Site Updates
Ongoing improvements, fixes, and status of known issues.
- In Progress
Fixed B–C paper counts undercounting drug mentions
The local literature index used to compute B–C (Disease–Compound) paper counts was only checking whether a paper formally listed a compound as a MeSH subject heading. In practice, most specific drugs are indexed by the National Library of Medicine via a separate chemical-substance field rather than as a subject heading — so many well-documented drug–disease connections were showing a B–C count of 0 when hundreds of supporting papers actually existed (verified example: benazepril and hypertension showed 0 despite 265+ papers directly connecting them). The indexer now also checks the chemical-substance field. Fixing this requires rebuilding the full literature index from NCBI's MEDLINE archive, which is in progress and expected to take a few hours; hypotheses will be rescored against the corrected counts once it completes. Until then, B–C counts — especially for drugs without their own dedicated MeSH heading — may still read lower than they should.
- Complete
Resilient database updates — staging swap and incremental refresh
The periodic data update process has been redesigned for reliability. Updates now build a complete new database in a staging file alongside the live one. The live database is only replaced once every import step succeeds — if any step fails partway through (e.g. a data source API times out), the staging file is discarded and the live database is left completely intact. Previously, a failed update would leave the database in a partial state with missing data. Additionally, updates are now incremental: each data source clears and replaces only its own records rather than wiping the entire database before rebuilding. The ChEMBL importer also received improved retry logic (6 attempts, 60s timeout, longer backoff on HTTP 500) to better handle transient API failures.
- Complete
Permanent hypothesis URLs, Cite This Tool page, and startup reliability
Hypothesis URLs are now permanently stable across database rebuilds. Each URL is derived from the three UMLS Concept Unique Identifiers (CUIs) that define the hypothesis — standard codes maintained by the US National Library of Medicine and used across NIH, FDA, and major biomedical databases. Because CUIs are internationally standardized and never change, the URLs will remain valid indefinitely regardless of how the underlying database is updated or rebuilt. A new Cite This Tool page (linked as CITE in the navbar) provides ready-to-copy APA and BibTeX citation blocks for academic use, and explains why the URLs are permanent. Each hypothesis detail page also includes a collapsible Cite This Result box with a pre-filled citation for that specific hypothesis.
- Complete
Insights tab: top pair leaderboards for A–B, A–C, and B–C
Three new leaderboard cards on the Insights tab show the top 5 most paper-supported pairings for each side of the ABC triangle. The A–B card ranks Disease × Bridge pairs by B↔A paper count, the A–C card ranks Bridge × Compound pairs by C↔A paper count, and the B–C card ranks Disease × Compound pairs by direct B–C paper count. The B–C leaderboard includes a note reminding readers that high counts reflect well-established connections — this app's primary targets are hypotheses where B–C = 0. All three leaderboards respect the active filters and tranche selection.
- Complete
Scoring formula v1.1, methodology page, and score delta indicators
Strength score formula updated to v1.1: log compression now applied per-side before the geometric mean (S = 1 − 1 / (1 + √(ln(1+B↔A) × ln(1+C↔A)))). The previous formula applied log after the geometric mean, which caused lopsided triangles (e.g. B↔A=2, C↔A=100) to incorrectly outscore balanced equivalents. Symmetric cases are mathematically unchanged — only lopsided hypotheses are affected. All hypothesis scores have been recomputed. A new Scoring Methodology page documents the formula rationale, behavior tables, known limitations, and full version history; it includes a version picker (v1.0 / v1.1) and a Track Changes toggle that overlays a diff of what changed between formula versions. The table page shows a scoring formula version badge (SCORING v1.1) linking to the methodology page, and after a rescore, each affected row shows a ▲/▼ badge indicating how many percentage points its score shifted.
- Complete
Discovery Landscape, Insights tab, and UX improvements
Major update across the main results page. A new Insights tab sits alongside the Table tab and shows aggregate analysis of the current filtered view: literature evidence distribution across five novelty tranches (Untested through Established), top 20 bridge targets by hypothesis count, score tier analysis for the top 1/5/10% of hypotheses, and auto-generated key findings. Clicking any tranche filters the table directly. A B–C column was added to the table showing direct disease–compound paper counts, color-coded by tranche. Pagination now supports typing a page number to jump directly. The 'What is this?' content moved to a dedicated About page linked from the navbar. Mobile layout improvements: a desktop recommendation banner and a 4-column table layout on narrow screens.
- Complete
PubMed novelty verification crawler
All 2,008,644 unique disease–compound pairs have been verified against PubMed. Novelty scores are now exact counts rather than estimates — the ~ prefix no longer appears. The cache survives database rebuilds so re-verification is not needed after a data update.
- Complete
Scoring formula correction
The Strength score was using a simple sum of B↔A and C↔A edge counts, which allowed a lopsided bridge (e.g. 99 papers on one side, 1 on the other) to score the same as a balanced one. Replaced with a geometric mean so both sides of the triangle must be well-evidenced. All 4.7M hypothesis scores are being recomputed.
- Complete
Filter state preserved on back navigation
Filters, sort order, and page are now encoded in the URL. Using the browser back button or the ← Back link on a hypothesis page restores your exact previous view.
- Complete
Score column shows active metric
When sorting by Novelty or Strength, the score pill in each row now shows that metric's value rather than always showing the combined Score.
- Complete
Public launch
Swanson's Apple is now publicly available at swansonsapple.org. The database currently tracks 4,746,394 hypotheses drawn from 6 biomedical sources: CTD, Open Targets, ChEMBL, DGIdb, DrugCentral, and DISEASES.