# GeneFoundry

Biomedical data for your AI tools. One MCP connection.

22 catalog-listed biomedical MCP servers; 285 listed tools.
Hosted endpoint: https://genefoundry.org/mcp
Browser sign-in required. Research use only. Not clinical decision support.
Catalog inventory is not a measurement of live availability. Client guides state their verification status.

- [GeneFoundry — Biomedical data for your AI tools](https://genefoundry.org/): Explore biomedical sources, review example research workflows, and connect your MCP client to the GeneFoundry gateway.
- [Biomedical data sources | GeneFoundry](https://genefoundry.org/sources/): Find biomedical sources by research task, identifier, or category. Review each source’s tools, documentation and limitations.
- [Connect your MCP client | GeneFoundry](https://genefoundry.org/connect/): Choose your AI client, review its documentation, and connect to GeneFoundry with browser sign-in. Check the setup verification status before use.
- [Research workflows | GeneFoundry](https://genefoundry.org/workflows/): Tested research workflows show how biomedical sources can contribute different kinds of evidence. Each step links to its source and limitations.
- [PubTator3 MCP tools | GeneFoundry](https://genefoundry.org/sources/pubtator/): Search biomedical literature and inspect machine-annotated entities and relations from PubTator3.
- [gnomAD MCP tools | GeneFoundry](https://genefoundry.org/sources/gnomad/): Explore population variation, gene constraint and coverage through the listed gnomAD integration.
- [Orphadata MCP tools | GeneFoundry](https://genefoundry.org/sources/orphanet/): Resolve rare disease concepts and explore Orphadata nomenclature, classifications and associations.
- [ClinGen MCP tools | GeneFoundry](https://genefoundry.org/sources/clingen/): Review ClinGen gene–disease validity, dosage, actionability and expert-panel evidence as distinct curation domains.
- [Human Phenotype Ontology MCP tools | GeneFoundry](https://genefoundry.org/sources/hpo/): Resolve phenotype terminology and explore the Human Phenotype Ontology hierarchy and curated associations.
- [MaveDB MCP tools | GeneFoundry](https://genefoundry.org/sources/mavedb/): Find multiplexed variant-effect experiments and inspect scores with their assay and calibration context.
- [UniProt MCP tools | GeneFoundry](https://genefoundry.org/sources/uniprot/): Explore protein function, features and cross-references through the UniProt integration.
- [MGI MCP tools | GeneFoundry](https://genefoundry.org/sources/mgi/): Explore mouse genes, alleles and phenotypes from Mouse Genome Informatics.
- [GeneReviews MCP tools | GeneFoundry](https://genefoundry.org/sources/genereviews/): Find expert-authored GeneReviews chapters and review passages in their chapter context.
- [Mondo MCP tools | GeneFoundry](https://genefoundry.org/sources/mondo/): Resolve disease terminology and inspect Mondo hierarchy and cross-ontology mappings.
- [ClinPGx MCP tools | GeneFoundry](https://genefoundry.org/sources/clinpgx/): Search curated pharmacogenomics datasets, gene-drug clinical annotations, CPIC and PharmGKB dosing guidelines, and variant-level drug responses.
- [GenCC MCP tools | GeneFoundry](https://genefoundry.org/sources/gencc/): Compare submitted gene–disease validity assertions in the Gene Curation Coalition resource.
- [MetaDome MCP tools | GeneFoundry](https://genefoundry.org/sources/metadome/): Explore protein tolerance landscapes and domain context for a resolved MetaDome transcript.
- [STRING MCP tools | GeneFoundry](https://genefoundry.org/sources/stringdb/): Explore STRING protein association networks and their supporting evidence channels.
- [GTEx Portal MCP tools | GeneFoundry](https://genefoundry.org/sources/gtex/): Explore tissue-level expression and regulatory associations in open-access GTEx Portal data.
- [HGNC MCP tools | GeneFoundry](https://genefoundry.org/sources/hgnc/): Resolve approved human gene symbols, aliases and cross-references using HGNC nomenclature.
- [PanelApp MCP tools | GeneFoundry](https://genefoundry.org/sources/panelapp/): Explore curated gene panels from Genomics England and PanelApp Australia.
- [AutoPVS1 MCP tools | GeneFoundry](https://genefoundry.org/sources/autopvs1/): Inspect AutoPVS1 loss-of-function evidence for sequence variants and copy-number changes.
- [SpliceAI Lookup MCP tools | GeneFoundry](https://genefoundry.org/sources/spliceai/): Inspect predicted splice effects through SpliceAI Lookup, with model and consequence context.
- [Ensembl VEP MCP tools | GeneFoundry](https://genefoundry.org/sources/vep/): Annotate sequence variants and inspect transcript consequences through Ensembl VEP.
- [ClinVar MCP tools | GeneFoundry](https://genefoundry.org/sources/clinvar/): Review submitted variant classifications, review status and condition context from ClinVar.
- [LitVar2 MCP tools | GeneFoundry](https://genefoundry.org/sources/litvar/): Find publications associated with genetic variants in NCBI LitVar2.
- [Connect Claude in your browser to GeneFoundry](https://genefoundry.org/connect/claude-ai/): Add GeneFoundry as a custom connector in Claude, then enable it in your conversation.
- [Connect ChatGPT in your browser to GeneFoundry](https://genefoundry.org/connect/chatgpt/): Connect GeneFoundry through ChatGPT’s custom MCP interface and select it when you ask a question.
- [Connect Claude Code to GeneFoundry](https://genefoundry.org/connect/claude-code/): Add the HTTP server from your terminal, then authenticate inside Claude Code.
- [Connect Codex CLI to GeneFoundry](https://genefoundry.org/connect/codex/): Register the remote server in Codex CLI and complete its OAuth login.
- [Connect Cursor to GeneFoundry](https://genefoundry.org/connect/cursor/): Add the GeneFoundry URL to Cursor’s MCP configuration.
- [Connect Gemini CLI to GeneFoundry](https://genefoundry.org/connect/gemini/): Configure GeneFoundry as a Streamable HTTP server in Gemini CLI.
- [Connect VS Code to GeneFoundry](https://genefoundry.org/connect/vscode/): Add a remote HTTP MCP server to VS Code and use it in agent chat.
- [What do gnomAD and ClinVar show for HNF1B? | GeneFoundry](https://genefoundry.org/workflows/variant-evidence/): One question brings together gene constraint and five source-linked variant records.
- [Which genes link renal cysts and diabetes? | GeneFoundry](https://genefoundry.org/workflows/phenotype-rare-disease/): Two phenotype searches found 13 shared genes. A ClinGen lookup added curated evidence for HNF1B.
- [What does CFTR p.Phe508del change? | GeneFoundry](https://genefoundry.org/workflows/variant-annotation/): Normalize an allele, compare transcript consequences and separate VEP annotation from ClinVar classification.
- [What do three studies show about HNF1B in kidney development? | GeneFoundry](https://genefoundry.org/workflows/literature-review/): A focused literature search turns three primary-study abstracts into a comparison of models, mechanisms and findings.
- [Draft a source-backed HNF1B gene summary | GeneFoundry](https://genefoundry.org/workflows/report-summary/): GeneReviews passages and ClinGen curation become a concise report draft that separates HNF1B-related disease from the broader 17q12 deletion syndrome.
- [How strong is the MYH7 link to different heart and muscle diseases? | GeneFoundry](https://genefoundry.org/workflows/gene-validity/): Compare five ClinGen relationships with GenCC assertions without turning one definitive association into a claim about every condition.
- [What evidence supports HNF1B p.Arg177Ter—and what is still missing? | GeneFoundry](https://genefoundry.org/workflows/acmg-evidence/): Build an ACMG/AMP research worksheet from an exact allele, a PVS1 suggestion and an unsuccessful population-frequency lookup.
- [Which Pax2 mouse models have kidney phenotypes? | GeneFoundry](https://genefoundry.org/workflows/animal-models/): Find annotated renal phenotypes, then keep the allele, genotype and genetic background together.
- [Where are HNF1B, PAX2 and GATA3 expressed? | GeneFoundry](https://genefoundry.org/workflows/tissue-expression/): Compare three genes across adult kidney cortex, kidney medulla and pancreas in GTEx.
- [About GeneFoundry](https://genefoundry.org/about/): How the GeneFoundry gateway connects MCP clients to biomedical source tools, how the project is maintained, and where to report an issue.
- [Research limitations | GeneFoundry](https://genefoundry.org/limitations/): Understand source coverage, release differences, tool availability and the limits of AI-assisted biomedical research before using GeneFoundry.
- [Imprint | GeneFoundry](https://genefoundry.org/imprint/): Legal notice and provider contact information for GeneFoundry, in English and German.