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Show HN: I mapped 8.5M research papers into interactive atlas (tomesphere.com)

1 points by leonickson ↗ HN
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.

29 comments

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murkt
I remember similar kind of visualization from a decade ago, called paperscape. Looked cool, worked on clustering using citations and references.

Never got any idea on any use case that would be covered by such visualizations, apart from looking cool.

gavinray
ResearchRabbit is free and has this feature!

https://www.researchrabbit.ai/

ConnectedPapers also has this but they started to limit unless you pay:

https://www.connectedpapers.com/

A few other ones I know of:

https://litmaps.com

https://consensus.app/home/features/citation-graph/

aziis98
I also made my own variant recently. I really liked the idea of litmaps but I didn't really like the UI/UX or "graph expand" feature (it uses some internal heuristic that is not very clear).

https://paper-explorer.aziis98.com/ (also on github https://github.com/aziis98/paper-explorer)

This uses OpenAlex as a source of articles and to let you explore the citation graph of papers. This is still a prototype mostly to test out how far I could go with vibecoding something without a js framework. Someday I think I will add more features to it, but now there is already a somewhat working version of import/export so I'm fine with it.

leonickson
Hello, I agree with you, viz are just cool and might not really have a usecase. In this project map is not the product, it is 1 of 4 parts and to be honest the least important. The value is what is under each dot, the enriched page (TLDR, genes/drugs/diseases, trials, protein structures, code, datasets, full text, images, reviews, etc) and the MCP for agents. You can ignore the map entirely and just use the pages or extension or MCP.
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figassis
Today you could plug this into your agent as a second brain to give it more insight on related topics and ground it's responses when doing research or building products that can benefit from cross polinating between fields.
gavinray
Neat! Two questions I had after using it:

1) Is there a way to filter the visual atlas by the search term? For instance, I searched "ribosome" and it gave me a list, but I couldn't seem to visualize the list

2) I notice there's an MCP tool. I've used https://paperclip.gxl.ai/ in the past to good effect, curious if there are any standout features from tomesphere?

leonickson
The project has four parts, and I think you may have used the search in the navigation bar. That search is for the paper page (detailed information about that specific paper). When you search, you get a list of results, and if you click one of them, it takes you to a paper page with all the in-depth details about that paper. I should have made the map UX better.

To highlight things in the atlas or map, you might want to go to the filter panel on the left side and scroll down a bit. You will see a search area that helps you search for genes, diseases, and proteins. However it might not highlight any dot for the “ribosome” because filter search for now is only connected to genes, diseases and protein. I noted this, and I will improve it. I may also move that filter search to a different place. Thank you so much.

Tomesphere includes web pages and a browser extension overlays all of this directly on the arXiv, PMC, bioRxiv, Google Scholar, and medRxiv pages you are already reading. I had noticed the Paperclip MCP before, and from what I can see, they have very good data. In some cases, they may even have better data. We also have some additional sources, such as peer review from OpenReview, video links from YouTube and SlidesLive, GitHub links, AlphaFold protein entities, citations, and semantic neighbors.

Thank you for the questions. Will improve the project more.

vignyBot
Just curious where do you source all those papers?
leonickson
It is all open, bulk-downloadable sources. Here are some links.

  - arXiv: bulk on S3 (https://info.arxiv.org/help/bulk_data_s3.html)
  - PubMed Central Open Access: AWS Open Data (s3://pmc-oa-opendata).
  - bioRxiv / medRxiv: their monthly S3 dumps
  - OpenAlex: for citations, metadata, abstracts (https://developers.openalex.org/download/download-to-machine) 
  - AlphaFold — structures (https://alphafold.ebi.ac.uk/download)
Thanks for the question.
goodwillhunting
this is fun! even for casual users. I searched "James Webb" and got 'James Webb Space Telescope: data, problems, and resolution A. D. Dolgov · 2023 · 1 cites' as my first result, but clicking it didn't do anything - I expected it to either zoom into or see the article contents. Was I doing something wrong? (Chrome, OSX).
VinayUPrabhu
This is amazing! Would love to collaborate on a position paper I've been authoring if you have bandwidth
leonickson
Thank you so much! I'd genuinely like to hear more, you can email me here - help@tomesphere.com
GymInMeCricket
I have a few questions:

1. I see there is a Chrome extension, but I have not used Chrome since their adblocker blocker announcement. Is a Firefox extension planned?

2. What is the business model? Is this an open beta of a paid product? If this is not a product, will the code be released at some point?

3. It would be helpful to be able to filter papers by institution or author. Is this planned or out of scope?

leonickson
Hello,

1. Yes, I am working on it, I will soon release it soon for Firefox and Safari (by this weekend). 2. For now I am just trying to see what people want, may be the business model is more focused on mcp for higher limits for labs, lets see where is goes. 3. The articl/paper search already has author search, I can add the university search soon in both the paper/article and altas/map search.

Thank you for all the questions and suggestions.

hadi121
This is super cool. Just one question. I noticed that papers have different spacing between them. Is that because a paper's placement is based on correlation with neighbors, or just random placement?
Kerbonut
Tailscale Aperture is having trouble doing the OAUth2 connection. Can you support oauth2_dcr or test with Aperture?
leonickson
Yes, DCR is supported (WorkOS exposes the registration endpoint). What error is Aperture throwing? I suspect a metadata-discovery detail.
rahulb0802
I really like the clustering aspect of this. It would be cool if there was a way to articulate some sort of relationship between two adjacent or nearby papers in this tool.
Jahnavi_Aleti
Jumping between arXiv, GitHub, and peer reviews is such a real pain. The “copy page as markdown for your LLM” feature is especially useful.Curious how accurate the entity linking is so far, genes/diseases/etc. That’s usually where these tools get messy.