How do I install the Bsmp2info skill?

Run npx skillmds add vimalinx/bsmp2info in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Bsmp2info safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: makes network calls. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Bsmp2info?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Bsmp2info free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Bsmp2info?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Bsmp2info by vimalinx — Agent Skill

Name: Bsmp2info
Rating: 4.666666666666667 (3 reviews)
Author: vimalinx

File contents

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

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.

---name: bsmp2infodescription: Use when converting BioSample `DocumentSummary` XML into a compact `BioSampleInfo` XML summary with accession, title, links, and harmonized attributes.--- # 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 ```bash # 1) Convert a local BioSample DocumentSummary XML snippet cat biosample_docsum.xml | bsmp2info ``` ```bash # 2) End-to-end after obtaining BioSample docsum XML esearch -db biosample -query 'SAMN38051082[ACCN]' | efetch -format docsum | bsmp2info ``` ```bash # 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.

Frequently asked questions