Help & Documentation

Retrieve raw data

The experimental data REST API provides access to data observations from experiments conducted for the Europhenome project and for the International Mouse Phenotype Consortium (IMPC) project. 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). 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. For example,

  • 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 the Solr Wiki, Solr Query Syntax and Common Query Parameters, 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 \
'https://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 \
'https://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 \
'https://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'

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