How do I install the Xtract skill?

Run npx skillmds@latest add vimalinx/xtract 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 Xtract safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: docs only, makes network calls. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Xtract?

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 Xtract free to use?

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

Who published Xtract?

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

Xtract by vimalinx — Agent Skill

Name: Xtract
Rating: 4.5 (4 reviews)
Author: vimalinx

Xtract

Use when parsing, extracting, or converting XML data from NCBI Entrez or other bioinformatics sources into tab-delimited tables. Use for selecting specific elements, filtering records, and restructuring hierarchical XML into flat formats for downstream analysis.

vimalinx Updated Aug 19, 2026 0 repo stars

File contents

xtract

Quick Start

Command: xtract
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/xtract
Full reference: See references/help.md for complete argument list and examples

When To Use This Tool

Convert Entrez XML into tab-delimited tables.
Extract selected elements or nested values from efetch, esummary, or elink XML output.
Filter records conditionally while flattening XML into rows.
Use this after you already know the XML structure you are parsing.

Common Patterns

# 1) Turn document summaries into a simple two-column table
esearch -db assembly -query 'GCF_000001405.40[accn]' | \
  efetch -format docsum | \
  xtract -pattern DocumentSummary -element Id AssemblyAccession

# 2) Extract PubMed summary IDs and titles
esearch -db pubmed -query 'ebola virus[Title/Abstract]' | \
  efetch -format docsum | \
  xtract -pattern DocumentSummary -element Id Title

# 3) Conditional extraction from linked records
elink -db pubmed -id 20210808 -cmd score | \
  xtract -pattern LinkSet -max Link/Score

Recommended Workflow

Feed XML from stdin or -input; xtract is not useful without structured input.
Define rows first with -pattern.
Add -element fields incrementally before reaching for -group, -block, or -if.
Save the exact extraction command alongside the analysis so XML-to-table logic remains reproducible.

Guardrails

xtract requires XML input from stdin or -input; otherwise it errors immediately.
-pattern defines row boundaries; choosing the wrong pattern is the fastest way to get nonsense tables.
Start with a minimal extraction and expand, rather than writing a huge one-liner blind.
Use -strict when embedded HTML or MathML is polluting the text you want to extract.

---name: xtractdescription: Use when parsing, extracting, or converting XML data from NCBI Entrez or other bioinformatics sources into tab-delimited tables. Use for selecting specific elements, filtering records, and restructuring hierarchical XML into flat formats for downstream analysis.---# xtract## Quick Start- **Command:** `xtract`- **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/xtract`- **Full reference:** See `references/help.md` for complete argument list and examples## When To Use This Tool- Convert Entrez XML into tab-delimited tables.- Extract selected elements or nested values from `efetch`, `esummary`, or `elink` XML output.- Filter records conditionally while flattening XML into rows.- Use this after you already know the XML structure you are parsing.## Common Patterns```bash# 1) Turn document summaries into a simple two-column tableesearch -db assembly -query 'GCF_000001405.40[accn]' | \ efetch -format docsum | \ xtract -pattern DocumentSummary -element Id AssemblyAccession``````bash# 2) Extract PubMed summary IDs and titlesesearch -db pubmed -query 'ebola virus[Title/Abstract]' | \ efetch -format docsum | \ xtract -pattern DocumentSummary -element Id Title``````bash# 3) Conditional extraction from linked recordselink -db pubmed -id 20210808 -cmd score | \ xtract -pattern LinkSet -max Link/Score```## Recommended Workflow1. Feed XML from stdin or `-input`; `xtract` is not useful without structured input.2. Define rows first with `-pattern`.3. Add `-element` fields incrementally before reaching for `-group`, `-block`, or `-if`.4. Save the exact extraction command alongside the analysis so XML-to-table logic remains reproducible.## Guardrails- `xtract` requires XML input from stdin or `-input`; otherwise it errors immediately.- `-pattern` defines row boundaries; choosing the wrong pattern is the fastest way to get nonsense tables.- Start with a minimal extraction and expand, rather than writing a huge one-liner blind.- Use `-strict` when embedded HTML or MathML is polluting the text you want to extract.

Frequently asked questions