Additional file 3 of Beyond gene-disease validity: capturing structured data on inheritance, allelic requirement, disease-relevant variant classes, and disease mechanism for inherited cardiac conditions
Bibliographic record
Abstract
Additional file 3: Table S1. A table showing the curation of syndromic forms of (hypertrophic) cardiomyopathy that can have isolated left ventricular hypertrophy as the presenting feature: structured representation of inheritance, allelic requirement, disease-associated variant consequence, and variant classes reported with evidence of pathogenicity for each gene-disease pair. Tables S2–S5. Details of the filtering process of each pipeline for the 3 datasets (Table S2 - Set 1, Table S3 - Set2a and Table S4 -Set2b). Details of the demographics of the cohorts used in Set2a and Set2b are available in Table S5. Tables S6–S8. The same information that is presented in Additional File 2 is included here in xls format. Table S6. (CardiacG2P) includes a structured representation of inheritance and mechanism data for all curated gene-disease pairs. In addition this also includes information for 7 genes related to a syndrome where LVH is seen only with overt syndromic features. Table S7. (Narr_sum) has narrative summaries for each gene-disease pair as plain free text. Table S8. (Other_limited) is a list of gene-disease pairs where there is no established relationship (gene disease validity assertion from ClinGen); these are included for completeness.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.003 | 0.032 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.746 | 0.189 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".