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OBO Semantic Engineering Training
Introduction to the SSSOM Toolkit
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GitHub
OBO Semantic Engineering Training
GitHub
About the course
Getting started with learning
Overview of lessons and tutorials
Contribute to the course
Courses
Courses
ICBO 2024 Tutorial
ICBO 2023 Tutorial
ICBO 2022 Tutorial
ICBO 2021 Tutorial
Monarch Ontology Training
Ontology Summit 2023
Pathways
Pathways
What is a pathway?
Early Career Data Scientist
Ontology Curator
Ontology Curator GO-style
Ontology Curator OBI-style
Ontology Engineer/Developer
Ontology Contributor
Lessons
Lessons
Contributing to OBO ontologies
Ontology Pipelines with ROBOT
Project Ontology Development
Analysing Linked Data
Automating Ontology Workflows
Developing an OBO Ontology
Ontology Design
Templates for OBO ontologies
Ontology Fundamentals
Modelling with Object Properties
Ontology Term Use
RDF Fundamentals
Semantic Entity Matching
Disease and Phenotype Ontologies
Basic concepts of phenotype data and ontologies
Hacking the OBOOK
Getting Hands on with Ontologies
Leveraging ChatGPT for ontology curation
Using Ontologies in Practice--LinkML can help
Licensing Data and Software
Vocabularies for bioinformatics
An Introduction to Synonyms in OBO Ontologies
Lessons In Development
Lessons In Development
Developing an Application Ontology
Ontology Development
Semantic Database Fundamentals
Tutorials
Tutorials
Protege
Protege
DL queries
Disjointness
Ontology Pipelines - ODK, ROBOT, etc
Ontology Pipelines - ODK, ROBOT, etc
ROBOT Mini-Tutorial 1 - Convert, Extract and Template
ROBOT Mini-Tutorial 2 - Annotate, Merge, Reason and Diff
ROBOT Mini-Tutorial QC - Quality Control with report, verify and query
ROBOT - Generating SPARQL table reports
ODK - Adding SPARQL table reports
ODK - Getting started with your own repo
ODK - 20 minute complete walk-through
ODK - Adding custom Quality Check
ODK - Managing imports
ODK - Managing ontology releases
ODK - Migrating to ODK
ODK - Using the ODK Toolbox
Templates
Templates
Getting started with DOSDP templates
DOSDP Templates Basic Tutorial
Introduction to Managing DOSDP Templates in ODK
Git, GitHub and Collaborative Workflows
Git, GitHub and Collaborative Workflows
GitHub Fundamentals for OBO Engineers
GitHub Issue for OBO Engineers
Managing OBO ontology projects
Pull requests
OntoGPT
OntoGPT
OntoGPT Introduction
OntoGPT in Practice
Dealing with Semantic Data
Dealing with Semantic Data
From Tables to Linked Data
Standardizing Prefixes, CURIEs, and URIs with the `curies` package
Units of Measurement
Basic SPARQL for OBO Engineers
Basic cypher on the Monarch Neo4j graph
Command line
Command line
Basic introduction to CLI 1
Basic introduction to CLI 2
Mappings and SSSOM
Mappings and SSSOM
Basic Tutorial
Lexical Matching with OAK Lexmatch
Introduction to the SSSOM Toolkit
Curating Mappings with Biomappings
General Ontology Modelling
General Ontology Modelling
Project Ontology Development
Family History Knowledge Base (FHKB) tutorial
Exomiser
Exomiser
Introduction to Exomiser
Information Extraction
Information Extraction
Named Entity Recognition with Gilda
Named Entity Normalization
Named Entity Standardization
How-to guides
How-to guides
General
General
Maximising impact as an open science engineer
Creating an ontology from scratch
Create an ontology overview
Prettify Markdown Files
Create Screenshot and paste into an issue
Set-up docker
Protege
Protege
Install Protégé
Setup Protege 5.5
Installing ELK in Protege
Setting up your ID range
Editing in Protege
Daily Workflow
Edit in Protege
Switching Ontologies in Protege
Browsing and Searching
Creating New Terms in Protege
Obsoleting a Term
Merging Terms
Adding Taxon Restrictions
Creating a new Slim (under construction)
ODK
ODK
Get set up for ODK-based ontology development
Setting up the ODK
Update to a newer ODK version
Creating a Repo with ODK
Dealing with Large Ontologies
Updating Imports with ODK
Import ORCIDIO
Running ODK with podman
Migrate an existing ontology Repo to ODK
Git and GitHub
Git and GitHub
Make term requests to existing ontologies
Clone a repository
Fork an ontology for editing
Create a GitHub Pull Request
Change a pull request
Fix conflicts
Automate tasks with GitHub actions
Revert a commit
Review a pull request
Quality control
Quality control
Deploy a custom OBO-Dashboard
Command line
Command line
How to filter a file based on another file
Mappings
Mappings
Are these two entities the same? A guide.
How to review disease mappings
Reference
Reference
Tools
Glossary of Terms
Frequently used ODK commands
Protege Interface
Protege FAQ
LLMs for the Semantic Engineer
Formatting your ontology annotations correctly
OBO-style term annotation
Ontology Matching
Ontology Matching
Semantic ETL
Git
Git
Intro to GitHub
GitHub Desktop
Git FAQ
Semantic Engineering Toolbox
Tables and Triples
Reasoning
A day in the life of an ontology curator
Protege interface
SPARQL
SPARQL
SPARQL basics
SPARQL templates
Tools for Managing Issues
Release Artefacts
Base Release
Synonym Properties
Synonym Types
Synonym Validation
Monkeying around with OWL
Ontology Development Kit (ODK)
Troubleshooting ROBOT
Common Errors in GitHub actions
Other useful resources
Medical Ontology landscape
A reference guide to Wikidata
OBOOK Maturity Indicator
ChatGPT
ChatGPT
Leveraging ChatGPT for ontology curation
Ontology User references
Explanations
Explanations
Introduction to Ontologies
Logical axiomatization of classes & use of reasoning
Term Comments
Introduction to Annotation Properties
Writing good issues
Ontology Matching
Which biomedical ontologies should we use?
OWL, OBO, JSON? Base, simple, full, basic? What should you use, and why?
What are taxon constraints?
The logical building blocks of OWL
SubClassOf versus EquivalentTo
Existential restrictions
OBOOK Editors
OBOOK Editors
Getting started for OBOOK editors
How to add images
How to embed videos
New lesson template
Case studies for teaching
Outreach
Outreach
Outreach materials
Introduction to the SSSOM Toolkit
¶
A basic tutorial
Documentation