get_toxicity_endpoints

Instructions

Get toxicity endpoint study data from ENDPOINT_STUDY table by TOX_ID.

Retrieves detailed toxicity endpoint records including NOAEL, LD50, and other
toxicity measurements from animal and in vitro studies. This tool provides the
experimental data used to assess the toxicological effects of food substances.

Args:
    tox_id: Single TOX_ID (int) or list of TOX_IDs (list[int]) to query.
           Use search_substance tool first to find TOX_IDs through the STUDY table.

Returns:
    JSON string containing a DataFrame with toxicity endpoint records. Each record
    includes endpoint type, toxicity values, study conditions, and target organs.

The returned data includes:
- Endpoint information: ENDPOINT, ENDPOINT_CODE (e.g., NOAEL, LD50, LOAEL)
- Toxicity values: VALUE, VALUE_MILLI, DOSEUNIT, DOSEUNITFULLTEXT
- Qualifier: QUALIFIER (e.g., "greater than", "less than")
- Study conditions: SPECIES, STRAIN, SEX, ROUTE, EXP_DURATION, DURATIONUNIT
- Target information: TARGETTISSUE, EFFECT_DESC
- Toxicity classification: TOXICITY (e.g., "acute", "chronic")
- Study details: TESTTYPE, GUIDELINE, GLP_COMPL, REMARKS

Note: Multiple records may be returned if multiple TOX_IDs are provided or if
a single study has multiple endpoints measured.

<dictionary_descriptions>
<name>STUDY_CATEGORY</name>
<description>Indicates the reason for testing Human health, Exotoxicology, Animal health (target) or Animal health (non target)</description>
<name>TESTSUBSTANCE</name>
<description>Description of the test material used in the toxocological study</description>
<name>TESTTYPE_CODE</name>
<description>Transmission code for the type of toxicological test</description>
<name>SPECIES_ID</name>
<description>Internal unique identifier of organism/cell culture used in the toxicological study</description>
<name>SPECIES</name>
<description>Description of the organism/cell culture used in the toxicological study</description>
<name>SEX</name>
<description>Indicates the sex of tested animals</description>
<name>NUMBER_INDIVIDUALS</name>
<description>Number of organisms dosed at each dose level of the toxicological study</description>
<name>CONTROL</name>
<description>Indicates whether and what type of concurrent control groups were used</description>
<name>EFFECT_DESC</name>
<description>Description of the effects observed in the toxicological study</description>
<name>REMARKS</name>
<description>Additional remarks on toxicological study. Free text on hazard assessment including (if necessary): 1) short explanation on how the study has been carried on; 2) any conclusions on the hazard identication (for example, explanation on why an hazard could not be identified)</description>
</dictionary_descriptions>

Implementation Reference

• src/mcp_openfoodtox/tools/get_toxicity_endpoints.py:5-57 (handler)

  The main handler function for the 'get_toxicity_endpoints' tool. It queries the 'endpoint_study' table using a helper function and returns the results as JSON.

  def get_toxicity_endpoints(tox_id: Union[int, list[int]]):
      """
      Get toxicity endpoint study data from ENDPOINT_STUDY table by TOX_ID.
  
      Retrieves detailed toxicity endpoint records including NOAEL, LD50, and other
      toxicity measurements from animal and in vitro studies. This tool provides the
      experimental data used to assess the toxicological effects of food substances.
  
      Args:
          tox_id: Single TOX_ID (int) or list of TOX_IDs (list[int]) to query.
                 Use search_substance tool first to find TOX_IDs through the STUDY table.
  
      Returns:
          JSON string containing a DataFrame with toxicity endpoint records. Each record
          includes endpoint type, toxicity values, study conditions, and target organs.
  
      The returned data includes:
      - Endpoint information: ENDPOINT, ENDPOINT_CODE (e.g., NOAEL, LD50, LOAEL)
      - Toxicity values: VALUE, VALUE_MILLI, DOSEUNIT, DOSEUNITFULLTEXT
      - Qualifier: QUALIFIER (e.g., "greater than", "less than")
      - Study conditions: SPECIES, STRAIN, SEX, ROUTE, EXP_DURATION, DURATIONUNIT
      - Target information: TARGETTISSUE, EFFECT_DESC
      - Toxicity classification: TOXICITY (e.g., "acute", "chronic")
      - Study details: TESTTYPE, GUIDELINE, GLP_COMPL, REMARKS
  
      Note: Multiple records may be returned if multiple TOX_IDs are provided or if
      a single study has multiple endpoints measured.
  
      <dictionary_descriptions>
      <name>STUDY_CATEGORY</name>
      <description>Indicates the reason for testing Human health, Exotoxicology, Animal health (target) or Animal health (non target)</description>
      <name>TESTSUBSTANCE</name>
      <description>Description of the test material used in the toxocological study</description>
      <name>TESTTYPE_CODE</name>
      <description>Transmission code for the type of toxicological test</description>
      <name>SPECIES_ID</name>
      <description>Internal unique identifier of organism/cell culture used in the toxicological study</description>
      <name>SPECIES</name>
      <description>Description of the organism/cell culture used in the toxicological study</description>
      <name>SEX</name>
      <description>Indicates the sex of tested animals</description>
      <name>NUMBER_INDIVIDUALS</name>
      <description>Number of organisms dosed at each dose level of the toxicological study</description>
      <name>CONTROL</name>
      <description>Indicates whether and what type of concurrent control groups were used</description>
      <name>EFFECT_DESC</name>
      <description>Description of the effects observed in the toxicological study</description>
      <name>REMARKS</name>
      <description>Additional remarks on toxicological study. Free text on hazard assessment including (if necessary): 1) short explanation on how the study has been carried on; 2) any conclusions on the hazard identication (for example, explanation on why an hazard could not be identified)</description>
      </dictionary_descriptions>
      """
      df = query_by_id(tox_id, "endpoint_study")
      return df.to_json()

• main.py:4-26 (registration)

  The tool is imported and registered with the MCP server using mcp.add_tool in the main server file.

  from src.mcp_openfoodtox.tools.get_toxicity_endpoints import get_toxicity_endpoints
  from src.mcp_openfoodtox.tools.get_genotox_details import get_genotox_details
  from src.mcp_openfoodtox.tools.get_opinions import get_opinions
  from src.mcp_openfoodtox.tools.substance_safety_assessment import get_substance_safety_assessment
  from src.mcp_openfoodtox.tools.list_substances_by_class_and_safety import (
      list_substances_by_class_and_safety,
  )
  from src.mcp_openfoodtox.tools.list_hazard_ids_by_assessment import list_hazard_ids_by_assessment
  from src.mcp_openfoodtox.tools.list_substances_by_assessment import list_substances_by_assessment
  
  # Initialize FastMCP server
  mcp = FastMCP("mcp-openfoodtox")
  
  # Add tools to the server
  mcp.add_tool(search_substance)
  mcp.add_tool(get_risk_assessments)
  mcp.add_tool(get_toxicity_endpoints)
  mcp.add_tool(get_genotox_details)
  mcp.add_tool(get_opinions)
  mcp.add_tool(get_substance_safety_assessment)
  mcp.add_tool(list_substances_by_class_and_safety)
  mcp.add_tool(list_hazard_ids_by_assessment)
  mcp.add_tool(list_substances_by_assessment)