supporting non-nlp experts in creating annotation schemas for extraction of clinical concepts 

Supporting Non-NLP Experts in Creating Annotation Schemas for Extraction of Clinical Concepts 

Wendy W. Chapman, PhD

Department of Biomedical InformaticsUniversity of Utah

Motivation

Common information models

– Enable interoperability

– Guide non-NLP experts in developing NLP apps

Creating Domain Knowledge Bases for NLP

User Domain Knowledge Base

User Domain Knowledge Base Schema OntologySchema Ontology

Modifier OntologyModifier OntologyDomain

Ontologies

Knowledge Author

Creating Domain Knowledge Bases for NLP

User Domain Knowledge Base

User Domain Knowledge Base Schema OntologySchema Ontology

Modifier OntologyModifier OntologyDomain

Ontologies

Knowledge Author

Schema Ontology

Semantic types (from cTAKES type system)– Allergy– Disease/Disorder– Encounter– Finding– Medication– Procedure/Intervention– Research Activity– Sign/ Symptom– Social History– Test

Schema Ontology: Elements

Schema Ontology: Relationships

Creating Domain Knowledge Bases for NLP

User Domain Knowledge Base

User Domain Knowledge Base Schema OntologySchema Ontology

Modifier OntologyModifier OntologyDomain

Ontologies

Knowledge Author

Modifier Ontology

Modifiers are important for interpreting text– Chest radiograph confirms pneumonia– Family history of pneumonia– No evidence of pneumonia

Allowable modifiersFor each clinical element

Modifier Ontology

Semantic Modifiers

• Dosage• Duration• Form• Frequency• Route• Status Change• Anatomic location• …

Linguistic Modifiers

• Negation• Uncertainty• Conditional• Experiencer• Future• Historical

Modifier Ontology

• Value Sets– NegEx and ConText lexicon– Value sets from existing

ontologies/vocabularies

• Labels for different languages– English– Swedish– German– French

ACTION: Forward CLOSURE: Because_Group BackwardPatient_GroupBidirectional But_GroupTerminate SecondaryTo_Group

Which_Group

CATEGORY: DefiniteExistence ITEMS: AlthoughDefiniteNegativeExistence As a part fromEquivocality As a cause for Experiencer (n

~400)FutureHistoricalIndicationProbableExistenceProbableNegatedExistencePseudoExperiencerPseudoFuturePseudoHistoricalPseudoNegation

ConText Elements

Modifier OntologyTypes of modifiersTypes of modifiers Linguistic

expressionsLinguistic

expressions

ActionsActions

TranslationsTranslations

Modifier Ontology: Elements

Schema Ontology Imports Modifier Ontology

Medications– Type– Dose– Frequency– Route

Diagnosis– Negation– Uncertainty– Severity– History– Experiencer

Creating Domain Knowledge Bases for NLP

User Domain Knowledge Base

User Domain Knowledge Base Schema OntologySchema Ontology

Modifier OntologyModifier OntologyDomain

Ontologies

Knowledge Author

Domain Knowledge Base for NLP

• Instance of schema ontology

• Clinical elements from a particular domain

Synonyms Misspellings

Regular expressions

Synonyms Misspellings

Regular expressions

Creating Domain Knowledge Bases for NLP

User Domain Knowledge Base

User Domain Knowledge Base Schema OntologySchema Ontology

Modifier OntologyModifier OntologyDomain

Ontologies

Knowledge Author

Map NLP Output to User KB

User’s ConceptsCough

DyspneaInfiltrate on CXR

WheezingFever

Cervical Lymphadenopathy

User’s ConceptsCough

DyspneaInfiltrate on CXR

WheezingFever

Cervical Lymphadenopathy

Controlled Vocabs

Dry cough Productive coughCoughHacking coughBloody cough

Controlled Vocabs

Dry cough Productive coughCoughHacking coughBloody cough

Which concepts?

User’s ConceptsCough

DyspneaInfiltrate on CXR

WheezingFever

Cervical Lymphadenopathy

User’s ConceptsCough

DyspneaInfiltrate on CXR

WheezingFever

Cervical Lymphadenopathy

Attribute-values

Temp 38.0CLow-grade temperature

Attribute-values

Temp 38.0CLow-grade temperature

What values?

Knowledge AuthorKnowledge Author

Disease: colon cancerExperiencer: familyNegation: noHistorical: yes

Disease: colon cancerExperiencer: familyNegation: noHistorical: yes

“Family history of colon cancer”

NLP Schema Domain Ontology

Knowledge Author

• Front end interface for users

• Back end– Schema ontology– Modifier ontology

• Output– Domain ontology– Schema for NLP system

B Scuba, F Fana, Liqin Wang, Mingyuan Zhang, Y Liu, M Kong, F Drews

Questions | Discussion

African American Adult

Ibuprofen

Ibuprofen p.o.

No family history of colon cancer

Linguistic modifiers

Suggests synonyms

Acknowledgments

• Lee Christensen• Melissa Tharp• Mike Conway• Danielle Mowery• Bill Scuba• Milan Kovacevich• Dieter Hillert• Samir Abdelrahman• Leah Willis• Bob Angell

• Harry Hochheiser

• Jan Wiebe

• Rebecca Hwa

• Guergana Savova

• Noemie Elhadad

• Michael Matheny

• Rob El-Kareh

• Ruth Reeves

• Qing Zeng

• Guy Divita

• Frank Drews

BLU Lab Collaborators• Sumithra Vellupilai• Maria Kvist• Maria Skeppstedt• Aron Henrikkson• Brian Chapman• David Carrell• Sascha Dublin• Zia Agha• Stephane Meystre• Scott DuVall• Jianlin Shi