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.
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 NAGenomics
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 NAICD-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 NALOINC
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 NASNOMED
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 NASpecimen
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> NAUnits 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.
