Comprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, adverse events (FAERS), pharmacogenomics, and approval history. Use for full drug investigation reports, 'tell me about drug X' queries, and assembling drug profiles for clinicians, researchers, or regulatory work.
Comprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, adverse events (FAERS), pharmacogenomics, and approval history. Use for full drug investigation reports, 'tell me about drug X' queries, and assembling drug profiles for clinicians, researchers, or regulatory work.
Drug Research Strategy
Comprehensive drug investigation using 50+ ToolUniverse tools across chemical databases, clinical trials, adverse events, pharmacogenomics, and literature.
KEY PRINCIPLES:
Report-first approach - Create report file FIRST, then populate progressively
Compound disambiguation FIRST - Resolve identifiers before research
Citation requirements - Every fact must have inline source attribution
Evidence grading - Grade claims by evidence strength (T1-T4)
Mandatory completeness - All sections must exist, even if "data unavailable"
English-first queries - Always use English drug/compound names in tool calls, even if the user writes in another language. Only try original-language terms as a fallback. Respond in the user's language
LOOK UP, DON'T GUESS
When asked about a drug, query ChEMBL/PubChem/DailyMed FIRST. Don't guess at mechanism, targets, or side effects — look them up. When you're not sure about a fact, your first instinct should be to SEARCH for it using tools, not to reason harder from memory.
Drug Mechanism Reasoning
When investigating a drug's mechanism of action, trace the full causal chain:
Target engagement - Which protein(s) does the drug bind, and with what affinity/selectivity?
Molecular effect - Does binding inhibit, activate, or modulate the target's function?
- Which signaling or metabolic pathway is altered downstream?
Pathway consequence
Cellular phenotype - What changes occur at the cell level (proliferation, apoptosis, secretion)?
Physiological outcome - How does the cellular effect translate to the therapeutic benefit in the patient?
Workflow Overview
1. Report-First Approach (MANDATORY)
DO NOT show the search process or tool outputs to the user. Instead:
Create the report file FIRST - [DRUG]_drug_report.md with all 11 section headers and [Researching...] placeholders. See REPORT_TEMPLATE.md for the full template.
Progressively update the report - Replace placeholders with findings as you query each tool.
Use ALL relevant tools - Query multiple databases for each data type; cross-reference across sources.
2. Citation Requirements (MANDATORY)
Every piece of information MUST include its source. Use inline citations:
*Source: PubChem via `PubChem_get_compound_properties_by_CID` (CID: 4091)*
Tools: DailyMed MOA -> ChEMBL activities (NOT ChEMBL_get_molecule_targets) -> ChEMBL target details -> DGIdb -> PubChem bioactivity
Critical: Derive targets from activities filtered to pChEMBL >= 6.0. Avoid ChEMBL_get_molecule_targets.
Output: FDA MOA text, target table with UniProt/potency, selectivity profile
PATH 3: ADMET Properties
Tools: ADMET-AI (bioavailability, BBB, CYP, clearance, toxicity)
Fallback: DailyMed clinical_pharmacology + pharmacokinetics + drug_interactions
Critical: If ADMET-AI fails, automatically use fallback. Never leave Section 4 empty.
PATH 4: Clinical Trials
Tools: search_clinical_trials -> compute phase counts -> extract outcomes/AEs -> fda_pharmacogenomic_biomarkers
Critical: Section 5.2 must show actual counts by phase/status in table format.
PATH 5: Post-Marketing Safety
Tools: FAERS (reactions, seriousness, outcomes, deaths, age) + DailyMed (DDI, dosing, warnings)
Critical: Include FAERS date window, seriousness breakdown, and limitations paragraph.
See TOOLS_REFERENCE.md for the complete tool listing with parameters and input format requirements.
Type Normalization
Many tools require string inputs. Always convert IDs before API calls:
ChEMBL IDs, PubMed IDs, NCT IDs: convert int -> str
SMILES for ADMET-AI: pass as list ["SMILES_STRING"]
FAERS drug names: use UPPERCASE (e.g., "METFORMIN")
ChEMBL IDs: full format "CHEMBL1431" not "1431"
PharmGKB IDs: PA prefix "PA450657" not "450657"
Common Use Cases
Use Case
Primary Sections
Light Sections
Approved Drug Profile
All 11 sections
None
Investigational Compound
1, 2, 3, 4, 9
5, 6, 7, 8
Safety Review
1, 5, 6, 7, 9
2, 3, 4, 8
ADMET Assessment
1, 2, 4
3, 5, 6, 7, 8, 9
Clinical Development Landscape
1, 5, 9
2, 3, 4, 6, 7, 8
Always maintain all section headers but adjust depth based on query focus and data availability.
When NOT to Use This Skill
Target research -> Use target-intelligence-gatherer skill
Disease research -> Use disease-research skill
Literature-only -> Use literature-deep-research skill
Single property lookup -> Call tool directly
Structure similarity search -> Use PubChem_search_compounds_by_similarity directly
Cross-Skill References
For drug interaction checking, run: python3 skills/tooluniverse-drug-drug-interaction/scripts/pharmacology_ref.py --type interaction --drug1 X --drug2 Y
