moalmanac-docs/mkdocs.yml at main · vanallenlab/moalmanac-docs · GitHub

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site_name: Molecular Oncology Almanac Documentation
theme:
  name: material
  features:
    - navigation.tabs
    - navigation.sections
    - toc.integrate
    - content.code.copy
  palette:
    primary: custom
    accent: custom

extra_css:
- stylesheets/extra.css

plugins:
  - search

markdown_extensions:
  - admonition
  - footnotes
  - tables
  - toc:
      permalink: true
  - pymdownx.details
  - pymdownx.superfences

nav:
  - Home: index.md
  - Start Here:
      - Overview: start-here/index.md
      - Quickstarts:
          - Reader: start-here/quickstarts/reader.md
          - Curator: start-here/quickstarts/curator.md
          - Developer: start-here/quickstarts/developer.md
  - Concepts:
      - Overview: concepts/index.md
      - Glossary: concepts/glossary.md
      - IDs and Namespaces: concepts/ids-and-namespaces.md
      - Referenced vs Dereferenced: concepts/referenced-vs-dereferenced.md
      - Provenance: concepts/provenance.md
      - Dates and Versioning: concepts/dates-and-versioning.md
      - URL Strategy: concepts/url-strategy.md
  - Database:
      - Overview: database/index.md
      - Service Overview:
          - Workflow: database/overview/workflow.md
          - Schema Diagram: database/overview/schema-diagram.md
          - Dereferencing Pipeline: database/overview/dereferencing-pipeline.md
          - Validation and QC: database/overview/validation-and-qc.md
          - Reviewer Guide: database/overview/reviewer-guide.md
          - Pitfalls and Edge Cases: database/overview/pitfalls-and-edge-cases.md
      - Schemas:
          - Overview: database/schemas/index.md
          - Referenced:
              - Overview: database/schemas/referenced/index.md
              - Documents: database/schemas/referenced/documents.md
              - Indications: database/schemas/referenced/indications.md
              - Agents: database/schemas/referenced/agents.md
              - URLs: database/schemas/referenced/urls.md
          - Dereferenced:
              - Overview: database/schemas/dereferenced/index.md
              - Documents: database/schemas/dereferenced/documents.md
              - Indications: database/schemas/dereferenced/indications.md
              - Agents: database/schemas/dereferenced/agents.md
              - URLs: database/schemas/dereferenced/urls.md
      - SOP:
          - Overview: database/sop/index.md
          - General:
              - Curation Workflow: database/sop/general/curation-workflow.md
              - Source Hierarchy: database/sop/general/source-hierarchy.md
              - Naming Normalization: database/sop/general/naming-normalization.md
              - Monitoring and Staying Up to Date: database/sop/general/monitoring-and-staying-up-to-date.md
              - PR Checklist: database/sop/general/pr-checklist.md
          - Agencies:
              - Overview: database/sop/agencies/index.md
              - FDA: database/sop/agencies/fda.md
              - EMA: database/sop/agencies/ema.md
              - HPRA: database/sop/agencies/hpra.md
              - HSE: database/sop/agencies/hse.md
  - API:
      - Overview: api/index.md
      - Quickstart: api/quickstart.md
      - Endpoints: api/endpoints.md
      - Schemas: api/schemas.md
      - Versioning: api/versioning.md
  - Browser:
      - Overview: browser/index.md
      - Deployment: browser/deployment.md
      - Configuration: browser/configuration.md
      - Troubleshooting: browser/troubleshooting.md
  - Algorithm:
      - Overview: algorithm/index.md
      - Service Overview: algorithm/overview.md
      - Inputs and Outputs: algorithm/inputs-and-outputs.md
      - Validation: algorithm/validation.md
  - Governance:
      - Overview: governance/index.md
      - Releases and Versioning: governance/releases-and-versioning.md
      - Schema Evolution: governance/schema-evolution.md
      - Deprecation Policy: governance/deprecation-policy.md
      - Citation and Attribution: governance/citation-and-attribution.md