BASIC PROTOCOL 2: PERFORMING A DATABASE SEARCH

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This protocol presents how to conduct a general search of WormBase

Necessary Resources

Hardware

   A standard computer with a reasonably fast connection to the Internet (cable modem, DSL, or Ethernet recommended)

Software

   Web browser such as Internet Explorer (http://www.microsoft.com) or Firefox (http://www.mozilla.org/firefox)

1. Go to the main page, either by entering its URL http://wormbase.org, or by clicking on the Home link at the top left of any WormBase Web page (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png).

2. Type a word or phrase into the search form (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png). For a search of the entire database, click the Search link after selecting Anything in the "Search for" pull-down menu.

3. Once the search has run, examine the results (if any). If a single data record is found, the search routine will sometimes go directly to the Web page for that record (it will automatically do this for Gene pages). However, it will usually instead have 0 or ‚â•2 results. In the latter case, the search will give one or more summary pages on which the data records found are listed.

Fig_1_8_02.png

4. Look at the page of summarized results, and consider whether there are too few or too many. If there are too few results, try different key words for the search; computers are literal-minded, and a particular search word may be almost but not quite recognized by the database. Conversely, if there are too many results, select a restricted subset of the database for the search from the "Search for" pull-down menu (e.g., "Any Gene"; (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png)), or check the "Exact match" box and resubmit the search by clicking the Search button.

5. If the search results look reasonable, then follow the hypertext links to the data records themselves.

6. To get a list of many data records all falling into a specific class, pick a subset of the database and search with a wildcard. For instance, if the "Any Gene" search is selected, and run with unc-* as the search term, WormBase will return links to 117 Locus records (snt-1 through vab-8, with 114 unc-* hits). When possible, WormBase recognizes and returns synonyms in searches (which is why a search for unc-* genes returns three non-unc-* gene names; these three genes have aliases of unc-107, unc-110, and unc-121).

7. Remember that search words can be anything of interest. While there is no guarantee that the database will give hits for any given search string, specific topics of interest can have useful results.

For instance, consider a search for' '''hyperplasia ''under all categories (i.e., by choosing Anything from the pull-down menu in (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png). Hyperplasia is a topic normally associated with cancer biology or endocrinology (Merke and Bornstein 2005; Simpson et al., 2005), but one might want to see the potential for C. elegans to serve as a model for the control of tissue proliferation. A search with this term reveals nine hits, including six genetic loci that either have hyperplastic phenotypes or are homologs of human disease genes with roles in deregulated proliferation.