Methods And Glossary · Gene-Disease Evidence Index

Release Scope

The current rendered resource is a fixed set of per-disease 120-association public preview scopes, not a complete inventory of all genes for those diseases or all possible gene-disease relationships. A missing gene or missing association means only that it is absent from these release scopes.

The website renders from the tagged public data packages. The live page may later move to newer releases, but each version remains traceable through its GitHub tag, integrity manifest, and downloadable archive:

Alzheimer disease (alzheimer-top120-v0.1.0-preview): Git tag, integrity, ZIP, data dictionary.
Parkinson disease (parkinson-top120-v0.1.0-preview): Git tag, integrity, ZIP, data dictionary.
Type 2 diabetes mellitus (type2-diabetes-top120-v0.1.0-preview): Git tag, integrity, ZIP, data dictionary.
Breast carcinoma (breast-carcinoma-top120-v0.1.0-preview): Git tag, integrity, ZIP, data dictionary.
Dilated cardiomyopathy (dilated-cardiomyopathy-top120-v0.1.0-preview): Git tag, integrity, ZIP, data dictionary.
Amyotrophic lateral sclerosis (amyotrophic-lateral-sclerosis-top120-v0.1.0-preview): Git tag, integrity, ZIP, data dictionary.
Huntington disease (huntington-disease-top120-v0.1.0-preview): Git tag, integrity, ZIP, data dictionary.
Cystic fibrosis (cystic-fibrosis-top120-v0.1.0-preview): Git tag, integrity, ZIP, data dictionary.
Schizophrenia (schizophrenia-top120-v0.1.0-preview): Git tag, integrity, ZIP, data dictionary.
Epilepsy (epilepsy-top120-v0.1.0-preview): Git tag, integrity, ZIP, data dictionary.
Inflammatory bowel disease (inflammatory-bowel-disease-top120-v0.1.0-preview): Git tag, integrity, ZIP, data dictionary.
Hypertrophic cardiomyopathy (hypertrophic-cardiomyopathy-top120-v0.1.0-preview): Git tag, integrity, ZIP, data dictionary.

Method Summary

Identifier normalization

Gene records are rendered with stable ids, symbols, names, aliases, and source provenance. Disease context is represented through source-attributed disease identifiers and labels.

Evidence rows

Source records are converted into evidence rows attached to a gene-disease association. An evidence row records source id, source record id, evidence type, statement, and source-reported metrics when available.

Association records

Associations group evidence rows by gene and disease. They carry a support tier, source coverage, caveats, review state, and stable id so future releases can report changes.

Source coverage

Supporting, silent, and conflicting source fields are part of the data model. Source silence is not hidden; it is rendered as release-specific context when available.

Freshness metadata

Source and snapshot freshness fields describe when metadata was assessed, whether refresh is recommended, and whether the condition blocks release promotion.

Release gates

120-association public preview release work checks schema shape, fixture leakage, source metadata, citation metadata, integrity manifests, clinical-use wording, and reader-facing boundaries.

Review Boundaries

Automatic checks and referee artifacts are advisory. They can surface objections, mark release concerns, and guide corrections, but they do not replace human control, final publication approval, or source and citation review.

Early referee work used controlled Claude Code and Codex harness capabilities with GPT-5.5 and Claude Opus 4.8. The relevant method boundary is the review contract: explicit roles, target artifacts, structured outputs, model metadata, stored findings, and human disposition.

At the current stage, the human review disposition is performed by Serkan. A 120-association public preview page should not be read as external peer review or clinical validation.

Narration Boundary

LLM-assisted narration may make structured evidence easier to read, but it must not create source evidence, alter deterministic identifiers, change support tiers, resolve source disagreement, or turn a hypothesis into a clinical claim.

A strong future release should keep narration reproducible from the release artifacts and record which model, prompt contract, target records, and reviewer role were used for each review artifact.

Glossary

120-association public preview: A per-disease draft release containing up to 120 ranked associations, suitable for public reader testing and traceability checks.
Observed unreviewed: A source-attributed signal exists in the included release data, but no reviewed brief or human scientific acceptance has been attached.
Automatic checks only: The record passed deterministic or controlled referee checks. This is not the same as human scientific review.
Support tier: A release-specific grouping of evidence strength. It is not a diagnosis, a clinical recommendation, or a universal truth score.
Source-reported score: A score imported from an upstream source, such as Open Targets. It is rendered as provenance-bound source context, not as a combined confidence score for this resource.
Source silence: An included source does not support an association in the current release. Silence is source- and release-specific; it is not evidence that no relationship exists.
Source disagreement: Included sources conflict or provide materially different signals. The project should expose disagreement instead of blending it away.
Freshness status: A release metadata field that says whether source or snapshot metadata is current, refresh-recommended, refresh-required, or unknown.
Release blocker: A condition that may be acceptable for a 120-association public preview but must be resolved before promotion to a stronger release status.

Current Sources

data repository

HGNC

License: CC0 1.0
Freshness: refresh recommended; assessed Jun 9, 2026; next review Jul 9, 2026
Citation: source citation

MONDO Disease Ontology

License: CC BY 4.0
Freshness: refresh recommended; assessed Jun 9, 2026; next review Jul 9, 2026
Citation: source citation

Open Targets Platform

License: CC0 1.0
Freshness: refresh recommended; assessed Jun 9, 2026; next review Jul 9, 2026
Citation: source citation

Snapshot api-v4-graphql-2026-06-14-paper120: 120 records, accessed Jun 14, 2026; freshness refresh recommended; assessed Jun 9, 2026; next review Jul 9, 2026.

ClinVar

License: NCBI public data; reuse subject to NCBI policies
Freshness: refresh recommended; assessed Jun 9, 2026; next review Jul 9, 2026
Citation: source citation

Snapshot gene_condition_source_id-2026-06-14-paper120: 6 records, accessed Jun 14, 2026; freshness refresh recommended; assessed Jun 9, 2026; next review Jul 9, 2026.

Snapshot gene_condition_source_id-2026-06-14-paper120: 12 records, accessed Jun 14, 2026; freshness refresh recommended; assessed Jun 9, 2026; next review Jul 9, 2026.

Snapshot gene_condition_source_id-2026-06-14-paper120: 21 records, accessed Jun 14, 2026; freshness refresh recommended; assessed Jun 9, 2026; next review Jul 9, 2026.

Snapshot gene_condition_source_id-2026-06-14-paper120: 0 records, accessed Jun 14, 2026; freshness refresh recommended; assessed Jun 9, 2026; next review Jul 9, 2026.

Snapshot gene_condition_source_id-2026-06-14-paper120: 17 records, accessed Jun 14, 2026; freshness refresh recommended; assessed Jun 9, 2026; next review Jul 9, 2026.

Snapshot gene_condition_source_id-2026-06-14-paper120: 1 record, accessed Jun 14, 2026; freshness refresh recommended; assessed Jun 9, 2026; next review Jul 9, 2026.

Snapshot gene_condition_source_id-2026-06-14-paper120: 2 records, accessed Jun 14, 2026; freshness refresh recommended; assessed Jun 9, 2026; next review Jul 9, 2026.