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?
• How do I select more than one item from this list?
• After I make my selection, strange things appear in the box. Why?
• Are there examples of what shows up in the box?
• Can I edit what's in the box? Add more terms?
• Is there a list of all the possible stems?

See also:

• Using Full-Text Searches 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
• Understanding Phenotypic Allele Summary Reports
• Understanding Phenotypic Allele Detail Reports
• 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) that MGI has phenotypes for. Selecting terms and clicking Add to query results in their 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

You can then 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.

How do I select more than one item from this list?

To pick two or more items from a selection list, do the following:

• On a PC, hold the control key down and click the desired items, or hold the shift key down and click two items to select them and all items in between.
• On a Macintosh, hold the command (Apple) key down and click the desired items, or hold the shift key down and click two items to select them and all the items in between.

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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 enclosed in parentheses to ensure that terms are considered as a whole and in order. Sometimes, this requires more than one set of parentheses. For terms such as endocrine, cardiovascular, and so on, the word system is understood and does not appear in the query box.
• Based on your selections the list, the Boolean operators AND and OR appear in the query box.
• A space between terms is interpreted as AND; any matches must contain the terms on either side of the AND. If you want a match on either term, type OR between them.
• Depending upon your intent, you can backspace and retype to substitute one for the other.
• Individual words may be enclosed in quotation marks. Occasionally, there are spaces before (or after) the 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.
• A space within quotation marks indicates that the search should treat it as a space. For example, if you only want results for eye, enter "eye " to prevent matches on, for example, Peyer's patch:.

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Are there examples of what shows up in the box?

When you select ... from the Phenotypes Selection List:	the Phenotype/Disease box contains...	because the system stems to ...	and adds...
behavior/neurological	(behavior OR neurological)	behavior, neurolog	Boolean OR and parentheses
cardiovascular system	(cardiovascular)	cardiovascular	parentheses ("system" is understood)
endocrine/exocrine glands	((endocrine OR exocrine) AND glands)	endocrin, gland, exocrin	outer parentheses for entire expression, internal parentheses for ORed terms
hearing/ear	("hearing" OR " ear " OR " ears")	hear, ear	Outer parentheses for entire expression, quotation marks to turn off partial word matching.
immune system	("immune")	immun	Quotation marks to turn off word stemming. If you want everything beginning with "immun," remove the quotation marks.
lethality/embryonic-perinatal	(lethality AND (embryonic OR perinatal))	lethal, embryon, perinat	Internal parentheses enclosed in external parentheses to ensure correct order of evaluation.
taste/olfaction	("taste" OR olfaction)	tast, olfaction	Stemming ("tast" retrieves e.g., metastasize, so taste must be enclosed in quotation marks.)
vision/eye	("vision" OR " eye")	vision, ey	Quotation marks turn off partial word matching; inserted white space prevents matches on words containing eye i.e., Peyer's patch.

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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. See Using Full-Text Searches on MGI Query Forms for additional information.

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Is there a list of all the possible stems?

Anatomical Systems Affected by Phenotypes term Stems to... adipose tissue adiopos, tissu behavioral/neurological behavioral, neurolog cardiovascular system cardiovascular, system cellular cellular craniofacial craniofaci digestive/alimentary system digestive, alimentari, system embryogenesis embryogenesi endocrine/exocrine glands endocrine, exocrin, gland growth/size growth, siz hearing/ear hearing, ear hematopoietic system hematopoiet, system homeostasis/metabolism homeostasis, metabol immune system immun, system lethality/embryonic-perinatal lethality, embryon, perinat lethality/postnatal lethality, postnat life span/aging life, span, ag nervous system nervou, system normal phenotype normal, phenotyp other phenotype other, phenotyp pigmentation pigment renal/urinary system renal, urinari, system reproductive system reproduct, system respiratory system respiratori skeleton skeleton touch/vibrissae touch, vibrassa tumorigenesis tumorigenesi vision/eye vision, ey

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