Finding Bugs in People: Developing an Entomology Ontology from the UMLS

Finding Bugs in People:Developing an

Entomology Ontology from the UMLS

Indra Neil Sarkar, PhDLewis B. & Dorothy Cullman Bioinformatics Associate

Division of Invertebrate Zoology

American Museum of Natural History

NKOS Workshop 10 June 2005

© 2005 Indra Neil Sarkar, PhD

Total Evidence Tree of Life

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Sequence Data


Structural Data


Phenotypes

Morphology

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Statements of Homology

Sequence Data Multiple Sequence Alignments

CLUSTAL, T-COFFEE, MUSCLE

Non-sequence Data Ontologies


Ontologies

“White” “Blanc” “Weiss”

White BlueRed

Color


Ogden-Richards Semiotic Triangle

“White” “Weiss”“Blanc” XVFD

Symbols

Thought/Reference

Referent


Ontology Development

Protégé http://protege.stanford.edu “Frame-based”


Ontology Development


Ontologies in Phylogenetics

“Wing” “Aile” “Flügel”

Wing ArmForeleg

Forelimb


Wing ArmForeleg

Forelimb

CATBATBIRD

111

Forelimb

Wing(2)

Arm(3)

Foreleg(1)

132

[Gene 1][Gene 1][Gene 1]

[Gene 2][Gene 2][Gene 2]

………




Genetic Information 99% of Earth’s biota are extinct!

Morphological Information Fossil record Morphological studies from extant organisms



Ontology Development Web Ontology Language (OWL) Structured Descriptive Data (SDD)

Can be exported to NEXUS, DELTA, Lucid

Ontology Acquisition and Markup Archival Resources Natural Language Processing


Unified Medical Language System (UMLS)

Metathesaurus One Million Concepts 100+ Biomedical Terminologies/Ontologies

Semantic Network 135 Semantic Types 15 Coarse Semantic Groups

SPECIALIST Lexicon English + Biomedical Words


Torre-Bueno Glossary of Entomology (TBGE)

Common Entomology Phrases 300 Primary Sources 15,010 Terms/Phrases


TBGE to UMLS

Question 1: Is Entomology Language Different than Biomedical Language? TBGE to SPECIALIST

Question 2: Can UMLS Be Used to Seed an Ontology for Entomology? TBGE to UMLS Metathesaurus Organize Results According to Semantic

Network


Q1: Is Entomology a Unique Language?

“Look-up” Individual Word Atoms in SPECIALIST

Complete Look-up 48% Coverage

Partial Look-up 66% Coverage

Not found 34% Not covered


Q2: Can UMLS Be Used to Seed Entomology Ontology?

Three-Tiered Mapping Approach Tier 1: Direct Mapping

Exact & Normalized String Matching Tier 2: Direct Mapping after Demodification

Remove nominal and adjectival modifiers Exact & Normalized String Matching

Tier 3: Approximate Matching MetaMap Application



Tier

(Approach)

1

(Direct)

2

(Demod)

3

(Approx)

% Mapped % Accuracy

Method Overall Method Overall

20 8620 86

37 7449 78

23 4161 71



Correct Mappings

0

500

1000

1500

2000

2500

3000

ACTIANATCHEMCONCDEVIDISOGENEGEOG

LIVBOBJCOCCUORGAPHENPHYSPROCSemantic Type

Number of Mappings

Approx

Demod

Direct

Incorrect Mappings

0

100

200

300

400

500

600

700

800

900

1000

ACTIANATCHEMCONCDEVIDISOGENEGEOG

LIVBOBJCOCCUORGAPHENPHYSPROC

Semantic Type

Number of Mappings

Approx

Demod

Direct



0

500

1000

1500

2000

2500

3000

SNOMED CT

MeSH

Other (30)

UWDANCBI MDR LCH CSP GO

Incorrect

Correct

Source Terminologies


TBGE-UMLS Implications

UMLS Semantic Network is a good Seed Ontology for Biological Domain Ontologies

Best Term-Concept Mappings into Anatomy


Bottom-Up vs. Top-Down


In Summary…

Ontologies are Needed for Phylogenetics Existing Biomedical Ontologies Are Useful

for New Domain Ontologies (especially UMLS)

Top-Down Strategy using UMLS is Tractable


End Goal


Sequence Data


Structural Data


Phenotypes

Morphology

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OWL SDD


Next Steps

Represent Seed Entomology Ontology in OWL

Link OWL Representation to SDD for use in Taxonomic Descriptions

Involve Team of Experts for Validation Go Beyond Morphology-- Location,

Biodiversity Data, etc.

Acknowledgements


Acknowledgements

Tom Moritz Rob DeSalle Mark Siddall David Figurski Susan Perkins Paul Planet

Gloria Coruzzi Olivier Bodenreider Carol Friedman Jim Cimino Bob Morris Mark Musen

National Institutes of Health

National Science Foundation

American Museum of Natural History

Thank [email protected]

Indra Neil Sarkar, Cullman Bioinformatics AssociateAmerican Museum of Natural History

http://www.GenomeCurator.org/people/sarkar

Finding Bugs in People: Developing an Entomology Ontology from the UMLS

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