cit2pmid(1)

Usage

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}]

Overview

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.

Releases

2 releases since Debian 12 (Bookworm); the text changed 1 time.

12
13

Referred to by

edict(1) HTTP server for EDirect local PubMed archive and search system xlink(1) look up related local NCBI Entrez Direct archive search results nquire(1) query NCBI Entrez Utilities, other parameter-based web services, or FTP xfetch(1) fetch records from a local NCBI Entrez Direct archive by UID esearch(1) search an NCBI Entrez database xsearch(1) search an indexed local NCBI Entrez Direct archive ecollect(1) list NCBI Entrez unique identifiers ref2pmid(1) match PubMed citations in Reference Index XML transmute(1) transform data, particularly within NCBI Entrez Direct fetch-pubmed(1) fetch records from a local NCBI PubMed archive by UID phrase-search(1) search an indexed local NCBI PubMed archive archive-pubmed(1) maintain a local NCBI PubMed archive