"Using Knowledge Base Files for Drafting, Writing, and Editing Documents" matching MCP servers:

This server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.

Enables editing and querying of Gene Ontology Causal Activity Models (GO-CAMs) through the Barista API. Supports model creation, individual and fact management, evidence addition, and causal pathway construction for biological knowledge representation.

Enables natural language control of UCSF ChimeraX for protein structure visualization, editing, and analysis through MCP clients.

Enables AI agents to search, filter, download files, and generate reports from the IGVF Data Portal using natural language commands.

Agent-callable canine genomics API providing breed-stratified allele frequencies, pathogenicity predictions, and variant-gene-breed-disease knowledge graph for dog DNA.

Enables AI assistants to perform quality control analysis on high-throughput sequencing data using FastQC and MultiQC. It supports single-file and batch processing of FASTQ/FASTA files and generates comprehensive, interactive summary reports.

Enables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.

Enables querying HERB 2.0's Traditional Chinese Medicine knowledge base for herbs, ingredients, gene targets, diseases, PubMed-cited papers, and GEO transcriptomic experiments, with each relationship tagged by evidence tier.

Provides access to UniProt protein sequence and function knowledge base, enabling search and retrieval of protein entries, proteomes, taxonomy, and feature annotations.

Enables AI assistants to query VCF files through MCP tools that summarize variants, identify pathogenic and carrier variants, interpret pharmacogenomic results, and determine APOE status, with web app and Claude Desktop support.

Enables natural language interface for single-cell RNA-Seq analysis using Liana. Supports reading/writing scRNA-Seq data, cell-cell communication analysis, and visualization through circle plots and dotplots.

Enables LLMs and AI agents to search a biomedical knowledge graph for concepts and study variables, traverse semantic relationships, and look up BioData Catalyst PIC-SURE paths for cohort building.

MCP server for querying BV-BRC biological data, submitting analysis jobs (assembly, annotation, BLAST, etc.), and managing workspace files via natural language.

Enables LLMs and AI agents to query a biomedical knowledge graph stored in RedisGraph, with tools for concept search, synonym enrichment, and study variable discovery through semantic relationships.

A Model Control Protocol implementation for SAMtools, providing a standardized interface for working with SAM/BAM/CRAM files.

Enables in-chat scientific viewers for molecular structures, sequence alignments, and slide images, plus data tools for searching structures, fetching sequences, aligning them, and drafting NGS analysis plans.

Enables querying and retrieving cell line records from the Cellosaurus knowledge base via its REST API, including searching, fetching by accession, and accessing release information.

An MCP server that grounds protein research in the UniProt SPARQL endpoint, providing tools for querying proteins, sequences, variants, diseases, and more via intent-named tools and raw SPARQL.

Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.

Grounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset, enabling resolution of gene symbols and IDs to canonical HGNC identifiers, plus cross-references and batch operations.