Social Pharmacy and Pharmacoepidemiology Lister Hill National Center for Biomedical Communications Text-based Discovery in Biomedicine The Architecture of the DAD-system Marc Weeber 1,2 , Henny Klein 1 , Alan R. Aronson 2 , Jim G. Mork 2 , Lolkje T. W. de Jong - van den Berg 1 , Rein Vos 1,3 1 Department of Social Pharmacy and Pharmacoepidemiology, Groningen University Institute for Drug Exploration, The Netherlands 2 Lister Hill National Center for Biomedical Communication, National Library of Medicine, Bethesda, MD 3 Health Ethics and Philosophy, Faculty of Health Sciences, University of Maastricht, The Netherlands
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Social Pharmacy and Pharmacoepidemiology Lister Hill National Center for Biomedical Communications Text-based Discovery in Biomedicine The Architecture.
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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