[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.