toward using ontologies to reason about disagreeing taxonomic experts dave thau uc davis...
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Toward Using Ontologies to Reason About Disagreeing
Taxonomic Experts
Dave ThauUC Davis
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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
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Why did the taxonomistscross the road?
So they couldproperlyidentify the chicken
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Representation Details
• Based on the Taxon Concept Schema (TCS)
• Represented using Description Logic–(OWL DL)
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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
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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
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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
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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.
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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
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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.
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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
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• 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
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Example of Theory Ordering
A
B C D
A
B C
A
B C E
T1 T2 T3
T1 T2 T3
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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
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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
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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
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R. aquatilis R. trichophyllus
Where In Greece Can I Find Ranunculus aquatilis?
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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)