performAccessionSearch: Perform an Accession Search

In TriticeaeToolbox/breedbase.R: breeDBase

Perform an Accession Search

Description

Search the provided Accession Search Database to find database terms that match the provided search terms.

Usage

performAccessionSearch(
  db,
  terms,
  config = getBBOption("accession_search_config")
)

Arguments

db	Accession Search Database
terms	Vector of accession search terms
config	Accession Search Configuration

Details

The accession search can be configured by providing a set of accession search configuration properties, which is a nested list with the following names:

NAME	DEFINITION	DEFAULT VALUE
database_terms	a list with the names: name, synonyms, accession_numbers
database_terms$name	flag to include accession names in the accession search	TRUE
database_terms$synonyms	flag to include accession synonyms in the accession search	TRUE
database_terms$accession_numbers	flag to include the accession numbers in the accession search	TRUE
search_routines	a list with the names: exact, punctuation, substring, prefix, edit_distance
search_routines$exact	flag to use the exact name search routine in the accession search	TRUE
search_routines$punctuation	flag to use the punctuation search routine in the accession search	TRUE
search_routines$substring	flag to use the substring search routine in the accession search	TRUE
search_routines$prefix	flag to use the prefix search routine in the accession search	FALSE
search_routines$edit_distance	flag to use the edit distance search routine in the accession search	FALSE
search_routine_options	a list that has names of the supported search routines with values set as a list of the search routine options
search_routine_options$substring$substring_length_min	the minimum length of a term to be included as a substring match	3
search_routine_options$prefix$prefixes	default prefixes to include	[]
search_routine_options$prefix$find_db_prefixes	scan the database terms to find common prefixes	TRUE
search_routine_options$prefix$prefix_length_min	when finding db prefixes, the minimum length of a prefix to include	2
search_routine_options$prefix$prefix_length_max	when finding db prefixes, the maximum length of a prefix to include	5
search_routine_options$prefix$threshold	when finding db prefixes, the minimum number of times a prefix is used before it is included	250
search_routine_options$edit_distance$max_edit_distance	the maximum number of changes for the edit distance comparison	2
case_sensitive	flag to perform a case-sensitive search	TRUE
return_records	flag to include the germplasm records with the search results	FALSE

Value

a tibble containing the search results. Example:

search_term	search_routine	germplasm_name	germplasm_id	database_term	database_term_type
jerry	Exact Match	JERRY	230227	JERRY	name
SY-Gold	Exact Match	00X0100-51	232633	Sy-Gold	synonym
PU0128A1_36	Remove Punctuation	0218A1-36	238801	PU0128A1-36	synonym

See Also

Other accessionSearch: createAccessionSearchDB(), getAccessionSearchCacheStatus(), getAccessionSearchConfig(), getAccessionSearchDB(), getAccessionSearchDBs(), getAccessionSearchServer(), updateAccessionSearchCache()

TriticeaeToolbox/breedbase.R documentation built on Aug. 8, 2024, 7:15 a.m.