More on RefSense usagepmid2text | pmid2bibtex | pmsearch | pmid2related | pmid2connotea | pmcomplete | taxonomy | lca | taxtree
pmid2text [<options>] [<pubmed identifier>+]
-u, -h, --help This text. -i No indentation of citations. -s Simple, no indentation and no PMID. -y Sort by publication year. -a Show abstract. -w Show an URL for retrieving article via PubMed. -www Show only the URL and nothing more. -rs Show a sole link to RefSense. -p Show a link to abstracts at PubMed. -nIf no PMID is given on the command line, STDIN is read until EOF and parsed for PMID:s. The expected format is a PMID first on each line, possibly followed by a space and any string.
pmid2bibtex [<option>] [<pubmed identifier>+]
-u, -h, --help This text. -y Sort by year. -ay BibTeX keys are composed as <1st author>If no PMID is given on the command line, STDIN is read until EOF and parsed for PMID:s. The expected format is a PMID first on each line, possibly followed by a space and any string.
pmsearch [<options>] <search terms>+
-u This text. -c Return the number of matching items. -d <int> The maximum number of PMID:s to report. Default: 100. -t <int> The number of days from today to include in search. -w <int> Warn when more than <int> identifiers are returned. Default: 100.
Search TermsA search term is either a lone word that can match anything in a PubMed entry. The complete query is a conjunction of its terms. You can for example write 'pmsearch eisen yeast' and get back (at this writing) 31 PubMed identifiers. You may also write these search terms using the PubMed qualifiers to specify to what record in an entry a term should match. For example, writing
author au abstract ab journal jo title ti year yeThe previous example is then written as
The journal titles can be hard to get right. Use either their full names (e.g. 'Molecular Biology and Evolution') or the official abbreviation ('Mol Biol Evol'). See the PubMed WWW site for details. In addition to the official abbreviations, pmsearch recognizes some additional common acronyms, which is translated to a name recognized by PubMed. Currently implemented are:
Key Journal psb = Pac Symp Biocomput jmb = J Mol Biol ismb = Proc Int Conf Intell Syst Mol Biol jme = J Mol Evol nar = Nucleic Acids Res mbe = Mol Biol Evol embo = EMBO J pnas = Proc Natl Acad Sci U S A cabios = Comput Appl Biosci jcb = J Comput Biol
pmid2related [<options>] [<pubmed identifier>+]If no PMIDs (PubMed identifiers) are provided on the commandline, then they are read from stdin instead. PMIDs from the input list is always removed from the output. Output is two columns with related PMID on the left and the relatedness score on the right.
-u This text. -c Only return the number of available linked entries. -1 Only first column, no score. -n <int> Limit to the best <int> related articles. -m <int> Minimum relatedness score. A score below this is ignored. -t <int> The number of days from today to include in search. -q Less verbose output.
pmid2connotea [<pubmed identifier>+]If no PMIDs (PubMed identifiers) are provided on the commandline, then they are read from stdin instead. PMIDs from the input list is always removed from the output.
pmcomplete <progname> <string> <string>
This utility is intended to be used by the completion system in BASH and in conjunction with the command pubmed. Typical usage is to instruct BASH as follows:
> complete -C pmcomplete pmid2text pmid2www pmid2bibtexAfter a pubmed-search, the result is cached in a file in the user's home directory and used to filter out candidate PMID:s.
> pubmed arvestad savolainen 11005171 Savolainen P, Arvestad L, Lundeberg J (2000) "A novel method for forensic DNA investigations: repeat-type sequence analysis of tandemly repeated mtDNA in domestic dogs." J Forensic Sci 45(5), 990-999 10742040 Savolainen P, Arvestad L, Lundeberg J (2000) "mtDNA tandem repeats in domestic dogs and wolves: mutation mechanism studied by analysis of the sequence of imperfect repeats." Mol Biol Evol 17(4), 474-488Now trying to retrieve the abstract for the paper in J Forensic Sci, we ask for completion on the text fragment 'for':
> pmid2text -a for<tab>This will result in the 'for' string to be converted to 11005171, the proper PMID. Completion is done on all parts of the search result from pubmed, including PMID, author names, journal name, and title.
journalcomplete <progname> <string> <string>
This utility is intended to be used by the completion system in BASH
and in conjunction with the
> complete -C journalcomplete pubmed pmsearchThis way, Bash will recognize when you are writing a journal name and hit TAB. For example, if you are composing a query for papers written by Smith in Nature Biotechnology, you write:
> pubmed au=Smith journal=naand then hit TAB. Bash will invoke journalcompete, which gives several suggestions:
Nat+Biotechnol Nat+Protoc Nat+Struct+Mol+Biol nar Nat+Cell+Biol Nat+Rev+Mol+Cell+Biol Natureby filling in "t+b" and hitting TAB again, you will find the full journal name (or abbreviation) on the command line:
> pubmed au=Smith journal=Nat+BiotechnolTry it out!
An important factor is that you need a file in your home directory
Proc Int Conf Intell Syst Mol Biol, ismb Proc Natl Acad Sci U S A, pnasdefines the shorthands