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Plant Genomics MCP

by musharnaco.huggingface.musharna/plant-genomics-mcp

Plant locus lookup across 7 public sources, over MCP

Install in Claude Code Other clients
  • Remote endpoint
  • 8 tools
  • MIT

Uptime

Checked  · every day

100%from 4 days of checks

Up without downtime on 4 of 4 days with data.

  • No downtime
  • Degraded
  • Down over 5 minutes
  • No data
  • Not checked yet

Response time

Median 1384 ms, slowest 5% 2150 ms for the handshake and the tool list, over 30 days.

2500 ms1250 ms0

How far each check got

  • Reached the address 83.3%
  • Completed the handshake 66.6%
  • Listed its tools 66.6%

8 tools at the last answer.

Every day
DayResultChecksMedian
3 Nov (today)No downtime1–
2 NovNo downtime1of 11412 ms
1 NovNo downtime1of 12150 ms
31 OctNo downtime31122 ms

A failure counts as down time only when a second check five minutes later fails too. How we check

Connect to the publisher's own endpoint

Run in a terminal:

claude mcp add --transport sse plant-genomics-mcp https://musharna-plant-genomics-mcp.hf.space/gradio_api/mcp/sse

Step by step for Claude Code

For agents: the install prompt

Every step above as one Markdown text, for an assistant installing it for you.

# Install the MCP server Plant Genomics MCP (`co.huggingface.musharna/plant-genomics-mcp`)

Its page: https://plug.directory/servers/co.huggingface.musharna/plant-genomics-mcp

It runs on the publisher's servers; the client connects to its URL.

Use the section for the person's client.

## Claude Desktop

Paste into Settings › Connectors › Add custom connector:

```text
https://musharna-plant-genomics-mcp.hf.space/gradio_api/mcp/sse
```

## Claude Code

Run in a terminal:

```sh
claude mcp add --transport sse plant-genomics-mcp https://musharna-plant-genomics-mcp.hf.space/gradio_api/mcp/sse
```

## Cursor, Devin Desktop, LM Studio, Gemini CLI, oterm, ECA

Merge into the place for the person's client:

- Cursor: ~/.cursor/mcp.json
- Devin Desktop: ~/.config/devin/mcp_config.json
- LM Studio: mcp.json (Program › Install › Edit mcp.json)
- Gemini CLI: ~/.gemini/settings.json
- oterm: config.json in oterm's data folder (~/Library/Application Support/oterm on macOS, ~/.local/share/oterm on Linux, %APPDATA%\oterm on Windows)
- ECA: ~/.config/eca/config.json (global) or .eca/config.json in the project

```json
{
  "mcpServers": {
    "plant-genomics-mcp": {
      "url": "https://musharna-plant-genomics-mcp.hf.space/gradio_api/mcp/sse"
    }
  }
}
```

## VS Code

Merge into .vscode/mcp.json:

```json
{
  "servers": {
    "plant-genomics-mcp": {
      "type": "sse",
      "url": "https://musharna-plant-genomics-mcp.hf.space/gradio_api/mcp/sse"
    }
  }
}
```

## Zed

This server's endpoint speaks only SSE, which this client's documentation does not list among its transports; use another client for it.

## Cline, AnythingLLM, Augment Code

Merge into the place for the person's client:

- Cline: cline_mcp_settings.json (MCP Servers › Configure › Configure MCP Servers)
- AnythingLLM: anythingllm_mcp_servers.json in the AnythingLLM storage plugins directory
- Augment Code: Augment Settings Panel – MCP section – Import from JSON (VS Code extension)

```json
{
  "mcpServers": {
    "plant-genomics-mcp": {
      "type": "sse",
      "url": "https://musharna-plant-genomics-mcp.hf.space/gradio_api/mcp/sse"
    }
  }
}
```

## Continue

Merge into ~/.continue/config.yaml:

```yaml
mcpServers:
  - name: "plant-genomics-mcp"
    type: sse
    url: "https://musharna-plant-genomics-mcp.hf.space/gradio_api/mcp/sse"
```

## Goose

This server's endpoint speaks only SSE, which this client's documentation does not list among its transports; use another client for it.

## Codex

This server's endpoint speaks only SSE, which this client's documentation does not list among its transports; use another client for it.

## mcp-client-cli, TUUI, BoltAI, Bob Shell, Kiro, Kiro CLI

This server's endpoint speaks only SSE, which this client's documentation does not list among its transports; use another client for it.

## Agenvoy

This server's endpoint speaks only SSE, which this client's documentation does not list among its transports; use another client for it.

## Amp

Merge into ~/.config/amp/settings.json (user) or .amp/settings.json (workspace):

```json
{
  "amp.mcpServers": {
    "plant-genomics-mcp": {
      "url": "https://musharna-plant-genomics-mcp.hf.space/gradio_api/mcp/sse"
    }
  }
}
```

Then restart the client, or reload its MCP servers, and ask it to list the server's tools to confirm it started.

Tools 8

  • plant_genomics_mcp_ensembl_plants_lookup_locus Fetch gene metadata for a plant locus from Ensembl Plants. Returns display name, coordinates, strand, biotype and description.
  • plant_genomics_mcp_gene_report One-shot "tell me about this gene" dossier, as rendered Markdown. Resolves the locus through Ensembl Plants and UniProt, then fans out in parallel to cross-references, KEGG pathways, STRING interactors, Europe PMC literature and QuickGO terms. Ensembl is the root: if it fails there is no dossier. Any single downstream backend failing degrades just that section to an "Unavailable" note; the rest still renders.
  • plant_genomics_mcp_go_enrichment GO and KEGG over-representation analysis for a gene LIST, via g:Profiler. Where go_annotations answers "what terms does this one gene carry", this answers "what is my gene SET enriched for" — the usual question for a differential-expression or co-expression cluster.
  • plant_genomics_mcp_gramene_homologs Orthologs and paralogs for a plant locus, from Gramene compara. The projection carries target locus, homology category and shared gene tree, but not per-row taxon or protein ID.
  • plant_genomics_mcp_locus_go_annotations Gene Ontology annotations for a plant locus, from QuickGO (EBI). The locus is first resolved to a UniProt accession, then QuickGO is queried by gene product. A locus with no UniProt entry cannot be queried, and that resolution failure is raised rather than returned as an empty result.
  • plant_genomics_mcp_locus_literature Search Europe PMC for literature mentioning a plant locus. For non-Arabidopsis species the common name is appended to the query to disambiguate locus IDs.
  • plant_genomics_mcp_resolve_locus_to_uniprot Resolve a plant locus to its canonical UniProtKB record. Prefers reviewed (Swiss-Prot) entries and falls back to unreviewed (TrEMBL) when no curated record exists, which is common outside Arabidopsis.
  • plant_genomics_mcp_string_interactions Protein-protein interaction partners from STRING-DB. Accepts a UniProt accession or a locus identifier; the latter is resolved through UniProt first. Returns first-neighbour partners with the combined STRING score and its per-channel sub-scores.

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