1. Introduction

2. phenodigm

2.1. Fields

Path Type Description

ontology

String

The ontology classification the experiment is associated with.

phenotype_id

String

Unique identifier for the phenotype.

phenotype_term

String

The term or description of the phenotype.

phenotype_synonym

Array

List of synonyms or alternate terms for the phenotype.

hp_id

String

Unique identifier for the human phenotype ontology (HPO) term.

hp_term

String

The term or description of the human phenotype (HP).

mp_id

String

Unique identifier for the mouse phenotype ontology (MPO) term.

mp_term

String

The term or description of the mouse phenotype (MP).

association_curated

Boolean

Boolean indicating if the gene-disease association was curated.

association_ortholog

Boolean

Boolean indicating if the gene-disease association is based on orthology.

marker_symbols_withdrawn

Array

List of withdrawn or obsolete marker symbols.

disease_matched_phenotypes

Array

List of phenotypes matched between the disease and the model.

model_matched_phenotypes

Array

List of phenotypes matched within the model.

disease_model_avg_raw

Number

The average raw score of the disease-model match.

disease_model_avg_norm

Number

The average normalized score of the disease-model match.

disease_model_max_raw

Number

The maximum raw score of the disease-model match.

disease_model_max_norm

Number

The maximum normalized score of the disease-model match.

search_qf

Array

List of fields considered when performing a search query.

human_curated_gene

Boolean

Boolean indicating if the gene has been curated by human effort.

impc_model_with_curated_gene

Boolean

Boolean indicating if the IMPC model includes genes curated by human effort.

mgi_model_with_curated_gene

Boolean

Boolean indicating if the MGI model includes genes curated by human effort.

impc_model_with_computed_association

Boolean

Boolean indicating if the IMPC model includes computed gene-disease associations.

mgi_model_with_computed_association

Boolean

Boolean indicating if the MGI model includes computed gene-disease associations.

type

String

The type classification of the experiment.

disease_id

String

Unique identifier for the associated disease.

disease_source

String

The source of the disease information.

disease_term

String

The term or name of the disease.

disease_alts

Array

Alternative names or identifiers for the disease.

disease_locus

String

The locus associated with the disease.

disease_classes

Array

Classification categories for the disease.

disease_phenotypes

Array

Phenotypic descriptions or identifiers associated with the disease.

gene_id

String

Unique identifier for the gene.

gene_symbol

String

The symbol representing the gene.

gene_symbols_withdrawn

Array

List of withdrawn or obsolete gene symbols.

gene_locus

String

The locus associated with the gene.

hgnc_gene_id

String

HGNC (HUGO Gene Nomenclature Committee) identifier for the gene.

hgnc_gene_symbol

String

HGNC symbol for the gene.

hgnc_gene_symbols_withdrawn

Array

List of withdrawn or obsolete HGNC gene symbols.

hgnc_gene_locus

String

The locus associated with the HGNC gene.

mouse_model

Boolean

Boolean indicating if a mouse model is used.

impc_model

Boolean

Boolean indicating if an IMPC (International Mouse Phenotyping Consortium) model is used.

model_id

String

Unique identifier for the mouse model (MGI gene identifier).

model_source

String

The source of the model.

model_description

String

A description of the model.

model_genetic_background

String

The genetic background of the model.

marker_id

String

Unique identifier for the marker.

marker_symbol

String

The symbol representing the marker.

marker_locus

String

The locus associated with the marker.

marker_num_models

Number

The number of models associated with the marker.

model_phenotypes

Array

Phenotypic descriptions or identifiers associated with the model.

2.2. Example Json

HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 2010

{
  "type" : "TypeExample",
  "disease_id" : "D12345",
  "disease_source" : "SourceExample",
  "disease_term" : "DiseaseTermExample",
  "disease_alts" : [ "Alt1", "Alt2" ],
  "disease_locus" : "LocusExample",
  "disease_classes" : [ "Class1", "Class2" ],
  "disease_phenotypes" : [ "Phenotype1", "Phenotype2" ],
  "gene_id" : "G12345",
  "gene_symbol" : "GeneSymbolExample",
  "gene_symbols_withdrawn" : [ "Withdrawn1", "Withdrawn2" ],
  "gene_locus" : "GeneLocusExample",
  "hgnc_gene_id" : "HGNC123",
  "hgnc_gene_symbol" : "HGNCGeneSymbolExample",
  "hgnc_gene_symbols_withdrawn" : [ "HGNCWithdrawn1" ],
  "hgnc_gene_locus" : "HGNCLocusExample",
  "mouse_model" : true,
  "impc_model" : false,
  "model_id" : "Model12345",
  "model_source" : "ModelSourceExample",
  "model_description" : "ModelDescriptionExample",
  "model_genetic_background" : "GeneticBackgroundExample",
  "marker_id" : "Marker12345",
  "marker_symbol" : "MarkerSymbolExample",
  "marker_locus" : "MarkerLocusExample",
  "marker_num_models" : 2,
  "model_phenotypes" : [ "ModelPhenotype1", "ModelPhenotype2" ],
  "ontology" : "OntologyExample",
  "phenotype_id" : "PhenotypeID12345",
  "phenotype_term" : "PhenotypeTermExample",
  "phenotype_synonym" : [ "Synonym1", "Synonym2" ],
  "hp_id" : "HP12345",
  "hp_term" : "HPTermExample",
  "mp_id" : "MP12345",
  "mp_term" : "MPTermExample",
  "association_curated" : true,
  "association_ortholog" : false,
  "marker_symbols_withdrawn" : [ "MarkerWithdrawn1" ],
  "disease_matched_phenotypes" : [ "MatchedPhenotype1" ],
  "model_matched_phenotypes" : [ "ModelMatchedPhenotype1" ],
  "disease_model_avg_raw" : 0.75,
  "disease_model_avg_norm" : 0.85,
  "disease_model_max_raw" : 0.95,
  "disease_model_max_norm" : 1.0,
  "search_qf" : [ "SearchQFExample1", "SearchQFExample2" ],
  "human_curated_gene" : true,
  "impc_model_with_curated_gene" : false,
  "mgi_model_with_curated_gene" : true,
  "impc_model_with_computed_association" : false,
  "mgi_model_with_computed_association" : true
}

3. Latest updates

  • 2024-04-15: Documentation Added