removing zev and gev from main dataset and adding responsive column

README.md

@@ -165,6 +165,139 @@ configs:
             local FDR (false discovery rate). Most users of the data will want
             to use this column.
           role: quantitative_measure
+        - name: responsive
+          dtype: bool
+          description: >-
+            This labels targets, for a given regulator, with abs(log2_shrunken_timecourses) `>` 0
+  - config_name: zev_gev
+    description: These are the Z3EV and GEV control strains (no specifically tagged TF)
+    default: true
+    dataset_type: annotated_features
+    metadata_fields: ["sample_id", "regulator_locus_tag", "regulator_symbol", "time", "mechanism", "restriction", "date", "strain"]
+    data_files:
+      - split: train
+        path: hackett_2020.parquet
+    dataset_info:
+      features:
+        - name: sample_id
+          dtype: integer
+          description: >-
+            unique identifier for a specific sample. The sample ID identifies a unique
+            (regulator_locus_tag, time, mechanism, restriction, date, strain) tuple.
+        - 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: time
+          dtype: float
+          description: time point (minutes)
+          role: experimental_condition
+        - name: mechanism
+          dtype:
+            class_label:
+              names: ["GEV", "ZEV"]
+          description: Synthetic TF induction system (GEV or ZEV)
+          role: experimental_condition
+          definitions:
+            GEV:
+              perturbation_method:
+                type: inducible_overexpression
+                system: GEV
+                inducer: beta-estradiol
+                description: "Galactose-inducible estrogen receptor-VP16 fusion system"
+            ZEV:
+              perturbation_method:
+                type: inducible_overexpression
+                system: ZEV
+                inducer: beta-estradiol
+                description: "Z3 (synthetic zinc finger)-estrogen receptor-VP16 fusion system"
+        - name: restriction
+          dtype:
+            class_label:
+              names: ["M", "N", "P"]
+          description: >-
+            nutrient limitation, one of P (phosphate limitation (20 mg/l).),
+            N (Nitrogen‐limited cultures were maintained at 40 mg/l ammonium sulfate) or
+            M (Not defined in the paper or on the Calico website)
+          role: experimental_condition
+          definitions:
+            P:
+              media:
+                nitrogen_source:
+                  - compound: ammonium_sulfate
+                    # Saldanha et al 2004: 5 g/l
+                    concentration_percent: 0.5
+                phosphate_source:
+                  - compound: potassium_phosphate_monobasic
+                    # Hackett et al 2020: 20 mg/l
+                    concentration_percent: 0.002
+            N:
+              media:
+                nitrogen_source:
+                  - compound: ammonium_sulfate
+                    # Hackett et al 2020: 40 mg/l
+                    concentration_percent: 0.004
+            M:
+              description: "Not defined in the paper or on the Calico website"
+        - name: date
+          dtype: string
+          description: date performed
+          role: experimental_condition
+        - name: strain
+          dtype: string
+          description: strain name
+          role: experimental_condition
+        - name: green_median
+          dtype: float
+          description: median of green (reference) channel fluorescence
+          role: quantitative_measure
+        - name: red_median
+          dtype: float
+          description: median of red (experimental) channel fluorescence
+          role: quantitative_measure
+        - name: log2_ratio
+          dtype: float
+          description: log2(red / green) subtracting value at time zero
+          role: quantitative_measure
+        - name: log2_cleaned_ratio
+          dtype: float
+          description: Non-specific stress response and prominent outliers removed
+          role: quantitative_measure
+        - name: log2_noise_model
+          dtype: float
+          description: estimated noise standard deviation
+          role: quantitative_measure
+        - name: log2_cleaned_ratio_zth2d
+          dtype: float
+          description: >-
+            cleaned timecourses hard-thresholded based on
+            multiple observations (or last observation) passing the noise model
+          role: quantitative_measure
+        - name: log2_selected_timecourses
+          dtype: float
+          description: >-
+            cleaned timecourses hard-thresholded based on single observations
+            passing noise model and impulse evaluation of biological feasibility
+          role: quantitative_measure
+        - name: log2_shrunken_timecourses
+          dtype: float
+          description: >-
+            selected timecourses with observation-level shrinkage based on
+            local FDR (false discovery rate). Most users of the data will want
+            to use this column.
+          role: quantitative_measure
+        - name: responsive
+          dtype: bool
+          description: >-
+            This labels targets, for a given regulator, with abs(log2_shrunken_timecourses) `>` 0
 ---
 # Hackett 2020
 

hackett_2020.parquet

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+size 433257326

zev_gev_strains.parquet

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