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 is 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.:

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 (also see metadata_group)
metadata list of strings Metadata is data that describes the conditions under which the data was collected (e.g. machine calibration date)
metadata_group string A collection of biological specimens that were all tested under the same experimental conditions. The experimental conditions are identified by the metadata_group tag. For more information, see the IMPReSS parameter documentation section Required For Data Analysis.
strain_name string Deprecated. Please see genetic_background description
strain_accession_id string The background strain MGI accession ID (or IMPC ID when MGI accession is not available)
genetic_background string 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
weight float indicating the weight of the specimen observed
weight_parameter_stable_id string indicating the particular weight parameter
weight_date date indicating the actual date the weight was observed
weight_days_old int indicating the age in days of the specimen when the weight was observed
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: Certain characters, most notably spaces and the "<" and ">" characters, must be url encoded (space = %20, < = %3c, > = %3e) for command line usage.

Retrieve all experimental results for parameter ESLIM_001_001_009 (Coat hair color) for colony Myo7aMyo7a<Hdb>

curl \
'http://www.ebi.ac.uk/mi/impc/solr/experiment/select?q=parameter_stable_id:ESLIM_001_001_009%20AND%20colony_id:Myo7aMyo7a%3cHdb%3e&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'