Documentation / Literature Evidence / Workflow
Literature Evidence Workflow
Literature retrieval normally runs near the end of a case pipeline and is non-blocking: a literature-stage failure does not invalidate the completed Variant Analysis result. When results are available, they are saved with the session and streamed to the interface.
Case Inputs
Genes
Reportable genes and clinically prioritized genes define the primary retrieval scope.
Variants
Protein and cDNA HGVS notation can be compared with variant mentions extracted from titles and abstracts.
Phenotype
Resolved HPO names can enrich ranking when patient phenotype is available; HPO IDs alone are not searched as publication text.
Publication Discovery
Indexed gene mentions
The local gene-mention table provides a structured path to publications in which a candidate gene was identified during ingestion.
Title and abstract fallback
A broader case-insensitive text lookup finds additional title or abstract records. This improves recall but can also introduce incidental or substring matches that require review.
Candidate PMIDs are deduplicated before evidence assembly. The scoring stage evaluates a bounded candidate set and returns a bounded list for the session rather than every matching PubMed record.
What Is Reported
PMID, title, abstract, authors, journal, publication date, DOI, and PubMed Central identifier when present.
Overall literature relevance and the visible phenotype, publication-context, gene-focus, functional, variant, and recency components.
Matched query genes, matched variant notation, and matched phenotype names.
A heuristic functional-data indicator and a Strong, Moderate, Supporting, or Weak triage label.
Links to PubMed and, when a PMC identifier exists, to PubMed Central full text.
How Results Appear
The interface groups publications by matched gene. Within each group, papers are ordered by literature relevance. Gene groups can also incorporate the Phenotype Matching clinical priority, display the associated clinical tier and phenotype rank, and be filtered by gene or tier.
Read the Source
Extraction operates on PubMed metadata, titles, abstracts, publication types, and MeSH descriptors. It does not interpret the full article. Methods, cohort details, transcript context, assay validity, segregation, conflicts, and limitations must be checked in the publication itself.
Continue with Relevance Ranking or review the Evidence Labels.