Can there be such a thing as Ontology Engineering?

Robert StevensBioHealth Informatics Group

University of Manchester

Introduction

A bit of ontology introduction if required; What is engineering? Predictability in ontology engineering The application of deterministic principles The role of strict semantics The role of philosophy Acquiring some level of reproducibility.

A World of Instances

The world (of information) is made up of things and lots of them Instances, individuals, objects, tokens, particulars. The Earth is a kind of Planet Robert Stevens (NE 67 41 58 A) is a Person All the individual Alpha Haemoglobins in my many Instances of Red Blood

Cell Each cell instance in my Body has copies of some 30,000 Genes A Word, language, idea, etc. This Table, those Chairs, Any Thing with “A”, “The”, “That”, etc. before it….

We Put things into Categories

All these instances hang about making our world Putting these things into categories is a fundamental part of human

cognition Psychologists study this as concept formation The same instances are put into a category The capitalised and italicised in the slide before last

We have Labels for the Categories and their Instances

We label categories with symbols: Words “Lion” is a category of big cat with big teeth Gene, Protein, Cell, Person, Hydrolase Activity, etc. …and, as we’ve already seen, each category can have many labels and

any particular label can refer to more than one category Semantic Heterogeneity “A lion” is an instance in that category Does the category “Lion” exist? Lions exist, but the category could just be a human way of talking about

lions … we like putting things into categories

A Controlled Vocabulary

A specified set of words and phrases for the categories in which we place instances

Natural language definitions for those words and phrases

A glossary defines, but doesn’t control The Uniprot keywords define and control Control is placed upon which labels are used to

represent the categories (concepts) we’ve used to describe the instances in the world

…, but there is nothing about how things in these categories are related

Biopolymer

DNA

Enzyme

Nucleic acid

mRNA

Polypeptide

snRNA

tRNA

We also like to Relate Things Together

Categories have subcategories Instances in one category can be related

in some way to instances in another Can relate instances to each other in

many different ways Is-a, part-of, develops-from, etc.axes We can use these relationships to classify

categories Things in category A are part is If all instances in category A are also in

category B then As are kinds of Bs

Biopolymer

Nucleic Acid Polypeptide

Enzyme

DNA RNA

tRNA mRNA smRNA

Categories and sub-categories

biopolymer

polypeptide Nucleic acid

enzymeDNA

RNA

Describing Category Membership

We can make conditions that any instance must fulfil in order to be a member of a particular category

A Phosphatase must have a phosphatase catalytic domain A Receptor must have a transmembrane domain A codon has three nucleotide residues A limb has part that is a joint A man has a Y chromosome and an X chromosome A woman has only an X chromosome

Relationships

These conditions made from a property and a successor relationship

isPartOf, hasPart isDerivedFrom DevelopsFrom isHomologousTo …and many, many more

A Structured Controlled Vocabulary

Not only can we agree on the labels we give categories

Can also agree on how the instances of categories are related

And agree on the labels we give he relations

Structure aids querying and captures knowledge with greater fidelity

Biopolymer

Nucleic Acid Polypeptide

Enzyme

DNA RNA

tRNA mRNA smRNAGene

regionOf

transcribedFrom

trans

lated

From

Manchester MercuryJanuary 1st 1754

Executed 18Found Dead 34Frighted 2Kill'd by falls and other

accidents 55Kill'd themselves 36Murdered 3Overlaid 40Poisoned 1Scalded 5Smothered 1Stabbed 1Starved 7Suffocated 5

Aged 1456

Consumption 3915

Convulsion 5977

Dropsy 794

Fevers 2292

Smallpox 774

Teeth 961

Bit by mad dogs 3

Broken Limbs 5

Bruised 5

Burnt 9

Drowned 86

Excessive Drinking 15

List of diseases & casualties this year

19276 burials

15444 christenings

Deaths by centile

Uses of Ontology in Bioinformatics

What is engineering?

American Engineers' Council for Professional Development defines "engineering" as:

“The creative application of scientific principles to design or develop structures, machines, apparatus, or manufacturing processes, or works utilizing them singly or in combination; or to construct or operate the same with full cognizance of their design; or to forecast their behavior under specific operating conditions; all as respects an intended function, economics of operation and safety to life and property.[2]”

Taken from http://en.wikipedia.org/wiki/Engineering

What Type of Artefact? The Rise of the Computer Science Ontology

A term borrowed from philosophy Not supposed to be the same thing, but… Meant to deliver formal, computational semantics to

applications and humans Necessarily involves consensus

Software engineering life cycle

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http://www.samsvb.co.uk

Ontology

Where are we in the Development of Ontology Engineering?

At about 1975… There’s a lot of craft involved; Too much reliance on gurus Could two independent sets of ontologist develop two

ontologies for the same domain with the same utility? Can we cost ontology building? Do we know when we have succcess?

The Waterfall Method

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RequirementsRequirements

ConceptualisationConceptualisation

Development +Coding

Development +Coding

Quality+TestingQuality+Testing

Maintenance +Support

Maintenance +Support

Getting it right first time

Something a bit more agile

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Requirements, scoping, Competency questions

Knowledge acquisition

Conceptualisation, pattern forming

Axiomatization

Testing / evaluation?

Repeated, small

iterations

Repeated, small

iterations

Users always involved

Users always involved

Four Broad Areas of Ontology Engineering

1. Technical aspects: Code repositories, issue trackers, editors, and so on

2. Coding styles and naming conventions, etc.

3. Choosing a class, placing it in a hierarchy and choosing relationships and entities by which it is described.

4. The rhetoric behind how (2) and (3) are done. One can have philosophical justification for any decision, or it can just be practically useful….

Getting the Requirements Right

Truth and beauty is an easy requirement to state Just model the world as it is and all else wil flow from this; Not necessarily helpful; Have to set a scope; Have to set priorities – what do we most need to represent? Competency questions – what do I need to be able to answer? Separating “what the ontology must answer” and “what the ontology

must enable to be answered”; Requirements change; keeping it “agile” Setting priorities.

Strict Semantics

Languages such as OWL have a strict semantics; Statements have a precise and interpretable meaning; Deductions can follow from a series of statements; Can be used to aid development and use of the ontology

Correct, but Wrong…

An automated reasoner for OWL can make sure all your axioms are coherent;

One can make sure the ontology is structurally robust The statements in the ontology can stil be rubbish

though… A strict semantics lends some kind of predictability to an

ontology; A pure description logic approach of all defined classes

has some appeal…

Total Definition

In OWL a defined class can find its own place in the hierarchy A parent is any person that has a child; A mother is any woman that has a child; As a woman is a kind of person, we can infer a mother to be a kind

of parent; Do this for all classes; press the button and you have an ontology Definition is hard (but that may be a good thing) and the tools may

lack Requires discipline from the authors …and it all grounds out to a primitive somewhere along the line…

Normalisation

An “engineering” method to manage polyhierarchies in ontology through reasoning;

Make a strict tree of primitive classes using one criterion; Put all other criteria as restrictions upon those classes; Re-establish the polyhierarchy through defined classes

with the “other” criteria…. http://ontogenesis.knowledgeblog.org/49

Authoring Tools

These are really just axiom editors Support for the surrounding processes are nascent Lots of “hand-crafting” of even large ontologies Knowledge gathering tools; organising tools; axiom

generation tools; checking and validation tools; …

Protégé 4

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Patterns and Components

Software Design Patterns: Accepted design solutions to common problems;

Application building at the level of components; Design pattern analogy in ontologies; Patterns or regularities that are not ODP; Ontologies tend to be repetitious and humans tend to be

bad at repetition – tedium kicks in…. Calls for automation

Ontology Pre-Processor Language

A cell type is equivalent to a cell type that is part of some anatomy

Pattern

Ontology Pre-Processor Language

?cell:CLASS, ?anatomyPart:CLASS, ?anatomy:CLASS =

(CL:0000000 part_of some ?anatomyPart)

BEGINADD ?cell equivalentTo ?anatomyEND;

Variables

Create axioms

A cell type is equivalent to a cell type that is part of some anatomy

Pattern

OPPL Script

Ontology Pre-Processor Language

?cell:CLASS, ?anatomyPart:CLASS, ?anatomy:CLASS =

(CL:0000000 part_of some ?anatomyPart)

BEGINADD ?cell equivalentTo ?anatomyEND;

A cell type is equivalent to a cell type that is part of some anatomy

Pattern

OPPL Script

Variable mapper ?cell -> ‘Kidney Cell’[CL:0003523]?anatomyPart -> ‘Kidney’[FMA:629093]

Resulting OWL axioms

Class: CL:0003523

Annotation:rdfs:label ‘Kidney Cell’

EquivalentTo:CL:0000000 and OBO_REL:part_of some FMA:629093

A ‘Kidney Cell’ is equivalent to a cell that is part of the ‘Kidney’

Example

Generated OWL (Manchester Syntax)

Automation

Moving from hand-crafting to production line Can try things out and then re-model (as long as the

entities involved don’t change) Documents what has been done; Ruthlessly consistent; Also need support in repetitious knowledge gathering as

well as axiom generation.

Populous

Generic tool for populating ontology templates Spreadsheet style interface Supports validation at the point of data entry Expressive Pattern language for OWL Ontology generation

http://www.e-lico.eu/populous

Evaluation

A big “can of worms” Closely linked to requirements Closely linked to what one believes an ontology to be…; “Just do what I say and it will be OK” isn’t an evaluation

strategy; Nor is saying “just model reality” and that’s all you need

to evaluate; No really convincing way of doing it.

The Role of philosophy

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BiologyComputer Science

Philosophy

Angels on the head of a pin

BiologyComputer Science

Philosophy

The role of philosophy

Can we have Ontology Engineering?

Probably, but you’ll have to wait; Not much predictability, except to say “it’s hard” and “people wil

disagree with you” So, much like software engineering; Much to learn from SE and it should be quicker; Programming is not software engineering Axiom authoring is not ontology engineering; At the moment we’re writing axioms, but realise we need to

engineer; Once wwe can demonstrate, with predictability, that two

independent groups can take a method and each produce an ontology that meets some needs then I’ll begin to relax.