JSON eMouseAtlas query using a URL

eMouseAtlas resources can be queried by url in a web browser or other web client. Results are returned in JSON format.

eMouseAtlas queries

• http://www.emouseatlas.org/jsonservice/json_service?service=info
  
  It returns statistics of the eMouseAtlas 3 resources (Atlas, eHistology, EMAGE):
  
  • stage
  • number of Mouse Atlas models
  • number of eHistology images
  • number of EMAGE entries at each stage


• http://www.emouseatlas.org/jsonservice/json_service?service=term
  
  It returns the anatomy term information for those which have been delineated in atlas models or annotated on high resolution histology images.
  The results can be filtered by adding 1 or more parameters: stage,which.
  
  The general form: http://www.emouseatlas.org/jsonservice/json_service?service=term&stage=value1,...,value2&which=value
  
  • Example values for stage are TS07, 9, TS03-5, TS04-TS07
  • The value for which is ema or kaufman
  
  

Atlas Ontology queries

• http://www.emouseatlas.org/jsonservice/json_service?service=ontology
  
  It returns ontology DAG. The resultant ontology can be filtered by adding 1 or more parameters: stage, accession,
  
  The general form: http://www.emouseatlas.org/jsonservice/json_service?service=ontology&stage=value1,...,value2&accession=value1,...,value2
  
  • Example values for stage are TS01, ..., TS28
  • Example values for accession are ontology accessions such as EMAPA:56766.
    This will result in a pruned ontology whose leaf nodes are the specified terms.
  
  
• http://www.emouseatlas.org/jsonservice/json_service?service=term_detail&accession=value
  
  It returns the detailed information of the specified term:
  
  • name
  • accession
  • synonym
  • stage range: start stage and end stage
  • wiki link
  • parents
  • paths
  • number of ema models where this term is delineated
  • number of histology images where this term is annotated
  • number of EMAGE entries where gene expression are observed in this term
  
  The results can be filtered by adding stage parameter.
  
  
• http://www.emouseatlas.org/jsonservice/json_service?service=domain&stage=value&model=value
  
  It returns the domain ontology: the smallest ontology DAG which contains all delineated terms of the specified model.
  The results can be filtered by adding section parameter.
  
  The general form: http://www.emouseatlas.org/jsonservice/json_service?service=domain&stage=value&model=value&x=number&y=number&z=number&theta=number&phi=number&dist=number
  It returns the smallest ontology DAG which contains all delineated terms of the specified section of the specified model.
  

Atlas Model queries

• http://www.emouseatlas.org/jsonservice/json_service?service=range
  
  It returns wholemount models, 3D voxel models at each stage.


• http://www.emouseatlas.org/jsonservice/json_service?service=ema
  
  It returns the details of all Mouse Atlas models: name, stage, whether having delineated terms, strain, preparation, embedding, number of delineated terms, image viewers. The resultant models can be filtered by adding 1 or more parameters stage, name, term.
  
  The general form: http://www.emouseatlas.org/jsonservice/json_service?service=ema&stage=value1,...,value2&name=value1,...,value2&term=value1,...,value2
  
  • Example values for stage are TS07, 9, TS03-5, TS04-TS07
  • Example values for name are atlas model names such as EMA7, EMA118.
  • Example values for term are ontology accessions or names such as EMAPA:56766 or eye. It returns Atlas models where the specified terms are delineated.
  
  

Kaufman High Resolution Histology Image queries

• http://www.emouseatlas.org/jsonservice/json_service?service=kaufman
  
  It returns the details of all high resolution histology images: accession, name, group accession, stage, age, orientation, image viewer, number of annotated terms. The resultant images can be filtered by adding 1 or more parameters stage, age, orientation, plate, term.
  
  The general form: http://www.emouseatlas.org/jsonservice/json_service?service=ema&stage=value1,...,value2&age=value1,...,value2&orientation=value1,...,value2&plate=value1,...,value2&term=value1,...,value2
  
  • Example values for stage are TS07, 9, TS03-5, TS04-TS07
  • Example values for age are 7, 6.5, E7.25, 7-10.5, E7-10, E1-E10
  • Example values for plate are plate numbers such as 33a, 34b used in Kaufman book
  • Example values for orientation are sagittal, transverse, frontal, coronal
  • Example values for term are ontology accessions or names such as EMAPA:56766 or heart. It returns only images where the specified term are annotated.
  
  

EMAGE gene expression queries

• http://www.emouseatlas.org/jsonservice/json_service?service=summarystatistics
  
  It returns the statistics of EMAGE gene expression database:
  • number of entries
  • number of entries of each type (ish, ihc, isr, enhancer, clonalAnalysis)
  • number of stages
  • number of genes
  • number of images