[
  {
    "term": "EVd3x",
    "short": "Source-attributed EV analysis platform.",
    "long": "EVd3x converts molecule or natural-language queries into a reusable state and surfaces separable evidence layers from query to export.",
    "aliases": ["EVd3x platform"],
    "related": ["Summary", "Source"],
    "sections": ["quick-start", "data-provenance"]
  },
  {
    "term": "Single mode",
    "short": "One resolved molecule, node-first interpretation.",
    "long": "Single mode auto-selects the node and opens node-level summary and module views for focused follow-up.",
    "aliases": ["single query mode"],
    "related": ["Collection mode", "Summary"],
    "sections": ["quick-start", "core-workflows"]
  },
  {
    "term": "Collection mode",
    "short": "Multiple molecules, system-first interpretation.",
    "long": "Collection mode preserves broad system context before node-level drilldown.",
    "aliases": ["system mode"],
    "related": ["Single mode", "Summary"],
    "sections": ["quick-start", "core-workflows"]
  },
  {
    "term": "Summary",
    "short": "First interpretation surface.",
    "long": "Summary confirms active context and should be reviewed before opening module-heavy tabs.",
    "aliases": ["overview"],
    "related": ["Single mode", "Collection mode"],
    "sections": ["quick-start", "interpreting-results"]
  },
  {
    "term": "miRNA",
    "short": "Regulatory RNA entity tracked in EVd3x.",
    "long": "miRNA nodes can contribute direct evidence and target-derived context through miRNA-mRNA support links.",
    "aliases": ["microRNA", "miR"],
    "related": ["mRNA", "target-derived"],
    "sections": ["analysis-modules", "interpreting-results"]
  },
  {
    "term": "mRNA",
    "short": "Gene/transcript context used across modules.",
    "long": "mRNA context links miRNA-target support to pathway and disease interpretation layers.",
    "aliases": ["gene transcript"],
    "related": ["miRNA", "Pathway", "Disease"],
    "sections": ["analysis-modules", "interpreting-results"]
  },
  {
    "term": "Protein",
    "short": "Protein-level entity in EVd3x.",
    "long": "Protein nodes connect to EV evidence, ligand-receptor context, and protein-protein interaction networks.",
    "aliases": ["protein cargo"],
    "related": ["PPI", "LR"],
    "sections": ["analysis-modules", "glossary-guide"]
  },
  {
    "term": "EV Evidence",
    "short": "Source-attributed EV support rows.",
    "long": "EV Evidence rows retain source and publication traceability for EV-related detectability review.",
    "aliases": ["EV support"],
    "related": ["Source", "PubMed_ID", "EV-TRACK ID"],
    "sections": ["analysis-modules", "data-provenance"]
  },
  {
    "term": "EV-TRACK ID",
    "short": "Record-level EV provenance field.",
    "long": "EV-TRACK metadata is preserved when present in source rows and should be interpreted with source and publication fields.",
    "aliases": ["EVTRACK"],
    "related": ["EV Evidence", "Source"],
    "sections": ["data-provenance", "troubleshooting"]
  },
  {
    "term": "Source",
    "short": "Origin database for each evidence row.",
    "long": "Source attribution enables row-level traceability and separates evidence layers from inferred context.",
    "aliases": ["source database"],
    "related": ["EV Evidence", "PubMed_ID"],
    "sections": ["data-provenance"]
  },
  {
    "term": "PubMed_ID",
    "short": "Publication identifier in evidence rows.",
    "long": "PubMed_ID helps audit supporting literature behind retrieved rows.",
    "aliases": ["PMID"],
    "related": ["Source", "EV-TRACK ID"],
    "sections": ["data-provenance"]
  },
  {
    "term": "Pathway",
    "short": "Annotation-level functional enrichment layer.",
    "long": "Pathway outputs rank enriched annotation programs for follow-up and should be interpreted with p-value and q-value settings.",
    "aliases": ["enrichment"],
    "related": ["q-value", "p-value"],
    "sections": ["analysis-modules", "interpreting-results"]
  },
  {
    "term": "Disease",
    "short": "Disease association ranking layer.",
    "long": "Disease outputs summarize curation-aware association context for prioritization, not causality.",
    "aliases": ["disease analysis"],
    "related": ["Pathway", "Source"],
    "sections": ["analysis-modules", "interpreting-results"]
  },
  {
    "term": "Cell specificity",
    "short": "Cell-context relevance ranking layer.",
    "long": "Cell specificity scores prioritize plausible cellular settings for follow-up interpretation.",
    "aliases": ["cell context"],
    "related": ["Cell communication", "LR"],
    "sections": ["analysis-modules"]
  },
  {
    "term": "Cell communication",
    "short": "Candidate sender-receiver communication layer.",
    "long": "Cell communication outputs rank plausible communication contexts using table-backed ligand and receptor support.",
    "aliases": ["communication module"],
    "related": ["LR", "Cell specificity"],
    "sections": ["analysis-modules"]
  },
  {
    "term": "LR",
    "short": "Ligand-receptor analysis layer.",
    "long": "LR analysis surfaces candidate ligand-receptor links and supporting rows for review.",
    "aliases": ["ligand-receptor"],
    "related": ["Cell communication", "Source"],
    "sections": ["analysis-modules"]
  },
  {
    "term": "PPI",
    "short": "Protein-protein interaction context layer.",
    "long": "PPI outputs surface interaction neighborhoods for ranking and triage, not standalone mechanistic proof.",
    "aliases": ["protein interaction"],
    "related": ["Protein", "STRING"],
    "sections": ["analysis-modules"]
  },
  {
    "term": "target-derived",
    "short": "Context inferred through supported targets.",
    "long": "Target-derived rows reflect inference through support links and should be separated from direct evidence in reporting.",
    "aliases": ["target inferred"],
    "related": ["miRNA", "mRNA"],
    "sections": ["interpreting-results"]
  },
  {
    "term": "Top-N",
    "short": "First-pass expansion cap.",
    "long": "Top-N is a processing guard for responsiveness and can be expanded for deeper review.",
    "aliases": ["N cap"],
    "related": ["Summary", "dominant metrics"],
    "sections": ["interpreting-results"]
  },
  {
    "term": "q-value",
    "short": "Benjamini-Hochberg FDR adjusted p-value.",
    "long": "q-value is used with p-value for enrichment interpretation within the same filter state.",
    "aliases": ["BH FDR"],
    "related": ["p-value", "Pathway"],
    "sections": ["interpreting-results", "analysis-modules"]
  },
  {
    "term": "p-value",
    "short": "Raw significance value.",
    "long": "p-value should be interpreted with q-value and current filter settings.",
    "aliases": ["significance"],
    "related": ["q-value", "Pathway"],
    "sections": ["interpreting-results", "analysis-modules"]
  },
  {
    "term": "machine-readable export",
    "short": "Structured export for downstream analysis.",
    "long": "Machine-readable exports preserve query state and source-attributed rows for reproducible review.",
    "aliases": ["csv export", "table export"],
    "related": ["Source", "Data provenance"],
    "sections": ["data-provenance", "chat-guidance"]
  }
]