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

A developer built an interactive atlas of 8.5 million research papers from arXiv, PubMed Central, bioRxiv, and medRxiv, embedding them into a 2D map with LLM-generated summaries, entity links, and an MCP server for AI agents. The free tool uses UMAP and WebGL to visualize clusters by topic, linking papers to genes, drugs, clinical trials, and code.

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. Comments URL: https://news.ycombinator.com/item?id=48840207 https://news.ycombinator.com/item?id=48840207 Points: 1 Comments: 0