Update README.md

README.md

@@ -183,8 +183,158 @@ configs:
       dtype: string
       description: Source identifier for the control dataset (m2025 or h2021)
     - name: condition
-      dtype: string
-      description: Experimental condition. 'standard' is YPD.
+      dtype:
+        class_label:
+          names: ["standard",
+                  "30", "37",
+                  "SM", "WT", "WT_SM", 
+                  "admut", "admut_SM",
+                  "cAD", "cAD_SM",
+                  "dbdmut", "dbdmut_SM",
+                  "nAD", "nAD_SM",
+                  "ncAD", "ncAD_SM",
+                  "galactose", "raffinose"]
+      role: experimental_condition
+      description: Experimental condition. Standard is YPD (synthetic complete media).
+      definitions:
+        standard:
+          description: Baseline growth condition in synthetic complete media
+          growth_conditions:
+            media:
+              name: synthetic_complete
+              composition:
+                yeast_nitrogen_base_g_per_l: 1.7
+                yeast_nitrogen_base_specs:
+                  - without_amino_acids
+                  - without_ammonium_sulfate
+                ammonium_sulfate_g_per_l: 5
+                adenine_sulfate_ug_per_ml: 40
+                amino_acid_dropout_mix_g_per_l: 0.6
+                amino_acid_dropout_mix_composition:
+                  - compound: Tyrosine
+                    g_per_l: 2
+                  - compound: Serine
+                    g_per_l: 2
+                  - compound: Valine
+                    g_per_l: 2
+                  - compound: Isoleucine
+                    g_per_l: 2
+                  - compound: Phenylalanine
+                    g_per_l: 2
+                  - compound: Aspartic_acid
+                    g_per_l: 2
+                  - compound: Proline
+                    g_per_l: 2
+                  - compound: Arginine
+                    g_per_l: 4
+                  - compound: Threonine
+                    g_per_l: 4
+                uracil_ug_per_ml: 2
+                other_amino_acids_percent: 0.01
+        "30":
+          description: No heat shock control at 30°C
+          growth_conditions:
+            temperature_celsius: 30
+            duration_minutes: 10
+        "37":
+          description: Heat shock condition at elevated temperature
+          growth_conditions:
+            temperature_celsius: 37
+            duration_minutes: 10
+        SM:
+          description: Amino acid starvation stress induced by sulfometuron methyl
+          growth_conditions:
+            media:
+              name: synthetic_complete_minus_isoleucine_valine
+            chemical_stress:
+              agent: sulfometuron_methyl
+              concentration_ug_per_ml: 0.5
+              duration_minutes: 60
+        WT:
+          description: Wild-type negative control to distinguish specific TF effects from non-specific IAA/DMSO treatment effects
+          strain_type: wildtype
+        WT_SM:
+          description: Wild-type strain treated with sulfometuron methyl to induce amino acid starvation
+          strain_type: wildtype
+          chemical_stress:
+            agent: sulfometuron_methyl
+            concentration_ug_per_ml: 0.5
+            duration_minutes: 60
+        admut:
+          description: Gcn4 activation domain mutant with inactivated activation domains but intact DNA-binding domain
+          strain_type: gcn4_mutant
+          mutation_type: activation_domain_deleted
+        admut_SM:
+          description: Gcn4 activation domain mutant treated with sulfometuron methyl
+          strain_type: gcn4_mutant
+          mutation_type: activation_domain_deleted
+          chemical_stress:
+            agent: sulfometuron_methyl
+            concentration_ug_per_ml: 0.5
+            duration_minutes: 60
+        cAD:
+          description: Gcn4 central activation domain inactivated by missense mutations
+          strain_type: gcn4_mutant
+          mutation_type: central_activation_domain_inactivated
+        cAD_SM:
+          description: Gcn4 central activation domain mutant treated with sulfometuron methyl
+          strain_type: gcn4_mutant
+          mutation_type: central_activation_domain_inactivated
+          chemical_stress:
+            agent: sulfometuron_methyl
+            concentration_ug_per_ml: 0.5
+            duration_minutes: 60
+        dbdmut:
+          description: Gcn4 DNA-binding domain mutant with triple mutation to inhibit specific DNA binding
+          strain_type: gcn4_mutant
+          mutation_type: dna_binding_domain_inactivated
+        dbdmut_SM:
+          description: Gcn4 DNA-binding domain mutant treated with sulfometuron methyl
+          strain_type: gcn4_mutant
+          mutation_type: dna_binding_domain_inactivated
+          chemical_stress:
+            agent: sulfometuron_methyl
+            concentration_ug_per_ml: 0.5
+            duration_minutes: 60
+        nAD:
+          description: Gcn4 N-terminal activation domain inactivated by missense mutations
+          strain_type: gcn4_mutant
+          mutation_type: n_terminal_activation_domain_inactivated
+        nAD_SM:
+          description: Gcn4 N-terminal activation domain mutant treated with sulfometuron methyl
+          strain_type: gcn4_mutant
+          mutation_type: n_terminal_activation_domain_inactivated
+          chemical_stress:
+            agent: sulfometuron_methyl
+            concentration_ug_per_ml: 0.5
+            duration_minutes: 60
+        ncAD:
+          description: Gcn4 mutant with both N-terminal and central activation domains inactivated
+          strain_type: gcn4_mutant
+          mutation_type: n_terminal_and_central_activation_domains_inactivated
+        ncAD_SM:
+          description: Gcn4 N-terminal and central activation domain double mutant treated with sulfometuron methyl
+          strain_type: gcn4_mutant
+          mutation_type: n_terminal_and_central_activation_domains_inactivated
+          chemical_stress:
+            agent: sulfometuron_methyl
+            concentration_ug_per_ml: 0.5
+            duration_minutes: 60
+        galactose:
+          description: Galactose induction condition for Gal4 transcription factor activation
+          growth_conditions:
+            induction:
+              inducer: D-galactose
+              concentration_percent: 2
+              duration_hours: 2
+        raffinose:
+          description: Non-inducing baseline growth medium for Gal4 experiments
+          growth_conditions:
+            media:
+              name: yeast_extract_peptone
+              carbon_source:
+                compound: D-raffinose
+                concentration_percent: 2
     - name: regulator_locus_tag
       dtype: string
       description: Systematic gene name (ORF identifier) of the transcription factor
@@ -205,12 +355,15 @@ configs:
       description: Strand orientation (+ or -) of the promoter/target
     - name: input_vs_target_log2_fold_change
       dtype: float64
+      role: quantitative_measure
       description: Log2 fold change of TF-tagged sample vs control (from DESeq2)
     - name: input_vs_target_p_value
       dtype: float64
+      role: quantitative_measure
       description: P-value for differential enrichment (from DESeq2)
     - name: input_vs_target_adj_p_value
       dtype: float64
+      role: quantitative_measure
       description: Adjusted p-value (FDR-corrected) for differential enrichment (from DESeq2)
 
 - config_name: rna_seq
@@ -275,55 +428,6 @@ This repo provides 5 datasets:
   m2025 from the Mahendrawada 2025 paper, and h2021 from a previous paper from the Hahn
   lab.
 
-The condition definitions are:
-
- - **30**: incubation for 10 min at 30 °C for no heat shock
- - **37**: incubation at 37 °C for 10 min for heat shock
- - **SM**: SM (sufometuron methyl) is a chemical agent used to
-   induce amino acid starvation, creating a stress condition to activate and study the transcription factor Gcn4.
- - **WT**: WT (Wild-type) serves as a negative control to
-   distinguish the specific effects of transcription factor depletion from non-specific side effects caused by the chemical treatment (IAA/DMSO).
- - **WT_SM**: WT_SM represents the Wild-Type strain (expressing native Gcn4)
-   treated with Sufometuron Methyl (SM) to induce amino acid starvation.
-   It acts as the activated stress condition to be compared against the
-   uninduced basal Wild-Type (WT) or Gcn4 mutants.
- - **admut**: admut refers to Gcn4 activation domain mutants, where the
-   protein's activation domains are inactivated (via deletion or missense
-   mutation) to inhibit their function while retaining the DNA-binding domain.
- - **admut_SM**: admut_SM refers to these specific mutant strains treated
-   with Sufometuron Methyl (SM) to induce amino acid starvation stress.      
- - **cAD**: cAD refers to the Gcn4 mutant where the central activation
-   domain is specifically inactivated by missense mutations.
- - **cAD_SM**: cAD_SM refers to this mutant strain measured under amino acid
-   starvation stress induced by Sufometuron Methyl (SM).
- - **dbdmut**: dbdmut refers to the Gcn4(DBD) mutant, which contains a triple
-   mutation in the DNA-binding domain designed to inhibit its specific DNA binding function.      
- - **dbdmut_SM**: dbdmut_SM refers to this same mutant strain treated with
-   Sufometuron Methyl (SM) to induce amino acid starvation, allowing
-   researchers to test if the Gcn4 protein can still target the genome
-   via its activation domain even when its DNA-binding domain is disabled.
- - **galactose**: Galactose refers to the induced condition
-   (2% galactose for 2 hours) specifically used to activate the transcription
-   factor Gal4 for functional analysis.
- - **nAD**: nAD refers to the Gcn4 mutant where the N-terminal activation
-   domain is specifically inactivated by missense mutations.
- - **nAD_SM**: nAD_SM refers to this mutant strain analyzed under amino acid
-   starvation stress induced by Sufometuron Methyl (SM).
- - **ncAD**: ncAD refers to the Gcn4 mutant where both the N-terminal and
-   central activation domains are inactivated.
- - **ncAD_SM**: ncAD_SM refers to this double mutant strain analyzed under
-   amino acid starvation stress induced by Sufometuron Methyl (SM).
- - **raffinose**: Raffinose refers to the non-inducing growth medium
-   (YEP with 2% raffinose) used as a baseline condition to cultivate cells
-   before triggering Gal4 activation with galactose.
- - **standard**：synthetic complete (SC) media (per litre: 1.7 g yeast
-   nitrogen base without ammonium sulfate or amino acids (BD Difco),
-   5 g ammonium sulfate, 40 μg ml−1 adenine sulfate, 0.6 g amino acid dropout
-   mix and supplemented with 2 μg ml−1 uracil and 0.01% other amino acids to
-   complement auxotrophic markers). Standard amino acid dropout mix contains
-   2 g each of Tyr, Ser, Val, Ile, Phe, Asp, Pro and 4 g each of Arg and
-   Thr.
-
 ## Usage
 
 The python package `tfbpapi` provides an interface to this data which eases