Pubmed Python Packages

data-aggregator-mcp

Unified research-data acquisition MCP — search & fetch datasets across Zenodo, DataCite, NCBI omics (GEO/SRA/BioProject), and literature (PubMed/OpenAIRE) behind one normalized model.

biomcp-python

BioMCP: Biomedical Model Context Protocol

local-deep-research

~95% on SimpleQA (e.g. Qwen3.6-27B on a 3090). Supports all local and cloud LLMs (llama.cpp, Ollama, Google, ...). 10+ search engines - arXiv, PubMed, your private documents. Everything Local & Encrypted.

biomcp-cli

BioMCP: Biomedical Model Context Protocol

pubmed-search-mcp

MCP SDK v2 server for PubMed and multi-source biomedical research, with resilient search, full text, citations, and tenant-safe deployment.

sci-etl-core

Async-first, domain-agnostic Python toolkit for mining scientific literature: LLM-powered ETL pipelines with pluggable extractors, parsers, exporters, and resumable state.

radiowriter

Search PubMed, screen the results and write a Radiopaedia article from them. Journal quartiles from SCImago and open access from Unpaywall. Unofficial.

paperscraper

A bibliometrics tool for publication metadata (pubmed, arxiv, medrxiv, biorxiv, chemrxiv) and citation analyses

nalaf

NLP framework in python for entity recognition and relationship extraction

pubmed-downloader

Automate downloading and processing PubMed in bulk

find-research-papers-mcp

MCP server for scientific grounding: search arXiv, OpenAlex, Crossref, Semantic Scholar, PubMed — references/citations from paywalled journals via public metadata

citevahti

Run unit tests on your manuscript. Check every manuscript claim against its cited evidence. Human-first, AI-second, Zotero-audited, local-first.

nature-academic-search

Academic Paper Search：中文科研用户的 Codex / Claude Code / DeepSeek Harness Skill + MCP；跨 CrossRef、PubMed、arXiv、OpenAlex、Europe PMC 检索去重，支持 MeSH、引用核验、引文图谱、试验检索与审计导出。

check-your-advisor

选导师前查课题组用的。输入导师名字，从 PubMed 和 OpenAlex 找出导师的论文，算出学生多久能发第一篇一作、一作主要给了谁、一般待几年，生成中英文报告。什么学科都能查。 For checking a PhD advisor's lab before you join. It pulls their papers from PubMed and OpenAlex and works out how long students wait for a first-author paper, who gets them, and how long people stay. Any field; reports in Chinese and English.

pmidcite

Get citation counts for a PubMed paper from the command line

pmcgrab

A PMC ID in. Clean, loss-aware article JSON out. Parse PubMed Central and JATS XML for biomedical AI, RAG, search, and literature pipelines.

bibaudit

Deterministic, field-level verification of bibliographies against Crossref, DataCite, PubMed, Europe PMC and Open Library. No language model in the verdict path.

bmlib

Shared Python library for biomedical literature tools — LLM abstraction, quality assessment, transparency analysis, full-text retrieval, publication ingestion, and database utilities.

findpapers

Findpapers: A tool for helping researchers who are looking for related works

bibtools-pkg

Fetch papers and metadata.

onecite

📚 Only Cite what you can verify

biolab-mcp

Hash-chained MCP server for auditable biological database queries — PubMed, Europe PMC, ClinicalTrials.gov, bioRxiv/medRxiv. Live, free to use, zero install.

pypubmed

Toolkits for NCBI Pubmed

okf-loremaster

Multi-agentic biomedical literature evidence extraction, curation, and summarization from PubMed/PMC in Open Knowledge Format (OKF) for downstream machine learning, feature selection, and agentic applications.