Using the Phenotypes Selection List

This help document answers the following questions:

• How do I make choices on the Anatomical Systems Affected by Phenotypes list?
• What if my term is not on that list?
• After I make my selection, strange things appear in the box. Why?
• Can I edit what's in the box? Add more terms?

See also:

• Full-Text Searching on MGI Query Forms (sections on Boolean operators, word stemming, partial word matching, quotation marks, parentheses)
• Using the Phenotypes, Alleles, and Disease Models Query Form
• Interpreting a Phenotypic Allele Summary
• Interpreting Phenotypic Allele Details
• MGI Glossary for unfamiliar terms (or for how MGI defines familiar terms) and acronyms

How do I make choices on the Anatomical Systems Affected by Phenotypes list?

The Anatomical Systems Affected by Phenotypes is a high-level phenotype term list consisting largely of systems (e.g., cardiovascular, digestive/alimentary) or syndromes (e.g., life span/aging) for which MGI has curated phenotypes. Selecting terms and clicking Add to query results in populating the Phenotype/Disease search box. The system takes the terms you enter, looks for that text in database records of the appropriate type, and returns a list of all records annotated to a phenotype term related to your system. For an explanation of what appears in the search box, see strange things .... If you can't find what you are looking for, see What if my term is not on that list?

Note: If you enter more than one term, the system returns only those records containing all your terms. It interprets a space between terms as AND. If you want the system to return records containing either term, type OR between terms.

See Using Full-Text Searches on MGI Query Forms for more details about using AND and OR, quotation marks, parentheses, partial word matching, and word stemming.

What if my term is not on that list?

Click Full Mammalian Phenotype (MP) Ontology and navigate the hierarchy. For example, to find aneurysm, the path is:

1. cardiovascular system phenotype
2. abnormal cardiovascular system morphology
3. aneurysm

Click on a term to see its definition and then you can copy and paste the term (or its MP identifier; for example, MP:0003279 is the ID for aneurysm) in the Phenotype/Disease search box.

See Using the Mammalian Phenotype (MP) Browser for additional help.

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After I make my selection, strange things appear in the box. Why?

When you click Anatomical Systems Affected by Phenotypes, select terms, and add them to your query, the system populates the Phenotype/Disease query box with your choices.

• Each choice is represented by its MP ID, such as MP:0005390 for skeletal system phenotypes.
• A space between terms is interpreted as OR; any matches may contain either of the terms on either side of the OR. If you want a match on both terms, type AND between them.

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Can I edit the box on the query form? Add more terms?

Yes to both questions. For example, you may wish to change an AND to an OR. You may wish to click the links beside Select or Browse and add more items from those lists. You may also wish to add your own terms. Individual words may be enclosed in quotation marks. Quotation marks "turn off" word stemming (cutting off words to retrieve matches that are close yet not exact). For example, you can enter diabetic or diabetes and get the same results because the system truncates your entry to diabet. Therefore, if you are entering a term (as opposed to selecting from a list), enclose anything that you do not want reduced to a stem in quotation marks. For example, if you want results for cardiac but not cardiovascular, enclose the former in quotes to prevent a return of everything beginning with cardio. On the other hand, if you want to look at every allele or phenotype involved in immunity, enter the stem, immun without the quotation marks. See Full-Text Searching on MGI Query Forms for additional information.

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