Oliver's mTOR Atlas
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": true
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| atlas_aboutA | Dataset version, corpus snapshot date, counts, evidence-code legend and how to cite the dataset. |
| search_studiesB | 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. |
| get_studyA | 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. |
| search_entitiesA | Find genes/proteins, complexes, drugs, diseases, processes, nutrients and outcomes by name or synonym. |
| get_entityA | 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. |
| find_relationsA | 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_relationA | One pathway relation by ID (e.g. "RHEB-MTORC1"): mechanism, boundary conditions, confidence, supporting and conflicting studies. |
| evidence_betweenB | 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?". |
| find_contradictionsB | Relations the Atlas marks as contested or that carry conflicting studies, with both sides of the evidence. Optionally limited to one entity. |
| list_questionsC | The Atlas's open questions (evidence gaps with testable hypotheses) and frontier questions. |
| get_questionB | 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. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 11 tools
Most tools target distinct resources (studies, entities, relations, questions) with clear get_/search_ pairs. However, evidence_between overlaps with find_relations (both return curated relations, the former just a special case for a two-entity pair), and find_contradictions overlaps with find_relations' contested-status filter. Descriptions help but an agent could still misselect among the relation-oriented tools.
The set is predominantly snake_case verb_noun (search_studies, get_study, find_relations, list_questions), which is readable and predictable. The main deviation is the inconsistent use of search_ vs find_ for essentially the same lookup semantics, plus the noun-only atlas_about.
11 tools is well-scoped for a read-only curated atlas, with each tool mapping to a distinct resource or query pattern. No tool feels redundant or trivially thin.
The surface covers the full read lifecycle for the domain: metadata (atlas_about), search+get for studies, entities, relations and questions, plus specialized views for evidence-between and contradictions. As a curated read-only dataset, no create/update/delete is needed, so coverage is complete.