bsmp2info

name	bsmp2info
description	Use when converting BioSample `DocumentSummary` XML into a compact `BioSampleInfo` XML summary with accession, title, links, and harmonized attributes.
disable-model-invocation	true
user-invocable	true

bsmp2info

Quick Start

• Command: ... | bsmp2info
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bsmp2info
• Output: formatted BioSampleInfo XML

When To Use This Tool

• Extract a compact XML summary from BioSample docsum records.
• Preserve accession, title, link IDs, and harmonized BioSample attributes in a simpler structure.
• Normalize attribute tag names to lowercase before downstream parsing.
• Keep BioSample extraction inside an EDirect XML pipeline.

Common Patterns

# 1) Convert a local BioSample DocumentSummary XML snippet
cat biosample_docsum.xml | bsmp2info

# 2) End-to-end after obtaining BioSample docsum XML
esearch -db biosample -query 'SAMN38051082[ACCN]' |
efetch -format docsum |
bsmp2info

# 3) Pull selected fields from the simplified XML
... | bsmp2info | xtract -pattern BioSampleInfo -element Accession,organism,tissue

Recommended Workflow

1. Start from BioSample DocumentSummary XML, whether from a local file or an EDirect fetch.
2. Pipe that XML into bsmp2info to collapse it to the key fields you actually need.
3. Inspect the emitted XML and confirm that expected harmonized attributes are present.
4. Continue with xtract or another XML-aware consumer instead of reparsing the original larger docsum structure.

Guardrails

• The wrapper expects BioSample DocumentSummary XML on stdin; it does not accept a bare accession or identifier list.
• Only attributes carrying harmonized_name are emitted, and their tag names are lowercased.
• Multiple Links/Link values are collapsed into one pipe-delimited Link element such as 123|456.
• There is no real help or version interface.
• Live BioSample EDirect requests may hit NCBI rate limits, so local fixture-based validation can be more reliable than repeated network probing.