Update file_simulated_dataset.yaml

openproblems-bio · Jul 9, 2024 · a22e0fc · a22e0fc
1 parent c691b01
commit a22e0fc
Showing 1 changed file with 31 additions and 13 deletions.
diff --git a/src/api/file_simulated_dataset.yaml b/src/api/file_simulated_dataset.yaml
@@ -9,24 +9,44 @@ info:
         name: counts
         description: Raw counts
         required: true
-      - type: double
-        name: normalized
-        description: Normalized counts
+      - type: integer
+        name: logcounts
+        description: Log-transformed counts
         required: true
     obs:
-      - ...
+      - type: double
+        name: col
+        description: Column index of the cell in the spatial grid.
+        required: true
+      - type: double
+        name: row
+        description: Row index of the cell in the spatial grid.
+        required: true
+      - type: double
+        name: sizeFactor
+        description: Size factor for the cell.
+        required: true
+      - type: integer
+        name: spatial_cluster
+        description: Spatial cluster assignment for the cell.
+        required: true
     var:
-      - ...
-    obsm:
-      - ...
+      - type: string
+        name: feature_id
+        description: Unique identifier for the feature, usually a ENSEMBL gene id.
+        required: false
+      - type: string
+        name: feature_name
+        description: A human-readable name for the feature, usually a gene symbol.
+        required: true
     uns:
       - type: string
         name: dataset_id
-        description: "A unique identifier for the dataset"
+        description: A unique identifier for the dataset. This is different from the `obs.dataset_id` field, which is the identifier for the dataset from which the cell data is derived.
         required: true
       - name: dataset_name
         type: string
-        description: Nicely formatted name.
+        description: A human-readable name for the dataset.
         required: true
       - type: string
         name: dataset_url
@@ -36,6 +56,7 @@ info:
         type: string
         description: Bibtex reference of the paper in which the dataset was published.
         required: false
+        multiple: true
       - name: dataset_summary
         type: string
         description: Short description of the dataset.
@@ -48,7 +69,4 @@ info:
         type: string
         description: The organism of the sample in the dataset.
         required: false
-      - type: string
-        name: normalization_id
-        description: "Which normalization was used"
-        required: true
+        multiple: true