DOWNLOAD-NCBI-DATA(1)

💾 download-ncbi-data(1) 💾

okay bestie, so this one lives in the NCBI Entrez Direct User's Manual, and it's literally your one-stop shop for pulling data straight off NCBI's FTP site 🫶

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✨ NAME ✨

download-ncbi-data — download specific data from NCBI's FTP site 💅

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🌸 SYNOPSIS 🌸

download-ncbi-data bioconcepts|generif|meshtree|taxnames|taxoninfo|
serials|journals|nihocc|pmc-oa|pmc-bioc|oa-list|oa-book accession|
carotene|globin|human|smear

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🦋 DESCRIPTION 🦋

download-ncbi-data</purl> drops the data you asked for right into your current directory. no extra steps, no drama, it's just there. ✨

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🎀 OPTIONS 🎀

• bioconcepts — grabs the mappings from chemical, disease, and gene names over to PubTatorCentral, unless it's already present (we don't re-download, we're not wasteful 💖).
• generif — downloads the GeneRif data, unless it's already present, and then extracts some summaries for you. little bonus treat 🍓
• taxnames — downloads a taxonomic database and whips up a table summarizing the correspondences between taxonomic IDs and their scientific or common names. taxonomy slay 🧚
• taxoninfo — downloads additional general taxonomic data. more tax stuff, we love to see it 🌈
• serials — downloads a database of serials indexed by NLM and extracts some summaries. iconic 🌟
• journals — downloads a database of journals indexed by PubMed and extracts some summaries. yes, journals as in those journals 👑
• meshtree — downloads MeSH data and extracts some summaries. tree structure but make it cute 🌸
• nihocc — downloads NIH Open Citation Collection data. periodt 💅
• pmc-oa — downloads PubMed Central open-access archives in traditional format, unless already present.
• pmc-bioc — downloads PubMed Central open-access archives in BioConcepts format, unless already present.
• oa-list — downloads a list of open access books, unless already present, and extracts a summary. two for one bestie 🫶
• oa-book accession — downloads the open access book with the specified accession. and if you need it, it'll first produce a list and summary as above before going for the book itself. so considerate 😭
• carotene — downloads and unzips sample PubmedArticleSet XML for carotene. 🥕 (yes the name is adorable, no I will not be elaborating)
• globin — downloads and unzips sample INSDSet XML for globin. 🔥
• human — downloads and unzips sample gene DocumentSummarySet XML for humans. main character energy fr fr 👑
• smear — downloads and unzips sample Seq-submit ASN.1 for a fruit fly nucleotide-protein set with annotations from GeneMachine and BLAST. yes that's a whole mouthful, no I'm not paraphrasing it, it's literally what it does 💀

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🌟 SEE ALSO 🌟

archive-pubmed(1), archive-taxonomy(1), download-flatfile(1), download-ncbi-software(1), download-pmc(1), download-pubmed(1), download-sequence(1), nquire(1), refseq-nm-cds(1), xfetch(1), xinfo(1), xlink(1), xsearch(1). xtract(1).

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and that's the whole page bestie, you ate that 💅✨

this one's brought to you by NCBI, dated 2025-05-26, and it's the DOWNLOAD-NCBI-DATA(1) page from the NCBI Entrez Direct User's Manual — go download something, ily, mwah 😘💖