Introduction

Use Case (karyotypes)

karyogram.png

Use Case (chromosomes)

ChromXISCN09.jpg

Use Case (karyotypes)

A partonomy?

Protege

protege-pizza.png

Protege

click.gif

Protege

click-fast.gif

Can we do this programmatically?

Can we do this programmatically?

OWLClass clsA = df.getOWLClass(IRI.create(pizza_iri + "#A"));
OWLClass clsB = df.getOWLClass(IRI.create(pizza_iri + "#B"));
// Now create the axiom
OWLAxiom axiom = df.getOWLSubClassOfAxiom(clsA, clsB);
// add the axiom to the ontology.
AddAxiom addAxiom = new AddAxiom(o, axiom);
// We now use the manager to apply the change
m.applyChange(addAxiom);

Brain

Brain brain = new Brain();
//Add the OWL classes
brain.addClass("Nucleus");
brain.addClass("Cell");
//Add the OWL object property
brain.addObjectProperty("part-of");
//Assert the axiom
brain.subClassOf("Nucleus", "part-of some Cell");

Ontology by pieces

Madaba_map.jpg

The Paragon

Constraints

Tawny-OWL

Ontologies in an IDE

Source

(defoproperty hasTopping
  :super hasIngredient
  :range PizzaTopping
  :domain Pizza)

Pizza Templates

Pizza Templates

(defn generate-named-pizza [& pizzalist]
  (doseq
      [[named & toppings] pizzalist]
    (owl-class
     named
     :super (some-only hasTopping toppings))))

Pizza Templates

Karyotypes

Karyotypes

(as-disjoint-subclasses
 Event
 (defclass Addition)
 (defclass Deletion)
 (defclass Duplication)
 (defclass Fission)
 (defclass Insertion)
 (defclass Inversion)
 (defclass Quadruplication)
 (defclass Translocation)
 (defclass Triplication))

Karyotypes

SIO

(defn owl-atom [name chebi]
 (owl-atom-annotation-maybe
  (owl-class (make-safe name)
             :subclass atom
             :label name)
  chebi))

Commodity tooling

Version Control

http://douroucouli.wordpress.com/2014/03/30/the-perils-of-managing-owl-in-a-version-control-system/

Unit Tests

OBO-style identifiers

(defclass OBI:0034322
     :subclass OBI:0034321)

Semantics-Free Identifiers

Continuous Integration

Dependency management

Driving Protege

Scalability

Rubbish

Literate Development

simple-literate.png

Literate Development

simple-literate-pdf-2.png

Tool Integration

Future Work

Conclusions

Acknowledgements

Links

tawny-cartoon-cropped-with-text.jpg