---
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


---
Source attribution: a5c-ai
Original project: https://github.com/a5c-ai/babysitter
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Dave AI.

## Upstream license notice

MIT License

Copyright (c) 2026 Gabriel Moreira

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Dave AI resource metadata

Creator / publisher: a5c-ai
Original project: https://github.com/a5c-ai/babysitter
Attribution basis: Upstream repository explicitly recorded in package mirror path

Fields of work: Data & Analytics, Education & Research, Healthcare & Life Sciences
Roles: Business Intelligence Analyst, Clinical Research, Data Analyst, Medical Writer, Researcher
Specialties: API
Tools: Biopython, Ncbi E Utilities, Pymed
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: 91c3c7bd97149861bda8f7b40f23639175553064c719c1dc4ea631093d9c2540