Invoking an EMAGE query using a URL

EMAGE queries can be invoked using a url in a web browser or other web client. Results are returned in HTML format (a web page).

Gene and/or anatomy queries

• Query for EMAGE entries by specifying a combination of genes, GO terms, anatomical structures, developmental stages and expression strengths.


• Names accepted for this type of query are all, genes, goterms, structures, stages, strengths, exactmatchgenes, includegenesynonyms, exactmatchgoterms, includegotermsynonyms, exactmatchstructures and includestructuresynonyms.


• The url includes name and value pairs in this general form:
  http://www.emouseatlas.org/emagewebapp/pages/emage_general_query_result.jsf?genes=value1,value2&structures=value1,value2&stages=value1,value2&strengths=value1,value2&exactmatchgenes=true&includegenesynonyms=true&exactmatchstructures=true&includestructuresynonyms=true

• Names that may have 1 or more values are genes, goterms, structures, stages, strengths.
  
  • The values for genes must be current MGI gene symbols unless includegenesynonyms=true (see below).
  • The values for goterms must be a gene ontology terms from the Gene Ontology GO project.
  • The values for structures must be terms or IDs from the EMAP anatomy ontology unless includestructuresynonyms=true (see below).
  • The values for stages must be numbers from the Theiler stage range 1 to 28, with or without the prefix "ts" or "TS".
  • The values for strengths must be "detected", "possible", or "not detected".
  • The values must be comma separated.
  • Example:
    http://www.emouseatlas.org/emagewebapp/pages/emage_general_query_result.jsf?genes=Fgf9,Fgf10&stages=14,15,16,17,20&strengths=detected
  
  
• Names that may only have the value "true" are exactmatchgenes, includegenesynonyms, exactmatchgoterms, includegotermsynonyms, exactmatchstructures and includestructuresynonyms
  
  • If exactmatchgenes=true the search will only return an exact match to the values given for genes.
    Otherwise an implicit wildcard is assumed and a value of "Fgf1" will also return results for "Fgf10","Fgf11", etc.
  • If includegenesynonyms=true the search will include synonyms, common IDs and orthologues of the values given for genes.
  • If exactmatchgoterms=true the search will only return an exact match to the values given for goterms.
    Otherwise an implicit wildcard is assumed.
  • If includegotermsynonyms=true the search will include synonyms of the values given for goterms.
  • If exactmatchstructures=true the search will only return an exact match to the values given for structures.
    Otherwise an implicit wildcard is assumed.
  • If includestructuresynonyms=true the search will include synonyms of the values given for structures.
  • Example:
    http://www.emouseatlas.org/emagewebapp/pages/emage_general_query_result.jsf?genes=MGI:1099809&structures=limb&includegenesynonyms=true&includestructuresynonyms=true
  
  
• Names that do not require a value are all
  
  • You cannot use any other names with all.
    
  • This query returns all possible results:
    http://www.emouseatlas.org/emagewebapp/pages/emage_general_query_result.jsf?all
  
  
• You only need to specify the names you are interested in.
  
  • This query gets you Fgf8 and Fgf9 at all stages, all structures and when not specified, strength defaults to "detected":
    http://www.emouseatlas.org/emagewebapp/pages/emage_general_query_result.jsf?genes=Fgf8,Fgf9
    
  
  
• If you don't specify any name/values you don't get anything.
  
• This query returns "No Results":
  http://www.emouseatlas.org/emagewebapp/pages/emage_general_query_result.jsf

EMAGE ID queries

• Query for EMAGE entries by specifying a list of EMAGE IDs.


• Names accepted for this type of query are all and emageIDs.


• The url includes name and value pairs in this general form:
  http://www.emouseatlas.org/emagewebapp/pages/emage_general_query_result.jsf?emageIDs=value1,value2

• The values for emageIDs must be numbers with or without the prefix "EMAGE:" e.g. "EMAGE:1000" or "1000".


• The values must be comma separated.


• Example:
  http://www.emouseatlas.org/emagewebapp/pages/emage_general_query_result.jsf?emageIDs=1000,EMAGE:2000


• This query returns all possible results:
  http://www.emouseatlas.org/emagewebapp/pages/emage_general_query_result.jsf?all

Spatial similarity queries

• Query for EMAGE entries that have spatially similar expression patterns to a given EMAGE entry .


• Names accepted for this type of query are spatialQueryID, spatialQueryStage and spatialQueryWholemount.
• Each name must be specified and be given a value.
• Each name may only have one value.


• The url includes name and value pairs in this general form:
  http://www.emouseatlas.org/emagewebapp/pages/emage_spatial_query_result.jsf?spatialQueryID=value&spatialQueryStage=value&spatialQueryWholemount=true

• The value for spatialQueryID must be a number with or without the prefix "EMAGE:" e.g. "EMAGE:1000" or "1000".


• The value for spatialQueryStage must be a number from the Theiler stage range 1 to 28, with or without the prefix "ts" or "TS".
• The value for spatialQueryStage must match the stage of the spatialQueryID EMAGE entry.


• The values for spatialQueryWholemount must be either "true" or "false".
• The value for spatialQueryWholemount should be "true" if the specimen type of the spatialQueryID EMAGE entry is wholemount, otherwise the value is "false" .


• Example:
  http://www.emouseatlas.org/emagewebapp/pages/emage_spatial_query_result.jsf?spatialQueryID=1000&spatialQueryStage=15&spatialQueryWholemount=true

 

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