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omophub (version 1.1.0)

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 mappings.

A list with concepts and any failures.

A list of suggestions.

Related concepts with scores and analysis.

Relationships with summary.

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
)

Arguments

concept_id

The OMOP concept ID.

include_relationships

Include related concepts. Default FALSE.

include_synonyms

Include concept synonyms. Default FALSE.

Method get_by_code()

Get a concept by vocabulary and code.

Usage

ConceptsResource$get_by_code(vocabulary_id, concept_code)

Arguments

vocabulary_id

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

concept_code

The concept code within the vocabulary.

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 = FALSE
)

Arguments

concept_ids

Vector of concept IDs (max 1000).

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 FALSE.

Method suggest()

Get concept suggestions (autocomplete).

Usage

ConceptsResource$suggest(query, vocabulary = NULL, domain = NULL, limit = 10)

Arguments

query

Search query (min 2 characters).

vocabulary

Filter to specific vocabulary.

domain

Filter to specific domain.

limit

Maximum suggestions (default 10, max 50).

Method related()

Get related concepts.

Usage

ConceptsResource$related(
  concept_id,
  relatedness_types = NULL,
  vocabulary_ids = NULL,
  domain_ids = NULL,
  min_relatedness_score = NULL,
  max_results = 50,
  include_scores = TRUE,
  standard_concepts_only = FALSE
)

Arguments

concept_id

The source concept ID.

relatedness_types

Types of relatedness (hierarchical, semantic, etc.).

vocabulary_ids

Filter to specific vocabularies.

domain_ids

Filter to specific domains.

min_relatedness_score

Minimum relatedness score.

max_results

Maximum results (default 50, max 200).

include_scores

Include score breakdown. Default TRUE.

standard_concepts_only

Only return standard concepts. Default FALSE.

Method relationships()

Get concept relationships.

Usage

ConceptsResource$relationships(
  concept_id,
  relationship_type = NULL,
  target_vocabulary = NULL,
  include_invalid = FALSE,
  page = 1,
  page_size = 20
)

Arguments

concept_id

The concept ID.

relationship_type

Filter by relationship type.

target_vocabulary

Filter by target vocabulary.

include_invalid

Include invalid relationships. Default FALSE.

page

Page number. Default 1.

page_size

Items per page. Default 20.

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.