Using the Quick Search Tool
Using the Quick Search Tool
This help document answers the following questions:
The Quick Search tool provides a swift overview of MGI data with linked results to deeper layers of information.
You can:
A toggle permits 4 options:
| Option | Comments |
|---|---|
| Keywords, Symbols, or IDs (exact phrase) | The default option searches for Keywords, Symbols, and IDs using an exact phrase. An exact match is given a 4-star score. |
| Keywords, Symbols, or IDs | This option also searches for Keywords, Symbols, and IDs but each "word" is searched separately. You can add quotes to include a phrase search of a portion of the included text. The wild card, an asterisk (*), is supported in this search option. |
| Mouse Location | Use the format Chr1:194732198-294732198, or Chr1:194732198 for a single coordinate, or Chr1 for an entire chromosome. |
| Human Location | Use the format Chr1:194732198-294732198 or Chr1 for an entire chromosome. This will return the mouse homologs of the human genes within the designated human coordinates. |
Notes:
For the first 2, non-coordinate, search options, the Quick Search attempts to find matches to your input text in several ways:
These three approaches compare your input text to:
In your input text, Quick Search:
Quick Search returns any matches in five tabs on a results page:
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 five separate tabs (Genome Features, Alleles, Vocabulary Terms, Strains and Stocks, Other Results by ID). For each tab, you can filter your search results. Filters for ontology terms feature subsets of selected highlevel terms. The filters are applied to the specific selected tab, and do not affect the other tabs' results. Items that appear beneath Vocabulary Terms in the results can teach you the "native language" used in each of the MGI vocabularies, 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.
In the Quick Search box, you can enter:
Entries can be:
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 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 or use the exact phrase search option.
- "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 We recommend not using more than 32 words. Use the MGI Batch Query for longer lists of genome features or accession IDs. Other special characters Quick Search replaces angle brackets and hyphens with spaces. It treats ampersands, embedded asterisks, parentheses, slashes, etc. as valid characters. The complete list is ~!@#$%^&*(_)+={}\|[]:;'?/
- 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 important when the occurance is 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.
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.
| Tabs: Genome Features | Alleles | Vocabulary Terms | Strains and Stocks | Other Results by ID Columns : Score | Best Match Other information: Search MGI with Google | Your Input Welcome |
The Quick Search Results include lists of:
From the Quick Search Results, you can:
- Genome Features
- The list includes genes, pseudogenes, QTLs, heritable phenotypic markers, cytogenetic genome features, and other genome features whose name, symbol, synonym, or accession ID matches some or all of your entry. See Genome Feature Types for a complete list.
- The list also includes genome features associated with vocabulary terms matching your search text. A search with a mouse anatomy term will return genome features whose expression has been detected in the structure.
- Cell line ID searches return only allele matches (and not both gene and allele matches).
- Items (in blue) are linked to their relevant MGI gene detail pages.
- Results are ranked by Score.
- Chr (chromosome), Location (genome coordinates), and Str (strand, + or -) appear for results with this data. Offsets (cM position or cytogenetic band) appear, if available, when there is no chromosome data.
- The Best Match column lists one of the best reasons why an item is returned.
- For large numbers of results, you can paginate through the full list of all matching genome features.
- You can filter your results by feature type, GO terms (molecular function, biological process, cellular component), expression, and phenotype and disease annotations.
- You have the option of forwarding your results to the MGI Batch Query, the GXD Batch Search, or MouseMine to obtain additional data associated with the features (see Using the MGI Batch Query, Using the Gene Expression Batch Search, and Using the MouseMine Data Warehouse).
- You can download your results as a text or spreadsheet file.
- See also Quick Search Examples and Questions for additional search and match information.
- Alleles
- The results display the allele type (see all allele types), official allele symbol and name, the genome location of the associated gene, and Best Match.
- Alleles existing as only cell lines are returned last within a given star rating.
- You can filter your results by feature type and phenotype and disease annotations. Note that MGI doesn't annotate phenotype and disease terms to genes or even alleles. The terms are assigned to genotypes—the combination of alleles and strain background.
- You have the option of forwarding the genes of the alleles to the Batch Query or via a toggle, the alleles to MouseMine.
- You can also download your results as a text or spreadsheet file.
- Vocabulary Terms
- This tab of Quick Search Results identifies and gives the best reason for any matches found in the MGI vocabularies (DO, GO, EMAPA, 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
- filter your results by high level vocabulary terms for Gene Ontology (GO: Molecular Function, Biological Process, and Cellular Component), Expression, Phenotype, and Disease
- download your results as a text or spreadsheet file.
- From this page, you can paginate through the full list of all matching vocabulary terms.
- The Associated Data column provides links to the Human Disease and Mouse Model Detail page where you can find information about mouse models and mouse/human orthologies. Note: MGI may not contain evidence that a mutation in a mouse gene presents a model for a disease, yet if that mouse gene is orthologous to a human gene associated with a disease, it is listed as a disease ortholog.
- See Scores and Best Match for information about the data appearing in these columns.
- Strains and Stocks
- The results display the name of the strain/stock, and when available, a link to the IMSR (International Mouse Strain Resource) which provides the state of the stock (i.e., embryo, sperm, live mice), and links to contact the repository of the stock, associated references, and Best Match.
- You can filter your results by phenotype and disease annotations.
- You can download your results as a text or spreadsheet file.
- Other Results by ID
- If your query contains one or more accession IDs for a non-genome feature or non-vocabulary object, such matches appear in this section. Results are linked to the sequence, orthology relationship, or other accession identifier matching a Quick Search box entry. These results can be filtered by feature type and downloaded as a text or spreadsheet file.
- Score
- Results are grouped into tiers and scored within these tiers by Best Match using a designation of four stars, three stars or two stars.
- Four stars There is an exact match between what you entered and an ID, symbol, name, synonym, or vocabulary item in MGI.
- Three stars
All the words you entered are present in the matched item, but the matched item also contains additional words.
Search engine scores determine the order of this tier. Results with better matches are at the top. The score takes into account such things as number and frequency of matching words, stemmed versus unstemmed results, and spacing. Results with the same score are sorted alphanumerically.- 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.
Within a star tier, a result may be boosted according to:
- Whether the match is at the start of the string
- Whether the words in the search string are in the same order (even if interrupted) in the matched string
- Whether the search string is an exact substring of the matched string
- Whether the match is to a non-stemmed field (prioritized over stemmed fields)
- When matching numbers, whether the whole number matched rather than just a prefix to a number
- Best Match
- The Best Match column displays the nomenclature, vocabulary terms, strains and stocks, or ID(s) that is 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 genome feature.
- 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.
- Search MGI with Google
- See: What is Search MGI with Google useful for?.
- 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.
Search results are automatically filtered into tabs. Within a given tab, further filtering options are available.
When you perform a Quick Search query, your search term also appears in the bottom section of your results, 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:
This search works following Google's algorithms on versions of pages 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.
See Querying by Accession ID - Results and Examples.
All search results tabs offer the ability to download your results as text or spreadsheet files.
Depending on the tab, you may have the option of forwarding your results to the MGI Batch Query, the GXD Batch Search, or MouseMine to obtain additional data associated with the results (see Using the MGI Batch Query, Using the Gene Expression Batch Search, and Using the MouseMine Data Warehouse).
It depends on what you are looking for and the depth of information you need. In general, use the Quick Search when you are looking for something specific or are expecting only a few results. You can also use the Quick Search to run a broad search to explore MGI and see the depth of our data. Like using Google to search the Internet, your Quick Search results can be hit or miss. You may get results you weren't expecting, though the best results will sort to the top.
The query forms give you more power over your search. One of the strengths of MGI is data integration. This allows you to search across multiple data sets. For example, you can use the Genes & Markers Query to find all the protein coding genes and microRNAs mapped to mouse Chromosome 2, whose products are involved in axon guidance and have alleles that show an eye phenotype. In this example you narrowed the mapping search to Chr 2, the Feature Types to just protein coding genes and microRNAs, the Gene Ontology to just axon guidance and its subterms, and the phenotype to just eye phenotypes. The Quick Search results allow you to narrow your results by filtering, however, the filters use high-level terms, whereas with the Query Forms, you can use the specific terms.
See Quick Search Examples and Questions.
Use the "Your Input Welcome" button, the Contact User Support form, or call (207) 288-6445 for help locating information relevant to your research.