Pharma Intelligence

Global Pharma Intelligence & Biomedical Research Skill

Systematic, source-prioritized search and synthesis across regulatory, clinical, academic, and commercial databases — covering all major pharmaceutical markets and 20+ biomedical research databases.

Sub-Skills — How to Invoke

This skill delegates all database work to the sub-skills bundled locally under skills/. Read the relevant sub-skill's SKILL.md before invoking it, then run its bundled script.

See references/sub-skills.md for the full mapping of research tasks to sub-skills and execution patterns.

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Core Principle: Tiered Source Priority

Every region follows a 3-tier hierarchy. Higher tiers override lower-tier claims; always cite the tier.

For the per-region source map (CN / US / EU / JP / KR / AU + global) with URLs and access notes, see references/sources-by-region.md.

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Tool Access Notes

web_fetch is the default tool for any URL in this skill that isn't covered by a bundled sub-skill. Some sites are JavaScript-rendered or block plain HTTP fetches — Google Patents is the most common offender, and CTIS, jRCT, and ANZCTR occasionally behave the same way — but this can happen on any site, not just those.

Rule: try web_fetch first. If it returns empty, blocked, or placeholder content, retry the exact same URL with browser_navigate before concluding that a source has no data. Every other section in this skill that mentions web_fetch defers to this rule rather than restating it.

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Search Workflow

Step 1 — Classify the Query (pick ONE intent)

Also capture: regions in scope (US / EU / JP / CN / KR / AU / global) and time horizon.

Step 2 — Execute the Per-Intent Sequence

Run the workflow for the chosen intent (see Per-Intent Workflows) in order. For sources without MCP coverage (CN NMPA/CDE, EMA EPAR, PMDA, jRCT, CTIS, CRIS, ANZCTR, Orange Book), use web_fetch only at the steps that name them, following the fallback rule in Tool Access Notes.

Resolve identifiers as needed:

• Free-text disease → MONDO/EFO ID via opentargets-skill or efo-ontology-skill
• Free-text gene → HGNC symbol via ncbi-clinicaltables-skill or ensembl-skill
• Cross-database ID conversion → ensembl-skill, uniprot-skill, or efo-ontology-skill

Step 3 — Resolve Conflicts

1. Higher-tier source wins (Tier 1 > Tier 2 > Tier 3).
2. More recent data wins within the same tier.
3. Flag unresolved conflicts; do not silently pick one.

Step 4 — Synthesize and Present

Structure output to match the intent of the question:

• Trial landscape → table of trials (NCT/registry ID, phase, status, sponsor, N, primary endpoint).
• Approval status → region × status × date × indications table.
• Safety → top FAERS reactions plus black-box / warnings.
• Pipeline → drug × company × phase × mechanism table.
• Patent → patent number, jurisdiction, expiry.

Always cite source, tier, and access date.

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Per-Intent Workflows

A. Trial Landscape

"What clinical studies / trials exist for [drug | target | indication]?"

Default scope = ALL regions. Only narrow if the user names a single region.

clinicaltrials-skill covers only ClinicalTrials.gov, which is primarily US-registered trials. Run each regional source in parallel.

1. United States — clinicaltrials-skill (action=studies).
   • Use query.intr for a drug, query.cond for a disease, both for combined.
   • For a target/class (e.g., "pan-RAS", "PD-L1 inhibitor"): pass the class term as query.intr plus a relevant query.cond.
   • Then re-run with an NCT ID in query.id for eligibility, endpoints, sponsor, and locations.
2. China — web_fetch:
   • http://www.chinadrugtrials.org.cn (mandatory CN IND registry)
   • https://www.chictr.org.cn (ChiCTR, WHO primary)
3. Europe — web_fetch:
   • https://euclinicaltrials.eu (CTIS — current EU register)
   • https://eudract.ema.europa.eu (EudraCT — legacy historical trials)
   • https://www.isrctn.com (ISRCTN, UK/global)
4. Japan — web_fetch:
   • https://jrct.niph.go.jp (jRCT — mandatory JP registry)
   • https://www.umin.ac.jp/ctr/ (UMIN-CTR — legacy)
5. South Korea — web_fetch https://cris.nih.go.kr.
6. Australia / New Zealand — web_fetch https://www.anzctr.org.au.
7. WHO ICTRP catch-all — web_fetch https://trialsearch.who.int for any WHO primary registry (covers India CTRI, Iran IRCT, Brazil ReBEC, etc.).
8. Published results — ncbi-entrez-skill (db=pubmed) with NCT ID or drug name to surface completed-trial papers.
9. US company-disclosed pipeline (optional) — web_fetch SEC EDGAR full-text search at https://efts.sec.gov/LATEST/search-index for US-listed sponsors.

For every regional web_fetch: query both INN and brand name; for CN also use the Chinese transliteration (see references/drug-naming.md). Aggregate results in one table with a "Registry" column.

B. Approval / Regulatory Status

"Is [drug] approved in [region]?"

1. US — web_fetch https://api.fda.gov/drug/label.json (openFDA) and https://dailymed.nlm.nih.gov/dailymed/services/v2/spls.json (label date anchors approval); web_fetch https://api.fda.gov/drug/ndc.json for orphan status.
2. Non-US — web_fetch the regional Tier 1 source (NMPA, EMA EPAR, PMDA, MFDS, TGA). For CN, also search Chinese characters.
3. chembl-skill (drug_indication.json?molecule_chembl_id=...) — cross-check approved indications and max phase.
4. Say "not approved" only when Tier 1 affirms denial/withdrawal. Otherwise: "no record found as of [date]".

C. Safety / Adverse Events

1. web_fetch https://api.fda.gov/drug/event.json (FAERS) filtering by drug name and seriousness.
2. web_fetch https://api.fda.gov/drug/label.json with sections=warnings and sections=contraindications.
3. chembl-skill (molecule/.json) — inspect the black_box_warning flag.
4. ncbi-entrez-skill (db=pubmed) with terms "adverse effect" OR "toxicity" for case reports and post-marketing literature.

D. Pipeline / Competitive Intelligence

"Who else is developing for [indication / target]? What's the global competitive landscape?"

Default scope = ALL regions. A competitive landscape without the active-trial picture is incomplete, so run the full multi-region trial sweep from Workflow A and then layer pipeline-specific sources on top.

1. Active trials — all regions — run Workflow A steps 1–7 in full, optionally adding filter.overallStatus=RECRUITING (or ACTIVE_NOT_RECRUITING) and a phase filter to focus on competitors at a specific stage.
2. Company disclosures — web_fetch SEC EDGAR full-text search at https://efts.sec.gov/LATEST/search-index for pipeline language in 10-K / 10-Q / 8-K (US-listed sponsors only).
3. Patent activity per company — web_fetch https://patents.google.com/?assignee=companyname (see Workflow E, step 1, for the exact query format and non-English name handling; or use WIPO PATENTSCOPE / Espacenet as alternatives).
4. Published results — ncbi-entrez-skill (db=pubmed) with NCT IDs or drug names to surface completed-trial papers.

Aggregate into one table: drug × company × phase × mechanism × registry/region.

E. Patent / IP / Exclusivity

All listed patent sources are free and require no API key.

1. Global patent search — web_fetch one or more of (see Tool Access Notes for the browser_navigate fallback):
   • https://patents.google.com (Google Patents — best full-text search, covers USPTO, EPO, WIPO, JPO, CNIPA, KIPO). To retrieve all patents assigned to a specific company, query https://patents.google.com/?assignee=companyname. If the company's name is non-English, first search with the original non-English name, then run a second search with the English translation/transliteration — assignee records are not always normalized across languages, so neither search alone is reliable.
   • https://patentscope.wipo.int (WIPO PATENTSCOPE — authoritative for PCT applications and national filings worldwide).
   • https://worldwide.espacenet.com (EPO Espacenet — strongest European and family-tree coverage).
2. US patents (structured) — uspto_ppubs_search_patents via MCP for granted patents and applications.
3. Patent family / cross-jurisdiction equivalents — Espacenet's "INPADOC patent family" view, or Google Patents' "Worldwide applications" section.
4. Orange Book (patent + exclusivity expiry for FDA-approved drugs) — web_fetch https://www.accessdata.fda.gov/scripts/cder/ob.
5. Orphan exclusivity — fda_orphan_search_exclusivity (7-year US orphan exclusivity).

F. Target / Mechanism / Drug Discovery

1. chembl-skill — search target/search.json?q= to resolve target ChEMBL ID, then mechanism.json?target_chembl_id=... for all drugs.
2. chembl-skill — mechanism.json?molecule_chembl_id=... for mechanism of action of each candidate.
3. chembl-skill — activity.json?target_chembl_id=... for IC50 / Kd / EC50 bioactivity comparisons.
4. uniprot-skill — uniprotkb/search with gene: AND organism_id:9606 for protein function and druggability context.
5. reactome-skill — pathway and disease-pathway context for the target.

G. Repurposing / Target Discovery

1. opentargets-skill — search for disease to resolve MONDO / EFO ID.
2. opentargets-skill — associatedTargets query with disease EFO ID → ranked targets by evidence score.
3. gwas-catalog-skill — associations for the disease EFO term to identify genetically supported targets.
4. web_fetch OMIM API at https://api.omim.org/api/entry/search for Mendelian basis (requires API key).
5. For each top target: chembl-skill — mechanism.json?target_chembl_id=... for all drugs.
6. clinicaltrials-skill with each drug as query.intr for prior-art trials.
7. web_fetch https://api.fda.gov/drug/event.json as a safety filter for non-trivial candidates.

H. Literature / Evidence Review

1. ncbi-entrez-skill (db=pubmed) — entry point; use MeSH terms for disease, chemical, and gene-aware filtering.
2. web_fetch Europe PMC REST (https://www.ebi.ac.uk/europepmc/webservices/rest/search) — broader: grants, preprints, non-MEDLINE.
3. biorxiv-skill — bioRxiv / medRxiv preprints only.
4. ncbi-pmc-skill or ncbi-entrez-skill (efetch, db=pmc) — abstract or full text for top hits.

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Combination Strategies (cross-intent)

Use only when a question genuinely spans multiple intents.

• Disease → Targets → Drugs → Trials: opentargets-skill (search + associations) → chembl-skill (mechanism by target) → clinicaltrials-skill
• Gene → Protein → Pathways → Drugs: ncbi-clinicaltables-skill or ensembl-skill → uniprot-skill → reactome-skill → chembl-skill (mechanism by target)
• Variant → Gene → Disease → Treatments: clinvar-variation-skill or gnomad-graphql-skill → ensembl-skill → opentargets-skill → chembl-skill (mechanism by target)
• Drug → Safety → Label → Trials: chembl-skill (mechanism) → web_fetch openFDA adverse events → web_fetch openFDA label → clinicaltrials-skill

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API Keys

Most APIs require no key. Exceptions:

All bundled sub-skills (ChEMBL, OpenTargets, PubMed via NCBI Entrez, ClinicalTrials.gov, Reactome, UniProt, GWAS Catalog, Ensembl) are public and require no key. Patent landscape work uses Google Patents, WIPO PATENTSCOPE, and Espacenet — no keys required.

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Output Quality Standards

• Never fabricate approval dates, trial IDs, or efficacy numbers.
• Attribute every claim to its source and tier.
• Flag gaps explicitly (e.g., "No registered trials found in jRCT as of [date]").
• Distinguish "no data found" from "not approved" — absence of evidence ≠ negative regulatory decision.
• For Chinese sources: note whether the search was conducted in Chinese characters; romanization alone may miss records.

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Troubleshooting

No results?

• Try alternative terms (INN vs brand name, gene symbol vs protein name).
• Use standardized IDs: MONDO/EFO for diseases, HGNC for genes, ChEMBL IDs for compounds, Ensembl for OpenTargets.
• Resolve IDs first with efo-ontology-skill, ncbi-clinicaltables-skill, ensembl-skill, or uniprot-skill.

Too many results?

• Add filters: max_items, filter.phase, filter.overallStatus, reviewed=true (UniProt).
• Apply date ranges where supported.

API key errors?

• OMIM requires a key; NCI and OpenFDA accept optional keys for higher rate limits.

Source not covered by a sub-skill?

• Use web_fetch directly for CDE/NMPA, EMA/EPAR, PMDA, jRCT, CTIS, CRIS, ANZCTR, Orange Book, openFDA, DailyMed, FAERS, and EDGAR.

web_fetch returns empty, blocked, or placeholder content?

• See Tool Access Notes: retry the same URL with browser_navigate before concluding the source has no data.

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References

• references/sub-skills.md — Mapping of pharma-intelligence tasks to bundled sub-skills, with execution patterns.
• references/drug-naming.md — INN / brand / Chinese / Japanese naming conventions and transliteration.
• references/regulatory-timelines.md — Review-clock lengths and milestones per agency (FDA, EMA, PMDA, CDE/NMPA, etc.).
• references/sources-by-region.md — Direct URLs and access notes for all regional regulatory databases.
• references/pharma-intelligence-workflow.md — End-to-end worked example (osimertinib in NSCLC).