askBrassica runs a public MCP server (Model Context Protocol). Connect it to an AI assistant such as Claude and the assistant can look up Brassica and Arabidopsis genes, find orthologues across Brassica genomes, check expression, query Brassica 60K SNP genotypes and search the literature, citing the source database for every answer. It is free, read-only and needs no account.
1 Get Claude (free)
- Create a free account at claude.ai.
- Use Claude in your web browser, or install the desktop app for macOS or Windows from claude.ai/download.
The free plan allows one custom connector, which is all askBrassica needs. Free accounts have usage limits; paid plans give more.
2 Add the askBrassica connector
https://askbrassica.plantdatabases.org/mcp- In Claude, open Customize → Connectors.
- Click + Add, then Add custom connector.
- Name:
askBrassica. Remote MCP server URL: the address above. Click Continue. - Under Authentication choose No sign in, then click Add.
Claude Team or Enterprise: an organisation Owner adds it once under Organization settings → Connectors → Add → Custom → Web (same name and URL, no sign in). Members then find askBrassica under Customize → Connectors and click Connect.
3 Turn it on in a chat
Start a new chat, click + (lower left) → Connectors, and switch askBrassica on. Then ask a question. Claude will ask permission the first time it uses an askBrassica tool.
4 Example questions
Click a question to copy it, then paste it into Claude.
Genes and orthologues
Expression
SNP genotypes (CropSNPdb)
Literature
Tips
- Brassica napus genes in Ensembl Plants use the Darmor-bzh v4.1 assembly (IDs GSBRNA2T…, names BnaA01g…). CropSNPdb uses Darmor v4.1 or v8.1 coordinates; positions differ between assemblies.
- Expression Atlas has only about a dozen Brassica experiments; Arabidopsis genes are included for orthology, not expression.
- Ask for links: every result carries a URL to the source database.
- AI assistants can make mistakes. Check IDs and positions against the linked source before using them.
Other AI tools
Any MCP client that supports remote servers (streamable HTTP) can use the same URL. For Claude Code:
claude mcp add --transport http askbrassica https://askbrassica.plantdatabases.org/mcp
Available tools
| Tool | What it does |
|---|---|
search_data | Full-text search across all resources, with filters by database, data type and species |
find_gene | Gene name or Ensembl ID → species, location, description and link (Ensembl Plants) |
genes_in_region | Genes in an interval of one genome (max 5 Mb) |
orthologues | Orthologues across plant genomes from Ensembl Plants Compara |
gene_expression | Where a gene is expressed (TPM by tissue/stage) and the treatments that change it, from Expression Atlas |
expression_genes | Tissue-specific or treatment-responsive genes in one Expression Atlas experiment |
expression_experiments | RNA-seq experiments held, with tissues/stages and contrasts |
snp_lines | SNP-genotyped lines in CropSNPdb (Brassica 60K datasets) by name or accession |
snp_genotypes | Genotype calls for named lines in a chromosome region |
snp_compare_lines | Identity between two lines and the regions where they differ |
snp_haplotype_carriers | Lines sharing a reference line's haplotype in a region (max 5 Mb) |
snp_markers | SNP array markers and positions in a region |
snp_phenotypes | Trait records for genotyped lines, where CropSNPdb has them |
search_literature | Publications and preprints in Europe PMC, restricted to the crop, with year, open-access and citation sorting |
get_paper | Abstract and full-text links for a DOI, PMID or PMCID |
data_sources | The databases behind the site and their record counts |
Your questions are processed by the AI provider you use. askBrassica receives only the tool requests the assistant makes and keeps standard web server logs. There is no login and no cost.