1. Introduction

2. gene

2.1. Fields

Path Type Description

allele_accession_id

Array

List of accession IDs for alleles.

allele_name

Array

List of names for alleles.

alt_mp_id

Array

List of alternative Mouse Phenotype (MP) IDs.

annotated_higher_level_ma_term_name

Array

List of annotated higher level Mouse Anatomy (MA) term names.

annotated_higher_level_mp_term_name

Array

List of annotated higher level Mouse Phenotype (MP) term names.

assignment_status

String

The assignment status.

ccds_id

Array

List of Consensus CDS (CCDS) IDs.

child_ma_id

Array

List of child Mouse Anatomy (MA) IDs.

child_ma_term

Array

List of child Mouse Anatomy (MA) terms.

child_ma_term_synonym

Array

List of synonyms for child MA terms.

child_mp_id

Array

List of child Mouse Phenotype (MP) IDs.

child_mp_term

Array

List of child MP terms.

child_mp_term_synonym

Array

List of synonyms for child MP terms.

chr_end

Number

Chromosome end position.

chr_name

String

Name of the chromosome.

chr_start

Number

Chromosome start position.

chr_strand

String

Chromosome strand.

clan_acc

Array

List of clan accession numbers.

clan_desc

Array

List of clan descriptions.

clan_id

Array

List of clan IDs.

conditional_allele_production_status

String

Production status of the conditional allele.

crispr_allele_production_status

String

Production status of the CRISPR allele.

data_type

String

The type of data.

datasets_raw_data

String

Raw data from datasets.

disease_alts

Array

List of alternative disease names.

disease_classes

Array

List of disease classes.

disease_human_phenotypes

String

Human phenotypes related to the disease.

disease_id

Array

List of disease IDs.

disease_source

Array

List of sources for disease data.

disease_term

Array

List of disease terms.

dmdd_image_data_available

Boolean

Indicates if DMDD image data is available.

dmdd_lethal_data_available

Boolean

Indicates if DMDD lethal data is available.

embryo_analysis_view_name

String

Name of the embryo analysis view.

embryo_analysis_view_url

String

URL for the embryo analysis view.

embryo_data_available

Boolean

Indicates if embryo data is available.

embryo_modalities

Array

List of modalities for embryo analysis.

ensembl_gene_id

Array

List of Ensembl gene IDs.

es_cell_production_status

String

Production status of the ES cell.

evid_code_rank

Number

Evidence code rank.

exp_name

Array

List of experiment names.

go_count

Number

Count of Gene Ontology (GO) terms associated.

go_term_def

Array

List of GO term definitions.

go_term_domain

Array

List of domains for GO terms.

go_term_evid

Array

List of evidence for GO terms.

go_term_id

Array

List of GO term IDs.

go_term_name

Array

List of GO term names.

go_uniprot

Array

List of UniProt IDs associated with GO terms.

has_qc

Number

Indicates if quality control (QC) has been performed.

hp_id

Array

List of Human Phenotype Ontology (HPO) IDs.

hp_term

Array

List of HPO terms.

human_curated

Array

Indicates if the gene has been curated by human experts.

human_gene_symbol

Array

List of human gene symbols associated with the gene.

human_symbol_synonym

Array

List of human gene Synonym associated with the gene.

impc_novel_predicted_in_locus

Array

Indicates if novel IMPC predictions exist within the gene locus.

impc_predicted

Array

Indicates if there are IMPC predictions for the gene.

impc_predicted_in_locus

String

Specific locus for the IMPC predicted gene.

impc_predicted_known_gene

Array

Indicates if known genes are predicted by IMPC within the locus.

inferred_child_ma_id

Array

List of inferred child Mouse Anatomy (MA) IDs.

inferred_child_ma_term

Array

List of inferred child MA terms.

inferred_child_ma_term_synonym

Array

List of synonyms for the inferred child MA terms.

inferred_ma_id

Array

List of inferred Mouse Anatomy (MA) IDs.

inferred_ma_term

Array

List of inferred MA terms.

inferred_ma_term_synonym

Array

List of synonyms for the inferred MA terms.

inferred_selected_top_level_ma_id

Array

List of IDs for the inferred selected top-level MA terms.

inferred_selected_top_level_ma_term

Array

List of inferred selected top-level MA terms.

inferred_selected_top_level_ma_term_synonym

Array

List of synonyms for the inferred selected top-level MA terms.

intermediate_mp_id

Array

List of intermediate Mouse Phenotype (MP) IDs.

intermediate_mp_term

Array

List of intermediate MP terms.

intermediate_mp_term_synonym

Array

List of synonyms for the intermediate MP terms.

is_idg_gene

Boolean

Indicates if the gene is part of the IDG (Illuminating the Druggable Genome) project.

is_umass_gene

Boolean

Indicates if the gene is associated with the University of Massachusetts.

ma_id

Array

List of Mouse Anatomy (MA) IDs.

ma_term

Array

List of MA terms.

ma_term_definition

Array

List of definitions for the MA terms.

ma_term_synonym

Array

List of synonyms for the MA terms.

marker_name

String

General name of the marker.

marker_symbol

String

Symbol representing the marker.

marker_synonym

Array

List of synonyms for the marker.

marker_type

String

Type of marker.

mgi_accession_id

String

MGI (Mouse Genome Informatics) accession ID for the gene.

mgi_novel_predicted_in_locus

Array

Indicates if novel MGI predictions exist within the gene locus.

mgi_predicted

Array

Indicates if there are MGI predictions for the gene.

mgi_predicted_in_locus

String

Specific locus for the MGI predicted gene.

mgi_predicted_known_gene

Array

Indicates if known genes are predicted by MGI within the locus.

mouse_curated

Array

Indicates if the gene has been curated by mouse experts.

mouse_production_status

String

The production status of the mouse model for the gene.

mp_id

Array

List of Mouse Phenotype (MP) IDs.

mp_term

Array

List of MP terms.

mp_term_definition

Array

List of definitions for the MP terms.

mp_term_synonym

Array

List of synonyms for the MP terms.

ncbi_id

Array

List of NCBI IDs associated with the gene.

not_significant_top_level_mp_terms

Array

List of top-level MP terms not deemed significant.

null_allele_production_status

String

Production status for null alleles.

p_value

Array

List of p-values associated with statistical tests.

parameter_name

Array

List of names for parameters used in experiments.

parameter_stable_id

Array

List of stable IDs for the experimental parameters.

pfama_acc

Array

List of Pfam A accession numbers.

pfama_go_cat

Array

GO categories associated with Pfam A entries.

pfama_go_id

Array

GO IDs associated with Pfam A entries.

pfama_go_term

Array

GO terms associated with Pfam A entries.

pfama_id

Array

List of Pfam A IDs.

pfama_json

Array

JSON data related to Pfam A entries.

phenotype_status

String

Status of the phenotyping effort for the gene.

phenotyping_centre

Array

List of centres where phenotyping has been conducted.

phenotyping_data_available

Boolean

Indicates if phenotyping data is available for the gene.

pipeline_name

Array

List of names for pipelines used in data generation.

pipeline_stable_id

Array

List of stable IDs for the pipelines.

proc_param_name

Array

List of names for procedure parameters.

proc_param_stable_id

Array

List of stable IDs for the procedure parameters.

procedure_name

Array

List of names for procedures.

procedure_stable_id

Array

List of stable IDs for the procedures.

production_centre

Array

List of centres responsible for producing the models.

scdb_id

Array

List of IDs from the Sanger Cancer Database.

scdb_link

Array

List of links to the Sanger Cancer Database.

selected_top_level_ma_id

Array

List of selected top-level Mouse Anatomy (MA) IDs.

selected_top_level_ma_term

Array

List of selected top-level MA terms.

selected_top_level_ma_term_id

String

ID of the selected top-level MA term.

selected_top_level_ma_term_synonym

Array

List of synonyms for the selected top-level MA terms.

seq_region_end

Number

End position on the sequence region.

seq_region_id

String

ID of the sequence region.

seq_region_start

Number

Start position on the sequence region.

significant_top_level_mp_terms

Array

List of significant top-level MP terms.

subtype

Array

List of subtypes associated with the gene.

top_level_mp_definition

String

Definition of the top-level MP term.

top_level_mp_id

Array

List of top-level MP IDs.

top_level_mp_term

Array

List of top-level MP terms.

top_level_mp_term_synonym

Array

List of synonyms for the top-level MP terms.

type

String

The type of document or data.

vega_id

Array

List of VEGA IDs associated with the gene.

xref

Array

List of cross-references for the gene.

2.2. Example Json

HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 6966

{
  "allele_accession_id" : [ "MGI:123456" ],
  "allele_name" : [ "Allele Name 1", "Allele Name 2" ],
  "alt_mp_id" : [ "MP:0000001", "MP:0000002" ],
  "annotated_higher_level_ma_term_name" : [ "Term 1", "Term 2" ],
  "annotated_higher_level_mp_term_name" : [ "Term 3", "Term 4" ],
  "assignment_status" : "Assigned",
  "ccds_id" : [ "CCDS:1234", "CCDS:5678" ],
  "child_ma_id" : [ "MA:0000001", "MA:0000002" ],
  "child_ma_term" : [ "Child MA Term 1", "Child MA Term 2" ],
  "child_ma_term_synonym" : [ "Synonym 1", "Synonym 2" ],
  "child_mp_id" : [ "MP:0000003", "MP:0000004" ],
  "child_mp_term" : [ "Child MP Term 1", "Child MP Term 2" ],
  "child_mp_term_synonym" : [ "Child Synonym 1", "Child Synonym 2" ],
  "chr_end" : 10000,
  "chr_name" : "Chr1",
  "chr_start" : 5000,
  "chr_strand" : "+",
  "clan_acc" : [ "Clan 1", "Clan 2" ],
  "clan_desc" : [ "Clan Desc 1", "Clan Desc 2" ],
  "clan_id" : [ "Clan ID 1", "Clan ID 2" ],
  "conditional_allele_production_status" : "Complete",
  "crispr_allele_production_status" : "Pending",
  "data_type" : "Genomic",
  "datasets_raw_data" : "RawData123",
  "disease_alts" : [ "Disease Alt 1", "Disease Alt 2" ],
  "disease_classes" : [ "Disease Class 1", "Disease Class 2" ],
  "disease_human_phenotypes" : "None",
  "disease_id" : [ "Disease ID 1", "Disease ID 2" ],
  "disease_source" : [ "Source 1", "Source 2" ],
  "disease_term" : [ "Disease Term 1", "Disease Term 2" ],
  "dmdd_image_data_available" : true,
  "dmdd_lethal_data_available" : false,
  "embryo_analysis_view_name" : "EmbryoView1",
  "embryo_analysis_view_url" : "http://example.com/embryo",
  "embryo_data_available" : true,
  "embryo_modalities" : [ "Modality 1", "Modality 2" ],
  "ensembl_gene_id" : [ "ENSG00000123456", "ENSG00000123457" ],
  "es_cell_production_status" : "In Progress",
  "evid_code_rank" : 1,
  "exp_name" : [ "Experiment 1", "Experiment 2" ],
  "go_count" : 5,
  "go_term_def" : [ "GO Definition 1", "GO Definition 2" ],
  "go_term_domain" : [ "Domain 1", "Domain 2" ],
  "go_term_evid" : [ "Evidence 1", "Evidence 2" ],
  "go_term_id" : [ "GO:0000001", "GO:0000002" ],
  "go_term_name" : [ "GO Name 1", "GO Name 2" ],
  "go_uniprot" : [ "UniProt 1", "UniProt 2" ],
  "has_qc" : 1,
  "hp_id" : [ "HP:0000001", "HP:0000002" ],
  "hp_term" : [ "HP Term 1", "HP Term 2" ],
  "human_curated" : [ true, false ],
  "human_gene_symbol" : [ "Gene Symbol 1", "Gene Symbol 2" ],
  "human_symbol_synonym" : [ "Synonym1", "Synonym2" ],
  "impc_novel_predicted_in_locus" : [ true, false ],
  "impc_predicted" : [ true, true ],
  "impc_predicted_in_locus" : "Locus1",
  "impc_predicted_known_gene" : [ true, false ],
  "inferred_child_ma_id" : [ "MA:0000003", "MA:0000004" ],
  "inferred_child_ma_term" : [ "Inferred Child MA Term 1", "Inferred Child MA Term 2" ],
  "inferred_child_ma_term_synonym" : [ "Inferred Synonym 1", "Inferred Synonym 2" ],
  "inferred_ma_id" : [ "MA:0000005", "MA:0000006" ],
  "inferred_ma_term" : [ "Inferred MA Term 1", "Inferred MA Term 2" ],
  "inferred_ma_term_synonym" : [ "Inferred Term Synonym 1", "Inferred Term Synonym 2" ],
  "inferred_selected_top_level_ma_id" : [ "MA:0000007", "MA:0000008" ],
  "inferred_selected_top_level_ma_term" : [ "Selected MA Term 1", "Selected MA Term 2" ],
  "inferred_selected_top_level_ma_term_synonym" : [ "Selected Term Synonym 1", "Selected Term Synonym 2" ],
  "intermediate_mp_id" : [ "MP:0000005", "MP:0000006" ],
  "intermediate_mp_term" : [ "Intermediate MP Term 1", "Intermediate MP Term 2" ],
  "intermediate_mp_term_synonym" : [ "Intermediate MP Synonym 1", "Intermediate MP Synonym 2" ],
  "is_idg_gene" : true,
  "is_umass_gene" : false,
  "ma_id" : [ "MA:0000009", "MA:0000010" ],
  "ma_term" : [ "MA Term 1", "MA Term 2" ],
  "ma_term_definition" : [ "MA Definition 1", "MA Definition 2" ],
  "ma_term_synonym" : [ "MA Synonym 1", "MA Synonym 2" ],
  "marker_name" : "Marker Name Example",
  "marker_symbol" : "MkSym",
  "marker_synonym" : [ "Marker Synonym 1", "Marker Synonym 2" ],
  "marker_type" : "Marker Type Example",
  "mgi_accession_id" : "MGI:0000001",
  "mgi_novel_predicted_in_locus" : [ true, false ],
  "mgi_predicted" : [ false, true ],
  "mgi_predicted_in_locus" : "In Locus Example",
  "mgi_predicted_known_gene" : [ true, true ],
  "mouse_curated" : [ true, false ],
  "mouse_production_status" : "Production Status Example",
  "mp_id" : [ "MP:0000007", "MP:0000008" ],
  "mp_term" : [ "MP Term 1", "MP Term 2" ],
  "mp_term_definition" : [ "MP Definition 1", "MP Definition 2" ],
  "mp_term_synonym" : [ "MP Synonym 1", "MP Synonym 2" ],
  "ncbi_id" : [ "NCBI:0000001", "NCBI:0000002" ],
  "not_significant_top_level_mp_terms" : [ "Not Significant MP Term 1", "Not Significant MP Term 2" ],
  "null_allele_production_status" : "Null Production Status Example",
  "p_value" : [ 0.01, 0.05 ],
  "parameter_name" : [ "Parameter Name 1", "Parameter Name 2" ],
  "parameter_stable_id" : [ "Stable ID 1", "Stable ID 2" ],
  "pfama_acc" : [ "Pfam Acc 1", "Pfam Acc 2" ],
  "pfama_go_cat" : [ "GO Category 1", "GO Category 2" ],
  "pfama_go_id" : [ "GO:0000003", "GO:0000004" ],
  "pfama_go_term" : [ "GO Term 1", "GO Term 2" ],
  "pfama_id" : [ "Pfam ID 1", "Pfam ID 2" ],
  "pfama_json" : [ "{\"key\": \"value\"}", "{\"key\": \"value2\"}" ],
  "phenotype_status" : "Phenotype Status Example",
  "phenotyping_centre" : [ "Centre 1", "Centre 2" ],
  "phenotyping_data_available" : true,
  "pipeline_name" : [ "Pipeline Name 1", "Pipeline Name 2" ],
  "pipeline_stable_id" : [ "Pipeline Stable ID 1", "Pipeline Stable ID 2" ],
  "proc_param_name" : [ "Param Name 1", "Param Name 2" ],
  "proc_param_stable_id" : [ "Param Stable ID 1", "Param Stable ID 2" ],
  "procedure_name" : [ "Procedure Name 1", "Procedure Name 2" ],
  "procedure_stable_id" : [ "Procedure Stable ID 1", "Procedure Stable ID 2" ],
  "production_centre" : [ "Production Centre 1", "Production Centre 2" ],
  "scdb_id" : [ "SCDB ID 1", "SCDB ID 2" ],
  "scdb_link" : [ "http://example.com/scdb1", "http://example.com/scdb2" ],
  "selected_top_level_ma_id" : [ "Selected MA ID 1", "Selected MA ID 2" ],
  "selected_top_level_ma_term" : [ "Selected MA Term 1", "Selected MA Term 2" ],
  "selected_top_level_ma_term_id" : "Selected MA Term ID Example",
  "selected_top_level_ma_term_synonym" : [ "Selected MA Term Synonym 1", "Selected MA Term Synonym 2" ],
  "seq_region_end" : 123456789,
  "seq_region_id" : "Region ID Example",
  "seq_region_start" : 987654321,
  "significant_top_level_mp_terms" : [ "Significant MP Term 1", "Significant MP Term 2" ],
  "subtype" : [ "Subtype 1", "Subtype 2" ],
  "top_level_mp_definition" : "Top Level MP Definition Example",
  "top_level_mp_id" : [ "Top MP ID 1", "Top MP ID 2" ],
  "top_level_mp_term" : [ "Top MP Term 1", "Top MP Term 2" ],
  "top_level_mp_term_synonym" : [ "Top MP Term Synonym 1", "Top MP Term Synonym 2" ],
  "type" : "Type Example",
  "vega_id" : [ "Vega ID 1", "Vega ID 2" ],
  "xref" : [ "Xref 1", "Xref 2" ]
}

3. Latest updates

  • 2024-04-15: Documentation Added