PhUSE Computational Science Working Groups Solutions Through - - PowerPoint PPT Presentation

PhUSE Computational Science Working Groups


Solutions Through Collaboration

PHUSE CS OVERVIEW

Paradigm Shift

Computational Science Collaboration

Mission: To provide an open, transparent, and collaborative forum in a non-competitive environment in which Academia, Regulators, Industry, and Technology providers can address computational science needs in support of product development and regulatory review, ultimately bringing safe and effective products to those who need them.

CS Collaboration Framework

Working Groups Symposium

Computa3onal Science Collabora3on

CS Working Groups

Steering Commi8ee Op3mizing Use of Data Standards Emerging Technologies Standard Scripts for Repor3ng and Analysis Non-Clinical Roadmap and Implementa3on Seman3c Technology

2016 CSS WRAP UP

CSS 2016 Highlights

• Over 300 attendees – SOLD OUT!
• Over 50 FDA attendees/2 from PMDA
• Lively panel discussion
• Engagement in every project
• Networking with new and old colleagues
• Great food!

OPTIMIZING THE USE OF
 DATA STANDARDS

CSS 2016 Project Summary

q Standards Implementa3on Nuances (by version)

§ Brain-storming sessions focused on Standards Implementa3on and Standards Nuances § Results of sessions will be used to scope the project § Possible project with CDISC for SDTM/ADaM FAQ

q Define v2.0 Implementa3on & Style Sheet Recommenda3ons

§ Two projects iden3fied and in the process of determining all co-leads

§ Define-XML 2.0 Implementa3on, "Comple3on Guidelines" document, focusing on best prac3ces for content and granularity § Define-XML 2.0 Stylesheet Recommenda3ons, scope to be clarified by team

q Study Data Standardiza3on Plan (SDSP)

§ Outstanding ques3ons answered & deliverables to be updated § Deliverables to be sent to FDA Champion by end of March § Deliverables for public review with Technical Conformance Guide updates

CSS 2016 Project Summary

q Legacy Data Conversion Plan & Report (LDCP)

§ Updated SDRG template will be sent to FDA for FDA PhUSE Working Group Review § SDRG Comple3on Guidelines and Example Document requires updates § Working group lead to schedule mee3ngs with team members

q Reviewer’s Guide & Define.xml

§ Reviewed notes and ques3ons from discussions over the last year with the broader group § Core team reviewed and edited introductory sec3ons of white paper and paper

• utline

q Standardizing Data within the Inspec3on Site Selec3on Process

§ Analysis of gaps between FDA expecta3ons and CDISC standards near comple3on § Reps from CDISC indicated they will consider new standards for this § PhUSE Standard Scripts group indicated they will consider standard specs and code for this

Roundtable Discussion Summary

• Working group met on Tuesday a^ernoon to discuss per3nent

topics and generate ideas for projects not already defined

Standards Scripts for Analysis and Reporting

What We Did

• Updated the whole group about our vision, motivation, and

progress

• Had the following breakout sessions:

– Whitepapers

• Discussed displays associated with adverse events, questionnaire data,

hepatotoxicity

– Repository

• Reviewed Git and Github
• Reviewed qualification process
• Reviewed FDA JumpStart scripts in the repository
• Reviewed the front-end of repository – index page
• Discussed name convention, version control and the goals
• Conducted workshop on github and the repository
• Met with Results Analysis Metadata WG and formed a

collaboration on creating a analysis result

Goals in PhUSE Year 2017

• Promote and Present FDA JumpStart

content

• Develop and present Central Tendency

package moving through the qualification process

• Develop and present traditional vs analysis

result metadata driven program using central tendency.

• Continue development of 4 analysis and

display white papers

Possible new projects

• Test Data Curation

– In order to have a good tests, we need to have test data sets containing different “issues” so that we could test scenarios that we plan to test – We need to have SDTM and ADaM data sets

• Mapping the whitepapers and scripts

– We need to create technical documents from the whitepapers to define what type of scripts that we need – We need to create the mapping between the whitepapers and scripts at the variable level

NON-CLINICAL IMPLEMENTATION AND ROADMAP

CSS2016: Nonclinical Working Group Outcomes

• Breakout A>endance and Ac?on be>er than ever

– over 60 a>endees represen?ng FDA, PMDA, Pharma, CROs and soHware vendors. – Nine project teams will go forward into the coming “PhUSE Year” to answer their highest priority data challenges

• Highlights

– Collabora?on Poster Award for the Nonclinical SDRG! – Assessment of current state of SEND-readiness in Industry

• Team conclusion: progress but room for improvement
• New Project Teams formed to tackle emerging implementa?on issues

– Extensive stakeholder discussions on Data Visualiza?on and Analysis

• Mul?ple needs iden?fied resul?ng on several key projects: one for

visualiza?on, one for analysis and one for script development

Nonclinical Projects Proposed for the Coming Year

• SEND Implementa?on

– SEND Implementa?on User Group – Nonclinical Study Data Reviewer’s Guide – Annual SEND Implementa?on Status Survey – Submission Data Consistency – Test Submission Forum

• Visualiza?on and Analysis

– Applica?on of SEND Data for Analysis – Visualiza?on of Group Differences in Histopathology Data – Nonclinical Analysis Scripts

CSS 2016 – Wrap up Ian Fleming Geoff Low

Emerging Trends and Technologies

Working Groups

• Alternate Transport Formats
• Cloud Adoption
• Data Transparency
• Data Visualisation
• Statistical Computing Environments

Alternative Transport Formats

• Achieved:

– Worked on a set of criteria for evaluating transport formats – Discussed transport and content issues

• Target:

– Finalise Criteria – Carry out Survey to prioritise criteria – Release white paper on evaluation of existing and new transport formats

Cloud Adoption

• Achieved

– Discussed Existing Framework document – Discussed Questions posed by EMA – Defined path for expansion and socialisation of Existing Framework

• Targets

– Update Framework to include Auditor section – Update Framework to incorporate data location – Develop Q&V section

Data Transparency

• Achieved

– Review EMA Policy 0070 – ADaM De-identification Scenarios

• extreme values,
• imputed dates
• Targets

– Blog Post on EMA 0070 – Questionnaire for previous downloaders – Release ADaM guidance for Public review

Data Visualisations

• Achieved

– Discussed and agreed future direction of Group

• Targets

– Risk-Based Monitoring & Data Visualisations – Implementations of Data Visualisations – Safety Graphics – Technology Comparisons – Interactive vs. Static Visualisations

Statistical Computing Environments

• Achieved

– Developed framework for describing user requirements for SCE (Acquire, Transform, Analyze, Visualize, Deliver) – Created list of requirements within this framework.

• Targets

– Dis3ll notes further and finalize framework – Request industry to share user requirement documents that they have developed – Develop best prac3ces as precursor to user requirements – Develop visual representa3on of SCE, clearly defining scope – Develop and publish user requirements

CSS 2016 Project Summaries

Semantic Technology Working Group

Workshop: Semantics 101 for Pharma


An introduction to Linked Data and the Semantic Web

• Over 50 attendees
• Groundwork for Semantic Technology Projects.

Future Offerings:

PhUSE CSS – EU Annual Conference, Barcelona

Marc Andersen, Tim Williams

Analysis Results & Metadata


Project Deliverables

Due end of June, 2016:

• White Paper, RDF Data Cube Tech. Specification, R Package.

Collaboration

• Standard Scripts, Use Cases

– R Package Hosting. – Code base and data for use cases.

Plans for 2016

• Use cases from Clinical Data Review Template (FDA

suggestion).

• Cloud solution.

Marc Andersen, Tim Williams

Clinical Program Design

White Paper Review and Development

• Reviewed original CPD suggestions.
• Reviewed and added tools for ST design in other industries.
• Reviewed sections and comments.
• Added Early Experiences with Design Tools.

Schedule

• Finish all WP sections and reviews : March – June 2016
• Send WP for PhUSE review by July 1, 2016
• Tool Development : June 2016 – April 2017

– Test CMAP and Neo4j for Design Activities. – Build Instructional materials for tools. – Validate nodes for Design Activities. Mary Banach, Laszlo Vasko

Regulations to RDF (REG2RDF)

Project Deliverables (by March, 2016)

• Key words for 21 CFR, reviewed by the FDA CDER/OSI.
• Web-based search 21 CFR.
• C-map graph representations of two of the 21 CFR sections.

Plans for 2016

• Interactive domain expert review tool for 21 CFR key words.
• Link 21 CFR regulation to:

– Relevant FDA guidances. – Regulations from other health authorities (e.g. EMA, ICH, PMDA, KMDA, and etc.). – Geographic locations.

• Change Management and Version Control.
• Cloud storage for public accessibility.

Mitra Rocca

Use Cases For Linked Data


Project Kick Off

• Collected Use Cases.

Collaboration

• Optimizing the Use of Data Standards.

– Additional Use Cases.

Plans for 2016

• 2-3 virtual round tables.
• Collate Use Cases, Draft White Paper.
• Consider development of proof of concept.

Scott Bahlavooni , Christine Fleeman

2016 EUROPEAN CSS

Why a European CSS?

• Collaboration and innovation are global
• European colleagues make significant

contributions to the CS Collaboration

– Steering Committee – Working Group Co-Leads – Project Co-Leads

• > 20% of US CSS attendees from Europe

European CSS Overview

• June 21-22 in Basel, Switzerland
• Focused on a subset of CS projects
• Free to PhUSE members

– Only 120 spots available – April 1: Registration opens to Working Group members – April 18: Registration opens to general public

European CSS Agenda

• Tuesday, June 21

– 14:00-16:00: Opening Session – 16:00-17:00: Working Group Breakout and Introductions – 17:00-18:30: Semantics 101 for Pharma Workshop

• Wednesday, June 22

– 9:00-15:00: Working Group Breakout Sessions – 15:00-17:00: Working Group Wrap Up and Closing Remarks

European CSS Projects

• Describe and develop requirements for an ideal

SCE

SCE Experiences

• Finalise evalua3on criteria survey

Alterna3ve Submission Transport Formats

• Con3nued development of ADaM de-

iden3fica3on rules

De-Iden3fica3on of ADaM

• Review of ongoing Working Group projects

Non-Clinical: SEND Implementa3on

• Joint CDISC/PhUSE project to address SDTM

implementa3on ques3ons

SDTM Implementa3on FAQ

• Define op3mal to enable new ways of working

and increase collaboraprocesses3on

PhUSE Future Forum: Process Op3miza3on

Questions