import { RestToolConfig } from "@mcp/rest-utils";
export const ensemblTools: RestToolConfig[] = [
{
name: "lookup_gene_by_symbol",
description: "Look up a gene by its symbol (e.g., BRCA2) and get detailed information including ID, location, and description",
method: "GET",
inputSchema: {
type: "object",
properties: {
symbol: {
type: "string",
description: "Gene symbol (e.g., BRCA2, TP53)",
},
species: {
type: "string",
description: "Species name (default: human)",
default: "human",
},
expand: {
type: "boolean",
description: "Expand transcripts information",
default: false,
},
},
required: ["symbol"],
},
endpoint: (args: any) => `/lookup/symbol/${args.species || "human"}/${args.symbol}`,
transformRequest: (args: any) => ({
method: "GET",
queryParams: args.expand ? { expand: 1 } : undefined,
}),
},
{
name: "lookup_gene_by_id",
description: "Look up a gene by its Ensembl stable ID (e.g., ENSG00000139618)",
method: "GET",
inputSchema: {
type: "object",
properties: {
id: {
type: "string",
description: "Ensembl gene stable ID (e.g., ENSG00000139618)",
},
expand: {
type: "boolean",
description: "Expand transcripts information",
default: false,
},
},
required: ["id"],
},
endpoint: (args: any) => `/lookup/id/${args.id}`,
transformRequest: (args: any) => ({
method: "GET",
queryParams: args.expand ? { expand: 1 } : undefined,
}),
},
{
name: "get_sequence",
description: "Get the DNA/RNA/protein sequence for a given region or feature",
method: "GET",
inputSchema: {
type: "object",
properties: {
id: {
type: "string",
description: "Ensembl stable ID (gene, transcript, or translation)",
},
type: {
type: "string",
enum: ["genomic", "cds", "cdna", "protein"],
description: "Type of sequence to retrieve",
default: "genomic",
},
},
required: ["id"],
},
endpoint: (args: any) => `/sequence/id/${args.id}`,
transformRequest: (args: any) => ({
method: "GET",
queryParams: { type: args.type || "genomic" },
}),
},
{
name: "get_variants_for_region",
description: "Get genetic variants for a genomic region",
method: "GET",
inputSchema: {
type: "object",
properties: {
species: {
type: "string",
description: "Species name",
default: "human",
},
region: {
type: "string",
description: "Genomic region (e.g., 7:140424943-140624564)",
},
},
required: ["region"],
},
endpoint: (args: any) => `/overlap/region/${args.species || "human"}/${args.region}`,
transformRequest: () => ({
method: "GET",
queryParams: { feature: "variation" },
}),
},
{
name: "get_homology",
description: "Get homologous genes/proteins across species",
method: "GET",
inputSchema: {
type: "object",
properties: {
id: {
type: "string",
description: "Ensembl gene stable ID",
},
species: {
type: "string",
description: "Species name for the gene",
default: "human",
},
target_species: {
type: "string",
description: "Target species for homology search (optional)",
},
type: {
type: "string",
enum: ["orthologues", "paralogues", "all"],
description: "Type of homology",
default: "orthologues",
},
},
required: ["id"],
},
endpoint: (args: any) => `/homology/id/${args.species || "human"}/${args.id}`,
transformRequest: (args: any) => {
const queryParams: Record<string, string> = {};
if (args.type && args.type !== "all") {
queryParams.type = args.type;
}
if (args.target_species) {
queryParams.target_species = args.target_species;
}
return { method: "GET", queryParams: Object.keys(queryParams).length > 0 ? queryParams : undefined };
},
},
{
name: "get_phenotype_by_gene",
description: "Get phenotype annotations associated with a gene",
method: "GET",
inputSchema: {
type: "object",
properties: {
gene_id: {
type: "string",
description: "Ensembl gene stable ID",
},
species: {
type: "string",
description: "Species name",
default: "human",
},
},
required: ["gene_id"],
},
endpoint: (args: any) => `/phenotype/gene/${args.species || "human"}/${args.gene_id}`,
},
{
name: "get_regulatory_features",
description: "Get regulatory features in a genomic region",
method: "GET",
inputSchema: {
type: "object",
properties: {
species: {
type: "string",
description: "Species name",
default: "human",
},
region: {
type: "string",
description: "Genomic region (e.g., X:1000000-1010000)",
},
},
required: ["region"],
},
endpoint: (args: any) => `/overlap/region/${args.species || "human"}/${args.region}`,
transformRequest: () => ({
method: "GET",
queryParams: { feature: "regulatory" },
}),
},
{
name: "overlap_region",
description: "Get features that overlap a given genomic region",
method: "GET",
inputSchema: {
type: "object",
properties: {
species: {
type: "string",
description: "Species name",
default: "human",
},
region: {
type: "string",
description: "Genomic region (e.g., 7:140424943-140624564)",
},
feature: {
type: "string",
enum: [
"gene",
"transcript",
"cds",
"exon",
"repeat",
"simple_feature",
"misc_feature",
"variation",
"structural_variation",
"somatic_variation",
"somatic_structural_variation",
"constrained",
"regulatory",
"motif",
"chipseq",
"array_probe"
],
description: "Type of feature to retrieve",
default: "gene",
},
},
required: ["region"],
},
endpoint: (args: any) => `/overlap/region/${args.species || "human"}/${args.region}`,
transformRequest: (args: any) => ({
method: "GET",
queryParams: { feature: args.feature || "gene" },
}),
},
{
name: "get_xrefs_by_gene",
description: "Get external references (cross-references) for a gene",
method: "GET",
inputSchema: {
type: "object",
properties: {
gene_id: {
type: "string",
description: "Ensembl gene stable ID",
},
external_db: {
type: "string",
description: "Filter by external database name (e.g., HGNC, UniProt)",
},
},
required: ["gene_id"],
},
endpoint: (args: any) => `/xrefs/id/${args.gene_id}`,
transformRequest: (args: any) => ({
method: "GET",
queryParams: args.external_db ? { external_db: args.external_db } : undefined,
}),
},
{
name: "get_xrefs_by_symbol",
description: "Get cross-references for a gene symbol",
method: "GET",
inputSchema: {
type: "object",
properties: {
species: {
type: "string",
description: "Species name",
default: "human",
},
symbol: {
type: "string",
description: "Gene symbol",
},
external_db: {
type: "string",
description: "Filter by external database",
},
},
required: ["symbol"],
},
endpoint: (args: any) => `/xrefs/symbol/${args.species || "human"}/${args.symbol}`,
transformRequest: (args: any) => ({
method: "GET",
queryParams: args.external_db ? { external_db: args.external_db } : undefined,
}),
},
{
name: "get_xrefs_by_name",
description: "Search cross-references by name",
method: "GET",
inputSchema: {
type: "object",
properties: {
species: {
type: "string",
description: "Species name",
default: "human",
},
name: {
type: "string",
description: "Name to search for",
},
},
required: ["species", "name"],
},
endpoint: (args: any) => `/xrefs/name/${args.species}/${args.name}`,
},
{
name: "map_assembly",
description: "Map coordinates between different genome assemblies",
method: "GET",
inputSchema: {
type: "object",
properties: {
species: {
type: "string",
description: "Species name",
default: "human",
},
asm_one: {
type: "string",
description: "Source assembly (e.g., GRCh37)",
},
region: {
type: "string",
description: "Region to map (e.g., X:1000000..1000100:1)",
},
asm_two: {
type: "string",
description: "Target assembly (e.g., GRCh38)",
},
},
required: ["species", "asm_one", "region", "asm_two"],
},
endpoint: (args: any) => `/map/${args.species}/${args.asm_one}/${args.region}/${args.asm_two}`,
},
{
name: "map_cdna_to_region",
description: "Map cDNA coordinates to genomic coordinates",
method: "GET",
inputSchema: {
type: "object",
properties: {
id: {
type: "string",
description: "Transcript stable ID",
},
region: {
type: "string",
description: "cDNA coordinates (e.g., 100..300)",
},
},
required: ["id", "region"],
},
endpoint: (args: any) => `/map/cdna/${args.id}/${args.region}`,
},
{
name: "map_cds_to_region",
description: "Map CDS coordinates to genomic coordinates",
method: "GET",
inputSchema: {
type: "object",
properties: {
id: {
type: "string",
description: "Transcript stable ID",
},
region: {
type: "string",
description: "CDS coordinates (e.g., 1..300)",
},
},
required: ["id", "region"],
},
endpoint: (args: any) => `/map/cds/${args.id}/${args.region}`,
},
{
name: "map_translation_to_region",
description: "Map protein coordinates to genomic coordinates",
method: "GET",
inputSchema: {
type: "object",
properties: {
id: {
type: "string",
description: "Translation stable ID",
},
region: {
type: "string",
description: "Protein coordinates (e.g., 1..100)",
},
},
required: ["id", "region"],
},
endpoint: (args: any) => `/map/translation/${args.id}/${args.region}`,
},
{
name: "get_ontology_by_id",
description: "Get ontology term information by ID",
method: "GET",
inputSchema: {
type: "object",
properties: {
id: {
type: "string",
description: "Ontology term ID (e.g., GO:0005667)",
},
},
required: ["id"],
},
endpoint: (args: any) => `/ontology/id/${args.id}`,
},
{
name: "get_ontology_ancestors",
description: "Get ancestor terms for an ontology term",
method: "GET",
inputSchema: {
type: "object",
properties: {
id: {
type: "string",
description: "Ontology term ID",
},
},
required: ["id"],
},
endpoint: (args: any) => `/ontology/ancestors/${args.id}`,
},
{
name: "get_ontology_descendants",
description: "Get descendant terms for an ontology term",
method: "GET",
inputSchema: {
type: "object",
properties: {
id: {
type: "string",
description: "Ontology term ID",
},
closest_terms: {
type: "boolean",
description: "Only return closest terms",
default: false,
},
},
required: ["id"],
},
endpoint: (args: any) => `/ontology/descendants/${args.id}`,
transformRequest: (args: any) => ({
method: "GET",
queryParams: args.closest_terms ? { closest_term: 1 } : undefined,
}),
},
{
name: "search_ontology_by_name",
description: "Search for ontology terms by name",
method: "GET",
inputSchema: {
type: "object",
properties: {
name: {
type: "string",
description: "Term name to search",
},
ontology: {
type: "string",
description: "Ontology to search (e.g., GO, SO)",
},
},
required: ["name"],
},
endpoint: (args: any) => `/ontology/name/${args.name}`,
transformRequest: (args: any) => ({
method: "GET",
queryParams: args.ontology ? { ontology: args.ontology } : undefined,
}),
},
{
name: "get_taxonomy_by_id",
description: "Get taxonomy information by ID",
method: "GET",
inputSchema: {
type: "object",
properties: {
id: {
type: "string",
description: "Taxonomy ID (e.g., 9606 for human)",
},
},
required: ["id"],
},
endpoint: (args: any) => `/taxonomy/id/${args.id}`,
},
{
name: "get_taxonomy_classification",
description: "Get taxonomic classification for a species",
method: "GET",
inputSchema: {
type: "object",
properties: {
id: {
type: "string",
description: "Taxonomy ID",
},
},
required: ["id"],
},
endpoint: (args: any) => `/taxonomy/classification/${args.id}`,
},
{
name: "search_taxonomy_by_name",
description: "Search taxonomy by name",
method: "GET",
inputSchema: {
type: "object",
properties: {
name: {
type: "string",
description: "Taxonomy name to search",
},
},
required: ["name"],
},
endpoint: (args: any) => `/taxonomy/name/${args.name}`,
},
{
name: "overlap_id",
description: "Get features that overlap a specific feature by ID",
method: "GET",
inputSchema: {
type: "object",
properties: {
id: {
type: "string",
description: "Ensembl stable ID",
},
feature: {
type: "string",
enum: ["gene", "transcript", "cds", "exon", "repeat", "simple_feature", "misc_feature", "variation", "structural_variation", "somatic_variation", "somatic_structural_variation", "constrained", "regulatory", "motif", "chipseq", "array_probe"],
description: "Type of feature to retrieve",
default: "gene",
},
},
required: ["id"],
},
endpoint: (args: any) => `/overlap/id/${args.id}`,
transformRequest: (args: any) => ({
method: "GET",
queryParams: { feature: args.feature || "gene" },
}),
},
{
name: "overlap_translation",
description: "Get features overlapping a translation (protein)",
method: "GET",
inputSchema: {
type: "object",
properties: {
id: {
type: "string",
description: "Translation stable ID",
},
feature: {
type: "string",
enum: ["protein_feature", "transcript_variation", "somatic_transcript_variation"],
description: "Type of feature to retrieve",
default: "protein_feature",
},
},
required: ["id"],
},
endpoint: (args: any) => `/overlap/translation/${args.id}`,
transformRequest: (args: any) => ({
method: "GET",
queryParams: { type: args.feature || "protein_feature" },
}),
},
{
name: "vep_region",
description: "Predict variant consequences for a genomic region using the Variant Effect Predictor (VEP). Returns detailed consequence predictions including transcript effects, protein changes, and regulatory impacts.",
method: "GET",
inputSchema: {
type: "object",
properties: {
species: {
type: "string",
description: "Species name (e.g., human, mouse)",
default: "human",
},
region: {
type: "string",
description: "Genomic region in format chr:start-end:strand (e.g., 9:22125503-22125502:1)",
},
allele: {
type: "string",
description: "Variant allele (e.g., C, T, DUP, DEL)",
},
// Transcript selection
canonical: {
type: "boolean",
description: "Use only canonical transcripts",
},
ccds: {
type: "boolean",
description: "Use CCDS transcripts",
},
gencode_basic: {
type: "boolean",
description: "Use GENCODE basic transcripts",
},
mane: {
type: "boolean",
description: "Use MANE (Matched Annotation from NCBI and EBI) transcripts",
},
refseq: {
type: "boolean",
description: "Use RefSeq transcripts",
},
merged: {
type: "boolean",
description: "Use merged Ensembl/RefSeq transcripts",
},
pick: {
type: "boolean",
description: "Pick one consequence per variant",
},
pick_allele: {
type: "boolean",
description: "Pick one consequence per variant allele",
},
pick_allele_gene: {
type: "boolean",
description: "Pick one consequence per variant allele and gene",
},
per_gene: {
type: "boolean",
description: "Use per-gene output",
},
// Annotation details
hgvs: {
type: "boolean",
description: "Include HGVS nomenclature",
},
protein: {
type: "boolean",
description: "Include protein sequence",
},
domains: {
type: "boolean",
description: "Include protein domains",
},
uniprot: {
type: "boolean",
description: "Include UniProt identifiers",
},
tsl: {
type: "boolean",
description: "Include transcript support level",
},
appris: {
type: "boolean",
description: "Include APPRIS annotation",
},
numbers: {
type: "boolean",
description: "Include affected exon/intron numbers",
},
variant_class: {
type: "boolean",
description: "Include Sequence Ontology variant class",
},
// Prediction plugins
AlphaMissense: {
type: "boolean",
description: "Include AlphaMissense pathogenicity predictions",
},
CADD: {
type: "boolean",
description: "Include CADD pathogenicity scores",
},
REVEL: {
type: "boolean",
description: "Include REVEL pathogenicity scores",
},
Conservation: {
type: "boolean",
description: "Include conservation scores",
},
LoF: {
type: "boolean",
description: "Include Loss of Function predictions",
},
SpliceAI: {
type: "boolean",
description: "Include SpliceAI splice-altering predictions",
},
// Other options
distance: {
type: "number",
description: "Distance to transcript (bp) for upstream/downstream variants",
},
minimal: {
type: "boolean",
description: "Return minimal output",
},
shift_3prime: {
type: "boolean",
description: "Shift variants to 3' end if possible",
},
transcript_version: {
type: "boolean",
description: "Include transcript version numbers",
},
},
required: ["region", "allele"],
},
endpoint: (args: any) => `/vep/${args.species || "human"}/region/${args.region}/${args.allele}`,
transformRequest: (args: any) => {
const queryParams: Record<string, number | string> = {};
// Boolean parameters - only add if true
const boolParams = [
'canonical', 'ccds', 'gencode_basic', 'mane', 'refseq', 'merged',
'pick', 'pick_allele', 'pick_allele_gene', 'per_gene',
'hgvs', 'protein', 'domains', 'uniprot', 'tsl', 'appris', 'numbers', 'variant_class',
'AlphaMissense', 'CADD', 'REVEL', 'Conservation', 'LoF', 'SpliceAI',
'minimal', 'shift_3prime', 'transcript_version'
];
boolParams.forEach(param => {
if (args[param]) queryParams[param] = 1;
});
// Number parameters
if (args.distance !== undefined) queryParams.distance = args.distance;
return {
method: "GET",
queryParams: Object.keys(queryParams).length > 0 ? queryParams : undefined,
};
},
},
];
