General Guidelines for MGI Query Form Searches

This help document answers the following questions:

See also:

Where can I find help using MGI query forms?

MGI is accessible on the Internet via the World Wide Web (WWW) and relies on online forms to present query options in an easy-to-use format. Help documentation is available on-line (click Help under the MGI logo). Our Mouse Genome Informatics home page is located at http://www.informatics.jax.org. You can contact User Support by e-mail or by phone at (207) 288-6445.

Is there a general method of querying the MGI databases?

A general procedure to build a query includes the following steps (select form, enter value(s), choose output, restrict/expand scope, execute).

The query results are usually a list of records in an abbreviated format. The display contains links to related information in the MGI database.

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What is a good search strategy?

A good search strategy ensures that your search executes quickly and retrieves the information you want. Here are some general guidelines:

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Can I do a full-text search on any of the forms?

Yes. The following query forms have fields that provide full-text search options:

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What are the parts of a query form?

A query form consists of a logical arrangement of data entry fields, selection lists, and various options and operators used to modify the search criteria or to format query results. Field names are linked to user documentation describing the fields; click any field name to go to the relevant part of the documentation.

The subsections below describe form elements.

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Selection lists

A selection list consists of a pre-defined list of values from which you may select one or more items. An example is the list of species on the Orthology query form. To specify a search for orthology information for a particular species, you select that species from the list. How you make the selection depends upon the browser you use.

Some selection lists allow you to specify more than one value. For example, you may wish to search for orthologies in species human or cat. In this case, you would select several options from the selection list. Again, the exact mechanism for doing this depends on your implementation.

Data entry fields

A data entry field requires you to type a value in the field. There are two types of data entry fields, numeric and text.

Numeric fields

Numeric fields require that you enter a number, possibly in a specified format. For example, the Year field in the Reference query form requires the year to be entered in the format: 20xx .

Comparison operators

Comparison operators provide a means to focus your search on a range or subset of records in the database. The following table describes the set of comparison operators used with numeric fields:

Operator Description
= is equal to (the DEFAULT value in all cases)
> is greater than
< is less than
>= is greater than or equal to
<= is less than or equal to
<> is not equal to
is null has no value (NOT equivalent to a value of "0")

The NOT operator

You can use the NOT operator to exclude a value or set of values. However, NOT also can be interpreted as EVERYTHING ELSE BUT..., and therein lies the danger of using the NOT operator.

Use NOT only when you put values in multiple fields on the query form. Use at least one descriptive field without NOT.

Text fields with comparison operators

Text fields accept alphanumeric characters. The table below lists the set of comparison operators for text fields:

Operator Description
= equals xxx
BEGINS begins with xxx
ends ends with xxx
contains contains the sequence xxx anywhere
like
partial match (MUST use 1 or more wild cards)

Select NOT to exclude a value or set of values.

Wild card with LIKE operator

Use wild cards only with the LIKE operator; do not use wild cards with BEGINS, ENDS, CONTAINS, or =.
Below is a list of wild cards to use with LIKE:

OperatorDescription
% May be any string of 0 or more characters
_(underscore) May be any single character
[a..n]
May be any character in the range of a to n
[abc]
May be any one of a, b, or c

Wild card and text

You can put a wild card symbol after or within the text you enter in the search field.
The following are examples of using wild cards to search for information on a marker by its symbol.

Enter To Find
Abc% all of the ATP-binding cassette genes
Abc[ab]% ATP-binding cassette genes, sub-families A and B
Abc_1 Abca1, Abcb1, Abcc1, Abcd1, Abce1, Abcf1, Abcg1
Lag%1 Lag-rs1
D%Mit% all of the MIT markers

Wild card as literal

If the string you are searching for contains a wild card character (%, _,[a,b,c]), you can still use the LIKE operator and treat the embedded wild card character as a literal, i.e., as ordinary text. To do so, enclose the embedded wild card character in square brackets [ ]. For example, suppose you want to search for strings containing the [ character. You could use LIKE and enter the search string %[[]%. (Translation: any string of characters, followed by a [, followed by any string of characters. Of course, for this example, you could also use the CONTAINS operator, with the search string [[].)

Button-activated options

There are selectable options, such as sort options and formatting options, that are used to modify the display of query results. You can click on the appropriate "button" to select an option.

For example, on the Genes and Markers Query Form, you have two SORT options for query results: by cM position or by Nomenclature. Click the appropriate button to select the option.

Can I view the results of a query in different ways?

The query forms offer several options for ordering query returns. For example, on the Genes and Markers Query Form you can specify that the returned list of markers be sorted by cM position or by Nomenclature. Choose the sort order by selecting the appropriate option from the list. For more details, refer to the documentation for specific forms. At the present time, multilevel sorting is not an option.

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Can I print or save the results of my query?

Options for printing and saving files vary with computer platform and browser. Refer to your browser and system documentation for information on how to print results or save them to a file.

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Can I e-mail the results of my query?

Some browsers provide a Web e-mail option so you can easily send query results to a colleague. The e-mail functions are browser and computer platform-dependent and usually require some configuration of browser preferences. See your system administrator for details.

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Can I change font sizes to make query forms and Help documents easier to read?

Yes. The setting for the font size on MGI web pages is specified in a style sheet. If you use Internet Explorer (IE), you can override this by doing the following:

  1. Click Tools (on the IE Toolbar). A menu appears.
  2. Click Internet Options . The Internet Options dialog box appears.
  3. Click Accessibility... The Accessibility dialog box appears.
  4. In the Formatting section, check Ignore Font Sizes .
  5. Click OK.
  6. Click OK (in the Internet Options dialog box).

Now you can increase (or decrease) the font sizes. To do this:

  1. Click View (on the IE Toolbar).
  2. Click Text Size and hold the mouse button down.
  3. Click one of the sizes (Largest, Large, Medium, Smaller, Smallest). The text on your page resizes.

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