ToxValDBCancer API Reference¶

`pycomptox.hazard.toxvaldbcancer.ToxValDBCancer` ¶

Bases: CachedAPIClient

Client for accessing ToxValDB cancer summary data from EPA CompTox Dashboard.

A carcinogen is a substance that may cause cancer and pose a health hazard. Carcinogens are subject to specific controls and regulations. National and international health agencies evaluate new and existing chemicals to determine if they are likely to be carcinogens through a process called cancer hazard identification. This process combines human and animal data with supporting evidence to characterize the weight-of-evidence (WOE) regarding the agent's potential as a human carcinogen.

The general categories recognized by the guidelines are: - Carcinogenic to humans - Likely to be carcinogenic to humans - Suggestive evidence of carcinogenic potential

This class provides methods for retrieving summary-level cancer data associated with chemicals.

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 ToxValDBCancer cancer = ToxValDBCancer()

Get cancer data for a chemical¶

data = cancer.get_data_by_dtxsid("DTXSID0021125") if data: ... print(f"Cancer classification: {data[0].get('classification')}")

Source code in src/pycomptox/hazard/toxvaldbcancer.py

class ToxValDBCancer(CachedAPIClient):
    """
    Client for accessing ToxValDB cancer summary data from EPA CompTox Dashboard.

    A carcinogen is a substance that may cause cancer and pose a health hazard. 
    Carcinogens are subject to specific controls and regulations. National and 
    international health agencies evaluate new and existing chemicals to determine 
    if they are likely to be carcinogens through a process called cancer hazard identification. 
    This process combines human and animal data with supporting evidence to characterize 
    the weight-of-evidence (WOE) regarding the agent's potential as a human carcinogen. 

    The general categories recognized by the guidelines are:
    - Carcinogenic to humans
    - Likely to be carcinogenic to humans
    - Suggestive evidence of carcinogenic potential

    This class provides methods for retrieving summary-level cancer data associated 
    with chemicals.

    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 ToxValDBCancer
        >>> cancer = ToxValDBCancer()
        >>> 
        >>> # Get cancer data for a chemical
        >>> data = cancer.get_data_by_dtxsid("DTXSID0021125")
        >>> if data:
        ...     print(f"Cancer classification: {data[0].get('classification')}")
    """

    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 ToxValDBCancer 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_data_by_dtxsid(self, dtxsid: str, 
                           use_cache: Optional[bool] = None) -> List[Dict[str, Any]]:
        """
        Get cancer summary data by DTXSID.

        Retrieves cancer hazard summary data for a specific chemical identified by 
        its DSSTox Substance Identifier (DTXSID). This includes cancer classifications,
        weight of evidence assessments, and carcinogenicity evaluations from various
        regulatory agencies and scientific organizations.

        Args:
            dtxsid: DSSTox Substance Identifier (e.g., 'DTXSID0021125')
            use_cache: Whether to use cache for this request. If None, uses
                the instance default setting.

        Returns:
            List of dictionaries containing cancer summary data with fields such as:
                - dtxsid (str): DSSTox Substance Identifier
                - classification (str): Cancer classification
                - source (str): Source of the assessment
                - woe (str): Weight of evidence
                - cancerType (str): Type of cancer
                - species (str): Test species
                - studyType (str): Type of study
                - evidence (str): Evidence description
                - route (str): Exposure route
                - Notes: Exact fields may vary based on the data source

        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 ToxValDBCancer
            >>> cancer = ToxValDBCancer()
            >>> 
            >>> # Get cancer data for benzene
            >>> data = cancer.get_data_by_dtxsid("DTXSID0021125")
            >>> 
            >>> if data:
            ...     for record in data:
            ...         print(f"Source: {record.get('source')}")
            ...         print(f"Classification: {record.get('classification')}")
            ...         if record.get('woe'):
            ...             print(f"Weight of Evidence: {record['woe']}")
            ...         if record.get('cancerType'):
            ...             print(f"Cancer Type: {record['cancerType']}")
            ...         print()
            >>> else:
            ...     print("No cancer data available for this chemical")

        Note:
            - Not all chemicals have cancer assessment data
            - Data may come from multiple sources (EPA, IARC, NTP, etc.)
            - Classifications and terminology vary by source
            - Weight of Evidence (WoE) indicates the strength and quality
              of evidence supporting the carcinogenicity assessment
        """
        if not dtxsid or not isinstance(dtxsid, str):
            raise ValueError("dtxsid must be a non-empty string")

        endpoint = f"hazard/cancer-summary/search/by-dtxsid/{dtxsid}"
        return self._make_cached_request(endpoint, use_cache=use_cache)

    def get_data_by_dtxsid_batch(self, dtxsids: List[str], 
                                 use_cache: Optional[bool] = None) -> List[Dict[str, Any]]:
        """
        Get cancer summary data for multiple chemicals in a single request.

        Batch retrieval of cancer hazard summary data for up to 200 chemicals.
        More efficient than making individual requests when querying multiple chemicals.

        Args:
            dtxsids: List of DSSTox Substance Identifiers (max 200)
            use_cache: Whether to use cache for this request. If None, uses
                the instance default setting.

        Returns:
            List of dictionaries containing cancer summary data for all
            requested chemicals. Each entry includes similar fields as
            get_data_by_dtxsid().

        Raises:
            ValueError: If dtxsids list is empty or contains more than 200 entries
            PermissionError: If API key is invalid
            RuntimeError: For other API errors

        Example:
            >>> from pycomptox.hazard import ToxValDBCancer
            >>> cancer = ToxValDBCancer()
            >>> 
            >>> # Get cancer data for multiple chemicals
            >>> dtxsids = ["DTXSID0021125", "DTXSID7020182", "DTXSID0020032"]
            >>> batch_data = cancer.get_data_by_dtxsid_batch(dtxsids)
            >>> 
            >>> # Group by chemical
            >>> by_chemical = {}
            >>> for record in batch_data:
            ...     dtxsid = record['dtxsid']
            ...     if dtxsid not in by_chemical:
            ...         by_chemical[dtxsid] = []
            ...     by_chemical[dtxsid].append(record)
            >>> 
            >>> # Display summary
            >>> for dtxsid, records in by_chemical.items():
            ...     print(f"{dtxsid}: {len(records)} cancer assessment(s)")
            ...     for record in records:
            ...         print(f"  - {record.get('source')}: {record.get('classification')}")

        Note:
            - Maximum 200 DTXSIDs per request
            - Results may include multiple assessments per chemical from different sources
            - Batch requests are more efficient than individual queries
        """
        if not dtxsids:
            raise ValueError("dtxsids list cannot be empty")

        if len(dtxsids) > 200:
            raise ValueError(f"Maximum 200 DTXSIDs allowed, got {len(dtxsids)}")

        endpoint = "hazard/cancer-summary/search/by-dtxsid/"
        return self._make_cached_request(
            endpoint, 
            json=dtxsids, 
            method='POST', 
            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 ToxValDBCancer 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/toxvaldbcancer.py

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 ToxValDBCancer 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_data_by_dtxsid(dtxsid, use_cache=None)` ¶

Get cancer summary data by DTXSID.

Retrieves cancer hazard summary data for a specific chemical identified by its DSSTox Substance Identifier (DTXSID). This includes cancer classifications, weight of evidence assessments, and carcinogenicity evaluations from various regulatory agencies and scientific organizations.

Parameters:

Name	Type	Description	Default
`dtxsid`	`str`	DSSTox Substance Identifier (e.g., 'DTXSID0021125')	required
`use_cache`	`Optional[bool]`	Whether to use cache for this request. If None, uses the instance default setting.	`None`

Returns:

Type Description

List[Dict[str, Any]]

List of dictionaries containing cancer summary data with fields such as: - dtxsid (str): DSSTox Substance Identifier - classification (str): Cancer classification - source (str): Source of the assessment - woe (str): Weight of evidence - cancerType (str): Type of cancer - species (str): Test species - studyType (str): Type of study - evidence (str): Evidence description - route (str): Exposure route - Notes: Exact fields may vary based on the data source

Raises:

Type	Description
`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 ToxValDBCancer cancer = ToxValDBCancer()

Get cancer data for benzene¶

data = cancer.get_data_by_dtxsid("DTXSID0021125")

if data: ... for record in data: ... print(f"Source: {record.get('source')}") ... print(f"Classification: {record.get('classification')}") ... if record.get('woe'): ... print(f"Weight of Evidence: {record['woe']}") ... if record.get('cancerType'): ... print(f"Cancer Type: {record['cancerType']}") ... print() else: ... print("No cancer data available for this chemical")

Note

Not all chemicals have cancer assessment data
Data may come from multiple sources (EPA, IARC, NTP, etc.)
Classifications and terminology vary by source
Weight of Evidence (WoE) indicates the strength and quality of evidence supporting the carcinogenicity assessment

Source code in src/pycomptox/hazard/toxvaldbcancer.py

def get_data_by_dtxsid(self, dtxsid: str, 
                       use_cache: Optional[bool] = None) -> List[Dict[str, Any]]:
    """
    Get cancer summary data by DTXSID.

    Retrieves cancer hazard summary data for a specific chemical identified by 
    its DSSTox Substance Identifier (DTXSID). This includes cancer classifications,
    weight of evidence assessments, and carcinogenicity evaluations from various
    regulatory agencies and scientific organizations.

    Args:
        dtxsid: DSSTox Substance Identifier (e.g., 'DTXSID0021125')
        use_cache: Whether to use cache for this request. If None, uses
            the instance default setting.

    Returns:
        List of dictionaries containing cancer summary data with fields such as:
            - dtxsid (str): DSSTox Substance Identifier
            - classification (str): Cancer classification
            - source (str): Source of the assessment
            - woe (str): Weight of evidence
            - cancerType (str): Type of cancer
            - species (str): Test species
            - studyType (str): Type of study
            - evidence (str): Evidence description
            - route (str): Exposure route
            - Notes: Exact fields may vary based on the data source

    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 ToxValDBCancer
        >>> cancer = ToxValDBCancer()
        >>> 
        >>> # Get cancer data for benzene
        >>> data = cancer.get_data_by_dtxsid("DTXSID0021125")
        >>> 
        >>> if data:
        ...     for record in data:
        ...         print(f"Source: {record.get('source')}")
        ...         print(f"Classification: {record.get('classification')}")
        ...         if record.get('woe'):
        ...             print(f"Weight of Evidence: {record['woe']}")
        ...         if record.get('cancerType'):
        ...             print(f"Cancer Type: {record['cancerType']}")
        ...         print()
        >>> else:
        ...     print("No cancer data available for this chemical")

    Note:
        - Not all chemicals have cancer assessment data
        - Data may come from multiple sources (EPA, IARC, NTP, etc.)
        - Classifications and terminology vary by source
        - Weight of Evidence (WoE) indicates the strength and quality
          of evidence supporting the carcinogenicity assessment
    """
    if not dtxsid or not isinstance(dtxsid, str):
        raise ValueError("dtxsid must be a non-empty string")

    endpoint = f"hazard/cancer-summary/search/by-dtxsid/{dtxsid}"
    return self._make_cached_request(endpoint, use_cache=use_cache)

`get_data_by_dtxsid_batch(dtxsids, use_cache=None)` ¶

Get cancer summary data for multiple chemicals in a single request.

Batch retrieval of cancer hazard summary data for up to 200 chemicals. More efficient than making individual requests when querying multiple chemicals.

Parameters:

Name	Type	Description	Default
`dtxsids`	`List[str]`	List of DSSTox Substance Identifiers (max 200)	required
`use_cache`	`Optional[bool]`	Whether to use cache for this request. If None, uses the instance default setting.	`None`

Returns:

Type	Description
`List[Dict[str, Any]]`	List of dictionaries containing cancer summary data for all
`List[Dict[str, Any]]`	requested chemicals. Each entry includes similar fields as
`List[Dict[str, Any]]`	get_data_by_dtxsid().

Raises:

Type	Description
`ValueError`	If dtxsids list is empty or contains more than 200 entries
`PermissionError`	If API key is invalid
`RuntimeError`	For other API errors

Example

from pycomptox.hazard import ToxValDBCancer cancer = ToxValDBCancer()

Get cancer data for multiple chemicals¶

dtxsids = ["DTXSID0021125", "DTXSID7020182", "DTXSID0020032"] batch_data = cancer.get_data_by_dtxsid_batch(dtxsids)

Group by chemical¶

by_chemical = {} for record in batch_data: ... dtxsid = record['dtxsid'] ... if dtxsid not in by_chemical: ... by_chemical[dtxsid] = [] ... by_chemical[dtxsid].append(record)

Display summary¶

for dtxsid, records in by_chemical.items(): ... print(f"{dtxsid}: {len(records)} cancer assessment(s)") ... for record in records: ... print(f" - {record.get('source')}: {record.get('classification')}")

Note

Maximum 200 DTXSIDs per request
Results may include multiple assessments per chemical from different sources
Batch requests are more efficient than individual queries

Source code in src/pycomptox/hazard/toxvaldbcancer.py

def get_data_by_dtxsid_batch(self, dtxsids: List[str], 
                             use_cache: Optional[bool] = None) -> List[Dict[str, Any]]:
    """
    Get cancer summary data for multiple chemicals in a single request.

    Batch retrieval of cancer hazard summary data for up to 200 chemicals.
    More efficient than making individual requests when querying multiple chemicals.

    Args:
        dtxsids: List of DSSTox Substance Identifiers (max 200)
        use_cache: Whether to use cache for this request. If None, uses
            the instance default setting.

    Returns:
        List of dictionaries containing cancer summary data for all
        requested chemicals. Each entry includes similar fields as
        get_data_by_dtxsid().

    Raises:
        ValueError: If dtxsids list is empty or contains more than 200 entries
        PermissionError: If API key is invalid
        RuntimeError: For other API errors

    Example:
        >>> from pycomptox.hazard import ToxValDBCancer
        >>> cancer = ToxValDBCancer()
        >>> 
        >>> # Get cancer data for multiple chemicals
        >>> dtxsids = ["DTXSID0021125", "DTXSID7020182", "DTXSID0020032"]
        >>> batch_data = cancer.get_data_by_dtxsid_batch(dtxsids)
        >>> 
        >>> # Group by chemical
        >>> by_chemical = {}
        >>> for record in batch_data:
        ...     dtxsid = record['dtxsid']
        ...     if dtxsid not in by_chemical:
        ...         by_chemical[dtxsid] = []
        ...     by_chemical[dtxsid].append(record)
        >>> 
        >>> # Display summary
        >>> for dtxsid, records in by_chemical.items():
        ...     print(f"{dtxsid}: {len(records)} cancer assessment(s)")
        ...     for record in records:
        ...         print(f"  - {record.get('source')}: {record.get('classification')}")

    Note:
        - Maximum 200 DTXSIDs per request
        - Results may include multiple assessments per chemical from different sources
        - Batch requests are more efficient than individual queries
    """
    if not dtxsids:
        raise ValueError("dtxsids list cannot be empty")

    if len(dtxsids) > 200:
        raise ValueError(f"Maximum 200 DTXSIDs allowed, got {len(dtxsids)}")

    endpoint = "hazard/cancer-summary/search/by-dtxsid/"
    return self._make_cached_request(
        endpoint, 
        json=dtxsids, 
        method='POST', 
        use_cache=use_cache
    )

ToxValDBCancer API Reference¶

pycomptox.hazard.toxvaldbcancer.ToxValDBCancer ¶

Get cancer data for a chemical¶

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

get_data_by_dtxsid(dtxsid, use_cache=None) ¶

Get cancer data for benzene¶

get_data_by_dtxsid_batch(dtxsids, use_cache=None) ¶

Get cancer data for multiple chemicals¶

Group by chemical¶

Display summary¶

`pycomptox.hazard.toxvaldbcancer.ToxValDBCancer` ¶

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

`get_data_by_dtxsid(dtxsid, use_cache=None)` ¶

`get_data_by_dtxsid_batch(dtxsids, use_cache=None)` ¶