Full-Text Searching on MGI Query Forms

This help document describes the MGI search engine that matches words and phrases and allows Boolean connectives between those searches for words and phrases.

See also:

What is a full-text searching?

In full-text searching, the system takes the term you enter, looks for that text in all database records of the appropriate type, and returns a list of all records containing the term in the search string.

Note: If you enter more than one term, you will get back records that contain all the terms. See Which Boolean operators are allowed? How do they work? Is there a default operator?.

Top

Which fields on MGI query forms support a full-text search?

The following MGI query forms support full-text searches:

Top

What database records are searched? What does the search return?

The system takes the text you enter in the phenotype/disease box on the query form and searches the following MGI database records:

The phenotype/disease box is located at the top of the query form in the Mouse phenotypes and models of human disease section (beneath Enter any combination of phenotype terms, disease terms or IDs).

The Human Disease Vocabulary has a flat structure and the Mammalian Phenotype (MP) Ontology is hierarchical. Thus:

Top

Which Boolean operators are allowed? How do they work? Is there a default operator?

 Two operators are allowed: AND and OR. NOT is currently unsupported but may be added at a future time. By default, a space between terms is interpreted as an AND.
 The format is:

term OPERATOR term ...

   Examples:

If you enter...the search tool returns...
heart AND defectEntries for heart defect but not for heart by itself or for defect by itself. Both expressions must appear in any matching terms.
heart OR defectEntries for either heart or defect.
heart defectEntries for heart defect but not for heart by itself or for defect by itself. (Same results as heart and defect, above.)
Top

How do I construct a query using multiple terms?

By default, the search tool interprets a space between terms as AND. Therefore, if you do not want results for something containing term1 and term2 and term3, be sure to enter or between terms: entering diabetes and Parkinsonism, for example, (probably) yields zero results because there are (currently in MGI) no diseases containing both terms.

  • When diseases names contain multiple word, numeral or letter designations, enclose expressions that go together in quotation marks; for example, entering diabetes and insulin resistance returns approximately 171 matches whereas entering diabetes and "insulin resistance" returns 36 matches.

    Top

    What if a term contains commas?

    Commas between terms (or within terms) are interpreted as ORs. Therefore, if the term itself contains a comma and you want to search on the exact phrase, enclose put the entire term in quotation marks (example: "cyclin B1, related sequence").

    Top

    Does case matter?

    No. The search engine is not case sensitive. Terms and operators may be uppercase, lowercase, or any mixture of the two.

    Top

    What are the rules for full-text searching?

    Top

    What is word stemming and how does it work?

    The MGI search engine stems (i.e., cuts off) at the word level 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.

    Top

    What is partial word matching and how does it work?

    The search engine performs partial matches on words: it looks for terms that begin, end, or are contained in other terms. For example, if you enter ear, the system not only returns results for ear, but also for early and heart.

    Therefore, be sure to put a space in front of any term that begins, ends, or is contained in another term and enclose the term in quotation marks. For example, if you want results for eye, you must enter “  eye”. If you don't, the system stems eye to ey and matches ey any where in a word, thus returning results for e.g., kidney as well as eye.

  • Top

    How do I use quotation marks?

    See Are there examples? for additional entries and results.

    Top

    How do I use parentheses?

    Parentheses tell the search engine the order in which it should interpret your terms. Consider two examples:

    a or b and c    e.g., cord or column and spinal
    (a or b) and c    e.g., (cord or column) and spinal
    By default, the engine interprets AND first, and so evaluates the first example as if you had put parentheses around b and c. The result is a return of anything containing spinal column, or cord, including accordance, record, and so on. The second example returns results for spinal cord or spinal column.

    See Which Boolean operators are allowed? How do they work? Is there a default operator? for how the search engine interprets AND and OR.

    Top

    Are there any restrictions on full-text searching?

    Top

    Are there examples?

    See also examples (with results specific to the Human Disease Vocabulary Browser).

    If you enter...you'll get results for...Why?
    membranemembrane, membranous; transmembrane anything containing membran Word stemming and partial word matching.
    hearing hear Word stemming.
    hearing hearing, heard, hears, heartPartial word matching.
    "hearing" hearing
    shearing
    Full word match
    Partial word matching.
    "ear" Anything containing ear including ears, hear, heart, earlyPartial word matching.
    " ear" ear, ears, early Quotation mark and white space at beginning eliminates partial word matches on hear, heart.
    " ear " Only earLeading and trailing quotation marks and white spaces prevent partial word matching at either end; no returns for early, hear, ears, or heart.
    spinal cord spinal cordImplicit AND operator.
    "spinal cord" spinal cordQuotation marks.
    spinal or cordAnything containing either spinal or cord OR operator.
    spinal and cord Anything containing both spinal and cord AND operator.
    spinal, cord Anything containing both spinal and cord AND operator. System ignores extraneous punctuation.
    spinal and (cord or column) Anything containing both spinal and cord or column AND parentheses, OR.
    spinal and (cord or column Error Opening parenthesis is present; closing parenthesis is missing.
    "abnormal spinal cord morphology Error Missing quotation mark.
    'abnormal spinal cord morphology abnormal spinal cord morphology results System ignores extraneous punctuation.
    Factor V Deficiency results for Factor V, VI, VII, etc. Partial match on V.
    "Factor V Deficiency" Factor V alone Quotation marks turn off stemming.
    cytochrome c, somatic (gene/marker symbol/name field) cytochrome c or somatic (~43 matches) Quotation marks needed if desired search is on entire term (searching on “cytochrome c, somatic” results in ~1 match).
    superimposed aqueductal stenosisOne allele with an allele name, chromosome and category information, but no observed effects or allelic composition (genetic background) dataThe Mammalian Phenotype (MP) Ontology is annotated at the genotype level. The allele appears because of a match in the Additional Notes Field but it has no genotypes that contribute to the query result.

    Top

    What should I do if I get an error message?

    Top

    What happens if my query returns no results?

    If your query returns no results, the resulting report:

    The probable causes are:

    Top