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).

EMAGE combination queries

• Query for EMAGE entries by specifying a combination of the following query types: genes, probe, annotation type, assay type, speciemen type, specimen strain, author, data source, genotype, GO terms, anatomical structures, developmental stages and expression strengths. The combination represent logic AND relationshps.


• Names accepted for this type of query are all, genes, annotationtype, specimentype, specimenstrain, author, genotype, probe, assaytype, datasource, 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, annotationtype, specimentype, specimenstrain, author, genotype, probe, assaytype, datasource, goterms, structures, stages, strengths.
  
  • The values for genes must be current MGI gene symbols unless includegenesynonyms=true (see below).
  • The values for annotationtype can be any annotation, spatial annotation, 3D spatial annotation, wholemount spatial annotation, text annotation, no annotation.
  • The values for specimentype can opt, section, wholemount, sectioned wholemount, wholemount plus section of wholemount, unknown.
  • The values for specimenstrain are substrings which are part of strain names.
  • The values for author are substrings which are part of author list.
  • The values for genotype are wild-type, substrings which are part of mutant allele names.
  • The values for probe are substrings which are part of probe names.
  • The values for assaytype are ish, ihc, isr, enhancer.
  • The values for datasource are emage, mgi, eurexpress, embryoExpress, facebase, vista, embrys
  • 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 part of gene 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.
    Otherwise, it only considers symbol and accession.
  • If exactmatchgoterms=true the search will only return an exact match to the values given for goterms.
    Otherwise part of go term is assumed.
  • If includegotermsynonyms=true the search will include synonyms of the values given for goterms.
    Otherwise, it only considers name and accession.
  • If exactmatchstructures=true the search will only return an exact match to the values given for structures.
    Otherwise part of anatomy is assumed.
  • If includestructuresynonyms=true the search will include synonyms of the values given for structures.
    Otherwise, it only considers name and accession.
  • 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

Gene expression overview queries

• Query for gene expression overview by specifying a combination of genes and developmental stages.
  For this query, you must have an extra argument infos=true.


• Names accepted for this type of query are genes and stages.


• The url includes name and value pairs in this general form:
  http://www.emouseatlas.org/emagewebapp/pages/emage_gene_result.jsf?infos=true&genes=value1,value2&stages=value1,value2

• Names that must have 1 or more values are genes.
  
  • The values for genes must be current MGI gene symbols.
  
  
• Names that may have 0 or more values are stages.
  
  • The values for stages must be numbers from the Theiler stage range 1 to 28, with or without the prefix "ts" or "TS".
  
  
• Examples:
  
  • http://www.emouseatlas.org/emagewebapp/pages/emage_gene_result.jsf?infos=true&genes=Fgf8,Wnt11
    It returns expression overview of Fgf8 and Wnt11 at all available stages
  • http://www.emouseatlas.org/emagewebapp/pages/emage_gene_result.jsf?infos=true&genes=Fgf8,Wnt11&stages=TS14
    It returns expression overview of Fgf8 and Wnt11 at Theiler stage 14
  
  

Spatially co-expression queries

• Query for gene expression overview by specifying a combination of genes and developmental stages.


• Names accepted for this type of query are genes and stages.


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

• Names that must have 1 value are genes.
  
  • The values for genes must be current MGI gene symbols.
  
  
• Names that may have 0 or more values are stages.
  
  • The values for stages must be numbers from the Theiler stage range 1 to 28, with or without the prefix "ts" or "TS".
  
  
• Examples:
  
  • http://www.emouseatlas.org/emagewebapp/pages/emage_gene_result.jsf?genes=Fgf8
    It returns expression overview of genes which co-express spatially with Fgf8 at all available stages
  • http://www.emouseatlas.org/emagewebapp/pages/emage_gene_result.jsf?genes=Fgf8&stages=TS14
    It returns expression overview of genes which co-express spatially with Fgf8 at Theiler stage 14
  
  

Gene expression in pathways queries

• Query for gene overview by specifying a combination of pathway and developmental stages.


• Names accepted for this type of query are pathways, stages and exactmatchpathway.


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

• Names that must have 1 or more values are pathways.
  
  • The values for pathways must be current Kegg pathway accession or definition.
  • If exactmatchpathway=true the search will only return an exact match to the values given for pathways.
    Otherwise an implicit wildcard is assumed.
  
  
• Names that may have 0 or more values are stages.
  
  • The values for stages must be numbers from the Theiler stage range 1 to 28, with or without the prefix "ts" or "TS".
  
  
• Examples:
  
  • http://www.emouseatlas.org/emagewebapp/pages/emage_gene_result.jsf?pathways=path:mmu04110&exactmatchpathway=true
    It returns expression overview of genes in pathway path:mmu04110 (Cell cycle) at all available stages
  • http://www.emouseatlas.org/emagewebapp/pages/emage_gene_result.jsf?pathways=ABC transporters&stages=TS23
    It returns expression overview of genes in pathway ABC transporters at Theiler stage 23

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

Publication queries

• Query for EMAGE entries by specifying DOI or PubMed ID.


• Names accepted for this type of query are doi, pubmed, exactmatchdoi and exactmatchpubmed.


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

• Both doi and pubmed may have 1 or more values. Values must be separated by commas.
  
  • The values for doi must be a DOI name.
  • If exactmatchdoi=true the search will only return an exact match to the values given for doi.
    Otherwise an implicit wildcard is assumed.
  • The values for pubmed must be a PubMed ID.
  • If exactmatchpubmed=true the search will only return an exact match to the values given for pubmed.
    If this value is set then the format of the ID must include the prefix PMID: e.g. PMID:9834182
    Otherwise an implicit wildcard is assumed.
• Examples:
  http://www.emouseatlas.org/emagewebapp/pages/emage_general_query_result.jsf?doi=10.1016/S0925-4773(01)00656-6
  http://www.emouseatlas.org/emagewebapp/pages/emage_general_query_result.jsf?pubmed=9834182
  http://www.emouseatlas.org/emagewebapp/pages/emage_general_query_result.jsf?pubmed=PMID:9834182&exactmatchpubmed=true

 

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