Update RO-Crate information (#6)

* Fix "contributing" link + chores

Conf.py added so sphinx-autobuild works.

* Fix links and fill a bit on RO-Crate

* Fix links and typos

* Contextualize MICrate with GIDE and more

* Link to RO-Crate use cases

* Fix spelling

* Remove conf.py

as it interferes with the build

* Update docs/specification/MICrate.md

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

Author: lubianat

.gitignore

@@ -0,0 +1,6 @@
+.ipynb_checkpoints/
+__pycache__/
+*.pyc
+
+# Ignore Jupyter Notebook build files
+_build/

docs/_config.yml

@@ -26,7 +26,7 @@ html:
   use_repository_button: true
   extra_footer: |
     <p>
-    Copyright: Licensed <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">CC-BY 4.0</a> unless mentioned otherwise. 
+    Copyright: Licensed <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">CC-BY 4.0</a> unless mentioned otherwise.
     Contributions and feedback are welcome.
     </p>
 sphinx:

docs/contributing/format.md

@@ -6,7 +6,7 @@ Add your **markdown files** to the section folders under `docs` and register the
 The **YML** files under `resources/` contain
 metadata about contributed material that is already published elsewhere.
 
-Their structure is examplified here:
+Their structure is exemplified here:
 ```
 resources
 - name: NFDI4BioImage Website

docs/guidelines/index.md

@@ -1,6 +1,6 @@
 # Guidelines
 
-## Which type of RO-Crate should I use (attache or detached)
+## Which type of RO-Crate should I use (attached or detached)
 ### Quick checklist – are you building the right type?
 
 1. Do you know the total size of the files?

docs/readme.md

@@ -6,22 +6,18 @@ Here you will find **standards**, **tooling** and **best practices** for “FAIR
 The entities described are intended to promote the reuse and exchange of bioimaging data.
 
 
-$\color{#D29922}\textsf{Warning: This knowledge base isn't complete}$ 
+$\color{#D29922}\textsf{Warning: This knowledge base isn't complete}$
 
 
 ## Contributing
 **Feedback and contributions are very welcome!**
 
-You find instructions in how to contribute on the [contributing page](/Contributing), e.g. as [github issue](https://github.com/NFDI4BIOIMAGE/FAIR-IO/issues).
+You can find instructions on how to contribute on the [contributing page](contributing/index.md), for example by opening a [GitHub issue](https://github.com/NFDI4BIOIMAGE/FAIR-IO/issues).
 Consider adding your favorite training resources so we can make sure they are findable and reusable.
 
 ## License
 All contents of this Jupyter book and the corresponding Github repository are licensed under [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/), unless mentioned otherwise.
 
 
 ## Acknowledgements
-This project is funded by the Deutsche Forschungsgemeinschaft (DFG, German  Research Foundation) under the National Research Data Infrasstructure – NFDI 46/1 – 501864659.
-
-
-
-
+This project is funded by the Deutsche Forschungsgemeinschaft (DFG, German  Research Foundation) under the National Research Data Infrastructure – NFDI 46/1 – 501864659.

docs/specification/MICrate.md

@@ -1,29 +1,29 @@
 # What is a FAIR-IO
 A FAIR-IO (FAIR Image Object) bundle combines acquisition and provenance metadata together with multi-resolution, chunked binary pixel data in a single cloud-compatible format for simplified sharing and re-use. As such, FAIR-IO implements
-a FAIR Digital Object (FDO, DOI:10.5281/zenodo.7824714) as illustrated below.
+a FAIR Digital Object (FDO, [DOI:10.5281/zenodo.7824714](https://doi.org/10.5281/zenodo.7824714)) as illustrated below.
 
 ![FAIR-IO concept](FAIR-IO_10.5281-zenodo.10512531.png)
 
 FAIR-IO is based on the following recommendations for binary (pixel) data and textual metadata.
-## Recommendations for easily sharable binary data: 
+## Recommendations for easily shareable binary data:
 <div>
 <table style="margin-left:5px;">
 <tr>
     <!--<td style="text-align:left;"><img src="FAIR-IO_inner.png" style="width:120px; float:left" ></td>-->
     <td>
         <ul>
           <li>Use data formats that store binary data with multiple resolutions in a single cloud-compatible, chunkable format. These enable web-optimised data access and high-performance cloud storage</li>
-          <li>Store data in a public available space accessible via a data specific URL</li> 
+          <li>Store data in a public available space accessible via a data specific URL</li>
         </ul>
-        <b>Example format:</b> ome-zarr (<a href="https://doi.org/10.1007/s00418-023-02209-1"> About</a> |<a href=""> Tools</a>)
     </td>
 </tr>
-
 </table>
 </div>
 
 
-## Recommendations for easily sharable metadata:
+**Example format**: OME-Zarr ([About](https://doi.org/10.1007/s00418-023-02209-1) | [Tools](../tools/index.md))
+
+## Recommendations for easily shareable metadata:
 <div>
 <table style="margin-left:5px;">
 <tr>
@@ -32,17 +32,11 @@ FAIR-IO is based on the following recommendations for binary (pixel) data and te
         <ul>
           <li>Ensure that the relationship and meaning of the data is clear described or linked</li>
           <li>Use metadata formats that store metadata in a machine readable form, that means </li>
-          <li>store data in a public available space accessible via a data specific URL</li> 
+          <li>store data in a public available space accessible via a data specific URL</li>
         </ul>
-        <b>Example formats:</b> JSON-LD (<a href=""> About</a> |<a href=""> Tools</a>), Turtle (<a href=""> About</a> |<a href=""> Tools</a>)
     </td>
 </tr>
 </table>
 </div>
 
-
-
-
-
-
-
+**Example formats**:JSON-LD ([About](https://json-ld.org/) | [Tools](../tools/index.md)), Turtle ([About](https://www.w3.org/TR/turtle/) | [Tools](../tools/index.md))

docs/specification/index.md

@@ -6,14 +6,15 @@
 * Crate = a container (think of a cardboard box).
 
 
-A **RO-Crate** is a **standardised digital box** that holds all the files plus a small metadata file that tells you what each file is, who created it, when, under which licence, etc.
-It can be compared to a ZIP folder + a “data sheet” that explains what each element is, who created it, and under what conditions it may be shared.
+A **RO-Crate** is a **standardised digital box** that holds all the files plus a small metadata file that tells you what each file is, who created it, when, under which licence, etc. It can be compared to a ZIP folder + a “data sheet” that explains what each element is, who created it, and under what conditions it may be shared.
 
-An **attached** RO-Crate bundles the actual data together with its metadata, giving you a self‑contained, portable snapshot. 
+An **attached** RO-Crate bundles the actual data together with its metadata, giving you a self‑contained, portable snapshot.
 
 A **detached** RO-Crate carries only the metadata and points to data that remains stored elsewhere, which keeps the crate lightweight but relies on the external locations staying accessible.
 Using RO-Crates makes your work **FAIR**, easier to cite, and ready for journal or archive submission.
 
+The details of how to build RO-Crates are developed openly as a [community project](https://www.researchobject.org/ro-crate/).
+
 ### Quick visual example
 **Attached crates** keep the data inside the box → fully portable but potentially large.
 ```
@@ -30,11 +31,10 @@ my-detached-crate/
 │
 └─ ro-crate-metadata.json       # "@id": "https://datahub.org/measurements.csv"
 ```
-### Key points detached ro-crate
-
-- exists without defined root directory,
-- not processed in a file-system context
-- referenced data entities are web-based
-- naming convention: ${prefix}-ro-crate-metadata.json
 
+### Key points of detached RO-Crates:
 
+- They exist without defined root directory,
+- They are not processed in a file-system context
+- The referenced data entities are web-based
+- They follow a naming convention: ${prefix}-ro-crate-metadata.json

docs/specification/ro-crate.md

@@ -14,4 +14,4 @@ Overview of software, libraries, and CLI tools that generate, read, or convert F
 
 * [**OMERO.forms**]()
 
-* [**RO-Crate Viewer**]((https://arunaengine.github.io/ro-crate-explorer/) for exploring and visualizing RO-Crates ([github](https://github.com/arunaengine/ro-crate-explorer)
+* [**RO-Crate Viewer**](https://arunaengine.github.io/ro-crate-explorer/) for exploring and visualizing RO-Crates ([GitHub](https://github.com/arunaengine/ro-crate-explorer)).

docs/tools/index.md

@@ -1,5 +1,11 @@
-# Community/ Use-Cases
+# Community/Use-Cases
 
-* [**OME-NGFF-Challenge**](https://ome.github.io/ome2024-ngff-challenge/) 422.89 TB of distributed public bioimage data including RO-Crate-compliant metadata
-* [**NGFF-RFC**](https://ngff.openmicroscopy.org/rfc) discuss and capture high-level decisions within the NGFF community.
+## Resources
 
+* [**OME-NGFF-Challenge**](https://ome.github.io/ome2024-ngff-challenge/): 422.89 TB of distributed public bioimage data including RO-Crate-compliant metadata.
+* [**NGFF-RFC**](https://ngff.openmicroscopy.org/rfc): discuss and capture high-level decisions within the NGFF community.
+* [**RO-Crate OME Use Cases**](https://research-object.org/ro-crate): overview the uses of RO-Crate in the Open Microscopy Environment.
+
+## Events
+
+* **SWAT4HCLS 2026**: poster presentation titled "RO-Crates for BioImaging" at the Semantic Web for Health Care and Life Sciences conference 2026, in Amsterdam ([abstract](https://www.swat4ls.org/workshops/amsterdam2026/programme/accepted-submissions/#RO-Crates_for_BioImaging)).