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Library and transport boundaries

bijux-proteomics-knowledge is a Python library and installs no executable or HTTP application. Evidence curation needs an explicit source corpus, annotation authority, storage decision, and review identity; a package-level command could not choose those safely on behalf of every deployment.

The root facade exposes high-value contracts and deterministic resolution operations:

  • EvidenceRecord, EvidenceBundle, and EvidenceClaim for scientific memory;
  • KnowledgeDecisionBrief for review handoff;
  • protein, pathway, complex, disease, drug-target, kinase-substrate, feature, ortholog, and coverage resolution;
  • stable TSV renderers for reviewer-facing tables;
  • schema compatibility evaluation for transported knowledge documents.
from bijux_proteomics_knowledge import (
    EvidenceBundle,
    EvidenceRecord,
    resolve_protein_ids,
)

Specialized graph, ingestion, reconciliation, reference, and review operations remain in their owner modules rather than expanding the root indefinitely.

Wrap the library without weakening it

Integration concern Owning layer
Evidence and claim meaning bijux-proteomics-knowledge typed contracts
Source authentication and access Importing application or service
Database transactions and retention Deployment repository implementation
CLI exit codes and terminal formatting Consuming command
HTTP authentication, pagination, and rate limits Publishing service
Runtime execution and run artifacts bijux-proteomics-runtime

A wrapper must return ambiguous, unresolved, stale, disputed, and held states as data. HTTP 200 or process exit code 0 means the request was processed; it does not mean an identifier resolved uniquely, a claim is supported, or a decision can advance.

Preserve the complete typed result when crossing a transport boundary: per-entity outcomes, unresolved inputs, policy identifiers, source locators, schema metadata, issue codes, and provenance. Do not reduce a resolution report to a dictionary of matched identifiers or a decision brief to its headline recommendation.

See Python API surface for the root capability map and Entrypoints and worked examples for concrete imports.