Questions for meeting on Friday 2023/11/03

[cmohl2013]

• ISA files (investigation file, study file etc) have set of mandatory keys (e.g. Investigation Identifier, Investigation Title). Is it mandatory, that all mandatory keys have a value? Are there at least some keys that must contain a value?

• Apart from keys that are defined in the ISA specification, is it allowed to include custom keys?

• ARCs can be created and manipulated with ARCommander and ARCtrl. ARCommander is a CLI, ARCtrl can be used in Javascript code. Is there a recommended way how to create and manipulate ARCs with Python?

• Adding Persons to an investigation:

  • Should we add the users of the omero group that is associated with the project?
  • Or should person data be stored in key value pairs with the omero project?
    If we think about importing of ARCs to OMERO in the future: We probably do not want that Persons defined in ARC will be automatically generated as Users in OMERO

• Studies and Assays: Is this correct: An Assay is always assigned to a study. A study can contain multiple assays.

• ARCommander: what does arc update do? The help says: Update items in the arc against each other

• ARCcommander: When I create a new ARC with arc init, a folder structure is generated. But the arc is not a git repository:

~/tmp/myarc$ git status
fatal: not a git repository (or any of the parent directories): .git

How does the versioning thing work then? I can not do git commit etc

• Which data should be placed into isa.assay.xlsx, should we define columns here?
• Which data should be placed into isa.study.xlsx, should we define columns here?
• Where should we place the image files? In the dataset folder of an assay? In what format should we store the images?
• Where do we save image metadata like pixel sizes and microscope settings? in protocols as unstructured text or in isa.assay.xlsx. The data comes out of OMERO as structured XML files.