Oliver's mTOR Atlas
Evidence-labelled mTOR research: studies, entities, pathway claims, contradictions, open questions.
Should I use this
Quality & Safety
Findings (2)
- LOWTool 'get_relation' description lacks action verbin get_relation
- LOWTool 'evidence_between' description lacks action verbin evidence_between
Based on automated analysis of tool definitions and protocol compliance.
Context Cost
This is the approximate number of tokens consumed each time the server's tools are loaded into a model's context. Higher counts reduce the attention available for other tasks.
Install
One-Click Install
Add this to your `claude_desktop_config.json` file:
{
"mcpServers": {
"mtor-atlas": {
"command": "npx",
"args": [
"mtor-atlas-mcp"
]
}
}
}Runnable packages
1.2.2stdioRemote endpoints
https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcpstreamable-httpWhat it can do
Tool inventory
Tools (11)
🟢atlas_about
Dataset version, corpus snapshot date, counts, evidence-code legend and how to cite the dataset.
Input Schema
{
"type": "object",
"properties": {}
}🟢search_studies(query, evidence_code, entity, year_from, year_to, ...)
Search the curated studies by keywords (title, finding, authors, journal, model system), optionally filtered by evidence code, a linked entity (gene, drug, disease...) and year range. Returns summary records with evidence codes and URLs.
Input Schema
{
"type": "object",
"properties": {
"query": {
"description": "Keywords, e.g. \"rapamycin lifespan mice\". Omit to list by filters only.",
"type": "string"
},
"evidence_code": {
"description": "Keep only these evidence codes, e.g. [\"H\",\"S\"] for human evidence.",
"type": "array",
"items": {
"type": "string",
"enum": [
"S",
"H",
"A",
"M",
"R",
"PP",
"RT"
]
}
},
"entity": {
"description": "Only studies linked to this entity (name, synonym or id), e.g. \"Rheb\".",
"type": "string"
},
"year_from": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991
},
"year_to": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991
},
"limit": {
"default": 20,
"type": "integer",
"minimum": 1,
"maximum": 50
},
"offset": {
"default": 0,
"description": "For the next page: pass next_offset from the previous answer.",
"type": "integer",
"minimum": 0,
"maximum": 9007199254740991
}
},
"$schema": "http://json-schema.org/draft-07/schema#"
}🟢get_study(sid)
Full record for one study by Atlas ID (e.g. "SAB1994"): abstract excerpt, extracted findings, linked entities, the relations it supports or contradicts, related open questions.
Input Schema
{
"type": "object",
"properties": {
"sid": {
"type": "string",
"description": "Atlas study ID, e.g. \"SAB1994\""
}
},
"required": [
"sid"
],
"$schema": "http://json-schema.org/draft-07/schema#"
}🟢search_entities(query, type, limit)
Find genes/proteins, complexes, drugs, diseases, processes, nutrients and outcomes by name or synonym.
Input Schema
{
"type": "object",
"properties": {
"query": {
"type": "string",
"description": "Name or synonym, e.g. \"raptor\", \"sirolimus\""
},
"type": {
"description": "Optional type filter, e.g. \"Drug\", \"Gene/Protein\", \"Disease\"",
"type": "string"
},
"limit": {
"default": 20,
"type": "integer",
"minimum": 1,
"maximum": 100
}
},
"required": [
"query"
],
"$schema": "http://json-schema.org/draft-07/schema#"
}🟢get_entity(entity, studies_limit)
One entity (gene/protein, complex, drug, disease, process...) with its linked studies as short cards (first studies_limit) and every pathway relation it takes part in as a one-line claim. Accepts an id, a name or a synonym.
Input Schema
{
"type": "object",
"properties": {
"entity": {
"type": "string",
"description": "e.g. \"mTORC1\", \"Rheb\", \"rapamycin\""
},
"studies_limit": {
"default": 25,
"type": "integer",
"minimum": 0,
"maximum": 50
}
},
"required": [
"entity"
],
"$schema": "http://json-schema.org/draft-07/schema#"
}🟢find_relations(entity, source, target, effect, contested_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.
Input Schema
{
"type": "object",
"properties": {
"entity": {
"description": "Entity on either end of the relation",
"type": "string"
},
"source": {
"type": "string"
},
"target": {
"type": "string"
},
"effect": {
"type": "string",
"enum": [
"activates",
"inhibits",
"binds",
"recruits",
"required-for",
"context-dependent",
"no-effect"
]
},
"contested_only": {
"description": "Only relations marked contested or with conflicting studies",
"type": "boolean"
},
"strongest_at_least": {
"description": "Keep relations whose best supporting study is at least this code in the order S > H > A > M",
"type": "string",
"enum": [
"S",
"H",
"A",
"M",
"R",
"PP",
"RT"
]
},
"limit": {
"default": 20,
"type": "integer",
"minimum": 1,
"maximum": 50
},
"offset": {
"default": 0,
"description": "For the next page: pass next_offset from the previous answer.",
"type": "integer",
"minimum": 0,
"maximum": 9007199254740991
}
},
"$schema": "http://json-schema.org/draft-07/schema#"
}🟢get_relation(id)
One pathway relation by ID (e.g. "RHEB-MTORC1"): mechanism, boundary conditions, confidence, supporting and conflicting studies.
Input Schema
{
"type": "object",
"properties": {
"id": {
"type": "string"
}
},
"required": [
"id"
],
"$schema": "http://json-schema.org/draft-07/schema#"
}🟢evidence_between(a, b)
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?".
Input Schema
{
"type": "object",
"properties": {
"a": {
"type": "string"
},
"b": {
"type": "string"
}
},
"required": [
"a",
"b"
],
"$schema": "http://json-schema.org/draft-07/schema#"
}🟢find_contradictions(entity, limit)
Relations the Atlas marks as contested or that carry conflicting studies, with both sides of the evidence. Optionally limited to one entity.
Input Schema
{
"type": "object",
"properties": {
"entity": {
"type": "string"
},
"limit": {
"default": 20,
"type": "integer",
"minimum": 1,
"maximum": 50
}
},
"$schema": "http://json-schema.org/draft-07/schema#"
}🟢list_questions(kind)
The Atlas's open questions (evidence gaps with testable hypotheses) and frontier questions.
Input Schema
{
"type": "object",
"properties": {
"kind": {
"type": "string",
"enum": [
"open-question",
"frontier"
]
}
},
"$schema": "http://json-schema.org/draft-07/schema#"
}🟢get_question(id)
One open or frontier question by ID (e.g. "H1", "F2"): the gap, what changed, what is still open, how it could be tested, linked studies.
Input Schema
{
"type": "object",
"properties": {
"id": {
"type": "string"
}
},
"required": [
"id"
],
"$schema": "http://json-schema.org/draft-07/schema#"
}Community
Evidence