How to setup MCP servers to access GBIF dataset from Claude Desktop

We will be setting up two MCP servers

1. A BigQuery MCP server to access GBIF dataset on BigQuery
2. A MCP server to provide context to LLMs (in this case, Claude) how to use the GBIF schema

BigQuery MCP

1. Clone https://github.com/ANewProfile/gbif-bigquery-mcp
2. Install dependencies and build code locally

git clone https://github.com/ANewProfile/gbif-bigquery-mcp
cd gbif-bigquery-mcp
npm install

# Build
npm run build

3. Add the following to your Claude desktop configuration fil ~/Library/Application Support/Claude/claude_desktop_config.json. Note this is if you are using Benjie's Google Cloud setup. Obtain the gbif_service_account_key.json file from Benjie. You can also create your own Google Cloud project and generate a service account key.

{
  "mcpServers": {
    "gbif-bigquery": {
      "command": "node",
      "args": [
        "<path-to-your-gbif-bigquery-mcp-working-directory>/dist/index.js",
        "--project-id",
        "gbif-data-if-i-can-get-it",
        "--key-file",
        "<path-to-benjie-gbif-service-account-key-file>/gbif_service_account_key.json"
      ]
    }
  }
}

4. If you start Claude Desktop, you should now be able to enter the following prompt and see Claude uses the MCP server (it will ask you for permission) to obtain the dataset schema.

Can you query GBIF database and get me schema for the occurrence table? It's
called bigquery-public-data.gbif.occurrences

MCP server to provide context about the GBIF dataset

1. Clone this repo, https://github.com/ANewProfile/gbif-custom-mcp
2. Run the following to update your Claude desktop configuration file

uv run mcp install gbif-context.py

3. Restart Claude Desktop, you should now be able to choose to "Attach from MCP" and select "gbif-context". Afterward, the folllowing prompt shoud work, and specifically if you look at the SQL, there is now a filter for the occurrencestatus field.

Can you query GBIF dataset to find count of mosquitos in the US in 2022?

4. Depends on how uv is installed on your OS and your path settings, you may need to explicitly specify the path to uv in the Claude desktop configuration file.