" --profile auto --json or MCP plan_literature_search first when source coverage matters.
Preserve DOI, PMID, PMCID, source, and trace fields.
Use resolve_identifiers or searchpaper resolve when merging or checking a known paper.
Use expand_from_work only after identifying a reliable seed paper.
Use search_literature_signals for biomedical entity/relation signals, but do not call those signals proof.
If results are sparse or suspicious, call get_source_status or searchpaper sources status. Use searchpaper sources tiers to report sources that are cataloged but not queried automatically.
Use PubMed utilities (searchpaper pubmed mesh, pubmed related, pubmed convert-ids) for MeSH strategy, related articles, and DOI/PMID/PMCID conversion.
Export machine-readable results with JSONL when passing results to downstream agents.

Interpretation Rules

A literature signal is not an evaluated conclusion.
A PubTator or abstract co-mention signal does not prove causality.
A single relevant paper is still a useful literature-backed record, but the agent must report its source and limitations.
Do not hide degraded or failed sources.
Do not retry a broken public API repeatedly.
Do not imply Scopus, Web of Science, Google Scholar, CNKI, or 万方 were searched unless an external/manual workflow actually checked them.

Output Rules

Read the full file on GitHub · 57 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

2mo ago First seen · 57 lines · 42 tokens per session scan A df0ee93425ad

Subscribe to this mod's changes

literature-search is a skill published in the GitHub repository FreddieWho/SearchPaper (0 stars, last pushed 18d ago), licensed MIT. It adds 42 tokens to every session and 541 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

Research Scientific

literature-search next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
literature-searchFreddieWho/SearchPaper	Skill	0	18d ago	MIT	A	42	Claude Code, Codex
instrument-data-to-allotropeanthropics/knowledge-work-plugins	Skill	35k	2d ago	Apache-2.0	A	123	Claude Code
exploratory-data-analysisK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	83	Claude Code
matlabK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	44	Claude Code
phylogeneticsK-Dense-AI/scientific-agent-skills	Skill	56k	4d ago	MIT	A	71	Claude Code, Codex
research-engineerdavila7/claude-code-templates	Skill	33k	yesterday	MIT	A	43	Claude Code, Codex
mapping-to-snomedmaziyarpanahi/openmed	Skill	5.8k	yesterday	Apache-2.0	A	205	Claude Code

SearchPaper: Skill for Claude Code