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IDEs

I need a nice IDE to recommend. Starting with Emacs may be problematic.

Gorilla REPL

Runs directly from lein command line – which means people need to be command line savvy and pre-install lein.

GUI is rather clunk and uses a lot of space. Difficult to go back and change.

NightCode

Single jar installation, including lein.

Pops up windows hard right on wrong screen.

Relatively easy to set up a project though.

Seems to crash

catnip

Requires lein, but cuter than gorilla

Display

Do the whole thing in org with reveal?

reveal does this irritating autozoom thing which is rather unfortunate. It means I have to be careful about the amount of stuff on screen, since I can’t scroll like I can with asciidoc/slidy.

This can be switched off, but the scroll bars don’t come back, so it’s useless.

Also, it doesn’t record what slide I am on, so the autoreload thing doesn’t work.

And I can’t do the single slide thing.

Syllabus

Section 1 – intro to hello world

Introduction

  • Welcome
  • What is the history (the karyotype ontology)
  • What is tawny (a programmatic API)

Key Features

  • Aimed at ontology building, NOT manipulation.
  • Unprogrammatic syntax, minimal baggage
  • Broadcasting
  • Fully extensible
  • Integrated reasoning
  • Build on commodity language
  • Access to fully programming tool chain (unit tests, git, build, dependency)

Tawny environment

  • Tawny architecture
  • Build on Clojure
  • Clojure is a lisp, build on JVM
  • Sits on top of OWL API

Pre-requisites

Clojure Hello World

  • Key Feature of Tawny
  • Also, key disadvantage over Protege/OBOedit
  • Need a working Clojure environment
  • Your mileage may vary – feel free to skip
  • Obtaining this tutorial: either git or download
  • Leiningen
  • Run lein catnip
  • Open Hello World, and run it.
  • Also try out the REPL
  • Other options
  • Emacs with CIDER
  • Eclipse with Counter-Clockwise
  • Cursive
  • Lighttable

How to follow

  • A complete leiningen project
  • src/tawny/lisbon
  • Place to try stuff in…
  • src/tawny/lisbon/hello_1.clj
  • Solutions (and all these slides)
  • src/tawny/lisbon/hello_1_s.clj

Tawny Hello World

  • Namespace declaration – this is a template, just copy it!
  • I should do all the namespaces
  • defontology form
  • defclass
  • Comments, labels and general tawny syntax
  • defoproperty
  • the use of the “owl-” prefix
  • save-ontology and open in protege

Section 2 – basic amino acid ontology

Introduction

  • We build a small ontology of amino acids
  • Nice because it’s tractable and well-defined.
  • Also start to build patterns

Define the class

  • AminoAcid
  • Glycine, Alanine
  • “super” keyword – not “subclassof”
  • Tawny is idempotent (generally)

as-subclasses

  • Painful, so introduce a pattern
  • as-subclasses
  • :disjoint
  • :cover
  • Interesting ontological question – the biologists will say this is correct
  • The chemists will not.

Defining the Properties

  • Want to define amino-acids by their properties
  • Are a set of standard characteristics we can use
  • Most are numerical
  • We build an abstraction which is the value partition
  • as-subproperty
  • Define a value partition by hand
  • Introduce as-facets

Formal Use of patterns

  • defpartition

Section 3 – Programmatic Considerations

Identifiers in Tawny

  • Tawny name, Clojure identifiers and URIs
  • How to build an OBO ID ontology
  • Building an ontology with strings
  • Why symbols are good

Importing, requiring and using an ontology

  • Introducing an external ontology
  • Why importing is not (necessarily) enough
  • read

AminoAcid with sio

  • equivalents and same as

How to program an autosave function

  • Clojure Java 101
  • Proxies
  • Listeners

The amino-acid pattern

  • Advanced
  • Build the pattern
  • Add SmallAminoAcid
  • Add SmallPolarAminoAcid
  • Reasoning
  • Add them all (do don’t show)
  • Filtering

Advanced Extensions

  • No more follow my leader

Questions

  • Can I add annotations on axioms
  • How does this affect ontology deployment?
  • How do you version your ontology?
  • How do you test your ontology?
  • How do you continously integrate your ontology?
  • What about advanced documentation for ontologies?
  • Can I internationalise my ontology?
  • Can I scaffolding your ontology from existing sources?
  • What happens if the labels of read ontologies change?
  • How do you convert an existing ontology to Tawny?
  • How fast is tawny?
  • Can I integrate more tightly with protege?
  • How does Tawny affect dependency management with ontologies
  • Can I link ontologies into software

The Future

  • Literate Ontologies
  • In Tawny pattern language (complete)
  • Manual!