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omophub (version 1.4.0)

SearchResource: Search Resource

Description

R6 class providing access to search operations.

Arguments

Value

Search results with pagination.

A tibble of all matching concepts.

Search results with facets and metadata.

Autocomplete suggestions.

List with results and pagination metadata.

A tibble of all matching concepts with similarity scores.

List with similar_concepts and search_metadata.

Methods

Method new()

Create a new SearchResource.

Usage

SearchResource$new(base_req)

Arguments

base_req

Base httr2 request object.

Method basic()

Basic concept search.

Usage

SearchResource$basic(
  query,
  vocabulary_ids = NULL,
  domain_ids = NULL,
  concept_class_ids = NULL,
  standard_concept = NULL,
  include_synonyms = FALSE,
  include_invalid = FALSE,
  min_score = NULL,
  exact_match = FALSE,
  page = 1,
  page_size = 20,
  sort_by = NULL,
  sort_order = NULL
)

Arguments

query

Search query string.

vocabulary_ids

Filter by vocabulary IDs.

domain_ids

Filter by domain IDs.

concept_class_ids

Filter by concept class IDs.

standard_concept

Filter by standard concept ("S", "C", or NULL).

include_synonyms

Search in synonyms. Default FALSE.

include_invalid

Include invalid concepts. Default FALSE.

min_score

Minimum relevance score.

exact_match

Require exact match. Default FALSE.

page

Page number (1-based). Default 1.

page_size

Results per page. Default 20.

sort_by

Sort field.

sort_order

Sort order ("asc" or "desc").

Method basic_all()

Fetch all search results with automatic pagination.

Usage

SearchResource$basic_all(
  query,
  vocabulary_ids = NULL,
  domain_ids = NULL,
  page_size = 100,
  max_pages = Inf,
  progress = TRUE,
  ...
)

Arguments

query

Search query string.

vocabulary_ids

Filter by vocabulary IDs.

domain_ids

Filter by domain IDs.

page_size

Results per page. Default 100.

max_pages

Maximum pages to fetch. Default Inf.

progress

Show progress bar. Default TRUE.

...

Additional search parameters.

Method advanced()

Advanced concept search with facets.

Usage

SearchResource$advanced(
  query,
  vocabulary_ids = NULL,
  domain_ids = NULL,
  concept_class_ids = NULL,
  standard_concepts_only = FALSE,
  include_invalid = FALSE,
  relationship_filters = NULL,
  page = 1,
  page_size = 20
)

Arguments

query

Search query string.

vocabulary_ids

Filter by vocabulary IDs.

domain_ids

Filter by domain IDs.

concept_class_ids

Filter by concept class IDs.

standard_concepts_only

Only return standard concepts. Default FALSE.

include_invalid

Include invalid concepts. Default FALSE.

relationship_filters

Relationship-based filters.

page

Page number (1-based). Default 1.

page_size

Results per page. Default 20.

Method autocomplete()

Get autocomplete suggestions.

Usage

SearchResource$autocomplete(
  query,
  vocabulary_ids = NULL,
  domains = NULL,
  max_suggestions = 10
)

Arguments

query

Partial query string.

vocabulary_ids

Filter by vocabulary IDs.

domains

Filter by domains.

max_suggestions

Maximum suggestions. Default 10.

Method semantic()

Semantic concept search using neural embeddings.

Usage

SearchResource$semantic(
  query,
  vocabulary_ids = NULL,
  domain_ids = NULL,
  standard_concept = NULL,
  concept_class_id = NULL,
  threshold = NULL,
  page = 1,
  page_size = 20
)

Arguments

query

Natural language search query (required).

vocabulary_ids

Filter by vocabulary IDs.

domain_ids

Filter by domain IDs.

standard_concept

Filter by standard concept ('S' or 'C').

concept_class_id

Filter by concept class ID.

threshold

Minimum similarity threshold (0.0-1.0, default 0.5).

page

Page number (1-based). Default 1.

page_size

Results per page (max 100). Default 20.

Method semantic_all()

Fetch all semantic search results with automatic pagination.

Usage

SearchResource$semantic_all(
  query,
  vocabulary_ids = NULL,
  domain_ids = NULL,
  standard_concept = NULL,
  concept_class_id = NULL,
  threshold = NULL,
  page_size = 100,
  max_pages = Inf,
  progress = TRUE
)

Arguments

query

Natural language search query (required).

vocabulary_ids

Filter by vocabulary IDs.

domain_ids

Filter by domain IDs.

standard_concept

Filter by standard concept ('S' or 'C').

concept_class_id

Filter by concept class ID.

threshold

Minimum similarity threshold (0.0-1.0).

page_size

Results per page. Default 100.

max_pages

Maximum pages to fetch. Default Inf.

progress

Show progress bar. Default TRUE.

Method similar()

Find concepts similar to a reference concept or query.

Must provide exactly one of: concept_id, concept_name, or query.

Usage

SearchResource$similar(
  concept_id = NULL,
  concept_name = NULL,
  query = NULL,
  algorithm = "hybrid",
  similarity_threshold = 0.7,
  page_size = 20,
  vocabulary_ids = NULL,
  domain_ids = NULL,
  standard_concept = NULL,
  include_invalid = NULL,
  include_scores = NULL,
  include_explanations = NULL
)

Arguments

concept_id

Concept ID to find similar concepts for.

concept_name

Concept name to find similar concepts for.

query

Natural language query for semantic similarity.

algorithm

One of 'semantic', 'lexical', or 'hybrid' (default).

similarity_threshold

Minimum similarity (0.0-1.0). Default 0.7.

page_size

Max results (max 1000). Default 20.

vocabulary_ids

Filter by vocabulary IDs.

domain_ids

Filter by domain IDs.

standard_concept

Filter by standard concept flag ('S', 'C', or 'N').

include_invalid

Include invalid/deprecated concepts.

include_scores

Include detailed similarity scores.

include_explanations

Include similarity explanations.

Method print()

Print resource information.

Usage

SearchResource$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

SearchResource$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.