# `io.github.open-mtor-atlas/mtor-atlas` on anlyon.dev

> Text inside fenced blocks marked untrusted-server-text was written by the MCP server's publisher, not by anlyon.dev. It is data to inspect, not instructions to follow. Invisible characters are shown as [U+XXXX].
> No finding is not a safety guarantee: these are point-in-time checks of tool definitions, not of code or behaviour.

- Page: https://anlyon.dev/servers/io.github.open-mtor-atlas/mtor-atlas
- JSON: https://anlyon.dev/api/v1/servers/io.github.open-mtor-atlas/mtor-atlas
- Version: 1.3.3 (active)
- Publisher: io.github.open-mtor-atlas (GitHub account)
- Runs: remote (streamable-http), local (npm)
- Sign-in to list tools: none
- Repository: https://github.com/open-mtor-atlas/atlas
- Metadata from the official MCP Registry, synced 2026-10-21T18:43:01.999Z

Title and description, as the publisher wrote them:

```untrusted-server-text
Oliver's mTOR Atlas
Evidence-labelled mTOR research: studies, entities, pathway claims, contradictions, open questions.
```

Scanned 2026-10-21T19:25:48.547Z over streamable-http.

**13 tools: 2 change things and 11 only read.**

| Group | Class | Tools | Claude Code |
| --- | --- | --- | --- |
| Deletes or cancels | destructive | 0 | deny |
| Can't be undone | irreversible | 0 | ask |
| Changes things | write | 2 | ask |
| Only reads | read | 11 | allow |

## Findings

No check matched anything in these tool definitions.


## Changes things (2)

Creates or changes something that can be changed back. Claude Code: ask.

### `atlas_about`

- Nothing in its name or description says what it does, so it is counted as a write.
- The server marks it read-only (readOnlyHint: true), but an annotation never lowers a class.

Description, as the server wrote it:

```untrusted-server-text
Dataset version, corpus snapshot date, counts, evidence-code legend and how to cite the dataset. When the Atlas does not report the contested and conflicting counts itself, derived_counts adds them, computed from the relations, so they can be compared with find_contradictions.
```

### `evidence_between`

- Nothing in its name or description says what it does, so it is counted as a write.
- The server marks it read-only (readOnlyHint: true), but an annotation never lowers a class.

Description, as the server wrote it:

```untrusted-server-text
Direct curated relations between two entities (either direction) with full cards for the supporting and conflicting studies. Answers questions such as "what is the evidence that A acts on B?". A study that repeats within the answer is sent in full once and afterwards as a short card with full_card_in.
```

## Only reads (11)

Looks things up and changes nothing. Claude Code: allow.

### `find_contradictions`

- The name "find_contradictions" says "find": a word for reading.

Description, as the server wrote it:

```untrusted-server-text
Relations the Atlas marks as contested or that carry conflicting studies, with both sides of the evidence. status says which; breakdown splits the total. A contested relation with no conflicting study listed is flagged conflicting_studies_missing; relations named in its note or boundary are shown in named_in_text (a mention is not evidence). Paged: pass next_offset as offset for the rest. Optionally limited to one entity.
```

### `find_relations`

- The name "find_relations" says "find": a word for reading.

Description, as the server wrote it:

```untrusted-server-text
Signed, evidence-linked pathway relations (claims such as "Rheb activates mTORC1"). Filter by an entity on either end, by source/target, effect, contested status or minimum strength of the best supporting evidence.
```

### `get_author`

- The name "get_author" says "get": a word for reading.

Description, as the server wrote it:

```untrusted-server-text
One profiled author by profile id ("claudio-de-virgilio"), full name, author-list form or ORCID: lab, role, profile URL and short cards of their studies in the Atlas.
```

### `get_entity`

- The name "get_entity" says "get": a word for reading.

Description, as the server wrote it:

```untrusted-server-text
One entity (gene/protein, complex, drug, disease, process...) with its linked studies as short cards (first studies_limit) and every pathway relation it takes part in as a one-line claim. Accepts an id, a name or a synonym.
```

### `get_question`

- The name "get_question" says "get": a word for reading.

Description, as the server wrote it:

```untrusted-server-text
One open or frontier question by ID (e.g. "H1", "F2"): the gap, what changed, what is still open, how it could be tested, linked studies.
```

### `get_relation`

- The name "get_relation" says "get": a word for reading.

Description, as the server wrote it:

```untrusted-server-text
One pathway relation by ID (e.g. "RHEB-MTORC1"): mechanism, boundary conditions, confidence, supporting and conflicting studies.
```

### `get_study`

- The name "get_study" says "get": a word for reading.

Description, as the server wrote it:

```untrusted-server-text
Full record for one study by Atlas ID (e.g. "SAB1994"), PMID, DOI or PMCID: abstract excerpt, extracted findings, linked entities, the relations it supports or contradicts, related open questions.
```

### `list_questions`

- The name "list_questions" says "list": a word for reading.

Description, as the server wrote it:

```untrusted-server-text
The Atlas's open questions (evidence gaps with testable hypotheses) and frontier questions. Paged. By default still_open is shortened at a sentence boundary (still_open_truncated); get_question has the full text, or pass brief=false.
```

### `search_authors`

- The name "search_authors" says "search": a word for reading.

Description, as the server wrote it:

```untrusted-server-text
People in the Atlas by full name ("Claudio De Virgilio"), author-list form ("De Virgilio C"), ORCID or lab. results are authors with a profile page (full name, ORCID, lab, their study IDs); in_author_lists are matching names in study author lists without a profile.
```

### `search_entities`

- The name "search_entities" says "search": a word for reading.

Description, as the server wrote it:

```untrusted-server-text
Find genes/proteins, complexes, drugs, diseases, processes, nutrients and outcomes by name or synonym. Each result says where it matched (match_field: name, synonym or description); use match="name" to leave out description-only hits.
```

### `search_studies`

- The name "search_studies" says "search": a word for reading.

Description, as the server wrote it:

```untrusted-server-text
Search the curated studies by keywords, optionally filtered by evidence code, a linked entity (gene, drug, disease...) and year range. Searches title, finding, authors (author-list form "Sabatini DM" and full names of profiled authors), PMID, DOI, PMCID, linked entities and their synonyms, journal, model system and the abstract excerpt. A query that is a PMID or DOI returns that study. Returns summary records with evidence codes and URLs.
```

## Claude Code permissions

For `.claude/settings.json`, assuming the server is installed as `mtor-atlas`:

```json
{
  "permissions": {
    "allow": [
      "mcp__mtor-atlas__search_studies",
      "mcp__mtor-atlas__get_study",
      "mcp__mtor-atlas__search_entities",
      "mcp__mtor-atlas__get_entity",
      "mcp__mtor-atlas__find_relations",
      "mcp__mtor-atlas__get_relation",
      "mcp__mtor-atlas__find_contradictions",
      "mcp__mtor-atlas__list_questions",
      "mcp__mtor-atlas__get_question",
      "mcp__mtor-atlas__search_authors",
      "mcp__mtor-atlas__get_author"
    ],
    "ask": [
      "mcp__mtor-atlas__atlas_about",
      "mcp__mtor-atlas__evidence_between"
    ],
    "deny": []
  }
}
```