AmiGO Manual: Live Search: Difference between revisions
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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: | 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: | ||
pleckstrin 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, if you click "RGD" under "Source" and input "pleckst", the items returned will contain "pleckst" and/or be sourced from RGD. | gives gene products that contain both. Finally, you may also use one of the various results filters to constrain your search. For example, if you click "RGD" under "Source" and input "pleckst", the items returned will contain "pleckst" and/or be sourced from RGD. | ||
Revision as of 20:47, 8 March 2010
Overview
In addition to the traditional search, AmiGO now provides a method of searching rapidly using pre-computed indexes.
Usage
The main feature of interest is that you can do an incremental search as you type. The search only initiates when you have over three characters entered and are typing forward (backspaces and the like will not initiate a search).
As an example, when using the gene product search (after clicking the "Gene Product" tab), typing:
pleckstrin 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:
pleckstrin 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, if you click "RGD" under "Source" and input "pleckst", the items returned will contain "pleckst" and/or be sourced from RGD.
For more information about the query syntax, please see the lucene documentation.
Additional Search Fields
In additional to typing search text, there are also special fields that you can add to constrain the search beyond the listed filters. These special fields are different depending on whether you are search for terms or gene products.
Term Search
TODO: complete list for terms
Gene Product Search
TODO: complete list for gene products
For example:
aatf and homolset:yes
gives all gene products that contain the string "aatf" and are also a member of a homolog set.
Experimental
On the AmiGO Labs server, there may also be similar implementations for searching dbxrefs and associations.
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.