Known limitations

Knowledge can preserve evidence and disagreement more faithfully than an unstructured summary. It cannot guarantee complete literature coverage, perfect biological identity resolution, source availability, or a final answer to every contradiction.

Evidence limits

Limitation	Consequence	Responsible interpretation
external databases and literature change on independent schedules	retained evidence can become stale without becoming structurally invalid	publish source version or retrieval date and freshness status
licensing and redistribution differ by source	a reference can be reviewable without its full upstream content being bundled	follow the source link and license record; do not infer local custody
protein, gene, isoform, ortholog, pathway, disease, drug, and complex identifiers are context-dependent	normalization can merge or split biologically distinct entities	retain namespace, species, isoform, mapping method, and ambiguity
source coverage is selective	absence from the graph is not evidence of biological absence	state the registries, corpora, and queries searched
several records may share one underlying experiment or database	record count can exaggerate independent support	inspect lineage before treating evidence as corroboration
contradiction can reflect context, method, population, or time	automated reconciliation may not yield one defensible truth	preserve competing contexts and use unresolved or hold dispositions
confidence depends on declared policy and inputs	it is not automatically a calibrated probability	report the scale and update rule with the value
retained fixtures prove deterministic handling of checked records	they do not prove that remote retrieval still succeeds or returns unchanged content	distinguish fixture replay from live-source verification

Knowledge boundary

flowchart LR
    W["world and external sources"] --> S["selected source snapshot"]
    S --> K["Knowledge records and graph"]
    K --> R["review disposition"]
    R --> D["downstream decision"]
    W -. incomplete coverage .-> K
    R -. advisory evidence state .-> D

The package can state what its selected sources support, contradict, or leave uncertain at a named revision. It cannot claim exhaustiveness unless the search space and retrieval result make that claim testable.

Report a grounded gap

Name the missing source class, unresolved identifier, stale retrieval, shared lineage, or contradiction context. “No evidence found” must include where and how the search was performed. “Reviewed” must include the evidence revision and disposition. Downstream recommendations remain bounded by these gaps even when their own policy is deterministic.