| 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
cat biosample_docsum.xml | bsmp2info
esearch -db biosample -query 'SAMN38051082[ACCN]' |
efetch -format docsum |
bsmp2info
... | bsmp2info | xtract -pattern BioSampleInfo -element Accession,organism,tissue
Recommended Workflow
- Start from BioSample
DocumentSummary XML, whether from a local file or an EDirect fetch.
- Pipe that XML into
bsmp2info to collapse it to the key fields you actually need.
- Inspect the emitted XML and confirm that expected harmonized attributes are present.
- 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.
