Introduction to Ontologies

1
Introduction to Ontologies

• Introduction
• Motivation
• Ontologies compared to other stuff
• Example first part
• Upper ontology specifics
• Example second part
• Discussion

2
Ground Rules

• Practical goal of providing basic grounding in
  knowledge engineering
• There are many alternatives, to make progress
  requires making choices and getting to work

3
Definitions

• An ontology is a shared conceptualization of a
  domain
• An ontology is a set of definitions in a formal
  language for terms describing the world

4
Motivation

• select EMPDAT from PERSTAB where POSmgmnt
• What does it mean?
• PERSTAB is a table which lists employee data
• Whats an employee? How is an employee different
  from a contractor? What if I want data on both?
• Even if this information is available in English,
  a machine has to read it

5
Motivation (2)

• "Parenthood is a more general relationship than
  motherhood."
• "Mary is the mother of Bill."
• "Who are Bill's parents?
• "Mary is the parent of Bill.
• that fact is not stated anywhere, but can be
  derived by a DAML application. Darpa Agent Markup
  Language- for Semantic web.

Example from Why Use DAML? lthttp//www.daml.org
/2002/04/why.htmlgt
6
Motivation (2) continued

• More formally stated, given the statements
• (motherOf subProperty parentOf)
• (Mary motherOf Bill)
• when stated in DAML, allows you to conclude
• (Mary parentOf Bill)
• Java code or a stored procedure could do this
  sort of inference for facts in XML or SQL
• But the DAML spec itself says the conclusion is
  true
• In contrast, different Java code could reach a
  different conclusion

7
Motivation (2) continued

• (Mary motherOf Bill)
• (parentOf inverse childOf)
• (Bill childOf ?X)
• ?X Mary
• The semantics of inverse is part of the DAML
  spec

8
Language Formality and Expressiveness
Human Language
Cyc
F-Logic
KIF
Machine Processing
OWL
OWLWeb ontology lang. More expressive than XML
RDF. It is the revision of DAMLOIL web ontology
lang.
Human Consumption
Machine Inference
SQL
Expressiveness
DAML
XML
Formality
9
Content Formality and Size
WordnetOnline lexical DB synonym concepts,
relations. UMLS NLMs Unified Medical Lang Sys
for knowledge rep and retrieval. Cyc Commonsense
reasoning engine. SUMO Suggested Upper Merged
Ontology- IEEE stad- Uses KIF. Dictionary. DOLCE
Descriptive Ontology for Linguistic and cognitive
engineering.
Cyc
WordNet
SUMOdomain
SUMO
UMLS
Yahoo!
DOLCE
Taxonomy
Lexicons
Formal Ontology
Size
Formality
10
Everything is not a Nail

• Ontology is not always the right tool for the job
• Face recognition, vehicle control systems etc
  not the right applications for ontology

11
Many Ways to Use Ontology

• As an information engineering tool
• Create a database schema
• Map the schema to an upper ontology
• Use the ontology as a set of reminders for
  additional information that should be included
• As more formal comments
• Define an ontology that is used to create a DB or
  OO system
• Use a theorem prover at design time to check for
  inconsistencies
• For taxonomic reasoning
• Do limited run-time inference in Prolog, a
  description logic, or even Java
• For first order logical inference
• Full-blown use of all the axioms at run time

12
Upper Ontology

• An attempt to capture the most general and
  reusable terms and definitions

13
Motivation

• Ontologies may have different names for the same
  things
• type a relation between a class and an instance
• instance a relation between a class and an
  instance
• isa a relation between a class and an instance
• Ontologies may have the same name for different
  things, and no corresponding terms
• before a relation between two time points
• before a relation between two time intervals
• Either use the same upper ontology, or at least
  map to a common upper ontology

14
Formal Upper Ontologies

• DOLCE
• Cyc
• SUMO

15
Simple Methodology

• Extract nouns and verbs from a source text
• Find classes in SUMO for the nouns and verbs.
  SUMO Suggested Upper Merged Ontology- IEEE stad-
  Uses KIF. Dictionary.
• Record a mapping as being either equal, subsuming
  or instance.
• type a single word that relates to the UBL term
  in the "SUMO term" or "English Word" text areas
  in the SUMO browser. UBLUniversal Business Lang.
• Create a subclass of SUMO if it's a subsuming
  mapping
• Add properties to the subclass
• reusing SUMO properties
• extending SUMO properties by creating a
  subrelation of an existing property
• Add English definition to the class
• define constraints that express how the subclass
  is more specific than the superclass
• Express the classes and properties in KIF and
  begin creating axioms, based on the English
  definitions created previously

16
Exercise

• Walk through the process of creating some
  ontology content from a source text
• Learn a general methodology
• Get practical familiarity with KIF and SUMO

17
First Exercise (1)

• Seven Turkish nationals of Chechen origin
  hijacked a Russia-bound Panamanian ferry in
  Trabzon. The hijackers initially threatened to
  kill all Russians on board unless Chechen
  separatists being held in Dagestan, Russia, were
  released. On 19 January 1998, the hijackers
  surrendered to Turkish authorities outside the
  entrance to the Bosporus. The passengers were
  unharmed.
• Identify items that need formalization start
  with nouns and verbs

18
First Exercise (2)

• Seven Turkish nationals of Chechen origin
  hijacked a Russia-bound Panamanian ferry in
  Trabzon. The hijackers initially threatened to
  kill all Russians on board unless Chechen
  separatists being held in Dagestan, Russia, were
  released. On 19 January 1998, the hijackers
  surrendered to Turkish authorities outside the
  entrance to the Bosporus. The passengers were
  unharmed.
• Now create terms that correspond to the nouns and
  verbs
• Remove redundancy
• Are there any background notions that are not
  explicit in the text?

19
First Exercise (3)

• Seven Turkish nationals of Chechen origin
  hijacked a Russia-bound Panamanian ferry in
  Trabzon. The hijackers initially threatened to
  kill all Russians on board unless Chechen
  separatists being held in Dagestan, Russia, were
  released. On 19 January 1998, the hijackers
  surrendered to Turkish authorities outside the
  entrance to the Bosporus. The passengers were
  unharmed
• Turkey, Chechnya, Nationality, Hijacking,
  Threatening, Killing, Releasing, Holding,
  Dagestan, Russia, Separatist, Entrance, Bosporus,
  Unharmed, Panama, Trabzon, Authority, Outside,
  boundFor, Ferry, onBoard

20
SUMO Overview

• Understanding whats in the upper ontology, in
  order to use it effectively

21
High Level Distinctions

• The first fundamental distinction is that between
  Physical (things which have a position in
  space/time) and Abstract (things which dont)
• Physical Abstract

22
High Level Distinctions

• Partition of Physical into Objects and
  Processes
• Physical
• Object Process

23
Objects

• Object
• SelfConnectedObject
• Substance
• CorpuscularObject
• Region
• Collection

24
Processes
IntentionalProcess IntentionalPsychologica
lProcess RecreationOrExercise
OrganizationalProcess Guiding
Keeping Maintaining Repairing
Poking ContentDevelopment
Making Searching
SocialInteraction Maneuver Motion
BodyMotion DirectionChange
Transfer Transportation Radiating
DualObjectProcess Substituting
Transaction Comparing Attaching
Detaching Combining
Separating InternalChange
BiologicalProcess QuantityChange
Damaging ChemicalProcess
SurfaceChange Creation
StateChange ShapeChange
25
Abstract

• SetOrClass
• Relation
• Proposition
• Quantity
• Number
• PhysicalQuantity
• Attribute
• Graph
• GraphElement

26
A Little Bit of Logic

• Instance GeorgeBush, Iraq, BobsRightBigToe
• Class Human, Nation
• Relation WWI before WWII, Bill childOf Mary
• gt (read as implies) - if X then Y
• and X and Y are true
• or X or Y (or both) are true
• not not X the opposite of the truth of X
• exists ?X there exists something about which
  the following is true

27
A Little Structural Ontology

• (instance GeorgeBush Human) GeorgeBush is an
  instance of the class of humans
• (exists (?X)
• (parent ?X GeorgeBush)) there exists
  something of which George Bush is the parent
• (instance parent BinaryPredicate) the relation
  of parent is a binary relation
• (domain parent 1 Organism) the first argument
  to the parent relation must be an instance of the
  class Organism
• (domain parent 2 Organism) similarly for the
  second argument

28
Linking to SUMO Terms

• Nation, Confining, Committing, SocialRole,
  TransportationDevice, Killing, Near, Injuring,
  citizen, (not), (exists)
• Terms from the exercise (may or may not be the
  same as SUMO terms)
• Turkey, Chechnya, Nationality, Hijacking,
  Threatening, Killing, Releasing, Holding,
  Dagestan, Russia, Separatist, Entrance, Bosporus,
  Unharmed, Panama, Trabzon, Authority, Outside,
  boundFor, Ferry, onBoard
• Use the terms in the first bullet to define the
  terms in the second bullet
• Use Nation to state (instance Turkey Nation)

29
Formalization

• (exists (?TURK )
• (and
• (citizen ?TURK Turkey))
• )

30
Formalization

• (exists (?TURK ?FERRY )
• (and
• (citizen ?TURK Turkey)
• (instance ?FERRY FerryBoat)
• )

31
Formalization

• (exists (?TURK ?FERRY ?HIJACK)
• (and
• (citizen ?TURK Turkey)
• (instance ?FERRY FerryBoat)
• (instance ?HIJACK Hijacking)
• (agent ?HIJACK ?TURK)
• (patient ?HIJACK ?FERRY)
• (earlier ?HIJACK
• (DayFn 19
• (MonthFn January
• (YearFn 1998))))))

32
Ontologies Working Group Goals

• Collect controlled vocabularies for sample
  descriptions.
• Define microarray concepts and their
  relationships.
• Provide bridge to ontologies from other knowledge
  domains.

33
What is an Ontology?
An ontology is a specification of a
conceptualization that is designed for reuse
across multiple applications and implementations.
a specification of a conceptualization is a
written, formal description of a set of concepts
and relationships in a domain of interest.
Peter Karp (2000) Bioinformatics 16269
34
Ontologies in Gene Expression Databases

• Controlled vocabulary
• Define relationships through hierarchy (e.g.,
  taxonomy)
• Schema
• Concepts as objects or relational tables
• Attributes and data types provide specification
• Relationships specified through subclassing
  (objects) or foreign keys (relational tables)
• Knowledge representation
• Link to other domains (gene sequence annotation,
  gene and protein roles, pathways)
• Facilitate data exchange by mapping common
  concepts

35
Anatomy Hierarchy
36
Experiment Tables
Experiment
37
MAML DTD -gt UML mappingArray platform-MicroArray
Makup Language
38
Other Domains

• Gene descriptions (Gene Ontology)
• Molecular function
• Biological process
• Subcellular localization
• Cellular and biochemical pathways (EcoCyc)
• Literature (MeSH)
• Phenotypes
• Others

Requires common set of terms (semantic mapping)
Or shared usage of identifiers (e.g. GenBank
accessions)
39
www.mged.org
40
Example Sample Descriptions

• Human
• Mouse

41
MIAME Ontology
Define MIAME concepts and their relationships
incorporating MAML. Minimum Info About a
Microarray Experiment The goal is to generate a
document that will provide a clear and common
understanding of what should be reported and how.
The tables are a draft to form the basis for
such a document. Located at Ontology Working
Group home page.