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README.md

@@ -6,13 +6,13 @@ tags:
 - chipexo
 - genomics
 - biology
+language:
+- en
 pretty_name: Rossi ChIP-exo 2021
 configs:
 - config_name: metadata
   description: Metadata describing the tagged regulator in each experiment
   default: true
-  dataset_type: metadata
-  applies_to: ["genome_map"]
   data_files:
   - split: train
     path: rossi_2021_metadata.parquet
@@ -32,7 +32,6 @@ configs:
       description: Sample identifier used by yeastepigenome.org
 - config_name: genome_map
   description: ChIP-exo 5' tag coverage data partitioned by sample accession
-  dataset_type: genome_map
   data_files:
   - split: train
     path: genome_map/*/*.parquet
@@ -47,14 +46,76 @@ configs:
     - name: pileup
       dtype: int32
       description: Depth of coverage (number of 5' tags) at this genomic position
-    partitioning:
-      enabled: true
-      partition_by: ["run_accession"]
-      path_template: "genome_map/accession={run_accession}/*.parquet"
-      filter_patterns:
-        - "accession=([^/]+)"
-language:
-- en
+- config_name: rossi_2021
+  description: ChIP-exo regulator-target binding features with peak statistics
+  dataset_type: annotated_features
+  default: true
+  metadata_fields:
+    - regulator_locus_tag
+    - regulator_symbol
+    - target_locus_tag
+    - target_symbol
+  data_files:
+    - split: train
+      path: yeastepigenome_annotatedfeatures.parquet
+  dataset_info:
+    features:
+      - name: sample_id
+        dtype: int32
+        description: >-
+          Unique identifier for each ChIP-exo experimental sample.
+      - name: pss_id
+        dtype: float64
+        description: >-
+          Current brentlab promotersetsig table id. This will eventually be removed.
+      - name: binding_id
+        dtype: float64
+        description: >-
+          Current brentlab binding table id. This will eventually be removed.
+      - name: yeastepigenome_id
+        dtype: float64
+        description: >-
+          Unique identifier in the yeastepigenome database.
+      - name: regulator_locus_tag
+        dtype: string
+        description: >-
+          Systematic ORF name of the regulator.
+        role: regulator_identifier
+      - name: regulator_symbol
+        dtype: string
+        description: >-
+          Common gene name of the regulator.
+        role: regulator_identifier
+      - name: target_locus_tag
+        dtype: string
+        description: >-
+          The systematic ID of the feature to which the effect/pvalue is
+          assigned. See hf/BrentLab/yeast_genome_resources
+        role: target_identifier
+      - name: target_symbol
+        dtype: string
+        description: >-
+          The common name of the feature to which the effect/pvalue is
+          assigned. If there is no common name, the `target_locus_tag` is
+          used.
+        role: target_identifier
+      - name: n_sig_peaks
+        dtype: float64
+        description: >-
+          Number of peaks in the promoter region of the the target gene
+        role: quantitative_measure
+      - name: max_fc
+        dtype: float64
+        description: >-
+          If there are multiple peaks in the promoter region, then the maximum is
+          reported. Otherwise, it is the fold change of the single peak in the
+          promoter.
+        role: quantitative_measure
+      - name: min_pval
+        dtype: float64
+        description: >-
+          The most significant p-value among peaks for this interaction. 
+        role: quantitative_measure
 ---
 
 # Rossi 2021