get_pathway_reactions

Retrieve all biochemical reactions for a specific Reactome pathway using its stable identifier to analyze pathway components and interactions.

Instructions

Get all biochemical reactions within a pathway

Input Schema

TableJSON Schema

Name	Required	Description	Default
`id`	Yes	Reactome pathway stable identifier

Implementation Reference

src/index.ts:878-941 (handler)

Main handler function that validates input, resolves pathway ID, fetches contained events from Reactome API, filters for reactions, and returns formatted reaction list.

private async handleGetPathwayReactions(args: any) {
  if (!isValidIdArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Pathway ID is required');
  }

  try {
    // Resolve pathway ID if it's a name
    const pathwayId = await this.resolvePathwayId(args.id);
    if (!pathwayId) {
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify({
              error: `No pathway found for identifier: ${args.id}`,
              suggestion: 'Try using a Reactome stable identifier (e.g., R-HSA-1640170) or search for the pathway first'
            }, null, 2),
          },
        ],
        isError: true,
      };
    }

    const response = await this.apiClient.get(`/data/pathway/${pathwayId}/containedEvents`);

    // Filter for reactions only
    const reactions = response.data?.filter((event: any) =>
      event.schemaClass === 'Reaction' || event.schemaClass === 'BlackBoxEvent'
    ) || [];

    const pathwayReactions = {
      pathwayId: pathwayId,
      originalQuery: args.id,
      reactionCount: reactions.length,
      reactions: reactions.map((reaction: any) => ({
        id: reaction.stId,
        name: reaction.name,
        type: reaction.schemaClass,
        reversible: reaction.reversible,
        species: reaction.species?.[0]?.name,
        url: `https://reactome.org/content/detail/${reaction.stId}`
      }))
    };

    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(pathwayReactions, null, 2),
        },
      ],
    };
  } catch (error) {
    return {
      content: [
        {
          type: 'text',
          text: `Error getting pathway reactions: ${error instanceof Error ? error.message : 'Unknown error'}`,
        },
      ],
      isError: true,
    };
  }
}

src/index.ts:296-302 (schema)

Input schema defining the required 'id' parameter for the tool.

inputSchema: {
  type: 'object',
  properties: {
    id: { type: 'string', description: 'Reactome pathway stable identifier' },
  },
  required: ['id'],
},

src/index.ts:293-303 (registration)

Tool registration in the ListTools response, including name, description, and input schema.

{
  name: 'get_pathway_reactions',
  description: 'Get all biochemical reactions within a pathway',
  inputSchema: {
    type: 'object',
    properties: {
      id: { type: 'string', description: 'Reactome pathway stable identifier' },
    },
    required: ['id'],
  },
},

src/index.ts:339-340 (registration)
Dispatcher case in the CallToolRequestSchema handler that routes to the specific handler function.
```
case 'get_pathway_reactions':
  return this.handleGetPathwayReactions(args);
```

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