NAME
download-ncbi-data - download specific data from NCBI's FTP site
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
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.
- taxoninfo
-
Download additional general taxonomic data.
- 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), 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).