Oliver's mTOR Atlas MCP

An MCP server that provides AI assistants with tools to search mTOR Atlas studies by evidence code, look up evidence for pathway claims including supporting and contradicting studies, and list contested claims and open questions. It connects to a hosted server or can be run locally via npm.

Visit Oliver's mTOR Atlas

Endpoint and access

No sign-in to connect and list tools. Individual tools may still need a vendor account, credentials, or permissions; check the documented prerequisites.

Community listingStreamable HTTPNo sign-inEndpoint checked 2026-11-07Published by Oliver's mTOR Atlas

MCP endpoint (Streamable HTTP)

https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp

Vendor documentation

What its tools do

13 tools, grouped by the hints the server advertises. Hints are self-declared, not verified behavior.

13 of 13 have a description · 13 of 13 declare behavior hints · 5 of 12 with parameters document them all

Checks and signals

Each line is separate evidence, not a trust score.

Passed Endpoint answered the live check · Nov 7, 2026, 1:19 PM UTC
Availability 1 of 1 checks passed in 30 days

What you can do with it

Search studies by evidence code
Look up evidence for a pathway claim with supporting and contradicting studies
List contested claims and open questions

Source and maintenance

Community listingRegistry 1.3.3

mcp-registry: io.github.open-mtor-atlas/mtor-atlas@1.3.3 Source repository Project website

Maintenance checked: Nov 7, 2026, 12:25 PM UTC

Protocol and capabilities

Server: mtor-atlas 1.3.3
MCP protocol negotiated in check: 2025-11-25
Tools: 13 advertised
Resources: Not advertised
Resource templates: Not advertised
Prompts: Not advertised

Server-advertised capabilities

{
  "tools": {
    "listChanged": true
  }
}

Server-provided instructions

Untrusted server output shown for inspection. It is not Koskamo guidance and is excluded from knowledge search.

Oliver's mTOR Atlas is a curated, evidence-labelled corpus of mTOR research (studies, entities, signed pathway relations, open questions). How to use it well: - Every study has an evidence code: S synthesis of human data, H human study, A animal model, M molecular/in vitro, R review, PP preprint, RT registered trial. The code describes the KIND of study, not its quality. Do not present an M finding as if it were shown in people. - A relation is a claim (source -> effect -> target) with supporting and conflicting studies, boundary conditions, a consensus flag and a human-relevance grade. Quote the boundary when you use a relation. - "Not in the Atlas" means not in this curated corpus, not "not known". Say so. - An empty search is not proof that something is missing. Look up a person with search_authors or get_author, and a paper with get_study by PMID or DOI, before saying the Atlas does not have it. - Cite the study or relation 'url' fields, and the dataset (doi:10.5281/zenodo.22059963) with the dataset_version, corpus_snapshot and source_commit from atlas_about. A dataset_version ending in "+unreleased" means the live data are newer than the archived Zenodo version; do not cite that version DOI for them.

Tools

13 advertised

atlas_about — About the Atlas

Advertised by the server during the last successful anonymous check.

Advertised read-only

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.

atlas_about input schema

{
  "type": "object",
  "properties": {}
}

atlas_about annotations

{
  "title": "About the Atlas",
  "readOnlyHint": true,
  "openWorldHint": false,
  "idempotentHint": true,
  "destructiveHint": false
}

search_studies — Search studies

Advertised by the server during the last successful anonymous check.

Advertised read-only

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.

search_studies input schema

{
  "type": "object",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "properties": {
    "limit": {
      "type": "integer",
      "default": 20,
      "maximum": 9007199254740991,
      "minimum": 1,
      "description": "Maximum 50; a larger value is capped at 50."
    },
    "query": {
      "type": "string",
      "description": "Keywords, e.g. \"rapamycin lifespan mice\", a person (\"Claudio De Virgilio\"), a PMID or a DOI. Omit to list by filters only."
    },
    "entity": {
      "type": "string",
      "description": "Only studies linked to this entity (name, synonym or id), e.g. \"Rheb\"."
    },
    "offset": {
      "type": "integer",
      "default": 0,
      "maximum": 9007199254740991,
      "minimum": 0,
      "description": "For the next page: pass next_offset from the previous answer."
    },
    "year_to": {
      "type": "integer",
      "maximum": 9007199254740991,
      "minimum": -10000
    },
    "year_from": {
      "type": "integer",
      "maximum": 9007199254740991,
      "minimum": -10000
    },
    "evidence_code": {
      "type": "array",
      "items": {
        "enum": [
          "S",
          "H",
          "A",
          "M",
          "R",
          "PP",
          "RT"
        ],
        "type": "string"
      },
      "description": "Keep only these evidence codes, e.g. [\"H\",\"S\"] for human evidence."
    }
  }
}

search_studies annotations

{
  "title": "Search studies",
  "readOnlyHint": true,
  "openWorldHint": false,
  "idempotentHint": true,
  "destructiveHint": false
}

get_study — Get one study

Advertised by the server during the last successful anonymous check.

Advertised read-only

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.

get_study input schema

{
  "type": "object",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "properties": {
    "id": {
      "type": "string",
      "description": "Alias of sid."
    },
    "doi": {
      "type": "string",
      "description": "Alias of sid, for a DOI."
    },
    "sid": {
      "type": "string",
      "description": "Atlas study ID (\"SAB1994\"), PMID (\"23716719\"), DOI or PMCID"
    },
    "pmid": {
      "type": "string",
      "description": "Alias of sid, for a PMID."
    },
    "pmcid": {
      "type": "string",
      "description": "Alias of sid, for a PMCID."
    },
    "study_id": {
      "type": "string",
      "description": "Alias of sid."
    }
  }
}

get_study annotations

{
  "title": "Get one study",
  "readOnlyHint": true,
  "openWorldHint": false,
  "idempotentHint": true,
  "destructiveHint": false
}

search_entities — Search entities

Advertised by the server during the last successful anonymous check.

Advertised read-only

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_entities input schema

{
  "type": "object",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "required": [
    "query"
  ],
  "properties": {
    "type": {
      "type": "string",
      "description": "Optional type filter, e.g. \"Drug\", \"Gene/Protein\", \"Disease\""
    },
    "limit": {
      "type": "integer",
      "default": 20,
      "maximum": 9007199254740991,
      "minimum": 1,
      "description": "Maximum 100; a larger value is capped at 100."
    },
    "match": {
      "enum": [
        "any",
        "name"
      ],
      "type": "string",
      "default": "any",
      "description": "\"any\" also searches descriptions; \"name\" searches names and synonyms only."
    },
    "query": {
      "type": "string",
      "description": "Name or synonym, e.g. \"raptor\", \"sirolimus\""
    },
    "offset": {
      "type": "integer",
      "default": 0,
      "maximum": 9007199254740991,
      "minimum": 0,
      "description": "For the next page: pass next_offset from the previous answer."
    }
  }
}

search_entities annotations

{
  "title": "Search entities",
  "readOnlyHint": true,
  "openWorldHint": false,
  "idempotentHint": true,
  "destructiveHint": false
}

get_entity — Get one entity

Advertised by the server during the last successful anonymous check.

Advertised read-only

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_entity input schema

{
  "type": "object",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "properties": {
    "id": {
      "type": "string",
      "description": "Alias of entity."
    },
    "entity": {
      "type": "string",
      "description": "e.g. \"mTORC1\", \"Rheb\", \"rapamycin\""
    },
    "studies_limit": {
      "type": "integer",
      "default": 25,
      "maximum": 9007199254740991,
      "minimum": 0,
      "description": "Maximum 50; a larger value is capped at 50."
    }
  }
}

get_entity annotations

{
  "title": "Get one entity",
  "readOnlyHint": true,
  "openWorldHint": false,
  "idempotentHint": true,
  "destructiveHint": false
}

find_relations — Find pathway relations

Advertised by the server during the last successful anonymous check.

Advertised read-only

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.

find_relations input schema

{
  "type": "object",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "properties": {
    "limit": {
      "type": "integer",
      "default": 20,
      "maximum": 9007199254740991,
      "minimum": 1,
      "description": "Maximum 50; a larger value is capped at 50."
    },
    "effect": {
      "enum": [
        "activates",
        "inhibits",
        "binds",
        "recruits",
        "required-for",
        "context-dependent",
        "no-effect"
      ],
      "type": "string"
    },
    "entity": {
      "type": "string",
      "description": "Entity on either end of the relation"
    },
    "offset": {
      "type": "integer",
      "default": 0,
      "maximum": 9007199254740991,
      "minimum": 0,
      "description": "For the next page: pass next_offset from the previous answer."
    },
    "source": {
      "type": "string"
    },
    "target": {
      "type": "string"
    },
    "contested_only": {
      "type": "boolean",
      "description": "Only relations marked contested or with conflicting studies"
    },
    "strongest_at_least": {
      "enum": [
        "S",
        "H",
        "A",
        "M",
        "R",
        "PP",
        "RT"
      ],
      "type": "string",
      "description": "Keep relations whose best supporting study is at least this code in the order S > H > A > M"
    }
  }
}

find_relations annotations

{
  "title": "Find pathway relations",
  "readOnlyHint": true,
  "openWorldHint": false,
  "idempotentHint": true,
  "destructiveHint": false
}

get_relation — Get one relation

Advertised by the server during the last successful anonymous check.

Advertised read-only

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

get_relation input schema

{
  "type": "object",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "required": [
    "id"
  ],
  "properties": {
    "id": {
      "type": "string"
    }
  }
}

get_relation annotations

{
  "title": "Get one relation",
  "readOnlyHint": true,
  "openWorldHint": false,
  "idempotentHint": true,
  "destructiveHint": false
}

evidence_between — Evidence between two entities

Advertised by the server during the last successful anonymous check.

Advertised read-only

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.

evidence_between input schema

{
  "type": "object",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "required": [
    "a",
    "b"
  ],
  "properties": {
    "a": {
      "type": "string"
    },
    "b": {
      "type": "string"
    },
    "dedupe": {
      "type": "boolean",
      "default": true,
      "description": "Send a repeated study in full only once. Pass false for a full card every time."
    }
  }
}

evidence_between annotations

{
  "title": "Evidence between two entities",
  "readOnlyHint": true,
  "openWorldHint": false,
  "idempotentHint": true,
  "destructiveHint": false
}

find_contradictions — Find contested claims

Advertised by the server during the last successful anonymous check.

Advertised read-only

Relations the Atlas marks as contested or that carry conflicting studies, with both sides of the evidence. status says which; breakdown splits the total. conflict carries WHY the studies disagree (Opposing result / Different context / Field dispute) with its basis. A contested relation with no conflicting study listed is flagged conflicting_studies_missing, and data_note says whether that is a real gap (Opposing result) or the recorded state because two published models compete (Field dispute, Different context); 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_contradictions input schema

{
  "type": "object",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "properties": {
    "brief": {
      "type": "boolean",
      "default": false,
      "description": "Shorten the long boundary and note text (text_truncated is set); get_relation has the full text."
    },
    "limit": {
      "type": "integer",
      "default": 20,
      "maximum": 9007199254740991,
      "minimum": 1,
      "description": "Maximum 50; a larger value is capped at 50."
    },
    "dedupe": {
      "type": "boolean",
      "default": true,
      "description": "Send a repeated study in full only once. Pass false for a full card every time."
    },
    "entity": {
      "type": "string"
    },
    "offset": {
      "type": "integer",
      "default": 0,
      "maximum": 9007199254740991,
      "minimum": 0,
      "description": "For the next page: pass next_offset from the previous answer."
    },
    "only_contested": {
      "type": "boolean",
      "default": false,
      "description": "Keep only relations the Atlas flags contested, not those that merely carry conflicting studies."
    }
  }
}

find_contradictions annotations

{
  "title": "Find contested claims",
  "readOnlyHint": true,
  "openWorldHint": false,
  "idempotentHint": true,
  "destructiveHint": false
}

list_questions — List open questions

Advertised by the server during the last successful anonymous check.

Advertised read-only

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.

list_questions input schema

{
  "type": "object",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "properties": {
    "kind": {
      "enum": [
        "open-question",
        "frontier"
      ],
      "type": "string"
    },
    "brief": {
      "type": "boolean",
      "default": true,
      "description": "Shorten still_open; false returns the full text."
    },
    "limit": {
      "type": "integer",
      "default": 20,
      "maximum": 9007199254740991,
      "minimum": 1,
      "description": "Maximum 50; a larger value is capped at 50."
    },
    "query": {
      "type": "string",
      "description": "Keywords to find questions by their title, gap, hypothesis or what is still open, e.g. \"rapamycin immune\"."
    },
    "offset": {
      "type": "integer",
      "default": 0,
      "maximum": 9007199254740991,
      "minimum": 0,
      "description": "For the next page: pass next_offset from the previous answer."
    }
  }
}

list_questions annotations

{
  "title": "List open questions",
  "readOnlyHint": true,
  "openWorldHint": false,
  "idempotentHint": true,
  "destructiveHint": false
}

get_question — Get one question

Advertised by the server during the last successful anonymous check.

Advertised read-only

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_question input schema

{
  "type": "object",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "required": [
    "id"
  ],
  "properties": {
    "id": {
      "type": "string"
    }
  }
}

get_question annotations

{
  "title": "Get one question",
  "readOnlyHint": true,
  "openWorldHint": false,
  "idempotentHint": true,
  "destructiveHint": false
}

search_authors — Search authors

Advertised by the server during the last successful anonymous check.

Advertised read-only

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_authors input schema

{
  "type": "object",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "required": [
    "query"
  ],
  "properties": {
    "limit": {
      "type": "integer",
      "default": 20,
      "maximum": 9007199254740991,
      "minimum": 1,
      "description": "Maximum 50; a larger value is capped at 50."
    },
    "query": {
      "type": "string",
      "description": "A name, ORCID or lab, e.g. \"Sabatini\", \"Claudio De Virgilio\", \"Fribourg\""
    },
    "offset": {
      "type": "integer",
      "default": 0,
      "maximum": 9007199254740991,
      "minimum": 0,
      "description": "For the next page: pass next_offset from the previous answer."
    }
  }
}

search_authors annotations

{
  "title": "Search authors",
  "readOnlyHint": true,
  "openWorldHint": false,
  "idempotentHint": true,
  "destructiveHint": false
}

get_author — Get one author

Advertised by the server during the last successful anonymous check.

Advertised read-only

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. If the name fits several people or has no profile page, the answer lists candidates (resolved: false) instead.

get_author input schema

{
  "type": "object",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "properties": {
    "id": {
      "type": "string",
      "description": "Alias of author."
    },
    "author": {
      "type": "string",
      "description": "e.g. \"Claudio De Virgilio\", \"De Virgilio C\", \"claudio-de-virgilio\""
    }
  }
}

get_author annotations

{
  "title": "Get one author",
  "readOnlyHint": true,
  "openWorldHint": false,
  "idempotentHint": true,
  "destructiveHint": false
}

Prompts

Not advertised

No prompt definitions available.

Resources

Not advertised

No resource definitions available.

30-day availability

Aggregated from read-only remote checks; this is not a tool-execution or security guarantee.

Successful checks: 1 of 1 (100%)
Average latency: 337 ms
95th percentile latency: 337 ms

Maintenance history

Public check and source-refresh events. Editorial and ownership records remain private.

Nov 7, 2026, 1:19 PM UTC · probe · passed · 337 ms · metadata changed · 13 tool(s)

Connect from your client

Each snippet registers the same endpoint; pick the client you use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Claude Code

Run this once in a terminal. It registers the remote server. Use --scope project to write .mcp.json for the repo.

Claude Code configuration

claude mcp add --transport http oliver-s-mtor-atlas-mcp https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp

Codex

Run this once. Codex stores MCP servers in ~/.codex/config.toml (or .codex/config.toml in a trusted project).

Codex configuration

codex mcp add oliver-s-mtor-atlas-mcp --url https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp

Cursor

Merge this server into .cursor/mcp.json in your project, then enable oliver-s-mtor-atlas-mcp in your MCP settings.

Cursor configuration

{
  "mcpServers": {
    "oliver-s-mtor-atlas-mcp": {
      "url": "https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp"
    }
  }
}

Cline

Merge this into cline_mcp_settings.json (Cline → MCP Servers → Configure).

Cline configuration

{
  "mcpServers": {
    "oliver-s-mtor-atlas-mcp": {
      "type": "streamableHttp",
      "url": "https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp",
      "disabled": false
    }
  }
}

VS Code

Merge this server into .vscode/mcp.json. Use MCP: List Servers to start oliver-s-mtor-atlas-mcp and inspect its tools.

VS Code configuration

{
  "servers": {
    "oliver-s-mtor-atlas-mcp": {
      "type": "http",
      "url": "https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp"
    }
  }
}

Gemini CLI

Run this once. It writes .gemini/settings.json in the current project; pass --scope user for ~/.gemini/settings.json.

Gemini CLI configuration

gemini mcp add --transport http oliver-s-mtor-atlas-mcp https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp

Claude Desktop

Open Claude Settings > Connectors > Add custom connector, enter this server URL and enable it for the conversation. This is a manual remote-connector handoff, not a desktop JSON configuration.

Claude Desktop configuration

https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp

Windsurf

Merge this into ~/.codeium/windsurf/mcp_config.json, then refresh MCP in Cascade. Windsurf remote servers use serverUrl, not url.

Windsurf configuration

{
  "mcpServers": {
    "oliver-s-mtor-atlas-mcp": {
      "serverUrl": "https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp"
    }
  }
}

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Oliver's mTOR Atlas MCP

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Checks and signals

What you can do with it

Source and maintenance

Protocol and capabilities

Server-provided instructions

Tools

Prompts

Resources

30-day availability

Maintenance history

Connect from your client

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Codex

Cursor

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VS Code

Gemini CLI

Claude Desktop

Windsurf

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