NAME¶

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

SYNOPSIS¶

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

DESCRIPTION¶

download-ncbi-data downloads the requested data to the current directory.

OPTIONS¶

bioconcepts

Download mappings from chemical, disease, and gene names to PubTatorCentral unless already present.

generif

Download GeneRif data, unless already present, and extract some summaries.

taxnames

Download a taxonomic database and produce a table summarizing correspondences between taxonomic IDs and scientific or common names.

serials

Download a database of serials indexed by NLM and extract some summaries.

journals

Download a database of journals indexed by PubMed and extract some summaries.

meshtree

Download MeSH data and extract some summaries.

nihocc

Download NIH Open Citation Collection data.

pmc-oa

Download PubMed Central open-access archives in traditional format, unless already present.

pmc-bioc

Download PubMed Central open-access archives in BioConcepts format, unless already present.

oa-list

Download a list of open access books, unless already present, and extract a summary.

oa-book accession

Download the open access book with the specified accession. First produce a list and summary as above if necessary.

carotene

Download and unzip sample PubmedArticleSet XML for carotene.

globin

Download and unzip sample INSDSet XML for globin.

human

Download and unzip sample gene DocumentSummarySet XML for humans.

smear

Download and unzip sample Seq-submit ASN.1 for a fruit fly nucleotide-protein set with annotations from GeneMachine and BLAST.

SEE ALSO¶

archive-pubmed(1), download-ncbi-software(1), download-pmc(1), download-pubmed(1), download-sequence(1), index-extras(1), index-pubmed(1), phrase-search(1), nquire(1), xtract(1).