AmiGO Manual: Live Search

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Overview

In addition to the traditional search, AmiGO now provides a powerful method of rapidly searching using pre-computed indexes.

The first column of results is a score for how much the search engine thought your query resembled the record. It is important to know that to generate this score, different fields are weighed differently; for example, the word "cho" appearing as a gene product's symbol weighs more than the same word appearing in a long list of gene product synonyms. For more control over this, please see the [Advanced Usage]

Basic Usage

The largest initial difference, when comapared to the traditional AmiGO search, is that results are returned incrementally as you type. It should be noted that the search only increments when there are over three characters entered and when you are typing forward (backspaces and the like will not increment the search). All examples in the Basic Usage section will assume that you are doing a gene product search (by clicking on the "Gene Product" tab in the search interface).

For our first example, let's say that you want to search for "pleckstrin". As you type it in, you will get results incrementally returned for "ple", "plec", and finally "pleckstrin". If you continued and entered:

pleckstrin domain

You would get a list of gene products that contain in their record "pleckstrin", "domain", or both. Finally, if you want to search for the phrase "pleckstrin domain", where the words occur side by side, you would have to put the phrase in quotes:

"pleckstrin domain"

Filtering

The term and gene product searches have different (and hopefully self-explanatory) filters that you can apply to them to reduce the number of returned results. Let's say that you've search for the phrase:

"pleckstrin domain"

And wish to just see the results for RGD. You can do this by clicking the "RGD" item in the "Data source" filter box. Multiple filters can be added by holding a control key (varies by operating system and browser) while clicking on filters. Any combination of filters may be added; to remove a filter set, click on "No filter" item, the first item in each filter set.

Boolean Operators

You may also use boolean logic and nesting in the search. For example, if you wanted to see all records that contain both "pleckstrin" and "domain" in them, you would enter:

pleckstrin and domain

Which 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.

Wildcards and Special Characters

For more information about the query syntax, please see the lucene documentation.

Advanced Usage

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 Live Search implementations for dbxrefs and associations.

Troubleshooting

  • Live Search may occasionally drop a packet of results as you type (especially for fast typers). If you think you should have gotten results, but the display seems "stuck", try erasing the last letter and retyping it.
  • Live Search is a new piece of software and some of the AmiGO_Labs caveats may apply as bugs are worked out. If you have a problem, please contact the GO Helpdesk.
  • While we aim to be functional on as wide a variety of platforms and browsers as possible, this software depends on features that may not be found in older systems. A complete compatibility list is currently under construction.