Experimental data REST API

REST API documentation for IMPC and Legacy experimental raw data access

The experimental data set contains data observations from experiments conducted for the Europhenome project (see http://www.europhenome.org) and for the International Mouse Phenotype Consortium (IMPC) project (see http://www.mousephenotype.org). A record in this resource represents a single data point for an experiment. The list of experiments performed are documented in the International Mouse Phenotyping Resource of Standardised Screens (IMPREeSS, see http://www.mousephenotype.org/impress). Individual data points are associated to an IMPReSS Parameter. Parameters are organised into Procedures. Procedures are organised into Pipelines.

There are many ways to select and filter experimental data records, e.g.:

• all data points for a parameter
• all data points for a gene for one experiment
• all data for a specific pipeline

The experimental data REST API provides the fields described in the table below. Each field may be used for restricting the set of experimental data you wish to receive. The full SOLR select syntax is available for use in querying the REST API. See http://wiki.apache.org/solr/SolrQuerySyntax and http://wiki.apache.org/solr/CommonQueryParameters for a more complete list of query options.

Field name	Datatype	Description
phenotyping_center	string	the name of the organisation that performed the experiment
gene_accession_id	string	the gene MGI ID (http://www.informatics.jax.org) of the mutant specimen used for the experiment
gene_symbol	string	the gene symbol of the mutant specimen used for the experiment
allele_accession_id	string	the allele MGI ID (http://www.informatics.jax.org) of the mutant specimen used for the experiment
allele_symbol	string	the allele symbol of the mutant specimen used for the experiment
zygosity	string	indicating the zygosity of the specimen
sex	string	indicating the sex of the specimen
biological_sample_group	string	indicating if the specimen was a member of the control group or the experimental group
strain_accession_id	string	indicating the background strain of the specimen
strain_name	string	indicating the background strain name of the specimen
pipeline_name	string	indicating the name of the pipeline where the experiment was conducted
pipeline_stable_id	string	indicating the IMPReSS ID of the pipeline
procedure_stable_id	string	indicating the IMPReSS ID of the procedure
procedure_name	string	indicating the full name of the procedure
parameter_stable_id	string	indicating the IMPReSS ID of the parameter
parameter_name	string	indicating the full name of the parameter
experiment_source_id	string	indicating the experiment identifier at the center that performed it
observation_type	string	indicating the type of parameter (categorical, unidimensional, multidimensional, time series, metadata)
colony_id	string	indicating the name of the colony of the specimen
date_of_birth	date	indicating the date the specimen was born
date_of_experiment	date	indicating the date the data was collected
data_point	float	indicates the measured data value (1) (2) (3)
order_index	int	indicating the order (2)
dimension	string	indicating the dimension (2)
time_point	string	indicating the time the data value was measured (3)
discrete_point	float	indicating the discrete point (3)
category	string	indicating the category to which the specimen has been classified (4)
value	string	the value of the metadata (5)

(1) - For unidimensional parameters (2) - For multidimensional parameters (3) - For time series parameters (4) - For categorical parameters (5) - For metadata parameters

Examples

NOTE: It may be necessary for spaces and double quotes to be url encoded (space = %20, double quote=%22) for command line usage

Retrieve all experimental results for parameter ESLIM_001_001_009 (Coat hair color) for colony HEPD0527_5_A04

curl \
'http://www.ebi.ac.uk/mi/impc/solr/experiment/select?q=parameter_stable_id:ESLIM_001_001_009%20AND%20colony_id:HEPD0527_5_A04&wt=json&indent=true'

Retrieve all experimental results for organisation WTSI

curl \
'http://www.ebi.ac.uk/mi/impc/solr/experiment/select?q=phenotyping_center:WTSI&wt=json&indent=true'

Retrieve all unidimensional experimental results for Harwell for pipeline EUMODIC Pipeline 1

curl \
'http://www.ebi.ac.uk/mi/impc/solr/experiment/select?q=phenotyping_center:%22MRC%20Harwell%22%20AND%20pipeline_name:%22EUMODIC%20Pipeline%201%22%20AND%20observation_type:unidimensional&wt=json&indent=true'