Update README.md

README.md

@@ -30,30 +30,40 @@ configs:
     - 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
+        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 transcription factor
+      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
+      description: >-
+        Identified DNA-binding domain(s) or protein family classification
     - name: sgd_description
       dtype: string
-      description: Functional description from Saccharomyces Genome Database (SGD)
+      description: >-
+        Functional description from Saccharomyces Genome Database (SGD)
     - name: essential
       dtype: bool
-      description: Boolean indicating whether the gene is essential for viability
+      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
+      description: >-
+        Boolean indicating whether overexpression experiments passed
+        quality control
     - name: del_passed_qc
       dtype: bool
-      description: Boolean indicating whether deletion experiments passed quality control
+      description: >-
+        Boolean indicating whether deletion experiments passed
+        quality control
 
 - config_name: overexpression
   description: Overexpression perturbation normalized log2 fold changes
@@ -61,27 +71,45 @@ configs:
   data_files:
   - split: train 
     path: overexpression.parquet
+  experimental_conditions:
+    growth_conditions:
+      media:
+        name: selective_medium
+        carbon_source:
+          compound: D-raffinose
+          concentration_percent: 2
+    induction:
+      inducer:
+        compound: D-galactose
+        concentration_percent: 2
+      duration_hours: 3
   dataset_info:
     features:
     - 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
+        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
+      description: >-
+        Systematic gene name (ORF identifier) of the
+        perturbed transcription factor
+      role: regulator_identifier
     - 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
+      description: >-
+        Systematic gene name (ORF identifier) of the
+        target gene measured
+      role: target_identifier
     - name: target_symbol
       dtype: string
       description: Standard gene symbol of the target gene measured
+      role: target_identifier
     - name: dye_plus
       dtype: float64
       role: quantitative_measure
@@ -98,8 +126,9 @@ configs:
       dtype: float64
       role: quantitative_measure
       description: >-
-        Average log2 fold change across dye orientations, providing a dye-independent
-        estimate of gene expression change upon transcription factor overexpression.
+        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
@@ -107,45 +136,60 @@ configs:
   data_files:
   - split: train
     path: knockout.parquet
+  experimental_conditions:
+    growth_conditions:
+      media:
+        name: synthetic_medium
+        carbon_source:
+          compound: D-glucose
+          concentration_percent: 2
   dataset_info:
     features:
     - 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
+        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
+      description: >-
+        Systematic gene name (ORF identifier) of the perturbed
+        transcription factor
+      role: regulator_identifier
     - name: regulator_symbol
       dtype: string
       description: Standard gene symbol of the perturbed transcription factor
+      role: regulator_identifier
     - name: target_locus_tag
       dtype: string
-      role: identifier
-      description: Systematic gene name (ORF identifier) of the target gene measured
+      description: >-
+        Systematic gene name (ORF identifier) of the
+        target gene measured
+      role: target_identifier
     - name: target_symbol
       dtype: string
       description: Standard gene symbol of the target gene measured
+      role: target_identifier
     - name: dye_plus
       dtype: float64
-      role: quantitative_measure
       description: >-
         Normalized log2 fold change for positive (+) dye orientation.
         Positive values indicate upregulation in response to deletion.
+      role: quantitative_measure
     - name: dye_minus
       dtype: float64
-      role: quantitative_measure
       description: >-
         Normalized log2 fold change for negative (-) dye orientation.
         Positive values indicate upregulation in response to deletion.
+      role: quantitative_measure
     - name: mean_norm_log2fc
       dtype: float64
-      role: quantitative_measure
       description: >-
         Average log2 fold change across dye orientations, providing a
-        dye-independent estimate of gene expression change upon transcription factor deletion.
+        dye-independent estimate of gene expression change upon
+        transcription factor deletion.
+      role: quantitative_measure
 ---
 # Hughes 2006