Show HN: I mapped 8.5M research papers into interactive atlas

leonickson1 pts0 comments

Reading a paper means opening a PDF, then hunting separately for the code, the citations, whether it replicated, and what genes/drugs it touches. I spent a few months trying to fix that.Two parts:1. The map: I embedded 8.5M papers (arXiv, PubMed Central, bioRxiv, medRxiv), ran UMAP to lay them out in 2D, and render them with a WebGL scatterplot. Every dot is a paper — click it for an LLM TLDR, key findings, citations, peer reviews (where they exist), and similar work. Zoom in and the clusters are labeled by topic.2. Rich paper pages + an MCP server: each paper is rebuilt with linked genes/proteins/diseases/drugs (normalized to real IDs via PubTator, not regex), clinical trials, 3D structures, code, and a citation graph. It s all exposed as an MCP server too, so you can point Claude or an agent at 8.5M papers instead of pasting PDFs.Stack: Next.js, Postgres (Neon), Cloudflare R2 for content, embeddings + UMAP/HDBSCAN for the map, a WebGL renderer. The hard part was the ingestion pipeline — 45+ heterogeneous sources normalized into one schema — and keeping entity links accurate, since papers use names not accession IDs (so curated link tables + PubTator beat regex every time).Free, no signup to explore. I d love feedback on the map UX and whether the TLDRs/entity links hold up for papers you know well.Known limits: Google indexing is still slow so title-search isn t great yet, some older arXiv figures are missing, and peer-review coverage is partial.

papers paper code citations whether genes

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