"Sublime Text" matching MCP servers:

A bridge connecting AI agents to NCBI's PubMed database through the Model Context Protocol, enabling seamless searching, retrieval, and analysis of biomedical literature and data.

Provides seamless access to UniProtKB protein database, enabling queries for protein entries, sequences, Gene Ontology annotations, full-text search, and ID mapping across 200+ database types.

Enables AI agents to search EBI BioSamples metadata for biological samples such as cell lines, tissues, and organisms by free-text keyword, and to fetch individual records by accession to retrieve taxId, organism, and characteristics like tissue, sex, and cell type. It can run as a hosted gateway endpoint or locally over stdio via npx.

Enables AI agents to resolve genes, diseases, chemicals, variants and species to normalized ids, search ~36M PubMed abstracts and PMC full texts by free text or entity, and retrieve the machine-extracted relations between them with the supporting sentences and PMIDs. Supports auditing individual relations with full evidence passages and pulling per-article entity annotations with character offsets.

MCP server for querying gene annotations, full-text gene search, and species taxonomy via MyGene.info. Enables AI agents to access gene data through natural language questions.

Enables users to look up yeast genes/loci, search genes and alleles by free text, and retrieve Gene Ontology annotations from the Saccharomyces Genome Database.

Resolves free-text condition and disease strings — trial-registry condition fields, drug-label indications, hand-typed wording — onto the Mondo Disease Ontology, returning the best term id and label along with a trustworthy match-quality label (exact label/synonym, broader, narrower, fuzzy, or no-match) plus cross-ontology xrefs. Optionally expands a resolved term to all of its descendant ids for building subtype-inclusive registry filters.

Enables querying and retrieving experimental protein structures from the RCSB Protein Data Bank, including text search, full entry records, polymer entities, ligands, and assemblies.

Enables searching and retrieving expert-curated biochemical reactions from the Rhea database by compound name, ChEBI id, EC number, keyword, or Rhea id, returning balanced plain-text reaction equations alongside EC, ChEBI, UniProt, and PubMed cross-references.