generate_submission_checklist

Instructions

Implementation Reference

• src/index.ts:311-320 (schema)

  Input schema and tool definition for generate_submission_checklist, defining submission_type and agency as required string parameters.

  name: "generate_submission_checklist",
  description: "Generate a submission readiness checklist for a given submission type and agency.",
  inputSchema: {
              type: "object",
              properties: {
                            submission_type: { type: "string", description: "Type: 'NDA', 'BLA', 'MAA', 'IND', 'CTA', 'IMPD'" },
                            agency: { type: "string", description: "Target agency: 'FDA', 'EMA', 'PMDA', 'Health Canada'" }
              },
              required: ["submission_type", "agency"]
  }

• src/index.ts:380-390 (handler)

  Handler for generate_submission_checklist that parses args, looks up hardcoded checklists for NDA/FDA, MAA/EMA, and IND/FDA, and returns a formatted markdown checklist.

  if (name === "generate_submission_checklist") {
          const { submission_type, agency } = z.object({ submission_type: z.string(), agency: z.string() }).parse(args);
          const checklists: Record<string, Record<string, string[]>> = {
                    NDA: { FDA: ["Cover letter and Form FDA 356h", "Module 1: Proposed labelling (PI, Medication Guide if applicable)", "Module 1: Patent certifications", "Module 1: Debarment certification", "Module 1: Financial disclosure (Form FDA 3454/3455)", "Module 2.3: Quality Overall Summary", "Module 2.4: Nonclinical Overview", "Module 2.5: Clinical Overview", "Module 2.6: Nonclinical Written and Tabulated Summaries", "Module 2.7: Clinical Summary", "Module 3: Full CMC documentation (3.2.S and 3.2.P)", "Module 4: All nonclinical study reports", "Module 5: All clinical study reports (pivotal trials)", "Module 5: Integrated Summary of Safety (ISS)", "Module 5: Integrated Summary of Efficacy (ISE)", "PREA compliance / iPSP or waiver/deferral", "REMS (if required based on safety profile)", "User fee payment confirmation (PDUFA)"] },
                    MAA: { EMA: ["Module 1.0: Cover letter", "Module 1.2: Application form (eAF)", "Module 1.3: Product information (SmPC, PIL, labelling)", "Module 1.7: EudraVigilance registration confirmation", "Module 1.8: Clinical trial information (EudraCT)", "Module 1.10: Pharmacovigilance system summary", "Module 1.11: Risk Management Plan (RMP)", "Module 2-5: Full CTD technical documentation", "Paediatric Investigation Plan (PIP) compliance", "CHMP scientific advice follow-up (if applicable)", "GMP compliance documentation for manufacturing sites", "ASMF or CEP for drug substance (if applicable)", "Environmental Risk Assessment (ERA)", "EMA application fee payment"] },
                    IND: { FDA: ["Form FDA 1571 (IND application cover sheet)", "Table of contents", "Introductory statement and general investigational plan", "Investigator's Brochure (IB)", "Protocol(s) and amendments", "Chemistry, Manufacturing, and Controls (CMC) information", "Pharmacology and toxicology information", "Previous human experience (if any)", "Additional information (PK, bioavailability)", "Institutional Review Board (IRB) confirmation", "Sponsor-investigator certifications"] }
          };
          const checklist = checklists[submission_type.toUpperCase()]?.[agency.toUpperCase()];
          if (!checklist) return { content: [{ type: "text", text: "Checklist for " + submission_type + " (" + agency + ") not available. Currently: NDA (FDA), MAA (EMA), IND (FDA)." }] };
          return { content: [{ type: "text", text: "# " + submission_type.toUpperCase() + " Submission Checklist (" + agency.toUpperCase() + ")\n\n" + checklist.map((item, i) => "- [ ] " + (i+1) + ". " + item).join("\n") + "\n\n**Total:** " + checklist.length + " items" }] };
  }

• src/index.ts:260-335 (registration)

  Tool registered in the ListToolsRequestSchema handler within the tools array returned by the server.

  server.setRequestHandler(ListToolsRequestSchema, async () => ({
        tools: [
          {
                    name: "lookup_ich_guideline",
                    description: "Look up an ICH guideline by code (e.g. E6(R3), M4, Q1A). Returns scope, key requirements, and official URL.",
                    inputSchema: {
                                type: "object",
                                properties: {
                                              guideline_code: { type: "string", description: "ICH guideline code, e.g. 'E6(R3)', 'M4(R4)', 'Q3D(R2)', 'M7(R2)'" }
                                },
                                required: ["guideline_code"]
                    }
          },
          {
                    name: "map_ctd_section",
                    description: "Map a document type or data package to the correct CTD/eCTD module and section. Returns the full section hierarchy.",
                    inputSchema: {
                                type: "object",
                                properties: {
                                              module: { type: "string", description: "CTD module number: '1', '2', '3', '4', or '5'" },
                                              submission_type: { type: "string", description: "Submission type: 'NDA', 'BLA', 'MAA', or 'JNDA'" }
                                },
                                required: ["module"]
                    }
          },
          {
                    name: "check_ctd_completeness",
                    description: "Check a list of provided CTD sections against required sections and identify gaps.",
                    inputSchema: {
                                type: "object",
                                properties: {
                                              provided_sections: { type: "array", items: { type: "string" }, description: "List of CTD sections already prepared" },
                                              submission_type: { type: "string", description: "Target submission type: 'NDA', 'BLA', or 'MAA'" },
                                              module: { type: "string", description: "Which module to check: '3', '4', or '5'" }
                                },
                                required: ["provided_sections", "submission_type", "module"]
                    }
          },
          {
                    name: "get_agency_deficiency_guidance",
                    description: "Retrieve common deficiency areas for FDA or EMA submissions by domain (CMC, Clinical, Labelling, Pharmacovigilance).",
                    inputSchema: {
                                type: "object",
                                properties: {
                                              agency: { type: "string", description: "Regulatory agency: 'FDA' or 'EMA'" },
                                              domain: { type: "string", description: "Area: 'CMC', 'Clinical', 'Labelling', or 'Pharmacovigilance'" }
                                },
                                required: ["agency", "domain"]
                    }
          },
          {
                    name: "generate_submission_checklist",
                    description: "Generate a submission readiness checklist for a given submission type and agency.",
                    inputSchema: {
                                type: "object",
                                properties: {
                                              submission_type: { type: "string", description: "Type: 'NDA', 'BLA', 'MAA', 'IND', 'CTA', 'IMPD'" },
                                              agency: { type: "string", description: "Target agency: 'FDA', 'EMA', 'PMDA', 'Health Canada'" }
                                },
                                required: ["submission_type", "agency"]
                    }
          },
          {
                    name: "check_ich_compliance",
                    description: "Check a description of a study or document against ICH guideline requirements and return a compliance assessment.",
                    inputSchema: {
                                type: "object",
                                properties: {
                                              description: { type: "string", description: "Description of the study or document to assess" },
                                              guideline_code: { type: "string", description: "ICH guideline to check against, e.g. 'E6(R3)', 'Q1A(R2)'" }
                                },
                                required: ["description", "guideline_code"]
                    }
          }
              ]
  }));