Man page - download-ncbi-data(1)
Packages contas this manual
- blst2tkns(1)
- pmc2bioc(1)
- hgvs2spdi(1)
- archive-nihocc(1)
- sort-by-length(1)
- print-missing-subranges(1)
- asn2ref(1)
- gene2range(1)
- xfetch(1)
- ini2xml(1)
- filter-genbank(1)
- sort-uniq-count-rank(1)
- archive-pmc(1)
- pair-at-a-time(1)
- xml2tbl(1)
- fuse-ranges(1)
- download-ncbi-data(1)
- jsonl2xml(1)
- epost(1)
- tbl2prod(1)
- find-in-gene(1)
- between-two-genes(1)
- efilter(1)
- gbf2info(1)
- filter-stop-words(1)
- exclude-uid-lists(1)
- archive-pubmed(1)
- print-columns(1)
- transmute(1)
- fsa2xml(1)
- quote-grouped-elements(1)
- esample(1)
- sort-uniq-count(1)
- download-pmc(1)
- pm-setup(1)
- archive-taxonomy(1)
- csv2xml(1)
- expand-current(1)
- esearch(1)
- download-sequence(1)
- archive-nmcds(1)
- reorder-columns(1)
- cit2pmid(1)
- fuse-segments(1)
- archive-pids(1)
- xml2fsa(1)
- scn2xml(1)
- refseq-nm-cds(1)
- elink(1)
- xy-plot(1)
- snp2hgvs(1)
- run-ncbi-converter(1)
- yaml2xml(1)
- gbf2ref(1)
- xinfo(1)
- xlink(1)
- efetch.ncbi(1)
- accn-at-a-time(1)
- bsmp2info(1)
- gbf2facds(1)
- json2xml(1)
- combine-uid-lists(1)
- gbf2fsa(1)
- spdi2tbl(1)
- args2slice(1)
- efetch(1)
- filter-columns(1)
- gbf2xml(1)
- download-pubmed(1)
- archive-nlmnlp(1)
- xtract(1)
- einfo.ncbi(1)
- intersect-uid-lists(1)
- custom-index(1)
- xfilter(1)
- ds2pme(1)
- amino-acid-composition(1)
- pm-clean(1)
- rchive(1)
- ref2pmid(1)
- pm-prepare(1)
- join-into-groups-of(1)
- difference-uid-lists(1)
- word-at-a-time(1)
- uniq-table(1)
- download-ncbi-software(1)
- tbl2xml(1)
- xsearch(1)
- skip-if-file-exists(1)
- nquire(1)
- esummary(1)
- filter-record(1)
- einfo(1)
- sort-table(1)
- edict(1)
- pm-collect(1)
- split-at-intron(1)
- systematic-mutations(1)
- just-top-hits(1)
- pma2pme(1)
- pm-refresh(1)
- ecollect(1)
- snp2tbl(1)
- gbf2tbl(1)
- gm2segs(1)
- disambiguate-nucleotides(1)
- gff-sort(1)
- align-columns(1)
- pmc2info(1)
- gff2xml(1)
- pma2apa(1)
- download-flatfile(1)
Package: ncbi-entrez-direct
apt-get install ncbi-entrez-direct
apt-get install ncbi-entrez-direct
Manuals in package:
Documentations in package:
Manual
| DOWNLOAD-NCBI-DATA(1) | NCBI Entrez Direct User's Manual | DOWNLOAD-NCBI-DATA(1) |
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).
| 2025-05-26 | NCBI |