fetch-pubmed - fetch records from a local NCBI PubMed archive by UID
fetch-pubmed [
-strict|
-mixed] [[
-path] dir ] [-all]
[-fresh]
[-asn|-xml|-pme]
[-turbo ]
fetch-pubmed reads a list of record IDs from standard input and prints to
standard output the corresponding portions of a local NCBI PubMed archive
produced by
archive-pubmed(1), typically for further processing by
xtract(1) or the like.
-
-strict|-mixed
- Run rchive(1) with -flag strict or
-flag mixed, respectively.
- [-path] dir
- Use the local archive in dir.
- -all
- Dump the entire archive.
- -fresh
- Dump the entire archive into filenames of the form
pubmed001.xml.gz, using any existing such files as a starting
point.
- -asn
- Retrieve ASN.1.
- -xml
- Retrieve XML (default).
- -pme
- Produce ASN.1 on the fly, via pma2pme.
- -turbo
- Add NEXT_RECORD_SIZE nodes to speed navigation.
- EDIRECT_PUBMED_MASTER
- Local archive directory to use in the absence of
-path. Expected to hold an absolute path; mandatory when not
supplying a path on the command line.
archive-pubmed(1),
cit2pmid(1),
ds2pme(1),
edict(1),
phrase-search(1),
pma2pme(1),
rchive(1),
stream-pubmed(1),
xtract(1).