BioCypher/mkdocs.nav.yml at main · jdreo/BioCypher · GitHub

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site_name: BioCypher

nav:
    - Home: index.md

    - About:
          - Project: biocypher-project/project.md
          - Design philosophy: biocypher-project/design-philosophy.md
          - Use Cases: biocypher-project/use-cases.md
          - BioCypher + LLMs: biocypher-project/biochatter-integration.md
          - R and Bioconductor: biocypher-project/r-bioc.md

    - Get Started:
          - Installation: installation.md
          - Quickstart: learn/quickstart.md
          - LLM Integration: llms.md


    - Learn:
          - Tutorials:
                - Basics: learn/tutorials/tutorial001_basics.md
                - Handling Ontologies: learn/tutorials/tutorial002_handling_ontologies.md
                - Adapters: learn/tutorials/tutorial003_adapters.md
                - BioCypher and Pandas: learn/tutorials/pandas_tutorial.ipynb
                - Agent API Guide: learn/tutorials/agent_api_guide.md
                - Hands-on Protein Graphs with BioCypher and Neo4j: learn/tutorials/tutorial_basics_neo4j_offline/tutorial_004_neo4j_offline.md

          - HowTo / FAQ:
                - learn/guides/index.md
                - Standalone Docker Image: learn/guides/htg001_standalone_docker_biocypher.md

          - Explanations:
                - learn/explanation/index.md
                - About Adapters: learn/explanation/adapters.md
                - About Ontologies: learn/explanation/ontologies.md
                - Schema Configuration Philosophy: learn/explanation/schema-config-philosophy.md
                - Graph Class Guide: learn/explanation/graph_class_guide.md
                - Architecture Migration Guide: learn/explanation/architecture-migration.md

    - Reference:
          - Reference Index: reference/index.md
          - API Documentation:
                - reference/source/index.md
                - BioCypher: reference/source/biocypher.md
                - BioCypherWorkflow: reference/source/biocypher-workflow.md
                - Graph Class: reference/source/graph-class.md
                - Output Writing: reference/source/output-write.md
                - Output In-Memory: reference/source/output-in-memory.md
                - Output Driver: reference/source/output-driver.md
                - Download and Cache: reference/source/download-cache.md
                - Ontology Handling: reference/source/ontology.md
                - Graph Handling: reference/source/graph-handling.md
                - Mapping and Translation: reference/source/translation.md
                - Logging: reference/source/logging.md
                - Miscellaneous Utility Functions: reference/source/utils.md
          - BioCypher Configuration: reference/biocypher-config.md
          - Output Configuration:
                - Overview: reference/outputs/index.md
                - Neo4j: reference/outputs/neo4j-output.md
                - SQLite: reference/outputs/sqlite-output.md
                - PostgreSQL: reference/outputs/postgresql-output.md
                - NetworkX: reference/outputs/networkx-output.md
                - Tabular Format: reference/outputs/tabular-output.md
                - RDF: reference/outputs/rdf-output.md
                - OWL: reference/outputs/owl-output.md
                - ArangoDB: reference/outputs/arangodb-output.md
          - Schema Configuration: reference/schema-config.md

    - Community:
          - Join Us: community/index.md
          - Where to Start: community/contribute.md
          - Contribute to the Documentation: community/contribute-docs.md
          - Contribute to the Code Base: community/contribute-codebase.md