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Searching RGD

There are a variety of ways to get to the information within the Rat Genome Database. The two most general methods provide the user an option to use a keyword or coordinates. The general keyword search function provides results based on matches such as locations, experimental data, descriptions (i.e. ASSOCIATED WITH hypertension (ortholog)), synonyms/aliases, database IDs, origin, name (i.e. spontaneous hypertension rat), trait, terms and term definitions, citations, titles, or abstracts. An advanced search function is available through OLGA.
For more about what terms you can use to search RGD and what data is searched, click here.

Jump to information about the:

Keyword Search
Object Search

Keyword Search

1. General searches are performed by entering text into the white “search term box” located in the banner of every page.

2. Full or partial terms can be used for the search function. For the purpose of this tutorial, the term ‘tnf’ will be used.

*Note* Using partial terms (for example ‘blood pressure’ versus ‘blo pres’ will not return the identical count of results).

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Keyword Search Result Matrix

1. The top table in the result matrix summarizes the number of objects found (i.e. External DB id, name, alias, etc.) for the categories listed in the left most column by species (across the top of the table). Clicking on the number under the species will redirect the user to the filtered object list results for that species. The values under the ‘All’ header will show a more detailed object list for all species in the chosen category.

2. The center table provides ontology results. Clicking on the ontology name or corresponding underlined number will take the user to the related ontology object list based on term and term definition matches.

3. Selecting either the term ‘Reference’ or the underlined number in the right column will take the user to the result list which matches the input term to citations, titles, or abstracts.

   
    
 
 
 

   

4. Selecting ‘View All’ in the top corner of the results matrix will redirect the user to a detailed result list.


 

 

5. The results can be manually filtered by the user by selecting the categories of interest from the left-hand menu.

*Note* Results in the Name/Term/Title column with an ‘A’ icon after them indicate annotation information is available. Clicking the branch icon after a term will bring it up in the ontology browser.

 

 

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Object Search

 
1. The form for searching by Object using coordinate information can be access by selecting ‘Search RGD’ from the Home drop-down menu located on the page banner.
 
 
 
  
  
 
 
 
 
 
 

2. Use the drop-down menus to select Species, Reference Assembly, and/or Chromosome.

3. Enter the base pair coordinates in the open text fields.

 
 

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Object Search Result Matrix

Four Tables are returned in the Object Search Result Matrix:
1. Summary of all objects in the selected regions by category.
2 – 4. Object results by category: 2. Genes, 3. QTLs and 4. SSLPs.

 
 

 


  
  
 
 
 
 

5. The Download icon (white arrow in blue box) will export results in a .csv formatted file. 
 
 

6. The Tools icon (wrench and screwdriver) allows the user to export the data into a RGD tool listed in the pop-up menu. 
 
 

7. Selecting the hyperlink in the ‘Symbol’ column will direct the user to the corresponding report page for that symbol.

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.