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 14+ biomedical research databases.

MCP Server — How to Invoke

There is no dedicated MCP tool in your toolbox. Call the unified endpoint over HTTP via web_fetch (POST) or run_in_terminal (curl):

https://mcp.sciminer.tech/tools/unified/mcp

Every call is a JSON-RPC POST. Always set Content-Type: application/json and Accept: application/json.

curl -X POST https://mcp.sciminer.tech/tools/unified/mcp \
  -H "Content-Type: application/json" -H "Accept: application/json" \
  -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"ctg_search_studies","arguments":{"intervention":"pan-RAS","condition":"cancer","max_results":20}},"id":1}'

See references/mcp-tools.md for every tool's parameters and return shape.

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.

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.

Resolve identifiers as needed:

• Free-text disease → MONDO/EFO ID via opentargets_search
• Free-text gene → HGNC symbol via mygene_search_genes
• Cross-database ID conversion → nodenorm_get_normalized_nodes

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.

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.

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

1. United States — ctg_search_studies via MCP.
   • Use intervention for a drug, condition for a disease, both for combined.
   • For a target/class (e.g., "pan-RAS", "PD-L1 inhibitor"): pass the class term as intervention plus a relevant condition.
   • Then ctg_get_study on top hits for eligibility, endpoints, sponsor, 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.). Also europepmc_search via MCP for ICTRP-linked publications.
8. Published results — pubmed_search_articles with NCT ID or drug name to surface completed-trial papers.
9. US company-disclosed pipeline (optional) — edgar_fulltext_search 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 — openfda_search_drug_labels + dailymed_search_drug_labels (label date anchors approval); fda_orphan_search_designations 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_get_drug_indications — 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. openfda_search_adverse_events (drug_name, seriousness=serious).
2. openfda_get_drug_label with section="warnings" and section="contraindications".
3. chembl_get_molecule for the black-box warning flag.
4. pubmed_search_articles with keywords: ["adverse effect", "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 recruitment_status=RECRUITING (or ACTIVE_NOT_RECRUITING) and a phase filter to focus on competitors at a specific stage.
2. Company disclosures — edgar_fulltext_search 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 with an assignee: filter (or WIPO PATENTSCOPE / Espacenet — see Workflow E).
4. Published results — pubmed_search_articles 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:
   • https://patents.google.com (Google Patents — best full-text search, covers USPTO, EPO, WIPO, JPO, CNIPA, KIPO).
   • 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_find_drugs_by_target (target_name = gene symbol, include_all_mechanisms=true).
2. chembl_get_mechanism for each candidate.
3. chembl_get_activities — IC50 / Kd / EC50 for bioactivity comparisons.
4. uniprot_search_proteins — protein function and druggability.
5. reactome_search_pathways or kegg_find_pathways — pathway context.

G. Repurposing / Target Discovery

1. opentargets_search (entity_type="disease") → MONDO ID.
2. opentargets_get_associations (disease_id, size 20–30) → ranked targets by evidence score.
3. gwas_search_associations — variants linking targets to disease.
4. omim_search_entries — Mendelian basis (requires API key).
5. For each top target: chembl_find_drugs_by_target (include_all_mechanisms=true).
6. ctg_search_studies with each drug as intervention for prior-art trials.
7. openfda_search_adverse_events as a safety filter for non-trivial candidates.

H. Literature / Evidence Review

1. pubmed_search_articles — entry point; use diseases, chemicals, genes for entity-aware filtering.
2. europepmc_search — broader: grants, preprints, non-MEDLINE.
3. europepmc_search_preprints — bioRxiv / medRxiv only.
4. pubmed_get_article — abstract or full text for top hits.

Combination Strategies (cross-intent)

Use only when a question genuinely spans multiple intents.

• Disease → Targets → Drugs → Trials: opentargets_search → opentargets_get_associations → chembl_find_drugs_by_target → ctg_search_studies
• Gene → Protein → Pathways → Drugs: mygene_search_genes → uniprot_get_protein → reactome_search_pathways → chembl_find_drugs_by_target
• Variant → Gene → Disease → Treatments: myvariant_get_variant → mygene_get_gene → omim_search_entries → chembl_find_drugs_by_target
• Drug → Safety → Label → Trials: chembl_get_mechanism → openfda_search_adverse_events → openfda_get_drug_label → ctg_search_studies

API Keys

Most APIs require no key. Exceptions:

All others (ChEMBL, OpenTargets, PubMed, ClinicalTrials.gov, Reactome, KEGG, UniProt, GWAS, Pathway Commons, MyGene / MyVariant / MyChem, Node Normalization, USPTO PPUBS) are public. Patent landscape work uses Google Patents, WIPO PATENTSCOPE, and Espacenet via web_fetch — no keys required.

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.

Troubleshooting

No results?

• Try alternative terms (INN vs brand name, gene symbol vs protein name).
• Use standardized IDs: MONDO for diseases, HGNC for genes, ChEMBL IDs for compounds, Ensembl for OpenTargets.
• Convert IDs across databases with nodenorm_get_normalized_nodes.

Too many results?

• Add filters: max_results, phase, recruitment_status, reviewed (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 MCP?

• Fall back to web_fetch for CDE/NMPA, EMA/EPAR, PMDA, jRCT, CTIS, CRIS, ANZCTR, Orange Book.

References

• references/mcp-tools.md — Parameters and call format for every MCP tool.
• 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 with curl commands (osimertinib in NSCLC).