find_pathways_by_disease

Discover biological pathways and mechanisms linked to specific diseases using Reactome pathway data. Input a disease name or DOID identifier to retrieve relevant pathways.

Instructions

Find disease-associated pathways and mechanisms

Input Schema

TableJSON Schema

Name	Required	Description	Default
`disease`	Yes	Disease name or DOID identifier
`size`	No	Number of pathways to return (1-100, default: 25)

Implementation Reference

src/index.ts:629-691 (handler)

The main handler function that implements the core logic for the 'find_pathways_by_disease' tool. It validates input, queries the Reactome search API for pathways matching the disease name, processes the results, and returns formatted pathway information.

private async handleFindPathwaysByDisease(args: any) {
  if (!isValidDiseaseArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid disease arguments');
  }

  try {
    // Search for disease-related pathways
    const searchResponse = await this.apiClient.get('/search/query', {
      params: {
        query: args.disease,
        types: 'Pathway',
        cluster: true
      }
    });

    // Extract pathway entries from result groups
    let pathwayEntries: any[] = [];
    if (searchResponse.data.results) {
      for (const group of searchResponse.data.results) {
        if (group.typeName === 'Pathway' && group.entries) {
          pathwayEntries = pathwayEntries.concat(group.entries);
        }
      }
    }

    // Limit results if specified
    if (args.size) {
      pathwayEntries = pathwayEntries.slice(0, args.size);
    }

    const diseasePathways = {
      disease: args.disease,
      pathwayCount: pathwayEntries.length,
      pathways: pathwayEntries.map((pathway: any) => ({
        id: pathway.stId || pathway.id,
        name: pathway.name?.replace(/<[^>]*>/g, '') || 'Unknown',
        type: pathway.exactType || pathway.typeName || 'Unknown',
        species: Array.isArray(pathway.species) ? pathway.species[0] : pathway.species || 'Unknown',
        description: (pathway.summation?.substring(0, 200) || 'No description available') + '...',
        url: `https://reactome.org/content/detail/${pathway.stId || pathway.id}`
      }))
    };

    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(diseasePathways, null, 2),
        },
      ],
    };
  } catch (error) {
    return {
      content: [
        {
          type: 'text',
          text: `Error finding pathways by disease: ${error instanceof Error ? error.message : 'Unknown error'}`,
        },
      ],
      isError: true,
    };
  }
}

src/index.ts:259-270 (schema)

The input schema definition for the 'find_pathways_by_disease' tool, registered in the ListToolsRequestSchema handler. Specifies the expected input parameters: disease (required string) and optional size (number).

{
  name: 'find_pathways_by_disease',
  description: 'Find disease-associated pathways and mechanisms',
  inputSchema: {
    type: 'object',
    properties: {
      disease: { type: 'string', description: 'Disease name or DOID identifier' },
      size: { type: 'number', description: 'Number of pathways to return (1-100, default: 25)', minimum: 1, maximum: 100 },
    },
    required: ['disease'],
  },
},

src/index.ts:333-334 (registration)
The switch case in the CallToolRequestSchema handler that routes calls to the 'find_pathways_by_disease' tool to its handler method.
```
case 'find_pathways_by_disease':
  return this.handleFindPathwaysByDisease(args);
```

src/index.ts:59-67 (helper)

Type guard and validation function for the input arguments of the 'find_pathways_by_disease' tool.

const isValidDiseaseArgs = (args: any): args is { disease: string; size?: number } => {
  return (
    typeof args === 'object' &&
    args !== null &&
    typeof args.disease === 'string' &&
    args.disease.length > 0 &&
    (args.size === undefined || (typeof args.size === 'number' && args.size > 0 && args.size <= 100))
  );
};

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