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, researc

Drug Research Strategy Comprehensive drug investigation using 50+ ToolUniverse tools across chemical databases, clinical trials, adverse events, pharmacogenomics, and literature. KEY PRINCIPLES : 1. Report first approach Create report file FIRST, then populate progressively 2. Compound disambiguation FIRST Resolve identifiers before research 3. Citation requirements Every fact must have inline source attribution 4. Evidence grading Grade claims by evidence strength (T1 T4) 5. Mandatory completeness All sections must exist, even if "data unavailable" 6. 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: 1. Target engagement Which protein(s) does the drug bind, and with what affinity/selectivity? 2. Molecular effect Does binding inhibit, activate, or modulate the target's function? 3. Pathway consequence Which signaling or metabolic pathway is altered downstream? 4. Cellular phenotype What changes occur at the cell level (proliferation, apoptosis, secretion)? 5. 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: 1. Create the report file FIRST [DRUG] drug report.md with all 11 section headers and [Researching...] placeholders. See [REPORT TEMPLATE.md](REPORT TEMPLATE.md) for the full template. 2. Progressively update the report Replace placeholders with findings as you query each tool. 3. 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: 3. Progressive Writing Workflow Compound Disambiguation (Phase 1) CRITICAL : Establish compound identity before any research. Identifier Resolution Chain Handle Naming Ambiguity Issue Example Resolution Salt forms metformin vs metformin HCl Note all CIDs; use parent compound Isomers omeprazole vs esomeprazole Verify SMILES; separate entries if distinct Prodrugs enalapril vs enalaprilat Document both; note conversion Brand confusion Different products same name Clarify with user Research Paths Summary Each path has detailed tool chains and output examples in [REPORT GUIDELINES.md](REPORT GUIDELINES.md). PATH 1: Chemical Properties & CMC Tools : PubChem properties ADMET AI physicochemical ADMET AI solubility DailyMed chemistry/description Output : Physicochemical table, Lipinski assessment, QED score, salt forms, formulation comparison PATH 2: Mechanism & Targets 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. PATH 6: Pharmacogenomics Tools : PharmGKB (search details annotations guidelines) Fallback : DailyMed pharmacogenomics section + PubMed literature PATH 7: Regulatory & Patents Tools : FDA Orange Book (search, approval history, exclusivity, patents, generics) + DailyMed (special populations via LOINC codes) Note : US only data; document EMA/PMDA limitation. PATH 8: Real World Evidence Tools : ClinicalTrials.gov (OBSERVATIONAL studies) + PubMed (real world, registry, surveillance) PATH 9: Comparative Analysis Tools : Abbreviated tool chains for each comparator + head to head trial search + PubMed meta analyses FDA Label Core Fields For approved drugs, retrieve these DailyMed sections early (after getting set id): Batch Sections Maps to Report Phase 1 mechanism of action, pharmacodynamics, chemistry Sections 2 3 Phase 2 clinical pharmacology, pharmacokinetics, drug interactions Sections 4, 6.5 Phase 3 warnings and cautions, adverse reactions, dosage and administration Sections 6, 8.2 Phase 4 pharmacogenomics, clinical studies, description, inactive ingredients Sections 5, 7 Fallback Chains Primary Tool Fallback Use When PubChem get CID by compound name ChEMBL search drugs Name not in PubChem ChEMBL get molecule targets Use ChEMBL search activities instead Always avoid this tool ChEMBL get activity PubChemBioAssay get assay summary No ChEMBL ID DailyMed search spls PubChemTox get acute effects DailyMed timeout PharmGKB search drugs DailyMed PGx sections + PubMed PharmGKB unavailable PharmGKB get dosing guidelines DailyMed pharmacogenomics section PharmGKB API error FAERS count reactions by drug event Document "FAERS unavailable" + use label AEs API error ADMETAI (all tools) DailyMed clinical pharmacology + pharmacokinetics Invalid SMILES or API error Quick Reference: Tools by Use Case Use Case Primary Tool Fallback Evidence Name CID PubChem get CID by compound name ChEMBL search drugs T1 Properties PubChem get compound properties by CID ADMET AI physicochemical T1/T2 FDA MOA DailyMed parse clinical pharmacology (mechanism of action) T1 Targets ChEMBL search activities ChEMBL get target DGIdb get drug info T1 ADMET ADMETAI predict (5 tools) DailyMed PK sections T2/T1 Trials search clinical trials T1 Trial outcomes extract clinical trial outcomes T1 FAERS FAERS count reactions by drug event Label adverse reactions T1 Dose mods DailyMed parse clinical pharmacology (dosage, warnings) T1 PGx PharmGKB search drugs DailyMed PGx + PubMed T2/T1 Label DailyMed search spls PubChemTox get acute effects T1 Literature PubMed search articles EuropePMC search articles Varies Regulatory FDA OrangeBook tools DailyMed label data T1 See [TOOLS REFERENCE.md](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 Additional Resources Report template : [REPORT TEMPLATE.md](REPORT TEMPLATE.md) Initial file template, citation format, evidence grading, scorecard, audit template Report guidelines : [REPORT GUIDELINES.md](REPORT GUIDELINES.md) Detailed section by section instructions with output examples Tool reference : [TOOLS REFERENCE.md](TOOLS REFERENCE.md) Complete tool listing with parameters and input formats Verification checklist : [CHECKLIST.md](CHECKLIST.md) Section by section pre delivery verification Examples : [EXAMPLES.md](EXAMPLES.md) Detailed workflow examples for different use cases

tooluniverse-drug-research