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README.md

@@ -16,10 +16,6 @@ tags:
 pretty_name: "Hughes 2006 Yeast Transcription Factor Perturbation Dataset"
 size_categories:
 - 100K<n<1M
-task_categories:
-- other
-source_datasets:
-- original
 configs:
 - config_name: metadata
   description: Transcription factor metadata including essentiality and QC status
@@ -30,87 +26,127 @@ configs:
     path: metadata.parquet
   dataset_info:
     features:
-      - name: regulator_locus_tag
-        dtype: string
-        description: Systematic gene name (ORF identifier) of the transcription factor
-      - name: regulator_symbol
-        dtype: string
-        description: Standard gene symbol of the transcription factor
-      - name: found_domain
-        dtype: string
-        description: Identified DNA-binding domain(s) or protein family classification
-      - name: sgd_description
-        dtype: string
-        description: Functional description from Saccharomyces Genome Database (SGD)
-      - name: essential
-        dtype: bool
-        description: Boolean indicating whether the gene is essential for viability
-      - name: oe_passed_qc
-        dtype: bool
-        description: Boolean indicating whether overexpression experiments passed quality control
-      - name: del_passed_qc
-        dtype: bool
-        description: Boolean indicating whether deletion experiments passed quality control
+    - name: sample_id
+      dtype: integer
+      description: >-
+        unique identifier for a specific sample. The sample ID identifies a unique regulator_locus_tag
+        and can be used to join the metadata to the other datasets in this repo
+    - name: regulator_locus_tag
+      dtype: string
+      role: identifier
+      description: Systematic gene name (ORF identifier) of the transcription factor
+    - name: regulator_symbol
+      dtype: string
+      description: Standard gene symbol of the transcription factor
+    - name: found_domain
+      dtype: string
+      description: Identified DNA-binding domain(s) or protein family classification
+    - name: sgd_description
+      dtype: string
+      description: Functional description from Saccharomyces Genome Database (SGD)
+    - name: essential
+      dtype: bool
+      description: Boolean indicating whether the gene is essential for viability
+    - name: oe_passed_qc
+      dtype: bool
+      description: Boolean indicating whether overexpression experiments passed quality control
+    - name: del_passed_qc
+      dtype: bool
+      description: Boolean indicating whether deletion experiments passed quality control
 
 - config_name: overexpression
   description: Overexpression perturbation normalized log2 fold changes
   dataset_type: annotated_features
+  applies_to: metadata
   data_files:
-  - split: train  
+  - split: train 
     path: overexpression.parquet
   dataset_info:
     features:
-      - name: regulator_locus_tag
-        dtype: string
-        description: Systematic gene name (ORF identifier) of the perturbed transcription factor
-      - name: regulator_symbol
-        dtype: string
-        description: Standard gene symbol of the perturbed transcription factor
-      - name: target_locus_tag
-        dtype: string
-        description: Systematic gene name (ORF identifier) of the target gene measured
-      - name: target_symbol
-        dtype: string
-        description: Standard gene symbol of the target gene measured
-      - name: dye_plus
-        dtype: float64
-        description: Normalized log2 fold change for positive (+) dye orientation
-      - name: dye_minus
-        dtype: float64
-        description: Normalized log2 fold change for negative (-) dye orientation
-      - name: mean_norm_log2fc
-        dtype: float64
-        description: Average log2 fold change across dye orientations
+    - name: sample_id
+      dtype: integer
+      description: >-
+        unique identifier for a specific sample. The sample ID identifies a unique regulator_locus_tag
+        and can be used to join to the other datasets in this repo, including the metadata
+    - name: regulator_locus_tag
+      dtype: string
+      role: identifier
+      description: Systematic gene name (ORF identifier) of the perturbed transcription factor
+    - name: regulator_symbol
+      dtype: string
+      description: Standard gene symbol of the perturbed transcription factor
+    - name: target_locus_tag
+      dtype: string
+      role: identifier
+      description: Systematic gene name (ORF identifier) of the target gene measured
+    - name: target_symbol
+      dtype: string
+      description: Standard gene symbol of the target gene measured
+    - name: dye_plus
+      dtype: float64
+      role: measurement
+      description: >- 
+        Normalized log2 fold change for positive (+) dye orientation.
+        Positive values indicate upregulation in response to overexpression.
+    - name: dye_minus
+      dtype: float64
+      role: measurement
+      description: >-
+        Normalized log2 fold change for negative (-) dye orientation.
+        Positive values indicate upregulation in response to overexpression.
+    - name: mean_norm_log2fc
+      dtype: float64
+      role: measurement
+      description: >-
+        Average log2 fold change across dye orientations, providing a dye-independent
+        estimate of gene expression change upon transcription factor overexpression.
 
 - config_name: knockout
   description: Deletion/knockout perturbation normalized log2 fold changes
   dataset_type: annotated_features
+  applies_to: metadata
   data_files:
   - split: train
     path: knockout.parquet
   dataset_info:
     features:
-      - name: regulator_locus_tag
-        dtype: string
-        description: Systematic gene name (ORF identifier) of the perturbed transcription factor
-      - name: regulator_symbol
-        dtype: string
-        description: Standard gene symbol of the perturbed transcription factor
-      - name: target_locus_tag
-        dtype: string
-        description: Systematic gene name (ORF identifier) of the target gene measured
-      - name: target_symbol
-        dtype: string
-        description: Standard gene symbol of the target gene measured
-      - name: dye_plus
-        dtype: float64
-        description: Normalized log2 fold change for positive (+) dye orientation
-      - name: dye_minus
-        dtype: float64
-        description: Normalized log2 fold change for negative (-) dye orientation
-      - name: mean_norm_log2fc
-        dtype: float64
-        description: Average log2 fold change across dye orientations
+    - name: sample_id
+      dtype: integer
+      description: >-
+        unique identifier for a specific sample. The sample ID identifies a unique regulator_locus_tag
+        and can be used to join to the other datasets in this repo, including the metadata
+    - name: regulator_locus_tag
+      dtype: string
+      role: identifier
+      description: Systematic gene name (ORF identifier) of the perturbed transcription factor
+    - name: regulator_symbol
+      dtype: string
+      description: Standard gene symbol of the perturbed transcription factor
+    - name: target_locus_tag
+      dtype: string
+      role: identifier
+      description: Systematic gene name (ORF identifier) of the target gene measured
+    - name: target_symbol
+      dtype: string
+      description: Standard gene symbol of the target gene measured
+    - name: dye_plus
+      dtype: float64
+      role: measurement
+      description: >-
+        Normalized log2 fold change for positive (+) dye orientation.
+        Positive values indicate upregulation in response to deletion.
+    - name: dye_minus
+      dtype: float64
+      role: measurement
+      description: >-
+        Normalized log2 fold change for negative (-) dye orientation.
+        Positive values indicate upregulation in response to deletion.
+    - name: mean_norm_log2fc
+      dtype: float64
+      role: measurement
+      description: >-
+        Average log2 fold change across dye orientations, providing a
+        dye-independent estimate of gene expression change upon transcription factor deletion.
 ---
 # Hughes 2006
 
@@ -214,4 +250,4 @@ WHERE regulator_locus_tag = 'CST6'
 
 result = conn.execute(query, [parquet_path]).fetchall()
 print(f"Found {len(result)} rows for CST6")
-```
+```