10,000 foot view of what I am
working on
Wendy W. Chapman, PhD
University of Pittsburgh
Dept of
Biomedical
Informatics
Biomedical Language
Understanding
U of Utah
1994
2000
Faculty DBMI
1992
Post-doc BMI
Wisconsin
PhD Medical Informatics
U of Utah
Chinese Literature
BA Linguistics
Background
U of Pittsburgh
2003
Biomedical Language Understanding
www.dbmi.pitt.edu/blulab
Henk Harkema, Danielle Mowery, Mike Conway,
Lee Christensen, Qi Li, Wendy Chapman
BLU Lab NLP Sampler
Topaz
Temporality
Schema
Onyx
Ontology
Enrichment
Results
Review/
Error
Analysis
NLP
Repository
Ontology
For
Syndromic
Surveillance
Anaphoric
Reference
BLU Lab NLP Sampler
Topaz
Temporality
Schema
Onyx
Ontology
Enrichment
Results
Review/
Error
Analysis
NLP
Repository
Ontology
For
Syndromic
Surveillance
Anaphoric
Reference
Topaz
Harkema, B Chapman, Hwa
• Named entity recognition
– Maps UMLS concepts to higher-level concepts
• Contextual property assignment (ConText)
– Existence (affirmed, negated)
– Experiencer (patient, other)
– Historicity (current, historical)
– Realis (actual, non-specific/hypothetical)
– Certainty (uncertain, certain)
– Reason for exam (yes, no)
– Quality of exam (diagnostic, limited)
ConText: Determine Values for
Contextual Properties
scope
Clinical condition: Cough
Negation:
Negated
Patient denies cough but complains of headache.
No change in the patient’s chest pain.
trigger term
pseudo-trigger
term
termination
term
ConText: Historical
scope
Past history of pneumonia presenting
today with cough and fever.
termination
term
trigger term
Clinical condition: Pneumonia
Temporality:
Historical
BLU Lab NLP Sampler
Topaz
Temporality
Schema
Onyx
Ontology
Enrichment
Results
Review/
Error
Analysis
NLP
Repository
Ontology
For
Syndromic
Surveillance
Anaphoric
Reference
Onyx
Haug, Schleyer
Eight mesial might have a slight translucency
Semantic
Models
Syntactic Analyzer
Onyx
Context-free
Grammar
Training
Corpus
Semantic Analyzer
At (translucency, numberEight) &
surfaceOf (numberEight, mesial) &
stateOf (translucency, possible)
Knowledge-rich
Frame-based Mapping
Semantic
Network
Probabilistic
Frames
- Frame slots map to semantic network
- Relationships between slots are probabilistic
Annotation Interface
with active learning and help from Onyx
Semantic Model
Templates
Speech  NLP  Chart
Dental Exams
Number one Is missing.
Two is fine. Caries on Tooth 3.
Onyx
Titus Schleyer, Lee Christensen, Peter Haug, Jeannie Irwin, Henk Harkema
BLU Lab NLP Sampler
Topaz
Temporality
Schema
Onyx
Ontology
Enrichment
Results
Review/
Error
Analysis
NLP
Repository
Ontology
For
Syndromic
Surveillance
Anaphoric
Reference
Ontology Development-Information Extraction (ODIE)
Rebecca Crowley, Mayo Clinic, Stanford NCBO
Information Extraction
Use ontology to improve
IE from text
Ontology
Text
Ontology Enrichment
Use IE to find new
concepts and
relationships to add
Surgical
Pathology
Chest
Radiography
View Overlap of Ontologies
Suggest Concepts
BLU Lab NLP Sampler
Topaz
Temporality
Schema
Onyx
Ontology
Enrichment
Results
Review/
Error
Analysis
NLP
Repository
Ontology
For
Syndromic
Surveillance
Anaphoric
Reference
Results Review/Error Analysis
BLU Lab NLP Sampler
Topaz
Temporality
Schema
Onyx
Ontology
Enrichment
Results
Review/
Error
Analysis
NLP
Repository
Ontology
For
Syndromic
Surveillance
Anaphoric
Reference
Schema for Clinical Condition Properties
Wiebe, Jordan, Mowery, Harkema
Properties of Condition Concept
Existence
Experiencer
Change
Yes, No
Patient, Other
Unmarked, Unchanging, Changing, Increasing, Decreasing,
Improving, Worsening, Recurrence
Intermittent
Unmarked, Yes, No
Certainty
Unmarked, High, Moderate, Low
Mental State
Yes, No
Generalized/
Conditional
Yes, No
Current Visit
Relation
Before, Meets_Overlaps, After
Schema for Temporal Relations
Time Words
Ordering Words
Aspectual Words
Points, Durations
Precedes, During, Follows
Initiation, Continuation, Culmination
BLU Lab NLP Sampler
Topaz
Temporality
Schema
Onyx
Ontology
Enrichment
Results
Review/
Error
Analysis
NLP
Repository
Ontology
For
Syndromic
Surveillance
Anaphoric
Reference
BLU Lab NLP Sampler
Topaz
Temporality
Schema
Onyx
Ontology
Enrichment
Results
Review/
Error
Analysis
NLP
Repository
Ontology
For
Syndromic
Surveillance
Anaphoric
Reference
Application Ontology for
Syndromic Surveillance
Consensus of developers/users across country
Conway, Buckeridge
BLU Lab NLP Sampler
Topaz
Temporality
Schema
Onyx
Ontology
Enrichment
Results
Review/
Error
Analysis
NLP
Repository
Ontology
For
Syndromic
Surveillance
Anaphoric
Reference
Anaphoric Reference in Clinical Reports
Crowey, Savova, Zeng
• Adapted MUC schema for clinical reports
• Three experts annotated 180 reports
Five types—Mayo, UPMC
• identity
• part/whole
• set/subset
• Characterize anaphoric reference in reports
• Train/test resolution algorithms