AmiGO Manual: OpenSearch

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Overview

AmiGO Labs now provides OpenSearch 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:

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 dashboard widget 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

  1. Go to https://addons.mozilla.org/
  2. Search for either "amigo" or "gene ontology"; both plugins should return as the top search results.
  3. Click the "Add to Firefox" button (you may have to check a "let me" box nearby).
  4. Agree to having it install.
  5. 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 (...)".
  6. Click on the default search icon again and select "Manage Search Engines...". In the new window, make sure that "Show search suggestions" is checked. Click "OK".
  7. Type away...

Internet Explorer

  1. Go to http://ieaddons.com/
  2. Search the gallery for "gene ontology"; both plugins should return as the top search results.
  3. Click the "Add to Internet Explorer" button.
  4. 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 "Add".
  5. 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].
  6. Type away...

Dashboard Widget (Mac OS X)

Although Safari does not directly support OpenSearch, there is a dashboard widget 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 gene_product and term.

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. 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 lucene documentation.

Troubleshooting

  • OpenSearch is still considered experimental software and may be offline for periods of time. All of the AmiGO_Labs caveats apply.
  • There is a bug (386591) that prevents Firefox from directly using the returned query URLs, which makes it not behave in a non-optimal way when searching. Please join the Mozilla bugzilla and vote this bug up so we can get it fixed.
  • If you consistently have problems using or installing the plugins, please contact Seth and let him know what's going on. He'll appreciate the feedback.