Lessons from teaching non-computer scientists OWL and ontologies

Robert StevensBio-health Informatics GroupSchool of Computer Science

University of manchesterOxford RoadManchester

United KingdomM13 9PL

Robert.Stevens@Manchester.ac.uk

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