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
- Choose a dedicated output directory before running the command because many subcommands emit multiple derived files.
- 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.
- Let the script finish its side products, such as
taxnames.txt, lineages.txt, meshconv.xml, meshtree.txt, or journal lookup tables.
- 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.
1---2name: download-ncbi-data3description: Use when downloading static NCBI reference datasets such as taxonomy, MeSH tree, bioconcepts, generif, journals, serials, or PMC open access files via CLI.4---5
6# download-ncbi-data
7
8## Quick Start
9- **Command:** `download-ncbi-data <dataset> [extra-arg]`
10- **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/download-ncbi-data`
11- **Full reference:** See `references/help.md`
12
13## When To Use This Tool
14
15- Download curated NCBI side datasets such as taxonomy tables, GeneRIF summaries, journal lists, MeSH resources, PMC OA bundles, or NIH Open Citation Collection files.
16- Build local lookup tables without manually browsing NCBI FTP trees.
17- Grab sample/demo payloads like `carotene`, `globin`, `human`, or `smear` for testing downstream EDirect tooling.
18
19## Common Patterns
20
21```bash
22# 1) Download taxonomy name and lineage tables
23download-ncbi-data taxnames
24```
25
26```bash
27# 2) Build MeSH helper tables in the current directory
28download-ncbi-data meshtree
29```
30
31```bash
32# 3) Mirror PubMed journal metadata or the NIH Open Citation Collection
33download-ncbi-data journals
34download-ncbi-data nihocc
35```
36
37```bash
38# 4) Download a specific OA book bundle after discovering its accession
39download-ncbi-data oa-book NBKXXXXXX
40```
41
42## Recommended Workflow
43
441. Choose a dedicated output directory before running the command because many subcommands emit multiple derived files.
452. 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.
463. Let the script finish its side products, such as `taxnames.txt`, `lineages.txt`, `meshconv.xml`, `meshtree.txt`, or journal lookup tables.
474. Treat the generated files as reusable local resources for later pipelines instead of re-downloading them each run.
48
49## Guardrails
50
51- This tool writes into the current directory and may create several companion files in addition to the primary download.
52- `oa-book` expects an accession argument after the subcommand; most other modes do not.
53- Some options are real datasets, while `carotene`, `globin`, `human`, and `smear` are sample payloads meant for testing.
54- The local script has no meaningful `--version` mode and depends heavily on live network access.
55- 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.
vimalinx