Fraunhofer ITMP ScreeningPort
Published April 17, 2025 | Version v2
Dataset Open

Supplementary data files for manuscript titled "From spreadsheet lab data templates to knowledge graphs: A FAIR data journey in the domain of AMR research"

Creators

  • 1. ROR icon Fraunhofer Institute for Translational Medicine and Pharmacology
  • 2. ROR icon Enveda Therapeutics (United States)

Description

This data repository contains all the necessary supplementary files for the manuscript titled "From spreadsheet lab data templates to knowledge graphs: A FAIR data journey in the domain of AMR research."
 
The repository is a copy of the GitHub page with the source code used to generate the graph and additional files required for the Lab Data Template.
 
Below we provide a brief overview of the data files in the `additional folder` and their underlying purpose:
  • The Data Survey collects relevant project and data set information to set up a Data Management Plan. It can serve as an input for Lab Data Template development.
  • The Lab Data Templates facilitate the collection of AMR research data (in vivo and in vitro) in several sub-tables. The Excel format is compatible with upload procedures into the data repository 'grit' and serves as input for a knowledge graph workflow.
  • The Data dictionary is connected to the Lab Data Templates and ensures harmonized data entries. In addition, the dictionaries collect metadata beyond the content of the Lab Data Template (e.g. bacterial strain information or compound information) and link to ontologies where possible.
  • The FAIR assessments have been used as a primer for improving the template. This report is generated using the FAIR-DSM model.
The templates have been used during the IMI2 GNA NOW project to collect information and have been improved according to FAIR standards in collaboration with the IMI FAIRplus project ("post FAIRification").

Files

GNA-NOW.zip

Files (1.9 MB)

Name Size Download all
md5:a393cebeb3efe1ba91d53333f04204de
1.9 MB Preview Download

Additional details

Related works

Is supplement to
Preprint: 10.1101/2024.07.18.604030 (DOI)

Funding

Innovative Medicines Initiative

Dates

Available
2025-04-17
Addition of usecase and updating Zenodo to be copy of GitHub

Software

Repository URL
https://github.com/IMI-COMBINE/template2graphs
Programming language
Python
Development Status
Active