BioOntology MCP Server

MIT License

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batch_annotate

Annotate multiple texts simultaneously using specified ontologies with options to return longest matches and whole-word-only annotations.

Instructions

Process multiple texts for annotation efficiently

Input Schema

Name	Required	Description
`longest_only`	No	Return only longest matches (default: true)
`ontologies`	No	Comma-separated ontology acronyms
`texts`	Yes	Array of texts to annotate (max 10)
`whole_word_only`	No	Match whole words only (default: true)

Input Schema (JSON Schema)

{
  "properties": {
    "longest_only": {
      "description": "Return only longest matches (default: true)",
      "type": "boolean"
    },
    "ontologies": {
      "description": "Comma-separated ontology acronyms",
      "type": "string"
    },
    "texts": {
      "description": "Array of texts to annotate (max 10)",
      "items": {
        "type": "string"
      },
      "maxItems": 10,
      "minItems": 1,
      "type": "array"
    },
    "whole_word_only": {
      "description": "Match whole words only (default: true)",
      "type": "boolean"
    }
  },
  "required": [
    "texts"
  ],
  "type": "object"
}

Install Server

HTTP connection URL

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