# Oliver's mTOR Atlas

> Evidence-labelled mTOR research: studies, entities, pathway claims, contradictions, open questions.

- name: io.github.open-mtor-atlas/mtor-atlas
- version: 1.3.3
- connection class: R0 (autonomous)
- trust: 96/100
- quality: 75/100 (good)
- owner: not claimed
- descriptor: https://api.protogrid.dev/v1/servers/io.github.open-mtor-atlas%2Fmtor-atlas
- tools: https://api.protogrid.dev/v1/servers/io.github.open-mtor-atlas%2Fmtor-atlas/tools

**An agent can connect right now, no human step.** Remote endpoint, no authentication, reachable on the last probe.

## Connection (mcpServers)

```json
{
  "mcpServers": {
    "mtor-atlas": {
      "type": "http",
      "url": "https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp"
    }
  }
}
```


## Trust

- hygiene: 100
- liveness: 98
- freshness: 100
- provenance: 90
- drivers: +repository +namespace-matches-repo +website +reachable +uptime-96% +updated-3d-ago
- Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed.

## Quality 75/100 (good)

### protocol: 75 (weight 25)

- warn `protocol.modern`: newest supported version is 2025-11-25; 2026-07-28 not supported, older versions are deprecated until 2027-07-28
- n/a `protocol.stateless`: only applies to 2026-07-28 servers
- pass `protocol.transport`: streamable HTTP
- n/a `protocol.list_ttl`: only applies to 2026-07-28 servers

### authorization: n/a (weight 15)

- n/a `auth.prm`, `auth.as_metadata`, `auth.cimd`: no remote uses OAuth
- n/a `auth.secret_in_url`: no templated URL

### tool hygiene: 100 (weight 30)

- pass `tools.descriptions`: every tool has a description
- pass `tools.description_length`: descriptions are concise
- pass `tools.schemas`: every tool has an object input schema
- pass `tools.annotations`: 13 of 13 tools declare readOnlyHint or destructiveHint
- pass `tools.directory_hints`: every tool declares readOnlyHint, destructiveHint, idempotentHint and openWorldHint
- pass `tools.token_cost`: about 2,804 tokens to load every tool
- pass `tools.api_dump`: tools are not a one-to-one API dump

### stability: 25 (weight 15)

- warn `stability.changes`: 38 tool changes in 30 days
- fail `stability.rug_pull`: 4 tools kept their name but changed most of their description in 30 days; review before trusting them

### dependencies: n/a (weight 15)

- n/a `deps.known_vulns`, `deps.mcp_sdk_version`, `deps.resolvable`: deps.dev does not know mtor-atlas-mcp@1.3.3

- tools: 13, about 2,804 tokens to load them all
- tool set hash: 576cabffbe589ed36e26302824c153f4
- tools last changed: 2026-10-17T22:29:47.225Z
- badge: [![protogrid quality](https://protogrid.dev/badge/io.github.open-mtor-atlas/mtor-atlas.svg)](https://protogrid.dev/servers/io.github.open-mtor-atlas/mtor-atlas)
- Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed.

### Tool changes

- 2026-10-17 `find_contradictions` changed (description)
  - before: 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 and shows related relations named in its text. Paged: pass next_offset as offset for the rest. Optionally limited to one entity.
  - after: 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.
- 2026-10-17 `atlas_about` changed (description)
  - before: Dataset version, corpus snapshot date, counts, evidence-code legend and how to cite the dataset. derived_counts adds figures computed from the relations (flagged contested, with conflicting studies, either) so they can be compared with find_contradictions.
  - after: 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.
- 2026-10-15 `get_author` added
  - 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.
- 2026-10-15 `search_authors` added
  - 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.
- 2026-10-15 `list_questions` changed (inputSchema)
- 2026-10-15 `get_study` changed (description, inputSchema)
  - before: 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.
  - after: 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.
- 2026-10-15 `search_studies` changed (description, inputSchema)
  - before: 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.
  - after: 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.
- 2026-10-13 `list_questions` changed (description, inputSchema) **meaning changed**
  - before: The Atlas's open questions (evidence gaps with testable hypotheses) and frontier questions.
  - after: 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.
- 2026-10-13 `find_contradictions` changed (description, inputSchema) **meaning changed**
  - before: Relations the Atlas marks as contested or that carry conflicting studies, with both sides of the evidence. Optionally limited to one entity.
  - after: 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 and shows related relations named in its text. Paged: pass next_offset as offset for the rest. Optionally limited to one entity.
- 2026-10-13 `evidence_between` changed (description, inputSchema)
  - before: 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?".
  - after: 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.

Full history: https://api.protogrid.dev/v1/servers/io.github.open-mtor-atlas%2Fmtor-atlas/changes

## Dependencies

- npm mtor-atlas-mcp@1.3.3: unknown

Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0.

## Remotes

- https://mtor-atlas-mcp.mtor-atlas.workers.dev/mcp (streamable-http, auth none, reachable true, uptime30d 0.9594595)

## Packages

- npm mtor-atlas-mcp@1.3.3

## Tools (13)

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