RiceMind Data API/MCP Server v1

Public data API/MCP server for RiceMind. Build, integrate, and explore the RiceMind Database programmatically.

Model Context Protocol (MCP) Integration

A major methodological innovation of RiceMind is the deployment of a standardized MCP server, distinguishing it from conventional static databases. To embrace the era of AI Agents, we present the RiceMind Database in a more advanced, LLM-friendly format. Designed strictly according to the latest official MCP specifications, our server utilizes Server-Sent Events (SSE) for transport and exposes our data APIs as standardized tool interfaces.

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MCP SSE Endpoint: http://117.72.82.63:8085/ricemind/mcp/sse
Transport Layer: Server-Sent Events (SSE)
Architecture: Official MCP Specification Compliant

RESTful API Architecture

The RiceMind API provides a standardized, high-performance interface to access our curated knowledge graph of Oryza sativa. Whether you are building bioinformatics pipelines, integrating LLM agents (like our MCP Agent), or conducting bulk data analysis, our API endpoints deliver precise, NLP-extracted evidence and multi-omics data.

Base URL: http://lit-evi.hzau.edu.cn/ricemind-api/
Format: JSON responses via HTTP GET.
Documentation: Interactive Swagger UI available for live testing.
Open Swagger UI to Explore Data API

1. Global Entity Retrieval

Fetch paginated, unified lists of all recognized entities in the database, automatically sorted by literature popularity.

GET /all-genes/

Returns a list of all normalized genes (e.g., sd1, Os01g0883800).

GET /all-traits/

Returns all phenotypic traits mapped to ontologies (PO, TO, GO).

GET /all-varieties/

Returns all registered rice varieties and cultivars.

2. Gene-Centric Profiling

Deep-dive into a specific gene to retrieve its omics profile, or discover all entities associated with it.

GET /gene-profile/

Parameters: ?gene={name}

Returns RAP IDs, CGSNL names, chromosome locations, and cross-database links.

GET /traits-by-gene/

Parameters: ?gene={name}

Returns all traits known to be associated with the given gene, grouped by confidence tiers.

GET /varieties-by-gene/

Parameters: ?gene={name}

Returns all varieties where the target gene is specifically mentioned or validated.

3. Single Entity Type Search

Retrieve raw literature sentences and evidence blocks that mention a specific entity.

GET /search-by-gene/

Search all evidence sentences for a given gene.

GET /search-by-trait/

Search all evidence sentences for a given trait.

GET /search-by-variety/

Search all evidence sentences for a given variety.

4. Two Entity Co-occurrence Search

The most powerful query type. Find direct literature evidence where two specific entities are linked.

GET /search-by-trait-and-gene/

Parameters: ?gene={name}&trait={name}

Returns Gene-Trait Association (GTA) metadata and exact sentence evidence.

GET /search-by-variety-and-gene/

Parameters: ?variety={name}&gene={name}

GET /search-by-variety-and-trait/

Parameters: ?variety={name}&trait={name}

5. Contextual Deep Dive

GET /sentence-context/

Parameters: ?pmid={id}&sent_id={id}&window={int}

Retrieve the surrounding textual context (N sentences before and after) from the original full-text article for a specific extracted sentence.