This help document answers the following questions:
You can narrow what the Quick Search returns by:
You can get additional information about Quick Search results by:
See also Is there an advantage to using Quick Search over an individual MGI query form? for more information about advanced searches.
TopAccession IDs associated directly with a genome feature and only with that feature, appear as an exact match under Genome Features. Accession IDs associated with one or more genome features AND with another object (for example, a sequence ID) return associated features as exact matches and accessioned objects in Other Results by ID. These include:
In addition, some accession IDs are not unique. As an example, query for 100678. HomoloGene uses this identifier for a mouse gene; NCBI uses it to identify a gene model sequence associated with another gene; OMIM uses it to identify a disease condition whose associated human gene has an orthologous gene in mouse.
See Accession ID types and examples for list of providers, sample IDs, and where to look for any matches in the Quick Search Results. TopYou may use any of these, and more. Searchable fields for exact matching include:
Quick Search handles special characters such as parentheses, commas, colons, semicolons, dashes, slashes, +/-. However, the text in this example consists of both the symbol (T(XA1?;InY)8Ei) and name (reciprocal translocation, Chr X and inverted Chr Y, Eicher 8). Enter either the symbol or the name in the query box. If you want an exact match on the name/symbol combination, enclose each group in quotation marks ("T(XA1?;InY)8Ei" "reciprocal translocation, Chr X and inverted Chr Y, Eicher 8").
TopAll synonym variations produce the same result. For example, whether you enter (K+ + H+)-ATPase activity or H+/K+-ATPase activity, or H,K-ATPase activity, you'll see identical matches.
TopIt is not necessary to enter both the term definition and the identifier. One or the other suffices to query for any matches. For best results, enclose the multi-word term in quotation marks, e.g. "hydrogen:potassium-exchanging ATPase activity."
TopQuick Search looks for terms (keywords), synonyms, and definitions from the vocabularies. If you want an exact match, put the word or phrase in quotation marks to ensure that Quick Search finds a complete term, synonym, or definition.
TopTop
Acronym Full Name Search is for... AD Anatomical Dictionary
The Mouse Anatomical Dictionary BrowserExpression GO Gene Ontology
GO BrowserFunction including molecular function, biological process, and cellular component MP Mammalian Phenotype
Mammalian Phenotype BrowserPhenotype OMIM Online Mendelian Inheritance in Man
Human Disease Vocabulary BrowserDisease (model or ortholog) PIRSF Protein Superfamily Vocabulary Browser
Protein superfamilyProtein family InterPro Protein data from EBI's InterPro database Protein domain
Note: Adult Mouse Anatomy (MA) matches do not appear beneath Vocabulary Terms, but (when available) do appear beneath Other Results by ID.
You can enter as many as 32 words, IDs, or other text items. Each piece of text in a phrase, even when enclosed in quotation marks, counts as a word.
TopYes, but only one type of wildcard (the asterisk) is allowed and you can only use it at the end of a word or symbol or term.
TopYes, as long as they do not contain more than 32 words.
TopNo, but they are helpful when you want Quick Search to match an exact word, term, or phrase.
TopNo. However, at the top of the Quick Search Results, anything that the tool does not find is highlighted in red, next to See Details for this Search. Frequently, this is a clue that a term is misspelled.
TopYes. See Accession ID types and examples for list of providers, sample IDs, and where to look for any matches in the Quick Search Results.
TopQuick Search identifies the "root" of a word by removing common suffixes. This is called stemming. (For more information, see stemming in Wikipedia.) As examples: translocation is stemmed to transloc-; immunization is stemmed to immun-. Click See Details for this Search on a Results page to see how Quick Search has stemmed any word or phrase in your search text.
Additional examples:
Term Stemmed to... alimentary alimentari- perinatal perinat- metabolism metabol- immune immun- embryonic embryon- postnatal postnat- aging age- pigmentation pigment- urinary system urinari-, system- respiratory respiratori- tumorigenesis tumorigenesi-
Note: For best results, use wildcards on scientific or medical terms that the stemming algorithm may not recognize. As examples, use:
See stop words in Wikipedia for a definition. Quick Search removes the following words (except when they are part of a gene name) from queries:
Top
a | an | and | as | be | but | if | is| it | or | such | that | the | their | then | there | these | they | this | was | will
If Quick Search doesn't return appropriate matches, or if you want more specific results, try using one of the MGI query forms accessible from the Search tab in the top menu bar. Click Search-->All Search Tools (on the MGI homepage) to see everything available. (http://www.informatics.jax.org/allsearch.shtml)
You can also consult the user documentation for detailed information about searches. As examples, see Using the Genes and Markers Query Form for information about searches on genes or genome features and Using the Accession IDs Query Form for a complete list of the types of accession ID cross-referenced in MGI.
Top
To find... For example... Look here An overview of MGI data lists of all MGI markers, sequence data, mammalian orthology, gene ontology, strains & polymorphisms, gene expression, alleles and phenotypes, nomenclature, references, clone collections MGI Data and Statistical Reports MGI query forms & other searches Genes, Genome Features & Maps; Phenotypes, Alleles & Disease Models; Gene Expression; GO Functional annotations; Strains, SNPs & Polymorphisms; Mammalian Orthology; Sequences; Probes & Clones; References; Vocabularies; and more All Search Tools Nomenclature symbols, names, synonyms for mouse genes, genome features, orthologs, alleles, mutations Genes, Genome Features & Maps
Mouse Nomenclature HomepageGene expression during development, from assays, in structures, during developmental stages, in cell-line or tissue Gene Expression Database (GXD) Embryonic development, postnatal mouse, anatomical structures, Theiler stages somite pair
pigmented retinal epitheliumThe Mouse Anatomical Dictionary Browser Functional annotations for mouse gene products GO:0004699
calcium-independent protein kinase C activity
regulation of signal transductionGO Browser Protein domains IPR016243
Immunoglobulin-like fold
Tyrosine-protein kinase, CSF-1/PDGF receptor
Protein kinase ATP binding, conserved siteInterpro IDs and domain names (MGI data report) or
EBI's InterPro databaseAnnotated phenotype data (terms, definitions and term relationships in a DAG) cellular phenotype
embryogenesis phenotype
homeostasis/metabolism phenotype
lethality-postnatalMammalian Phenotype Browser human genes and genetic disorders; diseases 607822
breast cancerHuman Disease Vocabulary Browser Super family classification name annotated to an MGI gene PIRSF017765
A-kinase anchor protein 8
acidProtein Superfamily Vocabulary Browser
Please feel free to contact User Support for help finding information relevant to your research. You can use the "Your Input Welcome" button to submit questions, use the Contact User Support form, or call (207) 288-6445.
TopMouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc |
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last database update 11/20/2009 MGI_4.31 Web browser compatibility |
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