Convenience wrapper that loads stop words, block patterns, and functional categories in one call. Returns a named list.
Value
List with keys: stop_words, block_patterns, functional_categories, strip_terms, corrections, isotope_lookup, unit_map, unit_synonyms, toxval_schema, media_map
Examples
cache_dir <- system.file("extdata", "reference_cache", package = "concert")
refs <- load_all_reference_lists(cache_dir)
#> Loading stop words from cache: /home/runner/work/_temp/Library/concert/extdata/reference_cache/stop_words.rds
#> Loading block patterns from cache: /home/runner/work/_temp/Library/concert/extdata/reference_cache/block_patterns.rds
#> Loading functional categories from cache: /home/runner/work/_temp/Library/concert/extdata/reference_cache/functional_categories.rds
#> Loading strip terms from cache: /home/runner/work/_temp/Library/concert/extdata/reference_cache/strip_terms.rds
#> Loading one-off corrections from cache: /home/runner/work/_temp/Library/concert/extdata/reference_cache/corrections.rds
#> Loading isotope lookup from cache: /home/runner/work/_temp/Library/concert/extdata/reference_cache/isotope_lookup.rds
#> Loading unit conversion map from cache: /home/runner/work/_temp/Library/concert/extdata/reference_cache/unit_conversion.rds
#> Loading unit synonyms from cache: /home/runner/work/_temp/Library/concert/extdata/reference_cache/unit_synonyms.rds
#> Loading ToxVal schema from cache: /home/runner/work/_temp/Library/concert/extdata/reference_cache/toxval_schema.rds
refs$stop_words
#> # A tibble: 50 × 6
#> term pattern match_mode source active notes
#> <chr> <chr> <chr> <chr> <lgl> <chr>
#> 1 not provided not provided literal_word legacy_seed TRUE NA
#> 2 unknown unknown literal_word legacy_seed TRUE NA
#> 3 unavailable unavailable literal_word legacy_seed TRUE NA
#> 4 undisclosed undisclosed literal_word legacy_seed TRUE NA
#> 5 no reportable no reportable literal_word legacy_seed TRUE NA
#> 6 none none literal_word legacy_seed TRUE NA
#> 7 na na literal_word legacy_seed TRUE NA
#> 8 ingredient ingredient literal_word legacy_review FALSE NA
#> 9 hazard hazard literal_word legacy_review FALSE NA
#> 10 blend blend literal_word legacy_review FALSE NA
#> # ℹ 40 more rows
refs$block_patterns
#> # A tibble: 50 × 6
#> term pattern match_mode source active notes
#> <chr> <chr> <chr> <chr> <lgl> <chr>
#> 1 propriet propriet regex legacy_seed TRUE NA
#> 2 proprietary proprietary regex legacy_seed TRUE NA
#> 3 confid confid regex legacy_seed TRUE NA
#> 4 confidential confidential regex legacy_seed TRUE NA
#> 5 cbi cbi regex legacy_seed TRUE NA
#> 6 conf bus info conf bus info regex legacy_seed TRUE NA
#> 7 secret secret regex legacy_seed TRUE NA
#> 8 trade secret trade secret regex legacy_seed TRUE NA
#> 9 tradesecret tradesecret regex legacy_seed TRUE NA
#> 10 withheld withheld regex legacy_seed TRUE NA
#> # ℹ 40 more rows
refs$functional_categories
#> # A tibble: 140 × 6
#> term pattern match_mode source active notes
#> <chr> <chr> <chr> <chr> <lgl> <chr>
#> 1 Abrasive Abrasive literal_w… Compt… TRUE NA
#> 2 Absorbent Absorbent literal_w… Compt… TRUE NA
#> 3 Adhesion/cohesion promoter Adhesion/cohes… literal_w… Compt… TRUE NA
#> 4 Adsorbent Adsorbent literal_w… Compt… TRUE NA
#> 5 Aerating and deaerating agents Aerating and d… literal_w… Compt… TRUE NA
#> 6 Alloying element Alloying eleme… literal_w… Compt… TRUE NA
#> 7 Anti-adhesive/cohesive Anti-adhesive/… literal_w… Compt… TRUE NA
#> 8 Anti-caking agent Anti-caking ag… literal_w… Compt… TRUE NA
#> 9 Anti-condensation agent Anti-condensat… literal_w… Compt… TRUE NA
#> 10 Anti-dandruff Anti-dandruff literal_w… Compt… TRUE NA
#> # ℹ 130 more rows
refs$strip_terms
#> # A tibble: 11 × 6
#> term pattern match_mode source active notes
#> <chr> <chr> <chr> <chr> <lgl> <chr>
#> 1 "modified" "modified" literal_word legacy_r… FALSE NA
#> 2 "\\d+%$" "\\d+%$" regex legacy_r… FALSE NA
#> 3 "part [a-z]:" "part [a-z]:" regex legacy_r… FALSE NA
#> 4 "pure" "pure" literal_word app_defa… TRUE NA
#> 5 "purified" "purified" literal_word app_defa… TRUE NA
#> 6 "technical" "technical" literal_word app_defa… TRUE NA
#> 7 "grade" "grade" literal_word app_defa… TRUE NA
#> 8 "chemical" "chemical" literal_word app_defa… TRUE NA
#> 9 "and its salts" "and its salts" literal_word app_defa… TRUE NA
#> 10 "and its \\w+ salts" "and its \\w+ salts" regex app_defa… TRUE NA
#> 11 "unspecified" "unspecified" literal_word app_defa… TRUE NA
refs$corrections
#> # A tibble: 0 × 2
#> # ℹ 2 variables: pattern <chr>, replacement <chr>
refs$isotope_lookup
#> $lookup
#> # A tibble: 656 × 7
#> symbol mass element_name shortcode canonical dtxsid source
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Ac 225 Actinium ac225 Actinium-225 DTXSID50931577 comptox_pt
#> 2 Ac 226 Actinium ac226 Actinium-226 DTXSID00942537 comptox_pt
#> 3 Ac 227 Actinium ac227 Actinium-227 DTXSID30873981 comptox_pt
#> 4 Ac 228 Actinium ac228 Actinium-228 DTXSID90873982 wqx_radioche…
#> 5 Ag 105 Silver ag105 Silver-105 DTXSID80933605 comptox_pt
#> 6 Ag 106 Silver ag106 Silver-106 DTXSID40931824 comptox_pt
#> 7 Ag 107 Silver ag107 Silver-107 DTXSID10162542 comptox_pt
#> 8 Ag 108 Silver ag108 Silver-108 DTXSID80891776 comptox_pt
#> 9 Ag 109 Silver ag109 Silver-109 DTXSID70162543 comptox_pt
#> 10 Ag 110 Silver ag110 Silver-110 DTXSID60891779 comptox_pt
#> # ℹ 646 more rows
#>
#> $elem_alt_names
#> cesium aluminum sulfur
#> "Caesium" "Aluminium" "Sulphur"
#>
refs$unit_map
#> # A tibble: 1,561 × 8
#> from_unit to_unit multiplier category confidence source offset
#> <chr> <chr> <dbl> <chr> <chr> <chr> <dbl>
#> 1 % % 1 dimensionless HIGH concert_enviro… 0
#> 2 % vol % v/v 1 dimensionless HIGH concert_enviro… 0
#> 3 % WSF % WSF 1 domain_unit HIGH concert_enviro… 0
#> 4 % sat % sat 1 domain_unit HIGH concert_enviro… 0
#> 5 pH pH 1 domain_unit HIGH concert_enviro… 0
#> 6 v/v v/v 1 dimensionless HIGH concert_enviro… 0
#> 7 % v/w % v/w 1 dimensionless HIGH concert_enviro… 0
#> 8 g% w/v mg/L 10000 concentration HIGH concert_enviro… 0
#> 9 no/eu count/eu 1 count HIGH concert_enviro… 0
#> 10 mg% mg/L 10 concentration MEDIUM concert_enviro… 0
#> # ℹ 1,551 more rows
#> # ℹ 1 more variable: conversion_type <chr>
refs$unit_synonyms
#> # A tibble: 28 × 4
#> input_pattern normalized_unit is_regex notes
#> <chr> <chr> <lgl> <chr>
#> 1 mg/kg bw/day mg/kg/d FALSE body weight qualifier
#> 2 ug/kg bw/day ug/kg/d FALSE body weight qualifier
#> 3 parts/billion (ppb) ppb FALSE SSWQS ppb label
#> 4 parts per billion ppb FALSE SSWQS ppb label
#> 5 ug/l ug/L FALSE SSWQS case
#> 6 micrograms/l ug/L FALSE SSWQS micro variant
#> 7 micrograms per liter ug/L FALSE SSWQS micro variant
#> 8 ng/l ng/L FALSE SSWQS case
#> 9 pg/l pg/L FALSE SSWQS case
#> 10 fg/l fg/L FALSE SSWQS case
#> # ℹ 18 more rows
refs$toxval_schema
#> # A tibble: 0 × 56
#> # ℹ 56 variables: dtxsid <chr>, casrn <chr>, name <chr>, source <chr>,
#> # sub_source <chr>, toxval_type <chr>, toxval_subtype <chr>,
#> # toxval_type_supercategory <chr>, qualifier <chr>, toxval_numeric <dbl>,
#> # toxval_units <chr>, risk_assessment_class <chr>, study_type <chr>,
#> # study_duration_class <chr>, study_duration_value <dbl>,
#> # study_duration_units <chr>, species_common <chr>, strain <chr>,
#> # latin_name <chr>, species_supercategory <chr>, sex <chr>, …
refs$media_map
#> # A tibble: 267 × 25
#> term canonical_media canonical_term term_id parent_id preferred_label rank
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 absin… absinthe absinthe FOODON… FOODON:0… absinthe cano…
#> 2 aceto… acetone acetone AMH:00… AMH:0000… acetone cano…
#> 3 aeros… aerosol aerosol AMH:00… ENVO:000… aerosol cano…
#> 4 air air air ENVO:0… ENVO:010… air cano…
#> 5 ambie… ambient air ambient air ENVO:0… ENVO:010… air cano…
#> 6 anima… feed feed AMH:00… ENVO:000… food alias
#> 7 anima… tissue tissue AMH:00… AMH:0000… tissue alias
#> 8 anima… tissue tissue AMH:00… AMH:0000… tissue alias
#> 9 apples apple apple FOODON… FOODON:0… apple alias
#> 10 aqueo… aqueous aqueous ENVO:0… ENVO:010… liquid water cano…
#> # ℹ 257 more rows
#> # ℹ 18 more variables: definition <chr>, envo_id <chr>, physical_phase <chr>,
#> # physical_state <chr>, is_water_based <lgl>, concert_unit_route <chr>,
#> # media_category <chr>, source <chr>, assertion_mode <chr>,
#> # confidence_tier <chr>, confidence <chr>, active <lgl>, canonical <chr>,
#> # ontology_node_id <chr>, artifact_version <chr>, parent <chr>,
#> # fetch_timestamp <chr>, ontology_path <chr>