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Biomedical literature mining using PubMed/MEDLINE for systematic review support
--- name: pubmed-literature-miner description: Biomedical literature mining using PubMed/MEDLINE for systematic review support allowed-tools: - Bash - Read - Write - Edit - Glob - Grep - WebFetch metadata: specialization: scientific-discovery domain: science category: literature-knowledge phase: 6 graph: domains: [domain:scientific-discovery] specializations: [specialization:scientific-research-methods] skillAreas: [skill-area:data-analysis, skill-area:statistical-analysis, skill-area:deep-web-research] workflows: [workflow:experiment-design, workflow:peer-review-cycle] roles: [role:research-engineer, role:computational-scientist] --- # PubMed Literature Miner ## Purpose Provides biomedical literature mining capabilities using PubMed/MEDLINE for systematic review support and PICO framework analysis. ## Capabilities - MeSH term-based search - PICO element extraction - Abstract screening automation - Citation deduplication - PRISMA flow diagram data generation - Full-text retrieval coordination ## Usage Guidelines 1. **MeSH Terms**: Use controlled vocabulary for precise searches 2. **PICO Framework**: Structure searches around population, intervention, comparison, outcome 3. **Screening**: Apply inclusion/exclusion criteria systematically 4. **PRISMA Compliance**: Generate required flow diagram data ## Tools/Libraries - Biopython - PyMed - NCBI E-utilities--- name: pubmed-literature-miner description: Biomedical literature mining using PubMed/MEDLINE for systematic review support allowed-tools: - Bash - Read - Write - Edit - Glob - Grep - WebFetch metadata: specialization: scientific-discovery domain: science category: literature-knowledge phase: 6 graph: domains: [domain:scientific-discovery] specializations: [specialization:scientific-research-methods] skillAreas: [skill-area:data-analysis, skill-area:statistical-analysis, skill-area:deep-web-research] workflows: [workflow:experiment-design, workflow:peer-review-cycle] roles: [role:research-engineer, role:computational-scientist] --- # PubMed Literature Miner ## Purpose Provides biomedical literature mining capabilities using PubMed/MEDLINE for systematic review support and PICO framework analysis. ## Capabilities - MeSH term-based search - PICO element extraction - Abstract screening automation - Citation deduplication - PRISMA flow diagram data generation - Full-text retrieval coordination ## Usage Guidelines 1. **MeSH Terms**: Use controlled vocabulary for precise searches 2. **PICO Framework**: Structure searches around population, intervention, comparison, outcome 3. **Screening**: Apply inclusion/exclusion criteria systematically 4. **PRISMA Compliance**: Generate required flow diagram data ## Tools/Libraries - Biopython - PyMed - NCBI E-utilities
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