README.md
In meerapatelmd/mOMOP: What the Package Does (One Line, Title Case)
mOMOP
The goal of mOMOP is to crosswalk the Minimal Common Oncology Data
Elements (mCode) with the OMOP
Vocabularies. mCode and the mCode Initiative provides a common data
language and model for data exchange between entities while the OMOP
Vocabularies integrate data elements into the OMOP Common Data Model to
serve analytics use cases. A crosswalk using the terminology service
will bridge the gap between data interoperability and analytical
application.
Installation
You can install mOMOP with:
library(devtools)
install_github("meerapatelmd/mOMOP")
Examples
library(mOMOP)
mCode Class Hierarchy
The end-product of this package is the MCODE_CLASS_HIERARCHY dataset,
which is a flattened taxonomy that serves a variety of use cases. For
example, it can be used to incorporate mCode into a lookup table in a
relational database such as the retrieval of a certain class of data
elements or it can be incorporated into an ontology.
head(MCODE_CLASS_HIERARCHY)
#> class
#> 1 CANCER_BODY_LOCATION
#> 2 CANCER_BODY_LOCATION
#> 3 CANCER_BODY_LOCATION
#> 4 CANCER_BODY_LOCATION
#> 5 CANCER_BODY_LOCATION
#> 6 CANCER_BODY_LOCATION
#> concept
#> 1 [V] [S] 4048384 Body structure [SNOMED 123037004] [Spec Anatomic Site] [Body Structure]
#> 2 [V] [S] 4002852 Buccal embrasure [SNOMED 110326006] [Spec Anatomic Site] [Body Structure]
#> 3 [V] [S] 36717763 Skin structure of left lower eyelid [SNOMED 719884003] [Spec Anatomic Site] [Body Structure]
#> 4 [V] [S] 4230944 Adenofibrosis [SNOMED 89115006] [Observation] [Morph Abnormality]
#> 5 [V] [S] 42605189 Intervertebral foramen of eighteenth thoracic vertebra [SNOMED Veterinary 336621000009107] [Spec Anatomic Site] [Body Structure]
#> 6 [V] [S] 4097829 Transitional cell carcinoma [SNOMED 27090000] [Observation] [Morph Abnormality]
Crosswalks from mCode to OMOP
The crosswalk between mCode value sets and OMOP concepts used to create
the MCODE_CLASS_HIERARCHY dataset can be accessed with the following
pre-packaged dataframes: CANCER_STAGING, GENOMICS, ICD10CM,
LOINC, SNOMED, SPECIMEN, UNITS_OF_MEASUREMENT.
Cancer Staging
head(CANCER_STAGING)
#> value_set_name code_system
#> 1 TNMDistantMetastasesCategoryVS http://cancerstaging.org
#> 2 TNMDistantMetastasesCategoryVS http://cancerstaging.org
#> 3 TNMDistantMetastasesCategoryVS http://cancerstaging.org
#> 4 TNMDistantMetastasesCategoryVS http://cancerstaging.org
#> 5 TNMDistantMetastasesCategoryVS http://cancerstaging.org
#> 6 TNMDistantMetastasesCategoryVS http://cancerstaging.org
#> logical_definition code
#> 1 includes codes from code system http://cancerstaging.org NA
#> 2 includes codes from code system http://cancerstaging.org NA
#> 3 includes codes from code system http://cancerstaging.org NA
#> 4 includes codes from code system http://cancerstaging.org NA
#> 5 includes codes from code system http://cancerstaging.org NA
#> 6 includes codes from code system http://cancerstaging.org NA
#> code_description concept_id
#> 1 NA 1537692
#> 2 NA 1537780
#> 3 NA 1537798
#> 4 NA 1537804
#> 5 NA 1537805
#> 6 NA 1537808
#> concept_name
#> 1 Vulvar Cancer cM1 TNM Finding by AJCC/UICC 8th edition
#> 2 Retinoblastoma cM0 TNM Finding by AJCC/UICC 8th edition
#> 3 Eyelid Carcinoma pM1 TNM Finding by AJCC/UICC 8th edition
#> 4 Uterine Corpus Leiomyosarcoma and Endometrial Stromal Sarcoma cM0 TNM Finding by AJCC/UICC 8th edition
#> 5 Esophagus and Esophagogastric Junction Cancer cM1 TNM Finding by AJCC/UICC 8th edition
#> 6 Duodenum and Ampulla of Vater Neuroendocrine Tumor cM1c TNM Finding by AJCC/UICC 8th edition
#> domain_id vocabulary_id concept_class_id standard_concept concept_code
#> 1 Measurement NCIt AJCC Category S cM1-50-8
#> 2 Measurement NCIt AJCC Category S cM0-68-8
#> 3 Measurement NCIt AJCC Category S pM1-64-8
#> 4 Measurement NCIt AJCC Category S cM0-54.1-8
#> 5 Measurement NCIt AJCC Category S cM1-16-8
#> 6 Measurement NCIt AJCC Category S cM1c-30-8
#> valid_start_date valid_end_date invalid_reason
#> 1 2018-01-01 2099-12-31 NA
#> 2 2018-01-01 2099-12-31 NA
#> 3 2018-01-01 2099-12-31 NA
#> 4 2018-01-01 2099-12-31 NA
#> 5 2018-01-01 2099-12-31 NA
#> 6 2018-01-01 2099-12-31 NA
Genomics
head(GENOMICS)
#> value_set_name code_system
#> 1 HGNCVS http://www.genenames.org/geneId
#> 2 HGNCVS http://www.genenames.org/geneId
#> 3 HGNCVS http://www.genenames.org/geneId
#> 4 HGNCVS http://www.genenames.org/geneId
#> 5 HGNCVS http://www.genenames.org/geneId
#> 6 HGNCVS http://www.genenames.org/geneId
#> logical_definition code code_description concept_id
#> 1 All codes in http://www.genenames.org/geneId NA NA 35944910
#> 2 All codes in http://www.genenames.org/geneId NA NA 35944911
#> 3 All codes in http://www.genenames.org/geneId NA NA 35944912
#> 4 All codes in http://www.genenames.org/geneId NA NA 35944913
#> 5 All codes in http://www.genenames.org/geneId NA NA 35944914
#> 6 All codes in http://www.genenames.org/geneId NA NA 35944916
#> concept_name domain_id vocabulary_id
#> 1 CCDC77 (coiled-coil domain containing 77) Variant Measurement HGNC
#> 2 INMT (indolethylamine N-methyltransferase) Variant Measurement HGNC
#> 3 ZNF117 (zinc finger protein 117) Variant Measurement HGNC
#> 4 CKAP2 (cytoskeleton associated protein 2) Variant Measurement HGNC
#> 5 ITPRIPL2 (ITPRIP like 2) Variant Measurement HGNC
#> 6 PEX19 (peroxisomal biogenesis factor 19) Variant Measurement HGNC
#> concept_class_id standard_concept concept_code valid_start_date
#> 1 Gene S 28203 2006-02-16
#> 2 Gene S 6069 1999-09-07
#> 3 Gene S 12897 1992-05-19
#> 4 Gene S 1990 1999-12-01
#> 5 Gene S 27257 2008-08-11
#> 6 Gene S 9713 1997-06-12
#> valid_end_date invalid_reason
#> 1 2099-12-31 NA
#> 2 2099-12-31 NA
#> 3 2099-12-31 NA
#> 4 2099-12-31 NA
#> 5 2099-12-31 NA
#> 6 2099-12-31 NA
ICD-10-CM
head(ICD10CM)
#> value_set_name code_system logical_definition code
#> 1 CancerDisorderVS ICD-10-CM NA C00.0
#> 2 CancerDisorderVS ICD-10-CM NA C00.1
#> 3 CancerDisorderVS ICD-10-CM NA C00.2
#> 4 CancerDisorderVS ICD-10-CM NA C00.3
#> 5 CancerDisorderVS ICD-10-CM NA C00.4
#> 6 CancerDisorderVS ICD-10-CM NA C00.5
#> code_description concept_id
#> 1 Malignant neoplasm of external upper lip 35206047
#> 2 Malignant neoplasm of external lower lip 35206048
#> 3 Malignant neoplasm of external lip, unspecified 35206049
#> 4 Malignant neoplasm of upper lip, inner aspect 35206050
#> 5 Malignant neoplasm of lower lip, inner aspect 35206051
#> 6 Malignant neoplasm of lip, unspecified, inner aspect 35206052
#> concept_name domain_id vocabulary_id
#> 1 Malignant neoplasm of external upper lip Condition ICD10CM
#> 2 Malignant neoplasm of external lower lip Condition ICD10CM
#> 3 Malignant neoplasm of external lip, unspecified Condition ICD10CM
#> 4 Malignant neoplasm of upper lip, inner aspect Condition ICD10CM
#> 5 Malignant neoplasm of lower lip, inner aspect Condition ICD10CM
#> 6 Malignant neoplasm of lip, unspecified, inner aspect Condition ICD10CM
#> concept_class_id standard_concept concept_code valid_start_date
#> 1 4-char billing code NA C00.0 2007-01-01
#> 2 4-char billing code NA C00.1 2007-01-01
#> 3 4-char billing code NA C00.2 2007-01-01
#> 4 4-char billing code NA C00.3 2007-01-01
#> 5 4-char billing code NA C00.4 2007-01-01
#> 6 4-char billing code NA C00.5 2007-01-01
#> valid_end_date invalid_reason
#> 1 2099-12-31 NA
#> 2 2099-12-31 NA
#> 3 2099-12-31 NA
#> 4 2099-12-31 NA
#> 5 2099-12-31 NA
#> 6 2099-12-31 NA
LOINC
head(LOINC)
#> value_set_name code_system logical_definition code
#> 1 TumorMarkerTestVS LOINC NA 1695-6
#> 2 TumorMarkerTestVS LOINC NA 31203-3
#> 3 TumorMarkerTestVS LOINC NA 1692-3
#> 4 TumorMarkerTestVS LOINC NA 1693-1
#> 5 TumorMarkerTestVS LOINC NA 1694-9
#> 6 TumorMarkerTestVS LOINC NA 72820-4
#> code_description
#> 1 5-Hydroxyindoleacetate [Mass/time] in 24 hour Urine
#> 2 5-Hydroxyindoleacetate [Mass/volume] in 24 hour Urine
#> 3 5-Hydroxyindoleacetate [Mass/volume] in Cerebral spinal fluid
#> 4 5-Hydroxyindoleacetate [Mass/volume] in Serum or Plasma
#> 5 5-Hydroxyindoleacetate [Mass/volume] in Urine
#> 6 5-Hydroxyindoleacetate [Mass/volume] in Urine by Confirmatory method
#> concept_id
#> 1 3005148
#> 2 3023028
#> 3 3014670
#> 4 3021106
#> 5 3021385
#> 6 43055680
#> concept_name
#> 1 5-Hydroxyindoleacetate [Mass/time] in 24 hour Urine
#> 2 5-Hydroxyindoleacetate [Mass/volume] in 24 hour Urine
#> 3 5-Hydroxyindoleacetate [Mass/volume] in Cerebral spinal fluid
#> 4 5-Hydroxyindoleacetate [Mass/volume] in Serum or Plasma
#> 5 5-Hydroxyindoleacetate [Mass/volume] in Urine
#> 6 5-Hydroxyindoleacetate [Mass/volume] in Urine by Confirmatory method
#> domain_id vocabulary_id concept_class_id standard_concept concept_code
#> 1 Measurement LOINC Lab Test S 1695-6
#> 2 Measurement LOINC Lab Test S 31203-3
#> 3 Measurement LOINC Lab Test S 1692-3
#> 4 Measurement LOINC Lab Test S 1693-1
#> 5 Measurement LOINC Lab Test S 1694-9
#> 6 Measurement LOINC Lab Test S 72820-4
#> valid_start_date valid_end_date invalid_reason
#> 1 1970-01-01 2099-12-31 NA
#> 2 1970-01-01 2099-12-31 NA
#> 3 1970-01-01 2099-12-31 NA
#> 4 1970-01-01 2099-12-31 NA
#> 5 1970-01-01 2099-12-31 NA
#> 6 2012-12-10 2099-12-31 NA
SNOMED
head(SNOMED)
#> value_set_name code_system
#> 1 CancerBodyLocationVS SNOMED CT
#> 2 CancerBodyLocationVS SNOMED CT
#> 3 CancerBodyLocationVS SNOMED CT
#> 4 CancerBodyLocationVS SNOMED CT
#> 5 CancerBodyLocationVS SNOMED CT
#> 6 CancerBodyLocationVS SNOMED CT
#> logical_definition ancestors_of
#> 1 includes codes descending from 123037004 | Body Structure NA
#> 2 includes codes descending from 123037004 | Body Structure NA
#> 3 includes codes descending from 123037004 | Body Structure NA
#> 4 includes codes descending from 123037004 | Body Structure NA
#> 5 includes codes descending from 123037004 | Body Structure NA
#> 6 includes codes descending from 123037004 | Body Structure NA
#> descendants_of code code_description all_codes concept_id
#> 1 123037004 NA NA 123037004 4048384
#> 2 123037004 NA NA 123037004 4002852
#> 3 123037004 NA NA 123037004 36717763
#> 4 123037004 NA NA 123037004 4230944
#> 5 123037004 NA NA 123037004 42605189
#> 6 123037004 NA NA 123037004 4097829
#> concept_name domain_id
#> 1 Body structure Spec Anatomic Site
#> 2 Buccal embrasure Spec Anatomic Site
#> 3 Skin structure of left lower eyelid Spec Anatomic Site
#> 4 Adenofibrosis Observation
#> 5 Intervertebral foramen of eighteenth thoracic vertebra Spec Anatomic Site
#> 6 Transitional cell carcinoma Observation
#> vocabulary_id concept_class_id standard_concept concept_code
#> 1 SNOMED Body Structure S 123037004
#> 2 SNOMED Body Structure S 110326006
#> 3 SNOMED Body Structure S 719884003
#> 4 SNOMED Morph Abnormality S 89115006
#> 5 SNOMED Veterinary Body Structure S 336621000009107
#> 6 SNOMED Morph Abnormality S 27090000
#> valid_start_date valid_end_date invalid_reason
#> 1 1970-01-01 2099-12-31 NA
#> 2 1970-01-01 2099-12-31 NA
#> 3 2017-01-31 2099-12-31 NA
#> 4 1970-01-01 2099-12-31 NA
#> 5 2014-01-31 2099-12-31 NA
#> 6 1970-01-01 2099-12-31 NA
Specimen
head(SPECIMEN)
#> concept_id value_set_name
#> 1 1027716 GeneticSpecimenTypeVS
#> 2 1032268 GeneticSpecimenTypeVS
#> 3 1033195 GeneticSpecimenTypeVS
#> 4 1033465 GeneticSpecimenTypeVS
#> 5 1033739 GeneticSpecimenTypeVS
#> 6 1585831 GeneticSpecimenTypeVS
#> code_system logical_definition code
#> 1 http://terminology.hl7.org/CodeSystem/v2-0487 NA SKN
#> 2 http://terminology.hl7.org/CodeSystem/v2-0487 NA PLC
#> 3 http://terminology.hl7.org/CodeSystem/v2-0487 NA SAL
#> 4 http://terminology.hl7.org/CodeSystem/v2-0487 NA SPT
#> 5 http://terminology.hl7.org/CodeSystem/v2-0487 NA WND
#> 6 http://terminology.hl7.org/CodeSystem/v2-0487 NA BON
#> code_description
#> 1 Skin
#> 2 Placenta
#> 3 Saliva
#> 4 Sputum
#> 5 Wound
#> 6 Bone
#> Observation
#> 1 [V] [N] 1027716 Skin [LOINC LP36760-4] [Observation] [LOINC System]
#> 2 [V] [N] 1032268 Placenta [LOINC LP7477-5] [Observation] [LOINC System]
#> 3 [V] [N] 1033195 Saliva [LOINC LP7565-7] [Observation] [LOINC System]
#> 4 [V] [N] 1033465 Sputum [LOINC LP7600-2] [Observation] [LOINC System]
#> 5 [V] [N] 1033739 Wound [LOINC LP7726-5] [Observation] [LOINC System]
#> 6 [V] [N] 1585831 Organ Transplant Description: Bone [PPI OrganTransplantDescription_Bone] [Observation] [Answer]
#> Condition Spec Anatomic Site Drug Meas Value Measurement Specimen X14
#> 1 <NA> <NA> <NA> <NA> <NA> <NA> NA
#> 2 <NA> <NA> <NA> <NA> <NA> <NA> NA
#> 3 <NA> <NA> <NA> <NA> <NA> <NA> NA
#> 4 <NA> <NA> <NA> <NA> <NA> <NA> NA
#> 5 <NA> <NA> <NA> <NA> <NA> <NA> NA
#> 6 <NA> <NA> <NA> <NA> <NA> <NA> NA
Units of Measurement
head(UNITS_OF_MEASUREMENT)
#> value_set_name code_system logical_definition code
#> 1 UnitsOfLengthVS http://unitsofmeasure.org NA pm
#> 2 UnitsOfLengthVS http://unitsofmeasure.org NA nm
#> 3 UnitsOfLengthVS http://unitsofmeasure.org NA mm
#> 4 UnitsOfLengthVS http://unitsofmeasure.org NA cm
#> 5 UnitsOfLengthVS http://unitsofmeasure.org NA m
#> 6 UnitsOfLengthVS http://unitsofmeasure.org NA ft-us
#> code_description concept_id concept_name domain_id vocabulary_id
#> 1 Picometer NA <NA> <NA> <NA>
#> 2 Nanometer NA <NA> <NA> <NA>
#> 3 Millimeter NA <NA> <NA> <NA>
#> 4 Centimeter NA <NA> <NA> <NA>
#> 5 Meter NA <NA> <NA> <NA>
#> 6 Foot NA <NA> <NA> <NA>
#> concept_class_id standard_concept concept_code valid_start_date
#> 1 <NA> <NA> <NA> <NA>
#> 2 <NA> <NA> <NA> <NA>
#> 3 <NA> <NA> <NA> <NA>
#> 4 <NA> <NA> <NA> <NA>
#> 5 <NA> <NA> <NA> <NA>
#> 6 <NA> <NA> <NA> <NA>
#> valid_end_date invalid_reason
#> 1 <NA> <NA>
#> 2 <NA> <NA>
#> 3 <NA> <NA>
#> 4 <NA> <NA>
#> 5 <NA> <NA>
#> 6 <NA> <NA>
Code of Conduct
Please note that the mOMOP project is released with a Contributor Code
of
Conduct.
By contributing to this project, you agree to abide by its terms.
meerapatelmd/mOMOP documentation built on June 15, 2021, 3:01 p.m.
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mOMOP
The goal of mOMOP is to crosswalk the Minimal Common Oncology Data Elements (mCode) with the OMOP Vocabularies. mCode and the mCode Initiative provides a common data language and model for data exchange between entities while the OMOP Vocabularies integrate data elements into the OMOP Common Data Model to serve analytics use cases. A crosswalk using the terminology service will bridge the gap between data interoperability and analytical application.
Installation
You can install mOMOP with:
library(devtools)
install_github("meerapatelmd/mOMOP")
Examples
library(mOMOP)
mCode Class Hierarchy
The end-product of this package is the MCODE_CLASS_HIERARCHY dataset,
which is a flattened taxonomy that serves a variety of use cases. For
example, it can be used to incorporate mCode into a lookup table in a
relational database such as the retrieval of a certain class of data
elements or it can be incorporated into an ontology.
head(MCODE_CLASS_HIERARCHY)
#> class
#> 1 CANCER_BODY_LOCATION
#> 2 CANCER_BODY_LOCATION
#> 3 CANCER_BODY_LOCATION
#> 4 CANCER_BODY_LOCATION
#> 5 CANCER_BODY_LOCATION
#> 6 CANCER_BODY_LOCATION
#> concept
#> 1 [V] [S] 4048384 Body structure [SNOMED 123037004] [Spec Anatomic Site] [Body Structure]
#> 2 [V] [S] 4002852 Buccal embrasure [SNOMED 110326006] [Spec Anatomic Site] [Body Structure]
#> 3 [V] [S] 36717763 Skin structure of left lower eyelid [SNOMED 719884003] [Spec Anatomic Site] [Body Structure]
#> 4 [V] [S] 4230944 Adenofibrosis [SNOMED 89115006] [Observation] [Morph Abnormality]
#> 5 [V] [S] 42605189 Intervertebral foramen of eighteenth thoracic vertebra [SNOMED Veterinary 336621000009107] [Spec Anatomic Site] [Body Structure]
#> 6 [V] [S] 4097829 Transitional cell carcinoma [SNOMED 27090000] [Observation] [Morph Abnormality]
Crosswalks from mCode to OMOP
The crosswalk between mCode value sets and OMOP concepts used to create
the MCODE_CLASS_HIERARCHY dataset can be accessed with the following
pre-packaged dataframes: CANCER_STAGING, GENOMICS, ICD10CM,
LOINC, SNOMED, SPECIMEN, UNITS_OF_MEASUREMENT.
Cancer Staging
head(CANCER_STAGING)
#> value_set_name code_system
#> 1 TNMDistantMetastasesCategoryVS http://cancerstaging.org
#> 2 TNMDistantMetastasesCategoryVS http://cancerstaging.org
#> 3 TNMDistantMetastasesCategoryVS http://cancerstaging.org
#> 4 TNMDistantMetastasesCategoryVS http://cancerstaging.org
#> 5 TNMDistantMetastasesCategoryVS http://cancerstaging.org
#> 6 TNMDistantMetastasesCategoryVS http://cancerstaging.org
#> logical_definition code
#> 1 includes codes from code system http://cancerstaging.org NA
#> 2 includes codes from code system http://cancerstaging.org NA
#> 3 includes codes from code system http://cancerstaging.org NA
#> 4 includes codes from code system http://cancerstaging.org NA
#> 5 includes codes from code system http://cancerstaging.org NA
#> 6 includes codes from code system http://cancerstaging.org NA
#> code_description concept_id
#> 1 NA 1537692
#> 2 NA 1537780
#> 3 NA 1537798
#> 4 NA 1537804
#> 5 NA 1537805
#> 6 NA 1537808
#> concept_name
#> 1 Vulvar Cancer cM1 TNM Finding by AJCC/UICC 8th edition
#> 2 Retinoblastoma cM0 TNM Finding by AJCC/UICC 8th edition
#> 3 Eyelid Carcinoma pM1 TNM Finding by AJCC/UICC 8th edition
#> 4 Uterine Corpus Leiomyosarcoma and Endometrial Stromal Sarcoma cM0 TNM Finding by AJCC/UICC 8th edition
#> 5 Esophagus and Esophagogastric Junction Cancer cM1 TNM Finding by AJCC/UICC 8th edition
#> 6 Duodenum and Ampulla of Vater Neuroendocrine Tumor cM1c TNM Finding by AJCC/UICC 8th edition
#> domain_id vocabulary_id concept_class_id standard_concept concept_code
#> 1 Measurement NCIt AJCC Category S cM1-50-8
#> 2 Measurement NCIt AJCC Category S cM0-68-8
#> 3 Measurement NCIt AJCC Category S pM1-64-8
#> 4 Measurement NCIt AJCC Category S cM0-54.1-8
#> 5 Measurement NCIt AJCC Category S cM1-16-8
#> 6 Measurement NCIt AJCC Category S cM1c-30-8
#> valid_start_date valid_end_date invalid_reason
#> 1 2018-01-01 2099-12-31 NA
#> 2 2018-01-01 2099-12-31 NA
#> 3 2018-01-01 2099-12-31 NA
#> 4 2018-01-01 2099-12-31 NA
#> 5 2018-01-01 2099-12-31 NA
#> 6 2018-01-01 2099-12-31 NA
Genomics
head(GENOMICS)
#> value_set_name code_system
#> 1 HGNCVS http://www.genenames.org/geneId
#> 2 HGNCVS http://www.genenames.org/geneId
#> 3 HGNCVS http://www.genenames.org/geneId
#> 4 HGNCVS http://www.genenames.org/geneId
#> 5 HGNCVS http://www.genenames.org/geneId
#> 6 HGNCVS http://www.genenames.org/geneId
#> logical_definition code code_description concept_id
#> 1 All codes in http://www.genenames.org/geneId NA NA 35944910
#> 2 All codes in http://www.genenames.org/geneId NA NA 35944911
#> 3 All codes in http://www.genenames.org/geneId NA NA 35944912
#> 4 All codes in http://www.genenames.org/geneId NA NA 35944913
#> 5 All codes in http://www.genenames.org/geneId NA NA 35944914
#> 6 All codes in http://www.genenames.org/geneId NA NA 35944916
#> concept_name domain_id vocabulary_id
#> 1 CCDC77 (coiled-coil domain containing 77) Variant Measurement HGNC
#> 2 INMT (indolethylamine N-methyltransferase) Variant Measurement HGNC
#> 3 ZNF117 (zinc finger protein 117) Variant Measurement HGNC
#> 4 CKAP2 (cytoskeleton associated protein 2) Variant Measurement HGNC
#> 5 ITPRIPL2 (ITPRIP like 2) Variant Measurement HGNC
#> 6 PEX19 (peroxisomal biogenesis factor 19) Variant Measurement HGNC
#> concept_class_id standard_concept concept_code valid_start_date
#> 1 Gene S 28203 2006-02-16
#> 2 Gene S 6069 1999-09-07
#> 3 Gene S 12897 1992-05-19
#> 4 Gene S 1990 1999-12-01
#> 5 Gene S 27257 2008-08-11
#> 6 Gene S 9713 1997-06-12
#> valid_end_date invalid_reason
#> 1 2099-12-31 NA
#> 2 2099-12-31 NA
#> 3 2099-12-31 NA
#> 4 2099-12-31 NA
#> 5 2099-12-31 NA
#> 6 2099-12-31 NA
ICD-10-CM
head(ICD10CM)
#> value_set_name code_system logical_definition code
#> 1 CancerDisorderVS ICD-10-CM NA C00.0
#> 2 CancerDisorderVS ICD-10-CM NA C00.1
#> 3 CancerDisorderVS ICD-10-CM NA C00.2
#> 4 CancerDisorderVS ICD-10-CM NA C00.3
#> 5 CancerDisorderVS ICD-10-CM NA C00.4
#> 6 CancerDisorderVS ICD-10-CM NA C00.5
#> code_description concept_id
#> 1 Malignant neoplasm of external upper lip 35206047
#> 2 Malignant neoplasm of external lower lip 35206048
#> 3 Malignant neoplasm of external lip, unspecified 35206049
#> 4 Malignant neoplasm of upper lip, inner aspect 35206050
#> 5 Malignant neoplasm of lower lip, inner aspect 35206051
#> 6 Malignant neoplasm of lip, unspecified, inner aspect 35206052
#> concept_name domain_id vocabulary_id
#> 1 Malignant neoplasm of external upper lip Condition ICD10CM
#> 2 Malignant neoplasm of external lower lip Condition ICD10CM
#> 3 Malignant neoplasm of external lip, unspecified Condition ICD10CM
#> 4 Malignant neoplasm of upper lip, inner aspect Condition ICD10CM
#> 5 Malignant neoplasm of lower lip, inner aspect Condition ICD10CM
#> 6 Malignant neoplasm of lip, unspecified, inner aspect Condition ICD10CM
#> concept_class_id standard_concept concept_code valid_start_date
#> 1 4-char billing code NA C00.0 2007-01-01
#> 2 4-char billing code NA C00.1 2007-01-01
#> 3 4-char billing code NA C00.2 2007-01-01
#> 4 4-char billing code NA C00.3 2007-01-01
#> 5 4-char billing code NA C00.4 2007-01-01
#> 6 4-char billing code NA C00.5 2007-01-01
#> valid_end_date invalid_reason
#> 1 2099-12-31 NA
#> 2 2099-12-31 NA
#> 3 2099-12-31 NA
#> 4 2099-12-31 NA
#> 5 2099-12-31 NA
#> 6 2099-12-31 NA
LOINC
head(LOINC)
#> value_set_name code_system logical_definition code
#> 1 TumorMarkerTestVS LOINC NA 1695-6
#> 2 TumorMarkerTestVS LOINC NA 31203-3
#> 3 TumorMarkerTestVS LOINC NA 1692-3
#> 4 TumorMarkerTestVS LOINC NA 1693-1
#> 5 TumorMarkerTestVS LOINC NA 1694-9
#> 6 TumorMarkerTestVS LOINC NA 72820-4
#> code_description
#> 1 5-Hydroxyindoleacetate [Mass/time] in 24 hour Urine
#> 2 5-Hydroxyindoleacetate [Mass/volume] in 24 hour Urine
#> 3 5-Hydroxyindoleacetate [Mass/volume] in Cerebral spinal fluid
#> 4 5-Hydroxyindoleacetate [Mass/volume] in Serum or Plasma
#> 5 5-Hydroxyindoleacetate [Mass/volume] in Urine
#> 6 5-Hydroxyindoleacetate [Mass/volume] in Urine by Confirmatory method
#> concept_id
#> 1 3005148
#> 2 3023028
#> 3 3014670
#> 4 3021106
#> 5 3021385
#> 6 43055680
#> concept_name
#> 1 5-Hydroxyindoleacetate [Mass/time] in 24 hour Urine
#> 2 5-Hydroxyindoleacetate [Mass/volume] in 24 hour Urine
#> 3 5-Hydroxyindoleacetate [Mass/volume] in Cerebral spinal fluid
#> 4 5-Hydroxyindoleacetate [Mass/volume] in Serum or Plasma
#> 5 5-Hydroxyindoleacetate [Mass/volume] in Urine
#> 6 5-Hydroxyindoleacetate [Mass/volume] in Urine by Confirmatory method
#> domain_id vocabulary_id concept_class_id standard_concept concept_code
#> 1 Measurement LOINC Lab Test S 1695-6
#> 2 Measurement LOINC Lab Test S 31203-3
#> 3 Measurement LOINC Lab Test S 1692-3
#> 4 Measurement LOINC Lab Test S 1693-1
#> 5 Measurement LOINC Lab Test S 1694-9
#> 6 Measurement LOINC Lab Test S 72820-4
#> valid_start_date valid_end_date invalid_reason
#> 1 1970-01-01 2099-12-31 NA
#> 2 1970-01-01 2099-12-31 NA
#> 3 1970-01-01 2099-12-31 NA
#> 4 1970-01-01 2099-12-31 NA
#> 5 1970-01-01 2099-12-31 NA
#> 6 2012-12-10 2099-12-31 NA
SNOMED
head(SNOMED)
#> value_set_name code_system
#> 1 CancerBodyLocationVS SNOMED CT
#> 2 CancerBodyLocationVS SNOMED CT
#> 3 CancerBodyLocationVS SNOMED CT
#> 4 CancerBodyLocationVS SNOMED CT
#> 5 CancerBodyLocationVS SNOMED CT
#> 6 CancerBodyLocationVS SNOMED CT
#> logical_definition ancestors_of
#> 1 includes codes descending from 123037004 | Body Structure NA
#> 2 includes codes descending from 123037004 | Body Structure NA
#> 3 includes codes descending from 123037004 | Body Structure NA
#> 4 includes codes descending from 123037004 | Body Structure NA
#> 5 includes codes descending from 123037004 | Body Structure NA
#> 6 includes codes descending from 123037004 | Body Structure NA
#> descendants_of code code_description all_codes concept_id
#> 1 123037004 NA NA 123037004 4048384
#> 2 123037004 NA NA 123037004 4002852
#> 3 123037004 NA NA 123037004 36717763
#> 4 123037004 NA NA 123037004 4230944
#> 5 123037004 NA NA 123037004 42605189
#> 6 123037004 NA NA 123037004 4097829
#> concept_name domain_id
#> 1 Body structure Spec Anatomic Site
#> 2 Buccal embrasure Spec Anatomic Site
#> 3 Skin structure of left lower eyelid Spec Anatomic Site
#> 4 Adenofibrosis Observation
#> 5 Intervertebral foramen of eighteenth thoracic vertebra Spec Anatomic Site
#> 6 Transitional cell carcinoma Observation
#> vocabulary_id concept_class_id standard_concept concept_code
#> 1 SNOMED Body Structure S 123037004
#> 2 SNOMED Body Structure S 110326006
#> 3 SNOMED Body Structure S 719884003
#> 4 SNOMED Morph Abnormality S 89115006
#> 5 SNOMED Veterinary Body Structure S 336621000009107
#> 6 SNOMED Morph Abnormality S 27090000
#> valid_start_date valid_end_date invalid_reason
#> 1 1970-01-01 2099-12-31 NA
#> 2 1970-01-01 2099-12-31 NA
#> 3 2017-01-31 2099-12-31 NA
#> 4 1970-01-01 2099-12-31 NA
#> 5 2014-01-31 2099-12-31 NA
#> 6 1970-01-01 2099-12-31 NA
Specimen
head(SPECIMEN)
#> concept_id value_set_name
#> 1 1027716 GeneticSpecimenTypeVS
#> 2 1032268 GeneticSpecimenTypeVS
#> 3 1033195 GeneticSpecimenTypeVS
#> 4 1033465 GeneticSpecimenTypeVS
#> 5 1033739 GeneticSpecimenTypeVS
#> 6 1585831 GeneticSpecimenTypeVS
#> code_system logical_definition code
#> 1 http://terminology.hl7.org/CodeSystem/v2-0487 NA SKN
#> 2 http://terminology.hl7.org/CodeSystem/v2-0487 NA PLC
#> 3 http://terminology.hl7.org/CodeSystem/v2-0487 NA SAL
#> 4 http://terminology.hl7.org/CodeSystem/v2-0487 NA SPT
#> 5 http://terminology.hl7.org/CodeSystem/v2-0487 NA WND
#> 6 http://terminology.hl7.org/CodeSystem/v2-0487 NA BON
#> code_description
#> 1 Skin
#> 2 Placenta
#> 3 Saliva
#> 4 Sputum
#> 5 Wound
#> 6 Bone
#> Observation
#> 1 [V] [N] 1027716 Skin [LOINC LP36760-4] [Observation] [LOINC System]
#> 2 [V] [N] 1032268 Placenta [LOINC LP7477-5] [Observation] [LOINC System]
#> 3 [V] [N] 1033195 Saliva [LOINC LP7565-7] [Observation] [LOINC System]
#> 4 [V] [N] 1033465 Sputum [LOINC LP7600-2] [Observation] [LOINC System]
#> 5 [V] [N] 1033739 Wound [LOINC LP7726-5] [Observation] [LOINC System]
#> 6 [V] [N] 1585831 Organ Transplant Description: Bone [PPI OrganTransplantDescription_Bone] [Observation] [Answer]
#> Condition Spec Anatomic Site Drug Meas Value Measurement Specimen X14
#> 1 <NA> <NA> <NA> <NA> <NA> <NA> NA
#> 2 <NA> <NA> <NA> <NA> <NA> <NA> NA
#> 3 <NA> <NA> <NA> <NA> <NA> <NA> NA
#> 4 <NA> <NA> <NA> <NA> <NA> <NA> NA
#> 5 <NA> <NA> <NA> <NA> <NA> <NA> NA
#> 6 <NA> <NA> <NA> <NA> <NA> <NA> NA
Units of Measurement
head(UNITS_OF_MEASUREMENT)
#> value_set_name code_system logical_definition code
#> 1 UnitsOfLengthVS http://unitsofmeasure.org NA pm
#> 2 UnitsOfLengthVS http://unitsofmeasure.org NA nm
#> 3 UnitsOfLengthVS http://unitsofmeasure.org NA mm
#> 4 UnitsOfLengthVS http://unitsofmeasure.org NA cm
#> 5 UnitsOfLengthVS http://unitsofmeasure.org NA m
#> 6 UnitsOfLengthVS http://unitsofmeasure.org NA ft-us
#> code_description concept_id concept_name domain_id vocabulary_id
#> 1 Picometer NA <NA> <NA> <NA>
#> 2 Nanometer NA <NA> <NA> <NA>
#> 3 Millimeter NA <NA> <NA> <NA>
#> 4 Centimeter NA <NA> <NA> <NA>
#> 5 Meter NA <NA> <NA> <NA>
#> 6 Foot NA <NA> <NA> <NA>
#> concept_class_id standard_concept concept_code valid_start_date
#> 1 <NA> <NA> <NA> <NA>
#> 2 <NA> <NA> <NA> <NA>
#> 3 <NA> <NA> <NA> <NA>
#> 4 <NA> <NA> <NA> <NA>
#> 5 <NA> <NA> <NA> <NA>
#> 6 <NA> <NA> <NA> <NA>
#> valid_end_date invalid_reason
#> 1 <NA> <NA>
#> 2 <NA> <NA>
#> 3 <NA> <NA>
#> 4 <NA> <NA>
#> 5 <NA> <NA>
#> 6 <NA> <NA>
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