Taverna & EU-ADR
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PEDRO LOPES [email protected] University of Manchester October 19 th , 2010 Exploring and Understanding Adverse Drug Reactions by Integrative Mining of Clinical Records and Biomedical Knowledge http:// euadr-project.org
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Presentation shown to Taverna development team to kick-off the discussion on how to improve and enhance Taverna usage in the EU-ADR Web Platform.
Transcript of Taverna & EU-ADR
PEDRO LOPES [email protected] of Manchester
October 19th, 2010
Exploring and Understanding Adverse Drug Reactions by Integrative Mining of Clinical Records and Biomedical Knowledgehttp://euadr-project.org
IntroductionGoals
Challenges
EU-ADR
Why?Taverna
UX
WORKFLOWS
ArchitectureTaverna
Open Issues
WEB PLATFORM
IntroductionGoals
Challenges
EU-ADR
Why?Taverna
UX
WORKFLOWS
ArchitectureTaverna
Open Issues
WEB PLATFORM
‣ DRUG
• “A pharmaceutical drug, also referred to as medicine, medication or medicament, can be loosely defined as any chemical substance intended for use in the medical diagnosis, cure, treatment, or prevention of disease.” Wikipedia
‣ ADVERSE DRUG REACTION
• “An adverse drug reaction (abbreviated ADR) is an expression that describes harm associated with the use of given medications at a normal dose. The meaning of this expression differs from the meaning of "side effect", as this last expression might also imply that the effects can be beneficial. The study of ADRs is the concern of the field known as pharmacovigilance.” Wikipedia
BACKGROUND
‣ DRUG
• “A pharmaceutical drug, also referred to as medicine, medication or medicament, can be loosely defined as any chemical substance intended for use in the medical diagnosis, cure, treatment, or prevention of disease.” Wikipedia
‣ ADVERSE DRUG REACTION
• “An adverse drug reaction (abbreviated ADR) is an expression that describes harm associated with the use of given medications at a normal dose. The meaning of this expression differs from the meaning of "side effect", as this last expression might also imply that the effects can be beneficial. The study of ADRs is the concern of the field known as pharmacovigilance.” Wikipedia
BACKGROUND
DRUG + ADR = SIGNALM01AH02 (Rofecoxib) + UGIB (Upper Gastro-Intestinal Bleeding)
‣ BEFORE THE MARKET
• Test with thousands of subjects
• Some Adverse Drug Reactions are not detected
‣ IN THE MARKET
• Clinicians must recognize and report suspected harmful “side effects”
‣ SPONTANEOUS REPORTING SYSTEMS
• Main pillar to detect signals in pharmacovigillance
LAUNCHING A NEW DRUG
‣ BEFORE THE MARKET
• Test with thousands of subjects
• Some Adverse Drug Reactions are not detected
‣ IN THE MARKET
• Clinicians must recognize and report suspected harmful “side effects”
‣ SPONTANEOUS REPORTING SYSTEMS
• Main pillar to detect signals in pharmacovigillance
LAUNCHING A NEW DRUG
There is an entire ecosystem associated with pharmacovigillance !
GOAL
The overall objective of the EU-ADR project is the design, development and validation of a computerized system that exploits data from electronic healthcare records and biomedical databases for the early detection of
adverse drug reactions.
GOAL
The overall objective of the EU-ADR project is the design, development and validation of a computerized system that exploits data from electronic healthcare records and biomedical databases for the early detection of
adverse drug reactions.
Some kind of intelligent application that finds ADRs in literature, patient data and other databases. ☺
‣ HOW TO BUILD THIS?
CHALLENGES
Application: (Search + Collect) x (Literature + Patient Data + Biomedical Databases) x User Interactions
‣ HOW TO BUILD THIS?
CHALLENGES
Application: (Search + Collect) x (Literature + Patient Data + Biomedical Databases) x User Interactions
‣ HOW TO BUILD THIS?
CHALLENGES
Application: (Search + Collect) x (Literature + Patient Data + Biomedical Databases) x User Interactions
Why?Taverna
UX
WORKFLOWS
IntroductionGoals
Challenges
EU-ADR
ArchitectureTaverna
Open Issues
WEB PLATFORM
Why?Taverna
UX
WORKFLOWS
IntroductionGoals
Challenges
EU-ADR
ArchitectureTaverna
Open Issues
WEB PLATFORM
Retrospective and Prospective System Validation
Signal Substantiation
Signal Detection
WORKFLOW
Literature
Known Side Effects
Pathway Analysis
In silico simulation
EHR n
EHR 2
EHR 1
Data Extraction
Text MiningTerminology Mapping
Data Mining
Ranked signal list
Re-ranked signal list
‣ DATABASES
• Public
‣ UniProt, DailyMed, DrugBank, PharmGKB, NCBI * ...
• Partner-specific
‣ Huge datasets
‣WEB SERVICES
• Public web services
• Partner-specific
HOW?
‣ DATABASES
• Public
‣ UniProt, DailyMed, DrugBank, PharmGKB, NCBI * ...
• Partner-specific
‣ Huge datasets
‣WEB SERVICES
• Public web services
• Partner-specific
HOW?
How to connect everything in a single system? ?
‣ DATABASES
• Public
‣ UniProt, DailyMed, DrugBank, PharmGKB, NCBI * ...
• Partner-specific
‣ Huge datasets
‣WEB SERVICES
• Public web services
• Partner-specific
HOW?
How to connect everything in a single system? ?
‣ DATA PRIVACY
• Sensitive, unpublished, data
• There’s money attached (pharmaceutical companies)
‣ USERS
• From clinicians to programmers
• Single lab scale (local data) vs Project scale (web environment)
‣ PERFORMANCE
• Huge datasets
‣ Thousands of signals
REQUIREMENTS
SECURITY
‣ TESTED
• Single Sign On
• OpenID
• Shibboleth
• OAuth
• OpenASelect
• HTTPS, WSDL-S
SECURITY
‣ SOLUTION
• WSO2 Platform
‣ Custom Identity Provider
‣ Secure web services
‣ Straightforward to install
‣ TESTED
• Single Sign On
• OpenID
• Shibboleth
• OAuth
• OpenASelect
• HTTPS, WSDL-S
SECURITY
‣ SOLUTION
• WSO2 Platform
‣ Custom Identity Provider
‣ Secure web services
‣ Straightforward to install
THANK YOU!☺
UX
UX
‣ LOCAL
• Local workflow execution
• Local data analysis
‣WEB
• Remote workflow execution
‣ Process the entire pipeline online
• Remote data analysis
‣ Analyze workflow results and provenance data
Web Platform = Taverna + Services + XSD !
UX
‣ LOCAL
• Local workflow execution
• Local data analysis
‣WEB
• Remote workflow execution
‣ Process the entire pipeline online
• Remote data analysis
‣ Analyze workflow results and provenance data
FIRST WORKFLOW
http://bioinformatics.ua.pt/euadr_test
ArchitectureTaverna
Open Issues
WEB PLATFORM
IntroductionGoals
Challenges
EU-ADR
Why?Taverna
UX
WORKFLOWS
ArchitectureTaverna
Open Issues
WEB PLATFORM
IntroductionGoals
Challenges
EU-ADR
Why?Taverna
UX
WORKFLOWS
WEB PLATFORM
‣WEB SERVICES
• Execute partner web services
• View results
‣WORKFLOWS
• Workflow management
• Search, browse and execute workflows
• Analyze and compare results
‣ DATASETS
• Process entire datasets
‣ All workflows x ~ 4000 signals per dataset
• Analyze and compare final and intermediate results
‣ “Signal evolution”
WEB PLATFORM
PIPELINE
1.UPLOAD DATASET
• From users’ desktop to web platform (.xls)
2.READ DATASET
• Web Platform reads file to database
3.PROCESS DATASET
• Generate workflow XML inputs
4.EXECUTE WORKFLOWS
• Launch threaded Taverna executions
5.STORE WORKFLOW RESULTS
• Save full XML output
6.UPDATE DATASET
• Update dataset information with output results
7.DISPLAY WORKFLOW RESULTS
• Show results in web platform
PIPELINE
ARCHITECTURE
ARCHITECTURE
security
Tave
rna
Conn
ect
CLI
‣ REQUIREMENTS
• Organize datasets into multiple workflow execution
‣ Workflow accepts any number of signals in input
• Output results as XML files
‣ One signal = One XML file
• Load files into web platform
‣ Read XML
‣ CONDITIONS
• Performance
• Time
• Efficiency
• Size
• Complexity
TAVERNA CONNECT
‣ REQUIREMENTS
• Organize datasets into multiple workflow execution
‣ Workflow accepts any number of signals in input
• Output results as XML files
‣ One signal = One XML file
• Load files into web platform
‣ Read XML
‣ CONDITIONS
• Performance
• Time
• Efficiency
• Size
• Complexity
TAVERNA CONNECT
BEST SOLUTION?syscalls, web services, disk access, web access, pooling, transmission, network, hosts...
‣ STRATEGY
• Define (static) workflow input/output directories
• Generate XML input
• Execute Java syscall (threaded)
• Read XML output
COMMAND LINE INTERFACE
Straightforward
Simple
Streamlined
Handles large files
Static
Time
Efficiency
“It’s a syscall!”
‣ STRATEGY
• Define (static) workflow input/output directories
• Generate XML input
• Execute Java syscall (threaded)
• Read XML output
COMMAND LINE INTERFACE
JAR package? Performance improvement? Full security? ...
Straightforward
Simple
Streamlined
Handles large files
Static
Time
Efficiency
“It’s a syscall!”
‣ STRATEGY
• Develop Java client package (do you have it?)
• Generate and transmit XML input
• Execute workflow
• Check for results
• Download results
TAVERNA SERVER
“It’s not a syscall!”
Modular (dynamic) design
Complexity
Efficiency
Network
Handles large files
‣ STRATEGY
• Develop Java client package (do you have it?)
• Generate and transmit XML input
• Execute workflow
• Check for results
• Download results
TAVERNA SERVER
“It’s not a syscall!”
Modular (dynamic) design
Complexity
Efficiency
Network
Handles large files
Simplified? Lighter? Performance? Client packages?
‣ STATUS
• Beta release soon
‣ NEXT
• More data
• More services
• More workflows
• More users
CONCLUDING
‣ STATUS
• Beta release soon
‣ NEXT
• More data
• More services
• More workflows
• More users
CONCLUDING
What’s next for Taverna?(What’s in it for us?)
What is the best path?
TAVERNA IS GREAT!
‣MIND | Microarray INformation Database
• http://bioinformatics.ua.pt/mind
‣ | Rare Disease Portal
• http://bioinformatics.ua.pt/diseasecard
‣ QuExT | Literature Query Expansion Tool
• http://bioinformatics.ua.pt/quext
‣ | Web Analysis of the Variome
• http://bioinformatics.ua.pt/WAVe
‣ GeneBrowser2
• http://bioinformatics.ua.pt/genebrowser2
http://bioinformatics.ua.pt
ME
/pdrlps
/pedrolopes
http://pedrolopes.net
THANK YOU!
