Update backend/main.py

backend/main.py

@@ -74,6 +74,7 @@ IMPORTANT RULES:
 - For CRISPR screens, always look for: MOI, library coverage, selection agent/duration, readout method, analysis software
 - For protein expression, always look for: induction conditions (IPTG concentration, OD600, temperature), purification steps, elution conditions"""
 
+
 COMPARISON_SYSTEM = """You are a senior peer reviewer specializing in bioengineering reproducibility. 
 Your job is to identify ALL methodological contradictions between protocols — including subtle ones most researchers miss.
 
@@ -101,12 +102,10 @@ Return ONLY valid JSON (no markdown, no extra text):
   "summary": {"total_contradictions": 0, "high": 0, "medium": 0, "low": 0}
 }
 
-SEVERITY ESCALATION RULES — apply these before assigning severity:
-- If one paper specifies a critical parameter and the other does not, this is a REPRODUCIBILITY GAP, not just low severity. 
-  Flag it as HIGH if the parameter is: MOI, cell line subtype, selection duration, packaging generation, or library coverage.
-  Flag it as MEDIUM if the parameter is: transfection reagent, serum concentration, or centrifugation speed.
-- "Not specified vs HEK293T" for cell line subtype = HIGH, because a researcher defaulting to HEK293 instead of HEK293T will see 3-10x lower viral titer.
-- Never rate Ampicillin vs mammalian selection agents as a contradiction — these operate in different biological contexts (bacterial vs mammalian). Flag this instead as a protocol scope difference.
+SEVERITY RULES:
+- HIGH: affects primary experimental outcome (e.g. MOI determines single vs multiple sgRNA integration; HEK293 vs HEK293T affects viral titer 3-10x; selection duration creates fitness bias)
+- MEDIUM: affects data quality or efficiency (e.g. library coverage affects statistical power; packaging ratios affect titer)
+- LOW: minor procedural difference unlikely to change conclusions
 
 CRITICAL CHECKS — always look for these specific contradictions:
 1. HEK293 vs HEK293T (SV40 T antigen affects transfection efficiency and episomal replication)