Merge pull request #28 from NBISweden/feature/schemav2

Update submission guidelines to metadata schema V2
NBISweden · Jan 28, 2025 · 9e9e255 · 9e9e255
2 parents 06d77f8 + ef842d6
commit 9e9e255
Showing 1 changed file with 35 additions and 34 deletions.
diff --git a/datasets/submission/preparation-guide.qmd b/datasets/submission/preparation-guide.qmd
@@ -5,46 +5,47 @@ Before you submit your data, please make sure
 
 1. The root folder of the submission should actually be the dataset folder which includes several subfolders. See the example of structure folder below:
 ```
-    DATASET_{IDENTIFIER}*
+    DATASET_{IDENTIFIER}
     |--- METADATA
-    |    |--- dataset.xml (contains: Dataset)
-    |    |--- policy.xml (contains: Policy)
-    |    |--- image.xml (contains: Images)
-    |    |--- annotation.xml (contains: Annotations) - optional+
-    |    |--- observation.xml (contains:  Observations)
-    |    |--- observer.xml (contains: Observers) - optional+
-    |    |--- sample.xml (contains: Biological Beings, Cases (if present), Specimens, Blocks and Slides)
-    |    |--- staining.xml (contains: Stainings)
-    |--- IMAGES
-    |    |--- IMAGE_{IDENTIFIER}**
-    |    |    |--- *.dcm files of an Image
-    |    |--- IMAGE_{IDENTIFIER}**
-    |    |    |--- *.dcm files of an Image
+    | |--- dataset.xml (contains: Dataset)
+    | |--- policy.xml (contains: Policy)
+    | |--- image.xml (contains: Images)
+    | |--- annotation.xml (contains: Annotations) 
+    | |--- observation.xml (contains: Observations)
+    | |--- observer.xml (contains: Observers)
+    | |--- sample.xml (contains: Biological Beings, Cases (if present), Specimens, Blocks and Slides)
+    | |--- staining.xml (contains: Stainings)
+    |---IMAGES
+    | |--- IMAGE_{IDENTIFIER}*
+    | | |--- *.dcm files of an Image
+    | |--- IMAGE_{IDENTIFIER}*
+    | | |--- *.dcm files of an Image
     |--- ANNOTATIONS+
-    |    |--- *.geojson
+    | |--- *.geojson
     |--- LANDING_PAGE***
-    |    |--- THUMBNAILS
-    |    |    |--- *.jpg
+    | |--- landingpage.xml (contains: Landing Page) 
+    | |--- THUMBNAILS
+    | | |--- *.jpg
     |--- PRIVATE**** - not shared with users
-    |    |--- DAC.xml (contains: DAC) - not shared with users
-    |    |--- submission.xml - not shared with users
+    | |--- rems.xml - not shared with users
+    | |--- organisation.xml - not shared with users
+    | |--- datacite.xml (contains: DataCite, optional) - not shared with users
 
-
-    *    The root of the folder must be the written as “DATASET_{IDENTIFIER}” with
-        IDENTIFIER being either the accession ID of the Dataset generated by the
-        repository (when data is downloaded), or the ALIAS defined by the submitter
-        at dataset creation and submission.
+    *    The root of the folder must be the written as "DATASET_{IDENTIFIER}" with
+         IDENTIFIER being either the accession ID of the Dataset generated by the
+         repository (when data is downloaded), or the ALIAS defined by the
+         submitter at dataset creation and submission.
     **   Folders containing WSIs files (I.e. *.dcm) must be named
-        “IMAGE_{IDENTIFIER}” with IDENTIFIER being either the accession ID of a
-        given Image the files relate to generated by the repository (when data is
-        downloaded), or the ALIAS defined by the submitter at dataset creation or
-        submission.
-    ***  This folder will eventually contain all relevant information needed to
-        generate a landing page for a given dataset.
-    +    If the dataset does not contain Annotations or Observers the respective
-        .xml files or directory can be omitted.
-    **** This folder contains metadata that will not be shared with users that have
-        gotten access to a dataset.
+         "IMAGE_{IDENTIFIER}" with IDENTIFIER being either the accession ID of a
+         given Image the files relate to generated by the repository (when data is
+         downloaded), or the ALIAS defined by the submitter at dataset creation or
+         submission.
+    ***  IMPORTANT: Anything in this folder should be expected to be visible to
+         the entire world.
+    +    If the dataset does not contain Annotations the respective .xml files
+         or directory can be omitted.
+    **** This folder contains metadata that will not be shared with users that
+         have gotten access to a dataset
 ```
 
 2. All the files should be encrypted with crypt4gh and the extensions must be `c4gh`, e.g: