Repository README File: Insights of Open Practices in Biosciences

Authors

Haya Deeb 1, Suzanna Creasey 1, Diego Lucini de Ugarte 1, George Strevens 1, Trisha Usman 1, Hwee Yun Wong 1, Megan A. M. Kutzer 1,2, Tomasz Zieliński 1, Andrew J. Millar 1*.

1: Centre for Engineering Biology and School of Biological Sciences, University of Edinburgh, EH9 3JF, UK. 2: Institute of Ecology and Evolution and School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9AA, UK

contact us:

General Queries and Data Management: bio_rdm@ed.ac.uk Principal Investigator and Corresponding Author: Andrew Millar (andrew.millar@ed.ac.uk) Orcid: 0000-0003-1756-3654

General Information

This reposotory contains the outcomes of a project executed at the Biosciences Institutes of the University of Edinburgh. This research project assesses the openness and FAIRness (Findable, Accessible, Interoperable, and Reusable) of data linked to publications from these institutes. Here, you will find datasets, analytical codes, and figures that detail our project’s methodology, results, and broader implications, aiming to enhance data-sharing practices and promote the adherence to FAIR principles within and beyond our community. Each folder within this repository contains a distinct dataset, enabling structured and organised access to diverse sets of data relevant to the same project's scope.

Protocol:

The protocol for this project can be found on Protocol.io, where detailed step-by-step guidelines are provided to ensure that the research methods are transparent and reproducible. https://www.protocols.io/view/a-protocol-for-assessing-open-data-practices-honou-kxygxyxmdl8j/v2

Repository Folder/File Overview

Branch: main (default)

|-- Project1January2024
|-- Project2November2024_Latest
|-- Licence

Branch: ODDPub_Fork

Main Branch: Folder Description

1. Project1January_2024

This folder conatins the outcomes of the first project, centered on publications in infectious diseases and non-communicable diseases. DataSet_v1 encompasses all relevant files from a sample of 193 publications dated between 2014 to 2022. These documents form the cornerstone of the findings presented in this preprint: https://doi.org/10.1101/2024.02.18.580901

2. Project2November_2024

This folder contains the outcomes of the second project, encompassing publications in biotechnology, regenerative medicine, infectious diseases, and non-communicable diseases. DataSetv2 includes all publications from the previous project (DataSetV1) plus new additions, totaling 555 publications from 2014 to 2023. This project builds upon the first by integrating prior data with new data, representing an advanced phase of our ongoing research. this folder, DataSet_v2, contains all the data outputs and analytical results of this comprehensive second project.

3. Licence

The licence file in this repository stipulates that all content is protected under the Creative Commons Attribution 4.0 International License (CC BY 4.0).

Branch ODDPub_fork

The "ODDPubfork" branch features the integration of the ODDPub algorithm, used as an automated step following manual assessment in Project 2 (November 2024). This branch includes the essential code of the ODDPub algorithm along with the datasets that were analysed from project 2 and the resulting datasets produced by the algorithm. To access and review the contents and contributions of this branch, please navigate using the branch navigation button at the top of the GitHub interface and select 'ODDPubfork'.