meta_down_analysis v1.0.0-paper

Paper release of a research prototype for interpreting GCST/trait upstream differential tables and ordinary metabolite tables.

This release freezes the repository version intended for manuscript code availability statements.

Scope:

• Parses GCST/trait differential tables and standard metabolite tables
• Uses local GCST annotation files to map GCST accessions to reported traits, metabolite candidates, ratio components, or stable compound IDs
• Connects parsed inputs to metabolite matching, graph evidence, literature support, ranking fields, confidence tiers, and interpretation boundaries
• Provides a web/CLI layer for auditable research explanations

Data dependency boundary:
GCST-only upstream tables require a local annotation table at raw_lake/European/European_trait_annotations.csv or raw_lake/European_point/European_trait_annotations.csv. The real annotation table is a research data artifact and is not distributed in this code repository. A schema template is provided in config/european_trait_annotations.template.csv.

Current limitations:
This research prototype requires further methodological validation and engineering refinement. Ambiguous GCST mappings, ratio traits, graph propagation, and model-only rankings should remain lower-confidence research signals. The software is not a clinical decision system and does not provide treatment recommendations.

Third-party data boundary:
The MIT License applies to original repository code and documentation. Third-party databases, literature-derived resources, external identifiers, and downloaded or rebuilt data remain subject to their original licenses and citation requirements.