Update README.md

README.md

@@ -20,29 +20,6 @@ task_categories:
 - other
 source_datasets:
 - original
-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: float
-      description: Normalized log2 fold change for positive (+) dye orientation
-    - name: dye_minus
-      dtype: float
-      description: Normalized log2 fold change for negative (-) dye orientation
-    - name: mean_norm_log2fc
-      dtype: float
-      description: Average log2 fold change across dye orientations; 0 when orientations have opposite signs, single value when only one orientation available
 configs:
 - config_name: metadata
   description: Transcription factor metadata including essentiality and QC status
@@ -50,16 +27,87 @@ configs:
   data_files:
   - split: train
     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
+
 - config_name: overexpression
   description: Overexpression perturbation normalized log2 fold changes
   data_files:
   - 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
+
 - config_name: knockout
   description: Deletion/knockout perturbation normalized log2 fold changes
   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
 ---
 # Hughes 2006
 
@@ -101,4 +149,41 @@ BrentLab/yeast_genome_resources
 | `del_passed_qc`       | Boolean indicating whether deletion experiments passed quality control                                                 |
 
 
+## Usage
+
+I recommend using `huggingface_hub.snapshot_download` to pull the repository. After that, use your favorite
+method of interacting with `parquet` files (eg duckDB, but you could use dplyr in R or pandas, too).
+
+```python
+from huggingface_hub import snapshot_download
+import duckdb
+import os
+
+repo_id = "BrentLab/hughes_2006"
+
+# Download entire repo to local directory
+repo_path = snapshot_download(
+    repo_id=repo_id,
+    repo_type="dataset"
+)
+
+print(f"Repository downloaded to: {repo_path}")
+
+# Construct path to the parquet file
+parquet_path = os.path.join(repo_path, "hughes_2006.parquet")
+print(f"Parquet file at: {parquet_path}")
+
+# Connect to DuckDB and query the parquet file
+conn = duckdb.connect()
+
+query = """
+SELECT * 
+FROM read_parquet(?)
+WHERE regulator_locus_tag = 'YJR060W'
+"""
+
+result = conn.execute(query, [parquet_path]).fetchall()
+print(f"Found {len(result)} rows for YJR060W")
+```
+
 **Dataset Author and Contact**: Chase Mateusiak [@cmatKhan](https://github.com/cmatkhan/)