download-ncbi-data - download specific data from NCBI's FTP
site
download-ncbi-data
bioconcepts|generif|meshtree|taxnames|serials|journals|nihocc|pmc-oa|pmc-bioc|oa-list|oa-book accession|carotene|globin|human|smear
download-ncbi-data downloads the requested data to the
current directory.
- 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.
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).