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mkdocs.yml
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site_name: OBO Semantic Engineering Training
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/[email protected]/dist/mermaid.min.js
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 2024 Tutorial: courses/icbo2024.md
- ICBO 2023 Tutorial: courses/icbo2023.md
- ICBO 2022 Tutorial: courses/icbo2022.md
- ICBO 2021 Tutorial: courses/icbo2021.md
- Monarch Ontology Training: courses/monarch-obo-training.md
- Ontology Summit 2023: courses/ontology-summit-2023.md
- Pathways:
- What is a pathway?: pathways/pathways.md
- Early Career Data Scientist: pathways/early-career-data-scientist.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
- Ontology Contributor: pathways/ontology-contributor.md
- Lessons:
- Contributing to OBO ontologies: lesson/contributing-to-obo-ontologies.md
- Ontology Pipelines with ROBOT: lesson/ontology-pipelines.md
- Project Ontology Development: tutorial/project-ontology-development.md
- Analysing Linked Data: lesson/analysing-linked-data.md
- Automating Ontology Workflows: lesson/automating-ontology-workflows.md
- Developing an OBO Ontology: lesson/developing-an-obo-ontology.md
- Ontology Design: lesson/ontology-design.md
- Templates for OBO ontologies: lesson/templates-for-obo.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 Entity Matching: lesson/entity-matching.md
- Disease and Phenotype Ontologies: lesson/using-disease-and-phenotype-ontologies.md
- Basic concepts of phenotype data and ontologies: lesson/phenotype-data.md
- Hacking the OBOOK: lesson/hackathon.md
- Getting Hands on with Ontologies: lesson/getting-hands-on.md
- Leveraging ChatGPT for ontology curation: lesson/chatgpt-ontology-curation.md
- Using Ontologies in Practice--LinkML can help: lesson/linkml-helps-with-ontology-use.md
- Licensing Data and Software: lesson/licensing-data-and-software.md
- Vocabularies for bioinformatics: lesson/vocabularies-for-bioinformatics.md
- An Introduction to Synonyms in OBO Ontologies: lesson/synonyms.md
- Lessons In Development:
- Developing an Application Ontology: lesson/developing-application-ontologies.md
- Ontology Development: lesson/ontology-development.md
- Semantic Database Fundamentals: lesson/semantic-database-fundamentals.md
- 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 - 20 minute complete walk-through: tutorial/odk-tutorial-2.md
- ODK - Adding custom Quality Check: tutorial/custom-qc.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
- ODK - Using the ODK Toolbox: tutorial/odk-toolbox.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
- Pull requests: tutorial/pull-requests.md
- ChatGPT:
- Leveraging ChatGPT for ontology curation: lesson/chatgpt-ontology-curation.md
- OntoGPT: tutorial/ontogpt.md
- Dealing with Semantic Data:
- From Tables to Linked Data: tutorial/linking-data.md
- Standardizing Prefixes, CURIEs, and URIs with the `curies` package: tutorial/curies.md
- Units of Measurement: tutorial/units.md
- Basic SPARQL for OBO Engineers: tutorial/sparql.md
- Basic cypher on the Monarch Neo4j graph: tutorial/monarch-kg-neo4j-basics.md
- Command line:
- Basic introduction to CLI 1: tutorial/intro-cli-1.md
- Basic introduction to CLI 2: tutorial/intro-cli-2.md
- Mappings and SSSOM:
- Basic Tutorial: tutorial/sssom-tutorial.md
- Lexical Matching with OAK Lexmatch: tutorial/lexmatch-tutorial.md
- Introduction to the SSSOM Toolkit: tutorial/sssom-toolkit.md
- Curating Mappings with Biomappings: tutorial/biomappings.md
- General Ontology Modelling:
- Project Ontology Development: tutorial/project-ontology-development.md
- Family History Knowledge Base (FHKB) tutorial: tutorial/fhkb.md
- Exomiser:
- Introduction to Exomiser: tutorial/exomiser-tutorial.md
- Information Extraction:
- Named Entity Recognition with Gilda: tutorial/named-entity-recognition.md
- Named Entity Normalization: tutorial/named-entity-normalization.md
- Named Entity Standardization: tutorial/named-entity-standardization.md
- How-to guides:
- General:
- Maximising impact as an open science engineer: howto/open-science-engineer.md
- Creating an ontology from scratch: howto/create-ontology-from-scratch.md
- Create an ontology overview: howto/ontology-overview.md
- Prettify Markdown Files: howto/prettify.md
- Create Screenshot and paste into an issue: howto/screenshot.md
- Set-up docker: howto/setup-docker.md
- Protege:
- Install Protégé: howto/install-protege.md
- Setup Protege 5.5: howto/set-up-protege.md
- 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
- Update to a newer ODK version: howto/odk-update.md
- Creating a Repo with ODK: howto/odk-create-repo.md
- Dealing with Large Ontologies: howto/deal-with-large-ontologies.md
- Updating Imports with ODK: howto/update-import.md
- Import ORCIDIO: howto/odk-add-orcidio-module.md
- Running ODK with podman: howto/run-odk-with-podman.md
- Git and GitHub:
- Make term requests to existing ontologies: howto/term-request.md
- Clone a repository: howto/clone-mondo-repo.md
- Fork an ontology for editing: howto/github-create-fork.md
- Create a GitHub Pull Request: howto/github-create-pull-request.md
- Change a pull request: howto/change-files-pull-request.md
- Fix conflicts: howto/fixing-conflicts.md
- Automate tasks with GitHub actions: howto/github-actions.md
- Revert a commit: howto/revert-commit.md
- Review a pull request: howto/review-pull-request.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
- Mappings:
- Are these two entities the same? A guide.: howto/are-two-entities-the-same.md
- How to review disease mappings: howto/review-disease-mappings.md
- Reference:
- Tools: reference/glossary.md
- Glossary of Terms: reference/glossary-of-terms.md
- Frequently used ODK commands: reference/frequently-used-odk-commands.md
- Protege Interface: reference/protege-interface.md
- Protege FAQ: reference/protege-faq.md
- LLMs for the Semantic Engineer: reference/llms.md
- Formatting your ontology annotations correctly: reference/formatting-license.md
- OBO-style term annotation: reference/go-style-annotation-property-practice.md
- Ontology Matching:
- Semantic ETL: reference/semantic-etl.md
- Git:
- Intro to GitHub: reference/github-intro.md
- GitHub Desktop: reference/github-desktop.md
- Git FAQ: reference/git-faq.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:
- SPARQL basics: reference/sparql-basics.md
- SPARQL templates: reference/sparql-reference.md
- Tools for Managing Issues: reference/managing-issues.md
- Release Artefacts: reference/release-artefacts.md
- Base Release: reference/base-specification.md
- Synonym Properties: reference/synonyms-properties.md
- Synonym Types: reference/synonyms-types.md
- Synonym Validation: reference/synonym-validation.md
- Monkeying around with OWL: reference/mungall-blog-radar.md
- Ontology Development Kit (ODK): reference/odk.md
- Troubleshooting ROBOT: reference/troublehooting-robot.md
- Common Errors in GitHub actions: reference/gh-actions-errors.md
- Other useful resources: reference/other-resources.md
- Medical Ontology landscape: reference/medical-ontology-landscape.md
- A reference guide to Wikidata: reference/wikidata.md
- OBOOK Maturity Indicator: reference/obook-maturity-indicator.md
- ChatGPT:
- Leveraging ChatGPT for ontology curation: reference/chatgpt-prompts-for-ontology-development.md
- Ontology User references: reference/ontology-user.md
- Explanations:
- Introduction to Ontologies: explanation/intro-to-ontologies.md
- Logical axiomatization of classes & use of reasoning: explanation/logical-axiomatization.md
- Term Comments: explanation/term-comments.md
- Introduction to Annotation Properties: explanation/annotation-properties.md
- Writing good issues: explanation/writing-good-issues.md
- Ontology Matching: explanation/ontology-matching.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
- The logical building blocks of OWL: explanation/owl-building-blocks.md
- SubClassOf versus EquivalentTo: explanation/subClassOf-vs-equivalentTo.md
- Existential restrictions: explanation/existential-restrictions.md
- OBOOK Editors:
- Getting started for OBOOK editors: getting-started-obook.md
- How to add images: images/index.md
- How to embed videos: howto/embed-video.md
- New lesson template: config/template.md
- Case studies for teaching: teaching/case-studies.md
- Outreach:
- Outreach materials: reference/outreach.md
repo_url: https://github.com/OBOAcademy/obook/
site_url: https://oboacademy.github.io/obook/
edit_uri: edit/master/docs/