# Noodle Biomedical Literature Discovery MCP (remote · api.helena.bio)

Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.

- Trust score: 81/100 (high trust)
- Change this week: +4
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-09-21

## Components

- remote · `api.helena.bio`: 81/100 (this document), [markdown](https://verifymcp.io/servers/helena-bioinformatics-noodle/noodle-v1-mcp.md), [page](https://verifymcp.io/servers/helena-bioinformatics-noodle/noodle-v1-mcp)

## Channel facts

- Endpoint: `https://api.helena.bio/noodle/v1/mcp`
- Transports: `streamable-http`
- Auth: `none`
- Version: `0.2.1`

## 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 2026-09-21.

- **Endpoint Security**: 66/100
  - The endpoint's TLS certificate is valid, in date, and uses a strong key.
  - No authorisation is required to call this server. Every tool declares its destructiveHint and none is destructive, so open access doesn't expose one.
  - HTTPS enforcement could not be verified: the plaintext port answered with HTTP 404, which proves neither a plaintext path nor enforcement.
  - HSTS check failed: the Strict-Transport-Security header is absent.
  - DNSSEC is configured correctly; the domain's records validate against the full chain to the root.
- **Transport & Reachability**: 100/100
  - Verified streamable-http transport via a live MCP handshake.
- **Schema Quality & AI Usability**: 86/100
  - 100% of prompts and resources have a non-trivial description (not blank, and not just the item's name).
  - AI-judged instruction clarity (excellent).
  - Tool/resource definitions use about 630 tokens (~78/item across 8 items; 7 tools + 1 resources), lean.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 77/100
  - Stability observed for 23 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.
  - Structured output schemas are declared (100% of tools); any adoption earns full credit.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 7 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 9 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a current MCP spec version (2026-07-28).

## Install

### How do I install the Noodle Biomedical Literature Discovery MCP server?

Noodle Biomedical Literature Discovery MCP is a hosted endpoint at https://api.helena.bio/noodle/v1/mcp, so there is nothing to install locally. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add --transport http helena-bioinformatics-noodle 'https://api.helena.bio/noodle/v1/mcp'
```

### Cursor

```json
{
  "mcpServers": {
    "helena-bioinformatics-noodle": {
      "url": "https://api.helena.bio/noodle/v1/mcp"
    }
  }
}
```

### VS Code

```json
{
  "servers": {
    "helena-bioinformatics-noodle": {
      "type": "http",
      "url": "https://api.helena.bio/noodle/v1/mcp"
    }
  }
}
```

### Codex

```toml
[mcp_servers.helena-bioinformatics-noodle]
url = "https://api.helena.bio/noodle/v1/mcp"
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "helena-bioinformatics-noodle": {
      "type": "remote",
      "url": "https://api.helena.bio/noodle/v1/mcp",
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add helena-bioinformatics-noodle --url 'https://api.helena.bio/noodle/v1/mcp' --transport streamable-http
```

### Hermes

```yaml
mcp_servers:
  helena-bioinformatics-noodle:
    url: "https://api.helena.bio/noodle/v1/mcp"
```

### Netclaw

```json
{
  "McpServers": {
    "helena-bioinformatics-noodle": {
      "Transport": "http",
      "Url": "https://api.helena.bio/noodle/v1/mcp"
    }
  }
}
```

### Vellum

```bash
assistant mcp add helena-bioinformatics-noodle -t streamable-http -u 'https://api.helena.bio/noodle/v1/mcp'
```

### Other

```json
{
  "mcpServers": {
    "helena-bioinformatics-noodle": {
      "type": "http",
      "url": "https://api.helena.bio/noodle/v1/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.

### 2026-09-21 (score 81, +1)

No change was recorded against any check on this day. Stability & Change Management went from 73 to 77. That category is still filling its 30-day observation window: 22 days of observed history at the previous scan, 23 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-09-19 (score 80, +1)

No change was recorded against any check on this day. Stability & Change Management went from 67 to 70. That category is still filling its 30-day observation window: 20 days of observed history at the previous scan, 21 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-09-17 (score 79, +1)

No change was recorded against any check on this day. Stability & Change Management went from 60 to 63. That category is still filling its 30-day observation window: 18 days of observed history at the previous scan, 19 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-09-15 (score 78, +1)

No change was recorded against any check on this day. Stability & Change Management went from 53 to 57. That category is still filling its 30-day observation window: 16 days of observed history at the previous scan, 17 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-09-13 (score 77, +1)

No change was recorded against any check on this day. Stability & Change Management went from 47 to 50. That category is still filling its 30-day observation window: 14 days of observed history at the previous scan, 15 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-09-11 (score 76, +1)

No change was recorded against any check on this day. Stability & Change Management went from 40 to 43. That category is still filling its 30-day observation window: 12 days of observed history at the previous scan, 13 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-09-08 (score 75, +1)

No change was recorded against any check on this day. Stability & Change Management went from 30 to 33. That category is still filling its 30-day observation window: 9 days of observed history at the previous scan, 10 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-09-06 (score 74, +1)

No change was recorded against any check on this day. Stability & Change Management went from 23 to 27. That category is still filling its 30-day observation window: 7 days of observed history at the previous scan, 8 at this one. The score rises as the window fills, whether or not the server changes.

## MCP tools (7)

### `search_biomedical_literature` (~173 tokens)

Search biomedical literature

Semantically search Noodle's public PubMed-derived biomedical corpus. Include known PMID, DOI, or PMCID identifiers in the query so they can act as exact anchors. Results are for literature discovery and professional review, not diagnosis or treatment.

Input parameters:

- `cursor`: Opaque continuation cursor from the preceding response for the same query and sort order; omit for the first page.
- `limit` (integer): Maximum number of publications to return, from 1 to 25.
- `query` (string, required): Natural-language literature question or exact PMID, DOI, PMCID, gene, variant, phenotype, HPO, or OMIM query. Include every known publication identifier when comparing or finding related papers.
- `sort` (string): Result ordering: relevance-ranked, newest publication first, or oldest publication first.

Output parameters:

- `contract_version` (string)
- `graph_degraded_reason`
- `graph_used` (boolean)
- `graph_version`
- `has_more` (boolean)
- `next_cursor`
- `query` (string)
- `results` (array)
- `returned_count` (integer)
- `searchable_fields` (array)
- `semantic_degraded_reason`
- `semantic_index_used` (boolean)
- `usage_boundary` (object)

### `get_publication_details` (~70 tokens)

Get publication details by PMID

Retrieve one complete public bibliographic record by PMID after search. Results are for literature discovery and professional review, not diagnosis or treatment.

Input parameters:

- `pmid` (string, required): One PubMed identifier to look up in Noodle's current public corpus, as 1 to 12 digits without a PMID prefix.

Output parameters:

- `contract_version` (string)
- `publication`
- `usage_boundary` (object)

### `get_work_details` (~52 tokens)

Get publication details by work ID

Retrieve one complete public bibliographic record by Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.

Input parameters:

- `work_id` (string, required): Canonical Noodle Literature Corpus work identifier.

Output parameters:

- `contract_version` (string)
- `publication`
- `usage_boundary` (object)

### `get_publication_neighborhood` (~72 tokens)

Explore a PMID literature neighborhood

Retrieve the bounded citation and semantic neighborhood around one PMID. Results are for literature discovery and professional review, not diagnosis or treatment.

Input parameters:

- `from_work_id`: Optional prior work ID for a reversible graph path.
- `pmid` (string, required): One PubMed identifier, as 1 to 12 digits.

Output parameters:

- `anchor_node_id` (string)
- `anchor_pmid`
- `anchor_work_id`
- `contract_version` (string)
- `edges` (array)
- `freshness` (string)
- `generated_at` (string)
- `graph_version` (string)
- `nodes` (array)
- `policy_version` (string)
- `release_channel` (string)
- `stale_after` (string)
- `usage_boundary`

### `get_work_neighborhood` (~72 tokens)

Explore a work literature neighborhood

Retrieve the bounded citation and semantic neighborhood around one Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.

Input parameters:

- `from_work_id`: Optional prior work ID for a reversible graph path.
- `work_id` (string, required): Canonical work identifier to place at the graph center.

Output parameters:

- `anchor_node_id` (string)
- `anchor_pmid`
- `anchor_work_id`
- `contract_version` (string)
- `edges` (array)
- `freshness` (string)
- `generated_at` (string)
- `graph_version` (string)
- `nodes` (array)
- `policy_version` (string)
- `release_channel` (string)
- `stale_after` (string)
- `usage_boundary`

### `get_corpus_summary` (~37 tokens)

Get corpus summary

Return public corpus coverage, source, freshness, and count metadata. Results are for literature discovery and professional review, not diagnosis or treatment.

Output parameters:

- `contract_version` (string)
- `counts`
- `deduplication_keys` (array)
- `generated_at` (string)
- `scope` (string)
- `sources` (array)

### `support_helena` (~35 tokens)

Support Helena's free scientific infrastructure

Learn about the separate Helena Good MCP. This opt-in information action initiates no payment or outreach and changes no scientific result.

## Diagnostics

Captured diagnostic sections: TLS, DNSSEC, Authorisation, Transports. The full working is on the page: https://verifymcp.io/servers/helena-bioinformatics-noodle/noodle-v1-mcp#diagnostics

## Score history

- 2026-09-21: 81
- 2026-09-20: 80
- 2026-09-19: 80
- 2026-09-18: 79
- 2026-09-17: 79
- 2026-09-16: 78
- 2026-09-15: 78
- 2026-09-14: 77
- 2026-09-13: 77
- 2026-09-12: 76
- 2026-09-11: 76
- 2026-09-10: 75
- 2026-09-09: 75
- 2026-09-08: 75
- 2026-09-07: 74
- 2026-09-06: 74
- 2026-09-05: 73
- 2026-09-04: 73
- 2026-09-03: 71
- 2026-09-02: 71
- 2026-09-01: 70
- 2026-08-31: 70
- 2026-08-30: 69
- 2026-08-29: 69

## Common questions

### What is the Noodle Biomedical Literature Discovery MCP server?

Noodle Biomedical Literature Discovery MCP is listed in the public MCP registry as io.github.helena-bioinformatics/noodle. Search biomedical papers, inspect publication records, and traverse citation or semantic graphs. This page covers its hosted endpoint (https://api.helena.bio/noodle/v1/mcp).

### Is the Noodle Biomedical Literature Discovery MCP server safe to use?

Noodle Biomedical Literature Discovery MCP scores 81 out of 100 on VerifyMCP. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.

### What tools does the Noodle Biomedical Literature Discovery MCP server expose?

Noodle Biomedical Literature Discovery MCP exposes 7 tools: search_biomedical_literature, get_publication_details, get_work_details, get_publication_neighborhood, get_work_neighborhood, and 2 more. Their descriptions and schemas cost roughly 511 tokens of context every time the server is loaded.

### Does the Noodle Biomedical Literature Discovery MCP server require authentication?

No. We connected to Noodle Biomedical Literature Discovery MCP without credentials and it answered, so anything it exposes is reachable by anyone who knows the address.

### Is the Noodle Biomedical Literature Discovery MCP server still maintained?

Noodle Biomedical Literature Discovery MCP is still listed as active in the MCP registry. We last reached this channel on 21 September 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

## Links

- Remote endpoint: https://api.helena.bio/noodle/v1/mcp
- Repository: https://github.com/helena-bioinformatics/noodle-mcp
- Website: https://noodle.helena.bio/
- Changelog RSS feed: https://verifymcp.io/servers/helena-bioinformatics-noodle/noodle-v1-mcp.xml
- Changelog JSON feed: https://verifymcp.io/servers/helena-bioinformatics-noodle/noodle-v1-mcp.json
- HTML version of this page: https://verifymcp.io/servers/helena-bioinformatics-noodle/noodle-v1-mcp