mkdocs.yaml

site_name: Uberon Multi-species Anatomy Ontology
theme:
  name: material
  icon:
    edit: material/pencil 
  features:
    - content.action.edit
    #- navigation.tabs
    #- toc.integrate
    #- navigation.sections
    #- navigation.top
    - search.suggest
    - search.highlight
    #- content.tabs.link
    - content.code.annotation
    - content.code.copy
    - content.code.select
plugins:
  - search
markdown_extensions:
  - toc:
      permalink: true
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_div_format
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.tabbed
  - pymdownx.critic
  - pymdownx.caret
  - pymdownx.details
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.tilde
  - attr_list
  - md_in_html
  - pymdownx.highlight:
      anchor_linenums: true
  - admonition
  - pymdownx.arithmatex:
      generic: true
  - footnotes
  - attr_list
  - md_in_html
  - tables

extra_javascript:
  - https://unpkg.com/mermaid@8.5.1/dist/mermaid.min.js

repo_url: https://github.com/obophenotype/uberon/
site_url: https://obophenotype.github.io/uberon/
edit_uri: edit/master/docs/

nav:
  - Home: index.md
  - About:
      - About Uberon: about.md
      - The Uberon team: team.md
      - Uberon on GitHub: https://github.com/obophenotype/uberon
      - Issue Tracker: https://github.com/obophenotype/uberon
      - Adopters: adopters.md
      - History: history.md
      - Acknowledgements: acknowledgements.md
      - Cite: cite.md
  - Browse:
      - OLS: https://www.ebi.ac.uk/ols4/ontologies/uberon
      - Ontobee: http://www.ontobee.org/ontology/UBERON
      - BioPortal: https://bioportal.bioontology.org/ontologies/UBERON
      - Bgee Anatomical Homology: https://bgee.org/?page=anat_similarities
  - Download:
      - Current release: current_release.md
      - Cross-species bridge files: bridges.md
      - Combined Multispecies Ontologies: combined_multispecies.md
      - Releases before 2020: old_releases.md
  - How-to guides:
      - How to contribute to Uberon: contributing.md
      - Standard ODK workflows:
          - Overview: odk-workflows/index.md
          - Editors Workflow: odk-workflows/EditorsWorkflow.md
          - Release Workflow: odk-workflows/ReleaseWorkflow.md
          - Manage your ODK Repository: odk-workflows/RepoManagement.md
          - Setting up Docker for ODK: odk-workflows/SettingUpDockerForODK.md
          - Imports management: odk-workflows/UpdateImports.md
          - Managing the documentation: odk-workflows/ManageDocumentation.md
          - Continuous Integration: odk-workflows/ContinuousIntegration.md
          - Manage automated checks: odk-workflows/ManageAutomatedTest.md
          - Manage components: odk-workflows/components.md
          - Your ODK Repository Overview: odk-workflows/RepositoryFileStructure.md
  - Uberon Internal Docs: 
      - Uberon Release: uberon-release.md
      - Standard Operating Procedure for Uberon Curators: uberon-editor-sop.md
      - Onboarding a new curator: onboarding.md
  - References:
      - Wiki: https://github.com/obophenotype/uberon/wiki
      - Uberon Manual: https://github.com/obophenotype/uberon/wiki/Manual
      - User Documentation: https://github.com/obophenotype/uberon/wiki/Manual#user-docs
      - Editors Documentation: https://github.com/obophenotype/uberon/wiki/Manual#editor-docs
      - Design Patterns: https://github.com/obophenotype/uberon/wiki/Manual#design-patterns
      - Anatomical Structures: https://github.com/obophenotype/uberon/wiki/Manual#anatomical-structures
      - Uberon Build Pipeline: uberon_build_pipeline.md