Linking assays and studies

[Mestizia]

This post is part of a series of suggestions endorsed by multiple data stewards involved daily in dataPLANT. Here, we propose enhancements to the intuitiveness of ARCs structure. Particularly, the changes relate to the organization of studies and assays and the visualization of their relationships.

1. Restore or Replace the Feature for Linking Studies and Assays:

Screenshot showing a previous version of ARCitect where it was possible to link assay to study when creating the assay

With the transition to the "light ISA" format, the ability to directly link assays to studies has been removed. This change was made to simplify the editing process, but it has also removed a useful organizational feature that some users relied on. We propose either restoring this functionality or providing a workaround, such as using placeholder samples to maintain the desired structure without directly linking files. Reintroducing or replacing this feature would allow users to organize their data on a "per chapter" basis, following the related publication structure making the ARCs easier to manage and understand.

2. Add an Interactive Visualization Map:
We propose adding an interactive visualization map feature to ARCitect to visually represent how studies and assays are linked within an ARC. Currently, the connections between different components are not easily understandable, especially for users unfamiliar with the structure. An interactive map would allow users to click on different elements to view their details, providing a clear and intuitive overview of the ARC’s structure. This feature would support users in creating and maintaining ARCs and could be a valuable addition to ARC publications, making the data more appealing and easier to interpret. This enhancement would likely increase the visibility of dataPLANT and encourage more citations in scientific literature.
This feature would be very important for the users that organize their data on a “per chapter” basis. Where you could have multiple assays linked to the same study and the links between them would be intuitively visualized.

3. Integrate Linking Functionality with the Interactive Map:
The need for direct links between studies and assays could be partially addressed by integrating this functionality into a proposed interactive visualization map. By visually displaying the connections, users could gain a comprehensive overview without needing to manually adjust data structures. This would provide the organizational clarity users want while maintaining the flexibility introduced by the light ISA format.

Specifically, these enhancements aim to improve the usability and accessibility of ARC creation and publication, helping both experienced and new users better manage their data within the dataPLANT framework.

Summary

These changes are intended to make ARCs more user-friendly and visually intuitive, enhancing the experience for creators and reviewers alike. By integrating linking functionality within the interactive map, adding this map to ARCitect, and restoring or replacing study and assay linking features, we believe we can significantly enhance the ARC publication routine.

We welcome any feedback or further discussion on these points to refine our approach. Thank you for considering these suggestions!

[Mestizia]

@Brilator @SabrinaZander @eik-dahms @AngelaKranz