monarchinitiative

@datafire/monarchinitiative

Client library for BioLink API

Installation and Usage

npm install --save @datafire/monarchinitiative

let monarchinitiative = require('@datafire/monarchinitiative').create();

.then(data => {
  console.log(data);
});

Description

API integration layer for linked biological objects.

Source: https://github.com/biolink/biolink-api/

Actions

get_associations_between

Given two entities (e.g. a particular gene and a particular disease), if these two entities are connected (directly or indirectly), then return the association objects describing the connection.

monarchinitiative.get_associations_between({
  "object": "",
  "subject": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • use_compact_associations boolean: If true, returns results in compact associations format
  • object required string: Return associations pointing to this node, e.g. MP:0013765. Can also be a biological entity such as a gene
  • subject required string: Return associations emanating from this node, e.g. MGI:1342287 (If ID is from an ontology then results would include inferred associations, by default)

Output

• output array
  • items AssociationResults

get_association_by_subject_category_search

Returns list of matching associations for a given subject category

monarchinitiative.get_association_by_subject_category_search({
  "subject_category": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • use_compact_associations boolean: If true, returns results in compact associations format
  • subject_taxon string: Subject taxon ID, e.g. NCBITaxon:9606 (Includes inferred associations, by default)
  • object_taxon string: Object taxon ID, e.g. NCBITaxon:10090 (Includes inferred associations, by default)
  • relation string: Filter by relation CURIE, e.g. RO:0002200 (has_phenotype), RO:0002607 (is marker for), RO:HOM0000017 (orthologous to), etc.
  • subject_category required string: Category of entity at link Subject (source), e.g. gene, disease, phenotype

Output

• output array
  • items AssociationResults

get_association_by_subject_and_object_category_search

Returns list of matching associations between a given subject and object category

monarchinitiative.get_association_by_subject_and_object_category_search({
  "object_category": "",
  "subject_category": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • use_compact_associations boolean: If true, returns results in compact associations format
  • subject string: Subject CURIE
  • object string: Object CURIE
  • subject_taxon string: Subject taxon ID, e.g. NCBITaxon:9606 (Includes inferred associations, by default)
  • object_taxon string: Object taxon ID, e.g. NCBITaxon:10090 (Includes inferred associations, by default)
  • relation string: Filter by relation CURIE, e.g. RO:0002200 (has_phenotype), RO:0002607 (is marker for), RO:HOM0000017 (orthologous to), etc.
  • object_category required string: Category of entity at link Object (target), e.g. gene, disease, phenotype
  • subject_category required string: Category of entity at link Subject (source), e.g. gene, disease, phenotype

Output

• output array
  • items AssociationResults

get_associations_from

Returns list of matching associations starting from a given subject (source)

monarchinitiative.get_associations_from({
  "subject": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • use_compact_associations boolean: If true, returns results in compact associations format
  • object_taxon string: Object taxon ID, e.g. NCBITaxon:10090 (Includes inferred associations, by default)
  • relation string: Filter by relation CURIE, e.g. RO:0002200 (has_phenotype), RO:0002607 (is marker for), RO:HOM0000017 (orthologous to), etc.
  • subject required string: Return associations emanating from this node, e.g. NCBIGene:84570, ZFIN:ZDB-GENE-050417-357 (If ID is from an ontology then results would include inferred associations, by default)

Output

• output array
  • items AssociationResults

get_associations_to

Returns list of matching associations pointing to a given object (target)

monarchinitiative.get_associations_to({
  "object": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • use_compact_associations boolean: If true, returns results in compact associations format
  • object required string: Return associations pointing to this node, e.g. specifying MP:0013765 will return all genes, variants, strains, etc. annotated with this term. Can also be a biological entity such as a gene

Output

• output array
  • items AssociationResults

get_association_by_subject_and_assoc_type

Returns list of matching associations of a given type

monarchinitiative.get_association_by_subject_and_assoc_type({
  "association_type": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • use_compact_associations boolean: If true, returns results in compact associations format
  • subject string: Subject CURIE
  • object string: Object CURIE
  • association_type required string: Association type, eg gene_phenotype

Output

• output array
  • items AssociationResults

get_association_object

An association connects, at a minimum, two things, designated subject and object, via some relationship. Associations also include evidence, provenance etc.

monarchinitiative.get_association_object({
  "id": ""
}, context)

Input

• input object
  • id required string: identifier for an association, e.g. f5ba436c-f851-41b3-9d9d-bb2b5fc879d4

Output

• output array
  • items AssociationResults

get_anatomy_gene_associations

Returns genes associated with a given anatomy

monarchinitiative.get_anatomy_gene_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of anatomical entity, e.g. GO:0005634 (nucleus), UBERON:0002037 (cerebellum), CL:0000540 (neuron). Equivalent IDs can be used with same results

Output

• output AssociationResults

get_anatomy_gene_by_taxon_associations

For example, + NCBITaxon:10090 (mouse)

monarchinitiative.get_anatomy_gene_by_taxon_associations({
  "taxid": "",
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • taxid required string: Species or high level taxon grouping, e.g NCBITaxon:10090 (Mus musculus)
  • id required string: CURIE identifier of anatomical entity, e.g. GO:0005634 (nucleus), UBERON:0002037 (cerebellum), CL:0000540 (neuron). Equivalent IDs can be used with same results

Output

Output schema unknown

get_case_disease_associations

Returns diseases associated with a case

monarchinitiative.get_case_disease_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier for a case

Output

• output AssociationResults

get_case_genotype_associations

Returns genotypes associated with a case

monarchinitiative.get_case_genotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier for a case

Output

• output AssociationResults

get_case_model_associations

Returns models associated with a case

monarchinitiative.get_case_model_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier for a case

Output

• output AssociationResults

get_case_phenotype_associations

Returns phenotypes associated with a case

monarchinitiative.get_case_phenotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier for a case

Output

• output AssociationResults

get_case_variant_associations

Returns variants associated with a case

monarchinitiative.get_case_variant_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier for a case

Output

• output AssociationResults

get_disease_case_associations

Returns cases associated with a disease

monarchinitiative.get_disease_case_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier of disease, e.g. MONDO:0007103, MONDO:0010918. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_disease_gene_associations

Returns genes associated with a disease

monarchinitiative.get_disease_gene_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • association_type string (values: causal, non_causal, both): Additional filters: causal, non_causal, both
  • id required string: CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_disease_genotype_associations

Returns genotypes associated with a disease

monarchinitiative.get_disease_genotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of disease, e.g. Orphanet:399158, DOID:0080008. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_disease_model_associations

In the association object returned, the subject will be the disease, and the object will be the model. The model may be a gene or genetic element.

If the query disease is a general class, the association subject may be to a specific disease.

In some cases the association will be direct, for example if a paper asserts a genotype is a model of a disease.

In other cases, the association will be indirect, for example, chaining over orthology. In these cases the chain will be reflected in the evidence graph

• TODO: provide hook into owlsim for dynamic computation of models by similarity

monarchinitiative.get_disease_model_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_disease_model_taxon_associations

See /disease//models route for full details

monarchinitiative.get_disease_model_taxon_associations({
  "taxon": "",
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon required string: CURIE of organism taxonomy class to constrain models, e.g NCBITaxon:10090 (M. musculus).
  • id required string: CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_disease_pathway_associations

Returns pathways associated with a disease

monarchinitiative.get_disease_pathway_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of disease, e.g. DOID:4450. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_disease_phenotype_associations

Returns phenotypes associated with disease

monarchinitiative.get_disease_phenotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of disease, e.g. OMIM:605543, Orphanet:1934, DOID:678. Equivalent IDs can be used with same results

Output

• output D2PAssociationResults

get_disease_publication_associations

Returns publications associated with a disease

monarchinitiative.get_disease_publication_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_disease_substance_associations

e.g. drugs or small molecules used to treat

monarchinitiative.get_disease_substance_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier of disease, e.g. DOID:2841 (asthma). Equivalent IDs not yet supported

Output

Output schema unknown

get_disease_variant_associations

Returns variants associated with a disease

monarchinitiative.get_disease_variant_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_function_associations

Returns annotations associated to a function term

monarchinitiative.get_function_associations({
  "id": ""
}, context)

Input

• input object
  • start integer: beginning row
  • rows integer: number of rows
  • evidence array: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • id required string: CURIE identifier of a function term (e.g. GO:0044598)

Output

Output schema unknown

get_function_gene_associations

Returns genes associated to a GO term

monarchinitiative.get_function_gene_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • relationship_type string (values: involved_in, involved_in_regulation_of, acts_upstream_of_or_within): relationship type ('involved_in', 'involved_in_regulation_of' or 'acts_upstream_of_or_within')
  • id required string: CURIE identifier of a GO term, e.g. GO:0044598

Output

• output AssociationResults

get_function_publication_associations

Returns publications associated to a GO term

monarchinitiative.get_function_publication_associations({
  "id": ""
}, context)

Input

• input object
  • start integer: beginning row
  • rows integer: number of rows
  • evidence array: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • id required string: CURIE identifier of a GO term, e.g. GO:0044598

Output

Output schema unknown

get_function_taxon_associations

Returns taxons associated to a GO term

monarchinitiative.get_function_taxon_associations({
  "id": ""
}, context)

Input

• input object
  • start integer: beginning row
  • rows integer: number of rows
  • evidence array: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • id required string: CURIE identifier of a GO term, e.g. GO:0044598

Output

Output schema unknown

get_gene_anatomy_associations

Returns anatomical entities associated with a gene

monarchinitiative.get_gene_anatomy_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of gene, e.g. NCBIGene:13434

Output

• output AssociationResults

get_gene_case_associations

Returns cases associated with a gene

monarchinitiative.get_gene_case_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier of gene, e.g. HGNC:613, HGNC:11025

Output

• output AssociationResults

get_gene_disease_associations

Returns diseases associated with gene

monarchinitiative.get_gene_disease_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • association_type string (values: causal, non_causal, both): Additional filters: causal, non_causal, both
  • id required string: CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_gene_expression_associations

Returns expression events for a gene

monarchinitiative.get_gene_expression_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_gene_function_associations

IMPLEMENTATION DETAILS

Note: currently this is implemented as a query to the GO/AmiGO solr instance. This directly supports IDs such as:

• ZFIN e.g. ZFIN:ZDB-GENE-050417-357

Note that the AmiGO GOlr natively stores MGI annotations to MGI:MGI:nn. However, the standard for biolink is MGI:nnnn, so you should use this (will be transparently mapped to legacy ID)

Additionally, for some species such as Human, GO has the annotation attached to the UniProt ID. Again, this should be transparently handled; e.g. you can use NCBIGene:6469, and this will be mapped behind the scenes for querying.

monarchinitiative.get_gene_function_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: id, e.g. NCBIGene:6469. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_gene_genotype_associations

Returns genotypes associated with a gene

monarchinitiative.get_gene_genotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of gene, e.g. ZFIN:ZDB-GENE-980526-166

Output

• output AssociationResults

get_gene_homolog_associations

Returns homologs for a gene

monarchinitiative.get_gene_homolog_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: Taxon CURIE of homolog, e.g. NCBITaxon:9606 (Can be an ancestral node in the ontology; includes inferred associations by default)
  • homology_type string (values: P, O, LDO): P (paralog), O (Ortholog) or LDO (least-diverged ortholog)
  • direct_taxon boolean: Set true to exclude inferred taxa
  • id required string: id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_gene_interactions

Returns interactions for a gene

monarchinitiative.get_gene_interactions({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_gene_model_associations

Returns models associated with a gene

monarchinitiative.get_gene_model_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of gene, e.g. NCBIGene:17988

Output

• output AssociationResults

get_gene_ortholog_disease_associations

Return diseases associated with orthologs of a gene

monarchinitiative.get_gene_ortholog_disease_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of gene, e.g. NCBIGene:4750

Output

• output AssociationResults

get_gene_ortholog_phenotype_associations

Return phenotypes associated with orthologs for a gene

monarchinitiative.get_gene_ortholog_phenotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of gene, e.g. NCBIGene:4750

Output

• output AssociationResults

get_gene_pathway_associations

Returns pathways associated with gene

monarchinitiative.get_gene_pathway_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of gene, e.g. NCBIGene:50846. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_gene_phenotype_associations

Returns phenotypes associated with gene

monarchinitiative.get_gene_phenotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results

Output

• output AssociationResults

get_gene_publication_associations

Returns publications associated with a gene

monarchinitiative.get_gene_publication_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of gene, e.g. NCBIGene:4750

Output

• output AssociationResults

get_gene_variant_associations

Returns variants associated with a gene

monarchinitiative.get_gene_variant_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of gene, e.g. HGNC:10896

Output

• output AssociationResults

get_genotype_case_associations

Returns cases associated with a genotype

monarchinitiative.get_genotype_case_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier of genotype, e.g. dbSNPIndividual:10440, dbSNPIndividual:22633

Output

• output AssociationResults

get_genotype_disease_associations

Returns diseases associated with a genotype

monarchinitiative.get_genotype_disease_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of genotype, e.g. dbSNPIndividual:11441 (if non-human will return models)

Output

• output AssociationResults

get_genotype_gene_associations

Returns genes associated with a genotype

monarchinitiative.get_genotype_gene_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607

Output

• output AssociationResults

get_genotype_genotype_associations

Genotypes may be related to one another according to the GENO model

monarchinitiative.get_genotype_genotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607

Output

• output AssociationResults

get_genotype_model_associations

Returns models associated with a genotype

monarchinitiative.get_genotype_model_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607

Output

• output AssociationResults

get_genotype_phenotype_associations

Returns phenotypes associated with a genotype

monarchinitiative.get_genotype_phenotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286

Output

• output AssociationResults

get_genotype_publication_associations

Returns publications associated with a genotype

monarchinitiative.get_genotype_publication_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607

Output

• output AssociationResults

get_genotype_variant_associations

Returns genotypes-variant associations

monarchinitiative.get_genotype_variant_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of genotype, e.g. MONARCH:FBgeno422705

Output

• output AssociationResults

get_goterm_gene_associations

Returns associations to GO terms for a gene

monarchinitiative.get_goterm_gene_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • relationship_type string (values: involved_in, involved_in_regulation_of, acts_upstream_of_or_within): relationship type ('involved_in', 'involved_in_regulation_of' or 'acts_upstream_of_or_within')
  • id required string: CURIE identifier of a GO term, e.g. GO:0044598

Output

• output AssociationResults

get_model_case_associations

Returns cases associated with a model

monarchinitiative.get_model_case_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier for a model, e.g. Coriell:GM22295, Coriell:HG02187

Output

• output AssociationResults

get_model_disease_associations

Returns diseases associated with a model

monarchinitiative.get_model_disease_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier for a model, e.g. MGI:5573196

Output

• output AssociationResults

get_model_gene_associations

Returns genes associated with a model

monarchinitiative.get_model_gene_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier for a model, e.g. MMRRC:042787

Output

• output AssociationResults

get_model_genotype_associations

Returns genotypes associated with a model

monarchinitiative.get_model_genotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier for a model, e.g. Coriell:NA16660

Output

• output AssociationResults

get_model_phenotype_associations

Returns phenotypes associated with a model

monarchinitiative.get_model_phenotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: id

Output

• output AssociationResults

get_model_publication_associations

Returns publications associated with a model

monarchinitiative.get_model_publication_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier for a model, e.g. MGI:5644542

Output

• output AssociationResults

get_model_variant_associations

Returns variants associated with a model

monarchinitiative.get_model_variant_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier for a model, e.g. MMRRC:042787

Output

• output AssociationResults

get_pathway_disease_associations

Returns diseases associated with a pathway

monarchinitiative.get_pathway_disease_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE any pathway element. E.g. REACT:R-HSA-5387390

Output

• output AssociationResults

get_pathway_gene_associations

Returns genes associated with a pathway

monarchinitiative.get_pathway_gene_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE any pathway element. E.g. REACT:R-HSA-5387390

Output

• output AssociationResults

get_pathway_phenotype_associations

Returns phenotypes associated with a pathway

monarchinitiative.get_pathway_phenotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE any pathway element. E.g. REACT:R-HSA-5387390

Output

• output AssociationResults

get_phenotype_anatomy_associations

Example IDs:

• MP:0008521 abnormal Bowman membrane

monarchinitiative.get_phenotype_anatomy_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier of phenotype, e.g. MP:0008521. Equivalent IDs can be used with same results

Output

• output array
  • items NamedObject

get_phenotype_case_associations

Returns cases associated with a phenotype

monarchinitiative.get_phenotype_case_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: Pheno class CURIE identifier, e.g HP:0011951 (Aspiration pneumonia), HP:0002450 (Abnormal motor neuron morphology)

Output

• output AssociationResults

get_phenotype_disease_associations

Returns diseases associated with a phenotype

monarchinitiative.get_phenotype_disease_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of phenotype, e.g. HP:0007359. Equivalent IDs can be used with same results

Output

• output D2PAssociationResults

get_phenotype_gene_by_taxon_associations

For example, MP:0001569 + NCBITaxon:10090 (mouse)

monarchinitiative.get_phenotype_gene_by_taxon_associations({
  "taxid": "",
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxid required string: Species or high level taxon grouping, e.g NCBITaxon:10090 (Mus musculus)
  • id required string: Pheno class CURIE identifier, e.g MP:0001569 (abnormal circulating bilirubin level)

Output

Output schema unknown

get_phenotype_gene_associations

Returns genes associated with a phenotype

monarchinitiative.get_phenotype_gene_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level),

Output

• output AssociationResults

get_phenotype_genotype_associations

Returns genotypes associated with a phenotype

monarchinitiative.get_phenotype_genotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)

Output

• output AssociationResults

get_phenotype_pathway_associations

Returns pathways associated with a phenotype

monarchinitiative.get_phenotype_pathway_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: Pheno class CURIE identifier, e.g MP:0001569 (abnormal circulating bilirubin level)

Output

• output AssociationResults

get_phenotype_publication_associations

Returns publications associated with a phenotype

monarchinitiative.get_phenotype_publication_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)

Output

• output AssociationResults

get_phenotype_variant_associations

Returns variants associated with a phenotype

monarchinitiative.get_phenotype_variant_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)

Output

• output AssociationResults

get_publication_disease_associations

Returns diseases associated with a publication

monarchinitiative.get_publication_disease_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier for a publication, e.g. PMID:11751940

Output

• output AssociationResults

get_publication_gene_associations

Returns genes associated with a publication

monarchinitiative.get_publication_gene_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier for a publication, e.g. PMID:11751940

Output

• output AssociationResults

get_publication_genotype_associations

Returns genotypes associated with a publication

monarchinitiative.get_publication_genotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier for a publication, e.g. PMID:11751940

Output

• output AssociationResults

get_publication_model_associations

Returns models associated with a publication

monarchinitiative.get_publication_model_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier for a publication, e.g. PMID:11751940

Output

• output AssociationResults

get_publication_phenotype_associations

Returns phenotypes associated with a publication

monarchinitiative.get_publication_phenotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier for a publication, e.g. PMID:11751940

Output

• output AssociationResults

get_publication_variant_associations

Returns variants associated with a publication

monarchinitiative.get_publication_variant_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier for a publication, e.g. PMID:11751940

Output

• output AssociationResults

get_substance_participant_in_associations

Examples relationships:

• substance is a metabolite of a process
• substance is synthesized by a process
• substance is modified by an activity
• substance elicits a response program/pathway
• substance is transported by activity or pathway

For example, CHEBI:40036 (amitrole)

monarchinitiative.get_substance_participant_in_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier of substance, e.g. CHEBI:40036

Output

• output array
  • items Association

get_substance_role_associations

Roles may be human-oriented (e.g. pesticide) or molecular (e.g. enzyme inhibitor)

monarchinitiative.get_substance_role_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier of substance, e.g. CHEBI:40036

Output

• output array
  • items Association

get_substance_treats_associations

e.g. drugs or small molecules used to treat

monarchinitiative.get_substance_treats_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier of substance, e.g. CHEBI:40036

Output

Output schema unknown

get_variant_case_associations

Returns cases associated with a variant

monarchinitiative.get_variant_case_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier of variant, e.g. OMIM:309550.0004, dbSNP:rs5030868

Output

• output AssociationResults

get_variant_disease_associations

Returns diseases associated with a variant

monarchinitiative.get_variant_disease_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of variant, e.g. ClinVarVariant:14925

Output

• output AssociationResults

get_variant_gene_associations

Returns genes associated with a variant

monarchinitiative.get_variant_gene_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783

Output

• output AssociationResults

get_variant_genotype_associations

Returns genotypes associated with a variant

monarchinitiative.get_variant_genotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8

Output

• output AssociationResults

get_variant_model_associations

Returns models associated with a variant

monarchinitiative.get_variant_model_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: CURIE identifier of variant, e.g. OMIM:607623.0012, dbSNP:rs5030868

Output

• output AssociationResults

get_variant_phenotype_associations

Returns phenotypes associated with a variant

monarchinitiative.get_variant_phenotype_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783

Output

• output AssociationResults

get_variant_publication_associations

Returns publications associated with a variant

monarchinitiative.get_variant_publication_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string: CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783

Output

• output AssociationResults

get_generic_object

Returns basic info on object of any type

monarchinitiative.get_generic_object({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • id required string: id, e.g. NCBIGene:84570

Output

• output BioObject

get_generic_associations

Returns associations for an entity regardless of the type

monarchinitiative.get_generic_associations({
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • taxon array: One or more taxon CURIE to filter associations by subject taxon; includes inferred associations by default
  • direct_taxon boolean: Set true to exclude inferred taxa
  • relation string: A relation CURIE to filter associations
  • sort string: Sorting responses <desc,asc>
  • q string: Query string to filter documents
  • id required string

Output

• output AssociationResults

get_generic_object_by_type

Return basic info on an object for a given type

monarchinitiative.get_generic_object_by_type({
  "type": "",
  "id": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start integer: beginning row
  • facet boolean: Enable faceting
  • facet_fields array: Fields to facet on
  • unselect_evidence boolean: If true, excludes evidence objects in response
  • exclude_automatic_assertions boolean: If true, excludes associations that involve IEAs (ECO:0000501)
  • fetch_objects boolean: If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload
  • use_compact_associations boolean: If true, returns results in compact associations format
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default) or a specific publication or other supporting object, e.g. ZFIN:ZDB-PUB-060503-2
  • direct boolean: Set true to only include direct associations, and false to include inferred (via subclass or subclass|part of), default=False
  • get_association_counts boolean: Get association counts
  • distinct_counts boolean: Get distinct counts for associations (to be used in conjunction with 'get_association_counts' parameter)
  • type required string (values: gene, variant, genotype, phenotype, disease, goterm, pathway, anatomy, substance, individual, publication, model, case): bioentity type
  • id required string: id, e.g. NCBIGene:84570

Output

Output schema unknown

get_entity_set_associations

Returns compact associations for a given input set

monarchinitiative.get_entity_set_associations({}, context)

Input

• input object
  • subject array: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
  • background array: Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests
  • object_category string: E.g. phenotype, function
  • object_slim string: Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED

Output

• output array
  • items AssociationResults

get_entity_set_summary

Summary statistics for objects associated

monarchinitiative.get_entity_set_summary({}, context)

Input

• input object
  • subject array: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
  • background array: Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests
  • object_category string: E.g. phenotype, function
  • object_slim string: Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED

Output

Output schema unknown

get_entity_set_graph_resource

TODO Graph object spanning all entities

monarchinitiative.get_entity_set_graph_resource({}, context)

Input

• input object
  • subject array: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
  • background array: Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests
  • object_category string: E.g. phenotype, function
  • object_slim string: Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED

Output

Output schema unknown

get_entity_set_homologs

Returns homology associations for a given input set of genes

monarchinitiative.get_entity_set_homologs({}, context)

Input

• input object
  • subject array: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387

Output

• output array
  • items AssociationResults

get_over_representation

Summary statistics for objects associated

monarchinitiative.get_over_representation({}, context)

Input

• input object
  • object_category string: E.g. phenotype, function
  • subject array: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
  • background array: Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests
  • subject_category string: Default: gene. Other types may be used e.g. disease but statistics may not make sense
  • max_p_value string: Exclude results with p-value greater than this
  • ontology string: ontology id. Must be obo id. Examples: go, mp, hp, uberon (optional: will be inferred if left blank)
  • taxon string: must be NCBITaxon CURIE. Example: NCBITaxon:9606

Output

Output schema unknown

get_entity_set_anatomy_slimmer

For a given gene(s), summarize its annotations over a defined set of slim

monarchinitiative.get_entity_set_anatomy_slimmer({
  "subject": [],
  "slim": []
}, context)

Input

• input object
  • subject required array: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
  • slim required array: Map objects up (slim) to a higher level category. Value can be ontology class ID (IMPLEMENTED) or subset ID (TODO)
  • exclude_automatic_assertions boolean: If set, excludes associations that involve IEAs (ECO:0000501)
  • rows integer: number of rows
  • start integer: beginning row

Output

Output schema unknown

get_entity_set_function_slimmer

For a given gene(s), summarize its annotations over a defined set of slim

monarchinitiative.get_entity_set_function_slimmer({
  "subject": [],
  "slim": []
}, context)

Input

• input object
  • relationship_type string (values: involved_in, acts_upstream_of_or_within): relationship type ('involved_in' or 'acts_upstream_of_or_within')
  • subject required array: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
  • slim required array: Map objects up (slim) to a higher level category. Value can be ontology class ID (IMPLEMENTED) or subset ID (TODO)
  • exclude_automatic_assertions boolean: If set, excludes associations that involve IEAs (ECO:0000501)
  • rows integer: number of rows
  • start integer: beginning row

Output

Output schema unknown

get_entity_set_phenotype_slimmer

For a given gene(s), summarize its annotations over a defined set of slim

monarchinitiative.get_entity_set_phenotype_slimmer({
  "subject": [],
  "slim": []
}, context)

Input

• input object
  • subject required array: Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387
  • slim required array: Map objects up (slim) to a higher level category. Value can be ontology class ID (IMPLEMENTED) or subset ID (TODO)
  • exclude_automatic_assertions boolean: If set, excludes associations that involve IEAs (ECO:0000501)
  • rows integer: number of rows
  • start integer: beginning row

Output

Output schema unknown

get_activity_collection

Returns list of models

monarchinitiative.get_activity_collection({}, context)

Input

• input object
  • title string: string to search for in title of model
  • contributor string: string to search for in contributor of model

Output

Output schema unknown

get_instance_object

Returns list of matches

monarchinitiative.get_instance_object({
  "id": ""
}, context)

Input

• input object
  • title string: string to search for in title of model
  • contributor string: string to search for in contributor of model
  • id required string

Output

• output array
  • items Association

get_model_instances

Returns list of all instances

monarchinitiative.get_model_instances(null, context)

Input

This action has no parameters

Output

Output schema unknown

get_model_collection

Returns list of ALL models

monarchinitiative.get_model_collection(null, context)

Input

This action has no parameters

Output

Output schema unknown

get_model_contributors

Returns list of all contributors across all models

monarchinitiative.get_model_contributors(null, context)

Input

This action has no parameters

Output

Output schema unknown

get_model_properties

Returns list of all properties used across all models

monarchinitiative.get_model_properties({}, context)

Input

• input object
  • title string: string to search for in title of model
  • contributor string: string to search for in contributor of model

Output

Output schema unknown

get_model_property_values

Returns list property-values for all models

monarchinitiative.get_model_property_values({}, context)

Input

• input object
  • title string: string to search for in title of model
  • contributor string: string to search for in contributor of model

Output

Output schema unknown

get_model_query

Returns list of models matching query

monarchinitiative.get_model_query({}, context)

Input

• input object
  • title string: string to search for in title of model
  • contributor string: string to search for in contributor of model

Output

Output schema unknown

get_model_object

Returns a complete model

monarchinitiative.get_model_object({
  "id": ""
}, context)

Input

• input object
  • id required string

Output

Output schema unknown

get_physical_interaction

Returns list of models

monarchinitiative.get_physical_interaction({}, context)

Input

• input object
  • title string: string to search for in title of model
  • contributor string: string to search for in contributor of model

Output

Output schema unknown

get_evidence_graph_object

Note that every association is assumed to have a unique ID

monarchinitiative.get_evidence_graph_object({
  "id": ""
}, context)

Input

• input object
  • id required string: association id, e.g. 68e686f6-d05b-46b8-ab1f-1da2fff97ada

Output

• output array
  • items Graph

get_evidence_graph_table

Note that every association is assumed to have a unique ID

monarchinitiative.get_evidence_graph_table({
  "id": ""
}, context)

Input

• input object
  • is_publication boolean: If true, considers dc:source as edge
  • id required string: association id, e.g. 68e686f6-d05b-46b8-ab1f-1da2fff97ada

Output

• output array
  • items AssociationResults

get_features_within_resource

Returns list of matches

monarchinitiative.get_features_within_resource({
  "build": "",
  "reference": "",
  "begin": "",
  "end": ""
}, context)

Input

• input object
  • build required string
  • reference required string
  • begin required string
  • end required string

Output

• output array
  • items SequenceFeature

get_edge_resource

Returns edges emanating from a given node

monarchinitiative.get_edge_resource({
  "id": ""
}, context)

Input

• input object
  • depth integer: How far to traverse for neighbors
  • direction string (values: INCOMING, OUTGOING, BOTH): Which direction to traverse (used only if relationship_type is defined)
  • relationship_type array: Relationship type to traverse
  • entail boolean: Include sub-properties and equivalent properties
  • graph string (values: data, ontology): Which monarch graph to query
  • id required string: CURIE e.g. HP:0000465

Output

• output array
  • items Graph

get_node_resource

A node is an abstract representation of some kind of entity. The entity may be a physical thing such as a patient, a molecular entity such as a gene or protein, or a conceptual entity such as a class from an ontology.

monarchinitiative.get_node_resource({
  "id": ""
}, context)

Input

• input object
  • id required string: CURIE e.g. HP:0000465

Output

• output array
  • items BioObject

get_identifier_mapper

TODO maps a list of identifiers from a source to a target

monarchinitiative.get_identifier_mapper({
  "source": "",
  "target": ""
}, context)

Input

• input object
  • source required string
  • target required string

Output

• output array
  • items Association

get_prefix_collection

Returns list of prefixes

monarchinitiative.get_prefix_collection(null, context)

Input

This action has no parameters

Output

Output schema unknown

get_prefix_contract

Returns contracted URI

monarchinitiative.get_prefix_contract({
  "uri": ""
}, context)

Input

• input object
  • uri required string: URI of entity to be contracted to identifier/CURIE, e.g "http://www.informatics.jax.org/accession/MGI:1"

Output

Output schema unknown

get_prefix_expand

Returns expanded URI

monarchinitiative.get_prefix_expand({
  "id": ""
}, context)

Input

• input object
  • id required string: ID of entity to be contracted to URI, e.g "MGI:1"

Output

Output schema unknown

get_pedigree

Returns list of matches

monarchinitiative.get_pedigree({
  "id": ""
}, context)

Input

• input object
  • id required string

Output

• output array
  • items Association

get_individual

Returns list of matches

monarchinitiative.get_individual({
  "id": ""
}, context)

Input

• input object
  • id required string

Output

• output array
  • items Association

get_mart_case_associations_resource

NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.

monarchinitiative.get_mart_case_associations_resource({
  "taxon": "",
  "object_category": ""
}, context)

Input

• input object
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • taxon required string: taxon of case, must be of form NCBITaxon:9606
  • object_category required string: Category of entity at link Subject (target), e.g. phenotype, disease

Output

Output schema unknown

get_mart_disease_associations_resource

NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.

monarchinitiative.get_mart_disease_associations_resource({
  "taxon": "",
  "object_category": ""
}, context)

Input

• input object
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • taxon required string: taxon of disease, must be of form NCBITaxon:9606
  • object_category required string: Category of entity at link Object (target), e.g. phenotype, disease

Output

Output schema unknown

get_mart_gene_associations_resource

NOTE: this route has a limiter on it, you may be restricted in the number of downloads per hour. Use carefully.

monarchinitiative.get_mart_gene_associations_resource({
  "taxon": "",
  "object_category": ""
}, context)

Input

• input object
  • slim array: Map objects up (slim) to a higher level category. Value can be ontology class ID or subset ID
  • taxon required string: taxon of gene, must be of form NCBITaxon:9606
  • object_category required string: Category of entity at link Object (target), e.g. phenotype, disease

Output

Output schema unknown

get_mart_ortholog_associations_resource

Bulk download of orthologs

monarchinitiative.get_mart_ortholog_associations_resource({
  "taxon2": "",
  "taxon1": ""
}, context)

Input

• input object
  • taxon2 required string: object taxon, e.g. NCBITaxon:10090
  • taxon1 required string: subject taxon, e.g. NCBITaxon:9606

Output

Output schema unknown

get_mart_paralog_associations_resource

Bulk download of paralogs

monarchinitiative.get_mart_paralog_associations_resource({
  "taxon2": "",
  "taxon1": ""
}, context)

Input

• input object
  • taxon2 required string: object taxon, e.g. NCBITaxon:9606
  • taxon1 required string: subject taxon, e.g. NCBITaxon:9606

Output

Output schema unknown

get_metadata_for_datasets

Get metadata for all datasets from SciGraph

monarchinitiative.get_metadata_for_datasets(null, context)

Input

This action has no parameters

Output

Output schema unknown

get_annotate

Annotate a given text using SciGraph annotator

monarchinitiative.get_annotate({}, context)

Input

• input object
  • content string: The text content to annotate
  • include_category array: Categories to include for annotation
  • exclude_category array: Categories to exclude for annotation
  • min_length string: The minimum number of characters in the annotated entity
  • longest_only boolean: Should only the longest entity be returned for an overlapping group
  • include_abbreviation boolean: Should abbreviations be included
  • include_acronym boolean: Should acronyms be included
  • include_numbers boolean: Should numbers be included

Output

Output schema unknown

post_annotate

Annotate a given text using SciGraph annotator

monarchinitiative.post_annotate({}, context)

Input

• input object
  • content string: The text content to annotate
  • include_category array: Categories to include for annotation
  • exclude_category array: Categories to exclude for annotation
  • min_length string: The minimum number of characters in the annotated entity
  • longest_only boolean: Should only the longest entity be returned for an overlapping group
  • include_abbreviation boolean: Should abbreviations be included
  • include_acronym boolean: Should acronyms be included
  • include_numbers boolean: Should numbers be included

Output

Output schema unknown

get_annotate_entities

Annotate a given content using SciGraph annotator and get all entities from content

monarchinitiative.get_annotate_entities({}, context)

Input

• input object
  • content string: The text content to annotate
  • include_category array: Categories to include for annotation
  • exclude_category array: Categories to exclude for annotation
  • min_length string: The minimum number of characters in the annotated entity
  • longest_only boolean: Should only the longest entity be returned for an overlapping group
  • include_abbreviation boolean: Should abbreviations be included
  • include_acronym boolean: Should acronyms be included
  • include_numbers boolean: Should numbers be included

Output

• output EntityAnnotationResult

post_annotate_entities

Annotate a given content using SciGraph annotator and get all entities from content

monarchinitiative.post_annotate_entities({}, context)

Input

• input object
  • content string: The text content to annotate
  • include_category array: Categories to include for annotation
  • exclude_category array: Categories to exclude for annotation
  • min_length string: The minimum number of characters in the annotated entity
  • longest_only boolean: Should only the longest entity be returned for an overlapping group
  • include_abbreviation boolean: Should abbreviations be included
  • include_acronym boolean: Should acronyms be included
  • include_numbers boolean: Should numbers be included

Output

• output EntityAnnotationResult

get_information_content_resource

IC = -log2( freq(t) / popSize )

Here the frequency and population is calculated for a particular dataset: e.g. all human disease-phenotype associations

monarchinitiative.get_information_content_resource({
  "subject_category": "",
  "object_category": "",
  "subject_taxon": ""
}, context)

Input

• input object
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)
  • subject_category required string
  • object_category required string
  • subject_taxon required string

Output

Output schema unknown

get_ontol_labeler_resource

Fetches a map from CURIEs/IDs to labels

monarchinitiative.get_ontol_labeler_resource({}, context)

Input

• input object
  • id array: List of ids

Output

Output schema unknown

get_extract_ontology_subgraph_resource

Extract a subgraph from an ontology

monarchinitiative.get_extract_ontology_subgraph_resource({
  "node": "",
  "ontology": ""
}, context)

Input

• input object
  • cnode array: Additional classes
  • include_ancestors boolean: Include Ancestors
  • include_descendants boolean: Include Descendants
  • relation array: Additional classes
  • include_meta boolean: Include metadata in response
  • node required string: class ID, e.g. HP:0001288
  • ontology required string: ontology ID, e.g. go, uberon, mp, hp

Output

Output schema unknown

post_extract_ontology_subgraph_resource

Extract a subgraph from an ontology

monarchinitiative.post_extract_ontology_subgraph_resource({
  "node": "",
  "ontology": ""
}, context)

Input

• input object
  • cnode array: Additional classes
  • include_ancestors boolean: Include Ancestors
  • include_descendants boolean: Include Descendants
  • relation array: Additional classes
  • include_meta boolean: Include metadata in response
  • node required string: class ID, e.g. HP:0001288
  • ontology required string: ontology ID, e.g. go, uberon, mp, hp

Output

Output schema unknown

get_ontology_terms_shared_ancestor

Returns the ancestor ontology terms shared by two ontology terms

monarchinitiative.get_ontology_terms_shared_ancestor({
  "subject": "",
  "object": ""
}, context)

Input

• input object
  • subject required string: CURIE identifier of a GO term, e.g. GO:0006259
  • object required string: CURIE identifier of a GO term, e.g. GO:0046483

Output

Output schema unknown

get_ontology_subset

Returns meta data of an ontology subset (slim)

monarchinitiative.get_ontology_subset({
  "id": ""
}, context)

Input

• input object
  • id required string: name of a slim subset, e.g. goslim_agr, goslim_generic

Output

Output schema unknown

get_ontology_term

Returns meta data of an ontology term

monarchinitiative.get_ontology_term({
  "id": ""
}, context)

Input

• input object
  • id required string: CURIE identifier of a GO term, e.g. GO:0003677

Output

Output schema unknown

get_ontology_term_graph

Returns graph of an ontology term

monarchinitiative.get_ontology_term_graph({
  "id": ""
}, context)

Input

• input object
  • graph_type string (values: topology_graph, regulates_transitivity_graph, neighborhood_graph, neighborhood_limited_graph): graph type ('topology_graph', 'regulates_transitivity_graph' or 'neighborhood_graph')
  • id required string: CURIE identifier of a GO term, e.g. GO:0000981

Output

Output schema unknown

get_ontology_term_subgraph

Extract a subgraph from an ontology term

monarchinitiative.get_ontology_term_subgraph({
  "id": ""
}, context)

Input

• input object
  • cnode array: Additional classes
  • include_ancestors boolean: Include Ancestors
  • include_descendants boolean: Include Descendants
  • relation array: Additional classes
  • include_meta boolean: Include metadata in response
  • id required string: CURIE identifier of a GO term, e.g. GO:0007275

Output

Output schema unknown

get_ontology_term_subsets

Returns subsets (slims) associated to an ontology term

monarchinitiative.get_ontology_term_subsets({
  "id": ""
}, context)

Input

• input object
  • id required string: CURIE identifier of a GO term, e.g. GO:0006259

Output

Output schema unknown

get_dl_query

Placeholder - use OWLery for now

monarchinitiative.get_dl_query({
  "query": ""
}, context)

Input

• input object
  • query required string

Output

• output array
  • items Association

get_sparql_query

Placeholder - use direct SPARQL endpoint for now

monarchinitiative.get_sparql_query({
  "query": ""
}, context)

Input

• input object
  • query required string

Output

• output array
  • items Association

get_pair_sim_jaccard_resource

Get pairwise similarity

monarchinitiative.get_pair_sim_jaccard_resource({
  "id2": "",
  "id1": ""
}, context)

Input

• input object
  • object_category string: e.g. disease, phenotype, gene. Two subjects will be compared based on overlap between associations to objects in this category
  • id2 required string: id, e.g. NCBIGene:1200; ZFIN:ZDB-GENE-980528-2059; UniProtKB:P12644
  • id1 required string: id, e.g. NCBIGene:10891; ZFIN:ZDB-GENE-980526-166; UniProtKB:Q15465

Output

Output schema unknown

get_relation_usage_resource

All relations used plus count of associations

monarchinitiative.get_relation_usage_resource({}, context)

Input

• input object
  • subject_taxon string: SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)

Output

• output array
  • items AssociationResults

get_relation_usage_between_resource

All relations used plus count of associations

monarchinitiative.get_relation_usage_between_resource({
  "subject_category": "",
  "object_category": ""
}, context)

Input

• input object
  • subject_taxon string: SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)
  • subject_category required string
  • object_category required string

Output

• output array
  • items AssociationResults

get_relation_usage_pivot_resource

Relation usage count for all subj x obj category combinations

monarchinitiative.get_relation_usage_pivot_resource({}, context)

Input

• input object
  • subject_taxon string: SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)

Output

• output array
  • items AssociationResults

get_relation_usage_pivot_label_resource

Relation usage count for all subj x obj category combinations, showing label

monarchinitiative.get_relation_usage_pivot_label_resource({}, context)

Input

• input object
  • subject_taxon string: SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
  • evidence string: Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)

Output

• output array
  • items AssociationResults

get_autocomplete

Returns list of matching concepts or entities using lexical search

monarchinitiative.get_autocomplete({
  "term": ""
}, context)

Input

• input object
  • fq array: fq string passed directly to solr, note that multiple filters will be combined with an AND operator. Combining fq_string with other parameters may result in unexpected behavior.
  • category array: e.g. gene, disease
  • prefix array: ontology prefix: HP, -MONDO
  • boost_fx array: boost function e.g. pow(edges,0.334)
  • boost_q array: boost query e.g. category:genotype^-10
  • taxon array: taxon filter, eg NCBITaxon:9606, includes inferred taxa
  • rows integer: number of rows
  • start string: row number to start from
  • highlight_class string: highlight class
  • min_match string: minimum should match parameter, see solr docs for details
  • minimal_tokenizer boolean: set to true to use the minimal tokenizer, good for variants and genotypes
  • term required string

Output

• output AutocompleteResults

get_search_hpo_entities

Returns list of matching concepts or entities using lexical search

monarchinitiative.get_search_hpo_entities({
  "term": ""
}, context)

Input

• input object
  • rows integer: number of rows
  • start string: row number to start from
  • phenotype_group string: phenotype group id
  • phenotype_group_label string: phenotype group label
  • anatomical_system string: anatomical system id
  • anatomical_system_label string: anatomical system label
  • highlight_class string: highlight class
  • term required string: search string, e.g. muscle atrophy, frequent infections

Output

• output LayResults

get_search_entities

Returns list of matching concepts or entities using lexical search

monarchinitiative.get_search_entities({
  "term": ""
}, context)

Input

• input object
  • fq array: fq string passed directly to solr, note that multiple filters will be combined with an AND operator. Combining fq_string with other parameters may result in unexpected behavior.
  • category array: e.g. gene, disease
  • prefix array: ontology prefix: HP, -MONDO
  • boost_fx array: boost function e.g. pow(edges,0.334)
  • boost_q array: boost query e.g. category:genotype^-10
  • taxon array: taxon filter, eg NCBITaxon:9606, includes inferred taxa
  • rows integer: number of rows
  • start string: row number to start from
  • highlight_class string: highlight class
  • min_match string: minimum should match parameter, see solr docs for details
  • minimal_tokenizer boolean: set to true to use the minimal tokenizer, good for variants and genotypes
  • term required string: search string, e.g. shh, parkinson, femur

Output

• output SearchResult

get_sim_compare

Compare a reference profile vs one profiles

monarchinitiative.get_sim_compare({}, context)

Input

• input object
  • is_feature_set boolean: set to true if all input ids are phenotypic features, else set to false
  • metric string (values: phenodigm, jaccard, simGIC, resnik, symmetric_resnik): Metric for computing similarity
  • ref_id array: A phenotype or identifier that is composed of phenotypes (eg disease, gene)
  • query_id array: A phenotype or identifier that is composed of phenotypes (eg disease, gene)

Output

• output SimResult

post_sim_compare

Compare a reference profile vs one or more profiles

monarchinitiative.post_sim_compare({
  "body": {}
}, context)

Input

• input object
  • body required CompareInput

Output

• output SimResult

get_annotation_score

Get annotation score

monarchinitiative.get_annotation_score({}, context)

Input

• input object
  • id array: Phenotype identifier (eg HP:0004935)
  • absent_id array: absent phenotype (eg HP:0002828)

Output

• output SufficiencyOutput

post_annotation_score

Get annotation score

monarchinitiative.post_annotation_score({
  "body": {}
}, context)

Input

• input object
  • body required SufficiencyPostInput

Output

• output SufficiencyOutput

get_sim_search

Search for phenotypically similar diseases or model genes

monarchinitiative.get_sim_search({}, context)

Input

• input object
  • is_feature_set boolean: set to true if all input ids are phenotypic features, else set to false
  • metric string (values: phenodigm, jaccard, simGIC, resnik, symmetric_resnik): Metric for computing similarity
  • id array: A phenotype or identifier that is composed of phenotypes (eg disease, gene)
  • limit integer: number of rows
  • taxon string: ncbi taxon id

Output

• output SimResult

get_variant_sets_collection

Returns list of variant sets

monarchinitiative.get_variant_sets_collection({}, context)

Input

• input object
  • page integer: Page number
  • per_page integer (values: 2, 10, 20, 30, 40, 50): Results per page {error_msg}

Output

• output Page_of_variant_sets

post_variant_sets_collection

Creates a new variant set

monarchinitiative.post_variant_sets_collection({
  "body": {
    "body": "",
    "title": ""
  }
}, context)

Input

• input object
  • body required variant_set

Output

Output schema unknown

get_variant_analyze

Returns list of matches

monarchinitiative.get_variant_analyze({
  "id": ""
}, context)

Input

• input object
  • id required string

Output

• output array
  • items Association

get_variant_sets_archive_collection

Returns list of variant sets from a specified time period

monarchinitiative.get_variant_sets_archive_collection({
  "year": 0,
  "month": 0,
  "day": 0
}, context)

Input

• input object
  • page integer: Page number
  • per_page integer (values: 2, 10, 20, 30, 40, 50): Results per page {error_msg}
  • year required integer
  • month required integer
  • day required integer

Output

• output Page_of_variant_sets

delete_variant_set_item

Deletes variant set

monarchinitiative.delete_variant_set_item({
  "id": ""
}, context)

Input

• input object
  • id required string

Output

Output schema unknown

get_variant_set_item

Returns a variant set

monarchinitiative.get_variant_set_item({
  "id": ""
}, context)

Input

• input object
  • id required string

Output

• output variant_set

put_variant_set_item

Updates a variant set

monarchinitiative.put_variant_set_item({
  "body": {
    "body": "",
    "title": ""
  },
  "id": ""
}, context)

Input

• input object
  • body required variant_set
  • id required string

Output

Output schema unknown

Definitions

A_page_of_results

• A_page_of_results object
  • page integer: Number of this page of results
  • pages integer: Total number of pages of results
  • per_page integer: Number of items per page of results
  • total integer: Total number of results

AbstractPropertyValue

• AbstractPropertyValue object
  • pred string: predicate (attribute) part
  • val string: value part
  • xrefs array: Xrefs provenance for property-value
    • items string

AnnotationExtension

• AnnotationExtension object
  • filler: Extension interpreted as OWL expression (r1 some r2 some .. some filler).
    • category array
      • items string: Type of object
    • id required string: ID or CURIE e.g. MGI:1201606
    • iri string: IRI
    • label string: RDFS Label
    • consider array
      • items string: Potential replacement object (if named object is obsoleted)
    • deprecated boolean: True if the node is deprecated/obsoleted.
    • description string: Descriptive text for the entity. For ontology classes, this will be a definition.
    • replaced_by array
      • items string: Direct 1:1 replacement (if named object is obsoleted)
    • synonyms array: list of synonyms or alternate labels
      • items SynonymPropertyValue
    • types array
      • items string: Type of object (direct)
  • relation_chain array: Relationship type. If more than one value, interpreted as chain
    • items Relation

Association

• Association object
  • evidence_graph: An indirect association is a join between two or more direct assocations, e.g. gene to disease via ortholog. We record the full set of associations as a graph object
    • edges array: All edges in graph
      • items Edge
    • nodes array: All nodes in graph
      • items Node
  • evidence_types array: Evidence types (ECO classes)
    • items EntityReference
  • id required string: Association/annotation unique ID
  • negated boolean: True if association is negated
  • object required: Object (sensu RDF), aka target, e.g. HP:0000448, MP:0002109, DOID:14330
    • category array
      • items string: Type of object
    • id required string: ID or CURIE e.g. MGI:1201606
    • iri string: IRI
    • label string: RDFS Label
    • taxon: Taxon to which the object belongs
      • id string: CURIE ID, e.g. NCBITaxon:9606
      • label string: RDFS Label
  • object_eq array: Equivalent identifiers to object node
    • items string
  • object_extensions array
    • items: Additional properties of the object in the context of this association. See http://www.biomedcentral.com/1471-2105/15/155
      • filler: Extension interpreted as OWL expression (r1 some r2 some .. some filler).
        • category array
          • items string: Type of object
        • id required string: ID or CURIE e.g. MGI:1201606
        • iri string: IRI
        • label string: RDFS Label
        • consider array
          • items string: Potential replacement object (if named object is obsoleted)
        • deprecated boolean: True if the node is deprecated/obsoleted.
        • description string: Descriptive text for the entity. For ontology classes, this will be a definition.
        • replaced_by array
          • items string: Direct 1:1 replacement (if named object is obsoleted)
        • synonyms array: list of synonyms or alternate labels
          • items SynonymPropertyValue
        • types array
          • items string: Type of object (direct)
      • relation_chain array: Relationship type. If more than one value, interpreted as chain
        • items Relation
  • provided_by array: Provider of association, e.g. Orphanet, ClinVar
    • items string
  • publications array: Publications supporting association, extracted from evidence graph
    • items EntityReference
  • qualifiers array: Qualifier on the association
    • items string
  • relation required: Relationship type connecting subject and object
    • category array
      • items string: Type of object
    • id required string: ID or CURIE e.g. MGI:1201606
    • iri string: IRI
    • label string: RDFS Label
    • inverse boolean: is relation inverted
  • slim array: Objects mapped to a slim
    • items string
  • subject required: Subject of association (what it is about), e.g. ClinVar:nnn, MGI:1201606
    • category array
      • items string: Type of object
    • id required string: ID or CURIE e.g. MGI:1201606
    • iri string: IRI
    • label string: RDFS Label
    • taxon: Taxon to which the object belongs
      • id string: CURIE ID, e.g. NCBITaxon:9606
      • label string: RDFS Label
  • subject_eq array: Equivalent identifiers to subject node
    • items string
  • subject_extensions array
    • items: Additional properties of the subject in the context of this association.
      • filler: Extension interpreted as OWL expression (r1 some r2 some .. some filler).
        • category array
          • items string: Type of object
        • id required string: ID or CURIE e.g. MGI:1201606
        • iri string: IRI
        • label string: RDFS Label
        • consider array
          • items string: Potential replacement object (if named object is obsoleted)
        • deprecated boolean: True if the node is deprecated/obsoleted.
        • description string: Descriptive text for the entity. For ontology classes, this will be a definition.
        • replaced_by array
          • items string: Direct 1:1 replacement (if named object is obsoleted)
        • synonyms array: list of synonyms or alternate labels
          • items SynonymPropertyValue
        • types array
          • items string: Type of object (direct)
      • relation_chain array: Relationship type. If more than one value, interpreted as chain
        • items Relation
  • type string: Type of association, e.g. gene-phenotype

AssociationResults

• AssociationResults
  • docs array: solr docs
    • items object
  • facet_counts object: Mapping between field names and association counts
  • highlighting object: Mapping between id and solr highlight
  • numFound integer: total number of associations matching query
  • associations array: Complete representation of full association object, plus evidence
    • items Association
  • compact_associations array: Compact representation in which objects (e.g. phenotypes) are collected for subject-predicate pairs
    • items CompactAssociationSet
  • objects array: List of distinct objects used
    • items string

AutocompleteResult

• AutocompleteResult object
  • category array: node categories
    • items string
  • has_highlight boolean: True if highlight can be interpreted as html, else False
  • highlight string: solr highlight
  • id string: curie formatted id
  • label array: primary label (rdfs:label)
    • items string
  • match string: matched part of document (may be primary label, synonym, id, etc)
  • taxon string: taxon as NCBITaxon curie
  • taxon_label string: taxon label

AutocompleteResults

• AutocompleteResults object
  • docs array: list of AutocompleteResult docs
    • items AutocompleteResult

BioObject

• BioObject
  • category array
    • items string: Type of object
  • id required string: ID or CURIE e.g. MGI:1201606
  • iri string: IRI
  • label string: RDFS Label
  • consider array
    • items string: Potential replacement object (if named object is obsoleted)
  • deprecated boolean: True if the node is deprecated/obsoleted.
  • description string: Descriptive text for the entity. For ontology classes, this will be a definition.
  • replaced_by array
    • items string: Direct 1:1 replacement (if named object is obsoleted)
  • synonyms array: list of synonyms or alternate labels
    • items SynonymPropertyValue
  • types array
    • items string: Type of object (direct)
  • association_counts object: association counts
  • taxon: Taxon to which the object belongs
    • id string: CURIE ID, e.g. NCBITaxon:9606
    • label string: RDFS Label
  • xrefs array: Database cross-references. These are usually CURIEs, but may also be URLs. E.g. ENSEMBL:ENSG00000099940
    • items string

BioObjectCore

• BioObjectCore
  • category array
    • items string: Type of object
  • id required string: ID or CURIE e.g. MGI:1201606
  • iri string: IRI
  • label string: RDFS Label
  • taxon: Taxon to which the object belongs
    • id string: CURIE ID, e.g. NCBITaxon:9606
    • label string: RDFS Label

CompactAssociationSet

• CompactAssociationSet object
  • objects required array: List of O, for a given (S,R) pair, yielding (S,R,O) triples. E.g. list of MPs for (MGI:nnn, has_phenotype)
    • items string
  • relation required string: Relationship type connecting subject and object list
  • subject required string: Subject of association (what it is about), e.g. MGI:1201606

CompareInput

• CompareInput object
  • query_ids array: list of query profiles
    • items array: list of ids
      • items string: curie formatted id
  • reference_ids array: list of ids
    • items string: curie formatted id

D2PAssociation

• D2PAssociation
  • evidence_graph: An indirect association is a join between two or more direct assocations, e.g. gene to disease via ortholog. We record the full set of associations as a graph object
    • edges array: All edges in graph
      • items Edge
    • nodes array: All nodes in graph
      • items Node
  • evidence_types array: Evidence types (ECO classes)
    • items EntityReference
  • id required string: Association/annotation unique ID
  • negated boolean: True if association is negated
  • object required: Object (sensu RDF), aka target, e.g. HP:0000448, MP:0002109, DOID:14330
    • category array
      • items string: Type of object
    • id required string: ID or CURIE e.g. MGI:1201606
    • iri string: IRI
    • label string: RDFS Label
    • taxon: Taxon to which the object belongs
      • id string: CURIE ID, e.g. NCBITaxon:9606
      • label string: RDFS Label
  • object_eq array: Equivalent identifiers to object node
    • items string
  • object_extensions array
    • items: Additional properties of the object in the context of this association. See http://www.biomedcentral.com/1471-2105/15/155
      • filler: Extension interpreted as OWL expression (r1 some r2 some .. some filler).
        • category array
          • items string: Type of object
        • id required string: ID or CURIE e.g. MGI:1201606
        • iri string: IRI
        • label string: RDFS Label
        • consider array
          • items string: Potential replacement object (if named object is obsoleted)
        • deprecated boolean: True if the node is deprecated/obsoleted.
        • description string: Descriptive text for the entity. For ontology classes, this will be a definition.
        • replaced_by array
          • items string: Direct 1:1 replacement (if named object is obsoleted)
        • synonyms array: list of synonyms or alternate labels
          • items SynonymPropertyValue
        • types array
          • items string: Type of object (direct)
      • relation_chain array: Relationship type. If more than one value, interpreted as chain
        • items Relation
  • provided_by array: Provider of association, e.g. Orphanet, ClinVar
    • items string
  • publications array: Publications supporting association, extracted from evidence graph
    • items EntityReference
  • qualifiers array: Qualifier on the association
    • items string
  • relation required: Relationship type connecting subject and object
    • category array
      • items string: Type of object
    • id required string: ID or CURIE e.g. MGI:1201606
    • iri string: IRI
    • label string: RDFS Label
    • inverse boolean: is relation inverted
  • slim array: Objects mapped to a slim
    • items string
  • subject required: Subject of association (what it is about), e.g. ClinVar:nnn, MGI:1201606
    • category array
      • items string: Type of object
    • id required string: ID or CURIE e.g. MGI:1201606
    • iri string: IRI
    • label string: RDFS Label
    • taxon: Taxon to which the object belongs
      • id string: CURIE ID, e.g. NCBITaxon:9606
      • label string: RDFS Label
  • subject_eq array: Equivalent identifiers to subject node
    • items string
  • subject_extensions array
    • items: Additional properties of the subject in the context of this association.
      • filler: Extension interpreted as OWL expression (r1 some r2 some .. some filler).
        • category array
          • items string: Type of object
        • id required string: ID or CURIE e.g. MGI:1201606
        • iri string: IRI
        • label string: RDFS Label
        • consider array
          • items string: Potential replacement object (if named object is obsoleted)
        • deprecated boolean: True if the node is deprecated/obsoleted.
        • description string: Descriptive text for the entity. For ontology classes, this will be a definition.
        • replaced_by array
          • items string: Direct 1:1 replacement (if named object is obsoleted)
        • synonyms array: list of synonyms or alternate labels
          • items SynonymPropertyValue
        • types array
          • items string: Type of object (direct)
      • relation_chain array: Relationship type. If more than one value, interpreted as chain
        • items Relation
  • type string: Type of association, e.g. gene-phenotype
  • frequency: Frequency of phenotype in patients with disease
    • id string: ID or CURIE e.g. MGI:1201606
    • label string: RDFS Label
  • onset: Onset of phenotype in disease process
    • id string: ID or CURIE e.g. MGI:1201606
    • label string: RDFS Label

D2PAssociationResults

• D2PAssociationResults
  • docs array: solr docs
    • items object
  • facet_counts object: Mapping between field names and association counts
  • highlighting object: Mapping between id and solr highlight
  • numFound integer: total number of associations matching query
  • associations array: Complete representation of full disease to phenotype association, plus evidence
    • items D2PAssociation
  • compact_associations array: Compact representation in which objects (e.g. phenotypes) are collected for subject-predicate pairs
    • items CompactAssociationSet
  • objects array: List of distinct objects used
    • items string

Edge

• Edge object
  • meta object: metadata about the Edge
  • obj string: Object (target) Node ID
  • pred string: Predicate (relation) ID
  • sub string: Subject (source) Node ID

EntityAnnotationResult

• EntityAnnotationResult object
  • content string
  • spans array: A marked-up span of text
    • items Span

EntityReference

• EntityReference object
  • id string: ID or CURIE e.g. MGI:1201606
  • label string: RDFS Label

Feature

• Feature object
  • id string: curie formatted id
  • isPresent boolean: is the feature present
  • label string: curie formatted id
  • type string: feature type (only phenotype supported)

Graph

• Graph object
  • edges array: All edges in graph
    • items Edge
  • nodes array: All nodes in graph
    • items Node

IcNode

• IcNode
  • id required string: ID or CURIE e.g. MGI:1201606
  • label string: RDFS Label
  • IC number: Information content

LayAutocomplete

• LayAutocomplete object
  • highlight string: solr highlight
  • id string: curie formatted id
  • label string: primary label (rdfs:label)
  • matched_synonym string: matched synonym

LayResults

• LayResults object
  • results array: list of AutocompleteResult docs
    • items LayAutocomplete

NamedObject

• NamedObject
  • category array
    • items string: Type of object
  • id required string: ID or CURIE e.g. MGI:1201606
  • iri string: IRI
  • label string: RDFS Label
  • consider array
    • items string: Potential replacement object (if named object is obsoleted)
  • deprecated boolean: True if the node is deprecated/obsoleted.
  • description string: Descriptive text for the entity. For ontology classes, this will be a definition.
  • replaced_by array
    • items string: Direct 1:1 replacement (if named object is obsoleted)
  • synonyms array: list of synonyms or alternate labels
    • items SynonymPropertyValue
  • types array
    • items string: Type of object (direct)

NamedObjectCore

• NamedObjectCore object
  • category array
    • items string: Type of object
  • id required string: ID or CURIE e.g. MGI:1201606
  • iri string: IRI
  • label string: RDFS Label

Node

• Node object
  • id required string: ID or CURIE e.g. MGI:1201606
  • label string: RDFS Label

Page_of_variant_sets

• Page_of_variant_sets
  • page integer: Number of this page of results
  • pages integer: Total number of pages of results
  • per_page integer: Number of items per page of results
  • total integer: Total number of results
  • items array
    • items variant_set

PairwiseMatch

• PairwiseMatch object
  • lcs: lowest common subsumer
    • id required string: ID or CURIE e.g. MGI:1201606
    • label string: RDFS Label
    • IC number: Information content
  • match: match id
    • id required string: ID or CURIE e.g. MGI:1201606
    • label string: RDFS Label
    • IC number: Information content
  • reference: reference id
    • id required string: ID or CURIE e.g. MGI:1201606
    • label string: RDFS Label
    • IC number: Information content

Relation

• Relation
  • category array
    • items string: Type of object
  • id required string: ID or CURIE e.g. MGI:1201606
  • iri string: IRI
  • label string: RDFS Label
  • consider array
    • items string: Potential replacement object (if named object is obsoleted)
  • deprecated boolean: True if the node is deprecated/obsoleted.
  • description string: Descriptive text for the entity. For ontology classes, this will be a definition.
  • replaced_by array
    • items string: Direct 1:1 replacement (if named object is obsoleted)
  • synonyms array: list of synonyms or alternate labels
    • items SynonymPropertyValue
  • types array
    • items string: Type of object (direct)

RelationRef

• RelationRef
  • category array
    • items string: Type of object
  • id required string: ID or CURIE e.g. MGI:1201606
  • iri string: IRI
  • label string: RDFS Label
  • inverse boolean: is relation inverted

SearchResult

• SearchResult object
  • docs array: solr docs
    • items object
  • facet_counts object: Mapping between field names and association counts
  • highlighting object: Mapping between id and solr highlight
  • numFound integer: total number of associations matching query

Seq

• Seq
  • category array
    • items string: Type of object
  • id required string: ID or CURIE e.g. MGI:1201606
  • iri string: IRI
  • label string: RDFS Label
  • consider array
    • items string: Potential replacement object (if named object is obsoleted)
  • deprecated boolean: True if the node is deprecated/obsoleted.
  • description string: Descriptive text for the entity. For ontology classes, this will be a definition.
  • replaced_by array
    • items string: Direct 1:1 replacement (if named object is obsoleted)
  • synonyms array: list of synonyms or alternate labels
    • items SynonymPropertyValue
  • types array
    • items string: Type of object (direct)
  • association_counts object: association counts
  • taxon: Taxon to which the object belongs
    • id string: CURIE ID, e.g. NCBITaxon:9606
    • label string: RDFS Label
  • xrefs array: Database cross-references. These are usually CURIEs, but may also be URLs. E.g. ENSEMBL:ENSG00000099940
    • items string
  • alphabet string: one of: DNA, RNA or AA
  • md5checksum string: checksum
  • residues string: string representing sequence of residues
  • seqlen string: length of sequence

SequenceFeature

• SequenceFeature
  • category array
    • items string: Type of object
  • id required string: ID or CURIE e.g. MGI:1201606
  • iri string: IRI
  • label string: RDFS Label
  • consider array
    • items string: Potential replacement object (if named object is obsoleted)
  • deprecated boolean: True if the node is deprecated/obsoleted.
  • description string: Descriptive text for the entity. For ontology classes, this will be a definition.
  • replaced_by array
    • items string: Direct 1:1 replacement (if named object is obsoleted)
  • synonyms array: list of synonyms or alternate labels
    • items SynonymPropertyValue
  • types array
    • items string: Type of object (direct)
  • association_counts object: association counts
  • taxon: Taxon to which the object belongs
    • id string: CURIE ID, e.g. NCBITaxon:9606
    • label string: RDFS Label
  • xrefs array: Database cross-references. These are usually CURIEs, but may also be URLs. E.g. ENSEMBL:ENSG00000099940
    • items string
  • homology_associations array
    • items Association
  • locations array
    • items SequenceLocation
  • seq Seq

SequenceLocation

• SequenceLocation
  • category array
    • items string: Type of object
  • id required string: ID or CURIE e.g. MGI:1201606
  • iri string: IRI
  • label string: RDFS Label
  • consider array
    • items string: Potential replacement object (if named object is obsoleted)
  • deprecated boolean: True if the node is deprecated/obsoleted.
  • description string: Descriptive text for the entity. For ontology classes, this will be a definition.
  • replaced_by array
    • items string: Direct 1:1 replacement (if named object is obsoleted)
  • synonyms array: list of synonyms or alternate labels
    • items SynonymPropertyValue
  • types array
    • items string: Type of object (direct)
  • association_counts object: association counts
  • taxon: Taxon to which the object belongs
    • id string: CURIE ID, e.g. NCBITaxon:9606
    • label string: RDFS Label
  • xrefs array: Database cross-references. These are usually CURIEs, but may also be URLs. E.g. ENSEMBL:ENSG00000099940
    • items string
  • end SequencePosition
  • phase integer
  • score integer
  • start SequencePosition
  • strand integer: Strand direction: 1=='+', -1=='-', 0 or null infers unknown.

SequencePosition

• SequencePosition object
  • position integer
  • reference string

SimMatch

• SimMatch
  • id required string: ID or CURIE e.g. MGI:1201606
  • label string: RDFS Label
  • taxon: taxon
    • id required string: ID or CURIE e.g. MGI:1201606
    • label string: RDFS Label
  • type string: node type (eg phenotype, disease)
  • pairwise_match array
    • items: list of pairwise matches
      • lcs: lowest common subsumer
        • id required string: ID or CURIE e.g. MGI:1201606
        • label string: RDFS Label
        • IC number: Information content
      • match: match id
        • id required string: ID or CURIE e.g. MGI:1201606
        • label string: RDFS Label
        • IC number: Information content
      • reference: reference id
        • id required string: ID or CURIE e.g. MGI:1201606
        • label string: RDFS Label
        • IC number: Information content
  • rank string: rank
  • score number: sim score
  • significance string: p-value

SimMetadata

• SimMetadata object
  • max_max_ic number: max IC

SimQuery

• SimQuery object
  • ids array
    • items: list of ids
      • id required string: ID or CURIE e.g. MGI:1201606
      • label string: RDFS Label
  • negated_ids array
    • items: list of ids
      • id required string: ID or CURIE e.g. MGI:1201606
      • label string: RDFS Label
  • reference: reference individual or class (eg gene, disease)
    • id required string: ID or CURIE e.g. MGI:1201606
    • label string: RDFS Label
    • taxon: taxon
      • id required string: ID or CURIE e.g. MGI:1201606
      • label string: RDFS Label
    • type string: node type (eg phenotype, disease)
  • target_ids array
    • items array
      • items: query ids
        • id required string: ID or CURIE e.g. MGI:1201606
        • label string: RDFS Label
  • unresolved_ids array: list of unresolved ids
    • items string: curie formatted id

SimResult

• SimResult object
  • matches array
    • items: list of matches
      • id required string: ID or CURIE e.g. MGI:1201606
      • label string: RDFS Label
      • taxon: taxon
        • id required string: ID or CURIE e.g. MGI:1201606
        • label string: RDFS Label
      • type string: node type (eg phenotype, disease)
      • pairwise_match array
        • items: list of pairwise matches
          • lcs: lowest common subsumer
          • match: match id
          • reference: reference id
      • rank string: rank
      • score number: sim score
      • significance string: p-value
  • metadata SimMetadata
  • query SimQuery

Span

• Span object
  • end integer: end of span text relative to content
  • start integer: start of span text relative to content
  • text string: span text
  • token array: A token or entity extracted from the span text
    • items Token

SufficiencyOutput

• SufficiencyOutput object
  • categorical_score number: categorical score
  • scaled_score number: scaled score
  • simple_score number: simple score

SufficiencyPostInput

• SufficiencyPostInput object
  • features array: list of features
    • items Feature
  • id string: curie formatted id

SynonymPropertyValue

• SynonymPropertyValue
  • pred string: predicate (attribute) part
  • val string: value part
  • xrefs array: Xrefs provenance for property-value
    • items string

Taxon

• Taxon object
  • id string: CURIE ID, e.g. NCBITaxon:9606
  • label string: RDFS Label

Token

• Token object
  • category array: entity categories
    • items string
  • id string: The CURIE for the entity or token
  • terms array: terms
    • items string

TypedNode

• TypedNode
  • id required string: ID or CURIE e.g. MGI:1201606
  • label string: RDFS Label
  • taxon: taxon
    • id required string: ID or CURIE e.g. MGI:1201606
    • label string: RDFS Label
  • type string: node type (eg phenotype, disease)

variant_set

• variant_set object
  • body required string: Article content
  • category string
  • category_id integer
  • id integer: The unique identifier of a variant set
  • pub_date string
  • title required string: Article title