GSoC Week 9

 Three production upgrades were shipped around data-source query strategy and annotation quality control:

  • Config-driven query strategy management

  • Target SBO term tracking

  • Smart reaction filtering to reduce LLM ambiguity

1) Config-Driven Query Strategy Management

Presets

  • Fast: BiGG only for the fastest response

  • Balanced: BiGG + KEGG for a balance of recall and latency

  • Comprehensive: all sources (BiGG/KEGG/SEED/Reactome) for maximum coverage

Custom configuration: users can arbitrarily combine any of the four databases.
Interactive UI: supports live edit, input validation, and exception handling to prevent task failures due to misconfiguration.

2) Target SBO Term Tracking

  • Maintain a set of parent SBO terms to identify reactions that require further LLM processing.

  • Perform in-pipeline monitoring during annotation; once a reaction matches a target term, immediately log details including the SBO term, list of EC numbers, and annotation source/adapter to enable later aggregation and manual review.

3) Smart Reaction Filtering

  • Single EC number: send directly to the LLM for fine-grained classification.

  • Multiple EC numbers: check whether the first digit is consistent:

    • If consistent → keep and generate a unified EC prefix identifier.

    • If inconsistent → treat as an EC number conflict and filter it out to avoid ambiguity for the LLM.

Goal: maximize disambiguation before entering the LLM, improving final annotation precision and interpretability.

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