Toward Using Ontologies to Reason About Disagreeing Taxonomic Experts Dave Thau UC Davis...

Toward Using Ontologies to Reason About Disagreeing

Taxonomic Experts

Dave ThauUC Davis

[email protected]

[email protected] NeSC RDF Workshop June 8, 2006 2/25

Why Did The Chicken Cross The Road?

• To get to the other side.

• To boldly go where no chicken has gone before.

• To prove it could never reach the other side.

• Chickens, over great periods of time, have been naturally selected so that they are now predisposed to cross roads.

Zeno of Elea


Why did the taxonomistscross the road?

So they couldproperlyidentify the chicken


Overview

• Quick primer on taxonomy

• Some types of disagreements between experts

• Problems this causes

• Using an ontology to represent taxonomic opinions

• Using the ontology to compare experts’ theories


Linnaean Taxonomy Basics

Ranks: kingdom, phylum, class, order, family, genus, species, variety (and others!)

Canidae

CanisVulpes Nyctereutes

Canis familiaris

Family Rank

Genus Rank

Species Rank Canis lupus Canis latrans


Things you may not know

• There is no big list of all the known species in the world

• This is partly because people don’t agree on the definitions of the species, genera, etc.

• Estimates are that 6% of the known taxa are changed every year

• This has been going on since Linnaeus published his classification scheme in 1735


Ranunculusaquatilis

R.a. varaquatilis

R.a. vardiffusus

R.a. varhispidulus

FNA-03, 1997

Ranunculusaquatilis

R.a. varcapillaceus

Benson, 1948

Types of Disagreement: The Basics

R.a. varcalvescens

This results in 512 (more than 240 million) possible sets of relationships.

B

A

A BA B

BA

A overlap B

BA

A disjoint B

B

A

A B


Types of Disagreement -Splitting and Lumping

Ranunculusflammula

R.f. vargenuiinus

R.f. varovalis

Benson, 1948

Ranunculusflammula

R.f. varfiliformis

Kartesz, 2004

Peet, 2005: B.1948:R.flammula is congruent to K.2004:R.flammula B.1948:R.f. genuiinus is included in K.2004:R.f.flammula B.1948:R.f.ovalis is included in K.2004:R.flammulaB.1948:R.f.filifomis is congruent to K.2004:R.f.filiformis

R.f. varfiliformis

R.f. varflammula


Ranunculusglaberrimus

R.g. varreconditus

R.g. varellipticus

R.g. vartypicus

Benson, 1948

Ranunculusglaberrimus

R.g. varellipticu

s

R.g. varglaberrimus

Kartesz, 2004

Types of Disagreement – Differing Extents

Peet, 2005: B.1948:R. glaberriums contains K.2004:R. glaberrimus B.1948:R.g.ellipticus is congruent to K.2004:R.g.ellipticusB.1948:R.g.typicus is congruent to K.2004:R.h.blaberrimusB.1948:R.g.reconditus is congruent to K.2004:R.tritenatus


Impact on Data Analysis

• Can’t find data– If A B, a search on A should retrieve B

• Can’t aggregate data– If B A, you should be able to combine data

from B into A


What to do in case of conflicting experts?

• Just listen to one expert you like

• Pick an expert you like and everyone who agrees with this expert (and each other)

• Choose experts who form the largest set of agreeing experts

• Choose experts whose opinions encompass the smallest or largest number of taxa


How can we find out which experts agree?

• Represent taxonomy using logic

• Use the logic to determine relations between expert opinions (theories)– Two theories may conflict– Two theories may be equivalent– One theory may encompass another


Representation Details

• Based on the Taxon Concept Schema (TCS)

• Represented using Description Logic–(OWL DL)


Example Ontology

Specimen Ranunculus (Kartesz, 2004)

hasSpecies

Ranunculus glaberrimus (Kartesz, 2004)

Things in the species Ranunculus glaberrimus

Things in the genus Ranunculus

Taxon Taxon Description

hasGenus


Fundamental Assumptions

• Each Taxa class has at least one instance

• Each Taxa class is defined as the union of its subclasses

• A class’s subclasses are defined to be mutually disjoint


Questions Ontology Can Answer

• Find the subclasses of a class

• Make sure the taxonomy is consistent

• See if two classes are equivalent

• Can also use it to compare expert opinions


Compatible Theories

• A theory is one expert’s set of classes and relations and all they imply.

• A set of theories is compatible if – Each theory is consistent and– The correspondences between classes in the

theories do not cause inconsistency.


Ranunculushydrocharoides

R.h. varnatans

R.h. varstolonifer

R.h. vartypicus

Benson, 1948

Ranunculushydrocharoides

R.h. varstolonife

r

R.h. vartypicus

Kartesz, 2004

Example Incompatibility

Peet, 2005: B.1948:R.h.stolonifer is congruent to K.2004:R.h.stoloniferB.1948:R.h.typicus is congruent to K.2004:R.h.typicusB.1948:R. hydrocharoides is congruent to K.2004:R. hydrocharoides


Example Incompatibility

Peet, 2005: B.1948:R. macranthus contains K.2004: R. petiolarisB.1948:R. petiolaris is contained by K. petiolaris

Ranunculuspetiolaris

…

Benson, 1948

Ranunculuspetiolaris

Kartesz, 2004

Ranunculus Ranunculus

Ranunculusmacranthus

…

B.48:R. petiolaris K.04:R. petiolaris B.48:R. macranthus contradictsB.48:R. macranthus and B.48:R. petiolaris are disjoint.


Inferring Unstated Correspondences

Ranunculusarizonicus

R.a. varchihuahua

R.a. vartypicus

Benson, 1948

Ranunculusarizonicus

Kartesz, 2004

Peet, 2005: B.1948:R.a.typicus is included in K.2004:R. arizonicusB.1948:R. arizonicus is congruent to K.2004:R. arizonicus


• Given two compatible theories, T and T’:

– The theories are equivalent if each class in theory T is equivalent to one class in T’ (and vice versa).

– T is smaller than ( ) T’ if each class in T either equals or is contained by a class in T’.

Comparing Theories


Example of Theory Ordering

A

B C D

A

B C

A

B C E

T1 T2 T3

T1 T2 T3


Whom to believe?

• Just listen to one expert you like– Easy! Don’t need any reasoning

• Pick an expert you like and everyone who can agree with this expert– Choose all experts with theories equivalent to the expert you like

• Choose experts who form the largest set of agreeing experts– Find largest equivalence class

• Choose experts whose opinions form the smallest or largest number of taxa– Bigger theories account for more taxa


Future Work

• Vetting the ontology

• Adding ‘intelligence’ to tools which build correspondences

• Implementing authority picker in a workflow system

• Efficient algorithm for determining theory hierarchy


Thanks! Questions?

• I’d like to acknowledge:– Bertram Ludäscher, Shawn Bowers, Serguei Krivov,

Richard Waldinger for many discussions on this topic.– Jessie Kennedy, Robert Kukla, Trevor Patterson,

Martin Graham for their work on the Taxon Concept Schema

– Bob Peet for the Ranunculus data set– Kirsten Menger-Anderson for Chicken Drawing– NSF, under SEEK awards 0225676, 0225665,

0225635, and 0533368


R. aquatilis R. trichophyllus

Where In Greece Can I Find Ranunculus aquatilis?


Beginnings of Biological Taxonomy

• Egypt, 1500 BC: Ebers medical papyrus, classification of medical plants

• Greece, 300 BC: Aristotle and Theophrastus

• China, 200 BC: Erh-ya dictionary (second century BC)

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