Using the Phenotypes Selection List
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This help document answers the following questions:

See also:

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:

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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.

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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 Full-Text Searching 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 tissueadiopos, tissu
behavioral/neurologicalbehavioral, neurolog
cardiovascular systemcardiovascular, system
cellularcellular
craniofacialcraniofaci
digestive/alimentary systemdigestive, alimentari, system
embryogenesisembryogenesi
endocrine/exocrine glandsendocrine, exocrin, gland
growth/size growth, siz
hearing/earhearing, ear
hematopoietic systemhematopoiet, system
homeostasis/metabolismhomeostasis, metabol
immune systemimmun, system
lethality/embryonic-perinatallethality, embryon, perinat
lethality/postnatallethality, postnat
life span/aginglife, span, ag
nervous systemnervou, 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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