Introduction

What are Ontologies?
How do we build Ontologies?
How we contextualize our ontologies

How do we ontologize our context

Ontologies

This is what makes [ontologies] fundamentally different from taxonomies. While [they] fulfil two of the conditions of taxonomy (connecting relating things and semantic expression), they do not fulfil the third, which is to map the structure of the domain in a way that is easy to grasp and navigate.

Patrick Lambe
— Organising Knowledge

Ontologies

Ontologies, in fact, pride themselves on their precision, and their impenetrability to humans.

Patrick Lambe
— Organising Knowledge

Our Motivation

The karyotype are a description of all chromosomes
The human karyotype is complex to describe

Our Motivation

Current, representation comes from ISCN
Written in a book, no computational representation

47,XXY
46,Xc,+21
46,XY,+21c,-21
45,XY,-10,der(10)t(10;17)(q22;p12)
46,XY,der(7)t(2;7)(q21;q22)ins(7;?)(q22;?)
46,XX,der(8)t(8;17)(p23;q21)inv(8)(p22q13)t(8;22)(q22;q12)
46,XX,der(9)del(9)(p12)t(9;22)(q34;q11.2),der(9)t(9;12)(p13;q22)inv(9)(q13q22)
We need an ontology!

Our Motivation

23 chromosome pairs, Over 800 bands
We have to do this programmatically
- Can generate all the chromosome bands
- Can change axiomatisation later

Tawny-OWL

Interactive environment, create new ontologies, classes
Built on Clojure, the JVM, OWL API and some reasoners!

Tawny-OWL

Karyotype patterns are too complex to get on a slide
This is the equivalent for pizza

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

(generate-named-pizza
        [MargheritaPizza TomatoTopping MozzarellaTopping]
        [CajunPizza MozzarellaTopping OnionTopping PeperonataTopping
         PrawnsTopping TobascoPepperSauce TomatoTopping])

Ontologies in an IDE

It turns out, we can now use a normal code environment
And normal build and deployment tools
And normal version control
And normal unit tests

Ontologies in an IDE

Tawny-OWL is the future of ontology development

— Anon

Ontologies in an IDE

Tawny-OWL is the future of ontology development or an uber-geek dead-end.

— Anon

Ontology Building

Ontologies are often difficult to understand
To remember why things were done in a certain way
Difficult to link to the world that it describes
True with programmatic code as well

Ontology Building

Literate Programming
A program is written as program logic and natural English
The English explains the logic
The logic gives a formal representation for the English
And the program runs

Literate Programming

We have adapted this for Tawny-OWL, as shown
In one form, we can edit ontology
In another form we can edit documentation.
In short, we can contextualize our ontology

Semantic Documents

Literate ontology is a semantic document
In this case, it’s an argument about cyclists and tax
The logic checks the argument
Here, we have ontologized the context

Semantic Music

We can combine with things other than literature
In this case, the Overtone music synthesis system
So, now we have music ontologies
Or ontologized music

The Future

So, where are we going with this technology
We have a number of bio-medical use cases

The Future: Mitochondria

Small biological system
Parts (genes, anatomy) already described, and can be automated
Hence, Programmatic development
Much cannot, and needs to relate to literature
Hence, Literate Ontologies

The Future: Clinical Guidelines

Are complex, difficult documents
Full of categorical statements
With lots of background data, and knowledge
Want to be able to link and formalize these
Hence, Semantic Documents

Conclusions

Tawny-OWL gives interactive, programmatic ontology building
We can integrate text and ontology statements
Giving literate ontologies
And semantic documents

Acknowledgements

Karyotype Ontology, Jennifer Warrender, Anthony Moorman Newcastle University
Integrated Music, Michael Bell, Newcastle University
Ignazio Palmisiano, Matthew Horridge OWL API
For Tawny-Overtone
EPSRC EP/J010375/1 http://semanticmedia.org.uk/

Semantic Documents and Literate Ontologies: A rose by any other name?

Introduction

Ontologies

Ontologies

Our Motivation

Our Motivation

Our Motivation

Tawny-OWL

Tawny-OWL

Ontologies in an IDE

Ontologies in an IDE

Ontologies in an IDE

Ontology Building

Ontology Building

Literate Programming

Semantic Documents

Semantic Music

The Future

The Future: Mitochondria

The Future: Clinical Guidelines

Conclusions

Acknowledgements

Links