Lessons from teaching non-computer scientists OWL and ontologies
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Transcript of Lessons from teaching non-computer scientists OWL and ontologies
Lessons from teaching non-computer scientists OWL and ontologies
Robert StevensBio-health Informatics GroupSchool of Computer Science
University of manchesterOxford RoadManchester
United KingdomM13 9PL
Why am I telling you all this?
• Having users is tremendous fun• (It is also very hard work)• But users do pay you back in the end – they’ll
bbring impact and they bbring interesting problems
• They may also enable wealth and fame…..
My favourite OWL question
person and hasPet some not Cat
• How many cats can this person have as a pet?• A real tester for OWL semantics – computer scientists included• Leading teaching by understanding the meaning of statements
in OWL• If authors understand the axioms then there’s a chance of
understanding the implications
Why the Pizza Ontology
• Domain specific examples can get in the way• An example that touches all the learning outcomes is
hard• No serious ontological issues in pizzas• They are naturally compositional• Raise most features and issues in OWL DL• Pizzas a bit weak on individuals and role chains• Pizzas are understood by most people and are fun• … but pizzas now a very well known example – almost
too well known
The customers
• Knowing your customers• For us, mainly life sciences, but all sorts• Assume they are bright, but not au fait with computer
science• Their research agenda are not your research agenda• Accommmodating their needs and your own is hard,
but worth while• Hundreds of people have taken the Pizza tutorial, with
many from industry• The Pizza Ontology has become one of those examples
Getting the language right
• Your customers’ language is not your language• You’re teaching OWL, not computer science• Talking logic doesn’t work• “r1 some c1 c2 blah” doesn’t work• “Each and every instance of C1 has at least one
relation r with an instance of c2” – is better• .., but better to use actual “words” rather than
c1 and c2
Manchester Syntax
• Grew out of the manchester OWL tutorials• (Essentially that of the Ontology Inference Layer)• Textual• Infix notation• Words like “some” and “only”• Relatively easy to read out• Lends itself to “pedantic paraphrasing”• “A cheesy pizza is any pizza that, among other things, has a
cheese topping”
Person and hasPet some not (Cat) Manchester: DL:
Person .hasPet Cat
Main issues in teaching OWL
• Subsumption as necessary implication• Disjointness• Open world assumption• Boolean logic• Confusion of universal and existential quantification• Universal quantification and trivial satisfiability• Domain and range constraints and their implications• Necessity and sufficiency – equivalence axioms
Pizza issuesClass: Margherita SubClassOf: NamedPizza,hasTopping some TomatoTopping,hasTopping only (MozzarellaTopping or TomatoTopping),
Class: VegetarianPizza
EquivalentTo:PizzaAnd (hasTopping some topping) and (hasTopping only (CheeseTopping or FruitTopping or HerbSpiceTopping or NutTopping or SauceTopping or VegetableTopping))
A new (advanced) tutorial
• Based on family history• Leads with individuals• Maximises use of inference• http://owl.cs.manchester.ac.uk/tutorials/
fhkbtutorial/
A lot of Individuals under the same category
RobertWilliam
Janet
Richard Charles HerbertIris Ellen
Margaret Grace Ian
William George Mark
JohnJames David
Violet Sylvia
Julie
Clare
Person
A complex property hierarchy
“You’re not using my DL properly!”
• Unless you’re using all the language and maximising inference you’re doing it wrong!
• This attitude won’t help• Compelling use case set around the core of
OWL’s capabilities• Maintaining subsumption hierarchies - Alan
Rector’s normalisaiton pattern• http://ontogenesis.knowledgeblog.org/49
The need for good tooling
• For impact tools are needed• You can have all the language and reasoners
you want….• …, but without some tools to use them, they
won’t be used• Protégé and the OWL API• Reasoners are now good enough to drive
applications in the life-sciences
Explanations
http://riotool.sourceforge.net/
Regularity Inspector for Ontologies (RIO)
Building a community
With the language, tools and training one can build a communityOnly if there’s actually a need…Building a community takes time and patienceDon’t expect too much too soon
BioPortalhttp://bioportal.bioontology.org/
The community pays back
• BioPortal (http://bioportal.bioontology.org/) is a fantastic ontology resource
• There are applications out there driven by OWL ontologies and their reasoners (http://openflyweb.org and http://owl.cs.manchester.ac.uk/goal)
• Vast amounts of data coded with ontologies• They can bring back useful problems
Things to do
EditorsExamples
API Repositories
Tutorial Training
The message
• Evangelise and build your community• Start teaching early• Give them tools to use• Manage their and your expectations• Know and understand your customers
Acknowledgements
• Uli Sattler• Eleni Mikroyannidi• And the rest of the Manchester people