literature-mining

name	literature-mining
description	Systematic literature mining and evidence synthesis for biopharma research. Automates literature search, screening, data extraction, and synthesis. Use when users ask for literature reviews, evidence synthesis, publication analysis, or systematic searches on a biomedical topic.
user-invocable	false

Literature Mining

Automated literature search, screening, and evidence synthesis for biopharma intelligence.

Data Sources

Gosset MCP Tools

• gosset_agent(prompt) — Deep research with literature synthesis capabilities
• find_drugs(query) — Context on drugs and mechanisms mentioned in literature
• find_trials(query) — Link publications to clinical trials

PubMed / Entrez (Free, via BioPython)

from Bio import Entrez
Entrez.email = "[e-mail]"

# Search PubMed
handle = Entrez.esearch(db="pubmed", term="CAR-T solid tumors", retmax=100, sort="date")
record = Entrez.read(handle)
id_list = record["IdList"]

# Fetch article details
handle = Entrez.efetch(db="pubmed", id=id_list, rettype="xml")
records = Entrez.read(handle)

for article in records['PubmedArticle']:
    medline = article['MedlineCitation']
    title = medline['Article']['ArticleTitle']
    # Extract: authors, journal, year, abstract, MeSH terms, etc.

Europe PMC (Free, no key)

import requests

# Full-text search with citation counts
r = requests.get("https://www.ebi.ac.uk/europepmc/webservices/rest/search", params={
    "query": "CAR-T solid tumors",
    "resultType": "core",
    "pageSize": 25,
    "sort": "CITED desc"
})

Web Search (supplementary)

• bioRxiv / medRxiv for preprints
• Google Scholar for citation analysis
• Conference abstract databases (ASCO, AACR, ASH, ESMO, etc.)

When to Use

• Systematic literature review on a therapeutic topic
• Evidence synthesis for due diligence
• Publication trend analysis (emerging targets, mechanisms)
• KOL identification through authorship analysis
• Competitive publication monitoring

Workflow

Step 1: Define Search Strategy

Clarify with the user:

• PICO framework: Population, Intervention, Comparator, Outcomes
• Scope: Therapeutic area, mechanism, time range
• Depth: Quick scan (10-20 papers) vs. systematic review (comprehensive)

Step 2: Execute Search

Quick Literature Scan:

gosset_agent(prompt="Find the 10 most important recent publications on [topic]. Focus on clinical data, mechanism of action studies, and review articles. Provide title, authors, journal, year, and key findings for each.")

Systematic Search:

gosset_agent(prompt="Perform a systematic literature search on [topic] using PICO: P=[population], I=[intervention], C=[comparator], O=[outcomes]. Search PubMed, identify relevant studies, and extract key data.")

Step 3: Data Extraction

For each relevant publication, extract:

Field	Description
Citation	Authors, title, journal, year
Study type	RCT, observational, meta-analysis, review
Population	N, demographics, disease stage
Intervention	Drug, dose, schedule
Comparator	Placebo, active comparator, SOC
Key endpoints	Primary and secondary endpoints
Key results	Effect sizes, p-values, confidence intervals
Safety	AE rates, SAEs, discontinuations
Conclusions	Author conclusions and implications

Step 4: Evidence Synthesis

Publication Landscape:

• Volume of publications over time (growing/declining interest)
• Key journals and conferences
• Authorship network and KOL identification

Evidence Quality:

• Study design hierarchy (meta-analysis > RCT > observational > case report)
• Sample sizes and statistical rigor
• Consistency across studies
• Risk of bias assessment

Key Findings Synthesis:

• Convergent evidence across studies
• Contradictory findings and potential explanations
• Evidence gaps and unanswered questions

Step 5: Report

1. Executive Summary — Key findings in 3-5 bullet points
2. Search Strategy — Terms, databases, inclusion/exclusion criteria
3. Evidence Map — Table of included studies with extracted data
4. Synthesis — Integrated findings by theme
5. Evidence Gaps — What remains unknown
6. Implications — Relevance for the user's specific question/decision