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This document answers the following questions:

• Where can I find help using MGI query forms?
• Is there a general method of querying the MGI databases?
• What is a good search strategy?
• Can I do a full-text search on any of the forms?
• What are the parts of a query form?
• Can I view the results of a query in different ways?
• Can I print or save the results of my query?
• Can I e-mail the results of my query?
• Can I change font sizes to make query forms and Help documents easier to read?

See also:

• Using Full-Text Searches on MGI Query Forms
• Help Using Wild Cards

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 our User Support staff by e-mail at mgi-help@informatics.jax.org 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:

1. Select the query form to use depending on the type of information you want to search for. The following forms are available:
   • Accession IDs Query Form
   • Adult Mouse Anatomical Dictionary Browser
   • Anatomical Dictionary Browser Query Refiner (accessible via searches from the Adult Mouse Anatomical Dictionary Browser)
   • cDNA Clone Query Form
   Genes and Markers Query Form
   • Gene Expression Literature Query Form
   • Gene Expression Data Query Form
   • Gene Expression Data Expanded Query Form
   • GO Browser
   • Human Disease Vocabulary Browser
   • Mammalian Orthology Query Form
   • Mammalian Phenotype Browser
   • MGI Batch Query
   • Molecular Probes and Clones Query Form (Probes, Clones and Primers)
   • The Mouse Anatomical Dictionary Browser
   • Mouse Sequence Query Form
   • Mouse SNP Query Form (Single Nucleotide Polymorphisms)
   • (Retrieve an) Oxford Grid
   • Phenotypes, Alleles, and Disease Models Query Form
   • References Query Form
   • RFLP/PCR Polymorphism Query Form
   • (Inbred) Strains (of Mice and Rats)

   In addition, you can use the following forms to retrieve mapping data and generate map displays:

   • Cytogenetic Map (Using Information from MGD)
   • DNA Mapping Panel Sets
   • Linkage Map (Using Information from MGD)
   • Recombinant Inbred Strain Distribution Patterns Query Form
   • Recombinant Congenic Strain Distribution Patterns Query Form

   See also All Search Tools for a lists of query forms arranged by function.

2. Enter (or select) values in one or more query form fields to use as search criteria. Use more descriptive fields (for example, Author or Title in the References Query Form) as primary search criteria. Use the general fields (for example, Year and Journal in the References Query Form) to further limit the scope of your search. Note that the search finds records that match all the criteria you enter as, for example,when you make the following choices on the Genes and Markers Query Form:

   Symbol/Name    begins    ak
   Chromosome    =    4

   The query returns any marker on Chr. 4 whose symbol or name begins with ak.

3. Select output format and sort options for your results.
   These options are useful when your query retrieves a large number of results, or if you want to generate a listing organized in a certain way. For example, you might want to see markers on a chromosome in linkage order.

4. If you think a search may be too broad, select a maximum number of items to return. Check these results to ensure you are getting the desired information. If not, expand or narrow your search, either by entering more parameters, or by being more specific in the ones you do enter, or by changing the number of records to return.

5. Execute searches by clicking Search .

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:

• Enter values in the search fields that specify the kind of information you are looking for. For example, on the Genes and Markers Query Form, if you are interested in data about the Histone gene complex on Chromosome 13, you might fill in the field and make a selection as follows:

  Symbol/Name   begins his
  Chromosome   in   13

  When you use multiple fields, the interpretation is "Search for all records that contain attribute A AND attribute B AND ...."

• Make your task easier by using appropriate comparison operators, especially for text fields. It is easier to use CONTAINS and type immunom than to type immunomodulation.

• Use a less-specific field along with a more descriptive field. For example, on the References Query Form, if you are interested only in more recent articles by Nadeau, then use Year along with Author.

  Author = Nadeau

  and specify
  

  Year    >   2004

  to further focus your search.
  
• Be wary of the NOT operator. Use it only when your search criteria include more than one search field and at least one descriptive field without the NOT operator. For example, if you want to retrieve mapping information on a particular gene but exclude work by a certain prolific author, use

  Marker Symbol/Name   =  cftr
  Author  NOT  begins  chapman

  
  
• Remember that there is a default in the field that determines the maximum number of items to return (for example, Max no of returns, or Maximum Returned; this field is usually located either at the top or the bottom of the query form near the sorting options.) Setting your own limit is useful when a query does not retrieve the results you want.
  • Set this to No limit (or type in a large number), for example, when you want a list of all genes in a chromosome.
  • Set this to a low number (if the query form allows this) when you have a rough idea of how many items your query might return but want a quick confirmation. For example, on the Mouse Sequence Query form, you could enter 20 as the limit; the summary report will display the total number of sequences your query actually found. If 20 of sequences 20 displayed appears, your search criteria are probably good. If 20 sequences of 600 displayed appears, you may want to refine these criteria.

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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:

• Genes and Markers, Phenotypes and Alleles, Sequences
  Use the Phenotype/Disease box to find potential mouse models for human diseases and phenotypic allele data in the MGI databases associated with any of the fields on the Genes and Markers Query Form.


• References
  Use the Abstract field to search for abstracts in MGI bibliographic records.


• Inbred Strains of Mice and Rats
  The text entry box at the end of the form is for full-text searching of Michael Festing's list of inbred strains. (This is a searchable index. Enter search keywords.)


• Gene Expression Literature
  The Abstract field is for full-text searching of abstracts in MGI bibliographic records. It functions the same way as the Abstract field on the References Query Form.


• Mouse Sequences
  The Mouse Sequence Query Form allows full-text searching in two fields: Description from Sequence Provider and Phenotype/Disease.


• Combined Mouse/Human Phenotypes Integrated MLC/OMIM Search - Integrated MLC/OMIM Search
  The text entry box at the end of the form is a searchable index.

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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.

• Selection lists
• Data entry fields
  • Numeric fields
  • Comparison operators
  • The NOT operator
  • Text fields with comparison operators
  • Wild card with LIKE operator
  • Wild card and text
  • Wild card as literal
• Button-activated options

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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.

• On a Macintosh, hold the command (Apple) key down and click on the desired items in the list; OR hold the shift key down and click on two items to select those and all items in between.
• On a PC, hold the control key down and click on the desired items in the list; OR hold the shift key down and click on two items to select those and all items in between.

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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.

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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 .

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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")

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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. For example, in References, you might be interested in finding articles where

Author BEGINS Chapman
Year = 1994
Journal NOT BEGINS Genom

This search yields the list of articles by Chapman written in 1994 appearing in any journal except Genomics (or any others with titles beginning Genom).

Click the NOT box next to the field to which you want to apply the negation.

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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.

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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:

Operator	Description
%	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

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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

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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 [[].)

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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.

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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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