Domain Specific Multi-Stage Query Language For Medical Document Repositories

to Advance Knowledge for Humanity
Domain Specific Multi-stage Query Language

for Medical Document Repositories
Aastha Madaan
University of Aizu
8/25/2013
VLDB Phd Workshop 2013
Introduction
Specialized Domains
Biomedical, agriculture, medical/healthcare
Require Effective search and query mechanisms
Insufficient Search Engine-like Keywords based search
Medical domain
Complex
Example,
Query general AIDS information
medical search tool, such as PubMed
Result 1000s of documents Different aspects of AIDS
Such as , treatment, drug therapy, transmission, diagnosis, and history
Medical professionals Specific technical articles (particular topic )

General public General information (disease or medicine).
How to retrieve medical information effectively

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Introduction (1)
Medical Information
Knowledge Evolved over 10s of years
Contains Well defined terms and processes
Available on the Web

Patient Specific Information
Knowledge-based Information
Web Documents
Patient-encounter
Recordings
Medical Literature
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Introduction (2)
Complexity Knowledge-based Resources
Heterogeneous End-user groups
Patients, researchers, doctors and other experts
Variation Information Requirements
Patient-treatment, self -diagnosis, general health information
Structure Medical Documents
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Scientific papers, encyclopedias and other literature

Unique, well-defined
Introduction (3): Specialized Documents

Case of medical encyclopedias
Comprehensive medical guide Patients and clinicians
Authoritative source NLM (National Library of Medicine)
Paper based resources Electronic format
Frequently referred Medical domain users

Example, MedlinePlus, WebMD, ADAMS,
Merriam-Webster Medical Dictionary
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Introduction (4): Why Query

External knowledge base Clinicians
Evidence based medicine

During different stages of point-of-care
Assessment plan of treatment

Patient diagnosis
Improve Quality of Care

Authoritative information required
Self Diagnosis
During Early appearance of symptoms
Personal Knowledge Patients and their relatives
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The Underlying Structure

The Hierarchical Structure
Topic of the Document
Miscellaneous/Related
Subtopics
Content
Subtopic 1
Subtopic 2
Subtopic n
Content topic 1
Content topic 2
Content topic n
Content
Content
Content
Content
Content
Content
Flow of Contents Organized as stages of point-of-care

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Introduction (5): The End Users

Variable
a.
b.
c.
Demographical Characteristics
Tasks/Purpose
Computer/Domain Expertise
Practitioners and Researchers
Well-versed
Domain knowledge and terminologies
Require
Precise, complete, accurate and timely results
Healthcare Workers
Specialized
Researchers
Patients and their relatives
NOT Well-versed
Domain knowledge and terminologies
Require
General information
Patients, their relatives
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The Medical Queries

Evidence-based Queries
Intent: Diagnostic
Raised by: Clinicians/Experts
Target resources: Online Medical Repositories (e.g. medical encyclopedia)
Example: Cases where helicobacter bacteria causes peptic ulcer
Hypothesis-directed Queries
Intent: Non-diagnostic
Raised by: Novice users/patients
Target resources: Online Medical Repositories (e.g. medical encyclopedia)
Example: Treatment in case of high fever and dizziness
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The Query Flows

Occurrence Evidence-based and hypothesis-directed queries
Represent Stages of information seeking
Comprise Varying levels of query complexity
2.
1.
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3.
4.
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The Research Gap

Healthcare Expert
Help Needed
Paper-based resources
Query: Find chances of "Cancer Risk" in patients showing symptom "Sleep Deprivation"
and have been exposed to "Radiation" (but not "Environmental Toxins" and does not have
"Genetic Disorder") .
Results Large in number, irrelevant
Failure Keyword search, domain-specific search tools

Require Precise and easy-to-use database style query methods
Key steps:
1. Schema understandable by users
2. Identify Resources to query
3. Identify Granularity of results
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Bridging the Gap

Aim: Effective Online Medical Information
Transform Document Repository User-Level Schema
Enable High-level Query Language
Target Audience Skilled and semi-skilled users

Utilize Query capabilities of a database query language
Assist Domain Experts Using Query language

Facilitate
In-depth Queries
Granular Results
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Querying the New Way

Resource
-
Results returned
Lack specificity
Long list of full documents
Trustworthiness of resources unknown
User-level
Schema
High-level Query Query

Method
language
Keyword
Search
Results returned
Specific, granular
Segments of documents query criteria
Trustworthy/Authoritative sources only
Medical
Expert
Medical
Expert
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Resource
Traditional
Method
Proposed
Method
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Proposed Approach
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Key Features
User-Level Schema
Universal , concept-level schema
Attributes
Understandable Domain experts and novice users
Query-able
Granular results
Multi-stage Query Language

Map multi-stage diagnostic process Step-by-step Query Flow
Interactive Querying View Results Add concept
Continuous query refinement
Supported Queries Simple, Medium, Complex, Recursive
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Outline
Two-step framework
Offline Process Create User-level schema
Online Process Enable Multi-stage Query Language
Offline Process
Use Web segmentation algorithm, Domain concepts
Result Automatic creation of a User-level schema
Online Process
Enable Multi-stage Query Language
Use User-level schema
Results Granular, segment-level, context-based
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The Method
Two-step Framework
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Data Model
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Data Model
Tree Structured Repository
H1
f1
f2
Example: MedlinePlus Medical Encyclopedia
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Data Model (1)
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Data Model (2):The Schema

Attributes Diagnostic concepts/terms
Understandable by expert and novice users
Do not change frequently
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Data Model (3): A XML Document

Document corresponding to Aarskog Syndrome
Title
Causes
Symptoms
Treatment
Example: MedlinePlus Medical Encyclopedia
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Data Model (4): Query Effort

Query: Find if "Oxygen therapy" work for the treatment of "Chronic Respiratory
Failure" and symptoms are "Lethargy" OR "Shortness of breath.
Not Possible
Easy-to-Use
Advanced search: MedlinePlus
Result segment
Proposed Method
SELECT attribute = Disease_name
WHERE
Attribute Disease_name = Chronic
Respiratory Failure
AND
Attribute Treatment = Oxygen therapy
AND
Attribute Symptoms =Lethargy
OR
Attribute Symptoms = Shortness of breath
Context of user-query
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Data Model (5): Granular Results

Each result is a segment, combination of
Concept/context in query
Item of concern (content enclosed in a
segment)
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Context
Granular
Queried
Attributes/Segments
Query Results
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An Example
Query: Find other symptoms where chronic kidney failure is
caused by anemia
Queried segment Symptoms
Segments in Query Causes = anemia and Disease_name
= Chronic kidney failure
Result Segment Symptoms
Context disease_name = chronic kidney failure & causes
= anemia (SYMPTOM - segment)
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Next Step Multi-stage Query Language
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Proposed Query Language (1)

XQBE Medical document repositories
Create queries Drag and drop interface
Query : Find cases where a person is inflicted with peptic ulcer due to
helicobacter pylon bacteria
Attributes understandable by end

users
1. Case = disease_name
Value = ??
2. Due to = Causes
Value = helicobacter pylon bacteria
3. Inflicted with = Symptoms
Value = peptic ulcer
Query Effort
Minimal learning curve
Computer-expertise not required
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Proposed Query Language (2)

Multi-stage Query-by-Concept
Concept Query-able attribute

Topic, sub-topic, medical concept
Query Effort
Dynamic selection of attributes
No computer expertise
An Example: Cases where fever is caused due

to infliction of Pneumonia and Tuberculosis
Query Process
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Another Example
Query: Find cases where 3 clinical concepts (cough, no
sore-throat, and had no sterol injection) occur in context of
symptoms occur along with a concept having sub-key (i.e. non
sterol injection at the left side)
Possible XQBE on Specialized Medical Repositories
Possible Multi-stage Query-by-concept Query Language
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Evaluation Plan
Data Sets
MedlinePlus document repository
Health topics (900+) , encyclopedia (4000+), drugs (12000+)
Set of Queries
50 test queries (multi-staged)
Using diseases and medication etc.
Quantitative Studies
Evaluation Metrics
Accuracy of segment extraction (schema creation) Precision and Recall
Reduction in search space
Qualitative Studies
Usability Studies
Actual End-users
Query Performance
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Initial Achievements
HTML XML as per proposed model
XQuery on XML
Integration with XQBE
Query by concept Enumeration using paper and
pencil
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Challenges
Scalability Similarly structured repositories
List Query operations needed

Implementation Above query operations
Query Language User Interface
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Related Work
Domain-specific Information Retrieval
Similarity and popularity based models Insufficient for domain experts
Information granulation needs to be considered in huge document repositories
Form-based Query Interfaces
Easy-to-use
Limited access to the database
Complex queries large number of forms
Varying medical concepts large number of fields in forms
Beyond single page web search results
Provide granular results for users search
Return segments from multiple or related web documents as results
High-level Graphical Query Languages
Easy-to-use and understand
Little or no programming effort required by the user
Common languages QBE, XQBE
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Summary and Conclusions

Proposed Multi-stage Query Language
1.
Aim Effective online medical resources
2.
Key feature User-Level Schema
3.
Facilitates Granular/Context-based Results
4.
Support Healthcare Experts
5.
Minimize Learning curve for novice users
6.
Reduce Dependency on general-purpose search engines
Provide Web user level activity no or little programming effort

Healthcare experts
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References (1)
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Questions
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