agentmods.dev

SearchPaper: Skill for Claude Code

.agents/skills/literature-search/SKILL.md

literature-search is a skill for Claude Code, Codex from FreddieWho/SearchPaper. It costs 42 tokens per session (541 once invoked), scanned A, original, MIT.

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.

In plain words
What is it for?
Finding papers, checking known identifiers, expanding searches from a seed paper, retrieving biomedical literature signals, and exporting literature records.
Why use it?
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.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one. Also seen: installed under .agents/ (shared by several agents).

This is FreddieWho/SearchPaper's own configuration. It tells Claude Code and Codex how to work on SearchPaper itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything SearchPaper configures →

not rated 0repo 2mo ago A scan 42 tokens original MIT
View source ↗ FreddieWho/SearchPaper
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.

agentmods badge for literature-search

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.

agentmods 80×15 button for literature-search

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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00042 $0.00541
Opus 5 $0.00021 $0.00270
Sonnet 5 $0.00008 $0.00108
Haiku 4.5 $0.00004 $0.00054

Measured 9d ago against content hash df0ee93425ad, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, 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 9d 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

  1. 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.
  2. Preserve DOI, PMID, PMCID, source, and trace fields.
  3. Use resolve_identifiers or searchpaper resolve when merging or checking a known paper.
  4. Use expand_from_work only after identifying a reliable seed paper.
  5. Use search_literature_signals for biomedical entity/relation signals, but do not call those signals proof.
  6. 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.
  7. Use PubMed utilities (searchpaper pubmed mesh, pubmed related, pubmed convert-ids) for MeSH strategy, related articles, and DOI/PMID/PMCID conversion.
  8. 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.

  1. 9d 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 2mo ago), licensed MIT. It adds 42 tokens to every session and 541 once invoked, about $0.0002 per session on Opus 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.

ResearchScientific
Related

Other skills, from other repositories

instrument-data-to-allotrope

Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…

anthropics/knowledge-work-plugins · 123 tokens

matlab

Build, review, migrate, and safely plan MATLAB or GNU Octave numerical workflows, including arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit Python interoperability.

K-Dense-AI/scientific-agent-skills · 42 tokens

exploratory-data-analysis

Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds. Other domain…

K-Dense-AI/scientific-agent-skills · 83 tokens

phylogenetics

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.

K-Dense-AI/scientific-agent-skills · 68 tokens

research-engineer

An uncompromising Academic Research Engineer. Operates with absolute scientific rigor, objective criticism, and zero flair. Focuses on theoretical correctness, formal verification, and optimal implementation across any required technology.

davila7/claude-code-templates · 43 tokens

mapping-to-snomed

Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a USER-SUPPLIED terminology server (the user's own Ontoserver, Snowstorm, or UMLS/UTS), never a bundled vocabulary. Use when the user wants to code findings, disorders, procedures, body structures, or substances to SNOMED CT, run an ECL…

maziyarpanahi/openmed · 205 tokens