Variable Name
labs_altRefreshed Date
2023-04
Files
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Tags
Level of Review
Data Model
Vocabularies
A concept set indicating that a patient received a laboratory measurement for alanine transaminase.
Variable Status
Funder(s)
Provenance
Original concept set developed for Preserving Kidney Function in Children with Chronic Kidney Disease (PRESERVE) study for alanine transaminase (ALT) labs. It was reused for the study "Natural History of Enteroviral Sepsis Using Real World Data" after slight modifications.
Description
This lab concept includes blood, serum, and plasma ALT labs. The original code list was generated by searching for all mention of ‘alanine’ and ‘trans’ in the concept_name, as well as mentions of ‘serum’, ‘plasma’ or ‘blood’, and limited to the LOINC vocabulary_id. Any mentions of aspartate in the name were filtered out. Body fluid concepts and other serum/blood concepts were added to improve the second version.
Medication Term Classes
Clinical Subjects Headings
Development Code
## ALT
# Alanine Aminotransferase
alt_cids <- c('3015912',
'3006923',
'3005755',
'3027388',
'3045928',
'3052018',
'46235106',
'46236949',
'37071721',
'37040912',
'37047736',
'37074219',
'37054637',
'40790133',
'4146380',
'3000784',
'3013721')
alt_name <- cdm_tbl('concept') %>%
filter(!concept_id %in% alt_cids) %>%
filter(domain_id == 'Measurement') %>%
filter(vocabulary_id == 'LOINC') %>%
mutate(msrt_name = tolower(concept_name)) %>%
filter(str_detect(msrt_name, 'alanine aminotransferase')) %>%
compute_new('alt_msrt_name')
alt_name <- alt_name %>% collect()
alt_cids <- c(alt_cids, alt_name$concept_id)
alt <- cdm_tbl('concept') %>%
filter(concept_id %in% alt_cids) %>%
select(concept_id, concept_code, concept_name, vocabulary_id, concept_class_id) %>%
collect()
alt_source <- cdm_tbl('measurement_labs') %>%
filter(!measurement_concept_id %in% alt_cids) %>%
mutate(source = tolower(measurement_source_value)) %>%
filter(str_detect(source, 'alanine aminotransferase')) %>%
compute_new('alt_source') # 3013721
alt <- cdm_tbl('concept') %>%
filter(concept_id %in% alt_cids) %>%
select(concept_id, concept_code, concept_name, vocabulary_id, concept_class_id) %>%
collect()
write_csv(alt, 'specs/lab_alt.csv')Creative Commons license
Except where otherwised noted, this item's license is described as a CC-BY Attribution 4.0 License.