• What are the Search Tools?
• How do I find information using the Search Tools
• How else can I search the database?
• What do the general search tool results look like?

"RGD provides a variety of search or query tools to allow users to find information within the database. These typically require a text query such as a gene or marker name that the user desired to find. The results returned depend on the tool being used but typically consist of a list of database records (hits) that match the query text."

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There are two main methods for finding information in RGD:

1. Using the General Search

The general RGD search available at the top of each page is a quick route to accessing data reports in RGD. The general search tool searches the following fields:

• RGD ID (Example: 2003)
• Genes: Symbol, name, description, aliases, curated annotations for both ontologies and curator notes
• Homologs: Symbol, name, description, functional annotations
• SSLPs: Symbol, name, aliases
• QTLs: Symbol, name,trait name, sub-trait name, aliases, curated annotations for both ontologies and curator notes
• Sequences: accession number
• ESTs: accession number, definition
• Strains: Symbol, aliases, genetics, origin, curated annotations for both ontologies and curator notes
• References: Title, citation
• Ontology terms: term, synonym, descendent terms, descendent synonyms annotated to RGD objects
• Maps: Not covered by general search tool, use the Map selection page instead. Information about individual markers (Genes, SSLPs, etc) is searchable.

Wildcard characters are allowed in the search fields, the asterisk '*' is the accepted wildcard character. It can be used to retrieve records matching a general search query as shown in the following table:

There is a list of query parameters and symbols that CANNOT be used with the * (wildcard).

The terms that may give unusual results are: OR, | , AND , & , ACCUM , ' , MINUS , - , NEAR , ; , NOT , ~ , EQUIV , = , {} , % , _ , $ , ? , ! , ()

The unusual results are due to using a special search function of Oracle 9i where the above listed terms tell Oracle to perform special functions with the query term.

If you wish to use operators such as; AND, OR, NOT, try using the Advanced Search tool.

If your search returns many hits, the results will be spread over mutiple pages grouped by database object (genes, QTLs, strains, etc.).

The summary page will be displayed if more than one RGD object (genes, QTLs, strains, etc.) matches the keywords used for searching or if the number of records found is greater than 10 for a single RGD object type. For example, if 12 gene records are found that match the keyword searched, the summary page will be displayed.

If your search returns less than 10 records for the same RGD object type (genes, QTLs, strains, etc.) the results page will be displayed directly.

The order in how the results are reported is based on the data found in the database. The results with exact matches to the keyword will be listed as the first group.  

Results that begin with the keyword will be grouped second in the list.

And results that contain the keyword will be grouped third in the list.

Within each grouping of results exact, begins with, or contains there will not be any specific order in the list. 

The user has the option to select the records he/she is interested in the group and view the records selected on the the Selected Items Report.

2. Using the individual object search tools

Each category of data within the database has an individual search tool that often provides more customizable search options, follow these links to read more about these individual tools:

• Gene search
• QTL search
• SSLPs search
• Sequence search
• EST search
• Strain search
• References search
• Ontology search
• Maps

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The search tools provide the main route into the RGD records, however, other databases link in to RGD and hence can also be used to find records within RGD by searching at these other sites. The following are some of the databases that link into RGD:

• LocusLink - NCBI database providing gene locus data for Rat, Mouse, Human and many other organisms.
• Ratmap - Ratmap database in Sweden
• KEGG - Kyoto encyclopedia of Genes and Genomes (Pathway database)
• Gene Ontology - Multi-organism database listing genes sharing common Molecular Processes, Cellular Components or Biological Pathways.

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The general search tool returns results such as shown below, the term 'atp1a*' was used in this example.

The keyword used in the search is shown along with a table of the matching results. The total number of results is shown at the top (in this example '4 genes, 2 strains, 4 homologs, and 2 sslps'  indicating this is showing hits 1 and 2 of two total hits).

In this example, following the hyperlinks to genes will take you to the genes results page.

There are serveral functions provided on the results page for user to easilly navigate through detailed information about the objects that match the search criteria.

• Allow to select all results on all pages by clicking on "Select all results" button
• Allow to un-select all results on all pages by clicking on "Unselect all results" button
• Allow to select all results on current page by clicking on the check box on the header line
• Allow to select wanted item by checking the checkbox at the beginning of each record
• Allow to navigate records by clicking on page number
• Allow to view all checked items in one page only by clicking on "Selected Items Report" button
• Allow to view all checked items in excel format by clicking on "Download Report" button
• Allow to go back to result summary page by clicking on "Results Summary Page" button
• Allow user to sort results the way user wants by clicking on the black triangle toggle icon in the grey header line

The Selected Items Report looks like the following example.

The quick search Download Report looks like the following report. The file can be saved as an Excel file by clicking on the File button in the upper left corner of the web browser window and saved by selecting Save as type: Microsoft Excel Workbook.

  View Advanced Search Help

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