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MCP servers by berntpopp
berntpopp publishes 19 live MCP servers on GitHub. Listed by trust score; the score reflects each repository's own health, security checks, and documentation.
Genefoundry Router
A thin FastMCP 3.x aggregator federating the GeneFoundry -link MCP fleet behind one Streamable-HTTP endpoint (collision-free namespacing, BM25 tool-search, pluggable auth).
Stringdb Link
MCP server for STRING v12: protein–protein association networks, interaction partners, and functional enrichment analysis — as typed tools for LLM agents.
Mgi Link
MCP server for MGI (Mouse Genome Informatics): mouse gene, allele, mutation and phenotype data — the MGI marker page as structured tools, served from a local SQLite index.
Genefoundry
A modular registry for trustworthy, evidence-based genomic analysis powered by Model Context Protocols (MCPs). Bridging AI and clinical genomics with traceable, validated data ret…
Hpo Link
MCP server for the Human Phenotype Ontology (HPO): phenotype term lookup, the is_a hierarchy, cross-ontology mapping, and gene–phenotype–disease associations from HPO and HPOA.
Gtex Link
MCP server for the GTEx Portal: tissue-specific gene expression — median and per-sample TPM, top expressed genes per tissue, and gene/transcript annotation — as typed tools for LL…
Genereviews Link
MCP server for GeneReviews: the expert-authored, peer-reviewed gene–disease chapters on NCBI Bookshelf, served as a searchable corpus of individually citable passages.
Autopvs1 Link
MCP server for AutoPVS1: automated ACMG PVS1 loss-of-function evidence for sequence variants and copy-number variants — variant interpretation as typed tools for LLM agents.
Litvar Link
MCP server for NCBI LitVar2: search the biomedical literature by genetic variant — the index linking variants to the publications that mention them, as typed tools for LLM agents.
Pubtator Link
MCP server for NCBI PubTator3: biomedical literature search with gene, variant, disease and chemical entity annotation — returns compact, citable passages instead of raw BioC.
Gnomad Link
MCP server for gnomAD (Genome Aggregation Database): variant allele frequencies, gene constraint, coverage, structural and mitochondrial variants, and liftover — as typed tools fo…
Mavedb Link
MCP server for MaveDB: quantitative variant-effect scores from Multiplexed Assays of Variant Effect (MAVE) and deep mutational scanning — functional evidence as typed tools for LL…
Mondo Link
MCP server for the Mondo Disease Ontology: disease term lookup, the is_a hierarchy, and cross-ontology mapping across OMIM, Orphanet, DOID, NCIT, UMLS and MeSH.
Uniprot Link
MCP server for UniProt: protein function, sequence, features and cross-references over the UniProt SPARQL endpoint — intent-named tools plus a guarded raw-SPARQL escape hatch.
Spliceailookup Link
MCP server for SpliceAI Lookup (Broad Institute): SpliceAI, Pangolin and SpliceAI-10k splice-impact predictions for variants, plus an Ensembl VEP-backed variant resolver.
Clingen Link
MCP server for ClinGen (Clinical Genome Resource): gene–disease validity, dosage sensitivity, clinical actionability, and expert-panel variant pathogenicity (ERepo) — as typed too…
Gencc Link
MCP server for GenCC (Gene Curation Coalition): harmonized gene–disease validity classifications across member submitters, with consensus and conflict detection per gene–disease p…
Metadome Link
MCP server for MetaDome: per-position missense tolerance (dN/dS) landscapes for human transcripts, Pfam domains, meta-domain homolog aggregation, and gnomAD/ClinVar per-position c…
Orphanet Link
MCP server for Orphanet (Orphadata): rare-disease nomenclature, gene–disease associations, phenotypes, epidemiology and cross-references, from the Orphadata scientific knowledge f…