How to Build an Ontology

How to Build an Ontology • Barry Smith • http://ontology.buffalo.edu/smith

Mission of the NCBO • To create software and support services for science-based ontology development and use in the biomedical domain • Science-based = ontologies for support of scientific research (taken as encompassing evidence-based medicine) • Science-based = using the scientific method as part of the process of ontology development and testing

Scientific ontologies have special features • Every term in a scientific ontology must be such that the developers of the ontology believe it to refer to some entity on the basis of the best current evidence

For scientific ontologies • reusability is crucial • compatibility with neighboring scientific ontologies is crucial  it should not be too easy to add new terms to an ontology • we want to introduce these features in clinical medicine ...

An Ontological Square

Problem of ensuring sensible cooperation in a massively interdisciplinary community • concept • type • instance • model • representation • data

from Handbook of Ontology(Semantic Web approach) • RetailPrice hasA Denomination InstanceOf Dollar (p. 101) • SI-Unit instanceof System-of-Units (p. 40)

from: Ontological Engineering(Semantic Web approach) • location =def. a spatial point identified by a name (p. 12) • arrivalPlace =def. a journey ends at a location (p. 13) • facet =def. ternary relation that holds between a frame, a slot, and the facet (p. 51)

Entity =def • anything which exists, including things and processes, functions and qualities, beliefs and actions, documents and software (Levels 1, 2 and 3)

First basic distinction • universal vs. instance • (science text vs. diary) • (man vs. Maximilian)

Instances  databasesFor scientific ontologies • it is generalizations that are important = universals, types, kinds, species

Catalog vs. inventory

Catalog of Universals/Types

Ontology Universals Instances

Ontology = A Representation of Universals

Ontology = A representation of universals • Each node of an ontology consists of: • preferred term (aka term) • term identifier (TUI, aka CUI) • synonyms • definition, glosses, comments

An ontology is a representation of universals • We learn about universals in reality from looking at the results of scientific experiments in the form of scientific theories – which describe not what is particular in reality but what is general

substance organism animal cat instances siamese universals mammal leaf class frog

Domain =def • a portion of reality that forms the subject-matter of a single science or technology or mode of study or administrative practice ...; • proteomics • HIV • epidemiology

Representation =def • an image, idea, map, picture, name or description ... of some entity or entities.

Ontologies are representational artifacts • comparable to science texts

The Periodic Table Periodic Table

Ontologies are here

or here

What do ontologies represent?

Ontologies do not represent concepts in people’s heads

They represent universals in reality

“leg” is not the name of a concept • concepts do not stand in • part_of • connectedness • causes • treats ... • relations to each other

instances universals

Inventory vs. Catalog:Two kinds of composite representational artifacts • Databases represent instances • Ontologies represent universals

How do we know which general terms designate universals? • Roughly: terms used by scientists to designate entities about which we have a plurality of different kinds of testable proposition • (cell, electron ...)

Problem: fiat demarcations • male over 30 years of age with family history of diabetes • abnormal curvature of spine • participant in trial #2030

Problem: roles • fist • patient • FDA-approved drug

Administrative ontologies often need to go beyond universals • Fall on stairs or ladders in water transport injuring occupant of small boat, unpoweredRailway accident involving collision with rolling stock and injuring pedal cyclistNontraffic accident involving motor-driven snow vehicle injuring pedestrian

universals vs. classes universals {a,b,c,...} classes

Class =def • a maximal collection of particulars determined by a general term • (‘cell’. ‘electron’), (‘ ‘restaurant in Palo Alto’, ‘Italian’) • the class A • = the collection of all particulars x for which ‘x is A’is true

Problem • The same general term can be used to refer both to universals and to collections of particulars. Consider: • HIV is an infectious retrovirus • HIV is spreading very rapidly through Asia

universals vs. classes universals {c,d,e,...} classes

Extension =def • The extension of a universal A is the class: instance of the universal A • (it is the class of A’s instances) • (the class of all entities to which the term ‘A’ applies)

universals vs. classes universals defined classes

universals vs. classes universals populations, ...

Defined class =def • a class defined by a general term which does not designate a universal • the class of all diabetic patients in Leipzig on 4 June 1952

OWL is a good representation of defined classes • sibling of Finnish spy • member of Abba aged > 50 years

Terminology =def. • a representational artifact whose representational units are natural language terms (with IDs, synonyms, comments, etc.) which are intended to designate universals together with defined classes.

universals, classes, concepts universals defined classes ‘concepts’

universals < defined classes < ‘concepts’ • ‘concepts’ which do not correspond to defined classes: • ‘Surgical or other procedure not carried out because of patient's decision’ • ‘Absent nipple’

(Scientific) Ontology =def. • a representational artifact whose representational units (which may be drawn from a natural or from some formalized language) are intended to represent • 1. universals in reality • 2. those relations between these universals which obtain universally (= for all instances) • lung is_a anatomical structure • lobe of lung part_of lung

How to Build an Ontology