# com.tomesphere/tomesphere

> Search 8.5M scientific papers with LLM TLDRs, citations, linked entities, figures, and full text.

- name: com.tomesphere/tomesphere
- version: 0.1.0
- connection class: unknown (unknown)
- trust: 54/100 flags: no-repository
- quality: 85/100 (good)
- owner: not claimed
- descriptor: https://api.protogrid.dev/v1/servers/com.tomesphere%2Ftomesphere
- tools: https://api.protogrid.dev/v1/servers/com.tomesphere%2Ftomesphere/tools

**Not classified yet.** The remote endpoints have not been probed successfully, or the listing has nothing to connect to.

## Connection (mcpServers)

```json
{
  "mcpServers": {
    "tomesphere": {
      "type": "http",
      "url": "https://mcp.tomesphere.com/api/mcp"
    }
  }
}
```


## Trust

- hygiene: 80
- liveness: 27
- freshness: 65
- provenance: 55
- drivers: +dns-namespace +website -unreachable(1 failures) ~updated-106d-ago -no-repository
- Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed.

## Quality 85/100 (good)

### protocol: 75 (weight 25)

- warn `protocol.modern`: newest supported version is 2025-03-26; 2026-07-28 not supported, older versions are deprecated until 2027-07-28
- n/a `protocol.stateless`: only applies to 2026-07-28 servers
- pass `protocol.transport`: streamable HTTP
- n/a `protocol.list_ttl`: only applies to 2026-07-28 servers

### authorization: n/a (weight 15)

- n/a `auth.prm`, `auth.as_metadata`, `auth.cimd`: no remote uses OAuth
- n/a `auth.secret_in_url`: no templated URL

### tool hygiene: 86 (weight 30)

- pass `tools.descriptions`: every tool has a description
- pass `tools.description_length`: descriptions are concise
- pass `tools.schemas`: every tool has an object input schema
- pass `tools.annotations`: 9 of 9 tools declare readOnlyHint or destructiveHint
- fail `tools.directory_hints`: no tool declares all four of readOnlyHint, destructiveHint, idempotentHint and openWorldHint; missing: citations (destructiveHint, idempotentHint); get_entities (destructiveHint, idempotentHint); get_paper (destructiveHint, idempotentHint); …
- pass `tools.token_cost`: about 1,140 tokens to load every tool
- pass `tools.api_dump`: tools are not a one-to-one API dump

### stability: 100 (weight 15)

- pass `stability.changes`: no tool changes in 30 days
- pass `stability.rug_pull`: no tool changed its meaning under the same name

### dependencies: n/a (weight 15)

- n/a `deps.known_vulns`, `deps.mcp_sdk_version`, `deps.resolvable`: no npm or PyPI package

- tools: 9, about 1,140 tokens to load them all
- tool set hash: 573f2e31c8b27cf95799b0da8872ad57
- badge: [![protogrid quality](https://protogrid.dev/badge/com.tomesphere/tomesphere.svg)](https://protogrid.dev/servers/com.tomesphere/tomesphere)
- Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed.

### Tool changes

_No tool definition changes recorded._

## Remotes

- https://mcp.tomesphere.com/api/mcp (streamable-http, auth none, reachable false, uptime30d 0.93043476)

## Packages

_none_

## Tools (9)

- `citations`: 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.
- `get_entities`: 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.
- `get_figures`: 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.
- `get_full_text`: 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/…).
- `get_paper`: 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.
- `get_structure`: 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.
- `references`: Get the papers that this paper cites (its bibliography). Use when the user asks 'what does X cite' or 'show me the references'.
- `search_papers`: 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'.
- `similar_papers`: 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'.