-*- mode: text -*- From 0.5 to 0.6 + Bugs removed in lca. Some species' lineages are not resolved enough, resulting in an "early" end. Consider $ taxonomy taxonomy sphyrna bull+shark where Sphyrna belongs to Carcharhinidae/Carcharhinus wile bull shark is Carcharhinidae. The lca is then Carcharhinidae, but lca could not handle that. Also, $taxonomy human homo+sapiens | lca would go into an infinite loop. From 0.4 to 0.5 + Name change: Biblio is now called RefSense. + The package is starting to be rewritten as a module to be submitted to CPAN. This includes having documentation adapted to Perl's POD, restructuring of libs, etc. Not quite there yet though. + New program: scholar. This is similar to 'pubmed', although the query is simply handed over to Googles Scholar system, using the web browser of your choice (including lynx). The RefSense search terms are not (yet) supported! + New programs: taxonomy and lca. With taxonomy, you access NCBI's taxonomy database and retrieve lineage information. For instance, try $ taxonomy human Scientific Name: Homo sapiens Common Name: human Common Name: man Rank: species Division: Primates Lineage: cellular organisms; Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa; Bilateria; Coelomata; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homo/Pan/Gorilla group; Homo (the wrap-around of the last line is not correct in this depiction!). You can have several taxa as arguments to 'taxonomy', and the program lca can read this and report the last common ancestor according to NCBI: $ taxonomy mouse human|lca Euarchontoglires From 0.3 to 0.4 + Programs now expect you to set PERL5LIB to point to libraries. + In pmid2text, -h is changed to -html. In all programs, -u, -h, and --help are all equivalent. + pmid2www: As before, mozilla is used by default, but the environment variable BIBLIO_BROWSER can be set to mozilla, netscape, firefox or konqueror to change the preferred browser. + pmid2text: You can now get a link to an abstract at NCBI's PubMed using option -p. + pmid2www: Two new options, -p and -b, let you choose to view articles at NCBI's site or at biblio.cgb.ki.se. Also more user friendly. + pubmed: Now caches last search to allow for command line completion. + pubmed: More userfriendly with a "usage string" and basic sanity checking. Thanks to Daniel Lundin. + All: Usage information is written to STDOUT, unless an error has occured. Thanks to Daniel Lundin. + All: Usage info has a pointer to the homepage, on a suggestion by Carlos MvEvilly. + pmcomplete: New program for generating completion information. A BASH user can register this command using for example complete -C pmcomplete pmid2text pmid2www pmid2bibtex to have those three commands pick PMIDs from the last search. The completion system is somewhat nonstandard. You can try to complete on both PMIDs and arbitrary text, such as authors. A completion is successful if either a unique PMID is derived or the matched text fragment is unique. In the latter case, an author name could be unique but exist several articles and all of them are returned. This feature might need some experimentation to appreciate. + Bugfix in Pubmed.pm, parse_article_medline: PMIDs starting with a zero were sometimes erroneosly handled. Contributed by E.A. Rödland. + An extension by E.A. Rödland makes Biblio handle substrings such as "Jr", "2nd", and "de la" in an agreeable fashion. From 0.2 to 0.3: + pmid2related: New program + Minor changes in PubMed.pm to support pmid2related. + pmid2text: New output option: Link to the web version of biblio. + Can now handle error occurring on NCBI's side, where there a MEDLINE request does not return a record. Previous symptom was that the record did not have a PMID. + pmsearch: Journal abbreviations (mbe, ismb, et.c.) now work correctly, and the help text was updated. + pmsearch: Year ranges have been implemented. For instance, you can write pmsearch author=gribskov year=2000-2002 pmsearch author=gribskov year=-2000 pmsearch author=gribskov year=2002- The range delimiter is either the pmsearch-specific but natural '-' as above, or PubMed's colon operator, i.e., year=2000:2002. --- From 0.1 to 0.2: + pmid2bibtex: You can get article URLs in records with option -w. + pmid2bibtex: AuthorYear keys in records now use four digit years. + pmid2bibtex: PMID is always included in records. + New program: pmid2seq, for downloading nucleotide and protein sequences linked to articles. --- From 0.0 to 0.1: 1. pmid2bibtex The bibtex key is by default composed as , where is the PubMed identifier. This guarantees a unique id (thanks to the pmid) and a little bit of mnemonic (thanks to the author name). However, it might not fit in with your usual key-generation scheme. Therefore, I have implemented an option '-ay' that sets the key to . So instead of "smith1234458948" you would get "smith03". The drawback with this scheme is of course that the keys are no longer guaranteed to be unique. I'd like to point out, that if you are using (x)emacs together with AUC-TeX and the reftex minor mode, the standard scheme is not a hassle, because you can search for citations and have them inserted automatically into your document. Actually, even without reftex you are pretty much set if you are using dynamic abbreviations (dabbrev). You write something like "\cite{smith" and hit the completion key. If your bib-file is in another buffer, the smith-references will be found. 2. pmid2text There are two new options: -w Output a URL that links to an online version of the article. This is through PubMed's elink utility and seems to work well for several journals. In some cases, the PDF is downloaded immediately, while in other cases (like Nature and Science) you get the full text in HTML. -www Output only the URL. This is mostly implemented for the next utility: 3. pmid2www This is a shell script that essentially is calling "pmid2text -www" with the arguments to pmid2www. Then it calls mozilla with "remote control" to open the running browser with the given URL. So no new browser window is opened. There is a slight delay too due to how the remote control feature works, but it is better than launching a brand new browser.Most likely, adapting this script to any version of netscape is simply a matter of replacing the call to "mozilla" with whatever the executable for netscape is called. Netscape has had this feature for a long time. Please note that pmid2www is more of a hack than the rest of the tools. If you know what you are looking for, you can download an article pretty quickly now. For example, try something like: pubmed year=2002 journal=science savolainen leitner | pmid2www I hope you'll find it useful. Please let me know if you use it, and if you have ideas for improvements.