The mappings between the mCode Value Sets and OMOP Concepts is converted into an RDF to view and edit in Protege.
There are 3 vocabulary-level datasets in this package that require additional parsing for appropriate categorization into owl: SNOMED, ICD10CM, and LOINC. This categarization is done by assessing the source mCode value sets each belongs to.
In mCode, LOINC is used only for tumor marker testing with no overlap with any other dataset.
unique(LOINC$value_set_name)
#> [1] "TumorMarkerTestVS"All the valuesets represented by ICD10CM overlaps with SNOMED.
unique(ICD10CM$value_set_name)
#> [1] "CancerDisorderVS"
#> [2] "ComorbidConditionVS"
#> [3] "PrimaryOrUncertainBehaviorCancerDisorderVS"
#> [4] "SecondaryCancerDisorderVS"
unique(SNOMED$value_set_name)
#> [1] "CancerBodyLocationVS"
#> [2] "CancerDisorderVS"
#> [3] "ComorbidConditionVS"
#> [4] "HistologyMorphologyBehaviorVS"
#> [5] "PrimaryOrUncertainBehaviorCancerDisorderVS"
#> [6] "SecondaryCancerDisorderVS"
#> [7] "CancerDiseaseStatusEvidenceTypeVS"
#> [8] "CancerRelatedSurgicalProcedureVS"
#> [9] "CancerStagingSystemVS"
#> [10] "ConditionStatusTrendVS"
#> [11] "LateralityVS"
#> [12] "RadiationProcedureVS"
#> [13] "RadiationTargetBodySiteVS"
#> [14] "TreatmentIntentVS"
#> [15] "TreatmentTerminationReasonVS"
#> [16] "YesNoUnknownVS"To manage the overlaps, ICD10CM and SNOMED are combined and split by value set.
ICD10CM_SNOMED <-
bind_rows(ICD10CM,
SNOMED) %>%
rubix::split_by(col = value_set_name)
names(ICD10CM_SNOMED)
#> [1] "CancerBodyLocationVS"
#> [2] "CancerDiseaseStatusEvidenceTypeVS"
#> [3] "CancerDisorderVS"
#> [4] "CancerRelatedSurgicalProcedureVS"
#> [5] "CancerStagingSystemVS"
#> [6] "ComorbidConditionVS"
#> [7] "ConditionStatusTrendVS"
#> [8] "HistologyMorphologyBehaviorVS"
#> [9] "LateralityVS"
#> [10] "PrimaryOrUncertainBehaviorCancerDisorderVS"
#> [11] "RadiationProcedureVS"
#> [12] "RadiationTargetBodySiteVS"
#> [13] "SecondaryCancerDisorderVS"
#> [14] "TreatmentIntentVS"
#> [15] "TreatmentTerminationReasonVS"
#> [16] "YesNoUnknownVS"The names are adjusted to following the uppercase snake format for this project.
nms <- names(ICD10CM_SNOMED)
nms <- str_remove_all(nms, "VS$")
nms <- str_replace_all(nms, "([a-z]{1})([A-Z]{1})","\\1_\\2")
nms <- toupper(nms)
names(ICD10CM_SNOMED) <- nms
names(ICD10CM_SNOMED)
#> [1] "CANCER_BODY_LOCATION"
#> [2] "CANCER_DISEASE_STATUS_EVIDENCE_TYPE"
#> [3] "CANCER_DISORDER"
#> [4] "CANCER_RELATED_SURGICAL_PROCEDURE"
#> [5] "CANCER_STAGING_SYSTEM"
#> [6] "COMORBID_CONDITION"
#> [7] "CONDITION_STATUS_TREND"
#> [8] "HISTOLOGY_MORPHOLOGY_BEHAVIOR"
#> [9] "LATERALITY"
#> [10] "PRIMARY_OR_UNCERTAIN_BEHAVIOR_CANCER_DISORDER"
#> [11] "RADIATION_PROCEDURE"
#> [12] "RADIATION_TARGET_BODY_SITE"
#> [13] "SECONDARY_CANCER_DISORDER"
#> [14] "TREATMENT_INTENT"
#> [15] "TREATMENT_TERMINATION_REASON"
#> [16] "YES_NO_UNKNOWN"The other datasets are combined into a list with LOINC renamed to TUMOR_MARKER_MEASUREMENT. Each dataset in the mcode_classes list is now divided by “Class” for the OWL class hierarchy.
other_value_sets <-
list(CANCER_STAGING = CANCER_STAGING,
GENOMICS = GENOMICS,
TUMOR_MARKER_MEASUREMENT = LOINC,
SPECIMEN = SPECIMEN,
UNITS_OF_MEASUREMENT = UNITS_OF_MEASUREMENT)
mcode_classes <-
c(ICD10CM_SNOMED,
other_value_sets)
names(mcode_classes)
#> [1] "CANCER_BODY_LOCATION"
#> [2] "CANCER_DISEASE_STATUS_EVIDENCE_TYPE"
#> [3] "CANCER_DISORDER"
#> [4] "CANCER_RELATED_SURGICAL_PROCEDURE"
#> [5] "CANCER_STAGING_SYSTEM"
#> [6] "COMORBID_CONDITION"
#> [7] "CONDITION_STATUS_TREND"
#> [8] "HISTOLOGY_MORPHOLOGY_BEHAVIOR"
#> [9] "LATERALITY"
#> [10] "PRIMARY_OR_UNCERTAIN_BEHAVIOR_CANCER_DISORDER"
#> [11] "RADIATION_PROCEDURE"
#> [12] "RADIATION_TARGET_BODY_SITE"
#> [13] "SECONDARY_CANCER_DISORDER"
#> [14] "TREATMENT_INTENT"
#> [15] "TREATMENT_TERMINATION_REASON"
#> [16] "YES_NO_UNKNOWN"
#> [17] "CANCER_STAGING"
#> [18] "GENOMICS"
#> [19] "TUMOR_MARKER_MEASUREMENT"
#> [20] "SPECIMEN"
#> [21] "UNITS_OF_MEASUREMENT"All the concepts in each class are converted to the chariot package’s strip format to represent them as single instances in OWL. For the SPECIMEN class specifically, the original mCode code and code description are carried over as instances to provide the appropriate gap coverage in the specimen representation.
mcode_classes2 <-
mcode_classes %>%
map(mutate_all, as.character) %>%
bind_rows(.id = "class") %>%
chariot::merge_strip(into = "concept") %>%
# Specimen domain has additional columns
unite(
col = "mcode_concept",
code, code_description,
sep = " ",
remove = FALSE,
na.rm = TRUE
) %>%
mutate(concept = coalesce(concept, Specimen, mcode_concept)) %>%
distinct() %>%
rubix::split_by(col = "class")The data is written to an Excel to load when calling the data function.
file <- file.path(getwd(), "data-raw/mcode_rdf.xlsx")
if (!file.exists(file)) {
openxlsx::write.xlsx(x = mcode_classes2,
file = file)
}
#> Warning in openxlsx::write.xlsx(x = mcode_classes2, file = file): Truncating
#> list names to 31 characters.
mcode_classes3 <-
mcode_classes2 %>%
map(select, concept)
mcode_classes3
#> $CANCER_BODY_LOCATION
#> # A tibble: 42,022 x 1
#> concept
#> <chr>
#> 1 [V] [S] 4048384 Body structure [SNOMED 123037004] [Spec Anatomic Site] [Body…
#> 2 [V] [S] 4002852 Buccal embrasure [SNOMED 110326006] [Spec Anatomic Site] [Bo…
#> 3 [V] [S] 36717763 Skin structure of left lower eyelid [SNOMED 719884003] [Spe…
#> 4 [V] [S] 4230944 Adenofibrosis [SNOMED 89115006] [Observation] [Morph Abnorma…
#> 5 [V] [S] 42605189 Intervertebral foramen of eighteenth thoracic vertebra [SNO…
#> 6 [V] [S] 4097829 Transitional cell carcinoma [SNOMED 27090000] [Observation] …
#> 7 [V] [S] 4265989 Structure of medial nuclei of hypothalamus [SNOMED 36501001]…
#> 8 [V] [S] 4143459 Structure of subarachnoid space of brain [SNOMED 33930006] […
#> 9 [V] [S] 4093877 Entire body of second thoracic vertebra [SNOMED 280839007] […
#> 10 [V] [S] 4300995 Structure of suprarenal vein [SNOMED 77905000] [Spec Anatomi…
#> # … with 42,012 more rows
#>
#> $CANCER_DISEASE_STATUS_EVIDENCE_TYPE
#> # A tibble: 6 x 1
#> concept
#> <chr>
#> 1 [V] [S] 4180938 Imaging [SNOMED 363679005] [Procedure] [Procedure]
#> 2 [V] [S] 4098214 Histopathology test [SNOMED 252416005] [Measurement] [Procedu…
#> 3 [V] [S] 46272623 Assessment of symptom control [SNOMED 711015009] [Procedure]…
#> 4 [V] [S] 4240345 Physical examination [SNOMED 5880005] [Procedure] [Procedure]
#> 5 [V] [S] 4353605 Tumor marker measurement [SNOMED 250724005] [Measurement] [Pr…
#> 6 [V] [S] 4303425 Laboratory data interpretation [SNOMED 386344002] [Procedure]…
#>
#> $CANCER_DISORDER
#> # A tibble: 58,222 x 1
#> concept
#> <chr>
#> 1 [V] [N] 35206047 Malignant neoplasm of external upper lip [ICD10CM C00.0] [C…
#> 2 [V] [N] 35206048 Malignant neoplasm of external lower lip [ICD10CM C00.1] [C…
#> 3 [V] [N] 35206049 Malignant neoplasm of external lip, unspecified [ICD10CM C0…
#> 4 [V] [N] 35206050 Malignant neoplasm of upper lip, inner aspect [ICD10CM C00.…
#> 5 [V] [N] 35206051 Malignant neoplasm of lower lip, inner aspect [ICD10CM C00.…
#> 6 [V] [N] 35206052 Malignant neoplasm of lip, unspecified, inner aspect [ICD10…
#> 7 [V] [N] 35206053 Malignant neoplasm of commissure of lip, unspecified [ICD10…
#> 8 [V] [N] 35206054 Malignant neoplasm of overlapping sites of lip [ICD10CM C00…
#> 9 [V] [N] 35206055 Malignant neoplasm of lip, unspecified [ICD10CM C00.9] [Con…
#> 10 [V] [N] 35206056 Malignant neoplasm of base of tongue [ICD10CM C01] [Conditi…
#> # … with 58,212 more rows
#>
#> $CANCER_RELATED_SURGICAL_PROCEDURE
#> # A tibble: 162 x 1
#> concept
#> <chr>
#> 1 [V] [S] 4067441 Destruction of lesion of anus [SNOMED 174337000] [Procedure]…
#> 2 [V] [S] 4171194 Excision of lesion of anus [SNOMED 49264007] [Procedure] [Pr…
#> 3 [V] [S] 4002559 Anus excision [SNOMED 119894003] [Procedure] [Procedure]
#> 4 [V] [S] 4087575 Operation on anus [SNOMED 24265000] [Procedure] [Procedure]
#> 5 [V] [S] 4170198 Destruction of lesion of bladder [SNOMED 48185007] [Procedur…
#> 6 [V] [S] 4029571 Bladder excision [SNOMED 108034003] [Procedure] [Procedure]
#> 7 [V] [S] 4010266 Partial cystectomy [SNOMED 112902005] [Procedure] [Procedure]
#> 8 [V] [S] 4270496 Complete cystectomy [SNOMED 63016009] [Procedure] [Procedure]
#> 9 [V] [S] 4273866 Radical cystectomy [SNOMED 64063003] [Procedure] [Procedure]
#> 10 [V] [S] 4119922 Urinary bladder reconstruction [SNOMED 287716007] [Procedure…
#> # … with 152 more rows
#>
#> $CANCER_STAGING
#> # A tibble: 1,617 x 1
#> concept
#> <chr>
#> 1 [V] [S] 1537692 Vulvar Cancer cM1 TNM Finding by AJCC/UICC 8th edition [NCIt…
#> 2 [V] [S] 1537780 Retinoblastoma cM0 TNM Finding by AJCC/UICC 8th edition [NCI…
#> 3 [V] [S] 1537798 Eyelid Carcinoma pM1 TNM Finding by AJCC/UICC 8th edition [N…
#> 4 [V] [S] 1537804 Uterine Corpus Leiomyosarcoma and Endometrial Stromal Sarcom…
#> 5 [V] [S] 1537805 Esophagus and Esophagogastric Junction Cancer cM1 TNM Findin…
#> 6 [V] [S] 1537808 Duodenum and Ampulla of Vater Neuroendocrine Tumor cM1c TNM …
#> 7 [V] [S] 1537809 Bone Cancer pM1b TNM Finding by AJCC/UICC 8th edition [NCIt …
#> 8 [V] [S] 1537821 Merkel Cell Carcinoma pM1 TNM Finding by AJCC/UICC 8th editi…
#> 9 [V] [S] 1537827 Jejunum and Ileum Neuroendocrine Tumor cM0 TNM Finding by AJ…
#> 10 [V] [S] 1537830 Thymic Tumor pM1 TNM Finding by AJCC/UICC 8th edition [NCIt …
#> # … with 1,607 more rows
#>
#> $CANCER_STAGING_SYSTEM
#> # A tibble: 3 x 1
#> concept
#> <chr>
#> 1 [V] [S] 40485522 American Joint Commission on Cancer, Cancer Staging Manual, …
#> 2 [V] [S] 40483646 American Joint Commission on Cancer, Cancer Staging Manual, …
#> 3 [V] [S] 4123019 UICC [SNOMED 258235000] [Measurement] [Staging / Scales]
#>
#> $COMORBID_CONDITION
#> # A tibble: 22,874 x 1
#> concept
#> <chr>
#> 1 [V] [N] 45537731 Syphilitic endocarditis [ICD10CM A52.03] [Condition] [5-cha…
#> 2 [V] [N] 35205769 Chronic viral hepatitis B with delta-agent [ICD10CM B18.0] …
#> 3 [V] [N] 35205770 Chronic viral hepatitis B without delta-agent [ICD10CM B18.…
#> 4 [V] [N] 35205771 Chronic viral hepatitis C [ICD10CM B18.2] [Condition] [4-ch…
#> 5 [V] [N] 35205776 Human immunodeficiency virus [HIV] disease [ICD10CM B20] [C…
#> 6 [V] [N] 35206047 Malignant neoplasm of external upper lip [ICD10CM C00.0] [C…
#> 7 [V] [N] 35206048 Malignant neoplasm of external lower lip [ICD10CM C00.1] [C…
#> 8 [V] [N] 35206049 Malignant neoplasm of external lip, unspecified [ICD10CM C0…
#> 9 [V] [N] 35206050 Malignant neoplasm of upper lip, inner aspect [ICD10CM C00.…
#> 10 [V] [N] 35206051 Malignant neoplasm of lower lip, inner aspect [ICD10CM C00.…
#> # … with 22,864 more rows
#>
#> $CONDITION_STATUS_TREND
#> # A tibble: 5 x 1
#> concept
#> <chr>
#> 1 [V] [S] 9190 Not detected [SNOMED 260415000] [Meas Value] [Qualifier Value]
#> 2 [V] [S] 4149524 Patient's condition improved [SNOMED 268910001] [Condition] […
#> 3 [V] [S] 4234874 Patient's condition stable [SNOMED 359746009] [Condition] [Cl…
#> 4 [V] [S] 4150631 Patient's condition worsened [SNOMED 271299001] [Condition] […
#> 5 [V] [S] 46271098 Patient condition undetermined [SNOMED 709137006] [Condition…
#>
#> $GENOMICS
#> # A tibble: 27,032 x 1
#> concept
#> <chr>
#> 1 [V] [S] 35944910 CCDC77 (coiled-coil domain containing 77) Variant [HGNC 282…
#> 2 [V] [S] 35944911 INMT (indolethylamine N-methyltransferase) Variant [HGNC 60…
#> 3 [V] [S] 35944912 ZNF117 (zinc finger protein 117) Variant [HGNC 12897] [Meas…
#> 4 [V] [S] 35944913 CKAP2 (cytoskeleton associated protein 2) Variant [HGNC 199…
#> 5 [V] [S] 35944914 ITPRIPL2 (ITPRIP like 2) Variant [HGNC 27257] [Measurement]…
#> 6 [V] [S] 35944916 PEX19 (peroxisomal biogenesis factor 19) Variant [HGNC 9713…
#> 7 [V] [S] 35944917 ZNF385D (zinc finger protein 385D) Variant [HGNC 26191] [Me…
#> 8 [V] [S] 35944920 EDDM3B (epididymal protein 3B) Variant [HGNC 19223] [Measur…
#> 9 [V] [S] 35944921 KLRC3 (killer cell lectin like receptor C3) Variant [HGNC 6…
#> 10 [V] [S] 35944922 GIMAP4 (GTPase, IMAP family member 4) Variant [HGNC 21872] …
#> # … with 27,022 more rows
#>
#> $HISTOLOGY_MORPHOLOGY_BEHAVIOR
#> # A tibble: 1,325 x 1
#> concept
#> <chr>
#> 1 [V] [S] 4264447 Acute myeloid leukemia with multilineage dysplasia following…
#> 2 [V] [S] 4029663 Acute myeloid leukemia, 11q23 abnormalities [SNOMED 12882900…
#> 3 [V] [S] 37311513 Biphenotypic sinonasal sarcoma [SNOMED 789405004] [Observat…
#> 4 [V] [S] 36403182 Papillary carcinoma follicular variant, in situ follicular …
#> 5 [V] [S] 4030124 Hepatoid adenocarcinoma [SNOMED 128706007] [Observation] [Mo…
#> 6 [V] [S] 4228267 Papillary carcinoma, clear cell [SNOMED 421630008] [Observat…
#> 7 [V] [S] 4029175 Prolymphocytic leukemia, T-cell type [SNOMED 128821006] [Obs…
#> 8 [V] [S] 4186244 Malignant immunoproliferative neoplasm [SNOMED 414646000] [O…
#> 9 [V] [S] 4267422 Malignant aortic body tumor [SNOMED 62512005] [Observation] …
#> 10 [V] [S] 4028856 Glomus tumor, malignant [SNOMED 128908003] [Observation] [Mo…
#> # … with 1,315 more rows
#>
#> $LATERALITY
#> # A tibble: 5 x 1
#> concept
#> <chr>
#> 1 [V] [S] 4197258 Right and left [SNOMED 51440002] [Observation] [Qualifier Val…
#> 2 [V] [S] 4161551 Midline [SNOMED 399488007] [Observation] [Qualifier Value]
#> 3 [V] [S] 4080761 Right [SNOMED 24028007] [Observation] [Qualifier Value]
#> 4 [V] [S] 4300877 Left [SNOMED 7771000] [Observation] [Qualifier Value]
#> 5 [V] [S] 4280221 Unilateral [SNOMED 66459002] [Observation] [Qualifier Value]
#>
#> $PRIMARY_OR_UNCERTAIN_BEHAVIOR_CANCER_DISORDER
#> # A tibble: 55,909 x 1
#> concept
#> <chr>
#> 1 [V] [N] 35206047 Malignant neoplasm of external upper lip [ICD10CM C00.0] [C…
#> 2 [V] [N] 35206048 Malignant neoplasm of external lower lip [ICD10CM C00.1] [C…
#> 3 [V] [N] 35206049 Malignant neoplasm of external lip, unspecified [ICD10CM C0…
#> 4 [V] [N] 35206050 Malignant neoplasm of upper lip, inner aspect [ICD10CM C00.…
#> 5 [V] [N] 35206051 Malignant neoplasm of lower lip, inner aspect [ICD10CM C00.…
#> 6 [V] [N] 35206052 Malignant neoplasm of lip, unspecified, inner aspect [ICD10…
#> 7 [V] [N] 35206053 Malignant neoplasm of commissure of lip, unspecified [ICD10…
#> 8 [V] [N] 35206054 Malignant neoplasm of overlapping sites of lip [ICD10CM C00…
#> 9 [V] [N] 35206055 Malignant neoplasm of lip, unspecified [ICD10CM C00.9] [Con…
#> 10 [V] [N] 35206056 Malignant neoplasm of base of tongue [ICD10CM C01] [Conditi…
#> # … with 55,899 more rows
#>
#> $RADIATION_PROCEDURE
#> # A tibble: 5 x 1
#> concept
#> <chr>
#> 1 [V] [S] 40489482 Megavoltage radiation therapy using photons [SNOMED 44838500…
#> 2 [V] [S] 4165039 Teleradiotherapy using electrons [SNOMED 45643008] [Procedure…
#> 3 [V] [S] 4024005 Teleradiotherapy protons [SNOMED 10611004] [Procedure] [Proce…
#> 4 [V] [S] 4213601 Teleradiotherapy neutrons [SNOMED 80347004] [Procedure] [Proc…
#> 5 [V] [S] 40317890 Brachytherapy [SNOMED 152198000] [Procedure] [Procedure]
#>
#> $RADIATION_TARGET_BODY_SITE
#> # A tibble: 66 x 1
#> concept
#> <chr>
#> 1 [V] [S] 4215878 Cervical lymph node structure [SNOMED 81105003] [Spec Anatom…
#> 2 [V] [S] 4055510 Entire lymph node of thorax [SNOMED 196374005] [Spec Anatomi…
#> 3 [V] [S] 4074816 Axillary lymph node group [SNOMED 245269009] [Spec Anatomic …
#> 4 [V] [S] 4075241 Supraclavicular lymph node group [SNOMED 245265003] [Spec An…
#> 5 [V] [S] 4075246 Internal mammary lymph node group [SNOMED 245282001] [Spec A…
#> 6 [V] [S] 4075247 Abdominal lymph node group [SNOMED 245284000] [Spec Anatomic…
#> 7 [V] [S] 4081786 Pelvic lymph node group [SNOMED 245294005] [Spec Anatomic Si…
#> 8 [V] [S] 4241958 Structure of lymph node [SNOMED 59441001] [Spec Anatomic Sit…
#> 9 [V] [S] 4353165 Entire eye [SNOMED 244486005] [Spec Anatomic Site] [Body Str…
#> 10 [V] [S] 4209428 Pituitary structure [SNOMED 56329008] [Spec Anatomic Site] […
#> # … with 56 more rows
#>
#> $SECONDARY_CANCER_DISORDER
#> # A tibble: 909 x 1
#> concept
#> <chr>
#> 1 [V] [N] 45532940 Secondary carcinoid tumors, unspecified site [ICD10CM C7B.0…
#> 2 [V] [N] 45552289 Secondary carcinoid tumors of distant lymph nodes [ICD10CM …
#> 3 [V] [N] 45542632 Secondary carcinoid tumors of liver [ICD10CM C7B.02] [Condi…
#> 4 [V] [N] 45542633 Secondary carcinoid tumors of bone [ICD10CM C7B.03] [Condit…
#> 5 [V] [N] 45532941 Secondary carcinoid tumors of peritoneum [ICD10CM C7B.04] […
#> 6 [V] [N] 45600534 Secondary carcinoid tumors of other sites [ICD10CM C7B.09] …
#> 7 [V] [N] 45566619 Secondary Merkel cell carcinoma [ICD10CM C7B.1] [Condition]…
#> 8 [V] [N] 45571543 Other secondary neuroendocrine tumors [ICD10CM C7B.8] [Cond…
#> 9 [V] [N] 35206319 Secondary and unspecified malignant neoplasm of lymph nodes…
#> 10 [V] [N] 35206320 Secondary and unspecified malignant neoplasm of intrathorac…
#> # … with 899 more rows
#>
#> $SPECIMEN
#> # A tibble: 3,928 x 1
#> concept
#> <chr>
#> 1 [V] [N] 1027716 NA [NA NA] [NA] [NA]
#> 2 [V] [N] 1032268 NA [NA NA] [NA] [NA]
#> 3 [V] [N] 1033195 NA [NA NA] [NA] [NA]
#> 4 [V] [N] 1033465 NA [NA NA] [NA] [NA]
#> 5 [V] [N] 1033739 NA [NA NA] [NA] [NA]
#> 6 [V] [N] 1585831 NA [NA NA] [NA] [NA]
#> 7 [V] [N] 1585833 NA [NA NA] [NA] [NA]
#> 8 [V] [N] 3310432 NA [NA NA] [NA] [NA]
#> 9 [V] [N] 3311979 NA [NA NA] [NA] [NA]
#> 10 [V] [N] 3326584 NA [NA NA] [NA] [NA]
#> # … with 3,918 more rows
#>
#> $TREATMENT_INTENT
#> # A tibble: 2 x 1
#> concept
#> <chr>
#> 1 [V] [S] 4162591 Curative - procedure intent [SNOMED 373808002] [Observation] …
#> 2 [V] [S] 4179711 Palliative intent [SNOMED 363676003] [Observation] [Qualifier…
#>
#> $TREATMENT_TERMINATION_REASON
#> # A tibble: 7 x 1
#> concept
#> <chr>
#> 1 [V] [S] 4082735 Treatment completed [SNOMED 182992009] [Observation] [Procedu…
#> 2 [V] [S] 4243225 Lack of drug action [SNOMED 58848006] [Observation] [Clinical…
#> 3 [V] [S] 4105886 Adverse reaction [SNOMED 281647001] [Condition] [Clinical Fin…
#> 4 [V] [S] 4052625 Financial problem [SNOMED 160932005] [Observation] [Clinical …
#> 5 [V] [S] 4019958 Refusal of treatment by patient [SNOMED 105480006] [Observati…
#> 6 [V] [S] 4030023 Patient transfer [SNOMED 107724000] [Observation] [Procedure]
#> 7 [V] [S] 4146955 Treatment not available [SNOMED 309846006] [Observation] [Con…
#>
#> $TUMOR_MARKER_MEASUREMENT
#> # A tibble: 160 x 1
#> concept
#> <chr>
#> 1 [V] [S] 3005148 5-Hydroxyindoleacetate [Mass/time] in 24 hour Urine [LOINC 1…
#> 2 [V] [S] 3023028 5-Hydroxyindoleacetate [Mass/volume] in 24 hour Urine [LOINC…
#> 3 [V] [S] 3014670 5-Hydroxyindoleacetate [Mass/volume] in Cerebral spinal flui…
#> 4 [V] [S] 3021106 5-Hydroxyindoleacetate [Mass/volume] in Serum or Plasma [LOI…
#> 5 [V] [S] 3021385 5-Hydroxyindoleacetate [Mass/volume] in Urine [LOINC 1694-9]…
#> 6 [V] [S] 43055680 5-Hydroxyindoleacetate [Mass/volume] in Urine by Confirmato…
#> 7 [V] [S] 3009461 5-Hydroxyindoleacetate [Moles/time] in 24 hour Urine [LOINC …
#> 8 [V] [S] 3010801 5-Hydroxyindoleacetate [Moles/volume] in 24 hour Urine [LOIN…
#> 9 [V] [S] 3051403 5-Hydroxyindoleacetate [Moles/volume] in Cerebral spinal flu…
#> 10 [V] [S] 44816667 5-Hydroxyindoleacetate [Moles/volume] in Platelet rich plas…
#> # … with 150 more rows
#>
#> $UNITS_OF_MEASUREMENT
#> # A tibble: 1,011 x 1
#> concept
#> <chr>
#> 1 pm Picometer
#> 2 nm Nanometer
#> 3 mm Millimeter
#> 4 cm Centimeter
#> 5 m Meter
#> 6 ft-us Foot
#> 7 in-us Prostate specific Ag/Prostate volume calculated from height, width and…
#> 8 [V] [S] 8478 avidity index [UCUM {ai}] [Unit] [Unit]
#> 9 [V] [S] 8479 centipoise [UCUM cP] [Unit] [Unit]
#> 10 [V] [S] 8480 Ehrlich unit [UCUM [EU]] [Unit] [Unit]
#> # … with 1,001 more rows
#>
#> $YES_NO_UNKNOWN
#> # A tibble: 1 x 1
#> concept
#> <chr>
#> 1 [V] [S] 4188539 Yes [SNOMED 373066001] [Meas Value] [Qualifier Value]