From dbb6566e2d7c02dafb997490ae9a11faeec369d6 Mon Sep 17 00:00:00 2001
From: Edern Deneuville <edern.deneuville@gmail.com>
Date: Sun, 2 Aug 2026 17:10:00 +0200
Subject: [PATCH] docs: add project README

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+# OpenHerbarium MCP
+
+**Botanical Knowledge MCP Server** — a Model Context Protocol server that gives AI agents structured, sourced botanical data from free/open sources.
+
+OpenHerbarium MCP is designed for a downstream agent such as **Hermes Agent Botaniste**. It is deliberately a knowledge-access layer only: it fetches, normalizes and cites botanical evidence, then lets the client agent reason, write, format and publish.
+
+## What this MCP does
+
+It exposes MCP tools for:
+
+- plant lookup by common or scientific name;
+- taxonomic information;
+- species information such as distribution, habitat and botanical descriptions;
+- horticultural care-source discovery;
+- image-source discovery with licence and author metadata;
+- targeted botanical source search through a local Firecrawl instance when configured.
+
+Every returned data point is wrapped with provenance:
+
+```json
+{
+  "value": "Marantaceae",
+  "source": "GBIF Backbone Taxonomy",
+  "url": "https://www.gbif.org/species/8184122",
+  "retrieved_at": "2026-08-02T12:00:00+00:00",
+  "confidence": "high"
+}
+```
+
+## What this MCP does **not** do
+
+OpenHerbarium MCP never:
+
+- creates final Markdown plant sheets;
+- writes to Outline;
+- manages Outline collections;
+- creates care calendars;
+- decides final horticultural recommendations;
+- replaces the reasoning/presentation layer of Hermes Agent.
+
+## MCP tools
+
+### `search_plant(name: str)`
+
+Returns:
+
+- accepted scientific name;
+- canonical name;
+- common/vernacular names when available;
+- synonyms;
+- family, genus, species and rank;
+- external identifiers such as GBIF keys and GBIF species URL;
+- best-effort Kew/POWO results when accessible.
+
+### `get_taxonomy(name: str)`
+
+Returns sourced taxonomy:
+
+- kingdom;
+- phylum/class/order when available;
+- family;
+- genus;
+- species;
+- scientific name;
+- botanical authorship;
+- taxonomic status;
+- synonyms.
+
+Priority sources:
+
+- GBIF Backbone Taxonomy;
+- Plants of the World Online, Kew, best-effort.
+
+### `get_species_information(name: str)`
+
+Returns raw evidence for:
+
+- botanical descriptions;
+- known distribution;
+- natural habitat where available;
+- additional source-search records when Firecrawl is configured.
+
+### `get_care_sources(name: str)`
+
+Returns raw source candidates for:
+
+- light;
+- temperature;
+- humidity;
+- watering;
+- substrate;
+- fertilisation;
+- repotting.
+
+It does **not** transform those sources into final care advice.
+
+### `get_image_sources(name: str, limit: int = 10)`
+
+Uses Wikimedia Commons to return:
+
+- image URL;
+- licence;
+- author;
+- source page.
+
+### `search_botanical_sources(query: str, limit: int = 5)`
+
+Uses a local Firecrawl instance if `FIRECRAWL_API_URL` is configured. If not configured, the tool returns source-constrained suggested queries rather than pretending to have scraped content.
+
+## Sources
+
+Implemented/targeted sources:
+
+- [GBIF](https://www.gbif.org/)
+- [Plants of the World Online, Kew](https://powo.science.kew.org/) best-effort connector
+- [Wikimedia Commons](https://commons.wikimedia.org/)
+- [Royal Horticultural Society](https://www.rhs.org.uk/) source candidates / Firecrawl search
+- [Tela Botanica](https://www.tela-botanica.org/) source candidates / Firecrawl search
+- public university horticultural resources via targeted Firecrawl search
+
+No paid API is required.
+
+## Installation
+
+### Requirements
+
+- Python 3.11+
+- `uv` recommended, or any Python package installer capable of creating a virtual environment
+
+### Local install with `uv`
+
+```bash
+git clone <YOUR_GITEA_URL>/openherbarium-mcp.git
+cd openherbarium-mcp
+uv sync --extra dev
+```
+
+Run tests:
+
+```bash
+uv run pytest
+```
+
+Run the MCP server over stdio:
+
+```bash
+uv run openherbarium-mcp
+```
+
+## Hermes Agent configuration
+
+Add the server to `~/.hermes/config.yaml`:
+
+```yaml
+mcp_servers:
+  openherbarium:
+    command: "uv"
+    args:
+      - "--directory"
+      - "/absolute/path/to/openherbarium-mcp"
+      - "run"
+      - "openherbarium-mcp"
+    timeout: 120
+    connect_timeout: 60
+```
+
+Restart Hermes Agent. Tools will be exposed with names similar to:
+
+- `mcp_openherbarium_search_plant`
+- `mcp_openherbarium_get_taxonomy`
+- `mcp_openherbarium_get_species_information`
+- `mcp_openherbarium_get_care_sources`
+- `mcp_openherbarium_get_image_sources`
+- `mcp_openherbarium_search_botanical_sources`
+
+## Firecrawl configuration
+
+Copy `.env.example` to `.env` and set:
+
+```bash
+FIRECRAWL_API_URL=http://localhost:3002
+FIRECRAWL_API_KEY=
+```
+
+If Firecrawl is not configured, source-search tools return explicit suggested queries and a `not_configured` status.
+
+## Development
+
+```bash
+uv sync --extra dev
+uv run pytest
+```
+
+Project layout:
+
+```text
+openherbarium-mcp/
+├── src/
+│   └── openherbarium_mcp/
+│       ├── server.py
+│       ├── gbif.py
+│       ├── kew.py
+│       ├── rhs.py
+│       ├── tela_botanica.py
+│       ├── wikimedia.py
+│       └── firecrawl.py
+├── tests/
+├── README.md
+├── pyproject.toml
+├── LICENSE
+└── .env.example
+```
+
+## Reliability model
+
+The server distinguishes between:
+
+- **high confidence**: exact/high-confidence API matches, mostly GBIF taxonomic matches;
+- **medium confidence**: sourced API records that still require interpretation;
+- **low confidence**: source candidates or search results that must be manually/agent verified.
+
+OpenHerbarium MCP prefers returning `status: unavailable`, `status: not_configured` or empty records over inventing missing data.
+
+## License
+
+MIT