CELO: A Cost-Effective System for Efficiently Building Informatics Solutions to Manage Biomedical...

CELO: A Cost-Effective System for CELO: A Cost-Effective System for Efficiently Building Informatics Solutions Efficiently Building Informatics Solutions

to Manage Biomedical Research Datato Manage Biomedical Research Data

Christine FongChristine FongUniversity of WashingtonUniversity of Washington

Biomedical and Health InformaticsBiomedical and Health Informatics

Master’s Thesis Committee: Master’s Thesis Committee: Jim Brinkley, Peter Tarczy-Hornoch, John ClarkJim Brinkley, Peter Tarczy-Hornoch, John Clark

May 17, 2005May 17, 2005

22

OutlineOutline

Data management needs of today's Data management needs of today's biomedical research labsbiomedical research labs

Existing informatics solutionsExisting informatics solutions Requirements for a successful systemRequirements for a successful system My approach to satisfy requirementsMy approach to satisfy requirements CELO System ArchitectureCELO System Architecture Using CELO to build a laboratory data Using CELO to build a laboratory data

management systemmanagement system CELO System EvaluationCELO System Evaluation Discussion and ConclusionsDiscussion and Conclusions

33

OutlineOutline




44

Traditional Data Management Traditional Data Management MethodsMethods

Lab Books

Spreadsheets

Word Documents

55

Trends in Biomedical ResearchTrends in Biomedical Research

Diversity of computerized data typesDiversity of computerized data types– Images, movies, etcImages, movies, etc– Domain specific applicationsDomain specific applications

Larger data setsLarger data sets– Recent digital technologiesRecent digital technologies– Large scale research effortsLarge scale research efforts

A need to share dataA need to share data– Large scale research effortsLarge scale research efforts– Multi-disciplinary research effortsMulti-disciplinary research efforts

66

OutlineOutline




77

Commercial LIMSCommercial LIMS Nearly a hundred optionsNearly a hundred options Generally targets specific markets (e.g. Generally targets specific markets (e.g.

environmental, pharmaceutical)environmental, pharmaceutical)

Feature-richFeature-rich

ExpensiveExpensiveUsually not open sourceUsually not open sourcePredefined types for targeted marketsPredefined types for targeted markets

88

Microsoft AccessMicrosoft Access

Commercial product for generic useCommercial product for generic use One of the more popular solutionsOne of the more popular solutions

Database and interface design toolsDatabase and interface design toolsSupport multimedia filesSupport multimedia filesStrong querying capabilitiesStrong querying capabilities

Difficult to make web-basedDifficult to make web-basedRequires substantial learning curveRequires substantial learning curveLarge databases require expensive upgrade

99

Open Source Approaches (1)Open Source Approaches (1)

NeuroSysNeuroSysWeb-basedWeb-basedUsers create user interfaces with set of widgetsUsers create user interfaces with set of widgetsCreating and querying data inefficientCreating and querying data inefficientDoes not support multimedia filesDoes not support multimedia files

SenseLabSenseLabWeb-basedWeb-basedTools for designing/evolving data representationsTools for designing/evolving data representationsQuerying not powerful and inefficientQuerying not powerful and inefficientDoes not support multimedia filesDoes not support multimedia files

1010

Open Source Approaches (2)Open Source Approaches (2)

Web-basedWeb-basedSupport for Multimedia FilesSupport for Multimedia FilesInformaticist needed to install and Informaticist needed to install and customizecustomize

WIRMWIRM

1111

OutlineOutline

Data management needs in today’s Data management needs in today’s biomedical research labsbiomedical research labs



1212

System RequirementsSystem Requirements

Inexpensive $$Inexpensive $$ Short development timeShort development time Customizable graphical user interfacesCustomizable graphical user interfaces Support for diverse data typesSupport for diverse data types Features to facilitate database designFeatures to facilitate database design Powerful querying capabilitiesPowerful querying capabilities Support for sharing over the internetSupport for sharing over the internet Plugins for customizationsPlugins for customizations Evolution of data representationsEvolution of data representations

1313

Review of Existing SystemsReview of Existing Systems

Commercial LIMS X X X X X

Microsoft Access X X X X X

NeuroSysX X X X X

SenseLabX X X X

WIRMX X X X X

Inexpensive

Short Develoment T

ime

Customiza

ble Gra

phical U

ser I

nterface

s

Featu

res F

acilita

ting D

atabase D

esign

Support for D

iverse D

ata Types

Powerful Q

uerying Capabilit

ies

Support for S

haring over t

he Intern

et

Plugins for C

ustomiza

tions

Evolution of D

ata Represe

ntations

1414

Comparison with CELOComparison with CELO

Commercial LIMS X X X X X

Microsoft Access X X X X X

NeuroSysX X X X X

SenseLabX X X X

WIRMX X X X X

CELOX X X X X X X

Inexpensive

Short Develoment T

ime

Customiza

ble Gra

phical U

ser I

nterface

s

Featu

res F

acilita

ting D

atabase D

esign

Support for D

iverse D

ata Types

Powerful Q

uerying Capabilit

ies

Support for S

haring over t

he Intern

et

Plugins for C

ustomiza

tions

Evolution of D

ata Represe

ntations

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OutlineOutline




1616

InexpensiveInexpensive

Reduce Costs by Distributing ResourcesReduce Costs by Distributing Resources

1717

Short Development TimeShort Development Time

Installation and Setup time reducedInstallation and Setup time reduced– Labs submit web registration formLabs submit web registration form– Automatic generation of database and Automatic generation of database and

webpagewebpage Generalizable features readily availableGeneralizable features readily available

– Determined by other system requirementsDetermined by other system requirements Web-based configuration toolsWeb-based configuration tools

– Help meet custom needs of labsHelp meet custom needs of labs– Allow researchers themselves to build systemAllow researchers themselves to build system

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Customizable graphical user Customizable graphical user interfacesinterfaces

Interfaces for creating and querying itemsInterfaces for creating and querying items– User friendly labelsUser friendly labels– Widgets for attribute valuesWidgets for attribute values

Web page contentWeb page content– Navigation barNavigation bar– Lab Home PageLab Home Page

Web page display settingsWeb page display settings– Color schemesColor schemes– Text stylesText styles

1919

Support for Diverse Data TypesSupport for Diverse Data Types

Predefined Data TypesPredefined Data Types– File (images, movies, documents, etc)File (images, movies, documents, etc)

Organizes and stores filesOrganizes and stores files Special handling of image filesSpecial handling of image files

– URLURL Customized Data TypesCustomized Data Types

2020

Features to Facilitate Database Features to Facilitate Database DesignDesign

Template SystemTemplate System– Predefined data types for particular research Predefined data types for particular research

areaarea– Automatically generates tables and Automatically generates tables and

relationshipsrelationships– Can be modified as neededCan be modified as needed– EfficientEfficient– Fosters consistency, reuse and sharingFosters consistency, reuse and sharing

2121

Powerful Querying CapabilitiesPowerful Querying Capabilities

Simple QueriesSimple Queries– Easy to use interfaceEasy to use interface– Quick way to find data from single tableQuick way to find data from single table

Advanced QueriesAdvanced Queries– User constructs SQL queriesUser constructs SQL queries– Can construct more detailed data viewsCan construct more detailed data views

2222

Support for sharing over the Support for sharing over the InternetInternet

Web-basedWeb-based Permissions systemPermissions system

– Controls who has access to various featuresControls who has access to various features– ConfigurableConfigurable

2323

OutlineOutline




2424

System ArchitectureSystem Architecture

Web Browser

CELO CGI Scripts

Client

WIRM Libraries CELO Libraries

CELO Server

Lab 1Data Files

Perl Modules

Lab 1 Database

Lab 1Data Files

XMLTemplates

Lab 2Data Files

...Lab 2

Database

...

CELO MainDatabase

CGI Scripts and Libraries

CELO Main Database

XML Templates Lab Databases

Lab Filesystem Directories

2525

CGI Scripts and LibrariesCGI Scripts and Libraries

CGI for web interfaceCGI for web interface WIRM LibrariesWIRM Libraries

– Image manipulationImage manipulation– Database functionsDatabase functions

Public Perl modulesPublic Perl modules– XML parsingXML parsing– HTML generationHTML generation

CELO LibrariesCELO Libraries– Set/Get Lab settingsSet/Get Lab settings– Generating interfacesGenerating interfaces

Web Browser

CELO CGI Scripts

Client


CELO Server

Lab 1Data Files

Perl Modules

Lab 1 Database

Lab 1Data Files

XMLTemplates

Lab 2Data Files

...

Lab 2Database

...

CELO MainDatabase

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CELO Main DatabaseCELO Main Database

One per CELO One per CELO installationinstallation

Table storing list of Table storing list of Research LabsResearch Labs

Table storing Table storing Template Template informationinformation

Web Browser

CELO CGI Scripts

Client


CELO Server

Lab 1Data Files

Perl Modules

Lab 1 Database

Lab 1Data Files

XMLTemplates

Lab 2Data Files

...

Lab 2Database

...

CELO MainDatabase

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Lab DatabasesLab Databases

Multiple per CELO Multiple per CELO installationinstallation

Each represents one Each represents one lablab– Research DataResearch Data– Custom Lab SettingsCustom Lab Settings

Web Browser

CELO CGI Scripts

Client


CELO Server

Lab 1Data Files

Perl Modules

Lab 1 Database

Lab 1Data Files

XMLTemplates

Lab 2Data Files

...

Lab 2Database

...

CELO MainDatabase

2828

Lab Database TablesLab Database Tables

Data_Storeds_id

ds_labelds_nickname

ds_labelds_derived

Data_Classdc_id

dc_of_datastore

dc_namedc_labeldc_desc

dc_showhome

Class_Attributeatt_of_classatt_nameatt_labelatt_typeatt_order

att_requiredatt_uniqueatt_inlabel

att_edit_widgetatt_query_widget

att_note

(lab specific)<dc_name>

oid<att_1><att_2>

...

Permissions System

Saved_Queryq_id

q_nameq_of_datastore

q_descq_dataclass

q_filterq_showq_orderq_viewq_edit

Fileoid

labeldomainlocatorsource

mime_typesubmit_datesubmitted_by

versioncontext

descriptionheightwidth

URLoid

url_labelurl_address

url_desc

User_Group

oidname

permissions

Useroid

loginfirst_namelast_name

emailpassword

user_group

Sessionsession_id

userlogin_datelogin_time

Default Data Types

Saved_SQLss_id

ss_namess_of_datastor

eq_descq_sql

q_viewq_edit

Data Representation and

Organization

Usage Log

Usage_Logul_id

ul_dateul_timeul_user

ul_actionul_param

Usage_Report

ur_filenameur_daterange

ur_usersur_actionsur_params

CustomizationLab_Settings

ls_namels_value

WirmFsaIndexoid

dest

WirmRepoTypesoid

rtype

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XML TemplatesXML Templates

Define data Define data representationsrepresentations

Define queriesDefine queries Transformed into Transformed into

database formatdatabase format– New table entriesNew table entries– New tablesNew tables

Web Browser

CELO CGI Scripts

Client


CELO Server

Lab 1Data Files

Perl Modules

Lab 1 Database

Lab 1Data Files

XMLTemplates

Lab 2Data Files

...

Lab 2Database

...

CELO MainDatabase

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XML Template FormatXML Template Format

Data_Classdc_id

dc_of_datastoredc_namedc_labeldc_desc

dc_showhome

Class_Attributeatt_of_classatt_nameatt_labelatt_typeatt_order

att_requiredatt_uniqueatt_inlabel

att_edit_widgetatt_query_widget

att_note

Saved_Queryq_id

q_nameq_of_datastore

q_descq_dataclass

q_filterq_showq_orderq_viewq_edit

<template> <id>1</id> <derived>original</derived> <name>Treatment Study</name> <desc>Study the effectiveness of treatments on animal subjects</desc> <author>CELO Developer</author> <author_id></author_id> <organization>Structural Informatics Group</organization> <date>February 4, 2004</date> <dataclass> <name>Treatment</name> <label>Treatment</label> <desc>A treatment being studied</desc> <showhome>1</showhome>

<attributes> <attribute> <order>1</order> <name>drug</name> <label>Drug</label> <type>char(50)</type> <required>1</required> <unique>0</unique> <inlabel>1</inlabel> <edit_widget>textfield(40,50)</edit_widget> <query_widget>textfield(40,50)</query_widget> <note>Name of drug being tested</note> </attribute> <attribute> <order>2</order>... </dataclass> <query> <name>All Treatments</name> <desc>List of all treatments being studied</desc> <q_dc>Treatment</q_dc> <filter></filter> <show>drug,amount</show> <order>drug</order> </query></template>

Template XML File Lab Database Tables

Treatmentdrugdose

dataclasses

attributes

queries

new tables

tableentries

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Lab Filesystem DirectoriesLab Filesystem Directories

Research Data FilesResearch Data Files– Uploaded through Uploaded through

browserbrowser– Automatically Automatically

organizedorganized Display Display

configuration filesconfiguration files– Cascading Style Cascading Style

SheetSheet– Banner logo imageBanner logo image

Web Browser

CELO CGI Scripts

Client


CELO Server

Lab 1Data Files

Perl Modules

Lab 1 Database

Lab 1Data Files

XMLTemplates

Lab 2Data Files

...

Lab 2Database

...

CELO MainDatabase

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OutlineOutline




3333

Register for a New SystemRegister for a New System

3434

LoginLogin

3535

Create User Groups and UsersCreate User Groups and Users

3636

Browse for and Use a TemplateBrowse for and Use a Template

3737

Enter ItemsEnter Items

3838

Simple QuerySimple Query

3939

Save a QuerySave a Query

4040

Customize Look of Lab Web PageCustomize Look of Lab Web Page

4141

OutlineOutline




4242

Evaluation ApproachEvaluation Approach

Test hypothesis:Test hypothesis:

CELO is able to efficiently build data management CELO is able to efficiently build data management systems that meet the specific needs of systems that meet the specific needs of biomedical laboratoriesbiomedical laboratories

Recreate 3 existing systemsRecreate 3 existing systems– Familiar with laboratory informatics needsFamiliar with laboratory informatics needs– Know most valuable featuresKnow most valuable features– Able to compare development timesAble to compare development times

Create a new systemCreate a new system– GeneralizabilityGeneralizability

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Evaluation Results SummaryEvaluation Results SummaryFeature Replicated Efficient

Eye Lab Image Repository

Controlling User Access ++ ++Organizing Data from Separate Experiments ++ ++Defining Representations of Data ++ ++Creating and Viewing Items ++ ++Finding Images ++ ++Creating Image Matrices for Image Comparison and

Analysisn/a

The Cortical Stimulation Mapping Database

Controlling User Access + ++Defining Representations of Data + ++Creating and Viewing Items + ++Access to Data + +System Navigation + ++Visual Brain Mapper Application n/a

Single Unit Recording Database

Defining Representations of Data ++ ++Access to Data ++ ++Creating and Viewing Items + ++Query Electrode Neuron by Patient n/a

Protein Interaction Study

Defining Representations of Data ++ +Creating and Viewing Items + ++

++ completely+ partially

++ very efficient+ somewhat efficient

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OutlineOutline




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DiscussionDiscussion

Revisit hypothesis:Revisit hypothesis:

CELO is able to efficiently build data management CELO is able to efficiently build data management systems that meet the specific needs of systems that meet the specific needs of biomedical laboratoriesbiomedical laboratories

Very efficient solutionVery efficient solution System able to satisfy needs of some labs System able to satisfy needs of some labs

more completely than othersmore completely than others More complex or unique features could not More complex or unique features could not

be recreated completely or not at allbe recreated completely or not at all

4646

Future WorkFuture Work

Satisfy 2 remaining requirementsSatisfy 2 remaining requirements– Plugins for customizationsPlugins for customizations– Evolution of data representationsEvolution of data representations

Additional tools for designing data Additional tools for designing data representationsrepresentations

Additional formatting options for Additional formatting options for customized interfacescustomized interfaces

Multi- SQL query data viewsMulti- SQL query data views Features for data integrationFeatures for data integration

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ConclusionConclusion

CELO can be a valuable tool for labs that CELO can be a valuable tool for labs that need an need an inexpensiveinexpensive and and quickquick solution for solution for

basicbasic data management needs data management needs

- Open source, free software- Shared resources

- Automatic installation and setup- Generalizable features readily available- Web-based configuration tools for customizations

- Strong support for basic organization, viewing, querying features- Weak support for unique formatting and complex features

Thank You!Thank You!

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