Mar 2, 2017 Meeting Notes

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Meeting minutes of Nonclinical_Script_Assessment_Project

March 2, 2017

Present First Name Last Name Affiliation
Yes Kevin Snyder FDA
Elaine Thompson FDA
Kevin Cahill EPL
Yes Bill Varady Boehringer-Ingelheim
Bob Dorsam FDA
Bob Friedman Xybion
Chris Eley Pfizer
Yes Stephen MacMannis Pfizer
Fred Mura PDS
Yes Anthony Fata PDS
Yes Hanming Tu Accenture
Yes Bill Houser Bristol-Myers Squibb
Carol Gleason Bristol-Myers Squibb
Yes Atul Mishra Pfizer
Peter Scaefer Validated Cloud Applications

Summary of Status of Nonclinical Script Assessment Projects:

  • R Scripts/Projects
    • CreatingXPT:
      • Bob Friedman’s tool for converting excel files into .xpt files (specifically tailored for the creation of a TS domain for legacy studies that are not required to contain SEND data). This project will be showcased in our poster at the CSS.
        • This may become the basis of other projects creating XPT files from Excel files.
    • Demographics:
      • An R script contributed by Bob Friedman during an earlier scriptathon for the clinical scripts working group that may be adapted to create useful tables from SEND data.
        • Bill Varady will look into leveraging this script for applications with SEND data.
    • Functions:
      • Several useful R functions have been created to make processing SEND data easier.
        • Hanming will contribute an additional file of functions.
        • The plan is to eventually turn this folder into an R package of coherently connected and well documented functions.
    • HistoGraphicApp:
      • This project adapts a tool called Krona that was developed to visualize metagenomic data for use in the visualization of SEND-formatted histopathology data.
        • Kevin Snyder is currently developing this application and will review the code with the group, focusing particularly on the use of R/Shiny to create GUI's.
    • Toxicokinetics:
      • An R script that Kevin Snyder contributed in the beginning of this collaboration to provide material for reviewing/learning R programming. It produces a rudimentary plot of toxicokinetics data from SEND, but is limited by ambiguities in the interpretation of the SEND standard with respect to the coding of time in the PC domain.
        • Going through this script as a group was a very helpful exercise, providing a practical introduction to R programming in the context of SEND data.
          • Occasionally going through portions of scripts like this that people are interested in or have questions about will be helpful in the future.
        • How does the group feel about actually coding during meetings?
          • The group general finds this practice to be helpful, provided that we have designated the meeting for this purpose with a particular goal in mind.
            • Potential coding meeting goals:
              • Redaction of identifiable data (i.e., dataset anonymization).
                • Perhaps start with a simple string search/removal function/tool.
                • Eventually work toward creating dictionary or key that can be used to convert back and forth between anonymization states.
                • They python script, SEND_STRIPPER.py, may be a good starting point for this project.
                  • Bill Houser will contact the author of this script and ask permission to add it to our repository.
              • Continue development of control animal data selection tool
    • Install ROracle:
      • An instruction set contributed by Hanming Tu, which allows users to access Oracle database data with R.
        • Hanming has integrated a .yml parameter file into this script (currently files are in development folder)
          • It would be good practice to use .yml parameter files for most of our scripts in the repository
        • Hanming's vision is that we should write scripts so that they can be sourced directly from repository without having to download them.
  • SAS Scripts/Projects
    • Histopath:
      • A SAS/css/javascript project that creates an .html file containing a tabular report of SEND histopathology data. This project was contributed by FDA, but was not authored by any members of our scripts group and to my knowledge is not undergoing further development.
        • There are no plans to continue development of this project at the moment.
          • The major roadblock to development of this project is unfamiliarity with SAS, CSS, and javascript languages and the lack an author to guide the project.
    • Utilities:
      • SAS scripts contributed by Bill Houser that perform various file type conversions, i.e. SEND --> Excel, SEND --> xml, SEND --> print.
        • Bill Houser will continue to make minor adjustments as necessary, but there are no goals for the group to develop this project at the moment.
  • Perl Scripts/Projects
    • PCandPPfromPDF
      • Perl scripts for the conversion of toxicokinetics data extracted from .pdf files into SEND PC and PP domains. This project could potentially be merged with the R Toxicokinetics project to produce visualizations of toxicokinetics data from .pdf files as the coding of time would be well defined by the perl scripts.
        • This project currently requires some manual editing after extracting data from .pdf.
        • Hanming may look into this project for further development.
        • This project may serve as an example of good encoding of PC domain time points, which Elaine Thompson was interested in getting the PhUSE Nonclinical Scripts Assessment Project to provide.

Potential New Projects:

  • Tool to allow FDA reviewers to look at body weight gain data so that Sponsor's do not have to submit this data to the FDA.
    • Questions/concerns regarding this project:
      • Should the output be .pdf or an .html graphical view?
      • What language/platform should be used?
        • Something like javascript/html may provide the necessary portability for use by FDA reviewers, but the team does not currently possess much expertise in this area.
      • Kevin will talk to Elaine Thompson to gain clarity regarding whether this project will be worth pursuing and if so, what the best approach might be.
  • Interaction/collaboration with other nonclinical PhUSE groups
    • Histopathology Visualization Project
      • Kevin is currently collaborating on Krona tool with this group
    • SEND Data Analysis Project
      • We will touch base with them at CSS

General Notes:

  • We should be mindful not to spread ourselves too thin across too many programming languages.
    • R is the preferred language to in-depth meeting discussions as most of the team is interested in learning to program better in R.
    • Other languages like SAS, perl, and python may be useful too, but it is not currently a priority of the group to delve deeper into these languages for purely educational purposes.
  • Of this meeting's attendee's, Tony Fata, Bill Houser, Bill Varady, Hanming Tu, and Kevin Snyder plan on attending the March 2017 CSS in Silver Spring, MD.