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mkdocs.yml
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site_name: OBO Semantic Engineering Training
theme:
name: 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: courses/icbo2021.md
- Monarch Ontology Training: courses/monarch-obo-training.md
- Pathways:
- What is a pathway?: pathways/pathways.md
- Ontology Curator: pathways/ontology-curator.md
- Ontology Curator GO-style: pathways/ontology-curator-go-style.md
- Ontology Curator OBI-style: pathways/ontology-curator-obi-style.md
- Ontology Engineer/Developer: pathways/ontology-engineer.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
- Documentation:
- Tutorials:
- Protege:
- DL queries: tutorial/basic-dl-query.md
- Disjointness: tutorial/disjointness.md
- 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, verify and query: tutorial/robot-tutorial-qc.md
- ROBOT - Generating SPARQL table reports: tutorial/sparql-report-robot.md
- ODK - Adding SPARQL table reports: tutorial/sparql-report-odk.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:
- Getting started with DOSDP templates: tutorial/dosdp-overview.md
- DOSDP Templates Basic Tutorial: tutorial/dosdp-template.md
- Introduction to Managing DOSDP Templates in ODK: tutorial/dosdp-odk.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
- Setting up your ID range: howto/idrange.md
- Editing in Protege: howto/edit-in-protege.md
- Daily Workflow: howto/daily-curator-workflow.md
- Edit in Protege: howto/edit-in-protege.md
- Switching Ontologies in Protege: howto/switching-ontologies.md
- Browsing and Searching: howto/protege-browse-search.md
- Creating New Terms in Protege: howto/create-new-term.md
- Obsoleting a Term: howto/obsolete-term.md
- Merging Terms: howto/merge-terms.md
- Adding Taxon Restrictions: howto/add-taxon-restrictions.md
- Creating a new Slim (under construction): howto/add-new-slim.md
- ODK:
- Get set up for ODK-based ontology development: howto/setup-ontology-development-odk.md
- Setting up the ODK: howto/odk-setup.md
- Creating a Repo with ODK: howto/odk-create-repo.md
- Dealing with Large Ontologies: howto/deal-with-large-ontologies.md
- Git and Github:
- Clone a repository: howto/clone-mondo-repo.md
- Fork an ontology for editing: 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
- Command line:
- How to filter a file based on another file: howto/filter-text-file.md
- Reference:
- Frequently used ODK commands: reference/frequently-used-odk-commands.md
- Protege Interface: reference/protege-interface.md)
- Formatting your ontology annotations correctly: reference/formatting-license.md
- OBO-style term annotation: reference/go-style-annotation-property-practice.md
- Glossary: reference/glossary.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
- Protege interface: reference/protege-interface.md
- SPARQL basics: reference/sparql-basics.md
- Git FAQ: reference/git-faq.md
- Tools for Managing Issues: reference/managing-issues.md
- Release Artefacts: reference/release-artefacts.md
- Synonyms: reference/synonyms-obo.md
- Monkeying around with OWL: reference/mungall-blog-radar.md
- Ontology Development Kit (ODK): reference/odk.md
- Troubleshooting ROBOT: reference/troublehooting-robot.md
- Other useful resources: reference/other-resources.md
- Explanation:
- Term Comments: explanation/term-comments.md
- Writing good issues: explanation/writing-good-issues.md
- Assert or Reason (under construction): explanation/deleting-asserted-sub-classes.md
- Which biomedical ontologies should we use?: explanation/which-ontology-to-use.md
- OWL, OBO, JSON? Base, simple, full, basic? What should you use, and why?: explanation/owl-format-variants.md
- What are taxon constraints?: explanation/taxon-constraints-explainer.md
- OBOOK Editors:
- Getting started for OBOOK editors: getting-started-obook.md
- 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/