download-ncbi-data

name	download-ncbi-data
description	Use when downloading static NCBI reference datasets such as taxonomy, MeSH tree, bioconcepts, generif, journals, serials, or PMC open access files via CLI.
disable-model-invocation	true
user-invocable	true

download-ncbi-data

Quick Start

• Command: download-ncbi-data <dataset> [extra-arg]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/download-ncbi-data
• Full reference: See references/help.md

When To Use This Tool

• Download curated NCBI side datasets such as taxonomy tables, GeneRIF summaries, journal lists, MeSH resources, PMC OA bundles, or NIH Open Citation Collection files.
• Build local lookup tables without manually browsing NCBI FTP trees.
• Grab sample/demo payloads like carotene, globin, human, or smear for testing downstream EDirect tooling.

Common Patterns

# 1) Download taxonomy name and lineage tables
download-ncbi-data taxnames

# 2) Build MeSH helper tables in the current directory
download-ncbi-data meshtree

# 3) Mirror PubMed journal metadata or the NIH Open Citation Collection
download-ncbi-data journals
download-ncbi-data nihocc

# 4) Download a specific OA book bundle after discovering its accession
download-ncbi-data oa-book NBKXXXXXX

Recommended Workflow

1. Choose a dedicated output directory before running the command because many subcommands emit multiple derived files.
2. Pick the dataset subcommand deliberately: taxnames/taxoninfo for taxonomy, meshtree for MeSH, serials/journals for literature metadata, pmc-oa or pmc-bioc for large content bundles.
3. Let the script finish its side products, such as taxnames.txt, lineages.txt, meshconv.xml, meshtree.txt, or journal lookup tables.
4. Treat the generated files as reusable local resources for later pipelines instead of re-downloading them each run.

Guardrails

• This tool writes into the current directory and may create several companion files in addition to the primary download.
• oa-book expects an accession argument after the subcommand; most other modes do not.
• Some options are real datasets, while carotene, globin, human, and smear are sample payloads meant for testing.
• The local script has no meaningful --version mode and depends heavily on live network access.
• In this local install, the human sample branch appears to contain a filename typo in the wrapper script, so verify that mode manually before depending on it.