Update rossi 2021 datacard

README.md

@@ -1,120 +1,156 @@
 ---
 license: mit
 tags:
-- transcription-factor
-- binding
-- chipexo
-- genomics
-- biology
+  - transcription-factor
+  - binding
+  - chipexo
+  - genomics
+  - biology
 language:
-- en
+  - en
 pretty_name: Rossi ChIP-exo 2021
 configs:
-- config_name: metadata
-  description: Metadata describing the tagged regulator in each experiment
-  data_files:
-  - split: train
-    path: rossi_2021_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: run_accession
-      dtype: string
-      description: GEO run accession identifier for the sample
-    - name: yeastepigenome_id
-      dtype: string
-      description: Sample identifier used by yeastepigenome.org
-- config_name: genome_map
-  description: ChIP-exo 5' tag coverage data partitioned by sample accession
-  data_files:
-  - split: train
-    path: 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 of the 5' tag
-    - name: pileup
-      dtype: int32
-      description: Depth of coverage (number of 5' tags) at this genomic position
-- config_name: rossi_annotated_features
-  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
+  - config_name: metadata
+    description: Metadata describing the tagged regulator in each experiment
+    dataset_type: metadata
+    data_files:
+      - split: train
+        path: rossi_2021_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: run_accession
+          dtype: string
+          description: GEO run accession identifier for the sample
+        - name: yeastepigenome_id
+          dtype: string
+          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
+    dataset_info:
+      features:
+        - name: chr
+          dtype: string
+          description: Chromosome name (e.g., chrI, chrII, etc.)
+        - name: pos
+          dtype: int32
+          description: Genomic position of the 5' tag
+        - name: pileup
+          dtype: int32
+          description: Depth of coverage (number of 5' tags) at this genomic position
+  - config_name: rossi_annotated_features
+    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
+  - config_name: reprocess_annotatedfeatures
+    description: >-
+      Annotated features reprocessed with updated peak
+      calling methodology
+    dataset_type: annotated_features
+    data_files:
+      - split: train
+        path: creprocess_annotatedfeatures.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: baseMean
+          dtype: float64
+          description: Average of normalized count values, dividing by size factors, taken over all samples
+        - name: log2FoldChange
+          dtype: float64
+          description: Log2 fold change between comparison and control groups
+        - name: lfcSE
+          dtype: float64
+          description: Standard error estimate for the log2 fold change estimate
+        - name: stat
+          dtype: float64
+          description: Value of the test statistic for the gene
+        - name: pvalue
+          dtype: float64
+          description: P-value of the test for the gene
+        - name: padj
+          dtype: float64
+          description: Adjusted p-value for multiple testing for the gene
 ---
 
 # Rossi 2021