Post on 21-Dec-2015
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
Text-based Discovery in Biomedicine
The Architecture of the DAD-system
Marc Weeber1,2, Henny Klein1,Alan R. Aronson2, Jim G. Mork2,
Lolkje T. W. de Jong - van den Berg1, Rein Vos1,3
1Department of Social Pharmacy and Pharmacoepidemiology, Groningen University Institute for Drug Exploration, The Netherlands
2Lister Hill National Center for Biomedical Communication, National Library of Medicine, Bethesda, MD
3Health Ethics and Philosophy, Faculty of Health Sciences, University of Maastricht, The Netherlands
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
Introduction• Goal:
Finding new biomedical knowledge through the combination of existing knowledge as represented in the medical literature
• Motivation:
Prevention of re-inventing the wheel, re-usage of specific knowledge outside the original domain of discovery
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
Swanson
• AB: Raynaud’s disease is characterized by high blood viscosity and high platelet aggregation
• BC: Fish oil is known to reduce blood viscosity and platelet aggregation
A CB?
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
Vos and Rikken
• Drugs instead of diet factors
• Intermediate (B) terms are adverse drug reactions
• Drug – Adverse drug reactions – Disease: The DAD-system
• Vos (1991) Drugs looking for diseases
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
Existing Techniques
• Swanson & Smalheiser:• Single words/multi word terms• MEDLINE titles• No statistics
• Gordon & Lindsay:• Single words/multi word terms• Information Retrieval statistics• Replication of Swanson’s discoveries
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
New Techniques
• Use of UMLS concepts
• PubMed
• MetaMap: mapping free text (MEDLINE titles and abstracts) to concepts
• Interactive web interface
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
Two-step Approach
• Open discovery, generating a hypothesis
A ??
• Closed discovery, testing a hypothesis
A C?
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
Why UMLS Concepts?
• Use of only biomedically relevant information
• Useful transition from single word to multi word term
• Semantic information (semantic types) for filtering (e.g. select only Disease or Syndrome)
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
DAD-system
Meta-thesaurus
SpecialistLexicon
PubMed SemanticNetwork
MetaMapKS
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
DAD-system
Meta-thesaurus
MySQLDatabase
SpecialistLexicon
PubMed SemanticNetwork
MetaMap
FilterTxt2ConQuery ShowSelect
KS
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
DAD-system
Meta-thesaurus
MySQLDatabase
SpecialistLexicon
PubMed SemanticNetwork
MetaMap
FilterTxt2ConQuery ShowSelect
KS
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A
Open Discovery
•Query (user input):
raynaud’s disease
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A
Open Discovery
•Mapping text to concept through MetaMap:
Raynaud's Disease [Disease or Syndrome]
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A
Open Discovery
•Synonym lookup:
Raynaud's syndrome Raynaud's disease /phenomenon
•Variant generation:
e.g. syndrome / syndromes
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A
Open Discovery
•PubMed query:
raynaud OR raynauds
•Processing: query in titles and abstracts
•Result: 1,246 MEDLINE citations
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A
Open Discovery
•Text to concept mapping of all citations
•Sentences with Raynaud’s disease
•Result: 1,278 UMLS concepts
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A
Open Discovery
•Select functional/physiological concepts•Semantic types in filter:
Body Location or RegionBiologic FunctionCell FunctionPhenomenon or ProcessPhysiologic FunctionTissue
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A B
Open Discovery
•Result: 57 Concepts
•Frequency range:
1- 18
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A B
Open Discovery
•Selected B-concepts:
Plasma Viscosity LevelBlood ViscosityPlatelet AdhesivenessPlatelet AggregationEffects, Blood
Coagulation
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A B
Open Discovery
•Variants:
plasma, plasmasviscosity, viscous,aggregation, aggregations,
aggregatingcoagulation, coagulating
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A B
Open Discovery
•PubMed query:
blood coagulation OR blood viscosity OR plasma viscosity OR platelet
adhesiveness OR platelet aggregation
•Result: 10,611 MEDLINE citations
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A B
Open Discovery
•Concepts in sentences with B-concepts:
7,702
•Concepts not in Raynaud sentences:
6,747
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A B
Open Discovery
•Filter for dietary related concepts
•Semantic types in filter:
VitaminLipidElement, Ion, or Isotope
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A B C
Open Discovery
Eicosapentaenoic AcidFish OilFatty Acids, Omega 3MAXEPAOmega-3
PolyunsaturatedFatty Acid
Cod Liver OilSalmon Oil
•Result: 206 Concepts
•Rank order on relations
•Fish oil related concepts:
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A C
Closed Discovery
Eicosapentaenoic AcidFish OilFatty Acids, Omega 3MAXEPAOmega-3
PolyunsaturatedFatty Acid
Cod Liver OilSalmon Oil
Raynaud’s Disease
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A C
Closed Discovery
1,246 citations1,278
concepts
479 common concepts
463 citations1,795
concepts
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A C
Closed Discovery
Functional / Physiological Filter
45 B-concepts
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
A C
Closed Discovery
B
•Known concepts:
Plasma viscosity level
Blood ViscosityPlatelet
AdhesivenessPlatelet AggregationEffects, Blood
Coagulation
•New concepts:
VasodilatationVeins, CapillariesDinoprostoneFibrinolysisDeformabilityRheology
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
Juxtaposition
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
Success / Failure +Simulation of Raynaud’s disease – fish
oil and migraine – magnesium
+Discovery of new therapeutic applications for thalidomide
- Mapping (Mg = milligram / magnesium)
- Association defined by co-occurrence
Social Pharmacy andPharmacoepidemiology
Lister Hill National Center forBiomedical Communications
Future
• Better semantic analysis:increase(A,B) and decrease(B,C)
• Better user interface
• More databasese.g. finding genetic bases for diseases