IMPC data portal documentation

Data Access and Submission

REST API documentation for Genotype associated phenotype calls

The International Mouse Phenotype Consortium (IMPC) is composed of several international research institutions. At each institute, mutant mice are phenotyped and the data produced is sent to a Data Coordination Center (DCC). Once the data has passed a set of Quality Control (QC) checks, the data is statistically analyzed.

Each institute has unique operating standards and must track specimen and phenotype data to allow downstream analysis. To facilitate this requirement, the DCC defined a method to uniquely identify a phenotyping effort. One key data point used for this is the Colony ID. The Colony ID is used to encapsulate phenotyping mutants from a single allele on a background strain. The colony ID is associated to an allele/gene/background strain for display and dissemination. Each center can use a different scheme for generating the colony ID, and the colony IDs are unique across the IMPC effort.

Internally, the IMPC uses the Colony ID (among other attributes) to assemble mutant and control data points into an appropriate data set used for analysis. If the analysis registers a significant change in the mutant due to the genotype effect, the IMPC generates an association between the mutant gene and a mammalian phenotype ontology (MP) term specific to the measured parameter as defined in IMPReSS.

The genotype-phenotype REST API provides programmatic access to the genotype to phenotype associations that the IMPC produces. The API also includes access to data from legacy projects (EuroPhenome and MGP legacy) which have been analyzed using the IMPC statistical pipeline. There are many ways to get information about the MP terms associated to the different KO genes. You can select data per:

  • phenotyping center (e.g.: UCD, Wellcome Trust Sanger Institute, JAX, etc.)
  • phenotyping procedure or parameter (e.g.: Procedure IMPC_VIA_001, Parameter IMPC_ABR_006_001, full IMPC procedure list available at IMPReSS)
  • allele name or MGI allele ID
  • background strain name or MGI strain ID
  • gene symbol or MGI gene ID
  • or a combination of all these fields

The genotype-phenotype REST API provides the fields described in the table below. Each field may be used for restricting the set of data you wish to retreive. 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
doc_idintthe unique ID of the document
mp_term_idstringthe term ID of the associated mammalian phenotype term
mp_term_namestringthe term name of the associated mammalian phenotype term
top_level_mp_term_idstringa list of the top level term ids of the associated mammalian phenotype term
top_level_mp_term_namestringa list of the top level term names of the associated mammalian phenotype term
top_level_mp_term_definitionstringa list of the top level term definitions of the associated mammalian phenotype term
top_level_mp_term_synonymstringa list of alternate strings for the top level term name of the associated mammalian phenotype term
intermediate_mp_term_idstringa list of the intermediate level term ids of the associated mammalian phenotype term
intermediate_mp_term_namestringa list of the intermediate level term names of the associated mammalian phenotype term
intermediate_mp_term_definitionstringa list of the intermediate level term definitions of the associated mammalian phenotype term
intermediate_mp_term_synonymstringa list of alternate strings for the intermediate level term name of the associated mammalian phenotype term
marker_symbolstringthe associated marker symbol
marker_accession_idstringthe associated marker accession ID
colony_idstringthe colony ID
allele_namestringthe name of the allele
allele_symbolstringthe allele symbol
allele_accession_idstringthe allele accession ID
strain_namestringDeprecated. Please see genetic_background description
strain_accession_idstringThe background strain MGI accession ID (or IMPC ID when MGI accession is not available)
genetic_backgroundstringThe background strain name of the specimen
phenotyping_centerstringthe center at which the phenotyping was performed
project_external_idstring(legacy) the identifier of the project at the phenotyping center at which the work was performed
project_namestringthe shortname of the project for which the phenotyping was performed
project_fullnamestringthe full name of the project for which the phenotyping was performed
resource_namestringthe resource for which the phenotyping was performed
resource_fullnamestringthe full name of the resource for which the phenotyping was performed
sexstringthe sex of the mutant specimens on which the association was made
zygositystringthe zygosity of the mutant specimens on which the association was made
pipeline_namestringthe name of the IMPReSS pipeline
pipeline_stable_idstringthe stable ID of the IMPReSS pipeline
pipeline_stable_keystringthe stable key of the IMPReSS pipeline
procedure_namestringthe name of the IMPReSS procedure performed
procedure_stable_idstringthe stable ID of the IMPReSS procedure performed
procedure_stable_keystringthe stable key of the IMPReSS procedure performed
parameter_namestringthe name of the IMPReSS parameter measured
parameter_stable_idstringthe stable ID of the IMPReSS parameter measured
parameter_stable_keystringthe stable key of the IMPReSS parameter measured
statistical_methodstringthe statistical method used to determine the P value
percentage_changestringfor continuous data, a standardized effect measure
p_valuedoublethe statistical significance of the association
effect_sizedoublethe size of the effect
external_idstring(legacy) internal ID of the association at the phenotyping center

Retrieve all genotype-phenotype associations

This is the basic request to get all the results from the Solr service in JSON format (open this link in browser)

A bit of explanation:

  • genotype-phenotype is the name of the Solr core service to query
  • select is the method used to query the Solr REST interface
  • q=*:* queries everything without any filtering on any field
  • rows limits the number of results returned
  • wt=json is the response format (try "csv" or "xml" instead of "json")
  • indent=1 or indent=true indents the output into a more human-readable form

Retrieve all genotype-phenotype associations for a specific marker using a command line tool, curl

We'll now constrain the results by adding a condition to the q (query) parameter using the specific marker_symbol field. For example, for Akt2, simply specify q=marker_symbol:Akt2

        curl \
        --basic \
        -X GET \
        'http://www.ebi.ac.uk/mi/impc/solr/genotype-phenotype/select?q=marker_symbol:Akt2&wt=json'
        

Retrieve all genotype-phenotype associations for a specific MP term

Now we constrain the results by adding a condition to the q (query) parameter using the specific mp_term_name field. To retrieve the genotype associated to "decreased body weight", simply specify q=mp_term_name:"decreased%20body%20weight"Note the use of  %20 replacing the spaces between the words.

Alternatively, we may filter by the MP term identifier by specifying the mp_term_id:

Retrieve all genotype-phenotype associations for a top level MP term

Now we constrain the results by adding a condition to the q (query) parameter using the specific top_level_mp_term_name field. This also works with top_level_mp_term_id if you pass an identifier instead of the MP term name. To retrieve the genotype associated to "decreased body weight", simply specify q=top_level_mp_term_name:"nervous system phenotype"

Note the use of  %20 replacing the space between "body" and "phenotype".

Retrieve all genotype-phenotype associations with a P value cut-off

In this example, we apply a cut-off to the previous query and add a condition to the q (query) command. In Solr, you can specify a range to retrieve results. For instance, if you want P values below 0.0001, you can add the condition p_value:[0 TO 0.0001] to retrieve the genotype associated to a nervous system phenotype with a P value cut-off of 0.00005.

Note the use of  %20 replacing the spaces between the words, and %5b and %5d replacing the "[" and "]" characters. Alternately, you could instead use the -g flag in the curl command

or, alternatively, you could replace the [ (%5b) and ] (%5d) encoding characters with the -g flag in the curl command:

Retrieve all genotype-phenotype associations for a specific phenotyping center

Now we constrain the results by adding a condition to the q (query) parameter using the specific phenotyping_center field. To retrieve all MP associations to the "WTSI" (Wellcome Trust Sanger Institute) phenotyping center, specify q=phenotyping_center:"WTSI"

Get the phenotyping resource names

Start by a simple request to get the different phenotyping resource names (EuroPhenome, MGP, IMPC). This will be the basis to filter historical phenotyping resources like EuroPhenome or active resources like the IMPC project.

Solr queries are based on filters and facets. Using facets enables the retrieval of distinct values from a specific field. Using filters enables us to sub-select specific fields to retrieve, or, alternatively, all the fields from a Solr document. In this example we want to retrieve the distinct phenotyping resource names. The fields we are interested in are resource_name and resource_fullname.

If you look carefully at the request:

  • parameter fl means 'filter': we want to filter the results and keep only the resource_fullname and resource-name fields
  • parameter facet=on means we want to have faceted results
  • parameter facet.field means we are looking at all the possible combinations of resource_name and resource_fullname
  • parameter q is the query parameter. q=* means we don't want any text matching and want to get all the resource_name and resource_fullname results.

Next, we look at more advanced query parameter examples.

Retrieve all the phenotyping projects

In this example, only the selected field changes. Use the project_name and/or project_fullname fields.

Retrieve all pipelines from a specific project

To retrieve all the phenotyping pipelines from EUMODIC, we'll use the fq (filter query) parameter to filter the query on project_name:EUMODIC. As we are only interested at the distinct pipeline names, we'll use the facet.field parameter to facet on pipeline_name.

Retrieve all procedures from a specific pipeline

Again, we'll use the fq command to filter the query on pipeline_name using double-quotes and select the facet.field called procedure_name.

Note the use of  %20 replacing the spaces between the words.

Retrieve all parameters from a specific procedure which produced an MP call

Note the use of  %20 replacing the spaces between the words.

Retrieve all MP calls grouped by top level MP terms first and then by resources (MGP, EuroPhenome)

REST API documentation for IMPC and Legacy statistical result access

The statistical-result REST API provides access to the detailed output generated as part of the statistical analysis process.

The API may be queried using

  • phenotyping center (UCD, Wellcome Trust Sanger Institute, JAX, etc.)
  • phenotyping program (legacy MGP, EUMODIC, etc.)
  • phenotyping resource (EuroPhenome, MGP, IMPC)
  • phenotyping pipeline (EUMODIC1, EUMODIC2, MGP, IMPC adult, IMPC embryonic, etc.)
  • phenotyping procedure or parameter
  • allele name or MGI allele ID
  • strain name or MGI strain ID
  • gene symbol or MGI gene ID
  • or a combination of all these fields

The statistical-result REST API provides the fields described in the table below. Each field may be used for restricting the set of statistical-results 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
doc_id string The ID of the solr document
db_id int The IMPC internal database identifier
data_type string The type of the underlying data for which the statistic was calculated
mp_term_id string The accession ID of the MP term associated to this result
mp_term_name string The name of the MP term associated to this result
top_level_mp_term_id string The accession ID of the top level MP term obtained by interrogating the MP ontology
top_level_mp_term_name string The name of the top level MP term obtained by interrogating the MP ontology
intermediate_mp_term_id string The accession ID of all intermediate level MP terms obtained by interrogating the MP ontology
intermediate_mp_term_name string The name of all intermediate level MP terms obtained by interrogating the MP ontology
phenotype_sex list of strings If the result produced a phenotype call, this lists all the sexes for which the call is significant
resource_name string The short name of the resource responsible for producing the data
resource_fullname string The full name of the resource responsible for producing the data
resource_id int The IMPC internal identifier of the resource responsible for producing the data
project_name string The consortium/project that produced the data
phenotyping_center string The center where the data was generated
pipeline_stable_id string IMPReSS pipeline identifier
pipeline_stable_key string IMPReSS pipeline stable key
pipeline_name string IMPReSS pipeline name
pipeline_id int IMPC internal ID representing the IMPReSS pipeline
procedure_stable_id string IMPReSS procedure stable ID
procedure_stable_key string IMPReSS procedure stable key
procedure_name string IMPReSS procedure name
procedure_id int IMPC internal ID representing the IMPReSS procedure
parameter_stable_id string IMPReSS parameter stable ID
parameter_stable_key string IMPReSS parameter stable key
parameter_name string IMPReSS parameter name
parameter_id int IMPC internal ID representing the IMPReSS parameter
colony_id string Phenotyping center specific colony name of the line used to generate the data
marker_symbol string Gene symbol
marker_accession_id string MGI ID of the gene
allele_symbol string Allele symbol
allele_name string Allele name
allele_accession_id string MGI ID of the allele
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
sex string The sex of the specimen
zygosity string The zygosity of the mutant specimen
control_selection_method string The strategy used to select the control set (options are baseline_all or concurrent)
dependent_variable string The variable being tested
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.
control_biological_model_id int IMPC internal ID of the biological model of the control group
mutant_biological_model_id int IMPC internal ID of the biological model of the experimental group
male_control_count int Count of male specimens in the control group
male_mutant_count int Count of male specimens in the experimental group
female_control_count int Count of female specimens in the control group
female_mutant_count int Count of female specimens in the experimental group
statistical_method string The statistical method used to calculate the P value
status string The status of the statistical calculation
additional_information string Any additional information about the calculation
raw_output string The actual R output produced while performing the calculation
p_value float The P value of the data
effect_size float The effect size of the data
categories string Categories of data [4]
categorical_p_value float The P value for categorical data [3]
categorical_effect_size float The effect size (max percentage change) for categorical data [3]
batch_significant boolean True/false if random variable "batch" is significant or not [1]
variance_significant boolean True/false if variance is significant [1]
null_test_p_value float The overall significance result of the calculation [1]
genotype_effect_p_value float The significance of the genotype effect to describe variation in the data [1]
genotype_effect_stderr_estimate float The estimate of the standard error of the genotype effect [1]
genotype_effect_parameter_estimate float The effect size estimate of the genotype effect [1]
sex_effect_p_value float The significance of sex to describe variation in the data [1]
sex_effect_stderr_estimate float The estimate of the standard error of the sex effect [1]
sex_effect_parameter_estimate float The effect size estimate of the sex effect [1]
weight_effect_p_value float The significance of weight to describe variation in the data [1]
weight_effect_stderr_estimate float The estimate of the standard error of the weight effect [1]
weight_effect_parameter_estimate float The effect size estimate of the weight effect [1]
group_1_genotype string The genotype of the first group (usually +/+)
group_1_residuals_normality_test float Significance that group 1 conforms to normal distribution
group_2_genotype string The genotype of the second group (usually the colony ID)
group_2_residuals_normality_test float Significance that group 2 conforms to normal distribution
blups_test float Best Linear Unbiased Prediction test
rotated_residuals_test float Additional statistical model details. See PhenStat documentation for more information
intercept_estimate float Additional statistical model details. See PhenStat documentation for more information
intercept_estimate_stderr_estimate float Additional statistical model details. See PhenStat documentation for more information
interaction_significant boolean True/false if the significance of sex*genotype interaction is significant [1]
interaction_effect_p_value float The significance of sex*genotype interaction to describe variation in the data [1]
female_ko_effect_p_value float If sex is significant, the significance of the female genotype [1]
female_ko_effect_stderr_estimate float If sex is significant, the standard error estimate of the female genotype [1]
female_ko_parameter_estimate float If sex is significant, the effect size estimate of the female genotype [1]
male_ko_effect_p_value float If sex is significant, the significance of the male genotype [1]
male_ko_effect_stderr_estimate float If sex is significant, the standard error estimate of the male genotype [1]
male_ko_parameter_estimate float If sex is significant, the effect size estimate of the male genotype [1]
classification_tag string A summary of the result [1]
[1] - For unidimensional parameters [2] - For multidimensional parameters [3] - For time series parameters [4] - For categorical parameters [5] - For metadata parameters

Command line examples

Retrieve all statistical-result calculations

This is the basic request to get the first 10 results from the Solr service in JSON

        curl \
        --basic \
        -X GET \
        'http://www.ebi.ac.uk/mi/impc/solr/statistical-result/select?q=*:*&rows=10&wt=json&indent=true'
        

A bit of explanation:

  • statistical-result is the name of the Solr core service to query
  • select is the method used to query the Solr REST interface
  • q=*:* means querying everything without any filtering on any field
  • rows allows to limit the number of results returned. Note: if you do not specify the rows parameter, the default is 10 rows.
  • wt=json return the results in json format (csv is an alternate format
  • indent=1 or indent=true indents the output into a more human-readable form

Retrieve all IMPC statistical results for a specific marker

We will constrain the results by adding a condition to the q (query) parameter using the specific marker_symbol field. For Akt2, simply specify q=marker_symbol:Akt2

        curl \
        --basic \
        -X GET \
        'http://www.ebi.ac.uk/mi/impc/solr/statistical-result/select?q=marker_symbol:Akt2&wt=json&indent=true'
        

More examples of how to use Solr to query and filter are available on the genotype-phenotype API documentation page.

URL examples

The following are example URLs that you can paste into your browsers location bar. The resulting documents will display like a web page.

NOTE: Certain characters, most notably spaces and the "<" and ">" characters, must be url encoded (space = %20, < = %3c, > = %3e) for command line usage.

Get a maximum of 500 statistical results for gene Car4

http://www.ebi.ac.uk/mi/impc/solr/statistical-result/select?q=marker_symbol:Car4&rows=500

Get a maximum of 500 statistical results for gene Car4 in CSV format

http://www.ebi.ac.uk/mi/impc/solr/statistical-result/select?q=marker_symbol:Car4&rows=500&wt=csv

Get a list of specific fields from statistical results for gene Car4 in CSV format

http://www.ebi.ac.uk/mi/impc/solr/statistical-result/select?q=marker_symbol:Car4&wt=csv&fl=parameter_stable_id,parameter_name,female_control_count,female_mutant_count,male_control_count,male_mutant_count,null_test_p_value,statistical_method,allele_name,status,marker_accession_id,marker_symbol,allele_accession_id,allele_symbol,colony_id,metadata_group,zygosity,strain_accession_id,strain_name,classification_tag,genotype_effect_p_value,effect_size,genotype_effect_stderr_estimate

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.:

  • 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 (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'

REST API documentation for IMPC images access

The experimental data set contains images 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 image records, e.g.:

  • all images for a parameter
  • all images for a gene for one experiment
  • all images for a specific pipeline

The impc images data REST API provides the fields described in the table below which are mostly the same as for the experiment API with some additions. Each field may be used to restrict the set of impc image 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.

Image specific parameters:

Field name Datatype Description
omero_id int the omero image id which uniquely signifies the image in the omero image system
download_url string Url from where the original image can be downloaded - the format can be one of many including dicom, tiff, jpeg
jpeg_url string Url where a high resolution jpeg of the image can be obtained

General experimental parameters:

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_group string a string indicating a group of experimental and control mice that have the same metadata (see also biological_sample_group)
metadata list of strings list showing all relevant metadata in effect when the data was collected
strain_name string Deprecated. Please see genetic_background description
strain_accession_id string Background strain MGI accession ID (or IMPC ID when MGI accession is not available)
genetic_background 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
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 the first 10 image results for parameter IMPC_XRY_034_001 "XRay Images Dorso Ventral", for colony MEAW

curl \
'http://www.ebi.ac.uk/mi/impc/solr/impc_images/select?q=parameter_stable_id:IMPC_XRY_034_001%20AND%20colony_id:MEAW&wt=json&indent=true'
            

Retrieve the first 1000 image results for parameter IMPC_XRY_034_001 "XRay Images Dorso Ventral", for colony MEAW (Same as above, except append &rows=1000)

curl \
'http://www.ebi.ac.uk/mi/impc/solr/impc_images/select?q=parameter_stable_id:IMPC_XRY_034_001%20AND%20colony_id:MEAW&wt=json&indent=true&rows=1000'
            

Retrieve impc image results for organisation WTSI

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

Retrieve impc image results for MRC Harwell for procedure name Echo

curl \
            'http://www.ebi.ac.uk/mi/impc/solr/impc_images/select?q=phenotyping_center:%22MRC%20Harwell%22%20AND%20procedure_name:%20Echo%20&wt=json&indent=true'
            

Data submission to IMPC

AttachmentSize
PDF icon ES cell culture conditions PDF432.68 KB
PDF icon STATUS CODE USAGE_0.pdf411.74 KB
PDF icon Production Statistical analysis of IMPC data737.33 KB
PDF icon IMPCdata.pdf138.43 KB
PDF icon Housing and Husbandry Report7.78 MB
PDF icon Experimental Workflow Report2.7 MB
PDF icon Ethical and Funding Report1.57 MB
PDF icon PhenStatUsersGuide.pdf1.75 MB
PDF icon How to guide - installing PhenStatV2.pdf367.08 KB