"Exploration of the term '.core' and its references" matching MCP servers:

Enables users to manage and navigate nf-core bioinformatics pipeline repositories, allowing list, search, and explore operations on pipeline configurations, workflows, and modules.

Enables AI agents to resolve scientific (Latin binomial) names to Open Tree of Life taxon IDs, retrieve full taxonomic details, synonyms, and ancestor lineages, and find the most recent common ancestor of up to 10 taxa within the synthetic tree of life. Runs keylessly over a hosted gateway endpoint or locally via npx.

Enables AI agents to resolve and cross-reference biological entities such as genes, proteins, and aliases across authoritative databases like HGNC, NCBI Entrez, and UniProt, with confidence scores and source citations.

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.

MCP server that provides tools for querying the Human Phenotype Ontology (HPO) including term lookup, hierarchy exploration, cross-ontology mappings, and gene-phenotype-disease associations, all grounded in a local SQLite database for fast offline lookups.

Enables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.

Enables AI agents and applications to search, retrieve, and analyze chemical compounds, substances, and bioassays from PubChem's vast chemical information database through comprehensive tools for chemical research and discovery.

A stateless, deterministic Bio-Robotics Core Engine converting biological data (UniProt API) to G-code.

A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

Enables AI assistants to query genetic variant data, gene constraints, and population genetics information from the gnomAD (Genome Aggregation Database) through its GraphQL API. Supports searching for genes and variants, retrieving constraint scores, analyzing population frequencies, and accessing genomic coverage data.

A Model Context Protocol server that lets you drive PyMOL with natural language, enabling structure loading, analytical views, measurements, and protein exploration through AI assistants.

Enables read-only exploration of Copick cryo-ET projects and discovery/validation of copick CLI commands for building processing pipelines.

Official public, read-only Helena Bioinformatics MCP for source-cited answers about the company and its published products.

Enables searching a manually curated database of stable macromolecular protein complexes by protein or complex name, gene, GO term, or biological process, and fetching individual records by accession to retrieve subunits with UniProt identifiers, biological roles, and stoichiometry. Complements UniProt, IntAct, and STRING, and can be used keyless over a hosted gateway endpoint or run locally over stdio.

Enables querying and browsing ontologies from the EBI Ontology Lookup Service, including searching for terms, retrieving term details, and navigating ontology hierarchies via natural language.

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 NCBI genome assemblies, gene details with cross-references, and taxonomy trees with per-node assembly and gene counts, providing structured answers about genomes, genes, and taxonomy.

Enables interaction with AnnData objects via the Model Context Protocol, allowing querying and manipulation of annotated data matrices for single-cell genomics.

An MCP server that wraps R scripts for microbiome and amplicon (16S/ITS) analysis, providing tools for alpha/beta diversity, differential abundance, networks, and more, with PNG/PDF outputs.

Enables term search, class lookup, and cross-ontology mappings across NCBO BioPortal's ~1,300 biomedical ontologies.