action monarchinitiative_get_annotate_entities {
  label: "Annotate a given content using SciGraph annotator and get all entities from content"
  provider: monarchinitiative
  method: GET
  path: "/nlp/annotate/entities"
  encoding: json
  input: {
    type: "object"
    properties: {
      content: {
        type: "string"
      }
      exclude_category: {
        type: "array"
        items: {
          type: "string"
        }
      }
      include_abbreviation: {
        type: "boolean"
      }
      include_acronym: {
        type: "boolean"
      }
      include_category: {
        type: "array"
        items: {
          type: "string"
        }
      }
      include_numbers: {
        type: "boolean"
      }
      longest_only: {
        type: "boolean"
      }
      min_length: {
        type: "string"
      }
    }
    additionalProperties: false
  }
  output: {
    type: "object"
    properties: {
      content: {
        type: "string"
      }
      spans: {
        type: "array"
        description: "A marked-up span of text"
        items: {
          type: "object"
          properties: {
            end: {
              type: "integer"
              description: "end of span text relative to content"
            }
            start: {
              type: "integer"
              description: "start of span text relative to content"
            }
            text: {
              type: "string"
              description: "span text"
            }
            token: {
              type: "array"
              description: "A token or entity extracted from the span text"
              items: {
                type: "object"
                properties: {
                  categories: {
                    type: "array"
                    description: "entity categories"
                    items: {
                      type: "string"
                    }
                  }
                  id: {
                    type: "string"
                    description: "The CURIE for the entity or token"
                  }
                  terms: {
                    type: "array"
                    description: "terms"
                    items: {
                      type: "string"
                    }
                  }
                }
              }
            }
          }
        }
      }
    }
  }
}