AmiGO Manual: OpenSearch: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
No edit summary
No edit summary
Line 8: Line 8:
* Internet Explorer Add-Ons site ([http://ieaddons.com/en/details/searchhelpers/AmiGO_Labs_gene_product/ gene product] and [http://ieaddons.com/en/details/searchhelpers/AmiGO_Labs_term/ term]).
* Internet Explorer Add-Ons site ([http://ieaddons.com/en/details/searchhelpers/AmiGO_Labs_gene_product/ gene product] and [http://ieaddons.com/en/details/searchhelpers/AmiGO_Labs_term/ term]).


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 something like [http://www.inquisitorx.com/safari/ Inquisitor] 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.  
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 something like [http://www.inquisitorx.com/safari/ Inquisitor] 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 =
= Installation =
Line 35: Line 35:
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:
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


You may also use boolean logic and nesting in the search. For example:
will give you a list of gene products that contain this string (or strings) appear 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


Finally, you may also use
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


More to come on this topic...
Gives things that contain "pleckst" and are sourced from RGD.
 
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 [http://lucene.apache.org/java/1_4_3/queryparsersyntax.html lucene documentation].


=Troubleshooting=
=Troubleshooting=

Revision as of 20:22, 3 June 2009

Overview

AmiGO Labs now has an OpenSearch plugin that you can use to search the GO from the comfort of your toolbar. It also allows for term and gene product suggestions while you type.

It 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 something like Inquisitor 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.
  4. Agree to having it install.
  5. Click the default search icon in the Firefox search bar (possibly a Google [G] in the lefthand 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...

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) appear 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

Gives things that contain "pleckst" and are sourced from RGD.

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.