tooluniverse-literature-deep-research

Conducts evidence-graded literature reviews across academic domains using 120+ ToolUniverse research tools.

Updated Mar 13, 2026
One-click install
npx skills add https://github.com/matt-grain/pharma-catalyst --skill tooluniverse-literature-deep-research-matt-grain
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-literature-deep-research
Source: https://github.com/matt-grain/pharma-catalyst/tree/main/.claude/skills/tooluniverse-literature-deep-research
Command: npx skills add https://github.com/matt-grain/pharma-catalyst --skill tooluniverse-literature-deep-research-matt-grain

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve? Manual literature reviews are slow, inconsistent, and often miss naming collisions or weak evidence. This Skill automates systematic literature research with subject disambiguation, citation network expansion, and evidence grading so every claim in the final report is traceable to a source. ## Core Features & Use Cases - Subject Disambiguation: Resolves identifiers (UniProt, Ensembl, ChEMBL, DrugBank) and detects naming collisions before searching, with domain-specific handling for genes, drugs, diseases, and general academic topics. - Systematic Search with Evidence Grading: Combines high-precision seed queries, citation network expansion, and collision-filtered broad queries across PubMed, ArXiv, Semantic Scholar, OpenAlex, and more; every claim is graded T1 (mechanistic) through T4 (mention). - Structured Deliverables: Produces a 15-section report with integrated biological model, testable hypotheses, and a JSON/CSV bibliography, plus a fast factoid mode for single-question verification. - Use Case: Ask "What does the literature say about ATP6V1A?" and receive a comprehensive report covering protein architecture, expression, disease links, research themes, and prioritized testable hypotheses with evidence grades. ## Quick Start Ask the agent to conduct a deep literature review on a gene, drug, disease, or research topic of your choice.

Frequently Asked Questions about tooluniverse-literature-deep-research

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run a deep literature review on a gene or protein target?▼

Provide the gene symbol or protein name and the skill resolves identifiers via UniProt, Ensembl, and MyGene, checks for naming collisions, then searches PubMed and citation networks. The output is a 15-section report with evidence-graded claims and a JSON bibliography.

What literature databases does this research workflow search?▼

It searches PubMed, PMC, Europe PMC, ArXiv, DBLP, Semantic Scholar, OpenAlex, Crossref, CORE, DOAJ, and preprint servers like bioRxiv and medRxiv. Citation expansion uses PubMed, Europe PMC, OpenCitations, and Semantic Scholar recommendations.

How does evidence grading work in literature synthesis?▼

Every claim is labeled T1 through T4: T1 for mechanistic or direct experimental evidence, T2 for functional studies, T3 for associations or correlations, and T4 for reviews or mentions. Grades appear inline with citations and are summarized per research theme.

Can it handle non-biomedical topics like machine learning papers?▼

Yes, general academic topics skip all bio annotation tools and search ArXiv, DBLP, Semantic Scholar, and OpenAlex directly. Cross-domain queries like graph neural networks for drug discovery resolve each domain component separately and merge results.

What happens when a literature search tool fails or is unavailable?▼

The workflow retries twice with backoff, then switches to a documented fallback chain, such as Europe PMC citations instead of PubMed cited-by, or HPA expression instead of GTEx. Unavailable data is marked in the report rather than omitted silently.

When should I use factoid mode instead of a full report?▼

Use factoid mode for single concrete questions like verifying which antibiotic a strain was evolved to resist. It returns a one-page fact-check report with a direct answer, evidence grade, and sources instead of the full 15-section deep-research report.