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README.md

@@ -13,9 +13,15 @@ pretty_name: Hackett, 2020 Overexpression
 size_categories:
 - 1M<n<10M
 experimental_conditions:
-  growth_medium: minimal
-  temperature: 30C
-  cultivation_method: chemostat
+  environmental_conditions:
+    temperature_celsius: 30
+    cultivation_method: chemostat
+    media:
+      name: minimal
+      carbon_source:
+        - compound: D-glucose
+          # Saldanha et al 2004: 10 g/l
+          concentration_percent: 1
 configs:
   - config_name: hackett_2020
     description: TF overexpression data from Hackett 2020
@@ -72,6 +78,19 @@ configs:
               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:
@@ -81,6 +100,27 @@ configs:
             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:
+              environmental_conditions:
+                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:
+              environmental_conditions:
+                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