This help document answers the following questions:

• What's the purpose of this tool?
• How does Quick Search work?
• What are the rules for entering text in the Quick Search box?
• About Quick Search Results (Genome Features, Vocabulary Terms, Other Results by ID, ...)
• Is there an advantage to using Quick Search over an individual MGI query form?
• Examples and more questions

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What's the purpose of this tool?

The Quick Search tool provides a swift overview of MGI data with linked results to deeper data layers.
You can:

• Enter gene symbols or names, text phrases, or accession IDs in the Quick Search box
• View the best matches, separated into Genome Features, Vocabulary Terms, and Other Results by ID (e.g. sequences, orthologies, references)
• Follow links to MGI data: genes and genome features, additional vocabulary, other objects
• Forward lists of genome features to the MGI Batch Query tool (to access and download additional MGI data such as genome location, phenotype, gene expression, genome attributes)
• Iterate your query to find ever more relevant results
• Search MGI's web pages including Help, FAQs, reference abstracts, detailed phenotype notes, sequence descriptions, and other text using Google.

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How does Quick Search work?

Quick Search attempts to find matches to your input text in several ways:

• To find an exact match, the tool uses your entire query phrase, intact, with no additional words.
• To accommodate lists, the tool searches for individual "words" (IDs, symbols, names, synonyms, and so on).
• To find data that may be related to your search, the tool uses as many of the "words" in your query phrase as possible.

These three approaches compare your input text to:

• individual mouse genome features and allele nomenclature (names, symbols, and synonyms)
• individual gene nomenclature for mouse orthologs in other organisms (human, rat, and so on)
• individual vocabulary terms, synonyms, and definitions in six of MGI's controlled vocabularies:
• Gene Ontology (GO)
• Mammalian Phenotype (MP)
• Human Disease (OMIM)
• InterPro
• Protein Superfamily (PIRSF)
• Mouse Anatomical Dictionary (AD)
• accession IDs from MGI and other data resources (e.g., Entrez Gene, NCBI, Ensembl, Vega, RefSeq) for many types of data objects
• genome features
• alleles
• sequences
• references
• expression images
• and more...

To your input text, Quick Search:

• applies stemming
• factors out special characters
• accepts wild cards for prefix searching
• recognizes quotation marks

Quick Search returns any matches in three sections on a result page:

• Genome Features - returns all that match, ordered by: best match.


• Vocabulary Terms - returns all that match, ordered by: best match.


• Other Results by ID - returns matches for anything other than genome features and vocabularies (i.e., no text is considered in matching).

Quick Search interprets queries as literally as possible and returns exact matches first, followed by less-than-exact matches. The tool parses your text entry into "words" and compares them to "words" in MGI nomenclature data, terms in any MGI-supported vocabulary, or any accession identifier stored in the MGI database. It assigns a score to the data it finds and determines the "goodness" of each match.

Once the results appear, you can look through the three separate categories (Genome Features, Vocabulary Terms, Other Results by ID), modify your input, and reiterate your search until you find the most relevant data. Items that appear beneath Vocabulary Terms in the results can teach you MGI's "native language," and this in turn can help you frame subsequent queries more accurately.

You can access the annotated data directly using links in the Quick Search Results.

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What are the rules for entering text in the Quick Search box?

Combining terms in a search | Stemming to root words | Order (of your entries) | Quotation marks | Case | Wild cards | Number of words allowed | Angle brackets | Other special characters | Separation characters | "Contains" searching | AND, OR, NOT |

In the Quick Search box, you can enter:

• single or multiple word search strings
• single or lists of accession IDs or symbols
• spaces or commas-plus-spaces between words, phrases, or IDs.

Entries can be:

• All of one type (e.g. identifiers such as accession IDs or Entrez Gene IDs; nomenclature such as gene names, symbols, synonyms, or orthologs)
• A mixed list of IDs and text (e.g. accession ID, gene synonym, allele name, keywords from an MGI vocabulary)

Issue	Rule	Examples
Combining terms in a search	Quick Search does not combine whatever you enter into "meaningful" associations. Rather, it attempts to match as much of your text as possible in individual nomenclature or vocabulary terms, synonyms, or definitions.	A search on cadherin hindbrain does not return genes in the cadherin family that are expressed in the hindbrain. To perform complex searches like this, consider using MGI's advanced query forms. Click Search-->All Search Tools for a complete list.
Stemming to root words	Quick Search stems words: it removes suffixes and searches using root words. Quick Search stems words even when they are enclosed in quotation marks.	A search for stem cell factor receptor binding searches for stem-, cell- (e.g. cellular), factor-, recept- (e.g. reception); bind- (e.g. binds). A search for cell division also looks for cell- divis-. .
Order (of your entries)	Does not matter (as long as you don't enclose the terms in quotation marks).	kit bmp4 returns the same list as bmp4 kit.
Quotation marks	Enclose any multi-word string (or part of a string) in quotation marks when searching for entire phrases.	"paired box gene 6" "kit ligand" "vitamin D metabolism" "forebrain;hippocampus" "left/right" patterning "interleukin 18" protein
Case	Quick Search is not case sensitive.	KIT returns same results as searching on Kit, kIt, or kit.
Wild cards	Use only the asterisk character, and only at the end of a word or text string. Currently, using a wild card on one word prevents stemming on all other words. To be sure to retrieve all words with the same root, use a wild card in the appropriate place on all words.	Kit* Kit lig* embry* develop* hippocamp* layer
	For best results, use wild cards on scientific or medical terms which the stemming algorithm may not recognize.	hippocamp*  finds hippocampus, hippocampi, hippocampal cell*  finds cell, cells, cellular, cell-like embry*  finds embryo, embryonic, embryonal, embryoes, embryogenesis nucle*  finds nucleus, nucleosis, nucleosome, nucleolar.
Number of words allowed	32	Use the MGI Batch Query for longer lists of genome features or accession IDs.
Angle brackets	Use to enclose superscripts in gene and allele nomenclature.	fas<lpr>
Other special characters	Quick Search treats ampersands, embedded asterisks, brackets, hyphens, parentheses, slashes, etc. as valid characters. The complete list is ~!@#$%^&*(_)-+={}\|[]:;'<>?/	RP23-100A23 Hprt<1tm1(UAS-Bmp4)Bhr> Tg(Igh-6-cre/ESR1)30Afst NM_001122899 Gt(pU21)103Imeg
Separation characters	The presence of some special characters is important when, for example, they occur within nomenclature, but not when within a text string.	A search for the text t cell or t-cell yields the same results.
"Contains" searching	Quick Search does not perform "contains" or "prefix" searches by default. Use a wild card when you want to do prefix searching. Use the advanced MGI query forms for "contains" searches.	Entering cardial does not return results for myocardial. Entering ax does not return results for Pax. Entering Trim returns results for Trat1 (because Trim is a synonym) and phenotypes annotated with whisper trimming, but if what you really want is a list of all tripartite motif-containing genes, use the wild card and enter Trim*. For a specific tripartite motif-containing gene, enter e.g. Trim10.
AND, OR NOT*	Do not use.	Quick Search handles both AND & OR Boolean searches automatically. * Use NOT only when it appears in the text of terms or definitions, especially in OMIM disease names.

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About Quick Search Results...

Sections:  Genome Features | Vocabulary Terms | Other Results by ID | Search MGI with Google Columns :   Score | Best Match Other information:   Helpful tips | See Details for this search | Your Input Welcome

The Quick Search Results include lists of:

• genome features (e.g. genes) that match your query
• vocabulary terms that match your query
• other results with an ID that matches query

From the Quick Search Results, you can:

• paginate through the results
• forward results to the MGI Batch Query tool
• search MGI using Google (this box is pre-populated with your search word or phrase)
• search again using the same word or phrase or modify your text
• reset the query (and type in new words or phrases for a new search)
• review the details for your search.

Sections on the Quick Search Results page

Genome Features

• The list includes genes, QTL, cytogenetic genome features, and other genome features whose name, symbol, synonym, or accession ID matched some or all of your entry.
• The list also includes genome features associated with vocabulary terms matching your search text.
• Items (in blue) are linked to their relevant MGI gene detail pages.
• See Score for how the results are ranked.
• The Best Match column lists one of the best reasons why an item is returned. Links from this column go to an All Matches page displaying additional reasons for the return.
• Get more data for genome features 1 through nn is linked to the MGI Batch Query where there is more data (symbols, MGI genome feature IDs, genome locations), more links, and some modification options (see Using the MGI Batch Query for complete details).

Depending on availability, the first ten matches appear in the display. A link at the bottom of this section provides access to the first 100 matching items. From this page, you can paginate through the full list of all matching genome features.

See also Quick Search Examples and Questions for additional search and match information.

Vocabulary Terms

This area of Quick Search Results identifies and gives the best reason for any matches found in the MGI vocabularies (GO, MA, MP, InterPro, OMIM, PIRSF), provides a link (when available) to that term in the given vocabulary, and to any associated MGI data (when available).

Use the Vocabulary Terms section to:

• learn MGI's official terms
• focus on detailed research topics
• explore related research areas
• investigate alternative paths to data.

Depending on availability, the first ten matches appear in the display. A link at the bottom of the vocabulary section provides access to the first 100 matching terms. From this page, you can paginate through the full list of all matching vocabulary terms.

See Scores and Best Match for information about the data appearing in these columns.

Other Results by ID

If your query:

• contains one or more accession IDs for a non-genome feature, non-vocabulary object, such matches appear in this section. Results are linked to the allele, sequence, orthology relationship, SNP, or other accession identifier matching a Quick Search box entry.


• contains a gene trap cell line ID that is:
  • associated with a marker, two records return:
    1. one for the marker associated with the ID, with a link to the marker's gene detail page
    2. one for the allele associated with the ID, with a link to the gene trapped allele detail page.
  
  
  • not associated with a marker, the summary report returns two records:
    1. one for the allele associated with the gene trap cell line ID, with a link to its allele detail page
    2. one for the sequence tag associated with the gene trap cell line ID, with a link to its sequence detail page.

  Note: A gene trap cell lines is not associated with with a marker if:

  • it is mixed (that is, it contains more than one likely gene trap insertion, as determined by sequence tags from separate chromosomes or at a greater distance from one another than would be covered by a single gene)
  • any associated sequence tags map to a location containing no known genes.
  • any associated sequences map to a location containing multiple genes.
  • any associated sequences map in the reverse orientation to a known marker.

Search MGI with Google

When you perform a Quick Search query, your search term also appears in the Search MGI with Google box. You can use it to locate MGI web pages containing this (or any other) term(s). The search extends to the following types of MGI web page content:

• FAQs
• Help text
• reference abstracts
• phenotypic details for alleles
• sequence descriptions
• image captions.

This search works following Google's algorithms on versions of pages it indexed from the MGI site. For example, enter: skeletal dysplasia, Pax6. The MGI Google Quick Search returns a list cached MGI pages where all the terms appeared.

Columns on the Quick Search Results page

Score

Results are grouped into tiers and scored within these tiers by best match using a designation of four stars, three stars, two stars, or one star.

• Four stars
  There is an exact match between what you entered and an ID or gene symbol, name, synonym, or vocabulary item in MGI. Genome features with nomenclature matches appear first, followed by genome features associated with vocabulary matches.


• Three stars
  All the words you entered are present in the matched item, but the matched item also contains additional words.
  Search engine (Lucene) scores determine the order of this tier. Genome features with better matches are at the top, and nomenclature matches appear before vocabulary matches. The score takes into account such things as number and frequency of matching words, stemmed versus unstemmed results, and spacing. Genome features or vocabulary terms with the same Lucene score are sorted alphanumerically by symbol.


• Two stars
  A single word or ID in your entry matches the nomenclature or ID of a genome feature, or the ID of a vocabulary term. For example, searching for absent hippocampus CA1 region returns genes associated with this phenotype term and also returns CA1 carbonic anhydrase 1 because CA1 matches the orthologous human gene symbol.


• One star
  Quick Search matched some but not all of your terms.
  Search engine (Lucene) scores determine order in this tier. Genome features with better matches appear at the top, and nomenclature matches appear before vocabulary matches. The score takes into account such things as number and frequency of matching words, stemmed versus unstemmed results, and spacing. Genome features or vocabulary terms with the same Lucene score are alphanumerically sorted by symbol.

Best Match

In the Genome Features section, the Best Match column displays the nomenclature, ID, or vocabulary terms associated with each gene which are the closest match to your query. Sometimes, a Best Match vocabulary term apparently has no matching text; this happens when a higher level, "parent" term matches your query. The displayed term is the more specific "child" term directly associated with the gene.

To see any additional associated nomenclature, IDs, or any vocabulary terms matching the query, click and more...

In the Vocabulary Terms section, this column displays the text element that is the closest match to the query. This may be the term itself, a synonym, or part of the term's definition. Where the text is lengthy, only the beginning of the best matching element appears.

Other information on the Quick Search Results page

Helpful Tips

Using your mouse, hover over an area of interest. If there is more information on a topic, a pop-up window appears.

See Details for this Search

Click to see a brief summary of how Quick Search performed this query. Some or all of the following appear:

• a list of what it tried to match (e.g. TS12, dysplasia, OTTMUSG00000015949)
• what words it stemmed to root words (e.g. metabolism is stemmed to metabol- so that additional material is matched).
• words, numbers, or letters excluded from this search (e.g. stop words, numbers 0-99, and single alpha characters with non-relevant results)
• wild card errors (e.g. only acceptable at the end of a term or symbol unless part of a gene name)

Terms that Quick Search cannot find appear (in red) next to See Details.... Frequently, this is a clue that a term is misspelled. A message also appears when Quick Search finds no matches whatsoever on your word(s) or phrase(s).

Note: Some mistakes in your entry text, such as an odd number of quotation marks, more than 32 words, or no search terms submitted, result in the appearance of a system message to that effect. Click OK, resolve the issue, and search again.

Your Input Welcome

Click to submit comments or questions about your query to our User Support staff. They will review them and take appropriate action.

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Is there an advantage to using Quick Search over an individual MGI query form?

Yes and no, depending on what you are looking for.

	Should I use MGI Quick Search?	or an MGI query form?
Are any results dependent upon established relationships among MGI data?	Yes. MGI's vocabularies are DAG structures or hierarchies.	Yes. (DAG, hierarchy)
Does it provide a quick view of all MGI data related to a term or phrase?	Yes. (Quick Search Results + linked data)	No.
Does it search all MGI vocabularies?	Yes. Any AD, GO, InterPro, OMIM, MP, or PIRSF results appear under Vocabulary Terms; Adult Mouse Anatomy results appear in Other Results by ID.	No. You must use the individual vocabulary query forms or separate vocabulary search boxes on the Genes & Markers; Phenotypes, Alleles & Disease Models; or Mouse Sequence query forms.
Does it find mouse orthologs for human disease genes? (possible research candidates)	Yes (Quick Search Results + linked data)	No.
Can it cross boundaries between subject areas? For example, can I find genes with a particular molecular function expressed in a specific tissue? ...combine a nomenclature query with a GO or MP term and a disease? ...confine the search to a specific coordinate range or Theiler stage?	No.	Yes. Click Search-->All Search Tools for a complete list of all available MGI query forms.
Can I choose how my results are sorted?	No.	Yes, many MGI query forms allow you to customize your output in this way.
"Contains" searching?	No.	Yes.

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Examples and more questions

See Quick Search Examples and Questions.

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Please feel free to ask User Support for help locating information relevant to your research. You can use the "Your Input Welcome" button or the Contact User Support form, or you can call (207) 288-6445.

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