atlas

# Oliver's mTOR Atlas

A curated, evidence-graded database of mTOR pathway research in which every claim carries its source, the conditions it was measured under, and the point where it stops holding. Studies are labelled by the kind of study behind them - from synthesis of human data down to mechanistic and in-vitro work - and traced back to their primary source, alongside a knowledge-graph view of genes, diseases, and interventions and a layer of open questions naming what the evidence does not yet resolve.

**Live site:** https://mtor-atlas.org

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.22059963.svg)](https://doi.org/10.5281/zenodo.22059963)

## What's inside

- 400+ hand-curated primary studies on the mTOR signaling pathway (mTORC1/mTORC2, autophagy, rapamycin and related interventions), each labelled by the kind of study behind it and linked back to its DOI/PubMed record.
- A knowledge-graph view connecting genes, diseases, and interventions.
- An "open questions" layer - evidence gaps identified across the corpus, each paired with a proposed testable experiment.
- A citation-grounded research assistant that answers pathway questions using only the indexed corpus, with links back to source studies.

## Evidence grading

Studies are hand-selected from PubMed / Europe PMC and labelled by **study design**, not by quality, importance, or citation count:

- **S** - synthesis of human data (systematic review / meta-analysis)
- **H** - human study (clinical trial or observational)
- **A** - animal model
- **M** - molecular / in-vitro (mechanistic)
- **R** - review

These codes ran A-D until September 2026. They were renamed because a lettered ladder reads as a quality grade, which it never was, and because the old bottom tier merged primary mechanistic work with narrative reviews - two different kinds of claim. The change was prompted by an external critique from a researcher in the field; the underlying data was not re-graded, only the labels shown to readers.

A mechanistic paper is not "worse" than a trial. The code says what kind of claim a study can support, not how good it is.

## About this project

Built and maintained independently by Oliver, a high-school student, together with his father Petr. Not affiliated with any lab, company, or institution. Feedback on the evidence grading, missing studies, or anything that looks wrong is very welcome - please open an issue. See [CONTRIBUTING.md](CONTRIBUTING.md).

## Programmatic access

- **JSON API** (read-only, no key): https://mtor-atlas.org/api/ - studies with evidence codes, entities, signed pathway relations with supporting and conflicting studies, open questions. OpenAPI 3.1: https://mtor-atlas.org/api/openapi.json
- **MCP server** for AI assistants: source and install instructions in [`mcp/`](mcp/).

## Citing this dataset

If you use this dataset, please cite it via its Zenodo record: https://doi.org/10.5281/zenodo.22059963

A single page with all identifiers, registrations (bio.tools, FAIRsharing, GitHub, ORCID) and a ready-to-use citation is at https://mtor-atlas.org/data/.

## License

This repository is dual-licensed, because it contains two different kinds of thing:

- **Curated content and data** - the study records, evidence grades, curated prose, gap hypotheses, and everything under `atlas_data/` and the generated pages - are licensed under **CC BY 4.0** (see [LICENSE](LICENSE)): https://creativecommons.org/licenses/by/4.0/
- **Source code** - the Python generators, validation and verification scripts, and site JavaScript - is licensed under the **MIT License** (see [LICENSE-CODE](LICENSE-CODE)).

If you reuse the data, attribute it. If you reuse the code, MIT terms apply.