1. Introduction

2. statistical-result

2.1. Fields

Path Type Description

doc_id

String

The document identifier unique to this dataset.

db_id

Number

The database identifier for the dataset.

data_type

String

The type of data represented in this dataset.

anatomy_term_id

Array

List of anatomy term identifiers related to the dataset.

anatomy_term_name

Array

List of anatomy term names related to the dataset.

intermediate_anatomy_term_id

Array

List of intermediate anatomy term identifiers.

intermediate_anatomy_term_name

Array

List of intermediate anatomy term names.

top_level_anatomy_term_id

Array

List of top-level anatomy term identifiers.

top_level_anatomy_term_name

Array

List of top-level anatomy term names.

mp_term_id_options

Array

List of optional MP term identifiers.

mp_term_name_options

Array

List of optional MP term names.

mp_term_id

String

The identifier for the MP term.

mp_term_name

String

The name of the MP term.

top_level_mp_term_id

Array

List of top-level MP term identifiers.

top_level_mp_term_name

Array

List of top-level MP term names.

intermediate_mp_term_id

Array

List of intermediate MP term identifiers.

intermediate_mp_term_name

Array

List of intermediate MP term names.

male_mp_term_id

String

The identifier for the male MP term.

male_mp_term_name

String

The name of the male MP term.

male_top_level_mp_term_id

Array

List of male top-level MP term identifiers.

male_top_level_mp_term_name

Array

List of male top-level MP term names.

male_intermediate_mp_term_id

Array

List of male intermediate MP term identifiers.

male_intermediate_mp_term_name

Array

List of male intermediate MP term names.

female_mp_term_id

String

The identifier for the female MP term.

female_mp_term_name

String

The name of the female MP term.

female_top_level_mp_term_id

Array

List of female top-level MP term identifiers.

female_top_level_mp_term_name

Array

List of female top-level MP term names.

female_intermediate_mp_term_id

Array

List of female intermediate MP term identifiers.

female_intermediate_mp_term_name

Array

List of female intermediate MP term names.

genetic_background

String

The genetic background of the subjects in the dataset.

production_center

String

The center where the data was produced.

external_db_id

Number

External database identifier associated with the dataset.

id

Number

Unique identifier for the dataset.

organisation_id

Number

Identifier of the organisation associated with the dataset.

phenotyping_center_id

Number

Identifier of the phenotyping center where the data was generated.

project_id

Number

Project identifier associated with the dataset.

male_control_mean

Number

The mean value for male controls.

male_mutant_mean

Number

The mean value for male mutants.

female_control_mean

Number

The mean value for female controls.

female_mutant_mean

Number

The mean value for female mutants.

genotype_effect_size_low_vs_normal_high

Number

Effect size for genotype low versus normal/high comparison.

genotype_effect_size_low_normal_vs_high

Number

Effect size for genotype low/normal versus high comparison.

female_effect_size_low_vs_normal_high

Number

Effect size for female low versus normal/high comparison.

female_effect_size_low_normal_vs_high

Number

Effect size for female low/normal versus high comparison.

male_effect_size_low_vs_normal_high

Number

Effect size for male low versus normal/high comparison.

male_effect_size_low_normal_vs_high

Number

Effect size for male low/normal versus high comparison.

categories

Array

Categories used in the statistical analysis.

categorical_p_value

Number

P-value for the categorical analysis.

categorical_effect_size

Number

Effect size for the categorical analysis.

batch_significant

Boolean

Indicates if batch effects are significant.

variance_significant

Boolean

Indicates if variance is significant.

null_test_p_value

Number

P-value for the null hypothesis test.

genotype_effect_p_value

Number

P-value for the genotype effect.

genotype_effect_stderr_estimate

Number

Standard error estimate for the genotype effect.

genotype_effect_parameter_estimate

Number

Parameter estimate for the genotype effect.

male_percentage_change

String

Percentage change for males.

female_percentage_change

String

Percentage change for females.

sex_effect_p_value

Number

P-value for the sex effect.

sex_effect_stderr_estimate

Number

Standard error estimate for the sex effect.

sex_effect_parameter_estimate

Number

Parameter estimate for the sex effect.

weight_effect_p_value

Number

P-value for the weight effect.

weight_effect_stderr_estimate

Number

Standard error estimate for the weight effect.

weight_effect_parameter_estimate

Number

Parameter estimate for the weight effect.

blups_test

Number

Results of the BLUPs test.

rotated_residuals_test

Number

Results of the rotated residuals test.

intercept_estimate

Number

Estimate of the intercept.

intercept_estimate_stderr_estimate

Number

Standard error estimate of the intercept estimate.

interaction_significant

Boolean

Indicates if interaction effects are significant.

interaction_effect_p_value

Number

P-value for the interaction effect.

soft_windowing_bandwidth

String

Bandwidth used in soft windowing.

soft_windowing_shape

String

Shape used in soft windowing.

soft_windowing_peaks

String

Peaks identified in soft windowing.

soft_windowing_min_obs_required

String

Minimum observations required for soft windowing.

soft_windowing_total_obs_or_weight

String

Total observations or weight for soft windowing.

soft_windowing_threshold

String

Threshold used in soft windowing.

soft_windowing_number_of_doe

String

Number of degrees of freedom in soft windowing.

soft_windowing_doe_note

String

Notes on the degree of evidence in soft windowing.

metadata

Array

List of metadata associated with the dataset.

resource_name

String

The name of the resource.

resource_fullname

String

The full name of the resource.

resource_id

Number

The unique identifier for the resource.

project_name

Array

List of names of projects associated with the dataset.

phenotyping_center

String

The name of the phenotyping center where the data was generated.

pipeline_stable_id

String

The stable identifier for the pipeline.

pipeline_stable_key

Number

The stable key for the pipeline.

pipeline_name

String

The name of the pipeline.

pipeline_id

Number

The unique identifier for the pipeline.

procedure_stable_id

Array

List of stable identifiers for the procedures.

procedure_stable_key

Array

List of stable keys for the procedures.

procedure_name

String

The name of the procedure.

procedure_id

Number

The unique identifier for the procedure.

parameter_stable_id

String

The stable identifier for the parameter.

parameter_stable_key

Array

List of stable keys for the parameter.

parameter_name

String

The name of the parameter.

parameter_id

Number

The unique identifier for the parameter.

colony_id

String

The identifier for the colony.

marker_symbol

String

The symbol for the genetic marker.

marker_accession_id

String

The accession ID for the genetic marker.

allele_symbol

String

The symbol for the allele.

allele_name

String

The name of the allele.

allele_accession_id

String

The accession ID for the allele.

strain_name

String

The name of the strain.

strain_accession_id

String

The accession ID for the strain.

sex

String

The sex of the organism.

zygosity

String

The zygosity of the organism.

control_selection_method

String

The method used for control selection.

dependent_variable

String

The dependent variable being measured.

metadata_group

String

The group classification of the metadata.

data_frame

String

The frame of data being referred to.

female_ko_effect_p_value

Number

The P-value for the knockout effect in females.

female_ko_effect_stderr_estimate

Number

The standard error estimate for the knockout effect in females.

female_ko_parameter_estimate

Number

The parameter estimate for the knockout effect in females.

female_effect_size

Number

The effect size for females.

male_ko_effect_p_value

Number

The P-value for the knockout effect in males.

male_ko_effect_stderr_estimate

Number

The standard error estimate for the knockout effect in males.

male_ko_parameter_estimate

Number

The parameter estimate for the knockout effect in males.

male_effect_size

Number

The effect size for males.

classification_tag

String

A classification tag for the dataset.

phenotype_sex

Array

List indicating the sex(es) for which phenotype data is available.

life_stage_acc

String

The accession code for the life stage.

life_stage_name

String

The name of the life stage.

significant

Boolean

Indicates whether the findings are statistically significant.

effect_size

Number

The measured effect size in the dataset.

female_control_count

Number

The number of female controls in the dataset.

female_mutant_count

Number

The number of female mutants in the dataset.

female_pvalue_low_normal_vs_high

Number

The P-value for females comparing low/normal versus high categories.

female_pvalue_low_vs_normal_high

Number

The P-value for females comparing low versus normal/high categories.

genotype_pvalue_low_normal_vs_high

Number

The P-value for genotype comparison between low/normal versus high categories.

genotype_pvalue_low_vs_normal_high

Number

The P-value for genotype comparison between low versus normal/high categories.

group_1_genotype

String

The genotype information for group 1.

group_1_residuals_normality_test

Number

Results of the residuals normality test for group 1.

group_2_genotype

String

The genotype information for group 2.

group_2_residuals_normality_test

Number

Results of the residuals normality test for group 2.

male_control_count

Number

The number of male controls in the dataset.

male_mutant_count

Number

The number of male mutants in the dataset.

male_pvalue_low_normal_vs_high

Number

The P-value for males comparing low/normal versus high categories.

male_pvalue_low_vs_normal_high

Number

The P-value for males comparing low versus normal/high categories.

p_value

Number

The general P-value associated with the statistical test.

statistical_method

String

The statistical method applied in the analysis.

status

String

The status of the dataset or analysis.

2.2. Example Json

HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 5648

{
  "doc_id" : "DOC123",
  "db_id" : 100,
  "data_type" : "Gene Expression",
  "anatomy_term_id" : [ "AID123", "AID456" ],
  "anatomy_term_name" : [ "Heart", "Liver" ],
  "intermediate_anatomy_term_id" : [ "IAID789", "IAID101" ],
  "intermediate_anatomy_term_name" : [ "Ventricle", "Lobe" ],
  "top_level_anatomy_term_id" : [ "TAID112", "TAID113" ],
  "top_level_anatomy_term_name" : [ "Circulatory System", "Digestive System" ],
  "mp_term_id_options" : [ "MPID123", "MPID456" ],
  "mp_term_name_options" : [ "Hypertrophy", "Necrosis" ],
  "mp_term_id" : "MPID789",
  "mp_term_name" : "Atrophy",
  "top_level_mp_term_id" : [ "TMPID123", "TMPID456" ],
  "top_level_mp_term_name" : [ "Muscle Structure", "Cell Death" ],
  "intermediate_mp_term_id" : [ "IMPID789", "IMPID101" ],
  "intermediate_mp_term_name" : [ "Muscle Size", "Apoptosis" ],
  "male_mp_term_id" : "MMPID123",
  "male_mp_term_name" : "Male Hypertrophy",
  "male_top_level_mp_term_id" : [ "MTMPID123", "MTMPID456" ],
  "male_top_level_mp_term_name" : [ "Male Muscle Structure", "Male Cell Death" ],
  "male_intermediate_mp_term_id" : [ "MIMPID789", "MIMPID101" ],
  "male_intermediate_mp_term_name" : [ "Male Muscle Size", "Male Apoptosis" ],
  "female_mp_term_id" : "FMPID123",
  "female_mp_term_name" : "Female Hypertrophy",
  "female_top_level_mp_term_id" : [ "FTMPID123", "FTMPID456" ],
  "female_top_level_mp_term_name" : [ "Female Muscle Structure", "Female Cell Death" ],
  "female_intermediate_mp_term_id" : [ "FIMPID789", "FIMPID101" ],
  "female_intermediate_mp_term_name" : [ "Female Muscle Size", "Female Apoptosis" ],
  "resource_name" : "Resource Name",
  "resource_fullname" : "Full Resource Name",
  "resource_id" : 200,
  "project_name" : [ "Project X", "Project Y" ],
  "phenotyping_center" : "Center Z",
  "pipeline_stable_id" : "PID123",
  "pipeline_stable_key" : 300,
  "pipeline_name" : "Pipeline Name",
  "pipeline_id" : 400,
  "procedure_stable_id" : [ "PRID123", "PRID456" ],
  "procedure_stable_key" : [ 500, 600 ],
  "procedure_name" : "Procedure Name",
  "procedure_id" : 700,
  "parameter_stable_id" : "PAID123",
  "parameter_stable_key" : [ 800 ],
  "parameter_name" : "Parameter Name",
  "parameter_id" : 900,
  "colony_id" : "Colony123",
  "marker_symbol" : "Gene123",
  "marker_accession_id" : "M123456",
  "allele_symbol" : "Allele123",
  "allele_name" : "Allele Name",
  "allele_accession_id" : "A123456",
  "strain_name" : "Strain Name",
  "strain_accession_id" : "S123456",
  "sex" : "Male",
  "zygosity" : "Homozygote",
  "control_selection_method" : "Random",
  "dependent_variable" : "Weight",
  "metadata_group" : "Group1",
  "data_frame" : "Frame1",
  "genetic_background" : "C57BL/6N",
  "production_center" : "EMBL-EBI",
  "external_db_id" : 101,
  "id" : 102,
  "organisation_id" : 103,
  "phenotyping_center_id" : 104,
  "project_id" : 105,
  "male_control_mean" : 0.5,
  "male_mutant_mean" : 1.5,
  "female_control_mean" : 0.4,
  "female_mutant_mean" : 1.4,
  "genotype_effect_size_low_vs_normal_high" : 0.5,
  "genotype_effect_size_low_normal_vs_high" : 0.6,
  "female_effect_size_low_vs_normal_high" : 0.7,
  "female_effect_size_low_normal_vs_high" : 0.8,
  "male_effect_size_low_vs_normal_high" : 0.9,
  "male_effect_size_low_normal_vs_high" : 1.0,
  "categories" : [ "Category 1", "Category 2" ],
  "categorical_p_value" : 0.07,
  "categorical_effect_size" : 1.1,
  "batch_significant" : true,
  "variance_significant" : false,
  "null_test_p_value" : 0.08,
  "genotype_effect_p_value" : 0.09,
  "genotype_effect_stderr_estimate" : 0.1,
  "genotype_effect_parameter_estimate" : 0.11,
  "male_percentage_change" : "10%",
  "female_percentage_change" : "20%",
  "sex_effect_p_value" : 0.12,
  "sex_effect_stderr_estimate" : 0.13,
  "sex_effect_parameter_estimate" : 0.14,
  "weight_effect_p_value" : 0.15,
  "weight_effect_stderr_estimate" : 0.16,
  "weight_effect_parameter_estimate" : 0.17,
  "blups_test" : 0.2,
  "rotated_residuals_test" : 0.21,
  "intercept_estimate" : 0.22,
  "intercept_estimate_stderr_estimate" : 0.23,
  "interaction_significant" : true,
  "interaction_effect_p_value" : 0.24,
  "female_ko_effect_p_value" : 0.25,
  "female_ko_effect_stderr_estimate" : 0.26,
  "female_ko_parameter_estimate" : 0.27,
  "female_effect_size" : 0.28,
  "male_ko_effect_p_value" : 0.29,
  "male_ko_effect_stderr_estimate" : 0.3,
  "male_ko_parameter_estimate" : 0.31,
  "male_effect_size" : 0.32,
  "classification_tag" : "Tag1",
  "phenotype_sex" : [ "Male", "Female" ],
  "life_stage_acc" : "LS:001",
  "life_stage_name" : "Adulthood",
  "significant" : true,
  "soft_windowing_bandwidth" : "Medium",
  "soft_windowing_shape" : "Gaussian",
  "soft_windowing_peaks" : "3",
  "soft_windowing_min_obs_required" : "10",
  "soft_windowing_total_obs_or_weight" : "50",
  "soft_windowing_threshold" : "0.05",
  "soft_windowing_number_of_doe" : "5",
  "soft_windowing_doe_note" : "Doe Note Example",
  "metadata" : [ "Metadata1", "Metadata2" ],
  "effect_size" : 8.3,
  "female_control_count" : 79,
  "female_mutant_count" : 7,
  "female_pvalue_low_normal_vs_high" : 6.3,
  "female_pvalue_low_vs_normal_high" : 8.5,
  "genotype_pvalue_low_normal_vs_high" : 9.2,
  "genotype_pvalue_low_vs_normal_high" : 4.1,
  "group_1_genotype" : "control",
  "group_1_residuals_normality_test" : 4.3,
  "group_2_genotype" : "experimental",
  "group_2_residuals_normality_test" : 4.3,
  "male_control_count" : 23,
  "male_mutant_count" : 21,
  "male_pvalue_low_normal_vs_high" : 9.2,
  "male_pvalue_low_vs_normal_high" : 9.2,
  "p_value" : 0.6,
  "statistical_method" : "Linear Mixed Model framework, LME, including Weight",
  "status" : "Successful"
}

3. Latest updates

  • 2024-04-15: Documentation Added