Search

SRAKE provides multi-backend search over local SRA metadata.

Search backends

Backend	Description	Use case
Bleve	Full-text search with BM25 ranking	General queries
SQLite FTS5	FTS5 virtual tables for high-volume data	Large datasets
Vector	SapBERT cosine similarity	Semantic/concept search
Hybrid	Weighted combination of text + vector	Default mode

Building the index

# Build Bleve index
srake index --build

# Include vector embeddings
srake index --build --with-embeddings

# Check index status
srake index --stats

Basic search

srake search "homo sapiens"
srake search "breast cancer RNA-Seq"

Search modes

# Full-text (Bleve BM25)
srake search "cancer" --search-mode text

# Vector similarity (SapBERT)
srake search "tumor gene expression" --search-mode vector

# Hybrid (default)
srake search "cancer" --search-mode hybrid

# Database only (SQLite)
srake search "SRP123456" --search-mode database

Advanced query syntax

Enable with --advanced:

# Boolean operators
srake search "organism:human AND library_strategy:RNA-Seq" --advanced

# NOT
srake search "cancer NOT organism:mouse" --advanced

# Phrase search
srake search "\"breast cancer\"" --advanced

# Wildcards
srake search "RNA*" --advanced

Field aliases: org (organism), plat (platform), lib/strat (library_strategy), inst (instrument_model), acc (accession).

Filtering

Combine text search with metadata filters:

srake search "cancer" \
  --organism "homo sapiens" \
  --platform ILLUMINA \
  --library-strategy RNA-Seq \
  --spots-min 1000000 \
  --date-from 2023-01-01

Quality control

# Set similarity threshold for vector results
srake search "cancer" --similarity-threshold 0.7

# Show confidence scores
srake search "cancer" --show-confidence

# Adjust hybrid weight (0.0=text only, 1.0=vector only)
srake search "cancer" --hybrid-weight 0.5

# Fuzzy search (tolerates typos)
srake search "hmuan" --fuzzy

Output formats

srake search "cancer" --format json
srake search "cancer" --format csv --output results.csv
srake search "cancer" --format tsv
srake search "cancer" --format accession  # accession numbers only
srake search "cancer" --fields "accession,organism,platform"

Pagination

srake search "human" --limit 100 --offset 0
srake search "human" --limit 100 --offset 100

Facets

srake search "cancer" --facets --format json

API access

Search is also available via the REST API:

curl "http://localhost:8080/api/v1/search?q=cancer&limit=10"
curl "http://localhost:8080/api/v1/search?q=RNA-Seq&organism=homo+sapiens"

See API Reference for details.

Resume SRAmetadb Export