Update README.md

README.md

@@ -16,9 +16,11 @@ tags:
 pretty_name: "Mahendrawada 2025 ChEC-seq and Nascent RNA-seq data"
 size_categories:
 - 100K<n<1M
+
 configs:
 - config_name: genomic_features
   description: Comprehensive genomic features and regulatory characteristics for yeast genes
+  dataset_type: genomic_features
   data_files:
   - split: train
     path: features_mahendrawada_2025.parquet
@@ -97,9 +99,62 @@ configs:
       dtype: string
       description: Standard gene symbol from yeast_genome_resources dataset
 
-- config_name: chec_seq
-  description: ChEC-seq transcription factor binding data with peak scores
+- config_name: chec_seq_metadata
+  description: Metadata for ChEC-seq experiments describing transcription factors and experimental conditions
+  dataset_type: genome_map_metadata
+  data_files:
+  - split: train
+    path: chec_seq_metadata_mahendrawada_2025.parquet
+  dataset_info:
+    features:
+    - name: accession
+      dtype: string
+      description: Unique identifier for each ChEC-seq experiment
+    - 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: strain_background
+      dtype: string
+      description: Yeast strain background used in the experiment
+    - name: experimental_condition
+      dtype: string
+      description: Experimental conditions (e.g., growth media, temperature)
+    - name: publication_doi
+      dtype: string
+      description: DOI of the publication describing this dataset
+    - name: data_processing_method
+      dtype: string
+      description: Method used for data processing and peak calling
+
+- config_name: chec_seq_genome_map
+  description: Raw ChEC-seq signal data partitioned by experiment accession showing genome-wide binding profiles
+  dataset_type: genome_map
+  data_files:
+  - split: train
+    path: chec_seq_genome_map/*/*.parquet
+  dataset_info:
+    features:
+    - name: chr
+      dtype: string
+      description: Chromosome name (e.g., chrI, chrII, etc.)
+    - name: pos
+      dtype: int32
+      description: Genomic position
+    - name: signal
+      dtype: float32
+      description: ChEC signal intensity at this genomic position, normalized to Drosophila spike-in control
+    partitioning:
+      enabled: true
+      partition_by: ["accession"]
+      path_template: "chec_seq_genome_map/accession={accession}/*.parquet"
+
+- config_name: mahendrawada_chec_seq
+  description: ChEC-seq transcription factor binding data with peak scores (original authors' processed data)
   default: true
+  dataset_type: annotated_features
   data_files:
   - split: train
     path: chec_mahendrawada_2025.parquet
@@ -120,9 +175,40 @@ configs:
     - name: peak_score
       dtype: float64
       description: ChEC signal around peak center (sum of ChEC signal from -150 to +150 bp from peak summit) normalized to Drosophila spike-in control
+    - name: processing_method
+      dtype: string
+      description: Method used for peak calling and quantification (original authors)
+
+- config_name: reprocessed_chec_seq
+  description: ChEC-seq transcription factor binding data reprocessed with updated peak calling methodology
+  dataset_type: annotated_features
+  data_files:
+  - split: train
+    path: chec_reprocessed_mahendrawada_2025.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: target_locus_tag
+      dtype: string
+      description: Systematic gene name (ORF identifier) of the target gene
+    - name: target_symbol
+      dtype: string
+      description: Standard gene symbol of the target gene
+    - name: enrichment
+      dtype: float64
+      description: ratio of experimental insertions to background insertions
+    - name: poisson_pval
+      dtype: float64
+      description: enrichment poisson pvalue
 
 - config_name: rna_seq
   description: Nascent RNA-seq differential expression data following transcription factor depletion using 4TU metabolic labeling
+  dataset_type: annotated_features
   data_files:
   - split: train
     path: rnaseq_mahendrawada_2025.parquet