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Contents • • • • • • • • Overview AmiGO Labs now provides plugins that you can use to search the GO from the comfort of your toolbar or dashboard. They also allow for term and gene product suggestions while you type. They is available directly from several add-ons sites: • Firefox Add-Ons site ( and ) • Internet Explorer Add-Ons site ( and ). • Dashboard widget (). • Direct XML download ( and ). These XML files should work with any browser that can use OpenSearch.
Unfortunately, this does not include Safari and Opera as of this writing. Safari users are encouraged to complain mightily and use the in the meantime. Opera users can mimic some of the functionality my manually adding the search to their search preferences using one of the XML files as a template. Installation Firefox • Go to • Search for either 'amigo' or 'gene ontology'; both plugins should return as the top search results. • Click the 'Add to Firefox' button (you may have to check a 'let me' box nearby). • Agree to having it install.
• Click the default search icon in the Firefox search bar (possibly a Google [G] in the left-hand part of the bar) and select '[A] AmiGO Labs (.)'. • Click on the default search icon again and select 'Manage Search Engines.' In the new window, make sure that 'Show search suggestions' is checked. Internet Explorer • Go to • Search the gallery for 'gene ontology'; both plugins should return as the top search results.
• Click the 'Add to Internet Explorer' button. • In the popup window, make sure that 'Use search suggestions from this provider' is checked and that you do not make this your default search engine. • Click the default search icon in the Internet Explorer search bar (possibly a stylized [G] in the lefthand part of the bar) and select AmiGO icon: [A].
Dashboard Widget (Mac OS X) Although Safari does not directly support OpenSearch, there is a for the Mac OS X Dashboard (the usual installation) that performs almost identically. All of the same caveats apply. XML files Some browsers do not support OpenSearch, but offer similar services.
To help in trying to apply the AmiGO OpenSearch service to your platform, we offer the raw XML files for. Usage The main useful feature of the plugins is that you can do an incremental search with completion as you type.
For example, using the gene product search, typing: pleckst pleckst domain will give you a list of gene products that contain this string (or strings) in one of the various gene product database fields. You may also use boolean logic and nesting in the search. For example: pleckst AND domain gives gene products that contain both. Finally, you may also use one of the various results filters to constrain your search. For example: source:RGD pleckst choc AND species:722 choc AND species:7227 The first gives things that contain 'pleckst' and/or are sourced from RGD. Prezi pro for mac. The second gives nothing, while the third gives us fly's 'chocolate'. Other filters might be: gptype:complex source:RGD species:10116 where the species number is the NCBI taxa id.
More to come on this topic later. For more information about the query syntax, please see the.
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Troubleshooting • OpenSearch is still considered experimental software and may be offline for periods of time. All of the caveats apply. • There is a bug () that prevents Firefox from directly using the returned query URLs, which makes it not behave in a non-optimal way when searching.