RGD Search Features

The RGD site search allows users to find objects in RGD based on keyword or position information.  Over 8.5 million terms have been  ranked and indexed to return Genes, QTLs, Strains, Markers, References, and Ontology terms.

Simply type one or more search terms into the search box and hit 'Search RGD'

    

Capitalization

Searching on RGD is NOT case sensitive.  Searching for BLOOD PRESSURE, blood pressure, or BlOoD PrEsSuRe will all return the same result

    

Automatic "and" queries

RGD only returns objects that have been indexed against all search terms entered. Searching for blood pressure will return all objects that have attributes containing the words blood and pressure. Objects that have been indexed against only one of the terms will not be returned.

    

Searching by RGD ID

If an integer value alone is in the search box, RGD will assume the search is for an RGD ID.  To get to the gene page for A2m you could enter it's RGD ID (2004) in the search box.

    

Searching with external identifiers

Over 4 million external identifiers have been indexed.  Since numeric values are assumed to be RGD ID's, adding a colon ( : ) to the front of the search box will tell RGD you want to run an external identifier search.  If the search term is not numeric, an external identifier search is always attempted.  The following searches will return references and genes based on PubMed and Entrez Gene IDs.

    
    
    
    

Automatic exclusion of common words

The RGD search excludes common words such as "is" and "then", as well single characters.

    

Phrase searches

Sometimes you will only want results that include an exact phrase. In this case, simply put quotation marks ( " )around your search terms. For example, searching for "hypertensive strain"  will return only objects that contain both terms seperated by a single space.

    

Negative terms

Adding a minus sign to the start of a term tells the search to exclude that word.  For example, if you want to return all objects that have been indexed to the word blood, and not pressure you could search for blood -pressure

    

Positional searching

The RGD search includes the ability to run a search by genomic position.  Users familiar with GBrowse will recognize the format.  Searching with the term chr2:12000000..130000000 will return objects on chromosome 2 between base pair 12000000 and 130000000.

    

Searching for object families/word variations

By default, RGD searches terms entered with a trailing wild card character.  This allows for retrieval of entire object families and acts as a basic stemming mechanism.  Searching for lepr will return all objects that have been indexed to terms starting with lepr.   

    

Using wildcards in search terms

It is sometimes convenient to search with a wild card within a term. Adding one or more asterisks ( * ) to a search term tells RGD to perform a wild card search.  If an asterisk is present, the terms will not will be automatically given a trailing wild card as in the default search. 

    

What is ranked and indexed?

Over 8.5 million terms have been ranked and indexed to return Genes, QTLs, Strains, Markers, and References housed at RGD.

  • All Symbols
  • All Descriptions
  • All Names
  • Aliases
  • QTL Traits
  • QTL Sub Traits
  • Strain Origins
  • Strain Sources
  • Reference Titles
  • Reference Citations
  • GO OntologyTerms
  • Pathway Ontology Terms
  • Mammalian Phenotype OntologyTerms
  • Disease Ontology Terms
  • External Database Identifiers
    • BIND
    • Ensembl Genes
    • Ensembl Protein
    • Ensembl Transcript
    • Entrez Gene
    • GenBank Nucleotide
    • GenBank Protein
    • Gene3D-CATH
    • Germonline
    • HGNC ID
    • HPRD ID
    • HomoloGene Group ID
    • IMAGE_CLONE ID
    • IPI
    • InterPro
    • KEGG Pathway
    • KEGG Report
    • MGC_CLONE ID
    • MGD
    • NCBI Nucleotide
    • OMIM
    • PANTHER
    • PIRSF
    • PRINTS
    • PROSITE
    • Pfam
    • PharmGKB
    • ProDom
    • PubMed
    • SMART
    • Superfamily-SCOP
    • TIGR
    • TIGRFAMs
    • Transposagen
    • UniGene
    • UniProtKB
    • UniSTS