Noodle Biomedical Literature Discovery MCP
REMOTE · API.HELENA.BIO
Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.
Available components
Last scanned (22 hours ago)
Scores higher than 89% of remote servers
Reachable. Last reached 4 Nov 2026.
Category Health and Science
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. How we score → Why this is hard to score →
Endpoint Security66
- The endpoint's TLS certificate is valid, in date, and uses a strong key. View diagnostics → Pass
- No authorisation is required to call this server. Every tool declares its destructiveHint and none is destructive, so open access doesn't expose one. See how to fix → View diagnostics → Partial
- HTTPS enforcement could not be verified: the plaintext port answered with HTTP 404, which proves neither a plaintext path nor enforcement. View diagnostics → Unverified
- HSTS check failed: the Strict-Transport-Security header is absent. See how to fix → View diagnostics → Fail
- DNSSEC is configured correctly; the domain's records validate against the full chain to the root. View diagnostics → Pass
Transport & Reachability100
- Verified streamable-http transport via a live MCP handshake. View diagnostics → Pass
Schema Quality & AI Usability86
- 100% of prompts and resources have a non-trivial description (not blank, and not just the item's name).Pass
- AI-judged instruction clarity (excellent).Pass
- Tool/resource definitions use about 630 tokens (~78/item across 8 items; 7 tools + 1 resources), lean.Pass
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management100
- No destabilizing schema changes in the last 30 days.Pass
Tool Coverage100
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 100% of tool parameters carry a description.Pass
- Structured output schemas are declared (100% of tools); any adoption earns full credit.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 7 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 9 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a current MCP spec version (2026-07-28).Pass
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 28 Sept 26 0
- We updated how we score, so this day's move reflects our rubric, not a change to the server See what changed → functional
- 25 Sept 26 0
- We updated how we score, so this day's move reflects our rubric, not a change to the server See what changed → functional
- 4 Sept 26 0
- DNSSEC: fail → pass ▲ security
- 30 Aug 26 0
- Stability: unverified → 0.03 ▲ functional
- Server version: 0.2.0 → 0.2.1 functional
- 29 Aug 26 0
First indexed and scored.
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 4 Nov 2026 · Probed https://api.helena.bio/noodle/v1/mcp
TLS valid
Negotiated TLS 1.3 with TLS_AES_256_GCM_SHA384 .
| Subject | Issuer | Valid from | Valid until | Key | Signature | Serial |
|---|---|---|---|---|---|---|
| CN=api.helena.bio | CN=YE2,O=Let's Encrypt,C=US | 29 Sept 2026 | 28 Dec 2026 | ECDSA 256 | ECDSA-SHA384 | 6b9210a8b41dd3d82604250e423d06961d7 |
| SANs: api.helena.bio | ||||||
| CN=YE2,O=Let's Encrypt,C=US (CA) | CN=Root YE,O=ISRG,C=US | 3 Sept 2025 | 2 Sept 2028 | ECDSA 384 | ECDSA-SHA384 | 4df3b15dd6c0784c507cd37b58e6f115 |
| CN=Root YE,O=ISRG,C=US (CA) | CN=ISRG Root X2,O=Internet Security Research Group,C=US | 13 May 2026 | 2 Sept 2032 | ECDSA 384 | ECDSA-SHA384 | 872165fc34b6e5fba8add5b3705fb53a |
| CN=ISRG Root X2,O=Internet Security Research Group,C=US (CA) | CN=ISRG Root X1,O=Internet Security Research Group,C=US | 13 May 2026 | 2 Sept 2032 | ECDSA 384 | SHA256-RSA | 6c8f1dc727c7117f7baf853ac980f9cd |
Background: What to check on a remote MCP endpoint →
DNSSEC secure
Validation of api.helena.bio. — Secure
| Zone | DS | Keys | Algorithms | Outcome |
|---|---|---|---|---|
| . | trust_anchor | 20326, 38696 | 8, 8 | Verified |
| bio. | present | 5606 | 8 | Verified |
| helena.bio. | present | 17027 | 13 | Verified |
| api.helena.bio. | Verified address RRset verified with the apex keys |
Authentication No authorisation required
The endpoint answered without asking for a token. Anyone who knows the URL can reach it.
| Result | No authorisation required |
|---|---|
| HTTP status | 200 |
Background: How OAuth 2.1 works in the 2026 MCP spec →
Transports 2 probes
| Transport | URL | Outcome | Status | Location |
|---|---|---|---|---|
| streamable-http | https://api.helena.bio/noodle/v1/mcp | Verified | 200 | |
| http (plaintext) | http://api.helena.bio/noodle/v1/mcp | Inconclusive | 404 |
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
get_corpus_summary Get corpus summary ~37
Return public corpus coverage, source, freshness, and count metadata. Results are for literature discovery and professional review, not diagnosis or treatment.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| contract_version | string | yes | – |
| counts | – | yes | – |
| deduplication_keys | array | yes | – |
| generated_at | string | yes | – |
| scope | string | yes | – |
| sources | array | yes | – |
No examples provided.
get_publication_details Get publication details by PMID ~70
Retrieve one complete public bibliographic record by PMID after search. Results are for literature discovery and professional review, not diagnosis or treatment.
| Name | Type | Req | Description |
|---|---|---|---|
| pmid | string | yes | One PubMed identifier to look up in Noodle's current public corpus, as 1 to 12 digits without a PMID prefix. |
| Name | Type | Req | Description |
|---|---|---|---|
| contract_version | string | yes | – |
| publication | – | yes | – |
| usage_boundary | object | yes | – |
No examples provided.
get_publication_neighborhood Explore a PMID literature neighborhood ~72
Retrieve the bounded citation and semantic neighborhood around one PMID. Results are for literature discovery and professional review, not diagnosis or treatment.
| Name | Type | Req | Description |
|---|---|---|---|
| from_work_id | – | – | Optional prior work ID for a reversible graph path. |
| pmid | string | yes | One PubMed identifier, as 1 to 12 digits. |
| Name | Type | Req | Description |
|---|---|---|---|
| anchor_node_id | string | yes | – |
| anchor_pmid | – | – | – |
| anchor_work_id | – | – | – |
| contract_version | string | yes | – |
| edges | array | yes | – |
| freshness | string | yes | – |
| generated_at | string | yes | – |
| graph_version | string | yes | – |
| nodes | array | yes | – |
| policy_version | string | yes | – |
| release_channel | string | yes | – |
| stale_after | string | yes | – |
| usage_boundary | – | yes | – |
No examples provided.
get_work_details Get publication details by work ID ~52
Retrieve one complete public bibliographic record by Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.
| Name | Type | Req | Description |
|---|---|---|---|
| work_id | string | yes | Canonical Noodle Literature Corpus work identifier. |
| Name | Type | Req | Description |
|---|---|---|---|
| contract_version | string | yes | – |
| publication | – | yes | – |
| usage_boundary | object | yes | – |
No examples provided.
get_work_neighborhood Explore a work literature neighborhood ~72
Retrieve the bounded citation and semantic neighborhood around one Noodle work identifier. Results are for literature discovery and professional review, not diagnosis or treatment.
| Name | Type | Req | Description |
|---|---|---|---|
| from_work_id | – | – | Optional prior work ID for a reversible graph path. |
| work_id | string | yes | Canonical work identifier to place at the graph center. |
| Name | Type | Req | Description |
|---|---|---|---|
| anchor_node_id | string | yes | – |
| anchor_pmid | – | – | – |
| anchor_work_id | – | – | – |
| contract_version | string | yes | – |
| edges | array | yes | – |
| freshness | string | yes | – |
| generated_at | string | yes | – |
| graph_version | string | yes | – |
| nodes | array | yes | – |
| policy_version | string | yes | – |
| release_channel | string | yes | – |
| stale_after | string | yes | – |
| usage_boundary | – | yes | – |
No examples provided.
search_biomedical_literature Search biomedical literature ~173
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.
| Name | Type | Req | Description |
|---|---|---|---|
| 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 | yes | 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. |
| Name | Type | Req | Description |
|---|---|---|---|
| contract_version | string | yes | – |
| graph_degraded_reason | – | – | – |
| graph_used | boolean | – | – |
| graph_version | – | – | – |
| has_more | boolean | – | – |
| next_cursor | – | – | – |
| query | string | yes | – |
| results | array | yes | – |
| returned_count | integer | yes | – |
| searchable_fields | array | yes | – |
| semantic_degraded_reason | – | – | – |
| semantic_index_used | boolean | – | – |
| usage_boundary | object | yes | – |
No examples provided.
support_helena Support Helena's free scientific infrastructure ~35
Learn about the separate Helena Good MCP. This opt-in information action initiates no payment or outreach and changes no scientific result.
Input schema present but exposes no named parameters.
Structured output declared, but exposes no named fields.
No examples provided.
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.
remote · api.helena.bio
claude mcp add --transport http helena-bioinformatics-noodle 'https://api.helena.bio/noodle/v1/mcp'
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 84 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 4 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.