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URL: ProTag: Web servicing the biological office
Submitted by Martin Szugat; posted on Monday, October 24, 2005
ProTag is open source software (licensed under the GPL) for Microsoft Office users. It integrates into the Office applications, Word, Excel and PowerPoint, and recognizes the names and (database) identifiers of proteins within free text, i.e. Office documents.
Protein names and identifiers are marked as a Smart Tag. A Smart Tag is similar to a hyperlink but offers multiple actions through a menu, e.g. to add all synonyms for a protein as a comment or to navigate to a certain online database. If a protein is not recognized as a Smart Tag, there is also the chance to perform a manual search from within Office using the ProTag command bar.
Currently, we support the databases Swiss-Prot, LocusLink, HUGO, SGD, RGD and MGI as well as the organisms Human, Yeast, Mouse and Rat through the Web Services LiMB and ProThesaurus [1]. Of course, it is possible to integrate additional Biological Name and Markup Services into ProTag, e.g. the BeThesaurus [1] service, which offers user-proposed protein names and identifiers.
Finally, ProTag can be used as a standalone application, i.e. without the need of running an Office application. There is also the possibility to use the ProTag functions within Excel formulas and within Visual Basic for Applications-macros. To extend ProTag, additional Smart Tag actions can be implemented using the .NET framework (a single class with only three methods has to be coded) and can be easily added to ProTag.
Jeff Perkel, an editor from The Scientist, said about ProTag: it is "a really cool tool" [2].
There is also an application note about ProTag that was presented at the ECCB '05 [3]:
Szugat,M., Güttler,D., Fundel,K., Sohler,F., Zimmer,R., Web servicing the biological office, Bioinformatics, ECCB/JBI, Vol. 21 Suppl. 2 2005, pages ii268-ii269
URL:
http://protag.sourceforge.net
References:
[1] http://services.bio.ifi.lmu.de/prothesaurus/
[2] http://media.the-scientist.com/blog/display/145/
[3] http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/suppl_2/ii268?ijkey=oqBS3nH1q9N7Xfj&keytype=ref
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