These materials are under construction and incomplete.
- Install Protege
- Complete OpenHPI Week 5: Ontology Engineering videos 5.1, 5.2, and 5.4 - 5.6 (~2.5 hours)
- We are skipping 5.3: Ontology Learning and both sections on MORE Ontology Evaluation (5.7 and 5.8)
- Complete part of the Ontologies 101 Tutorial (~2 hours)
- Clone the Ontologies 101 repository, then open the folder
BDK14_exercisesfrom your file system
basic-subclass/chromosome-parts.owlin Protégé, then do the following exercises:
- Basic Subclass Hierarchy (review) - make sure to look at the "detailed instructions" for adding annotations here, as it will go over adding annotations on annotation assertions
- Object Properties - note that you will rarely, if ever, be making object properties, as most of the properties you'll ever need are defined in the Relation Ontology
- OWL Class Restrictions
basic-restriction/er-sec-complex.owlin Protégé, then do the following exercise:
- Basic Restrictions
basic-dl-query/cc.owlin Protégé, then do the following exercises:
- DL Query Tab - note that
owl:Nothingis defined as the very bottom node of an ontology, therefore the DL query results will show
owl:Nothingas a subclass. This is expected and does not mean there is a problem with your ontology! It's only bad when something is a subclass of
owl:Nothingand therefore unsatisfiable (more on that below).
- Basic DL Queries
basic-classification/ubiq-ligase-complex.owlin Protégé, then do the following exercises:
- Basic Classification
- Read (I can't get no) satisfiability (~10 minutes)
- Optional: Open a new ontology in Protégé. Try creating an inconsistent ontology using the classes and instances in the first Pets example (hint: you'll also need to create the "eats" object property)... what happens when you run the reasoner? Don't spend too much time on this if you get stuck, we'll look at an example of an inconsistent ontology in our session.
What is delivered as part of the course¶
Description: Learn the fundamentals of ontologies.
- OpenHPI course review: questions? (~15 minutes)
- OWL ontology serializations ("formats") (~15 minutes)
- Converting between serializations with
robot convert(Review; ~15 minutes)
- Creating modules from existing ontologies (~30 minutes)
- What is a module?
- How do we use the modules in our ontologies?
- Extraction methods: MIREOT vs. SLME
- Creating a module to import with
robot extract(Review; ~15 minutes)
- Ontology design patterns (~15 minutes)
- Real world example: Ontology for Biomedical Investigations (OBI)
- Using design patterns in
robot template(Review; ~15 minutes)
- Including your modules in your ontology as imports
Additional materials and resources¶
- add name/ORCID here