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.
- What is full-text searching?
- Which fields on MGI Query Forms support the full-text search?
- What database records are searched? What does the search return?
- Which Boolean operators are allowed? How do they work? Is there a default operator?
- How do I construct a query using multiple terms?
- What if a term contains commas?
- Does case matter?
- What are the rules for full-text searching?
- How do I use quotation marks?
- Are there any restrictions on full-text searching?
- Are there examples?
- What happens if my query returns no results?
See also:
- MGI Glossary for unfamiliar terms (or for how MGI defines familiar terms) and acronyms
- General Guidelines for MGI Query Form Searches
- Using Wildcards on MGI Query Forms
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 either term. See Which Boolean operators are allowed? How do they work? Is there a default operator?
Which fields on MGI query forms support a full-text search?
The following MGI query forms support full-text searches:
- Genes and Markers Query Form (phenotype/disease field)
- Gene Expression Literature Search (Text field)
- Phenotypes, Alleles, and Disease Models Query Form (phenotype/disease field)
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:
- MP term names, synonyms, accession IDs and annotation notes (General and Background-Sensitive notes)
- Allele Additional Information Field
- human disease vocabulary terms, synonyms, and accession IDs.
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 Ontology (DO) and the Mammalian Phenotype (MP) Ontology are hierarchical. Thus:
- For MP or DO term entries, the search also returns an allele if the genotype for that allele is lower down in the ontology hierarchy. For example, entering a high level term such as heart returns not just alleles annotated to heart, but all genotypes annotated to cardiac hypertrophy, dilated atria, and so on.
Which Boolean operators are allowed? How do they work? Is there a default operator?
Four operators are allowed: AND, OR, NOT, or AND NOT in all-uppercase. By default, a space between terms is interpreted as an OR.
The format is:
term OPERATOR term ...
- If you enter term1 AND term2, the search locates all records containing both terms in any order.
- If you enter term1 OR term2, the search locates all records containing either term1 or term2 or both terms.
Examples:
If you enter... the search tool returns... heart AND defect Entries for heart defect but not for heart by itself or for defect by itself. Both expressions must appear in any matching terms. heart OR defect Entries for either heart or defect. heart defect Entries for either heart or defect. (Same results as heart OR defect, above.)
How do I construct a query using multiple terms?
By default, the search tool interprets a space between terms as OR. Therefore, if you want results for something containing term1 and term2 and term3, be sure to enter AND between the terms.
When diseases names contain multiple word, numeral or letter designations, enclose expressions that go together in quotation marks; for example, entering insulin resistance returns over 9000 matches whereas entering "insulin resistance" returns over 300 matches.
What if a term contains commas?
Commas between terms (or within terms) are ignored. 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").
Does case matter?
The MGI search engine is not case sensitive. Terms may be uppercase, lowercase, or any mixture of the two. Boolean operators, however, are the one exception. Operators must be upper case. A lower case and is ignored.
What are the rules for full-text searching?
- Enter one or more terms or multi-word terms (e.g., circulatory, "immune system").
- Separate words or phrases with one of the operators: AND or OR. Example: liver AND pancreas
- Enclose text in quotation marks if you want the search to return only items containing that phrase; e.g., "endocrine system". See How do I use quotation marks?
How do I use quotation marks?
- If the term you are entering contains a comma, put the entire term in quotation marks to ensure that the search is on the exact phrase (example: “cyclin B1, related sequence”).
- Be sure that all quotation marks are balanced. There must be one pair before and after each search term (e.g., “abnormal morphology”).
- Use only double quotation marks (single quotation marks - i.e, ‘cardio’ - are invalid).
See Are there examples? for additional entries and results.
Are there any restrictions on full-text searching?
- If you do not enter an operator, the default is OR between terms.
- The system ignores variations in punctuation and spacing. The results for each of the following entries are the same:
- heart, defect
- heart defect
- heart OR defect
- heart, defect
Are there examples?
| If you enter... | you'll get results for... | Why? |
|---|---|---|
| hearing | hear, hearing | Word stemming. |
| spinal cord | Anything containing either spinal or cord | Implicit OR operator |
| "spinal cord" | Anything containing the phrase, spinal cord | Quotation marks |
| spinal OR cord | Anything containing either spinal or cord | OR operator |
| spinal AND cord | Anything containing both spinal and cord | AND operator |
| spinal, cord | Anything containing either spinal or cord | OR operator. System ignores extraneous punctuation |
| spinal AND cord OR column | Anything containing both spinal and cord or column | AND, OR. By default, OR is interpreted first. |
| spinal and cord | Anything containing either spinal or cord | Implicit OR operator. Lower case boolean operators are ignored. |
| "abnormal spinal cord morphology | Anything containing abnormal OR spinal OR cord OR morphology | Missing quotation mark. System ignores extraneous punctuation |
| MP:0001463 | Anything annotated to the term, "abnormal spatial learning" | MP:0001463 is the ID for the term, "abnormal spatial learning" |
| MP:0001463 AND NOT Alzheimer | Anything annotated to the term, "abnormal spatial learning" and is NOT an Alzheimer disease model | AND NOT operator |
What happens if my query returns no results?
If your query returns no results, the resulting report:
- Summarizes your query parameters
- Indicates that there were 0 matches
- May list additional resources to help refine your query.
The probable causes are:
- There is something wrong with your selection from one of the browsers (i.e., did you copy and paste the entire term/ID?). See the following help documentation for clarification:
- There is an error in the text search string in the Phenotypes/Diseases box. For example, did you enclose multi-word terms in quotation marks? See examples for help.
- The allele nomenclature is incorrect (see Quick Guide to Nomenclature for Alleles and Mutations).
- The database does not contain your term yet.