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omophub (version 1.4.0)

ConceptsResource: Concepts Resource

Description

R6 class providing access to concept operations.

Arguments

Value

A list containing the concept data.

A list containing the concept data with optional relationships and synonyms.

A list with concepts and any failures.

A list with suggestions and pagination metadata.

Related concepts with relationship scores.

Relationships data.

Recommendations grouped by source concept ID with pagination metadata.

Methods

Method new()

Create a new ConceptsResource.

Usage

ConceptsResource$new(base_req)

Arguments

base_req

Base httr2 request object.

Method get()

Get a concept by ID.

Usage

ConceptsResource$get(
  concept_id,
  include_relationships = FALSE,
  include_synonyms = FALSE,
  include_hierarchy = FALSE,
  vocab_release = NULL
)

Arguments

concept_id

The OMOP concept ID.

include_relationships

Include related concepts (parents/children). Default FALSE.

include_synonyms

Include concept synonyms. Default FALSE.

include_hierarchy

Include hierarchy information. Default FALSE.

vocab_release

Specific vocabulary release (e.g., "2025.2"). Default NULL.

Method get_by_code()

Get a concept by vocabulary and code.

Usage

ConceptsResource$get_by_code(
  vocabulary_id,
  concept_code,
  include_relationships = FALSE,
  include_synonyms = FALSE,
  include_hierarchy = FALSE,
  vocab_release = NULL
)

Arguments

vocabulary_id

The vocabulary ID (e.g., "SNOMED", "ICD10CM").

concept_code

The concept code within the vocabulary.

include_relationships

Include related concepts (parents/children). Default FALSE.

include_synonyms

Include concept synonyms. Default FALSE.

include_hierarchy

Include hierarchy information. Default FALSE.

vocab_release

Specific vocabulary release (e.g., "2025.2"). Default NULL.

Method batch()

Get multiple concepts by IDs.

Usage

ConceptsResource$batch(
  concept_ids,
  include_relationships = FALSE,
  include_synonyms = FALSE,
  include_mappings = FALSE,
  vocabulary_filter = NULL,
  standard_only = TRUE
)

Arguments

concept_ids

Vector of concept IDs (max 100).

include_relationships

Include related concepts. Default FALSE.

include_synonyms

Include concept synonyms. Default FALSE.

include_mappings

Include concept mappings. Default FALSE.

vocabulary_filter

Filter results to specific vocabularies.

standard_only

Only return standard concepts. Default TRUE.

Method suggest()

Get concept suggestions (autocomplete).

Usage

ConceptsResource$suggest(
  query,
  page = 1,
  page_size = 10,
  vocabulary_ids = NULL,
  domain_ids = NULL,
  vocab_release = NULL
)

Arguments

query

Search query (min 2 characters, max 100 characters).

page

Page number (default 1).

page_size

Number of suggestions per page (default 10, max 100).

vocabulary_ids

Filter to specific vocabularies (character vector).

domain_ids

Filter to specific domains (character vector).

vocab_release

Specific vocabulary release (e.g., "2025.2").

Method related()

Get related concepts.

Usage

ConceptsResource$related(
  concept_id,
  relationship_types = NULL,
  min_score = NULL,
  page_size = 20,
  vocab_release = NULL
)

Arguments

concept_id

The source concept ID.

relationship_types

Filter by relationship types (e.g., c("Is a", "Maps to")).

min_score

Minimum relationship score (0.0-1.0).

page_size

Maximum number of results (default 20, max 100).

vocab_release

Specific vocabulary release (e.g., "2025.1").

Method relationships()

Get concept relationships.

Usage

ConceptsResource$relationships(
  concept_id,
  relationship_ids = NULL,
  vocabulary_ids = NULL,
  domain_ids = NULL,
  include_invalid = FALSE,
  standard_only = FALSE,
  include_reverse = FALSE,
  vocab_release = NULL
)

Arguments

concept_id

The concept ID.

relationship_ids

Filter by relationship type IDs (character vector or comma-separated string).

vocabulary_ids

Filter by target vocabulary IDs (character vector or comma-separated string).

domain_ids

Filter by target domain IDs (character vector or comma-separated string).

include_invalid

Include relationships to invalid concepts. Default FALSE.

standard_only

Only include relationships to standard concepts. Default FALSE.

include_reverse

Include reverse relationships. Default FALSE.

vocab_release

Specific vocabulary release version. Default NULL.

Method recommended()

Get recommended concepts using OHDSI Phoebe algorithm.

Usage

ConceptsResource$recommended(
  concept_ids,
  relationship_types = NULL,
  vocabulary_ids = NULL,
  domain_ids = NULL,
  standard_only = TRUE,
  include_invalid = FALSE,
  page = 1,
  page_size = 100
)

Arguments

concept_ids

Vector of source concept IDs (1-100).

relationship_types

Filter by relationship types (max 20).

vocabulary_ids

Filter to specific vocabularies (max 50).

domain_ids

Filter to specific domains (max 50).

standard_only

Only return standard concepts. Default TRUE.

include_invalid

Include invalid/deprecated concepts. Default FALSE.

page

Page number. Default 1.

page_size

Results per page (default 100, max 1000).

Method print()

Print resource information.

Usage

ConceptsResource$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

ConceptsResource$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.