Toxicology Assessment via Adverse Outcome Pathways & Signal Detection

Systematic toxicology analysis that links molecular initiating events (MIEs) through adverse outcome pathways (AOPs) to apical adverse outcomes, then triangulates with real-world FAERS signals, FDA label data, and toxicogenomic associations.

Domain Reasoning

Toxicity has many mechanisms, and the first interpretive question is temporal: is this acute toxicity (immediate effect from a high dose) or chronic toxicity (cumulative damage from long-term low-dose exposure)? Acute and chronic toxicity operate through different mechanisms — acute hepatotoxicity may reflect direct mitochondrial damage, while chronic hepatotoxicity may involve fibrosis from repeated low-level inflammation. They also have different regulatory frameworks: acute toxicity is captured by LD50 and emergency protocols, while chronic toxicity requires long-term carcinogenicity and repeat-dose studies.

LOOK UP DON'T GUESS

• Adverse outcome pathways for a chemical: query AOPWiki_list_aops and AOPWiki_get_aop; do not describe mechanisms from memory.
• FAERS adverse event signals: retrieve from FAERS_count_reactions_by_drug_event and FAERS_calculate_disproportionality; never estimate PRR values.
• FDA label warnings: call DailyMed_parse_adverse_reactions and related tools; do not state boxed warnings from memory.
• CTD chemical-gene and chemical-disease associations: query CTD_get_chemical_gene_interactions and CTD_get_chemical_diseases; do not infer gene targets without database evidence.
• EPA CompTox hazard values and ToxCast/Tox21 bioactivity: query CompTox_get_hazard_data and CompTox_get_bioactivity_summary/CompTox_get_bioactivity_assays; never estimate an LD50, a hazard classification, or an assay hit-call rate from memory — this is exactly the kind of chemical-specific quantitative data that must come from the database.

COMPUTE, DON'T DESCRIBE

When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.

When to Use This Skill

Triggers:

• "What are the toxicity mechanisms for [drug/chemical]?"
• "Find adverse outcome pathways for [chemical]"
• "What AOPs are relevant to [target/organ/effect]?"
• "FAERS signal analysis for [drug]"
• "Toxicogenomic profile for [chemical]"
• "What is the mechanism of hepatotoxicity / cardiotoxicity / neurotoxicity for [drug]?"

Use Cases:

1. AOP Tracing: Map chemical MIE through key events to apical outcome using AOPWiki
2. Real-World Signal Detection: Quantify FAERS adverse event signals with PRR/ROR
3. Label Safety Mining: Extract FDA boxed warnings, contraindications, nonclinical toxicology
4. Toxicogenomics: Chemical-gene-disease associations from CTD
5. Integrated Mechanism Report: Combine AOP pathway + real-world signals into unified narrative

KEY PRINCIPLES

1. AOP-first thinking - Frame all toxicity in terms of MIE → Key Events → Adverse Outcome
2. Report-first approach - Create report file FIRST, update progressively
3. Evidence grading mandatory - T1 (regulatory/clinical) through T4 (computational/AOP annotation)
4. Distinguish mechanism from signal - AOPWiki = mechanism; FAERS = real-world signal
5. Disambiguation first - Resolve drug/chemical identity before any queries
6. English-first queries - Always use English names in tool calls

Evidence Grading

Workflow Overview

Chemical/Drug Query
|
+-- PHASE 0: Disambiguation
|   Resolve name -> identifiers (ChEMBL, PubChem CID, SMILES)
|
+-- PHASE 1: Adverse Outcome Pathway Mapping (AOPWiki)
|   List AOPs by keyword; retrieve key events, MIEs, and biological plausibility scores
|
+-- PHASE 2: Real-World Adverse Event Signals (FAERS)
|   Top reactions by drug; disproportionality (PRR); serious event filter
|
+-- PHASE 3: FDA Label Safety Mining
|   Boxed warnings, contraindications, nonclinical toxicology, adverse reactions
|
+-- PHASE 4: Toxicogenomics (CTD)
|   Chemical-gene interactions; chemical-disease associations
|
+-- PHASE 4c: Quantitative Hazard & HTS Bioactivity (EPA CompTox)
|   Curated dose-based hazard values (ToxVal); ToxCast/Tox21 assay hit rates
|
+-- SYNTHESIS: Integrated Toxicology Report
    AOP-linked mechanism + FAERS signal + CTD gene targets + Risk classification

Phase 0: Disambiguation

Objective: Establish compound identity before any database queries.

Tools:

• PubChem_get_CID_by_compound_name (name: str) — get CID + SMILES
• ChEMBL_search_drugs (query: str) — get ChEMBL ID and max phase

Capture: generic name, SMILES, PubChem CID, ChEMBL ID, drug class.

Phase 1: Adverse Outcome Pathway Mapping

Objective: Find AOPs relevant to the chemical's known or suspected toxicity mechanisms.

Tools

AOPWiki_list_aops:

• Input: keyword (str) — e.g., organ ("liver", "kidney"), effect ("apoptosis", "inflammation"), or target ("AhR", "PPARalpha")
• Output: List of AOP IDs, titles, and short descriptions
• Use: Discovery scan to identify candidate AOPs

AOPWiki_get_aop:

• Input: aop_id (int) — ID from list_aops result
• Output: Full AOP details including MIE, key events (KEs), key event relationships (KERs), biological plausibility, and weight-of-evidence
• Use: Retrieve mechanistic pathway details for selected AOPs

Workflow

1. Query AOPWiki_list_aops with organ-level keyword (e.g., "hepatotoxicity", "nephrotoxicity")
2. Query again with mechanism-level keyword (e.g., "oxidative stress", "mitochondria")
3. Select top 3-5 most relevant AOPs by title relevance
4. Call AOPWiki_get_aop for each selected AOP
5. Extract: MIE (molecular initiating event), key events in order, apical adverse outcome, biological plausibility score

Decision Logic

• AOP found: Extract full pathway; note plausibility level (high/moderate/low)
• No direct AOP match: Try broader organ or mechanism terms; document as "no AOP directly mapped"
• Multiple AOPs: Report all; highlight shared key events as high-confidence mechanisms

AOP Table Format

Phase 2: Real-World Adverse Event Signals (FAERS)

Objective: Quantify observed adverse events with statistical signal measures.

Tools

FAERS_count_reactions_by_drug_event:

• Input: drug_name (str), limit (int, default 50)
• Output: Top adverse reactions with counts
• Note: param is drug_name not drug

FAERS_calculate_disproportionality:

• Input: drug_name (str), reaction_meddra_pt (str)
• Output: PRR, ROR, IC with confidence intervals

FAERS_filter_serious_events:

• Input: drug_name (str), serious_type (str: "death", "hospitalization", "life-threatening")
• Output: Serious event count and case details

FAERS_stratify_by_demographics:

• Input: drug_name (str), reaction_meddra_pt (str)
• Output: Age/sex breakdown for specific reaction

Workflow

1. Get top 25 reactions via FAERS_count_reactions_by_drug_event
2. Filter to organ-system clusters matching the AOP outcomes from Phase 1
3. Calculate PRR for top 10 reactions via FAERS_calculate_disproportionality
4. Check serious events (deaths, hospitalizations) for highest-PRR reactions

Signal Thresholds

Phase 3: FDA Label Safety Mining

Objective: Extract regulatory safety findings from approved drug labels.

Tools

• DailyMed_parse_adverse_reactions (drug_name: str)
• DailyMed_parse_contraindications (drug_name: str)
• DailyMed_parse_clinical_pharmacology (drug_name: str)
• DailyMed_parse_drug_interactions (drug_name: str)

Note: These tools apply to FDA-approved drugs only. Environmental chemicals will have no label data — document explicitly.

Workflow

1. Extract adverse reactions and note which match FAERS signals
2. Extract contraindications (highest evidence tier [T1])
3. Note pharmacological mechanism from clinical pharmacology section

Phase 4: Toxicogenomics (CTD)

Objective: Map chemical-gene interactions and chemical-disease associations.

Tools

CTD_get_chemical_gene_interactions:

• Input: input_terms (str) — chemical name or MeSH ID
• Output: Gene targets with interaction type (increases/decreases expression)
• Use: Find molecular targets mediating toxicity

CTD_get_chemical_diseases:

• Input: input_terms (str) — chemical name or MeSH ID
• Output: Disease associations with evidence type (curated/inferred)
• Use: Find downstream disease endpoints

Workflow

1. Query CTD with compound name; note curated (higher confidence) vs inferred entries
2. Cross-reference gene targets with Phase 1 AOP key events
3. Note which CTD disease endpoints match AOP apical outcomes

Phase 4c: Quantitative Hazard & HTS Bioactivity (EPA CompTox)

Objective: Get curated, dose-based hazard values and quantitative high-throughput screening (HTS) bioactivity data — the kind of numeric, assay-level evidence AOPWiki (mechanism) and FAERS (real-world signal) don't provide.

Requires EPA_COMPTOX_API_KEY (free; request by emailing [email protected]). Without the key, these tools are excluded from tu list entirely (same gating pattern as Addgene/USPTO) rather than failing loudly — check for their presence before relying on this phase.

Tools

CompTox_search_chemical (word: str — name, CASRN, or InChIKey):

• Output: Matching dtxsid/dtxcid/casrn/preferredName records
• Use: Resolve chemical identity to a DTXSID — required input for every other CompTox call. Run this immediately after Phase 0's PubChem/ChEMBL disambiguation; DTXSID is a separate identifier space from PubChem CID / ChEMBL ID.

CompTox_get_hazard_data (dtxsid: str):

• Output: ToxVal records — points of departure (NOAEL/LOAEL/BMDL), lethality effect levels (LD50/LC50), reference doses, exposure limits, each tagged with source, species, and study type
• Use: The quantitative dose-response counterpart to AOPWiki's qualitative mechanism and DailyMed's label text — grade as T1/T2 per source (regulatory sources like EPA IRIS/ECOTOX rank higher than screening-level estimates; check the source field per record)

CompTox_get_bioactivity_summary (dtxsid: str):

• Output: Aggregate ToxCast/Tox21 hit counts (activeMc/totalMc, activeSc/totalSc) and cytotoxicity burst point (cytotoxMedianUm)
• Use: A fast "how promiscuous and how cytotoxic does this chemical look across ~700+ HTS assays" check before deciding whether per-assay drill-down is worth it

CompTox_get_bioactivity_assays (dtxsid: str):

• Output: Per-assay hit-call records (aeid, hitCall, ac50) — which specific biological targets/pathways the chemical activated
• Use: Drill into which assay endpoints (aeid) drove the summary hit count; cross-reference specific aeids against Phase 1's AOP key events when a mechanistic link is claimed — do not assume an HTS hit implies the AOP mechanism without checking the assay's actual target

Workflow

1. CompTox_search_chemical on the compound name to get its DTXSID
2. CompTox_get_hazard_data for curated dose-based hazard values; note source/species per record
3. CompTox_get_bioactivity_summary for the HTS overview; if activeMc/totalMc shows meaningful activity, drill into CompTox_get_bioactivity_assays
4. Cross-reference high-hit-rate assay targets against Phase 1's AOP key events and Phase 4's CTD gene targets — convergent evidence across three independent sources (AOP mechanism, CTD gene interaction, ToxCast assay target) is much stronger than any one alone

Decision Logic

• No DTXSID match: The compound may not be in the CompTox universe (common for very new drugs or non-registered mixtures) — document as "not in CompTox" rather than treating it as zero hazard
• Hazard records but no bioactivity: Chemical has traditional tox study data but hasn't been through ToxCast/Tox21 screening — do not infer bioactivity from hazard data or vice versa, they measure different things
• High assay hit rate with low `cytotoxMedianUm`: A large fraction of "hits" may just reflect general cytotoxicity (cell stress triggers many unrelated assays) rather than a specific mechanism — check whether hit aeids cluster around one pathway or are scattered, and flag a low cytotoxicity burst point as a reason to discount isolated hits

Phase 4b: Toxin Reference Lookup (T3DB) — currently broken upstream, verified

Objective: Cross-reference a chemical/toxin against T3DB's curated toxin profiles (mechanism of toxicity, health effects, routes of exposure) via T3DB_search_toxins (query: str) and T3DB_get_toxin (toxin_id: str, e.g. T3D0001).

Live-verified status: both tools currently fail with HTTP 403 on every attempt (confirmed on multiple retries, both the search endpoint and a direct get_toxin call by known ID) — t3db.ca appears to be blocking the underlying request pattern entirely, not a transient outage tied to a specific query. Do not fabricate a toxin profile, mechanism, or health-effect list if this 403s — report T3DB as unavailable and fall back to CTD (Phase 4) and AOPWiki (Phase 1) for mechanistic toxicology instead, or DailyMed (Phase 3) if the chemical is also an FDA-approved drug. Re-check T3DB's live status with a cheap call before assuming this is still broken — it may be fixed by the time you read this.

Synthesis: Integrated Toxicology Report

Structure:

# Toxicology Report: [Compound Name]
**Generated**: YYYY-MM-DD

## Executive Summary
Risk tier: CRITICAL / HIGH / MEDIUM / LOW / INSUFFICIENT DATA
Key finding summary (2-3 sentences)

## 1. Compound Identity
(disambiguation table)

## 2. Adverse Outcome Pathways [T3-T4]
(AOP table; pathway diagrams in text form)

## 3. Real-World Adverse Event Signals [T1-T2]
(FAERS top reactions + PRR table + serious events)

## 4. FDA Label Safety [T1]
(boxed warnings, contraindications, adverse reactions)

## 5. Toxicogenomics [T2-T4]
(CTD gene targets + disease associations)

## 6. Mechanistic Integration
(How AOP key events map to observed FAERS signals and CTD gene targets)

## 7. Risk Classification
(Final tier with rationale)

## Data Gaps & Limitations
(Missing data, confidence caveats)

Risk Classification

Fallback Chains

Tool Parameter Reference (Critical)

Limitations

• AOPWiki: AOPs are in development; many lack high plausibility scores
• FAERS: Observational data; confounding by indication; underreporting bias
• CTD: Inferred associations have high false-positive rate
• T3DB: Both tools verified returning HTTP 403 as of this writing (upstream request-blocking, not a per-query issue) — treat as unavailable until re-verified live
• EPA CompTox: requires a free API key (EPA_COMPTOX_API_KEY, request via [email protected]) — schemas verified against the live production OpenAPI specs, but full response shapes were not live-tested end-to-end in this environment since no real key was available; DTXSID coverage skews toward chemicals with US regulatory/environmental relevance and may be sparse for newer or purely investigational drugs
• DailyMed: FDA-approved drugs only; no environmental chemical coverage
• Environmental chemicals: Primarily Phase 1 (AOP) + Phase 4 (CTD) data available
• Food additive/ingredient identity: This skill assesses a chemical's toxicity once you know what it is; it does not look up which foods/products actually contain a given additive or allergen, or a product's nutrient/ingredient label — for that, use tooluniverse-nutrition-food-composition (USDA FoodData Central, Open Food Facts) first, then bring the additive's identity here for hazard assessment

References

• AOPWiki: https://aopwiki.org
• FAERS: https://www.fda.gov/drugs/questions-and-answers-fdas-adverse-event-reporting-system-faers
• CTD: http://ctdbase.org
• DailyMed: https://dailymed.nlm.nih.gov
• OpenFDA: https://open.fda.gov
• EPA CompTox: https://comptox.epa.gov/dashboard/ (API docs: https://comptox.epa.gov/ctx-api/docs/)