# com.tomesphere/tomesphere (remote · mcp.tomesphere.com)

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

- Trust score: 66/100 (medium)
- Change this week: +3
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-08-03

## Components

- remote · `mcp.tomesphere.com`: 66/100 (this document), [markdown](https://verifymcp.io/servers/com-tomesphere-tomesphere/api-mcp.md), [page](https://verifymcp.io/servers/com-tomesphere-tomesphere/api-mcp)

## Channel facts

- Endpoint: `https://mcp.tomesphere.com/api/mcp`
- Transports: `streamable-http`
- Auth: `none`
- Version: `0.1.0`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically against the live server, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-08-03.

- **Endpoint Security**: 63/100
  - The endpoint's TLS certificate is valid, in date, and uses a strong key.
  - Authorisation not fully verified: no authorisation is required to call this server, and 9 tool(s) never declared a destructiveHint. The MCP spec treats an absent hint as destructive by default, so we cannot call this surface safe.
  - HTTPS is enforced; there's no plaintext access path.
  - The HSTS (Strict-Transport-Security) header is present.
  - DNSSEC check failed: this domain isn't protected by DNSSEC.
- **Transport & Reachability**: 100/100
  - Verified streamable-http transport via a live MCP handshake.
- **Schema Quality & AI Usability**: 76/100
  - AI-judged instruction clarity (excellent).
  - Context-footprint check failed: tool/resource definitions use about 1029 tokens (~114/item across 9 items; 9 tools + 0 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 27/100
  - Stability observed for 8 of 30 days with no destabilising changes; credit accrues until the full window elapses.
- **Tool Coverage**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% of tool parameters carry a description.
- **Capabilities**: 40/100
  - Spec-recency check failed: implements MCP spec 2025-03-26; the latest is 2026-07-28.

## Install

### Claude

```bash
claude mcp add --transport http com-tomesphere-tomesphere https://mcp.tomesphere.com/api/mcp
```

### Codex

```toml
[mcp_servers.com-tomesphere-tomesphere]
url = "https://mcp.tomesphere.com/api/mcp"
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "com-tomesphere-tomesphere": {
      "type": "remote",
      "url": "https://mcp.tomesphere.com/api/mcp",
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add com-tomesphere-tomesphere --url https://mcp.tomesphere.com/api/mcp --transport streamable-http
```

### Hermes

```yaml
mcp_servers:
  com-tomesphere-tomesphere:
    url: "https://mcp.tomesphere.com/api/mcp"
```

### Other

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

The mcpServers block is a cross-client convention. Remote transports vary, so check your client's docs.

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-08-02 (score 66, +1)

No change was recorded against any check on this day. Stability & Change Management went from 20 to 23. That category is still filling its 30-day observation window: 6 days of observed history at the previous scan, 7 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-07-31 (score 65, 0)

- [functional] We updated how we score, so this day's move reflects our rubric, not a change to the server

### 2026-07-30 (score 65, +1)

No change was recorded against any check on this day. Stability & Change Management went from 10 to 13. That category is still filling its 30-day observation window: 3 days of observed history at the previous scan, 4 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-07-28 (score 64, +1)

No change was recorded against any check on this day. Stability & Change Management went from 3 to 7. That category is still filling its 30-day observation window: 1 days of observed history at the previous scan, 2 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-07-27 (score 63, +1)

- [functional] We updated how we score, so this day's move reflects our rubric, not a change to the server

### 2026-07-26 (score 62)

First indexed and scored.

## MCP tools (9)

### `search_papers` (~170 tokens)

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'.

Input parameters:

- `k` (integer): Number of results (default 10, max 25).
- `query` (string, required): Natural-language search query. E.g. 'transformer attention efficiency', 'graph neural networks for molecular property prediction'.
- `year_max` (integer): Latest publication year.
- `year_min` (integer): Earliest publication year, e.g. 2024.

### `get_paper` (~149 tokens)

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.

Input parameters:

- `id` (string, required): arXiv ID like '2401.12345' or OpenAlex Work ID like 'W4390723197'.

### `similar_papers` (~93 tokens)

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'.

Input parameters:

- `id` (string, required): arXiv ID or OpenAlex Work ID.
- `k` (integer): Number of neighbors (default 10, max 25).

### `citations` (~92 tokens)

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.

Input parameters:

- `id` (string, required): arXiv ID or OpenAlex Work ID.
- `k` (integer): Max citing papers (default 25, max 100).

### `references` (~69 tokens)

Get the papers that this paper cites (its bibliography). Use when the user asks 'what does X cite' or 'show me the references'.

Input parameters:

- `id` (string, required): arXiv ID or OpenAlex Work ID.
- `k` (integer): Max references (default 25, max 100).

### `get_full_text` (~103 tokens)

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/…).

Input parameters:

- `id` (string, required): arXiv ID, PMC ID, or 10.1101/… DOI.

### `get_figures` (~82 tokens)

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.

Input parameters:

- `id` (string, required): arXiv ID, PMC ID, or 10.1101/… DOI.

### `get_entities` (~87 tokens)

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.

Input parameters:

- `id` (string, required): arXiv ID, PMC ID, or 10.1101/… DOI.

### `get_structure` (~91 tokens)

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.

Input parameters:

- `name` (string, required): Gene/protein symbol (TP53, CD44) or UniProt accession (P04637).

## Diagnostics

Captured diagnostic sections: TLS, DNSSEC, Authorisation, Transports. The full working is on the page: https://verifymcp.io/servers/com-tomesphere-tomesphere/api-mcp#diagnostics

## Score history

- 2026-08-03: 66
- 2026-08-02: 66
- 2026-08-01: 65
- 2026-07-31: 65
- 2026-07-30: 65
- 2026-07-29: 64
- 2026-07-28: 64
- 2026-07-27: 63
- 2026-07-26: 62

## Links

- Remote endpoint: https://mcp.tomesphere.com/api/mcp
- Website: https://tomesphere.com/mcp
- Changelog RSS feed: https://verifymcp.io/servers/com-tomesphere-tomesphere/api-mcp/changelog.xml
- Changelog JSON feed: https://verifymcp.io/servers/com-tomesphere-tomesphere/api-mcp/changelog.json
- HTML version of this page: https://verifymcp.io/servers/com-tomesphere-tomesphere/api-mcp