NAME
cit2pmid - find candidate NCBI PubMed identifiers for a citation
SYNOPSIS
cit2pmid [-debug] [-strict] [-remote|-eutils|-local|-exact|-verify] [-asn file|-cit file] [-title|-TITL str] [-author|-FAUT|-LAUT str] [-journal|-JOUR str] [-year|-YEAR|-PDAT str] [-volume|-VOL str] [-issue|-ISS str] [-page[s]|-PAGE str]
DESCRIPTION
cit2pmid tries to identify NCBI PubMed identifiers corresponding to a supplied citation. Some modes search an indexed local NCBI PubMed archive (as prepared by archive-pubmed(1)).
OPTIONS
- -debug
-
Trace some aspects of execution.
- -strict
-
Perform stricter matching (only in -local mode, at least for now).
- -remote
-
Use nquire -citmatch remote service (default).
- -eutils
-
Use esearch remote service.
- -local
-
Use transmute -r2p (ref2pmid) for relaxed search with local archive.
- -exact
-
Use xsearch -exact for strict matching with local archive.
- -verify
-
Query against local archive with strict (but not -exact) matching then confirm positive candidates via citmatch.
- -asn file
-
Read NCBI Pub ASN.1 from file (- for standard input). Must be the only query specification.
- -cit file
-
Read CITATION XML from file (- for standard input). Must be the only query specification.
- -title|-TITL str
-
Article title; may need other fields to disambiguate, especially if incomplete.
- -author str
-
Author name (last name, optionally followed by initials); may appear twice, for first and last authors. (Otherwise, taken to be first author only.)
- -FAUT str
-
Explicitly name first author.
- -LAUT str
-
Explicitly name last author.
- -journal|-JOUR str
-
Journal name.
- -year|-YEAR|-PDAT str
-
Publication year.
- -volume|-VOL str
-
Journal volume.
- -issue|-ISS str
-
Journal issue.
- -page[s]|-PAGE str
-
Journal page, or hyphenated range.
ENVIRONMENT
- EDIRECT_LOCAL_ARCHIVE
-
Local archive directory to use. Expected to hold an absolute path; mandatory for any mode besides -remote and -eutils.
- EDIRECT_LOCAL_WORKING
-
Directory to hold intermediate subtrees; expected to hold an absolute path. Defaults to the local archive directory when not set.
SEE ALSO
archive-pubmed(1), ecollect(1), edict(1), esearch(1), nquire(1), ref2pmid(1), transmute(1), xfetch(1), xlink(1), xsearch(1).