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Draft of MICrate as profile for storing extensible metadata alongside the OME-Zarr images#1

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sukunis wants to merge 14 commits intoNFDI4BIOIMAGE:mainfrom
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Draft of MICrate as profile for storing extensible metadata alongside the OME-Zarr images#1
sukunis wants to merge 14 commits intoNFDI4BIOIMAGE:mainfrom
sukunis:main

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@sukunis
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@sukunis sukunis commented Apr 4, 2025

follow up on RO-Crate metadata minimal design

First DRAFT for a RO-Crate profile defining a detached RO-Crate.

Things to discuss:

  1. Agreeing on MUST, SHOULD, COULD for properties
  2. context extensions and their mapping
  3. design decision in terms of specimen: is specimen a property of the root data entity:
    MicCrate V2

or of entity for acquisition_mode:

MicCrate V1

@joshmoore
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Few thoughts:

  1. Agreeing on MUST, SHOULD, COULD for properties

Outside the challenge I could see specimen not being a MUST.

  1. context extensions and their mapping

i.e. how do other people add in the extensions? Is there any way to do this at a higher-level of abstraction rather than on a field-by-field basis? I'm thinking of how to allow in an entire block of community metadata specified externally.

a detached RO-Crate.

So what makes this detached is the fact that the about @id and the Dataset @id point to a remote URL, right?

@sukunis
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sukunis commented May 6, 2025

So what makes this detached is the fact that the about @id and the Dataset @id point to a remote URL, right?

Key points detached ro-crate:

  • without defined root directory,
  • not processed in a file-system context
  • referenced data entities are web-based
  • naming: ${prefix}-ro-crate-metadata.json

https://www.researchobject.org/ro-crate/specification/1.2-DRAFT/structure.html#detached-ro-crate-package

sukunis and others added 8 commits May 20, 2025 11:13
change python version
change python version to 3.9.21
- Add sphinx with minimal version 7.4.7 to dependencies.
- Moving some sentences around and adding a few clarifying statements.
- Suggesting linguistic and typographic fixes here and there.
- Add walkthrough
- Restructure sections
- Streamline format description
Merging upstream, fixing NFDI4BIOIMAGE#2, review comments
@sukunis
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sukunis commented May 23, 2025

comments on that from @JensWendt (see issue#3)

@sukunis sukunis closed this Mar 4, 2026
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2 participants