unified_search

🔍 Unified Search - Single entry point for multi-source academic search.

Automatically analyzes your query and searches the best sources. No need to choose between PubMed, OpenAlex, CrossRef, etc.

═══════════════════════════════════════════════════════════════════ WHAT IT DOES: ═══════════════════════════════════════════════════════════════════

1. Analyzes your query (complexity, intent, PICO elements)

2. Automatically selects best sources based on query type

3. Searches multiple sources in parallel

4. Deduplicates and merges results

5. Ranks by configurable criteria

6. Enriches with OA links (Unpaywall)

7. Auto-detects ICD-9/10 codes and expands to MeSH terms

8. Optionally searches preprints (arXiv, medRxiv, bioRxiv)

═══════════════════════════════════════════════════════════════════ EXAMPLES (most calls only need 1-2 params): ═══════════════════════════════════════════════════════════════════

Simple (1 param): unified_search("remimazolam ICU sedation")

With limit (2 params): unified_search("machine learning in anesthesia", limit=20)

Specify sources: unified_search("CRISPR gene therapy", sources="pubmed,openalex")

Auto minus one source: unified_search("sepsis biomarkers", sources="auto,-semantic_scholar")

Search all enabled sources except enrichment-only CrossRef: unified_search("icu sedation", sources="all,-crossref")

Clinical filters: unified_search("diabetes treatment", filters="year:2020-2025, age:aged, clinical:therapy")

Include preprints + shallow search: unified_search("COVID-19 vaccine", options="preprints, shallow")

Full control: unified_search("propofol vs remimazolam", sources="pubmed,semantic_scholar,europe_pmc", ranking="impact", filters="year:2020-, sex:female, species:humans", options="preprints, no_relax")

ICD Code Auto-Detection: unified_search("E11 complications") → Auto-expands E11 to "Diabetes Mellitus, Type 2"[MeSH]

Args: query: Your search query (natural language, ICD codes, or structured) limit: Maximum results per source (default 10, max 100) sources: Comma-separated list of sources to search. Available: "pubmed", "openalex", "semantic_scholar", "europe_pmc", "crossref", "core". Commercial connectors may also appear when enabled via env, e.g. "scopus" when SCOPUS_ENABLED=true and SCOPUS_API_KEY are configured, or "web_of_science" when WEB_OF_SCIENCE_ENABLED=true and WEB_OF_SCIENCE_API_KEY are configured. Default: auto-select based on query complexity. Supports "auto" and "all" with exclusions. Examples: "pubmed,openalex", "auto,-semantic_scholar", or "all,-crossref" Global disable env: PUBMED_SEARCH_DISABLED_SOURCES Example: PUBMED_SEARCH_DISABLED_SOURCES=semantic_scholar,core ranking: Ranking strategy: - "balanced": Default, considers all factors - "impact": Prioritize high-citation papers - "recency": Prioritize recent publications - "quality": Prioritize high-evidence studies (RCTs, meta-analyses) output_format: "markdown" (human-readable), "json", or "toon" (programmatic) filters: Comma-separated key:value pairs for filtering results. Supported keys: year:2020-2025 → publication year range year:2020- → from 2020 onwards year:-2025 → up to 2025 year:2024 → from 2024 onwards age: → age group filter (PubMed). Values: newborn, infant, preschool, child, adolescent, young_adult, adult, middle_aged, aged, aged_80 sex: → sex filter: male, female species: → species filter: humans, animals lang: → language filter: english, chinese, etc. clinical: → clinical query filter (PubMed EBM). Values: therapy, therapy_narrow, diagnosis, diagnosis_narrow, prognosis, prognosis_narrow, etiology, etiology_narrow, clinical_prediction, clinical_prediction_narrow Example: "year:2020-2025, age:aged, sex:female, clinical:therapy" options: Comma-separated flags to toggle behaviors. Supported flags: preprints → also search arXiv, medRxiv, bioRxiv all_types → include non-peer-reviewed articles no_oa → skip Unpaywall OA link enrichment no_analysis → hide query analysis section in output no_scores → hide similarity/relevance scores compact → compact structured JSON/TOON output no_next → hide next-tool suggestions in structured output no_provenance → hide section provenance in structured output no_relax → disable auto-relaxation on 0 results shallow → disable deep search (faster, keyword-only) Example: "preprints, shallow" or "no_analysis, no_scores" pipeline: YAML/JSON string defining a multi-step search pipeline. When provided, other parameters (except output_format) are ignored and the pipeline DAG is executed instead.

         Accepts **YAML** (recommended, human-friendly) or **JSON** format.

         **Template mode — YAML** (shortcut for common workflows):
           template: pico
           params:
             P: ICU patients
             I: remimazolam
             C: propofol
             O: sedation

         Other templates:
           template: comprehensive
           params:
             query: CRISPR gene therapy

           template: exploration
           params:
             pmid: "12345678"

           template: gene_drug
           params:
             term: BRCA1

         **Custom pipeline — YAML** (full DAG control, max 20 steps):
           name: My Custom Search
           steps:
             - id: s1
               action: search
               params:
                 query: remimazolam ICU
                 sources: pubmed,europe_pmc
                 limit: 50
             - id: s2
               action: search
               params:
                 query: propofol ICU
                 sources: pubmed
                 limit: 50
             - id: merged
               action: merge
               inputs: [s1, s2]
               params:
                 method: rrf
             - id: enriched
               action: metrics
               inputs: [merged]
           output:
             format: markdown
             limit: 20
             ranking: impact

         Shared params:
           globals: default params inherited by every step
           variables: values available as ${name} placeholders

         Debugging controls:
           dry_run: validate/preview the pipeline without searches
           stop_at: execute through one step id, e.g. "merged"

         **JSON also supported** (for programmatic use):
           {"template": "pico", "params": {"P": "ICU patients", "I": "remimazolam"}}

         Available actions:
           search      — literature search (params: query, sources, limit, min_year, max_year)
           pico        — PICO elements (params: P, I, C, O)
           expand      — MeSH/synonym expansion (params: topic)
           details     — fetch article details (params: pmids)
           related     — find related articles (params: pmid, limit)
           citing      — find citing articles (params: pmid, limit)
           references  — get article references (params: pmid, limit)
           metrics     — enrich with iCite citation metrics (inputs only)
           merge       — combine results (params: method=union|intersection|rrf)
           filter      — post-filter (params: min_year, max_year, article_types, min_citations, has_abstract)

Returns: Formatted search results with: - Query analysis (complexity, intent, PICO) - ICD code expansions (if detected) - Search statistics (sources, dedup count) - Ranked articles with metadata - Open access links where available - Preprints (if options includes "preprints") - Relaxation info (if auto_relax triggered) - Pipeline step summary (if pipeline mode)