get_protein_interactions

Retrieve protein-protein interaction networks for a UniProt accession number to analyze molecular relationships and biological pathways.

Instructions

Protein-protein interaction networks

Input Schema

TableJSON Schema

Name	Required	Description	Default
`accession`	Yes	UniProt accession number

Implementation Reference

src/index.ts:1401-1439 (handler)

The handler function for the 'get_protein_interactions' tool. Fetches detailed protein information from the UniProt API and extracts relevant interaction data including cross-references to STRING and IntAct databases, as well as INTERACTION and SUBUNIT comments.

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

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

    const protein = response.data;
    const interactionInfo = {
      accession: protein.primaryAccession,
      stringReferences: protein.uniProtKBCrossReferences?.filter((ref: any) => ref.database === 'STRING') || [],
      intactReferences: protein.uniProtKBCrossReferences?.filter((ref: any) => ref.database === 'IntAct') || [],
      interactionComments: protein.comments?.filter((c: any) => c.commentType === 'INTERACTION') || [],
      subunitComments: protein.comments?.filter((c: any) => c.commentType === 'SUBUNIT') || [],
    };

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

src/index.ts:570-579 (registration)

Registration of the 'get_protein_interactions' tool in the listTools response, including name, description, and input schema definition.

  name: 'get_protein_interactions',
  description: 'Protein-protein interaction networks',
  inputSchema: {
    type: 'object',
    properties: {
      accession: { type: 'string', description: 'UniProt accession number' },
    },
    required: ['accession'],
  },
},

src/index.ts:759-760 (registration)
Registration of the tool handler in the CallToolRequestSchema switch statement, mapping the tool name to its handler method.
```
case 'get_protein_interactions':
  return this.handleGetProteinInteractions(args);
```

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

Input validation function used by the handler to validate arguments, effectively serving as schema enforcement for the tool's input.

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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