General Guidelines for MGI Query Form Searches
This help 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?
- How can I save the results of my query?
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), restrict/expand scope, execute).
- Select the query form to use depending on the type of information you want to search for. The following forms are available:
- Adult Mouse Anatomical Dictionary Browser
- Genes and Markers Query Form
- Gene Expression Literature Query Form
- Gene Expression Data Query Form
- GO Browser
- Human Disease Vocabulary Browser
- Mammalian Phenotype Browser
- MGI Batch Query
- Mouse Developmental Anatomy Browser
- Mouse dbSNP Query Form (Single Nucleotide Polymorphisms)
- Phenotypes, Alleles, and Disease Models Query Form
- References Query Form
See also: All Search Tools for a list of query forms arranged by function.
- 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 hox*
Chromosome 6The query returns any marker on Chr. 6 whose symbol, name or synonym begins with hox.
- Execute searches by clicking Search.
- Your search results may offer sort options. Click on the column headings or the up/down arrowheads ( ▼ ▲) to change the sort order of your results. For example, you might want to see markers on a chromosome in the order of their genome coordinates.
- If your search was too broad or narrow, click the banner at the top of the page (Click to modify search). (The banner title changes to Click to hide search.) The window that appears contains your original search criteria. You can then expand or narrow your search, either by entering more parameters, or by being more specific in the ones you do enter.
The query results are usually a list of records in an abbreviated format. The display contains links to related information in the MGI database.
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 hist*
Chromosome 13When you use multiple fields, the interpretation is "Search for all records that contain attribute A AND attribute B AND ...."
- 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 Joseph H. Nadeau, then use Year along with Author.
Author Nadeau JH
and specify
Year 2010-
to further focus your search.
Many query results now allow you to modify your search and requery. Use the Click to modify search button to view your previous search parameters and make refinements.
Alternately, many Query Forms allow you to filter your results. So in the previous search, you could filter JH Nadeau's publications to just those published in Mamm Genome.
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
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. - 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.
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
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 Chromosomes on some query forms. To limit your search to specific chromosomes, you make your selections 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 multiple chromosomes. 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.
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 .
Wild card and text
MGI supports the asterisk a wild card symbol before or after the text you enter in the search field.
The following are examples of using the wild card 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 |
| *rik | all RIKEN cDNA genes |
Can I view the results of a query in different ways?
The query forms offer several options for sorting query returns. For example, in the results of a Genes and Markers Query Form search, you can specify that the returned list of markers be sorted by Genome Coordinates, Feature Type or Symbol. Use the up/down triangles in a column header to sort by that column.
How can I save the results of my query?
Many query forms provide the option to export your results as a text file or in a spreadsheet format. Several also allow you to get additional information on genes by exporting your results to the MGI Batch Query or MouseMine.