# LOTUS Explore-rs

> Explore LOTUS with taxon filters, structure search, and Wikidata curation workflows.

All URLs below are absolute: the app is served from a subpath, so a
root-relative link resolves to the domain root and 404s.

## Core information

- **Official name**: LOTUS Explore-rs
- **Short name**: LOTUS-rs
- **Purpose**: Interactive exploration of chemical entity occurrence data
- **Data domain**: Natural products, chemical compounds, taxonomy, scientific references
- **Access model**: Free, web-based, no authentication required
- **Interface**: Four locales (en, fr, de, it); light and dark themes
- **Machine interface**: A WebMCP tool surface, see Discovery

## Features

- Search by taxon filters and structure input (SMILES or Molfile V2000/V3000)
- Draw a structure in the embedded Ketcher editor, then copy Daylight SMILES or MOL V3000 back into search
- Filter by mass range, publication year, and formula presence
- Browse taxonomy and references for each result
- Export results as CSV, JSON, RDF, or SPARQL
- Import TSV rows and generate QuickStatements for Wikidata curation
- A guided FAQ at https://lotus-initiative.github.io/lotus-explore-rs/faq

## Docs

In the repository. These are design and operations notes rather than user
documentation, and are not served from the site itself.

- [Architecture](https://github.com/lotusnprod/lotus-explore-rs/blob/main/apps/lotus-explore-rs/docs/ARCHITECTURE.md)
- [Design system](https://github.com/lotusnprod/lotus-explore-rs/blob/main/apps/lotus-explore-rs/docs/DESIGN_SYSTEM.md)
- [Performance](https://github.com/lotusnprod/lotus-explore-rs/blob/main/apps/lotus-explore-rs/docs/PERFORMANCE.md)
- [Deployment](https://github.com/lotusnprod/lotus-explore-rs/blob/main/apps/lotus-explore-rs/docs/DEPLOYMENT.md)
- [Citation](https://github.com/lotusnprod/lotus-explore-rs/blob/main/apps/lotus-explore-rs/docs/CITATION.md)
- [Curation share links](https://github.com/lotusnprod/lotus-explore-rs/blob/main/apps/lotus-explore-rs/docs/CURATION_SHARE_LINKS.md)

## Discovery

Machine-readable descriptions of this app, for agents.

- [AI capability catalog](https://lotus-initiative.github.io/lotus-explore-rs/.well-known/ai-catalog.json)
- [API catalog](https://lotus-initiative.github.io/lotus-explore-rs/.well-known/api-catalog.json)
- [Agent skills](https://lotus-initiative.github.io/lotus-explore-rs/.well-known/agent-skills.json)
- [Security policy](https://lotus-initiative.github.io/lotus-explore-rs/.well-known/security.txt)
- [robots.txt](https://lotus-initiative.github.io/lotus-explore-rs/robots.txt)
- [sitemap.xml](https://lotus-initiative.github.io/lotus-explore-rs/sitemap.xml)
- Structured data: JSON-LD in the page head

Every entry above is also linked from the document head, because the one
live host ignores `_headers` and a `Link:` header alone is discoverable by
nobody. The `WebMCP` surface is not a separate endpoint: there is no MCP
server. It is registered by the page itself, twice over. The forms carry
declarative annotations -- `toolname`, `tooldescription`, and a
`toolparamdescription` per control -- and `assets/js/webmcp.js` registers
the same capabilities imperatively with
`document.modelContext.registerTool` before the app has booted. The
second registration is not redundancy: the forms are rendered by the
WASM client, so the annotations do not exist until seconds after the
document loaded, and an agent (or an audit) looking for tools at document
start would otherwise find none.

- `search_lotus` -- fills and submits the search form, then reports the
top rows of the result table. Arguments: `taxon`, `reference`, `smiles`,
`mass_min`, `mass_max`, `year_min`, `year_max`, `formula_exact`,
`formula_enabled`, `stype`.
- `get_lotus_search_state` -- reads the criteria currently in the form,
for confirming what a previous `search_lotus` call applied.
- `add_curation_row`, `import_curation_tsv` -- registered on the curation
route only, because a tool whose form the agent cannot reach is context
it has to spend tokens on and then fail to use.

The tools drive the real controls, so a human watching sees the same
fields fill and the same results appear. What they return comes from
Wikidata and third-party services and is flagged `untrustedContentHint`.

- Search form: https://lotus-initiative.github.io/lotus-explore-rs/search
- Curation forms: https://lotus-initiative.github.io/lotus-explore-rs/curation

## Data sources

- [Wikidata Query Service](https://query.wikidata.org/)
- [QLever Wikidata endpoint](https://qlever.cs.uni-freiburg.de/wikidata)
- [DOI metadata](https://doi.org/)
- [LOTUS initiative](https://lotus-initiative.github.io)

## Citation

- [Paper](https://elifesciences.org/articles/70780)
- [DOI](https://doi.org/10.7554/eLife.70780)
- [BibTeX](https://lotus-initiative.github.io/lotus-explore-rs/docs/references.bib)

## Licensing

- App: [AGPL-3.0](https://www.gnu.org/licenses/agpl-3.0.html)
- Data: [CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/)

## Project

- [App](https://lotus-initiative.github.io/lotus-explore-rs/)
- [Repository and source](https://github.com/lotusnprod/lotus-explore-rs)
- [Issues](https://github.com/lotusnprod/lotus-explore-rs/issues)
- [Discussions](https://github.com/lotusnprod/lotus-explore-rs/discussions)