Ncbi Python Packages

eutils

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

gget

🧬 gget enables efficient querying of genomic reference databases

genomepy

genes and genomes at your fingertips

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.

pubmed-search-mcp

🔬 Professional MCP server for biomedical literature research — 40 tools, multi-source search (PubMed, Europe PMC, CORE, OpenAlex), full-text access, citation networks, PICO analysis, and more

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

taxadb

:hatching_chick: locally query the ncbi taxonomy

omicsmeta

Automated harmonization of public omics metadata

pmidcite

Turbocharge a PubMed literature search using citation data from the NIH

multitax

A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

clinvar-this

ClinVar Submission API Made Easy

elastic-blast

ElasticBLAST runs BLAST searches faster by distributing its work to multiple cloud instances. This allows larger numbers of queries to be searched in less time compared to BLAST+ on a single host. Use of the cloud facilitates collaboration, sharing of results, datasets and pipelines on a common platform. The National Center for Biotechnology Information ([NCBI](https://www.ncbi.nlm.nih.gov)), part of the National Library of Medicine at the NIH, developed and maintains ElasticBLAST.

medirect

multiprocessed ncbi edirect

pypubmed

Toolkits for NCBI Pubmed

http-stream-xml

Parse XML in HTTP response on the fly, by chunks - for example NCBI (PubMed) Entrez.

taxonomy-ranks

To get taxonomy ranks information with ETE3 from NCBI Taxonomy database.

ncbitax2lin

A tool that converts NCBI taxonomy dump into lineages

ncbi-submit

A tool to prepare files and run/monitor programmatic submissions to NCBI

taxidtools

A Python Toolkit for Taxonomy

orthoevol

This package aids in the analysis of orthologous genes.

pyncbi

Simple API for Python Integration with NCBI GEO Database

bioinformatics-mcp-server

MCP server for bioinformatics data — genes, proteins, PubMed, ClinVar and sequences via NCBI & UniProt (free, no API key)

genome-collector

Easily download and store taxID genomes from NCBI

enigmadatabase

NCBI DNA Database Builder and Dataset Loader for ML pipelines (Enigma2).