Script Metadata for Sharing

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Project Overview

Since the PhUSE-Scrips repository was created i GitHub in 2013, many scripts were contributed and hosted in the repository. The Standard Analyses and Code Sharing Working Group (SACS) in PhUSE recommended style and guideline and developed qualification process to review, develop and share the scripts. Many developers from other working groups started using the repository to share and host their scripts as well. FDA contributed the JumpStart script packages to the repository as well. The script discovery and acquisition team in the working group has gone through two-round reviews of the the JumpStart scripts.

The working group has recommended folder structure, file naming convention, and initial script metadata in YML format. The difficulties facing the users are:

  • Not easy to find scripts due to a) script metadata are not defined thus the metadata files are not consistent; b) the index page based on metadata files are not updated promptly

  • Not easy to navigate in the repository due to a) scripts are not well organised; b) the folders are deep and complicated

  • Not easy to use the scripts due to a) need to download the scripts; b) modify the scripts. You usually need to make change to the original script to make it work in your own environment.

Wouldn't it be nice if you could automatically download and execute a script once you know the name of a script and only need to provide a few parameters in a configuration file (script metadata file)? This project will explore how to use script metadata to increase the accessibility, reusability and automation of scripts in the repository.

The goal of this project is to clearly define script metadata in a white paper and conduct a proof of concept using the script metadata to drive the sharing and executing scripts in the repository. The scrips written in both R and SAS will be tested. Script metadata provides the information about the scripts purpose, version, execution environment, library and data files used, inputs, outputs, review history, ratings etc. The metadata will make it easy to share, access and execute scripts in the repository.

This project will be based on the paper published and presented in PhUSE EU annual conference by Hanming Tu

Paper: Defining Script Metadata for Sharing: Using PhUSE R Package as an example
Presentation: Defining Script Metadata for Sharing : Using PhUSE R Package as an example

Project Leads

Hanming Tu Project Lead Frontage
Wendy Dobson Project Co-ordinator PhUSE

Project Participants

Aiming Yang Participant Merck
Bob Friedman Participant Xybion
Jared Slain Participant MPI Research
Hal Li Participant Merck
Hongli Lu Participant Boehringer-Ingelheim
Mary Nilsson Participant Lilly
Mike Rubison Participant Capish
Peter Schaefer Participant VCA
James Gaiser Participant Prometrika
Sally Cassells Participant Next Step Clinical Systems
Steve Noga Participant Rhworld
Valerie Williams Participant Iconplc
Nancy Brucken Participant Inventivhealth
Raphael Noirfalise Participant JNJ
Vishwas Jadhav Participant Independent
Loizos Nikolaou Participant Clinbay

Project Updates

Objectives and Timelines

List proposed project deliverables and timelines.

Objective Timeline
Project Kick Off and Information Sharing Q12018
White Paper development and public review Q2/3 2018
PhUSE team follows up on adopting and using script metadata Q42018

Project Activities

Team Presentation Slide Deck 11.01.18

Meeting Minutes

Team Minutes 11.01.18

Archived Content