[Feature Request] export of ARCs investigation, study, assay Excel files to ISA-TAB compatible files

[langeipk]

Is your feature request related to a problem? Please describe.
In the created ARC structure the ISA model is represented as folder structure. In order to publish ISA-TAB compatible data sets, a export featrure would be neccessary.

Describe the solution you'd like
An transformation process could generate ISA-TAB compatible format as described in the technical ISA-TAB documentation: https://isatab.sourceforge.net/docs/ISA-TAB_release-candidate-1_v1.0_24nov08.pdf
The ARC splits investigation file. The study section is extracted into several study files. In ISA-TAB standard thes are part of the investigation file. Whereass the additional template tabs in ARcs study files, like source material description are equivalent to the ISA-TAB standard study files. All study files need to be referencd in the study section of the investigation file.

Describe alternatives you've considered
We going to merge the study files in the study section handcrafted way.

Additional context
This feature is required for repositories and data journal that support ISA-TAB format

[JonasLukasczyk]

I think this is a job for ARCtrl @HLWeil. Can you please transfer the issue?

[Freymaurer]

@langeipk would ISA-JSON be sufficient as this format is already supported by us? 🙂

[HLWeil]

Hey @langeipk,

Thanks a lot for your input!

As @Freymaurer suggested, the ARC always represents valid ISA-JSON for exchange purposes, although we now recommend using ARC RO-Crate.

I just tested the json2isatab from the ISA-API on our isa-json output, but it is IMO overly strict, hindering this conversion without further action.

To elaborate a bit on the differences between ISA-XLSX and ISA-Tab: The tabular model has been slightly modified to address specific user requirements, with the primary goal of enhancing the collaborative work experience. For example, when you modify a study, needing to edit multiple files and track these changes in Git can significantly increase the likelihood of merge conflicts in a collaborative setting. Additionally, a directory branch should be reusable and self-contained, including all necessary information for a partial checkout.

That being said, we would be very happy to piggyback on an existing ISA-JSON to ISA-Tab conversion pathway or find another way altogether, e.g. by implementing such functionality in ARCtrl. I'll take a quick look into how such an implementation could look like. Alternatively, we see this feature as an ideal project to tackle at the next ARC Hackathon, which will be announced very soon.

[HLWeil]

As @JonasLukasczyk suggested, will move to ARCtrl