Application of SEND Data for Analysis

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Welcome to the site for the "Application of SEND Data for Analysis" project.

This project was conducted in 2015-2016 as part of the FDA/PhUSE Computational Sciences Nonclinical Working Group. The project is now closed, but the work done is available publically. This page provides the details and deliverables from the project. To Learn more about the larger working group, and it's many other projects past and present, go to Nonclinical Topics Working Group.

Project Overview

The project focused on use cases for SEND data related to analyses provided on tables for general toxicology studies. Commonly, the nonclinical study analyses in industry practice are performed using raw data extracts, while the SEND datasets are created outside of this in a separate process. This project examined these purposes and identified some standard analyses that could be performed using the SEND package.
The intent was to understand how these analyses relate to SEND data, and demonstrate the data quality and fitness for use possible using SEND data sets for analysis. It was the project's objective that this effort can be used to create standard scripts and fitness for use checks on SEND data.

Identified Need/Challenge

As the implementation and exchange of SEND data is becoming more prevalent in the industry, focus is directed towards the usability and fitness for use of the SEND data. The usability of SEND data is essential in order to harvest the benefits of more efficient review and analysis.

Project Scope

The project focused on individual SEND domains in a prioritized manor (FW, CL, MA, MI mainly). Scientific questions that may arise during review of SEND data were discussed. SEND domain specific analyses using example analysis keys (i.e. SEND variables) were identified to aid in getting the right answers from the SEND datasets.
Certain SEND variables lend themselves better to computational analysis by being subject to controlled terminology, formats and/or expectancy requirements by the standard, while other variables are under the control of the sponsor (either with population by need or choice or through sponsor controlled vocabularies). The project proposed recommendations for which variables are minimum information for any review of the data.
Analyses is defined for this project as review of SEND data, and does not refer to the statistical outcomes of the study.

Vision

To describe use cases for SEND data that may provide the industry with a common platform to communicate and assess how SEND supports data "fitness for use" and provides quality context for review of study data.

Transverse Collaborative Investigations


Deliverables

SEND Domains Examined

Domain Name Data Type Source System Link to document page
FW Individual Non-rodent PDS - ToxData 2016-08-12
FW Individual Rodent Provantis 2016-08-26
FW Cage-based Rodent Provantis 2016-08-26
FW Individual Non-rodent Pristima 2016-09-09
CL (Qualitative Food) Individual Non-rodent PDS - ToxData 2016-09-09
MA Group summary non-rodent PDS - ToxData 2016-11-04
MA Group summary non-rodent PDS - ToxData 2016-11-04 continued
MA Individual Non-rodent Provantis 2016-11-04

SEND Variable Annotation Examples

Document Name Link to document page
ePaper
Minute Template File:Minute Template.docx
Tox tables mapped to SEND File:Tox tables to SEND mapping.xlsx
Tox table illustration File:Table illustration.docx
Sample BW report with annotation File:Bw summary with individual.pdf
Sample BG Individual listing with annotation File:IND BG Example.pdf
Sample LB Clin Chem Individual listing with annotation File:LB Clinical Chemistry individual data.pdf
Sample LB urinalysis data - individual and summary File:LB urinalysis examples reduced size.pdf
Sample CL data - individual and summary File:CL examples2.pdf
Sample CL data 2 - Individual File:Clin Obs Example.pdf
Sample CL data 3 - Individual Media:Clinical_Sign_report.gif
Thomas' overview of study data File:Framework for discussion of classification of information.pptx
Master Thesis, Thomas File:Analysis of SEND LB data (MSc thesis).zip
Master Thesis, Thomas, Presentation File:Analysis of SEND LB data (MSc thesis) - Examination slides final.pptx

Work Group Participants

The team was established at the PhUSE CSS March 2015, composed of those interested in the scientific output and quality of SEND datasets, with the following areas of expertise:

  • Toxicologists
  • FDA reviewers
  • IT vendors (with a special interest in the data quality aspect of SEND)
  • Nonclinical data managers (with focus on the fitness for use aspect of SEND data)
  • Biostatisticians (currently working or planning to work of SEND data)

Lead for this project was: Gitte Frausing (gfrausing@datastandardsdecisions.com).
Participants:

  • Gitte Frausing, Data Standards Decisions (lead), gfrausing@datastandardsdecisions.com
  • Wenxian Wang, Xybion
  • Dan Potenta, PDS Life Sciences
  • Elyse Hoffmann, Boehringer-Ingelheim
  • Jaga Virayah, Bayer
  • Thomas Gade Bjerregaard, Novo Nordisk
  • Rihab Kordane, Charles River Laboratories
  • Rachel Harper, Covance
  • Brian Argo, MPI Research
  • Christy Kubin, MPI Research
  • Paul Brown, FDA
  • Anisa Scott, SAS Institute
  • Kristi Johnson, PointCross Life Sciences
  • Laura Kaufmann, PDS Life Sciences
  • Robert Dorsam, FDA


Meeting Minutes

Date Link to minutes
2015
2015-04-10 TC1 Minutes
2015-04-24 TC2 Minutes
2015-05-08 TC3 Minutes
2015-05-22 TC4 Minutes
2015-06-05 TC5 Minutes
2015-07-31 TC7 Minutes
2015-08-14 TC8 Minutes
2015-09-11 TC9 Minutes
2015-09-25
2015-10-09 TC11 Minutes
2015-10-23 TC12 Minutes
2015-12-04 TC13 Minutes
2015-12-18 TC14 Minutes
2016
2016-01-15 TC15 Minutes
2016-02-26 TC17 Minutes
2016-05-06 TC18 Minutes
2016-05-20 TC19 Minutes
2016-06-17 TC20 Minutes
2016-08-12 TC21 Minutes
2016-08-26 TC22 Minutes
2016-09-09 TC23 Minutes
2016-10-07 TC24 Minutes
2016-11-04 TC25 Minutes

Last revision by Laurenwhite, 2019-03-5