3.0.0 • Published 5 years ago

@datafire/monarchinitiative v3.0.0

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License
MIT
Repository
github
Last release
5 years ago

@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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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
datafire
@infinitebrahmanuniverse/nolb-_datafire_m@everything-registry/sub-chunk-222@zalastax/nolb-_datafire_m
3.0.0

5 years ago