7 Glossary

Glossary

Relevant source files

The following files were used as context for generating this wiki page:

• CHANGELOG.md
• INTERVIEW.md
• LICENSE
• README.md
• src/core/stats.js

Purpose and Scope

This section provides precise definitions of domain-specific concepts (biology and genomics) and codebase architecture terms used throughout VariantScope. Each entry includes its functional role, mathematical or logical definition where applicable, and direct file pointers to the implementation code or documentation.

---

Domain Terms

pLDDT

• Definition: Predicted Local Distance Difference Test. An per-residue confidence score assigned by AlphaFold ranging from 0 to 100 stored in the B-factor column of PDB files.
• Codebase Role: Used to colorize the 3D molecular viewer and evaluate structural confidence bands (PLDDT_CONFIDENT >= 70).
• Implementation: src/core/stats.js:11-12, src/ui/viewer3d.js

Sources: src/core/stats.js:11-12, README.md:32

VUS

• Definition: Variant of Uncertain Significance. A genetic variant whose clinical impact cannot yet be definitively determined based on current medical and scientific evidence.
• Codebase Role: Represented in variant tallies, filtered in tables, and styled distinctly (gray spheres) in the 3D structure and lollipop plot.
• Implementation: CHANGELOG.md:44, src/core/stats.js

Sources: CHANGELOG.md:44, README.md:34

LOEUF

• Definition: Loss-of-Function Observed/Expected Upper Bound Fraction. A gnomAD gene constraint metric representing the upper bound of the confidence interval for the ratio of observed to expected loss-of-function variants. Lower values indicate strong intolerance to variation.
• Codebase Role: Displayed as a gene-level constraint score alongside pLI and missense Z scores.
• Implementation: CHANGELOG.md:45, src/core/gnomad.js

Sources: CHANGELOG.md:45, README.md:5

matchedBy

• Definition: An attribute indicating the join strategy used to link a ClinVar clinical record with a gnomAD population frequency record.
• Codebase Role: Distinguishes between genomic coordinate matching ('coordinates'), protein-change fallback matching ('protein'), or failed matching ('none'), preventing ambiguous allele frequency attribution.
• Implementation: src/core/join.js:1-50, README.md:46

Sources: src/core/join.js:1-50, README.md:46

Rarity Buckets

• Definition: Categorization thresholds applied to allele frequencies (AF) derived from gnomAD population data.
• Codebase Role: Classifies variants into discrete bins: 'absent', 'ultra-rare' (< 1e-5), 'rare' (< 1e-4), 'low-frequency' (< 1e-2), 'common', or 'unknown'.
• Implementation: src/core/stats.js:3-34

Sources: src/core/stats.js:3-34, CHANGELOG.md:45

---

Codebase and Architecture Terms

Panels

• Definition: Modular UI container components rendering distinct analytical views of gene data (e.g., 3D Viewer, Lollipop Plot, Variant Table, Summary Cards, and Plain Language Explanations).
• Codebase Role: Orchestrated by main application logic to synchronize state selections across views.
• Implementation: CHANGELOG.md:41-42, src/ui/cards.js, src/ui/table.js

Sources: CHANGELOG.md:41-42, src/ui/cards.js

Banners

• Definition: Top-level notification strips providing transient or persistent status alerts, such as offline status ("Offline: showing cached data") or data expiration ("Out of date").
• Codebase Role: Rendered dynamically based on network state and data timestamp checks.
• Implementation: CHANGELOG.md:30-31, src/main.js

Sources: CHANGELOG.md:30-31, src/main.js

vs:library

• Definition: The internal state schema and storage namespace representing saved user gene collections, metadata, and folder hierarchies.
• Codebase Role: Persists opened gene analyses across sessions in browser localStorage or desktop JSON files.
• Implementation: README.md:39-50, src/core/library.js, src/core/folders.js

Sources: README.md:39-50, CHANGELOG.md:9-16

api-cache

• Definition: The local persistence directory or storage store containing raw JSON responses retrieved from public APIs (UniProt, AlphaFold, ClinVar, gnomAD).
• Codebase Role: Enables offline operation in the desktop app and fast loading times without redundant network requests.
• Implementation: README.md:49-50, electron/disk-cache.js

Sources: README.md:49-50, electron/disk-cache.js

Bridge

• Definition: The secure Inter-Process Communication (IPC) boundary established via Electron context bridge, exposing a strictly limited set of functions from the main process to the renderer sandbox.
• Codebase Role: Limits exposed surface area to exactly six functions (fetchJson, saveFile, loadCache, listCache, deleteCache, getAppVersion).
• Implementation: CHANGELOG.md:28, electron/preload.cjs:1-25

Sources: CHANGELOG.md:28, electron/preload.cjs:1-25

Shard

• Definition: A parallel execution partition within GitHub Actions CI workflows.
• Codebase Role: Splits end-to-end web test suites across concurrent runner jobs to minimize pipeline duration.
• Implementation: README.md:61, .github/workflows/ci.yml

Sources: README.md:61, .github/workflows/ci.yml

Dry Run

• Definition: A verification or test execution phase that simulates actions (such as packaging builds or publishing releases) without committing persistent changes or pushing external artifacts.
• Codebase Role: Used in release pipelines and validation scripts to catch configuration or syntax errors early.
• Implementation: .github/workflows/release.yml, package.json

Sources: .github/workflows/release.yml, package.json

---

Domain Space to Code Entity Mapping

Diagram illustrating how abstract genomic and structural domain concepts map directly to underlying core JavaScript modules and functions.

graph TD
    subgraph "NaturalLanguageSpace"
        A["pLDDT Confidence"]
        B["Variant Rarity Bucket"]
        C["Coordinate vs Protein Join"]
    end

    subgraph "CodeEntitySpace"
        D["src/core/stats.js:PLDDT_CONFIDENT"]
        E["src/core/stats.js:rarityFromAf()"]
        F["src/core/join.js:matchVariants()"]
    end

    A --> D
    B --> E
    C --> F

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Sources: src/core/stats.js:3-34, src/core/join.js:1-50

---

System Architecture Space to Code Entity Mapping

Diagram illustrating how architectural concepts (api-cache, bridge, vs:library) correspond to implementation files and runtime objects in the codebase.

graph TD
    subgraph "ArchitecturalSpace"
        G["api-cache Disk Store"]
        H["Electron Preload Bridge"]
        I["Saved Library Storage"]
    end

    subgraph "CodeEntitySpace"
        J["electron/disk-cache.js"]
        K["electron/preload.cjs"]
        L["src/core/library.js"]
    end

    G --> J
    H --> K
    I --> L

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Sources: electron/disk-cache.js, electron/preload.cjs:1-25, src/core/library.js