import { RestToolConfig } from "@mcp/rest-utils";
export const stringTools: RestToolConfig[] = [
{
name: "get_string_ids",
description: "Map protein names, synonyms, and UniProt identifiers to STRING identifiers. Species parameter uses NCBI taxon IDs (e.g., 9606 for human, 10090 for mouse).",
method: "POST",
inputSchema: {
type: "object",
properties: {
identifiers: {
type: "string",
description: "Protein names or IDs, newline or space-separated (e.g., 'TP53 BRCA1' or 'P04637')",
},
species: {
type: "number",
description: "NCBI taxon ID (e.g., 9606 for human, 10090 for mouse)",
default: 9606,
},
limit: {
type: "number",
description: "Maximum number of STRING identifiers to return per query protein",
default: 1,
},
echo_query: {
type: "boolean",
description: "Include the submitted identifier in the output",
default: true,
},
},
required: ["identifiers"],
},
endpoint: "/api/json/get_string_ids",
transformRequest: (args: any) => ({
method: "POST",
body: {
identifiers: args.identifiers,
species: args.species || 9606,
limit: args.limit || 1,
echo_query: args.echo_query !== false ? 1 : 0,
},
}),
},
{
name: "get_network",
description: "Retrieve protein-protein interaction network for given proteins. Returns network edges with confidence scores.",
method: "POST",
inputSchema: {
type: "object",
properties: {
identifiers: {
type: "string",
description: "Protein names or STRING IDs, newline or space-separated",
},
species: {
type: "number",
description: "NCBI taxon ID",
default: 9606,
},
required_score: {
type: "number",
description: "Minimum interaction confidence score (0-1000)",
default: 400,
},
network_type: {
type: "string",
enum: ["functional", "physical"],
description: "Type of network (functional includes all evidence, physical only direct interactions)",
default: "functional",
},
add_nodes: {
type: "number",
description: "Number of additional nodes to add to the network",
default: 0,
},
},
required: ["identifiers"],
},
endpoint: "/api/json/network",
transformRequest: (args: any) => ({
method: "POST",
body: {
identifiers: args.identifiers,
species: args.species || 9606,
required_score: args.required_score || 400,
network_type: args.network_type || "functional",
add_nodes: args.add_nodes || 0,
},
}),
},
{
name: "get_interaction_partners",
description: "Get all STRING interaction partners for your proteins. Returns a list of interacting proteins with confidence scores.",
method: "POST",
inputSchema: {
type: "object",
properties: {
identifiers: {
type: "string",
description: "Protein names or STRING IDs, newline or space-separated",
},
species: {
type: "number",
description: "NCBI taxon ID",
default: 9606,
},
limit: {
type: "number",
description: "Maximum number of interaction partners to return per query protein",
default: 10,
},
required_score: {
type: "number",
description: "Minimum interaction confidence score (0-1000)",
default: 400,
},
network_type: {
type: "string",
enum: ["functional", "physical"],
description: "Type of network",
default: "functional",
},
},
required: ["identifiers"],
},
endpoint: "/api/json/interaction_partners",
transformRequest: (args: any) => ({
method: "POST",
body: {
identifiers: args.identifiers,
species: args.species || 9606,
limit: args.limit || 10,
required_score: args.required_score || 400,
network_type: args.network_type || "functional",
},
}),
},
{
name: "get_enrichment",
description: "Perform functional enrichment analysis for a set of proteins. Tests for over-representation in Gene Ontology terms, KEGG pathways, etc.",
method: "POST",
inputSchema: {
type: "object",
properties: {
identifiers: {
type: "string",
description: "Protein names or STRING IDs, newline or space-separated",
},
species: {
type: "number",
description: "NCBI taxon ID",
default: 9606,
},
background: {
type: "string",
description: "Background proteins for enrichment (optional, newline or space-separated)",
},
},
required: ["identifiers"],
},
endpoint: "/api/json/enrichment",
transformRequest: (args: any) => {
const body: any = {
identifiers: args.identifiers,
species: args.species || 9606,
};
if (args.background) {
body.background_string_identifiers = args.background;
}
return { method: "POST", body };
},
},
{
name: "get_ppi_enrichment",
description: "Test if your protein set has more interactions than expected by chance. Returns enrichment p-value.",
method: "POST",
inputSchema: {
type: "object",
properties: {
identifiers: {
type: "string",
description: "Protein names or STRING IDs, newline or space-separated",
},
species: {
type: "number",
description: "NCBI taxon ID",
default: 9606,
},
required_score: {
type: "number",
description: "Minimum interaction confidence score (0-1000)",
default: 400,
},
},
required: ["identifiers"],
},
endpoint: "/api/json/ppi_enrichment",
transformRequest: (args: any) => ({
method: "POST",
body: {
identifiers: args.identifiers,
species: args.species || 9606,
required_score: args.required_score || 400,
},
}),
},
{
name: "get_homology",
description: "Get homology information for proteins across species using STRING.",
method: "POST",
inputSchema: {
type: "object",
properties: {
identifiers: {
type: "string",
description: "Protein names or STRING IDs, newline or space-separated",
},
species: {
type: "number",
description: "Source species NCBI taxon ID",
default: 9606,
},
target_species: {
type: "number",
description: "Target species NCBI taxon ID (optional)",
},
},
required: ["identifiers"],
},
endpoint: "/api/json/homology",
transformRequest: (args: any) => {
const body: any = {
identifiers: args.identifiers,
species: args.species || 9606,
};
if (args.target_species) {
body.target_species = args.target_species;
}
return { method: "POST", body };
},
},
{
name: "get_homology_best",
description: "Get the best homology match for proteins in a target species.",
method: "POST",
inputSchema: {
type: "object",
properties: {
identifiers: {
type: "string",
description: "Protein names or STRING IDs, newline or space-separated",
},
species: {
type: "number",
description: "Source species NCBI taxon ID",
default: 9606,
},
target_species: {
type: "number",
description: "Target species NCBI taxon ID",
},
},
required: ["identifiers", "target_species"],
},
endpoint: "/api/json/homology_best",
transformRequest: (args: any) => ({
method: "POST",
body: {
identifiers: args.identifiers,
species: args.species || 9606,
target_species: args.target_species,
},
}),
},
{
name: "resolve_proteins",
description: "Resolve protein names to their preferred names in STRING database.",
method: "POST",
inputSchema: {
type: "object",
properties: {
identifiers: {
type: "string",
description: "Protein names or STRING IDs, newline or space-separated",
},
species: {
type: "number",
description: "NCBI taxon ID",
default: 9606,
},
},
required: ["identifiers"],
},
endpoint: "/api/json/resolve",
transformRequest: (args: any) => ({
method: "POST",
body: {
identifiers: args.identifiers,
species: args.species || 9606,
},
}),
},
{
name: "get_version",
description: "Get the current version of the STRING database.",
method: "GET",
inputSchema: {
type: "object",
properties: {},
},
endpoint: "/api/json/version",
},
];
