get_protein_pathways

Retrieve biological pathways (KEGG, Reactome) for a protein using its UniProt accession number to understand its functional context.

Instructions

Associated biological pathways (KEGG, Reactome)

Input Schema

TableJSON Schema

Name	Required	Description	Default
`accession`	Yes	UniProt accession number

Implementation Reference

src/index.ts:1361-1398 (handler)

The handler function that implements the core logic of the 'get_protein_pathways' tool. It validates input, fetches detailed protein information from the UniProt REST API, extracts relevant pathway data (KEGG/Reactome cross-references and comments), formats it as JSON, and returns it.

private async handleGetProteinPathways(args: any) {
  if (!isValidProteinInfoArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid protein pathways arguments');
  }

  try {
    const response = await this.apiClient.get(`/uniprotkb/${args.accession}`, {
      params: { format: 'json' },
    });

    const protein = response.data;
    const pathwayInfo = {
      accession: protein.primaryAccession,
      keggReferences: protein.uniProtKBCrossReferences?.filter((ref: any) => ref.database === 'KEGG') || [],
      reactomeReferences: protein.uniProtKBCrossReferences?.filter((ref: any) => ref.database === 'Reactome') || [],
      pathwayComments: protein.comments?.filter((c: any) => c.commentType === 'PATHWAY') || [],
      biologicalProcess: protein.comments?.filter((c: any) => c.commentType === 'FUNCTION') || [],
    };

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

src/index.ts:559-567 (registration)

Registration of the 'get_protein_pathways' tool in the list of available tools, including its name, description, and input schema definition.

name: 'get_protein_pathways',
description: 'Associated biological pathways (KEGG, Reactome)',
inputSchema: {
  type: 'object',
  properties: {
    accession: { type: 'string', description: 'UniProt accession number' },
  },
  required: ['accession'],
},

src/index.ts:757-758 (registration)
Dispatch registration in the CallToolRequestSchema switch statement that routes calls to the handler function.
```
case 'get_protein_pathways':
  return this.handleGetProteinPathways(args);
```

src/index.ts:79-89 (helper)

Shared input validation helper function used by get_protein_pathways (and other protein info tools) to validate the accession parameter.

const isValidProteinInfoArgs = (
  args: any
): args is { accession: string; format?: string } => {
  return (
    typeof args === 'object' &&
    args !== null &&
    typeof args.accession === 'string' &&
    args.accession.length > 0 &&
    (args.format === undefined || ['json', 'tsv', 'fasta', 'xml'].includes(args.format))
  );
};

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