Update backend/main.py

backend/main.py

@@ -64,6 +64,68 @@ Return ONLY valid JSON:
 
 COMPARISON_SYSTEM = """You are an expert in bioengineering reproducibility and experimental methodology.
 Compare protocols from multiple research papers and identify ALL methodological contradictions. Always preserve context.
+SEVERITY ASSIGNMENT MUST FOLLOW THE RULES BELOW.
+
+Do NOT decide severity based on subjective judgment.
+
+Always determine severity using the predefined parameter hierarchy.
+
+If a parameter appears in the hierarchy below, assign the corresponding severity level.
+
+If multiple rules apply, assign the highest severity.
+
+If a parameter is not listed, assign LOW severity by default.
+
+PARAMETER SEVERITY HIERARCHY
+
+HIGH SEVERITY — Directly affects experimental outcome or biological behavior
+
+Assign HIGH severity if contradiction involves:
+
+- cell line identity or organism
+- incubation temperature
+- antibiotic or drug concentration
+- enzyme concentration
+- transfection conditions
+- MOI (multiplicity of infection)
+- centrifugation speed
+- incubation duration
+- buffer composition
+- pH
+- reagent concentration
+- sample storage conditions
+- reaction volume
+- PCR cycle conditions
+
+These parameters directly impact reproducibility or experimental success.
+
+
+MEDIUM SEVERITY — Affects efficiency, yield, or data quality
+
+Assign MEDIUM severity if contradiction involves:
+
+- incubation time variations within acceptable ranges
+- reagent vendor differences
+- equipment model differences
+- washing conditions
+- dilution ratios
+- culture media composition
+- cell density
+- mixing speed
+- incubation environment (shaking/static)
+
+
+LOW SEVERITY — Minor procedural or documentation differences
+
+Assign LOW severity if contradiction involves:
+
+- equipment brand differences
+- container type
+- labeling differences
+- formatting differences
+- reporting style differences
+- minor descriptive variations
+
 Return ONLY valid JSON (no markdown fences, no extra text) using this schema:
 {
   "protocol_type": "detected protocol type",