AmiGO Manual: Live Search: Difference between revisions
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= Overview = | = Overview = | ||
In addition to the [[AmiGO_Manual:_Search | traditional search]], AmiGO now provides a powerful method of rapidly searching using pre-computed indexes. In addition to speed, | In addition to the [[AmiGO_Manual:_Search | traditional search]], AmiGO now provides a powerful method of rapidly searching using pre-computed indexes. In addition to speed, Live Search provides: boolean operators, wildcards, and fuzzy searches. | ||
When searching, 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 section. | When searching, 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 section. | ||
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== Fuzzy Searches == | == Fuzzy Searches == | ||
TODO | TODO (in the meantime, please see the [http://lucene.apache.org/java/1_4_3/queryparsersyntax.html lucene documentation]) | ||
== Boosting and Score Weights == | |||
TODO (in the meantime, please see the [http://lucene.apache.org/java/1_4_3/queryparsersyntax.html lucene documentation]) | |||
= Experimental = | = Experimental = |
Revision as of 18:49, 10 March 2010
Overview
In addition to the traditional search, AmiGO now provides a powerful method of rapidly searching using pre-computed indexes. In addition to speed, Live Search provides: boolean operators, wildcards, and fuzzy searches.
When searching, 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 section.
Basic Usage
The largest initial difference, when compared 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 with standard characters (spaces, 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 (and/or/not)
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
To exclude "domain" from "pleckstrin" results, you would enter:
pleckstrin and not domain
Also note that:
pleckstrin or domain pleckstrin domain
Are functionally equivalent.
Wildcards
For example, let's sat that we search for "top". In our results, we can see that the fly gene that we were looking for, Topoisomerase 1 with the symbol Top1, is not in the results. Unlike the AmiGO_Manual:_OpenSearch widgets available for AmiGO, Live Search does not automatically search for words where "top" is only part of it--you must explicitly instruct the search engine to look for these things by adding a wildcard at the end of the word: "*". By entering:
top*
You will now see the fly gene you were searching for returned as the first result.
Advanced Usage
For full information about the query syntax and special characters, please see the lucene documentation.
TODO
Additional Search Fields
TODO
Term Search
TODO: complete usage for term special fields
- acc
- name
- ontology
- synonym
Gene Product Search
TODO: complete usage for gene product special fields
- dbxref
- full_name
- symbol
- species
- scientific
- source
- gptype
- gpsynonym
- homolset
- association
Fuzzy Searches
TODO (in the meantime, please see the lucene documentation)
Boosting and Score Weights
TODO (in the meantime, please see the lucene documentation)
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.