◎OpenBio

For AI Agents

Tool Definitions

Copy-pasteable tool definitions for the three core OpenBio endpoints. Available in OpenAI function calling format and Anthropic tool use format.

get_subject_evidence

Retrieve evidence assertions for a single subject. The most commonly used tool — call this before answering any question about a specific patient or organism.

{
  "name": "get_subject_evidence",
  "description": "Retrieve evidence assertions for a biological subject from OpenBio. Returns typed assertions with trust scores and provenance.",
  "parameters": {
    "type": "object",
    "properties": {
      "subject_id": {
        "type": "string",
        "description": "The OpenBio subject identifier (e.g. 'james-58')"
      },
      "trust_layers": {
        "type": "array",
        "items": {
          "type": "string",
          "enum": ["source_fact", "normalized_fact", "extracted_annotation", "derived_feature", "model_output", "hypothesis"]
        },
        "description": "Trust layers to include. Omit for all layers."
      },
      "evidence_types": {
        "type": "array",
        "items": { "type": "string" },
        "description": "Evidence types to filter (e.g. ['lab_result', 'genomic_variant'])"
      },
      "max_assertions": {
        "type": "integer",
        "default": 50,
        "description": "Maximum number of assertions to return"
      }
    },
    "required": ["subject_id"]
  }
}

query_cohort

Find subjects matching multi-criteria evidence conditions. Use when your agent needs to reason about populations, not just individuals.

{
  "name": "query_cohort",
  "description": "Query OpenBio for subjects matching multi-criteria evidence conditions. Supports cross-species queries.",
  "parameters": {
    "type": "object",
    "properties": {
      "criteria": {
        "type": "array",
        "items": {
          "type": "object",
          "properties": {
            "type": { "type": "string" },
            "code": { "type": "string" },
            "value": {
              "type": "object",
              "properties": {
                "lt": { "type": "number" },
                "gt": { "type": "number" },
                "eq": { "type": "number" }
              }
            }
          },
          "required": ["type"]
        },
        "description": "Evidence criteria — subjects must match ALL criteria"
      },
      "subject_types": {
        "type": "array",
        "items": { "type": "string" },
        "description": "Organism types to search (human, canine, primate, cell_line, microbial)"
      },
      "trust_layers": {
        "type": "array",
        "items": { "type": "string" }
      }
    },
    "required": ["criteria"]
  }
}

get_provenance_chain

Retrieve the full transformation history for a single assertion. Use when your agent needs to cite its sources or explain how a value was derived.

{
  "name": "get_provenance_chain",
  "description": "Retrieve the full provenance chain for an evidence assertion — source, transformation history, and trust level at each step.",
  "parameters": {
    "type": "object",
    "properties": {
      "assertion_id": {
        "type": "string",
        "description": "The OpenBio assertion identifier"
      }
    },
    "required": ["assertion_id"]
  }
}