openapi: 3.1.0
info:
  title: Orphan Disease Venture & Translational Opportunity API (Static S3 Feed)
  version: 1.0.0
  summary: Zero-auth static JSON & Markdown endpoints for AI agents, Custom GPT Actions, and OpenAPI tool callers.
  description: >
    Machine-readable startup blueprints, biological tractability, FDA Orphan Drug Act unit economics,
    non-dilutive SBIR/venture-philanthropy grants, and ethical clinical validation pathways.
    Flagship Deep-Dive #1 covers JAK2 V617F-positive Myelofibrosis (`jak2-myelofibrosis`).
    Hosted statically on S3/CloudFront with zero authentication required so Custom GPTs and OpenAPI
    agents can query live structured data directly.
  contact:
    name: Rare Disease Venture Atlas
    url: https://rare-disease-atlas.github.io
  license:
    name: CC-BY-4.0
    url: https://creativecommons.org/licenses/by/4.0/

servers:
  - url: https://rare-disease-atlas.github.io
    description: Production static S3 + CloudFront distribution

paths:
  /opportunities.json:
    get:
      operationId: getOrphanDiseaseOpportunityAtlas
      summary: Fetch full structured dataset of founder opportunities, JAK2+ Myelofibrosis case study, non-dilutive grants, and ethical validation communities.
      description: >
        Returns the complete JSON atlas powering `rare-disease-atlas.github.io` and `orphan-disease-opportunity-mcp`.
        Agents should inspect `opportunities` (filtering by `backgrounds`, `capital_tier`, and `wet_lab_required`),
        `case_studies.jak2-myelofibrosis`, `non_dilutive_grants`, and `validation_communities`.
      responses:
        "200":
          description: Full structured opportunity, biology, grant, and validation atlas.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/OpportunityAtlas"

  /llms.txt:
    get:
      operationId: getLlmsSiteMap
      summary: Retrieve concise LLM-optimized markdown index of rare-disease-atlas.github.io.
      description: Lightweight `llmstxt.org` compliant overview mapping founder tracks, key biological hypotheses, and structured resource links.
      responses:
        "200":
          description: Markdown executive summary for LLMs and RAG agents.
          content:
            text/plain:
              schema:
                type: string

  /llms-full.txt:
    get:
      operationId: getLlmsFullBriefing
      summary: Retrieve full single-file Markdown translational & venture briefing.
      description: Complete concatenated narrative briefing covering JAK2 V617F JH2 structural biology, ruxolitinib failure modes, startup blueprints, and grants.
      responses:
        "200":
          description: Complete Markdown playbook.
          content:
            text/plain:
              schema:
                type: string

  /.well-known/mcp.json:
    get:
      operationId: getMcpDiscoveryManifest
      summary: Discover Model Context Protocol (MCP) server package, tools, resources, and prompts for this domain.
      responses:
        "200":
          description: MCP server capability manifest.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/McpDiscoveryManifest"

components:
  schemas:
    OpportunityAtlas:
      type: object
      required:
        - schema_version
        - atlas_name
        - flagship_disease_id
        - opportunities
      properties:
        schema_version:
          type: string
          example: "1.0.0"
        atlas_name:
          type: string
          example: "Rare Disease Venture & Translational Opportunity Atlas"
        canonical_url:
          type: string
          format: uri
        license:
          type: string
          example: "CC-BY-4.0"
        flagship_disease_id:
          type: string
          example: "jak2-myelofibrosis"
        opportunities:
          type: array
          items:
            $ref: "#/components/schemas/FounderOpportunity"
        case_studies:
          type: object
          additionalProperties:
            $ref: "#/components/schemas/DiseaseCaseStudy"
        non_dilutive_grants:
          type: array
          items:
            $ref: "#/components/schemas/GrantProgram"
        validation_communities:
          type: object
          additionalProperties:
            $ref: "#/components/schemas/ValidationCommunityGroup"

    FounderOpportunity:
      type: object
      required:
        - id
        - disease_id
        - title
        - backgrounds
        - capital_tier
        - wet_lab_required
        - problem_wedge
        - solution_blueprint
      properties:
        id:
          type: string
        disease_id:
          type: string
        title:
          type: string
        backgrounds:
          type: array
          items:
            type: string
            enum:
              - computational-ai-bio
              - public-health
              - venture-novel-financing
        capital_tier:
          type: string
          enum:
            - bootstrapped-grant
            - seed
            - series-a-platform
        capital_range_usd:
          type: string
        wet_lab_required:
          type: boolean
        problem_wedge:
          type: string
        solution_blueprint:
          type: string
        unit_economics:
          type: object
          additionalProperties:
            type: string
        regulatory_pathway:
          type: string
        first_90_days_milestones:
          type: array
          items:
            type: string
        open_datasets:
          type: array
          items:
            type: string

    DiseaseCaseStudy:
      type: object
      properties:
        disease_id:
          type: string
        name:
          type: string
        identifiers:
          type: object
        epidemiology:
          type: object
        biological_tractability:
          type: object
        standard_of_care_failure_modes:
          type: object
        regulatory_and_commercial_incentives:
          type: object
        open_datasets_and_tools:
          type: array
          items:
            type: object

    GrantProgram:
      type: object
      properties:
        id:
          type: string
        name:
          type: string
        track:
          type: string
          enum:
            - sbir-sttr
            - foundation
            - venture-philanthropy
            - regulatory-orphan
            - federal-translational
        typical_award_usd:
          type: string
        equity_dilution:
          type: string
        focus_areas:
          type: string
        url:
          type: string
          format: uri

    ValidationCommunityGroup:
      type: object
      properties:
        disease_id:
          type: string
        institutional_and_patient_communities:
          type: array
          items:
            type: object
        ethical_discovery_guidelines:
          type: array
          items:
            type: string

    McpDiscoveryManifest:
      type: object
      properties:
        name:
          type: string
        version:
          type: string
        homepage:
          type: string
          format: uri
        tools:
          type: array
          items:
            type: string
        resources:
          type: array
          items:
            type: string
        prompts:
          type: array
          items:
            type: string