Skip to content

Dashboard: data-driven evidence summary + top candidates per pool - #60

Merged
sr320 merged 2 commits into
mainfrom
docs/evidence-summary-data-driven
Oct 15, 2026
Merged

sr320 merged 2 commits into
mainfrom
docs/evidence-summary-data-driven

Conversation

@sr320

@sr320 sr320 commented Oct 15, 2026 •

Copy link
Copy Markdown
Owner

Rewrites the What the evidence says so far section of https://sr320.github.io/AREE/ so that every sentence comes from data.json instead of hardcoded prose.

What was out of date on the live page

  • It said "All real studies so far are RNA-seq pathogen challenges", which stopped being true once the heat, OA and starvation studies were added.
  • It listed single-study phenotypes as pools with "0 genes measured in both", and said "both" for a 3-study pool.
  • The next step it gave ("a second stressor class") is already done.

What the section now computes

  • Stressor and assay coverage, plus which assays actually have harmonized evidence.
  • Cross-study pools (k ≥ 2 only) as a list. Single-study phenotypes are named as awaiting replication.
  • Tier and evidence-class counts.
  • Caveats that only show when they apply: the top list being disease-only, the multi-omics tier being empty.
  • Next curation steps, worked out from unharmonized assays, unreplicated phenotypes and QC failures.

Tested by rendering against the live data.json and against an older local build (10 studies, one pool). Also guarded the CI case with no evidence.
Top candidates per pool (second commit)

  • The overall top-15 list is filled entirely by the 3-study disease-susceptibility pool, so thermal tolerance's replicated candidates never appeared.
  • aree build-dashboard now also writes top_real_by_phenotype / top_simulated_by_phenotype: the top 5 per phenotype, each with its evidence card and gene annotations.
  • The home page adds a Top candidates per pool section with one table per cross-study (k ≥ 2) pool. The existing overall table is unchanged.
  • New test assertions cover per-phenotype ranking order and size limits, and check that the field is empty when nothing has run. Full suite: 564 passed; ruff clean.

🤖 Generated with Claude Code

sr320 and others added 2 commits October 15, 2026 05:38
The section's prose was hardcoded and went stale as studies were added: it
said every real study was an RNA-seq pathogen challenge after heat, OA and
starvation studies landed, and it listed single-study phenotypes as pools
with '0 genes measured in both'.

Every sentence is now derived from data.json: stressor and assay coverage,
only k>=2 pools (with 'at least two studies' for 3-study pools), single-study
phenotypes named as awaiting replication, tier counts, caveats that fire only
when true, and next curation steps from unharmonized assays, unreplicated
phenotypes and QC failures.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
The overall top list is filled by whichever pool has the most studies, so
thermal tolerance's replicated candidates never appeared beside disease
susceptibility's. The builder now writes the top 5 per phenotype
(top_real_by_phenotype / top_simulated_by_phenotype, with cards and gene
annotations), and the home page shows one table per k>=2 pool.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@sr320
sr320 force-pushed the docs/evidence-summary-data-driven branch from 1295ea3 to fcd6c3d Compare October 15, 2026 12:38
@sr320 sr320 changed the title Dashboard: compute 'What the evidence says so far' from the data Dashboard: data-driven evidence summary + top candidates per pool Oct 15, 2026
@sr320
sr320 merged commit ed1dbf4 into main Oct 15, 2026
6 checks passed
@sr320
sr320 deleted the docs/evidence-summary-data-driven branch October 15, 2026 12:54
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant