mcp server
tomesphere
Search 8.5M scientific papers with LLM TLDRs, citations, linked entities, figures, and full text.
Description as published by the maintainer. Source
- version 0.1.0
- active
- retrieval
active — Registry entry last updated 2026-07-06. Dashed tags are derived by ZBS Index from the published description, not stated by the maintainer.
What this server can do
9 functions, named and described by the server itself. Parameter names are shown because they say more about what a function does than its name usually does.
citations(k, id)- Get papers that cite the given paper (who refers to this work). Use when the user asks 'who cites X', 'what's the impact', or wants follow-up work. Note: 2024+ citation coverage is sparse; indexing in progress. Required: id.
get_entities(id)- Get the biomedical entities linked to a paper: genes, proteins, chemicals, diseases, species, mutations, cell lines, and clinical-trial (NCT) IDs. Accepts an arXiv ID, PMC ID, or bioRxiv/medRxiv DOI. Required: id.
get_figures(id)- Get a paper's real figure images — URLs, labels, and captions. Most biomedical papers have figures; arXiv papers often don't. Accepts an arXiv ID, PMC ID, or bioRxiv/medRxiv DOI. Required: id.
get_full_text(id)- Fetch a paper's full body text as Markdown (methods, results, protocols, inline tables) — use for deep questions the abstract can't answer. Accepts an arXiv ID (2401.12345), a PMC ID (PMC5339222), or a bioRxiv/medRxiv DOI (10.1101/…). Required: id.
get_paper(id)- Fetch a paper's full metadata: title, authors, year, abstract, TLDR (LLM-generated), key findings, citation count, GitHub repos, HuggingFace models/datasets, videos, peer reviews, and links. Accepts an arXiv ID (e.g. '2401.12345' or '1706.03762v5') or an OpenAlex Work ID (e.g. 'W4390723197'). Use when the user names a specific paper or pastes an arXiv link. Required: id.
get_structure(name)- Resolve a gene/protein name (e.g. 'TP53', 'CD44') or UniProt accession to its 3D structure — returns the UniProt accession + AlphaFold model URL (and PDB when available). Great for a gene named in a paper's entities. Required: name.
references(k, id)- Get the papers that this paper cites (its bibliography). Use when the user asks 'what does X cite' or 'show me the references'. Required: id.
search_papers(k, query, year_max, year_min)- Search 8.5 million academic papers (arXiv + biomedical: PMC / bioRxiv / medRxiv, all disciplines) by topic, keyword, author, or linked entity (gene / protein / disease). Each hit returns id, title, TLDR, type, and links. Use to find papers about a topic, e.g. 'transformer efficiency' or 'CRISPR base editing'. Required: query.
similar_papers(k, id)- Find papers semantically similar to a given paper using SPECTER2 embeddings (trained on scientific-citation triplets). Returns nearest neighbors with TLDR. Use when the user wants 'papers like X' or 'what's adjacent to this work'. Required: id.
Last successful function declaration observed on . Source: https://mcp.tomesphere.com/api/mcp. We list what the server declared; we do not call any of these functions.
Endpoint status observed on . Source: https://mcp.tomesphere.com/api/mcp.
Signals
These are separate measurements of different things. They are deliberately not combined into one score, because a popularity number that mixes website traffic with saves and stars cannot be checked or acted on.
| Signal | Value | What it measures | Window | Observed | Source |
|---|---|---|---|---|---|
| Latest published version | 0.1.0 | Latest version string the maintainer published to the registry. | as of fetch | Model Context Protocol | |
| Registry record last updated | 2026-07-06 | When the registry record was last updated by its maintainer. | point in time | Model Context Protocol | |
| First listed in the MCP Registry | 2026-07-06 | Date this server was first published to the official MCP Registry. Not a usage or quality measure. | point in time | Model Context Protocol | |
| mcp tools declared | 9 tools | Number of functions the server itself declared when asked to list them. This is what the server offers an agent, not a measure of how well any of them work. | as of probe | mcp.tomesphere.com | |
| mcp endpoint status | ok | The server listed 9 functions when asked. | as of probe | mcp.tomesphere.com |
Where to get it
This record as data
Every field on this page, with its source and observation date, is in the catalog JSON. Fetch the whole kind at once instead of parsing this HTML.
GET /api/v1/entries/mcp_server.json