Text-based Discovery in Biomedicine The Architecture of the DAD -system

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

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

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

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

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

New Techniques

• Use of UMLS concepts

• PubMed

• MetaMap: mapping free text (MEDLINE titles and abstracts) to concepts

• Interactive web interface

Two-step Approach

• Open discovery, generating a hypothesis

• Closed discovery, testing a hypothesis

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)

DAD-system

Meta-thesaurus

SpecialistLexicon

PubMed SemanticNetwork

MetaMapKS

DAD-system

Meta-thesaurus

MySQLDatabase

SpecialistLexicon

MetaMap

FilterTxt2ConQuery ShowSelect

DAD-system

Meta-thesaurus

MySQLDatabase

SpecialistLexicon

MetaMap

FilterTxt2ConQuery ShowSelect

Open Discovery

•Query (user input):

raynaud’s disease

Open Discovery

•Mapping text to concept through MetaMap:

Raynaud's Disease [Disease or Syndrome]

Open Discovery

•Synonym lookup:

Raynaud's syndrome Raynaud's disease /phenomenon

•Variant generation:

e.g. syndrome / syndromes

Open Discovery

•PubMed query:

raynaud OR raynauds

•Processing: query in titles and abstracts

•Result: 1,246 MEDLINE citations

Open Discovery

•Text to concept mapping of all citations

•Sentences with Raynaud’s disease

•Result: 1,278 UMLS concepts

Open Discovery

•Select functional/physiological concepts•Semantic types in filter:

Body Location or RegionBiologic FunctionCell FunctionPhenomenon or ProcessPhysiologic FunctionTissue

Open Discovery

•Result: 57 Concepts

•Frequency range:

Open Discovery

•Selected B-concepts:

Plasma Viscosity LevelBlood ViscosityPlatelet AdhesivenessPlatelet AggregationEffects, Blood

Coagulation

Open Discovery

•Variants:

plasma, plasmasviscosity, viscous,aggregation, aggregations,

aggregatingcoagulation, coagulating

Open Discovery

•PubMed query:

blood coagulation OR blood viscosity OR plasma viscosity OR platelet

adhesiveness OR platelet aggregation

•Result: 10,611 MEDLINE citations

Open Discovery

•Concepts in sentences with B-concepts:

•Concepts not in Raynaud sentences:

Open Discovery

•Filter for dietary related concepts

•Semantic types in filter:

VitaminLipidElement, Ion, or Isotope

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:

Closed Discovery

Eicosapentaenoic AcidFish OilFatty Acids, Omega 3MAXEPAOmega-3

PolyunsaturatedFatty Acid

Cod Liver OilSalmon Oil

Raynaud’s Disease

Closed Discovery

1,246 citations1,278

concepts

479 common concepts

463 citations1,795

concepts

Closed Discovery

Functional / Physiological Filter

45 B-concepts

Closed Discovery

•Known concepts:

Plasma viscosity level

Blood ViscosityPlatelet

AdhesivenessPlatelet AggregationEffects, Blood

Coagulation

•New concepts:

VasodilatationVeins, CapillariesDinoprostoneFibrinolysisDeformabilityRheology

Juxtaposition

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

Future

• Better semantic analysis:increase(A,B) and decrease(B,C)

• Better user interface

• More databasese.g. finding genetic bases for diseases

Text-based Discovery in Biomedicine The Architecture of the DAD -system

Documents

Publishing in biomedicine sentences

Biomedicine & Pharmacotherapy - UiT

Biomedicine and Health Innovation OCDE

Rich Dad Poor Dad

Lecture 8 Biomedicine

A Fast Neighbor Discovery and DAD Scheme for Fast Handover in Mobile.pdf

Biomedicine and Big Data

Centre for Biomedicine & Society

Main figures biomedicine (Biopol'H)

Bioinformatics drives discovery in BiomedicineKeywords: Bioinformatics, multi-omics, big data, opportunities and biomedicine Description: The human genome sequencing project was the

Biomedicine & Pharmacotherapy - Patanjali Research Institute

University of Copenhagen Molecular Biomedicine the office of the Director of Studies in Molecular Biomedicine University of Copenhagen Molecular Biomedicine Course information on obligatory

An Anthropology of Biomedicine - Startseite · An Anthropology of Biomedicine Second Edition Margaret Lock and Vinh‐Kim Nguyen. ... Title: An anthropology of biomedicine / by Margaret

Deep Learning for Biomedicine - GitHub Pages · Deep Learning for Biomedicine. 11/07/2019 2 Deep Learning. Biomedicine. Deep Knowledge. 11/07/2019 3 ... Epidemiology meets Data Mining

MOFs in Biomedicine

TRIBE TRANSLATIONAL RESEARCH IN BIOMEDICINE

Knowledge Discovery in Biomedicine Limsoon Wong Institute for Infocomm Research

Discipline Guide Health Biomedicine

Biomedicine and bioinformatics databases (module ... · Biomedicine and bioinformatics databases (module Fundamentals of ... Biomedicine and bioinformatics databases Module Fundamentals

Nano Frontiers in Biomedicine Report