Hazard Module¶

The Hazard Module provides comprehensive access to toxicological hazard data from the EPA CompTox Dashboard. This module enables retrieval of various types of hazard information including toxicity values, study data, and health assessments.

Overview¶

The hazard module contains multiple specialized classes for accessing different types of hazard data:

Toxicity Reference Values¶

PPRTV: Provisional Peer-Reviewed Toxicity Values for chemicals without established IRIS assessments
IRIS: EPA Integrated Risk Information System assessments including RfDs, RfCs, and cancer assessments

ToxRefDB (Toxicity Reference Database)¶

ToxRefDBEffects: Dose-effect relationships from guideline toxicity studies
ToxRefDBSummary: Study-level summaries including NOAEL, LOAEL, and endpoint information
ToxRefDBData: Detailed dose-treatment group-effect information across all endpoints
ToxRefDBObservation: Endpoint observation status distinguishing true negatives from missing data
ToxRefDBBatch: Batch access to ToxRefDB data for multiple chemicals

ToxValDB (Toxicity Values Database)¶

ToxValDB: Comprehensive toxicity values database aggregating data from multiple sources
ToxValDBCancer: Cancer hazard identification and weight-of-evidence data
ToxValDBSkinEye: Skin and eye irritation/corrosion test data
ToxValDBGenetox: Genotoxicity test data including Ames, Comet, micronucleus, and chromosomal aberration tests

Health Assessments & Toxicokinetics¶

HAWC: EPA Health Assessment Workspace Collaborative project links
ADMEIVIVE: Toxicokinetics data (Absorption, Distribution, Metabolism, Excretion) including in vitro, in vivo, and in silico predictions

Quick Start¶

from pycomptox.hazard import (
    PPRTV, IRIS, ToxRefDBEffects, ToxRefDBSummary,
    ToxValDB, ToxValDBCancer, ToxValDBGenetox,
    ADMEIVIVE, HAWC
)

# Get IRIS assessment data
iris = IRIS()
iris_data = iris.get_data_by_dtxsid("DTXSID7020637")  # Formaldehyde

# Get genotoxicity data
genetox = ToxValDBGenetox()
genetox_summary = genetox.get_summary_by_dtxsid("DTXSID0021125")  # Benzene

# Get toxicokinetics data
adme = ADMEIVIVE()
adme_data = adme.get_all_data_by_dtxsid_ccd_projection("DTXSID7020182")  # Bisphenol A

# Get ToxRefDB dose-effect data
toxref = ToxRefDBEffects()
effects = toxref.get_data_by_dtxsid("DTXSID1037806")

# Batch operations
from pycomptox.hazard import ToxRefDBBatch
batch = ToxRefDBBatch()
dtxsids = ["DTXSID0021125", "DTXSID7020182", "DTXSID0020032"]
batch_data = batch.get_data_by_dtxsid_batch(dtxsids)

Key Features¶

Comprehensive Hazard Data Coverage¶

Toxicity Values: Reference doses (RfDs), reference concentrations (RfCs), NOAEL, LOAEL values
Study Data: Guideline toxicity studies with detailed dose-response information
Health Effects: Cancer assessments, reproductive/developmental toxicity, systemic effects
Specialized Testing: Genotoxicity, skin/eye irritation, neurotoxicity
Toxicokinetics: ADME parameters, clearance rates, bioavailability

Data Quality Features¶

Observation Status: Distinguishes tested endpoints (true negatives) from untested endpoints (missing data)
Weight of Evidence: Cancer hazard identification with strength of evidence assessments
Guideline Compliance: Study data mapped to regulatory guideline requirements
Multiple Sources: Data aggregated from ToxRefDB, ToxValDB, IRIS, HAWC, httk, and CvTdb

Flexible Access Patterns¶

Single Chemical Queries: Get all hazard data for one chemical
Batch Queries: Retrieve data for up to 200 chemicals in one request
Study-Based Access: Query by study type or specific study ID
Filtered Results: Use projections for dashboard-specific data formats

Common Use Cases¶

Hazard Assessment Workflow¶

from pycomptox.hazard import ToxValDB, ToxValDBCancer, ToxValDBGenetox, IRIS

dtxsid = "DTXSID7020182"  # Bisphenol A

# 1. Get general toxicity values
toxval = ToxValDB()
tox_data = toxval.get_data_by_dtxsid(dtxsid)

# 2. Check for cancer hazard
cancer = ToxValDBCancer()
cancer_data = cancer.get_data_by_dtxsid(dtxsid)

# 3. Check genotoxicity
genetox = ToxValDBGenetox()
genetox_data = genetox.get_summary_by_dtxsid(dtxsid)

# 4. Get EPA IRIS assessment if available
iris = IRIS()
iris_data = iris.get_data_by_dtxsid(dtxsid)

# Analyze combined data for comprehensive hazard profile

Comparative Toxicity Analysis¶

from pycomptox.hazard import ToxRefDBSummary

# Compare similar chemicals
dtxsids = ["DTXSID0021125", "DTXSID7020182", "DTXSID0020032"]

toxref = ToxRefDBSummary()

for dtxsid in dtxsids:
    summary = toxref.get_data_by_dtxsid(dtxsid)

    if summary:
        # Find lowest NOAEL across all studies
        noaels = [s.get('noael') for s in summary if s.get('noael')]
        if noaels:
            print(f"{dtxsid}: Lowest NOAEL = {min(noaels)}")

Toxicokinetics Modeling¶

from pycomptox.hazard import ADMEIVIVE

adme = ADMEIVIVE()

# Get all ADME parameters
data = adme.get_all_data_by_dtxsid_ccd_projection("DTXSID7020182")

# Extract key parameters for modeling
if data:
    params = {}
    for record in data:
        param_name = record.get('parameter')
        param_value = record.get('value')
        if param_name and param_value:
            params[param_name] = param_value

    # Use in PBPK/toxicokinetic models
    print(f"Clearance: {params.get('Clint', 'N/A')}")
    print(f"Fraction Unbound: {params.get('Fup', 'N/A')}")
    print(f"Volume of Distribution: {params.get('Vd', 'N/A')}")

Data Sources¶

The hazard module integrates data from multiple authoritative sources:

ToxRefDB: EPA's Toxicity Reference Database of guideline studies
ToxValDB: Aggregated toxicity values from multiple databases
IRIS: EPA Integrated Risk Information System
HAWC: Health Assessment Workspace Collaborative
httk: High-Throughput Toxicokinetics R package
CvTdb: Concentration vs. Time database
invivoPKfit: In vivo pharmacokinetics fitting package

Best Practices¶

Caching¶

All hazard classes support caching to minimize API calls:

from pycomptox.hazard import ToxRefDBEffects

# Enable caching (default)
toxref = ToxRefDBEffects()
data1 = toxref.get_data_by_dtxsid("DTXSID1037806", use_cache=True)

# Subsequent calls use cached data
data2 = toxref.get_data_by_dtxsid("DTXSID1037806", use_cache=True)

Batch Processing¶

Use batch methods when querying multiple chemicals:

from pycomptox.hazard import ToxValDBGenetox

genetox = ToxValDBGenetox()

# Efficient batch query (single API call)
dtxsids = ["DTXSID0021125", "DTXSID7020182", "DTXSID0020032"]
batch_data = genetox.get_summary_by_dtxsid_batch(dtxsids)

# Less efficient individual queries (multiple API calls)
# for dtxsid in dtxsids:
#     data = genetox.get_summary_by_dtxsid(dtxsid)

Error Handling¶

from pycomptox.hazard import IRIS

iris = IRIS()

try:
    data = iris.get_data_by_dtxsid("DTXSID7020637")
    if data:
        print(f"Found IRIS assessment")
    else:
        print("No IRIS assessment available")
except ValueError as e:
    print(f"Invalid input: {e}")
except PermissionError as e:
    print(f"API key issue: {e}")
except RuntimeError as e:
    print(f"API error: {e}")

API Classes Reference¶

For detailed documentation on each class, see: