Bringing Biology to the Office

The latest e-TOC from the journal Bioinformatics contains an application note on a really cool tool. ProTag is a Microsoft Office extension that uses biological name and markup services called ProThesaurus and LiMB to find protein names and database identifiers in Word, Excel, and Powerpoint documents. From there, you can perform a range of actions on that text, all without ever leaving the Office. So, for instance, if you type the phrase ?TIM4_HUMAN is the SwissProt identifier for tissu

Written byJeff Perkel

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The latest e-TOC from the journal Bioinformatics contains an application note on a really cool tool. ProTag is a Microsoft Office extension that uses biological name and markup services called ProThesaurus and LiMB to find protein names and database identifiers in Word, Excel, and Powerpoint documents. From there, you can perform a range of actions on that text, all without ever leaving the Office. So, for instance, if you type the phrase ?TIM4_HUMAN is the SwissProt identifier for tissue inhibitor of metalloproteinase 4? in Word and wait a few seconds, the program will underline the terms TIM4_HUMAN and ?tissue inhibitor of metalloproteinase 4?. Right-clicking on either term pulls up a context sensitive menu that allows you to pull up (and insert) related synonyms, database accession numbers, Life Science Identifiers, and Web database records (eg., from HUGO or SWISSPROT), all without the annoying cut-and-paste, browser-switching dance we?ve all gotten used to over the years. If nothing else, ProTag allows you to make sure your protein names are spelled correctly, and can force consistency in your documents. It has other useful features too. Users can suggest new protein names and synonyms through a service called BeThesaurus, which other users can query if they so desire. Excel users can replace static fields with dynamic formulae, like ?=GetSynonyms (?SWISSPROT:TIM4_HUMAN?)?, which retrieves all synonyms of that symbol. ProTag features can be implemented into Visual Basic macros, and the application can be extended, for instance to modify the context-sensitive menus that appear in Word.The brainchild of Martin Szugat, a bioinformatics student in Munich, Germany, who runs a blog on biological Web Services for Office, ProTag requires Office 2003 or Office XP. But even earlier versions of Office will load the ProTag toolbar, which allows you to select a term manually and search on it in a helper application. Users who lack Office, or who want to search on items they read in other programs (in Adobe Acrobat documents, for instance), can use the helper application as a standalone tool.