Data Wrangling: Universal Access Patterns

Reference for downloading and parsing scientific data from any source. Write and run Python code via Bash for every step.

When to Use

• ToolUniverse tool returned metadata/search results but you need raw or bulk data
• Data is in a format tools don't parse (VCF, h5ad, BAM, SDF, GCT)
• You need a multi-step API workflow (search -> filter -> download -> parse)
• The data source has no ToolUniverse tool at all
• You need thousands of records, not the 10-100 a tool returns

Decision: Tool vs Code