Documentation / Literature Evidence / Relevance Ranking
Relevance Ranking
Folklore assigns each candidate publication a normalized relevance score for ordering the review list. The score combines six visible evidence dimensions. It represents search relevance to this case, not study quality, pathogenicity, or ACMG evidence strength.
Signals Used
Phenotype overlap
Compares resolved patient HPO names with structured MeSH-derived terms and words in the title and abstract. Morphological normalization helps with common word forms but is not ontology-based semantic similarity.
Publication context
Uses the indexed publication type to distinguish clinical reports, studies, general journal articles, reviews, and other publication contexts.
Gene focus
Uses the available mention count as a signal for whether a query gene is central to the abstract or merely incidental.
Functional-study indicator
Looks for curated MeSH descriptors and title or abstract language associated with models, assays, expression, splicing, or other experimental work.
Variant match
Compares the query gene and supplied protein or cDNA notation with variant mentions extracted from the publication record.
Recency
Adds publication age as a ranking signal. Older evidence is not treated as invalid; recency only influences ordering.
Phenotype Matching in Literature
The literature ranker uses the human-readable name of each selected HPO term. It can match a MeSH-derived term directly or find morphologically related words in the title and abstract. Multi-word terms require their meaningful word components to be present, but the components do not have to form an exact phrase.
This is intentionally different from the ontology-based semantic similarity used by the dedicated Phenotype Matching service. A missing literature phenotype match does not mean the publication is clinically unrelated.
Variant and Functional Signals
Exact variant indicator
Requires the same gene and compatible supplied HGVS protein or cDNA notation in the extracted publication record. It does not confirm transcript equivalence, allelic phase, zygosity, or patient-level applicability.
Functional-data indicator
Signals that the metadata or abstract appears to describe experimental work. It does not assess assay calibration, biological relevance, reproducibility, or whether PS3/BS3 can be applied.
How to Read the Number
Use a higher relevance score as a prompt to review a paper earlier. Compare the component breakdown and matched entities before deciding why the score is high. Do not compare the number with an ACMG probability, a confidence interval, or a validated evidence-strength calibration.
Result Boundaries
Very low-relevance candidates are omitted from the returned review set.
Only a bounded number of candidate publications are scored and returned for a case.
When no patient HPO terms are present, the phenotype component contributes no signal and scores are not directly comparable with phenotype-enriched searches.
The user interface can combine literature relevance with Phenotype Matching clinical priority when ordering gene groups; publication cards continue to show the literature score itself.