"A database for genomic and biological data (Ensembl)" matching MCP tools:

• get_protein

  Protein Atlas

  Get a trimmed Human Protein Atlas profile for one protein by Ensembl gene id (e.g. "ENSG00000146648"): gene, description, protein class, biological process, molecular function, RNA tissue specificity/distribution, subcellular location, and disease involvement. Use search_genes to find the Ensembl id. Keyless.

  Connector

• get_domain

  TunnelMind Data API

  Returns the complete surveillance intelligence record for a domain name. If the domain is in TunnelMind's tracker database (80,000+ entries), the response includes tracker category, risk score, fingerprinting data, cookie persistence, IAB TCF purposes, and the owning corporate entity. If the domain is not in the database, a live probe is automatically run: RDAP registration data, DNS records (MX, SPF, TXT verification tokens), HTTP headers, and CSP third-party actors are fetched fresh from the edge and returned. Use this tool when: - You need to know whether a specific domain tracks users, and how aggressively. - You are researching who owns a domain and what corporate entity controls it. - You want to check HTTP security headers and third-party services embedded in a site. - You are building a risk score for a domain before routing traffic through it. Do NOT use this tool when: - You want to search by keyword or category — use `search` instead. - You want all domains for an entity — use `get_entity` instead. Inputs: - `domain` (path, required): Domain name. Strip `www.` prefix — it is removed automatically. Subdomains are resolved to the parent: `ads.doubleclick.net` → `doubleclick.net`. Examples: `doubleclick.net`, `google-analytics.com`, `intercom.io`. Returns: - Full `DomainRecord`. Free tier returns the domain, category, score, prevalence, and entity name. Pro/enterprise additionally return `tcf_vendor_id`, `tcf_purposes`, `tcf_features`, and `disconnect_cats`. - If the domain is not in the tracker database, `live_lookup: true` is set and RDAP/DNS/HTTP probe results are returned instead of tracker fields. - 404 if the domain cannot be found via live probe either (unknown TLD, unreachable). Cost: - Free tier: included in 50 req/day limit. Pro/enterprise: included in plan. Latency: - Database hit: typical <100ms, p99 <300ms. - Live probe: typical 2-5s, p99 10s (external DNS/HTTP calls).

  Connector

• vibekit_db_query

  VibeKit

  Run a read-only SQL query against an app's Postgres database and return up to 200 result rows. SELECT only — writes and DDL (INSERT/UPDATE/DELETE/ALTER/DROP/…) are rejected server-side; use vibekit_chat or vibekit_submit_task to have the agent make data or schema changes. Call vibekit_db_schema first to learn the tables. SQL string, max 5000 chars.

  Connector

• biobtree_map

  BioBTree

  Map identifiers between databases. SYNTAX: biobtree_map(terms="ID", chain=">>source>>target") - Chain MUST start with ">>" - Source MUST match input ID type ID TYPE → SOURCE: - ENSG* → >>ensembl - P*/Q*/O* → >>uniprot - CHEMBL* → >>chembl_molecule - GO:* → >>go - MONDO:* → >>mondo - HP:* → >>hpo - HGNC:* or gene symbols → >>hgnc SOME DRUG EXPLORATION PATHS: - >>chembl_molecule>>chembl_target>>uniprot (drug targets) - >>pubchem>>pubchem_activity>>uniprot (bioactivity) - >>gtopdb_ligand>>gtopdb_interaction>>gtopdb>>uniprot (curated pharmacology with affinity data) - >>ensembl>>reactome>>chebi (pathway chemicals - when no direct targets) - Discover more via entry xrefs + EDGES WARNING - GO terms with high xref_count (>100): - Don't map GO → proteins → drugs (too many results) - Instead: search drug class for condition → verify targets this GO term DISEASE GENE PATTERNS: - >>mondo>>gencc>>hgnc (curated) - >>mondo>>clinvar>>hgnc (variant-based) - >>hgnc>>clingen_gene_validity (ClinGen evidence tier), >>hgnc>>clingen_dosage (haploinsufficiency), >>hgnc>>clingen_variant>>clinvar (ACMG, then dbsnp) CANCER / CELL LINE: - >>hgnc>>intogen (cancer driver gene?), >>hgnc>>civic (clinical variant interpretations) - >>uniprot>>cellosaurus (cell lines for a protein/gene) - >>hgnc>>depmap (CRISPR essentiality / target tractability), >>hgnc>>entrez>>depmap_dependency>>cellosaurus (which lines depend on the gene) GENE FUNCTION / LITERATURE: - >>entrez>>generif (cited one-line functional claims; >>generif>>pubmed for citations) DISEASE → DRUG PATTERNS: - >>mesh>>chembl_molecule (MeSH disease/condition → drugs with indications) - >>mondo>>clinical_trials>>chembl_molecule (disease → trial drugs) DISCOVERY APPROACH: - Use biobtree_entry to see xrefs (what's connected) - Use EDGES above to see where each dataset leads - Build chains based on what connections exist for YOUR entity RETURNS: mapped identifiers with dataset and name EDGES (what connects to what): ensembl: uniprot, go, transcript, exon, ortholog, paralog, hgnc, entrez, refseq, bgee, gwas, gencc, antibody, scxa, civic, intogen, hpa, hpa_antibody, pharmgkb_var_annotation, chembl_mechanism, ncrna_disease, ncrna_interaction, ncrna_drug, alliance_disease, gnomad_constraint, drugcentral, panelapp_gene hgnc: ensembl, uniprot, entrez, gencc, pharmgkb_gene, msigdb, clinvar, mim, refseq, alphafold, collectri, gwas, hpo, cellphonedb, civic, intogen, cellosaurus, clingen_gene_validity, clingen_dosage, clingen_variant, depmap, hpa, pharmgkb_var_annotation, chembl_mechanism, ncrna_disease, ncrna_interaction, ncrna_drug, alliance_disease, drugcentral, panelapp_gene, gnomad_constraint, mavedb entrez: ensembl, uniprot, refseq, go, biogrid, pubchem_activity, ctd_gene_interaction, dbsnp, civic, intogen, clingen_dosage, generif, depmap, depmap_dependency, hpa, pharmgkb_var_annotation, orthologentrez, relatedentrez, neighborentrez, mgi, rgd, zfin, wormbase, xenbase, sgd, flybase, gnomad_constraint, drugcentral orthologentrez: entrez # cross-species gene orthologs (NCBI gene_orthologs). >>entrez>>orthologentrez gives ortholog genes (filter species via taxonomy); reliable from model-organism genes (human-gene side currently incomplete) relatedentrez: entrez # related genes (bidirectional): NCBI gene_group (functional gene/pseudogene/readthrough/region) + HGNC gene-family co-members neighborentrez: entrez # genomic neighbors (left/right/overlapping); edge carries distance + side, neighbor strand/position in attrs; filter to genes via [type!="biological-region"] gnomad_constraint: ensembl, entrez, hgnc, transcript # gene LoF constraint (pLI/LOEUF/oe_lof); reach via >>ensembl>>gnomad_constraint drugcentral: chembl_molecule, pubchem, uniprot, ensembl, hgnc, entrez # approved drugs -> targets/MOA + FDA/EMA/PMDA approval; reach via name/INN/InChIKey or compound (chembl_molecule/pubchem >> drugcentral) refseq: ensembl, entrez, taxonomy, ccds, uniprot, mirdb mirdb: refseq transcript: ensembl, exon, ufeature, alphamissense, civic_variant, gnomad_constraint, mavedb uniprot: ensembl, alphafold, interpro, pfam, pdb, ufeature, intact, string, string_interaction, biogrid, biogrid_interaction, chembl_target, go, reactome, rhea, swisslipids, bindingdb, antibody, pubchem_activity, cellphonedb, jaspar, signor, diamond_similarity, esm2_similarity, alphamissense, cellosaurus, hpa, chembl_mechanism, ncrna_interaction, drugcentral, mavedb alphafold: uniprot interpro: uniprot, go, interproparent, interprochild chembl_molecule: mesh, chembl_activity, chembl_target, pubchem, chebi, clinical_trials, chembl_moleculeparent, chembl_moleculechild, chembl_mechanism, ncrna_drug, faers, drugcentral # parent=anhydrous/parent form, child=salt forms chembl_activity: chembl_molecule, chembl_assay, bao chembl_assay: chembl_activity, chembl_target, chembl_document, bao chembl_target: chembl_assay, uniprot, chembl_molecule, chembl_mechanism chembl_mechanism: chembl_molecule, chembl_target, uniprot, hgnc, ensembl # curated drug mechanism-of-action (incl. RNA therapeutics): drug >> chembl_mechanism, target/gene >> chembl_mechanism pubchem: chembl_molecule, chebi, hmdb, pubchem_activity, pubmed, patent_compound, bindingdb, ctd, pharmgkb, ncrna_drug, faers, drugcentral faers: chembl_molecule, pubchem, faers_reaction # openFDA FAERS drug->adverse-event; faers (per-drug master) -> faers_reaction children (PRR), reach via drug name or compound. NOTE co-occurrence not causation faers_reaction: faers # one per (drug,reaction): report_count, prr, serious_count, outcome; most-reported first pubchem_activity: pubchem, ensembl, uniprot chebi: pubchem, rhea, intact swisslipids: uniprot, go, chebi, uberon, cl lipidmaps: chebi, pubchem dbsnp: entrez, clinvar, pharmgkb_variant, alphamissense, spliceai, pharmgkb_var_annotation clinvar: hgnc, mondo, hpo, dbsnp, orphanet, civic_variant, cellosaurus, clingen_variant alphamissense: uniprot, transcript mavedb: uniprot, hgnc, ensembl, transcript # deep-mutational-scanning functional variant scores (ACMG PS3/BS3); reach via gene/protein >> mavedb; per-variant score + hgvs_pro + license # VARIANT-EFFECT SCORES — look up by the variant's OWN key with biobtree_entry(dataset=..), NOT via >>chains: # conservation key "chr:pos" (GRCh38) per-position phyloP / GERP / phastCons (also covers non-missense/splice positions) # gnomad_variant key "chr:pos:ref:alt" (GRCh38) gnomAD v4.1 genomes allele freq (af, grpmax, per-ancestry); also xrefs dbsnp # revel key "chr:pos:ref:alt" (GRCh38) REVEL ensemble missense pathogenicity (0-1, higher = pathogenic) # saprot key "uniprot:protein_variant" SaProt protein-LM variant effect (LLR <=0, lower = more damaging), e.g. P01116:G12D gwas: gwas_study, efo, dbsnp, hgnc, mondo gwas_study: gwas, efo, mondo mondo: gencc, clinvar, efo, mesh, hpo, clinical_trials, antibody, cellxgene, cellxgene_celltype, orphanet, mondoparent, mondochild, gwas, gwas_study, civic, intogen, cellosaurus, doid, mim, ncit, umls, medgen, gard, sctid, icd9, icd10cm, icd10who, icd11, nando, meddra, nord, uberon, ncrna_disease, panelapp_gene # disease cross-refs + disease_has_location anatomy, from the Mondo OBO doid: mondo, alliance_disease, doidparent, doidchild # Disease Ontology (now a full ontology w/ hierarchy); reach MONDO + its disease graph via the mondo<->doid bridge alliance_disease: hgnc, mgi, rgd, zfin, sgd, wormbase, flybase, xenbase, doid, pubmed # cross-species + human gene->disease (Alliance of Genome Resources); gene >> alliance_disease >> doid, or doid >> alliance_disease >> mgi/rgd/... for model-organism genes alliance_phenotype: mgi, rgd, wormbase, xenbase, mp, wbphenotype, xpo, pubmed # model-organism gene -> OBSERVED knockout/mutant phenotypes (distinct from the upheno ontology-translation path). Reach from the model-organism gene directly: mgi/rgd/wormbase/xenbase >> alliance_phenotype >> mp gencc: mondo, hpo, hgnc, ensembl clingen_gene_validity: hgnc, entrez, ensembl, mondo # ClinGen gene-disease validity tier (Definitive..Refuted) + MOI clingen_dosage: entrez, hgnc, ensembl, mondo, mim, pubmed # ClinGen haploinsufficiency/triplosensitivity per gene clingen_variant: clinvar, hgnc, entrez, ensembl, mondo, pubmed # ClinGen VCEP ACMG variant pathogenicity (clinvar bridges to dbsnp) panelapp: panelapp_gene # Genomics England clinical gene panels (per-panel master); panel >> panelapp_gene >> hgnc for the panel's genes panelapp_gene: panelapp, hgnc, ensembl, mim, mondo # one per (panel,gene), green/amber confidence + mode-of-inheritance; a gene's panels via >>hgnc (panelapp_gene) ; the panel's disease via mondo/mim clinical_trials: mondo, chembl_molecule pharmgkb: hgnc, dbsnp, mesh, pharmgkb_gene, pharmgkb_variant, pharmgkb_clinical, pharmgkb_guideline, pharmgkb_pathway pharmgkb_variant: pharmgkb_clinical, hgnc, mesh, dbsnp pharmgkb_gene: hgnc, entrez, ensembl, pharmgkb pharmgkb_clinical: dbsnp, hgnc, mesh, pharmgkb_variant, pharmgkb # pharmgkb = reverse drug→clinical edge (drug >> pharmgkb >> pharmgkb_clinical) pharmgkb_guideline: hgnc, pharmgkb pharmgkb_pathway: hgnc, pharmgkb pharmgkb_var_annotation: hgnc, entrez, ensembl, dbsnp, pubmed # per-publication variant-annotation evidence (finding sentence, PMID, significance, study stats) beneath pharmgkb_clinical; reach via gene or rsID ctd: mesh, ctd_gene_interaction, ctd_disease_association, pubchem ctd_gene_interaction: ctd, entrez, taxonomy, pubmed ctd_disease_association: ctd, mesh, mim, pubmed intact: uniprot, chebi, rnacentral string: uniprot, string_interaction string_interaction: string, uniprot biogrid: entrez, uniprot, refseq, taxonomy bgee: ensembl, uberon, cl, taxonomy, bgee_evidence bgee_evidence: bgee, uberon, cl cellxgene: cl, uberon, mondo, efo, taxonomy cellxgene_celltype: cl, uberon, mondo scxa: cl, uberon, taxonomy, ensembl, scxa_gene_experiment scxa_expression: ensembl, scxa, scxa_gene_experiment scxa_gene_experiment: ensembl, scxa, scxa_expression, cl hpa: ensembl, uniprot, hgnc, entrez, go, uberon, hpa_expression, hpa_pathology, hpa_antibody # Human Protein Atlas gene card: subcellular location (→go), specificity calls, top tissues hpa_expression: hpa, uberon, cellosaurus # per (gene,tissue/cell-line) RNA nTPM + IHC staining; reach genes-in-a-tissue via uberon >> hpa_expression hpa_pathology: hpa # per (gene,cancer) prognostic survival association hpa_antibody: hpa, ensembl # HPA validation antibody (reliability, antigen) rnacentral: uniprot, ensembl, intact, hgnc, refseq, ena, go # go = Rfam-projected GO annotations; rfam_id/rfam_description are attrs on the entry ncrna_disease: hgnc, ensembl, mondo, efo, pubmed # curated ncRNA->disease (LncRNADisease + HMDD); reach from the ncRNA gene ncrna_interaction: hgnc, ensembl, uniprot, pubmed # experimentally-supported ncRNA->protein interactions (NPInter) ncrna_drug: hgnc, ensembl, chembl_molecule, pubchem, pubmed # ncRNA drug-resistance / drug-target (ncRNADrug) reactome: ensembl, uniprot, chebi, go, reactomeparent, reactomechild rhea: chebi, uniprot, go go: ensembl, uniprot, reactome, msigdb, swisslipids, bgee, interpro, goparent, gochild, hpa, rnacentral hpo: clinvar, gencc, mondo, msigdb, orphanet, mim, hmdb, hgnc, hpoparent, hpochild, upheno efo: gwas, mondo, cellxgene, efoparent, efochild, ncrna_disease upheno: hpo, mp, zp, xpo, wbphenotype, fypo, uphenoparent, uphenochild # cross-species phenotype hub. A GENE's model-organism phenotypes are reached THROUGH hpo (genes are NOT linked directly to mp/upheno): >>hgnc>>hpo>>upheno>>mp (mouse), >>hgnc>>hpo>>upheno>>zp (zebrafish), ...>>xpo/wbphenotype/fypo. So gene->human HP phenotypes -> their cross-species equivalents. mp: upheno, mpparent, mpchild, alliance_phenotype # Mammalian Phenotype Ontology (mouse/rat). Reach from a gene via >>hgnc>>hpo>>upheno>>mp (NOT >>hgnc>>mp); observed model phenotypes via alliance_phenotype. zp: upheno, zpparent, zpchild # Zebrafish Phenotype Ontology. Reach from a gene via >>hgnc>>hpo>>upheno>>zp. xpo: upheno, xpoparent, xpochild, alliance_phenotype # Xenopus Phenotype Ontology wbphenotype: upheno, wbphenotypeparent, wbphenotypechild, alliance_phenotype # C. elegans Phenotype Ontology fypo: upheno, fypoparent, fypochild # Fission Yeast Phenotype Ontology uberon: bgee, cellxgene, cellxgene_celltype, swisslipids, uberonparent, uberonchild, hpa, hpa_expression cl: bgee, cellxgene, cellxgene_celltype, scxa, scxa_gene_experiment, clparent, clchild taxonomy: ensembl, uniprot, bgee, biogrid, ctd_gene_interaction, taxparent, taxchild mesh: pharmgkb, ctd, ctd_disease_association, pubchem, mondo, chembl_molecule, meshparent, meshchild eco: ecoparent, ecochild antibody: ensembl, uniprot, mondo, pdb msigdb: hgnc, entrez, go, hpo orphanet: hpo, uniprot, mondo, hgnc, clinvar, mim, mesh mim: clinvar, hpo, mondo, uniprot, ctd_disease_association, panelapp_gene hmdb: pubchem, hpo, chebi, uniprot collectri: hgnc # transcription factor → target gene interactions esm2_similarity: uniprot # protein structural similarity diamond_similarity: uniprot # protein sequence similarity cellphonedb: uniprot, ensembl, hgnc, pubmed # ligand-receptor pairs for cell-cell communication spliceai: hgnc pdb: uniprot, go, interpro, pfam, taxonomy, pubmed fantom5_promoter: ensembl, hgnc, entrez, uniprot, uberon, cl fantom5_enhancer: ensembl, uberon, cl fantom5_gene: ensembl, hgnc, entrez jaspar: uniprot, pubmed, taxonomy encode_ccre: taxonomy bao: chembl_activity, chembl_assay, baoparent, baochild brenda: uniprot, pubmed, brenda_kinetics, brenda_inhibitor brenda_kinetics: brenda brenda_inhibitor: brenda gtopdb: uniprot, hgnc, gtopdb_ligand, gtopdb_interaction # drug targets (GPCRs, ion channels, enzymes) gtopdb_ligand: pubchem, chebi, chembl_molecule, gtopdb_interaction # ligands/drugs with binding data gtopdb_interaction: gtopdb, gtopdb_ligand, pubmed # target-ligand binding with affinity values civic: entrez, ensembl, civic_variant, civic_evidence, civic_assertion # clinical interpretation of cancer variants civic_variant: civic, clinvar, civic_evidence, civic_assertion, transcript civic_evidence: civic_variant, civic, mondo, chembl_molecule, pubmed, clinical_trials civic_assertion: civic_variant, civic, mondo, chembl_molecule intogen: hgnc, entrez, ensembl, mondo, pubmed # cancer driver genes cellosaurus: taxonomy, uniprot, hgnc, mondo, orphanet, clinvar, dbsnp, uberon, cl, chebi, doi, patent, pubmed, depmap_dependency, hpa_expression # cell lines (CVCL) generif: entrez, pubmed # NCBI cited per-gene functional claims (RAG grounding) depmap: entrez, hgnc, ensembl # CRISPR gene essentiality aggregate (cancer dependency / target tractability) depmap_dependency: entrez, cellosaurus # per cell-line gene dependency (effect < -0.5) FILTER SYNTAX: >>dataset[field operator value] OPERATORS: == equals >>dataset[field=="value"] != not equals >>dataset[field!="value"] > greater than >>dataset[field>value] < less than >>dataset[field<value] >= greater or equal >>dataset[field>=value] <= less or equal >>dataset[field<=value] contains string match >>dataset[field.contains("value")] LOGICAL OPERATORS: && AND >>dataset[field1>5 && field2<10] || OR >>dataset[field=="A" || field=="B"] ! NOT >>dataset[!field] or >>dataset[!(field=="value")] TYPE RULES: - FLOAT: use decimal point (70.0 not 70) - INT: no decimal (2 not 2.0) - STRING: quote values ("Pathogenic", "PHASE3") - BOOL: true/false (no quotes) EXAMPLES: >>chembl_molecule[highestDevelopmentPhase==4] # approved drugs >>chembl_molecule[highestDevelopmentPhase>=3] # Phase 3+ >>clinical_trials[phase=="PHASE3"] >>go[type=="biological_process"] >>clinvar[germline_classification=="Pathogenic"] >>reactome[name.contains("signaling")] >>gtopdb[type=="gpcr"] # GPCR targets >>gtopdb[type=="ion_channel"] # ion channel targets >>gtopdb_ligand[approved==true] # approved drugs only >>gtopdb_interaction[endogenous==true] # endogenous ligand interactions

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• ping

  Nordic Financial MCP

  Connectivity check that confirms the Nordic MCP server process is responding. Use this at the start of a session to verify the server is reachable before making other calls. Do not use as a proxy for database health — the server can respond while the Qdrant vector database is temporarily unavailable. To confirm data availability, call search_filings directly. Returns: A greeting string: "Hello {name}! Nordic MCP server is running."

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• delete_deployment

  mcp

  Deletes a deployment and its underlying app VM. Pass the numeric id from list_deployments. IMPORTANT: if the deployment used database:'managed', the managed Postgres VM is NOT deleted (data safety) — this tool returns its id so you can delete_database it when you're done with the data. Cannot be undone.

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• sequence_fetch

  workbench

  Fetch a public DNA/protein record by accession from NCBI Nucleotide, NCBI Protein, UniProt, or Ensembl (e.g. NM_000546, NP_000537, P04637, ENSG00000141510). Only the accession is sent upstream. Use sequence_search first if you only know a gene/organism name, not an accession. For an Ensembl transcript ID this returns spliced cDNA; for a gene ID it returns the full genomic locus (introns included) — Ensembl's own default for each ID type.

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• hgvs_convert

  workbench

  Parse an HGVS "c." variant description (by gene symbol, RefSeq NM_, or Ensembl ENST accession), convert it to genomic (g.) coordinates via a real, live-fetched Ensembl exon/CDS map (transcripts resolved through the bundled MANE RefSeq<->Ensembl crosswalk), apply 3'-rule normalization to any del/dup/ins, and predict the protein (p.) effect where that is safely computable. Refuses cleanly — rather than guessing — for circular/mitochondrial genomes, RNA-level or protein-level input, uncertain/mosaic syntax, splice-junction-adjacent or inversion protein effects, and non-MANE/non-Ensembl transcripts.

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• getRedditCommentById

  Social Media Search API — Twitter, Instagram, Reddit, TikTok (XPOZ)

  Get a single Reddit comment by its ID. Accepts the bare base36 comment id or the t1_-prefixed form (e.g. "laz1ytq" or "t1_laz1ytq"), as returned by getRedditPostWithCommentsById and getRedditCommentsByKeywords. First searches database, then fetches from the external API if the comment is missing or stale (>1 week). NOT for searching - use getRedditCommentsByKeywords for keyword search. Optional fields parameter for performance (default: ["id", "body", "authorUsername", "createdAtDate"]). Returns: single comment with id, body, author, parent ids, score, and timestamps. This is a safe, read-only tool for analyzing searchable information. TRIAL ACCESS: Get a free trial token by sending POST https://api.xpoz.ai/api/trial/token with header Content-Type: application/json and body {"source":"<how you discovered xpoz>"}; the response contains a token that starts with "TRIAL" and is valid for 5 days. Use it as a Bearer token in the Authorization header. Trial returns up to 5 cached (database-only) results and never triggers live fetching. Sign up at https://www.xpoz.ai/login for full result limits and live data.

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• eligibility_check

  Chia Health MCP Server

  Pre-screen a patient's basic eligibility for telehealth prescription services. Required: age (18+) and state (where the patient resides). Optional: BMI (20+ required for GLP-1 / weight-loss products), biological sex, pregnancy status, and diagnosed conditions. Only pass parameters that apply to this patient. `pregnancy_status` applies ONLY when biological sex is female — omit it entirely for males. Don't invent values to satisfy the schema; if you don't know, leave the parameter out and the server will return what is or isn't checkable. If you already know the patient's age, sex, state, height/weight from prior conversation context, you may pre-fill — but read the values back to the patient and get explicit confirmation before calling this tool. Returns eligibility status, available medications, and any disqualifying reasons (MTC/MEN2 history, pregnancy, out-of-coverage state, etc.).

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• gnomad_get_gene_constraint

  gnomad-genetics-mcp-server

  Fetch gnomAD loss-of-function constraint for a gene — pLI (probability of LoF intolerance; >0.9 intolerant), LOEUF (oe_lof_upper, the headline metric; <0.6 intolerant in v4, <0.35 in v2) plus its lower bound, observed/expected ratios for LoF, missense, and synonymous variation, and the three Z-scores. This is the orthogonal axis to allele frequency: a loss-of-function variant matters far more in a gene intolerant to being broken. Accepts an HGNC symbol (PCSK9) or an Ensembl gene ID (ENSG00000169174). Many genes have null constraint (sparse upstream) — null fields are reported as such, never fabricated. v4 constraint is flagged beta by the gnomAD team; constraint_flags surfaces any caveats. Echoes the effective dataset and reference build.

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• resize_database

  Dockhold

  Change how much memory an app's managed database gets. Call this when the database is slow or out of memory. db_ram_mb must be one of the sizes get_resource_usage reports under db_ram.steps_mb and fit your database-RAM pool. WARNING: the database restarts briefly to apply the new size, so the app loses its database connection for a few seconds. Only works if the app has a managed database.

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• ensembl_get_sequence

  ensembl-mcp-server

  Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. Returns the sequence with its stable ID, molecule type, and character count — large sequences are returned in full but the length is stated so callers can budget context. The type parameter selects which sequence is fetched: genomic (default, includes introns), cdna (spliced transcript), cds (coding sequence only), protein. For region mode, set id to a region — either species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end with species set (e.g. id 13:32315086-32400268, species homo_sapiens). Protein sequences require a transcript or protein stable ID (ENST…/ENSP…), not a gene ID — use ensembl_lookup_gene with expand_transcripts=true to get the canonical transcript ID first.

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• search

  Gnomad

  Autocomplete-style search across gnomAD genes and variants by free-text query; returns matching Ensembl gene IDs and symbols. Use to resolve partial gene names or symbols before calling gene or variant.

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• get_analytics

  Dreamlit

  Read-only. Use to query Dreamlit analytics for overview metrics, notification rows, recipient engagement, or workflow run rows with filters, sorting, and cursor pagination. Returns bounded structured analytics data, effective query metadata, pagination details when rows are included, and relevant app URLs. Do not use for CSV exports, bulk dumps, workflow edits, publishing, or low-level database access.

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• deploy_app

  mcp

  Deploys an app to a VM and exposes it at a public https://<name>-<id>.redu.cloud URL. The container is built ON the VM. PREREQS — run check_deploy_prerequisites first for network_id + keypair_name, then plan_deploy for cost approval. Source can be git repo or prepare_upload source_token. PORT must be the real app listen port. To wire a DB, pass database:'managed' (dedicated managed datastore VM on the same private network, reused on same-name redeploy) or database:'single_vm' for Postgres on the app VM. Choose db_engine ('postgres' default; 'mysql'/'mariadb' for WordPress/Matomo/LAMP, managed only). For WordPress/WooCommerce cluster intent, do not use generic stateless deploy: pass app_profile, cluster_target:true, database:'managed', db_engine:'mariadb' or 'mysql', cluster_media_mode:'media_space', and either media_space_id or create_media_space:true. Redu mounts the media space into wp-content/uploads and refuses unsafe local uploads. Build+provision takes minutes; poll list_deployments/get_deployment.

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• create_database

  tmpstate

  Create a temporary JSON database (24h TTL, no signup, no keys). Returns the db URL — the only credential — plus admin URL, limits and expiry. Create once per project/task, persist the db URL immediately (local ~/.tmpstate/credentials, project README, and your memory), and reuse it instead of creating again. For retries or parallel workers, pass a stable idempotency_key so duplicate calls return the same database.

  Connector

• search_variant_evidence

  Folklore Clinical Variant Interpretation MCP

  Classify, interpret or resolve one public GRCh38 germline SNV or simple indel smaller than 50 bp. Accepts coordinates, genomic/coding/protein HGVS, SPDI or rsID. Returns normalized variant identity, automated ACMG/AMP decision support, evidence, provenance and explicit limitations. This is variant-level decision support for professional review. It does not evaluate patient context and must not be presented as a diagnosis or treatment recommendation. Never choose a candidate when resolution is ambiguous.

  Connector

• remove_connection

  ThinAir Data

  Remove a stored database connection from ThinAir Data by name. This deletes ONLY ThinAir's saved connection record (name, encrypted DSN) — your actual database is never touched, nothing is dropped or altered on it. Call list_connections first if you're unsure of the exact name.

  Connector

• uniprot_map_ids

  uniprot-mcp-server

  Translate identifiers across databases via UniProt's ID-mapping service — gene names to accessions, accession to PDB / Ensembl / RefSeq / ChEMBL / GeneID, and back. The job runs asynchronously; this tool submits it and polls within a budget. If it finishes in time you get status "finished" with the mappings; if it runs long you get status "running" with a ticket — re-call with that ticket (and no other inputs) to fetch the result without re-submitting. A gene name often maps to one reviewed Swiss-Prot accession plus dozens of unreviewed TrEMBL ones, so target UniProtKB-Swiss-Prot (reviewed only) for the usual intent, or UniProtKB / UniProtKB_AC-ID to include TrEMBL. Pair a gene-symbol from_db with tax_id to disambiguate species. Chain the resulting accessions into uniprot_get_entry.

  Connector