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mkdocs.yml
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site_name: OBO Semantic Engineering Training
theme: material
markdown_extensions:
- toc:
permalink: true
nav:
- About the course: index.md
- Getting started with learning: getting_started.md
- Overview of lessons and tutorials: overview.md
- Contribute to the course: contributing.md
- Courses:
- ICBO 2021 Tutorial: tutorial/icbo2021.md
- Monarch Ontology Training: courses/monarch-obo-training.md
- Lessons:
- Contributing to OBO ontologies: lesson/contributing_to_obo_ontologies.md
- Ontology Pipelines with ROBOT: lesson/ontology_pipelines.md
- Analysing Linked Data: lesson/analysing_linked_data.md
- Application Ontology Development: lesson/application_ontology_development.md
- Automating Ontology Workflows: lesson/automating_ontology_workflows.md
- Developing an OBO Ontology: lesson/developing_an_obo_ontology.md
- Developing an Application Ontology: lesson/developing_application_ontologies.md
- Ontology Design: lesson/ontology_design.md
- Templates for OBO ontologies: lesson/templates_for_obo.md
- Ontology Development: lesson/ontology_development.md
- Ontology Fundamentals: lesson/ontology_fundamentals.md
- Modelling with Object Properties: lesson/modelling_with_object_properties.md
- Ontology Term Use: lesson/ontology_term_use.md
- RDF Fundamentals: lesson/rdf.md
- Semantic Database Fundamentals: lesson/semantic_database_fundamentals.md
- Disease and Phenotype Ontologies: lesson/using_disease_and_phenotype_ontologies.md
- Tutorials:
- Ontology Pipelines - ODK, ROBOT, etc:
- ROBOT Mini-Tutorial 1 - Convert, Extract and Template: tutorial/robot_tutorial_1.md
- ROBOT Mini-Tutorial 2 - Annotate, Merge, Reason and Diff: tutorial/robot_tutorial_2.md
- ROBOT Mini-Tutorial QC - Quality Control with report and query: tutorial/robot_tutorial_qc.md
- ODK - Getting started with your own repo: tutorial/setting-up-project-odk.md
- ODK - Managing imports: tutorial/managing-dynamic-imports-odk.md
- ODK - Managing ontology releases: tutorial/managing-ontology-releases-odk.md
- ODK - Migrating to ODK: tutorial/migrating-ontology-to-odk.md
- Templates:
- DOSDP Templates: tutorial/dosdp_template.md
- Git, GitHub and Collaborative Workflows:
- GitHub Fundamentals for OBO Engineers: tutorial/github_fundamentals.md
- GitHub Issue for OBO Engineers: tutorial/github_issues.md
- Managing OBO ontology projects: tutorial/managing-ontology-project.md
- Dealing with Semantic Data:
- From Tables to Linked Data: tutorial/linking-data.md
- Basic SPARQL for OBO Engineers: tutorial/sparql.md
- General Ontology Modelling:
- Family History Knowledge Base (FHKB) tutorial: tutorial/fhkb.md
- How-to guides:
- Protege:
- Installing ELK in Protege: howto/installing_elk_in_protege.md
- Switching Ontologies in Protege: howto/switching_ontologies.md
- Browsing and Searching: howto/protege_browse_search.md
- ODK:
- Get set up for ODK-based ontology development: howto/setup_ontology_development_odk.md
- Setting up the ODK: howto/odk_setup.md
- Git and Github:
- Clone a repository: howto/clone_mondo_repo.md
- Creating an GitHub Fork: howto/github_create_fork.md
- Creating an GitHub Pull Request: howto/github_create_pull_request.md
- Change a pull request: howto/change_files_pull_request.md
- Fixing conflicts: howto/fixing-conflicts.md
- Quality control:
- Deploy a custom OBO-Dashboard: howto/deploy_custom_obo_dashboard.md
- Reference:
- Glossary: reference/glossary.md
- Other useful resources: reference/other_resources.md
- GitHub Desktop: reference/github_desktop.md
- Semantic Engineering Toolbox: reference/semantic_engineering_toolbox.md
- Tables and Triples: reference/tables-and-triples.md
- Reasoning: reference/reasoning.md
- A day in the life of an ontology curator: reference/ontology-curator.md
- Git FAQ: reference/git_faq.md
- OWL, OBO, JSON? Base, simple, full, basic? What should you use, and why?: reference/owl_formats_variants.md
- Monkeying around with OWL: reference/mungall_blog_radar.md
- Ontology Development Kit (ODK): reference/odk.md
- OBOOK Editors:
- How to add images: images/index.md
- New lesson template: config/template.md
- Case studies for teaching: teaching/case_studies.md
repo_url: https://github.com/OBOAcademy/obook/