mkdocs.yml

---
site_name: "OntoGPT"
theme:
  name: material
  analytics:
    gtag: G-2SYBSJVZ23
  palette:
    - media: '(prefers-color-scheme: light)'
      scheme: default
      primary: teal
      accent: amber
      toggle:
        icon: material/lightbulb
        name: Switch to light mode
    - media: '(prefers-color-scheme: dark)'
      scheme: slate
      primary: teal
      accent: amber
      toggle:
        icon: material/lightbulb-outline
        name: Switch to dark mode
  features:
    - content.tabs.link
plugins:
  - search
  - mermaid2:
      version: 9.3.0
nav:
  - Introduction: index.md
  - Setup: setup.md
  - Operation: operation.md
  - Custom Schemas: custom.md
  - OWL Exports: owl_exports.md
  - Evaluations: evaluations.md
  - Functions: functions.md
  - Starting with OWL: start_with_owl.md
  - Troubleshooting: troubleshooting.md
  - SPIRES Templates:  # Note these are autogenerated
      - Core Upper Level Schema: core/index.md
      - Alzheimer's Disease: alzrd/index.md
      - Biochemical Reactions: reaction/index.md
      - Biological Processes: biological_process/index.md
      - Biotic Interactions: biotic_interaction/index.md
      - Cell Types: cell_type/index.md
      - Chemical to Disease: ctd/index.md
      - Chemical to Disease (Entities Only): ctd_ner/index.md
      - Datasheets for Datasets: data_sheets_schema/index.md
      - Diagnostic Procedures: diagnostic_procedure/index.md
      - Dietitian Notes: dietitian_notes/index.md
      - Drugs and Mechanisms: drug/index.md
      - EMAPA (Mouse Developmental Anatomy Ontology): emapa_simple/index.md
      - Environmental Samples: environmental_sample/index.md
      - Error Analysis: error_analysis/index.md
      - Figures: figure/index.md
      - GO Terms: go_terms/index.md
      - GO Terms (Entities Only): go_simple/index.md
      - Go Terms and Relations: go_terms_relational/index.md
      - GO-CAMs and Pathways: gocam/index.md
      - Human Phenotypes: human_phenotype/index.md
      - Irritable Bowel Diseases and Literature: ibd_literature/index.md
      - Medical Actions: maxo/index.md
      - Mendelian Diseases: mendelian_disease/index.md
      - Metabolic Processes: metabolic_process/index.md
      - Metagenome Studies: metagenome_study/index.md
      - MONDO Diseases (Entities Only): mondo_simple/index.md
      - NMDC Schema Data: nmdc_schema_data/index.md
      - Ontology Classes: ontology_class/index.md
      - Ontology Issues: ontology_issue/index.md
      - Ontology Usage: onto_usage/index.md
      - Recipes: recipe/index.md
      - STORMS Checklist: storms/index.md
      - Traits of a Taxon: traits/index.md
      - Treatments: treatment/index.md
  - HALO Schema: halo/index.md
site_url: https://monarch-initiative.github.io/ontogpt/
repo_url: https://github.com/monarch-initiative/ontogpt/