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ADMEIVIVE API Reference

pycomptox.hazard.admeivive.ADMEIVIVE

Bases: CachedAPIClient

Client for accessing ADME-IVIVE (Absorption, Distribution, Metabolism, Excretion - In Vitro to In Vivo Extrapolation) toxicokinetics data from EPA CompTox Dashboard.

This class provides access to toxicokinetics data describing how chemicals behave in the human body. Data values are:

  1. Measured - either in vitro or in vivo
  2. Predicted - from chemical properties using in silico tools
  3. Computed - with mathematical models simulating toxicokinetics

Key Parameters: - Intrinsic hepatic clearance - Fraction unbound in plasma - Volume of distribution - PK half-life - Steady-state plasma concentration

Data Sources: - httk R package: In vitro measured values (https://CRAN.R-project.org/package=httk) - CvTdb: In vivo concentration vs. time data (https://doi.org/10.1038/s41597-020-0455-1) - invivoPKfit: In vivo estimates (https://github.com/USEPA/CompTox-ExpoCast-invivoPKfit)

Note: Some measured values may be assumed from surrogate species data. The Data Source Species column identifies the species source for measured data. These assumed measured values are used in calculations to estimate other outcomes.

Parameters:

Name Type Description Default
api_key str

CompTox API key. If not provided, will attempt to load from saved configuration or COMPTOX_API_KEY environment variable.

 None
base_url str

Base URL for the CompTox API. Defaults to EPA's endpoint.

 'https://comptox.epa.gov/ctx-api/'
time_delay_between_calls float

Delay in seconds between API calls for rate limiting. Default is 0.0 (no delay).

 0.0
use_cache bool

Whether to use caching by default. Default is True.

 required
Example

from pycomptox.hazard import ADMEIVIVE adme = ADMEIVIVE()

Get ADME-IVIVE data for bisphenol A

data = adme.get_all_data_by_dtxsid_ccd_projection("DTXSID7020182")

if data: ... for record in data: ... param = record.get('parameter', 'Unknown') ... value = record.get('value', 'N/A') ... units = record.get('units', '') ... print(f"{param}: {value} {units}")

Source code in src/pycomptox/hazard/admeivive.py 
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class ADMEIVIVE(CachedAPIClient):
    """
    Client for accessing ADME-IVIVE (Absorption, Distribution, Metabolism, Excretion - 
    In Vitro to In Vivo Extrapolation) toxicokinetics data from EPA CompTox Dashboard.

    This class provides access to toxicokinetics data describing how chemicals behave 
    in the human body. Data values are:

    1. **Measured** - either in vitro or in vivo
    2. **Predicted** - from chemical properties using in silico tools
    3. **Computed** - with mathematical models simulating toxicokinetics

    Key Parameters:
    - Intrinsic hepatic clearance
    - Fraction unbound in plasma
    - Volume of distribution
    - PK half-life
    - Steady-state plasma concentration

    Data Sources:
    - **httk R package**: In vitro measured values (https://CRAN.R-project.org/package=httk)
    - **CvTdb**: In vivo concentration vs. time data (https://doi.org/10.1038/s41597-020-0455-1)
    - **invivoPKfit**: In vivo estimates (https://github.com/USEPA/CompTox-ExpoCast-invivoPKfit)

    Note: Some measured values may be assumed from surrogate species data. The Data 
    Source Species column identifies the species source for measured data. These 
    assumed measured values are used in calculations to estimate other outcomes.

    Args:
        api_key (str, optional): CompTox API key. If not provided, will attempt
            to load from saved configuration or COMPTOX_API_KEY environment variable.
        base_url (str): Base URL for the CompTox API. Defaults to EPA's endpoint.
        time_delay_between_calls (float): Delay in seconds between API calls for
            rate limiting. Default is 0.0 (no delay).
        use_cache (bool): Whether to use caching by default. Default is True.

    Example:
        >>> from pycomptox.hazard import ADMEIVIVE
        >>> adme = ADMEIVIVE()
        >>> 
        >>> # Get ADME-IVIVE data for bisphenol A
        >>> data = adme.get_all_data_by_dtxsid_ccd_projection("DTXSID7020182")
        >>> 
        >>> if data:
        ...     for record in data:
        ...         param = record.get('parameter', 'Unknown')
        ...         value = record.get('value', 'N/A')
        ...         units = record.get('units', '')
        ...         print(f"{param}: {value} {units}")
    """

    def __init__(
        self,
        api_key: Optional[str] = None,
        base_url: str = "https://comptox.epa.gov/ctx-api/",
        time_delay_between_calls: float = 0.0,
        **kwargs: Any
    ):
        """
        Initialize the ADMEIVIVE client.

        Args:
            api_key: CompTox API key (optional, will be loaded from config if not provided)
            base_url: Base URL for the CompTox API
            time_delay_between_calls: Delay between API calls in seconds
            kwargs: Additional arguments for CachedAPIClient (cache_manager, use_cache)

        Raises:
            ValueError: If no API key is provided or found in configuration
        """
        super().__init__(
            api_key=api_key,
            base_url=base_url,
            time_delay_between_calls=time_delay_between_calls,
            **kwargs
        )

    def get_all_data_by_dtxsid_ccd_projection(
        self, 
        dtxsid: str, 
        projection: Optional[str] = None,
        use_cache: Optional[bool] = None
    ) -> List[Dict[str, Any]]:
        """
        Get ADME-IVIVE toxicokinetics data by DTXSID.

        Retrieves all ADME-IVIVE (Absorption, Distribution, Metabolism, Excretion - 
        In Vitro to In Vivo Extrapolation) data for a chemical. Optionally use 
        projection for CompTox Dashboard-specific formatting.

        The data includes toxicokinetic parameters such as:
        - Intrinsic hepatic clearance (CLint)
        - Fraction unbound in plasma (Fup)
        - Volume of distribution (Vd)
        - Pharmacokinetic half-life (t½)
        - Steady-state plasma concentration (Css)
        - Oral bioavailability
        - Renal clearance
        - Blood:plasma ratio

        Data types include:
        - **In vitro measured**: Direct measurements from in vitro assays
        - **In vivo measured**: Derived from concentration-time data (CvTdb)
        - **In silico predicted**: Predictions from chemical properties
        - **Computed**: Calculated using httk or invivoPKfit models

        Args:
            dtxsid: DSSTox Substance Identifier (e.g., 'DTXSID7020182')
            projection: Optional projection name. Use 'ccd-adme-data' for 
                CompTox Dashboard ADME-IVIVE page format. If None, returns 
                default ADME-IVIVE data.
            use_cache: Whether to use cache for this request. If None, uses
                the instance default setting.

        Returns:
            List of dictionaries containing ADME-IVIVE data with fields such as:
                - dtxsid (str): Chemical identifier
                - parameter (str): ADME parameter name
                - value (float): Parameter value
                - units (str): Units of measurement
                - dataType (str): Type of data (measured/predicted/computed)
                - source (str): Data source (httk, CvTdb, in silico tool)
                - species (str): Species for measured data
                - method (str): Measurement or prediction method
                - reference (str): Literature reference
                - confidence (str): Confidence level or quality indicator
                - Notes: Exact fields vary by projection

        Raises:
            ValueError: If dtxsid is not a valid non-empty string
            PermissionError: If API key is invalid
            RuntimeError: For other API errors

        Example:
            >>> from pycomptox.hazard import ADMEIVIVE
            >>> adme = ADMEIVIVE()
            >>> 
            >>> # Get ADME-IVIVE data for bisphenol A
            >>> data = adme.get_all_data_by_dtxsid_ccd_projection("DTXSID7020182")
            >>> 
            >>> if data:
            ...     print(f"Found {len(data)} ADME-IVIVE parameters")
            ...     
            ...     # Group by data type
            ...     by_type = {}
            ...     for record in data:
            ...         dtype = record.get('dataType', 'Unknown')
            ...         if dtype not in by_type:
            ...             by_type[dtype] = []
            ...         by_type[dtype].append(record)
            ...     
            ...     print(f"\nData types available:")
            ...     for dtype, records in sorted(by_type.items()):
            ...         print(f"  {dtype}: {len(records)} parameter(s)")
            ...     
            ...     # Show key parameters
            ...     print(f"\nKey toxicokinetic parameters:")
            ...     key_params = ['Clint', 'Fup', 'Vd', 't1/2', 'Css']
            ...     for record in data:
            ...         param = record.get('parameter', '')
            ...         if any(kp in param for kp in key_params):
            ...             value = record.get('value', 'N/A')
            ...             units = record.get('units', '')
            ...             source = record.get('source', 'Unknown')
            ...             print(f"  {param}: {value} {units} ({source})")
            >>> 
            >>> # Get with CompTox Dashboard projection
            >>> ccd_data = adme.get_all_data_by_dtxsid_ccd_projection(
            ...     "DTXSID7020182", 
            ...     projection="ccd-adme-data"
            ... )
            >>> 
            >>> # Compare in vitro vs in vivo data
            >>> if data:
            ...     in_vitro = [r for r in data if 'in vitro' in str(r.get('dataType', '')).lower()]
            ...     in_vivo = [r for r in data if 'in vivo' in str(r.get('dataType', '')).lower()]
            ...     print(f"\nIn vitro parameters: {len(in_vitro)}")
            ...     print(f"In vivo parameters: {len(in_vivo)}")

        Note:
            - Data may include measured, predicted, and computed values
            - Some measured values may be from surrogate species
            - Check 'species' field to identify data source species
            - Computed values are derived using httk or invivoPKfit R packages
            - Use projection='ccd-adme-data' for dashboard-formatted data
        """
        if not dtxsid or not isinstance(dtxsid, str):
            raise ValueError("dtxsid must be a non-empty string")

        endpoint = f"hazard/adme-ivive/search/by-dtxsid/{dtxsid}"
        params = {"projection": projection} if projection else None

        return self._make_cached_request(endpoint, params=params, use_cache=use_cache)

__init__(api_key=None, base_url='https://comptox.epa.gov/ctx-api/', time_delay_between_calls=0.0, **kwargs)

Initialize the ADMEIVIVE client.

Parameters:

Name Type Description Default
api_key Optional[str]

CompTox API key (optional, will be loaded from config if not provided)

 None
base_url str

Base URL for the CompTox API

 'https://comptox.epa.gov/ctx-api/'
time_delay_between_calls float

Delay between API calls in seconds

 0.0
kwargs Any

Additional arguments for CachedAPIClient (cache_manager, use_cache)

 {}

Raises:

Type Description
ValueError

If no API key is provided or found in configuration
Source code in src/pycomptox/hazard/admeivive.py 
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def __init__(
    self,
    api_key: Optional[str] = None,
    base_url: str = "https://comptox.epa.gov/ctx-api/",
    time_delay_between_calls: float = 0.0,
    **kwargs: Any
):
    """
    Initialize the ADMEIVIVE client.

    Args:
        api_key: CompTox API key (optional, will be loaded from config if not provided)
        base_url: Base URL for the CompTox API
        time_delay_between_calls: Delay between API calls in seconds
        kwargs: Additional arguments for CachedAPIClient (cache_manager, use_cache)

    Raises:
        ValueError: If no API key is provided or found in configuration
    """
    super().__init__(
        api_key=api_key,
        base_url=base_url,
        time_delay_between_calls=time_delay_between_calls,
        **kwargs
    )

get_all_data_by_dtxsid_ccd_projection(dtxsid, projection=None, use_cache=None) 

    Get ADME-IVIVE toxicokinetics data by DTXSID.

    Retrieves all ADME-IVIVE (Absorption, Distribution, Metabolism, Excretion - 
    In Vitro to In Vivo Extrapolation) data for a chemical. Optionally use 
    projection for CompTox Dashboard-specific formatting.

    The data includes toxicokinetic parameters such as:
    - Intrinsic hepatic clearance (CLint)
    - Fraction unbound in plasma (Fup)
    - Volume of distribution (Vd)
    - Pharmacokinetic half-life (t½)
    - Steady-state plasma concentration (Css)
    - Oral bioavailability
    - Renal clearance
    - Blood:plasma ratio

    Data types include:
    - **In vitro measured**: Direct measurements from in vitro assays
    - **In vivo measured**: Derived from concentration-time data (CvTdb)
    - **In silico predicted**: Predictions from chemical properties
    - **Computed**: Calculated using httk or invivoPKfit models

    Args:
        dtxsid: DSSTox Substance Identifier (e.g., 'DTXSID7020182')
        projection: Optional projection name. Use 'ccd-adme-data' for 
            CompTox Dashboard ADME-IVIVE page format. If None, returns 
            default ADME-IVIVE data.
        use_cache: Whether to use cache for this request. If None, uses
            the instance default setting.

    Returns:
        List of dictionaries containing ADME-IVIVE data with fields such as:
            - dtxsid (str): Chemical identifier
            - parameter (str): ADME parameter name
            - value (float): Parameter value
            - units (str): Units of measurement
            - dataType (str): Type of data (measured/predicted/computed)
            - source (str): Data source (httk, CvTdb, in silico tool)
            - species (str): Species for measured data
            - method (str): Measurement or prediction method
            - reference (str): Literature reference
            - confidence (str): Confidence level or quality indicator
            - Notes: Exact fields vary by projection

    Raises:
        ValueError: If dtxsid is not a valid non-empty string
        PermissionError: If API key is invalid
        RuntimeError: For other API errors

    Example:
        >>> from pycomptox.hazard import ADMEIVIVE
        >>> adme = ADMEIVIVE()
        >>> 
        >>> # Get ADME-IVIVE data for bisphenol A
        >>> data = adme.get_all_data_by_dtxsid_ccd_projection("DTXSID7020182")
        >>> 
        >>> if data:
        ...     print(f"Found {len(data)} ADME-IVIVE parameters")
        ...     
        ...     # Group by data type
        ...     by_type = {}
        ...     for record in data:
        ...         dtype = record.get('dataType', 'Unknown')
        ...         if dtype not in by_type:
        ...             by_type[dtype] = []
        ...         by_type[dtype].append(record)
        ...     
        ...     print(f"

Data types available:") ... for dtype, records in sorted(by_type.items()): ... print(f" {dtype}: {len(records)} parameter(s)") ...
... # Show key parameters ... print(f" Key toxicokinetic parameters:") ... key_params = ['Clint', 'Fup', 'Vd', 't1/2', 'Css'] ... for record in data: ... param = record.get('parameter', '') ... if any(kp in param for kp in key_params): ... value = record.get('value', 'N/A') ... units = record.get('units', '') ... source = record.get('source', 'Unknown') ... print(f" {param}: {value} {units} ({source})") >>> >>> # Get with CompTox Dashboard projection >>> ccd_data = adme.get_all_data_by_dtxsid_ccd_projection( ... "DTXSID7020182", ... projection="ccd-adme-data" ... ) >>> >>> # Compare in vitro vs in vivo data >>> if data: ... in_vitro = [r for r in data if 'in vitro' in str(r.get('dataType', '')).lower()] ... in_vivo = [r for r in data if 'in vivo' in str(r.get('dataType', '')).lower()] ... print(f" In vitro parameters: {len(in_vitro)}") ... print(f"In vivo parameters: {len(in_vivo)}")

    Note:
        - Data may include measured, predicted, and computed values
        - Some measured values may be from surrogate species
        - Check 'species' field to identify data source species
        - Computed values are derived using httk or invivoPKfit R packages
        - Use projection='ccd-adme-data' for dashboard-formatted data
Source code in src/pycomptox/hazard/admeivive.py 
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def get_all_data_by_dtxsid_ccd_projection(
    self, 
    dtxsid: str, 
    projection: Optional[str] = None,
    use_cache: Optional[bool] = None
) -> List[Dict[str, Any]]:
    """
    Get ADME-IVIVE toxicokinetics data by DTXSID.

    Retrieves all ADME-IVIVE (Absorption, Distribution, Metabolism, Excretion - 
    In Vitro to In Vivo Extrapolation) data for a chemical. Optionally use 
    projection for CompTox Dashboard-specific formatting.

    The data includes toxicokinetic parameters such as:
    - Intrinsic hepatic clearance (CLint)
    - Fraction unbound in plasma (Fup)
    - Volume of distribution (Vd)
    - Pharmacokinetic half-life (t½)
    - Steady-state plasma concentration (Css)
    - Oral bioavailability
    - Renal clearance
    - Blood:plasma ratio

    Data types include:
    - **In vitro measured**: Direct measurements from in vitro assays
    - **In vivo measured**: Derived from concentration-time data (CvTdb)
    - **In silico predicted**: Predictions from chemical properties
    - **Computed**: Calculated using httk or invivoPKfit models

    Args:
        dtxsid: DSSTox Substance Identifier (e.g., 'DTXSID7020182')
        projection: Optional projection name. Use 'ccd-adme-data' for 
            CompTox Dashboard ADME-IVIVE page format. If None, returns 
            default ADME-IVIVE data.
        use_cache: Whether to use cache for this request. If None, uses
            the instance default setting.

    Returns:
        List of dictionaries containing ADME-IVIVE data with fields such as:
            - dtxsid (str): Chemical identifier
            - parameter (str): ADME parameter name
            - value (float): Parameter value
            - units (str): Units of measurement
            - dataType (str): Type of data (measured/predicted/computed)
            - source (str): Data source (httk, CvTdb, in silico tool)
            - species (str): Species for measured data
            - method (str): Measurement or prediction method
            - reference (str): Literature reference
            - confidence (str): Confidence level or quality indicator
            - Notes: Exact fields vary by projection

    Raises:
        ValueError: If dtxsid is not a valid non-empty string
        PermissionError: If API key is invalid
        RuntimeError: For other API errors

    Example:
        >>> from pycomptox.hazard import ADMEIVIVE
        >>> adme = ADMEIVIVE()
        >>> 
        >>> # Get ADME-IVIVE data for bisphenol A
        >>> data = adme.get_all_data_by_dtxsid_ccd_projection("DTXSID7020182")
        >>> 
        >>> if data:
        ...     print(f"Found {len(data)} ADME-IVIVE parameters")
        ...     
        ...     # Group by data type
        ...     by_type = {}
        ...     for record in data:
        ...         dtype = record.get('dataType', 'Unknown')
        ...         if dtype not in by_type:
        ...             by_type[dtype] = []
        ...         by_type[dtype].append(record)
        ...     
        ...     print(f"\nData types available:")
        ...     for dtype, records in sorted(by_type.items()):
        ...         print(f"  {dtype}: {len(records)} parameter(s)")
        ...     
        ...     # Show key parameters
        ...     print(f"\nKey toxicokinetic parameters:")
        ...     key_params = ['Clint', 'Fup', 'Vd', 't1/2', 'Css']
        ...     for record in data:
        ...         param = record.get('parameter', '')
        ...         if any(kp in param for kp in key_params):
        ...             value = record.get('value', 'N/A')
        ...             units = record.get('units', '')
        ...             source = record.get('source', 'Unknown')
        ...             print(f"  {param}: {value} {units} ({source})")
        >>> 
        >>> # Get with CompTox Dashboard projection
        >>> ccd_data = adme.get_all_data_by_dtxsid_ccd_projection(
        ...     "DTXSID7020182", 
        ...     projection="ccd-adme-data"
        ... )
        >>> 
        >>> # Compare in vitro vs in vivo data
        >>> if data:
        ...     in_vitro = [r for r in data if 'in vitro' in str(r.get('dataType', '')).lower()]
        ...     in_vivo = [r for r in data if 'in vivo' in str(r.get('dataType', '')).lower()]
        ...     print(f"\nIn vitro parameters: {len(in_vitro)}")
        ...     print(f"In vivo parameters: {len(in_vivo)}")

    Note:
        - Data may include measured, predicted, and computed values
        - Some measured values may be from surrogate species
        - Check 'species' field to identify data source species
        - Computed values are derived using httk or invivoPKfit R packages
        - Use projection='ccd-adme-data' for dashboard-formatted data
    """
    if not dtxsid or not isinstance(dtxsid, str):
        raise ValueError("dtxsid must be a non-empty string")

    endpoint = f"hazard/adme-ivive/search/by-dtxsid/{dtxsid}"
    params = {"projection": projection} if projection else None

    return self._make_cached_request(endpoint, params=params, use_cache=use_cache)