Comprehensive literature deep research across any academic domain using 120+ ToolUniverse tools. Conducts subject disambiguation, systematic literature search with citation network expansion, evidence grading (T1-T4), and structured theme extraction. Produces detailed reports with mandatory completeness checklists, integrated models, and testable hypotheses. Use when users need thorough literature reviews, target/drug/disease profiles, topic deep-dives, claim verification, or systematic evidence synthesis. Supports biomedical (genes, proteins, drugs, diseases), computer science, social science, and general academic topics. For single factoid questions, uses a fast verification mode with inline answer.
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Systematic literature research: disambiguate, search with collision-aware queries, grade evidence, produce structured reports.
KEY PRINCIPLES: (1) Disambiguate first (2) Right-size deliverable (3) Grade every claim T1-T4 (4) All sections mandatory even if "limited evidence" (5) Source attribution for every claim (6) English-first queries, respond in user's language (7) Report = deliverable, not search log
Search PubMed/EuropePMC FIRST before reasoning. A published paper beats memory.
Factoid search strategy:
EuropePMC_search_articles(query="term1 term2 term3", limit=5)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.
Phase 0: Clarify + Mode Select → Phase 1: Disambiguate + Profile → Phase 2: Literature Search → Phase 3: Report
| Mode | When | Deliverable |
|---|---|---|
| Factoid | Single concrete question | 1-page fact-check report + bibliography |
| Mini-review | Narrow topic | 1-3 page narrative |
| Full Deep-Research | Comprehensive overview | 15-section report + bibliography |
# [TOPIC]: Fact-check Report
## Question / ## Answer (with evidence rating) / ## Source(s) / ## Verification Notes / ## Limitations
| Pattern | Domain | Action |
|---|---|---|
| Gene/protein symbol | Biological target | Full bio disambiguation |
| Drug name | Drug | Drug disambiguation (1.5) |
| Disease name | Disease | Disease disambiguation (1.6) |
| CS/ML topic | General academic | Skip bio tools, literature-only |
| Cross-domain | Interdisciplinary | Resolve each entity in its domain |
tooluniverse-target-researchtooluniverse-drug-researchtooluniverse-disease-researchUse this skill for literature synthesis. Use specialized skills for entity profiling. For max depth, run both.
UniProt_search → UniProt_get_entry_by_accession → UniProt_id_mapping
ensembl_lookup_gene → MyGene_get_gene_annotation
Check first 20 results. If >20% off-topic, build negative filter: NOT [collision1] NOT [collision2].
Gene family: "ADAR" NOT "ADAR2" NOT "ADARB1". Cross-domain: add context terms.
InterPro_get_protein_domains, UniProt_get_ptm_processing_by_accession, HPA_get_subcellular_location,
GTEx_get_median_gene_expression, GO_get_annotations_for_gene, Reactome_map_uniprot_to_pathways,
STRING_get_protein_interactions, intact_get_interactions, OpenTargets_get_target_tractability_by_ensemblID
GPCR targets: delegate to tooluniverse-target-research.
Identity: OpenTargets_get_drug_chembId_by_generic_name, ChEMBL_get_drug, PubChem_get_CID_by_compound_name, drugbank_get_drug_basic_info_by_drug_name_or_id
Targets: ChEMBL_get_drug_mechanisms, OpenTargets_get_associated_targets_by_drug_chemblId, DGIdb_get_drug_gene_interactions
Safety: OpenTargets_get_drug_adverse_events_by_chemblId, OpenTargets_get_drug_indications_by_chemblId, search_clinical_trials
OpenTargets disease search → EFO/MONDO IDs
DisGeNET_get_disease_genes, DisGeNET_search_disease
CTD_get_disease_chemicals
Resolve both entities, then cross-reference via CTD_get_chemical_gene_interactions, CTD_get_chemical_diseases, OpenTargets drug-target/drug-disease tools. Intersect shared targets/pathways.
Non-bio: skip bio tools, use ArXiv/DBLP/OSF. Cross-domain: resolve bio entities with 1.1-1.3, search CS/general in parallel, merge and cross-reference.
Methodology stays internal. Report shows findings, not process.
Step 1: Seeds (15-30 core papers): domain-specific title searches with date/sort filters.
Step 2: Citation expansion: PubMed_get_cited_by, EuropePMC_get_citations/references, PubMed_get_related, SemanticScholar_get_recommendations, OpenCitations_get_citations
Step 3: Collision-filtered broader queries: "[TERM]" AND ([context]) NOT [collision]
Biomedical: PubMed_search_articles, PMC_search_papers, EuropePMC_search_articles, PubTator3_LiteratureSearch
Biology (ecology/evolution/plant): EuropePMC as PRIMARY (PubMed returns 0-1 for non-clinical biology). Also openalex_literature_search.
CS/ML: ArXiv_search_papers, DBLP_search_publications, SemanticScholar_search_papers
General: openalex_literature_search, Crossref_search_works, CORE_search_papers, DOAJ_search_articles
Preprints: BioRxiv_get_preprint, MedRxiv_get_preprint, OSF_search_preprints, EuropePMC_search_articles(source='PPR')
Multi-source: advanced_literature_search_agent (12+ DBs; needs Azure key -- fallback: query PubMed+ArXiv+SemanticScholar+OpenAlex individually)
Citation impact: iCite_search_publications (RCR/APT), iCite_get_publications (by PMID), scite_get_tallies (support/contradict). PubMed-only; for CS use SemanticScholar.
Full-text: see FULLTEXT_STRATEGY.md for three-tier strategy.
CRITICAL: PubMed returns 0 for ~30% of valid queries. Always retry with EuropePMC when PubMed returns empty. This is not optional.
Retry once -> fallback tool. Key fallbacks: PubMed_get_cited_by -> EuropePMC_get_citations -> OpenCitations. OA: Unpaywall if configured, else Europe PMC/PMC/OpenAlex flags.
| Tier | Label | Bio Example | CS/ML Example |
|---|---|---|---|
| T1 | Mechanistic | CRISPR KO + rescue, RCT | Formal proof, controlled ablation |
| T2 | Functional | siRNA knockdown phenotype | Benchmark with baselines |
| T3 | Association | GWAS, screen hit | Observational, case study |
| T4 | Mention | Review article | Survey, workshop abstract |
Inline: Target X regulates Y [T1: PMID:12345678]. Per theme: summarize evidence distribution.
| File | Mode |
|---|---|
[topic]_report.md | Full |
[topic]_factcheck_report.md | Factoid |
[topic]_bibliography.json + .csv | All |
Progressive update: create report with all section headers immediately. Fill after each phase. Write Executive Summary LAST.
Use 15-section template from REPORT_TEMPLATE.md. Domain adaptations: bio (architecture/expression/GO/disease), drug (properties/MOA/PK/safety), disease (epi/patho/genes/treatments), general (history/theories/evidence/applications).
Brief progress updates only: "Resolving identifiers...", "Building paper set...", "Grading evidence..." Do NOT expose: raw tool outputs, dedup counts, search round details.
TOOL_NAMES_REFERENCE.md -- 123 tools with parametersREPORT_TEMPLATE.md -- template, domain adaptations, bibliography, completeness checklistFULLTEXT_STRATEGY.md -- three-tier full-text verificationWORKFLOW.md -- compact cheat-sheetEXAMPLES.md -- worked examples