Various uses will be shown by chapter
source('codeToRun.R')## Reading prepared vocab data (may take 2-8 minutes)
## Vocab data all loaded.
## Time difference of 1.306024 minslibrary(DT);library(knitr)Of classes
get_version()## vocabulary_id vocabulary_name vocabulary_reference
## 1 None OMOP Standardized Vocabularies OMOP generated
## vocabulary_version vocabulary_concept_id
## 1 v5.0 09-JUL-19 44819096kable(overview_class())| concept_class_id | n |
|---|---|
| Marketed Product | 457353 |
| 11-digit NDC | 358943 |
| 9-digit NDC | 207316 |
| Branded Drug Box | 202829 |
| Physical Object | 190218 |
| OTC Drug | 189471 |
| Pharma/Biol Product | 175634 |
| Branded Drug | 169016 |
| AMPP | 146937 |
| Prescription Drug | 145743 |
| Branded Drug Comp | 142362 |
| Clinical Finding | 131876 |
| AMP | 131774 |
| Branded Drug Form | 114910 |
| ICD10PCS Hierarchy | 110632 |
| Clinical Drug Box | 107889 |
| Brand Name | 104404 |
| Clinical Drug | 103955 |
| 8th level | 102089 |
| Read | 101953 |
| LOINC Hierarchy | 97469 |
| Quant Branded Drug | 89291 |
| Clinical Drug Comp | 88064 |
| Drug Product | 84383 |
| Quant Branded Box | 82685 |
| ICD10PCS | 79758 |
| Procedure | 79261 |
| Quant Clinical Drug | 77352 |
| Quant Clinical Box | 70261 |
| 10th level | 62708 |
| Organism | 61769 |
| ICDO Condition | 58512 |
| Lab Test | 52593 |
| Clinical Drug Form | 51395 |
| 7-char billing code | 50012 |
| LLT | 47269 |
| Diagnosis | 37061 |
| Body Structure | 35795 |
| NAACCR Value | 30708 |
| VMPP | 30493 |
| GCN_SEQNO | 29658 |
| Ingredient | 29081 |
| Substance | 27977 |
| PT | 23708 |
| Clinical Observation | 23138 |
| Containered Pack | 21456 |
| Branded Dose Group | 20914 |
| 9th level | 20631 |
| Trade Product Pack | 20227 |
| VMP | 20148 |
| Answer | 19993 |
| VA Product | 18666 |
| Med Product Pack | 18388 |
| Clinical Dose Group | 15842 |
| Qualifier Value | 15757 |
| SPL | 14684 |
| Observable Entity | 14196 |
| ICD10 code | 13248 |
| Trade Product Unit | 13054 |
| CPT4 | 12029 |
| Device | 11598 |
| Chemical Structure | 10474 |
| Survey | 10048 |
| Multum | 9770 |
| 6-char billing code | 9747 |
| Supplier | 9362 |
| 6-char nonbill code | 9337 |
| 6th level | 8572 |
| 5-dig billing code | 8212 |
| OXMIS | 8118 |
| HCPCS | 7819 |
| Pharma Preparation | 7680 |
| Drug | 7554 |
| 4-dig billing code | 7524 |
| 5-char nonbill code | 6992 |
| Main Heading | 6957 |
| 7th level | 6574 |
| LOINC Group | 6542 |
| 5-char billing code | 6498 |
| Context-dependent | 5567 |
| 4-char billing code | 5452 |
| Social Context | 5367 |
| Med Product Unit | 5291 |
| ATC 5th | 4949 |
| Ind / CI | 4873 |
| Morph Abnormality | 4851 |
| 4-char nonbill code | 4496 |
| Trade Product | 4363 |
| Suppl Concept | 4338 |
| CPT4 Hierarchy | 3367 |
| Medicinal Product | 3163 |
| Precise Ingredient | 2856 |
| Staging / Scales | 2097 |
| AU Substance | 2065 |
| ICD10 Hierarchy | 2049 |
| Specimen | 1942 |
| Location | 1866 |
| Physiologic Effect | 1866 |
| NAACCR Variable | 1861 |
| Branded Pack | 1768 |
| HLT | 1737 |
| 4-dig nonbill code | 1730 |
| 3-char nonbill code | 1687 |
| 11th level | 1632 |
| Question | 1598 |
| Regimen | 1546 |
| Clinical Pack | 1523 |
| 3-dig nonbill code | 1505 |
| ICDO Histology | 1368 |
| ATC 4th | 1298 |
| 4-dig billing E code | 1247 |
| Record Artifact | 1185 |
| Attribute | 1102 |
| Dose Form | 1054 |
| Finding | 1026 |
| Misc | 986 |
| Field | 869 |
| Unit | 855 |
| MS-DRG | 752 |
| APC | 715 |
| Model Comp | 710 |
| CDT | 699 |
| NFC | 692 |
| NAACCR Procedure | 679 |
| Plasma Derivative | 674 |
| 5-dig billing V code | 634 |
| Mechanism of Action | 628 |
| Pharmacologic Class | 625 |
| Claims Attachment | 615 |
| ATC 3rd | 585 |
| 5th level | 567 |
| Visit | 564 |
| Component | 555 |
| Branded Pack Box | 550 |
| Physician Specialty | 546 |
| Relationship | 542 |
| Revenue Code | 538 |
| VA Class | 486 |
| Vaccine | 478 |
| Permissible Range | 475 |
| 4-dig billing V code | 474 |
| Provider | 453 |
| Clinical Pack Box | 439 |
| Event | 433 |
| Supplement | 432 |
| ICDO Topography | 400 |
| CPT4 Modifier | 393 |
| HCPCS Modifier | 363 |
| Concept Class | 361 |
| 4th level | 354 |
| Disposition | 340 |
| HLGT | 337 |
| Component Class | 333 |
| Test | 327 |
| Admin Concept | 321 |
| SMQ | 318 |
| 3-dig billing code | 313 |
| LOINC Class | 301 |
| Animal Drug | 232 |
| Namespace Concept | 230 |
| 3-char billing code | 223 |
| Physical Force | 196 |
| CVX | 195 |
| NAACCR Schema | 195 |
| Non-Stand Allergenic | 194 |
| ATC 2nd | 183 |
| Currency | 180 |
| 3-dig nonbill E code | 171 |
| 12th level | 165 |
| Payer | 162 |
| 4-dig nonbill V code | 159 |
| Doc Subject Matter | 151 |
| AU Qualifier | 146 |
| Doc Type of Service | 141 |
| ConvSet | 136 |
| Form | 133 |
| Radiology | 130 |
| Anatomy | 123 |
| LOINC Document Type | 121 |
| Vocabulary | 110 |
| Cosmetic | 108 |
| Condition Type | 104 |
| Navi Concept | 101 |
| 2-dig nonbill code | 100 |
| Procedure Type | 97 |
| Standard Allergenic | 97 |
| CDT Hierarchy | 95 |
| 3-dig nonbill V code | 89 |
| Drug form | 88 |
| Cohort | 78 |
| Life circumstance | 73 |
| Topic | 72 |
| Doc Kind | 68 |
| LabSet | 64 |
| Pharmacokinetics | 59 |
| Race | 57 |
| UB04 Pt dis status | 55 |
| Table | 53 |
| Domain | 51 |
| Units of Measure | 49 |
| Place of Service | 48 |
| Dose Form Group | 45 |
| 3-dig billing E code | 44 |
| Death Type | 42 |
| Symptom/Finding | 37 |
| Canonical Unit | 35 |
| Cellular Therapy | 34 |
| Misc Order | 34 |
| Context | 33 |
| Frequency | 33 |
| ATC 1st | 30 |
| NAACCR Proc Schema | 30 |
| Therapeutic Class | 30 |
| Doc Role | 29 |
| 3rd level | 28 |
| Observation | 27 |
| SOC | 27 |
| Summary | 27 |
| MDC | 26 |
| Detail | 24 |
| UB04 Point of Origin | 22 |
| 2nd level | 19 |
| Doc Setting | 18 |
| Regimen type | 18 |
| Visit Type | 18 |
| MedSet | 17 |
| Drug Type | 16 |
| Food | 16 |
| Observation Type | 15 |
| Symptom | 15 |
| Discharge Status | 14 |
| Drug Class | 14 |
| Plan Stop Reason | 13 |
| Route | 13 |
| Admitting Source | 12 |
| Medical supply | 12 |
| Meas Type | 11 |
| Procedure Code Type | 11 |
| CDM | 10 |
| Module | 10 |
| Note Type | 10 |
| Linkage Assertion | 9 |
| US Census Division | 9 |
| VTM | 9 |
| Inactive Concept | 8 |
| State | 7 |
| Undefined | 7 |
| Benefit | 6 |
| Obs Period Type | 6 |
| PPI Modifier | 6 |
| Sponsor | 6 |
| UB04 Pri Typ of Adm | 6 |
| Cost Type | 5 |
| Encounter Type | 5 |
| Episode Type | 5 |
| Gender | 5 |
| Metal level | 5 |
| Aggregate Meas | 4 |
| Device Type | 4 |
| Diagnosis Code Type | 4 |
| Enrollment Basis | 4 |
| Program | 4 |
| US Census Region | 4 |
| Blood Pressure Pos | 3 |
| Diagnosis Type | 3 |
| Disease Episode | 3 |
| Workflow | 3 |
| Biobank Flag | 2 |
| Chart Availability | 2 |
| Discharge Dispo | 2 |
| DRG Type | 2 |
| Ethnicity | 2 |
| Hispanic | 2 |
| Treatment Episode | 2 |
| Vital Source | 2 |
| 3-dig billing V code | 1 |
| Episode of Care | 1 |
| Special Concept | 1 |
| Specimen Type | 1 |
#dummyOverview of vocabularies
kable(overview_vocab())| vocabulary_id | n |
|---|---|
| RxNorm Extension | 1687745 |
| SNOMED | 720493 |
| NDC | 574890 |
| SPL | 354274 |
| dm+d | 338959 |
| LOINC | 207875 |
| OSM | 203339 |
| RxNorm | 199835 |
| ICD10PCS | 190390 |
| Read | 101953 |
| ICD10CM | 94444 |
| AMT | 76706 |
| MedDRA | 73078 |
| ICDO3 | 60280 |
| DPD | 55976 |
| CIEL | 48997 |
| JMDC | 35962 |
| NAACCR | 33948 |
| SNOMED Veterinary | 32390 |
| BDPM | 31561 |
| GCN_SEQNO | 29658 |
| NDFRT | 26427 |
| VA Product | 18666 |
| ICD9CM | 17552 |
| CPT4 | 15837 |
| ICD10 | 15297 |
| GGR | 13417 |
| MeSH | 11295 |
| OPCS4 | 10994 |
| Multum | 9770 |
| HCPCS | 8182 |
| OXMIS | 8118 |
| ATC | 6150 |
| HemOnc | 4678 |
| ICD9Proc | 4657 |
| PPI | 4316 |
| CDM | 932 |
| EphMRA ATC | 895 |
| UCUM | 890 |
| NUCC | 845 |
| CDT | 794 |
| DRG | 752 |
| APC | 715 |
| NFC | 692 |
| Relationship | 542 |
| Revenue Code | 538 |
| VA Class | 486 |
| Concept Class | 361 |
| SMQ | 318 |
| UB04 Typ bill | 298 |
| CVX | 195 |
| Currency | 180 |
| PHDSC | 162 |
| HES Specialty | 157 |
| Condition Type | 118 |
| Medicare Specialty | 116 |
| Vocabulary | 110 |
| ABMS | 97 |
| Procedure Type | 97 |
| PCORNet | 81 |
| Cohort | 78 |
| CMS Place of Service | 60 |
| UB04 Pt dis status | 55 |
| Cost | 51 |
| Domain | 51 |
| Race | 50 |
| Observation Type | 29 |
| MDC | 26 |
| UB04 Point of Origin | 22 |
| Visit Type | 18 |
| Drug Type | 16 |
| Death Type | 14 |
| Plan Stop Reason | 13 |
| US Census | 13 |
| Visit | 12 |
| Meas Type | 11 |
| Plan | 11 |
| Note Type | 10 |
| Episode | 6 |
| Obs Period Type | 6 |
| Sponsor | 6 |
| UB04 Pri Typ of Adm | 6 |
| Cost Type | 5 |
| Episode Type | 5 |
| Device Type | 4 |
| MMI | 4 |
| Provider | 4 |
| Ethnicity | 2 |
| Gender | 2 |
| None | 1 |
| Specimen Type | 1 |
| Supplier | 1 |
Overview of vocabularies with more data on concept status about each vocabulary (look for S and C mostly)
kable(overview_vocab_standard())| vocabulary_id | V1 | C | S |
|---|---|---|---|
| RxNorm Extension | 65415 | NA | 1622330 |
| SNOMED | 191112 | NA | 529381 |
| OSM | NA | NA | 203339 |
| ICD10PCS | NA | NA | 190390 |
| RxNorm | 15153 | 36801 | 147881 |
| LOINC | NA | 104433 | 103442 |
| ICDO3 | 5178 | NA | 55102 |
| SNOMED Veterinary | 396 | NA | 31994 |
| NAACCR | 8572 | NA | 25376 |
| dm+d | 318608 | NA | 20351 |
| CPT4 | 172 | 3367 | 12298 |
| NDC | 566259 | NA | 8631 |
| HCPCS | 1322 | NA | 6860 |
| AMT | 73761 | NA | 2945 |
| OPCS4 | 8618 | NA | 2376 |
| ICD9Proc | 2434 | NA | 2223 |
| HemOnc | 2748 | 351 | 1579 |
| PPI | 3068 | NA | 1248 |
| JMDC | 34735 | NA | 1227 |
| CDM | NA | NA | 932 |
| UCUM | NA | NA | 890 |
| CDT | NA | NA | 794 |
| DRG | NA | NA | 752 |
| APC | NA | NA | 715 |
| NUCC | 148 | NA | 697 |
| GGR | 12872 | NA | 545 |
| Revenue Code | NA | NA | 538 |
| CVX | NA | NA | 195 |
| Currency | NA | NA | 180 |
| PHDSC | 4 | NA | 158 |
| Condition Type | NA | NA | 118 |
| Medicare Specialty | 9 | NA | 107 |
| Procedure Type | NA | NA | 97 |
| ABMS | 10 | NA | 87 |
| HES Specialty | 93 | NA | 64 |
| CMS Place of Service | 9 | NA | 51 |
| Cost | NA | NA | 51 |
| Race | NA | NA | 50 |
| Observation Type | NA | NA | 29 |
| MDC | NA | NA | 26 |
| Visit Type | NA | NA | 18 |
| Drug Type | NA | NA | 16 |
| Death Type | NA | NA | 14 |
| Plan Stop Reason | NA | NA | 13 |
| US Census | NA | NA | 13 |
| Relationship | 530 | NA | 12 |
| Visit | NA | NA | 12 |
| Meas Type | NA | NA | 11 |
| Plan | NA | NA | 11 |
| Note Type | NA | NA | 10 |
| Episode | NA | NA | 6 |
| Obs Period Type | NA | NA | 6 |
| Sponsor | NA | NA | 6 |
| UB04 Pri Typ of Adm | NA | NA | 6 |
| Cost Type | NA | NA | 5 |
| Episode Type | NA | NA | 5 |
| Device Type | NA | NA | 4 |
| MMI | NA | NA | 4 |
| Provider | NA | NA | 4 |
| UB04 Typ bill | 294 | NA | 4 |
| Ethnicity | NA | NA | 2 |
| Gender | NA | NA | 2 |
| PCORNet | 79 | NA | 2 |
| Specimen Type | NA | NA | 1 |
| Supplier | NA | NA | 1 |
| ATC | NA | 6150 | NA |
| BDPM | 31561 | NA | NA |
| CIEL | 48997 | NA | NA |
| Cohort | NA | 78 | NA |
| Concept Class | 361 | NA | NA |
| Domain | 51 | NA | NA |
| DPD | 55976 | NA | NA |
| EphMRA ATC | NA | 895 | NA |
| GCN_SEQNO | 29658 | NA | NA |
| ICD10 | 15297 | NA | NA |
| ICD10CM | 94444 | NA | NA |
| ICD9CM | 17552 | NA | NA |
| MedDRA | NA | 73078 | NA |
| MeSH | 11295 | NA | NA |
| Multum | 9770 | NA | NA |
| NDFRT | 26427 | NA | NA |
| NFC | NA | 692 | NA |
| None | 1 | NA | NA |
| OXMIS | 8118 | NA | NA |
| Read | 101953 | NA | NA |
| SMQ | NA | 318 | NA |
| SPL | 14684 | 339590 | NA |
| UB04 Point of Origin | 22 | NA | NA |
| UB04 Pt dis status | 55 | NA | NA |
| VA Class | 486 | NA | NA |
| VA Product | 18666 | NA | NA |
| Vocabulary | 110 | NA | NA |
Overview of
kable(overview_domain())| domain_id | n |
|---|---|
| Drug | 3458270 |
| Condition | 439532 |
| Device | 402473 |
| Procedure | 300786 |
| Observation | 234332 |
| Geography | 203352 |
| Measurement | 199257 |
| Meas Value | 48403 |
| Spec Anatomic Site | 37806 |
| Metadata | 3123 |
| Type Concept | 2681 |
| Unit | 2237 |
| Specimen | 1993 |
| Provider | 1632 |
| Visit | 641 |
| Revenue Code | 538 |
| Race | 473 |
| Place of Service | 468 |
| Relationship | 260 |
| Route | 183 |
| Currency | 180 |
| Condition/Obs | 164 |
| Payer | 162 |
| Cost | 51 |
| Gender | 16 |
| Episode | 14 |
| Plan Stop Reason | 13 |
| Plan | 11 |
| Sponsor | 6 |
| Meas Value Operator | 5 |
| Condition/Procedure | 3 |
| Spec Disease Status | 3 |
| Ethnicity | 2 |
| Obs/Procedure | 2 |
| Condition/Meas | 1 |
Overview of
kable(overview_domain_and_vocab())| domain_id | vocabulary_id | n |
|---|---|---|
| Condition | SNOMED | 110558 |
| Condition | ICD10CM | 86665 |
| Condition | ICDO3 | 58512 |
| Condition | MedDRA | 52487 |
| Condition | Read | 48356 |
| Condition | CIEL | 38139 |
| Condition | ICD9CM | 15728 |
| Condition | ICD10 | 13935 |
| Condition | MeSH | 5964 |
| Condition | OXMIS | 5704 |
| Condition | SNOMED Veterinary | 3093 |
| Condition | SMQ | 318 |
| Condition | Cohort | 66 |
| Condition | OPCS4 | 6 |
| Condition | HCPCS | 1 |
| Condition/Meas | OXMIS | 1 |
| Condition/Obs | OXMIS | 164 |
| Condition/Procedure | OXMIS | 3 |
| Cost | Cost | 51 |
| Currency | Currency | 180 |
| Device | dm+d | 192567 |
| Device | SNOMED | 190673 |
| Device | NDC | 8631 |
| Device | HCPCS | 3433 |
| Device | AMT | 2945 |
| Device | SPL | 1262 |
| Device | JMDC | 1227 |
| Device | GGR | 545 |
| Device | BDPM | 478 |
| Device | CDT | 335 |
| Device | Read | 271 |
| Device | SNOMED Veterinary | 67 |
| Device | OXMIS | 16 |
| Device | CIEL | 12 |
| Device | OPCS4 | 11 |
| Drug | RxNorm Extension | 1687745 |
| Drug | NDC | 566259 |
| Drug | SPL | 352888 |
| Drug | RxNorm | 199835 |
| Drug | SNOMED | 185145 |
| Drug | dm+d | 146392 |
| Drug | AMT | 73761 |
| Drug | DPD | 55976 |
| Drug | JMDC | 34735 |
| Drug | BDPM | 31083 |
| Drug | GCN_SEQNO | 29658 |
| Drug | NDFRT | 26426 |
| Drug | VA Product | 18666 |
| Drug | GGR | 12872 |
| Drug | Multum | 9770 |
| Drug | CIEL | 7673 |
| Drug | ATC | 6150 |
| Drug | HemOnc | 4594 |
| Drug | MeSH | 4364 |
| Drug | HCPCS | 1242 |
| Drug | EphMRA ATC | 895 |
| Drug | NFC | 692 |
| Drug | VA Class | 486 |
| Drug | SNOMED Veterinary | 372 |
| Drug | Read | 242 |
| Drug | CVX | 195 |
| Drug | CPT4 | 113 |
| Drug | NAACCR | 26 |
| Drug | Cohort | 12 |
| Drug | OXMIS | 3 |
| Episode | NAACCR | 8 |
| Episode | Episode | 6 |
| Ethnicity | Ethnicity | 2 |
| Gender | SNOMED | 11 |
| Gender | Read | 3 |
| Gender | Gender | 2 |
| Geography | OSM | 203339 |
| Geography | US Census | 13 |
| Meas Value | NAACCR | 31084 |
| Meas Value | LOINC | 17086 |
| Meas Value | SNOMED | 223 |
| Meas Value | Read | 10 |
| Meas Value Operator | SNOMED | 5 |
| Measurement | LOINC | 170767 |
| Measurement | SNOMED | 13452 |
| Measurement | MedDRA | 10096 |
| Measurement | CPT4 | 1687 |
| Measurement | NAACCR | 1438 |
| Measurement | Read | 683 |
| Measurement | CIEL | 395 |
| Measurement | OXMIS | 183 |
| Measurement | MeSH | 163 |
| Measurement | HCPCS | 126 |
| Measurement | ICD9CM | 72 |
| Measurement | OPCS4 | 63 |
| Measurement | ICD10CM | 60 |
| Measurement | ICD10 | 37 |
| Measurement | PPI | 33 |
| Measurement | SNOMED Veterinary | 2 |
| Metadata | SNOMED | 1027 |
| Metadata | CDM | 932 |
| Metadata | Relationship | 542 |
| Metadata | Concept Class | 361 |
| Metadata | Vocabulary | 110 |
| Metadata | Read | 61 |
| Metadata | Domain | 51 |
| Metadata | SNOMED Veterinary | 24 |
| Metadata | NAACCR | 13 |
| Metadata | NDFRT | 1 |
| Metadata | None | 1 |
| Obs/Procedure | OXMIS | 2 |
| Observation | SNOMED | 128999 |
| Observation | Read | 30932 |
| Observation | SNOMED Veterinary | 27401 |
| Observation | LOINC | 20022 |
| Observation | ICD10CM | 7391 |
| Observation | PPI | 4283 |
| Observation | HCPCS | 2640 |
| Observation | MedDRA | 1962 |
| Observation | CIEL | 1945 |
| Observation | ICDO3 | 1768 |
| Observation | ICD9CM | 1458 |
| Observation | ICD10 | 1124 |
| Observation | OXMIS | 845 |
| Observation | DRG | 752 |
| Observation | APC | 715 |
| Observation | CPT4 | 667 |
| Observation | NAACCR | 627 |
| Observation | OPCS4 | 291 |
| Observation | CDT | 242 |
| Observation | SPL | 124 |
| Observation | PCORNet | 81 |
| Observation | MDC | 26 |
| Observation | UB04 Typ bill | 19 |
| Observation | UB04 Pri Typ of Adm | 6 |
| Observation | HES Specialty | 4 |
| Observation | MMI | 4 |
| Observation | NUCC | 4 |
| Payer | PHDSC | 162 |
| Place of Service | SNOMED | 374 |
| Place of Service | CPT4 | 48 |
| Place of Service | Read | 46 |
| Plan | Plan | 11 |
| Plan Stop Reason | Plan Stop Reason | 13 |
| Procedure | ICD10PCS | 190390 |
| Procedure | SNOMED | 50064 |
| Procedure | Read | 18433 |
| Procedure | CPT4 | 13322 |
| Procedure | OPCS4 | 9741 |
| Procedure | MedDRA | 8533 |
| Procedure | ICD9Proc | 4657 |
| Procedure | OXMIS | 1193 |
| Procedure | MeSH | 804 |
| Procedure | NAACCR | 752 |
| Procedure | HCPCS | 740 |
| Procedure | CIEL | 644 |
| Procedure | SNOMED Veterinary | 389 |
| Procedure | ICD10CM | 328 |
| Procedure | ICD9CM | 294 |
| Procedure | CDT | 217 |
| Procedure | ICD10 | 201 |
| Procedure | HemOnc | 84 |
| Provider | NUCC | 662 |
| Provider | SNOMED | 509 |
| Provider | HES Specialty | 149 |
| Provider | Read | 124 |
| Provider | ABMS | 97 |
| Provider | Medicare Specialty | 86 |
| Provider | Provider | 4 |
| Provider | Supplier | 1 |
| Race | SNOMED | 302 |
| Race | Read | 117 |
| Race | Race | 50 |
| Race | OXMIS | 4 |
| Relationship | SNOMED | 194 |
| Relationship | Read | 66 |
| Revenue Code | Revenue Code | 538 |
| Route | SNOMED | 183 |
| Spec Anatomic Site | SNOMED | 33991 |
| Spec Anatomic Site | Read | 1888 |
| Spec Anatomic Site | SNOMED Veterinary | 922 |
| Spec Anatomic Site | OPCS4 | 882 |
| Spec Anatomic Site | CIEL | 123 |
| Spec Disease Status | SNOMED | 3 |
| Specimen | SNOMED | 1805 |
| Specimen | SNOMED Veterinary | 120 |
| Specimen | Read | 51 |
| Specimen | CIEL | 17 |
| Sponsor | Sponsor | 6 |
| Type Concept | SNOMED | 1678 |
| Type Concept | Read | 669 |
| Type Concept | Condition Type | 118 |
| Type Concept | Procedure Type | 97 |
| Type Concept | Observation Type | 29 |
| Type Concept | Visit Type | 18 |
| Type Concept | Drug Type | 16 |
| Type Concept | Death Type | 14 |
| Type Concept | Meas Type | 11 |
| Type Concept | Note Type | 10 |
| Type Concept | Obs Period Type | 6 |
| Type Concept | Cost Type | 5 |
| Type Concept | Episode Type | 5 |
| Type Concept | Device Type | 4 |
| Type Concept | Specimen Type | 1 |
| Unit | SNOMED | 1297 |
| Unit | UCUM | 890 |
| Unit | CIEL | 49 |
| Unit | Read | 1 |
| Visit | UB04 Typ bill | 279 |
| Visit | NUCC | 179 |
| Visit | CMS Place of Service | 60 |
| Visit | UB04 Pt dis status | 55 |
| Visit | Medicare Specialty | 30 |
| Visit | UB04 Point of Origin | 22 |
| Visit | Visit | 12 |
| Visit | HES Specialty | 4 |
kable(vocabulary)| vocabulary_id | vocabulary_name | vocabulary_reference | vocabulary_version | vocabulary_concept_id |
|---|---|---|---|---|
| Cost Type | OMOP Cost Type | OMOP generated | 5029 | |
| PCORNet | National Patient-Centered Clinical Research Network (PCORI) | OMOP generated | 44819148 | |
| dm+d | Dictionary of Medicines and Devices (NHS) | https://isd.hscic.gov.uk/trud3/user/authenticated/group/0/pack/1/subpack/24/releases | dm+d Version 1.4.0 20190128 | 232 |
| Device Type | OMOP Device Type | OMOP generated | 44819151 | |
| Plan | Health Plan - contract to administer healthcare transactions by the payer, facilitated by the sponsor | OMOP generated | 32471 | |
| Medicare Specialty | Medicare provider/supplier specialty codes (CMS) | http://www.cms.gov/Medicare/Provider-Enrollment-and-Certification/MedicareProviderSupEnroll/Taxonomy.html | 2018-06-26 Specialty | 44819138 |
| PHDSC | Source of Payment Typology (PHDSC) | http://www.phdsc.org/standards/payer-typology-source.asp | Version 3.0 | 32473 |
| Provider | OMOP Provider | OMOP generated | 32573 | |
| VA Product | VA National Drug File Product (VA) | http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html | RXNORM 2018-08-12 | 44819120 |
| NAACCR | NAACCR Data Dictionary | http://datadictionary.naaccr.org/?c=10 | NAACCR v18 | 32642 |
| NDFRT | National Drug File - Reference Terminology (VA) | http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html | RXNORM 2018-08-12 | 44819103 |
| MEDRT | Medication Reference Terminology MED-RT (VA) | https://nciterms.nci.nih.gov/ncitbrowser/pages/vocabulary.jsf?dictionary=MED-RT | MED-RT 2018-09-04 | 32537 |
| Cohort Type | OMOP Cohort Type | OMOP generated | 44819234 | |
| ICDO3 | International Classification of Diseases for Oncology, Third Edition (WHO) | https://seer.cancer.gov/icd-o-3/ | ICDO3 SEER Site/Histology Released 09/18/2015 | 581426 |
| UB04 Pri Typ of Adm | UB04 Claim Inpatient Admission Type Code (CMS) | https://www.resdac.org/cms-data/variables/Claim-Inpatient-Admission-Type-Code | 32046 | |
| Read | NHS UK Read Codes Version 2 (HSCIC) | http://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html | NHS READV2 21.0.0 20160401000001 + DATAMIGRATION_25.0.0_20180403000001 | 44819113 |
| Revenue Code | UB04/CMS1450 Revenue Codes (CMS) | http://www.mpca.net/?page=ERC_finance | 2010 Release | 44819133 |
| Death Type | OMOP Death Type | OMOP generated | 44819135 | |
| DRG | Diagnosis-related group (CMS) | http://www.cms.gov/Medicare/Medicare-Fee-for-Service-Payment/AcuteInpatientPPS/Acute-Inpatient-Files-for-Download.html | 2011-18-02 | 44819130 |
| MedDRA | Medical Dictionary for Regulatory Activities (MSSO) | http://www.meddramsso.com/subscriber_download.asp | MedDRA Version 22.0 | 44819111 |
| ICD10PCS | ICD-10 Procedure Coding System (CMS) | http://www.cms.gov/Medicare/Coding/ICD10/index.html | ICD10PCS 2019 | 44819125 |
| Domain | OMOP Domain | OMOP generated | 44819147 | |
| OPCS4 | OPCS Classification of Interventions and Procedures version 4 (NHS) | http://systems.hscic.gov.uk/data/clinicalcoding/codingstandards/opcs4 | 2018 Release | 44819143 |
| Visit Type | OMOP Visit Type | OMOP generated | 44819150 | |
| HemOnc | HemOnc | https://hemonc.org | HemOnc 2019-05-30 | 32613 |
| AMT | Australian Medicines Terminology (NEHTA) | https://www.nehta.gov.au/implementation-resources/terminology-access | AMT 01-SEP-17 | 238 |
| Concept Class | OMOP Concept Class | OMOP generated | 44819233 | |
| Ethnicity | OMOP Ethnicity | OMOP generated | 44819134 | |
| EphMRA ATC | Anatomical Classification of Pharmaceutical Products (EphMRA) | http://www.ephmra.org/Anatomical-Classification | EphMRA ATC 2016 | 243 |
| UCUM | Unified Code for Units of Measure (Regenstrief Institute) | http://aurora.regenstrief.org/~ucum/ucum.html#section-Alphabetic-Index | Version 1.8.2 | 44819107 |
| NFC | New Form Code (EphMRA) | http://www.ephmra.org/New-Form-Codes-Classification | NFC 20160704 | 245 |
| ABMS | Provider Specialty (American Board of Medical Specialties) | http://www.abms.org/member-boards/specialty-subspecialty-certificates | 2018-06-26 ABMS | 45756746 |
| Drug Type | OMOP Drug Exposure Type | OMOP generated | 44819126 | |
| MMI | Modernizing Medicine (MMI) | MMI proprietary | 581367 | |
| CVX | CDC Vaccine Administered CVX (NCIRD) | https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx | CVX Code Set 20180831 | 581400 |
| Supplier | OMOP Supplier | OMOP generated | 32574 | |
| Plan Stop Reason | Plan Stop Reason - Reason for termination of the Health Plan | OMOP generated | 32474 | |
| Cohort | Legacy OMOP HOI or DOI cohort | OMOP generated | 44819123 | |
| Multum | Cerner Multum (Cerner) | http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html | 2013-07-10 | 44819112 |
| Race | Race and Ethnicity Code Set (USBC) | http://www.cdc.gov/nchs/data/dvs/Race_Ethnicity_CodeSet.pdf | Version 1.0 | 44819109 |
| CPT4 | Current Procedural Terminology version 4 (AMA) | http://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html | 2019 Release | 44819100 |
| APC | Ambulatory Payment Classification (CMS) | http://www.cms.gov/Medicare/Medicare-Fee-for-Service-Payment/HospitalOutpatientPPS/Hospital-Outpatient-Regulations-and-Notices.html | 2018-January-Addendum-A | 44819132 |
| Specimen Type | OMOP Specimen Type | OMOP generated | 581376 | |
| Note Type | OMOP Note Type | OMOP generated | 44819146 | |
| GGR | Commented Drug Directory (BCFI) | http://www.bcfi.be/nl/download | GGR 20190401 | 581450 |
| Episode | OMOP Episode | OMOP generated | 32523 | |
| Visit | OMOP Visit | OMOP generated | 44819119 | |
| ICD10CM | International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS) | http://www.cdc.gov/nchs/icd/icd10cm.htm | ICD10CM FY2019 code descriptions | 44819098 |
| Condition Type | OMOP Condition Occurrence Type | OMOP generated | 44819127 | |
| Procedure Type | OMOP Procedure Occurrence Type | OMOP generated | 44819128 | |
| JMDC | Japan Medical Data Center Drug Code (JMDC) | OMOP generated | JMDC 2019-03-11 | 32557 |
| Episode Type | OMOP Episode Type | OMOP generated | 32542 | |
| Meas Type | OMOP Measurement Type | OMOP generated | 44819152 | |
| MDC | Major Diagnostic Categories (CMS) | http://www.cms.gov/Medicare/Medicare-Fee-for-Service-Payment/AcuteInpatientPPS/Acute-Inpatient-Files-for-Download.html | 2013-01-06 | 44819131 |
| ATC | WHO Anatomic Therapeutic Chemical Classification | FDB UK distribution package | RXNORM 2018-08-12 | 44819117 |
| Cost | OMOP Cost | OMOP generated | 581457 | |
| Currency | International Currency Symbol (ISO 4217) | http://www.iso.org/iso/home/standards/currency_codes.htm | 2008 | 44819153 |
| SNOMED | Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO) | http://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html | Snomed Release 20190131 | 44819097 |
| VA Class | VA National Drug File Class (VA) | http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html | RXNORM 2018-08-12 | 44819122 |
| None | OMOP Standardized Vocabularies | OMOP generated | v5.0 09-JUL-19 | 44819096 |
| CDM | OMOP Common DataModel | https://github.com/OHDSI/CommonDataModel | CDM v6.0.0 | 32485 |
| HCPCS | Healthcare Common Procedure Coding System (CMS) | http://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html | 20180101 Alpha Numeric HCPCS File | 44819101 |
| MeSH | Medical Subject Headings (NLM) | http://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html | 2019 Release | 44819136 |
| ICD10 | International Classification of Diseases, Tenth Revision (WHO) | http://www.who.int/classifications/icd/icdonlineversions/en/ | 2016 Release | 44819124 |
| UB04 Typ bill | UB04 Type of Bill - Institutional (USHIK) | https://ushik.ahrq.gov/ViewItemDetails?&system=apcd&itemKey=196987000 | 32044 | |
| BDPM | Public Database of Medications (Social-Sante) | http://base-donnees-publique.medicaments.gouv.fr/telechargement.php | BDPM 17-JUL-17 | 236 |
| Vocabulary | OMOP Vocabulary | OMOP generated | 44819232 | |
| Relationship | OMOP Relationship | OMOP generated | 44819235 | |
| RxNorm | RxNorm (NLM) | http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html | RxNorm 20190603 | 44819104 |
| RxNorm Extension | RxNorm Extension (OMOP) | OMOP generated | RxNorm Extension 2019-06-10 | 252 |
| Obs Period Type | OMOP Observation Period Type | OMOP generated | 44819149 | |
| SMQ | Standardised MedDRA Queries (MSSO) | http://www.meddramsso.com/secure/smq/SMQ_Spreadsheet_14_0_English_update.xlsx | Version 14.0 | 44819121 |
| OXMIS | Oxford Medical Information System (OCHP) | Codes extracted from GPRD database, courtesy of GSK | 44819114 | |
| OSM | OpenStreetMap | https://www.openstreetmap.org/copyright/en, https://wambachers-osm.website/boundaries/ | OSM Release 2019-02-21 | 32541 |
| US Census | United States Census Bureau | https://www.census.gov/geo/maps-data/data/tiger-cart-boundary.html | US Census 2017 Release | 32570 |
| ICD9CM | International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS) | http://www.cms.gov/Medicare/Coding/ICD9ProviderDiagnosticCodes/codes.html | ICD9CM v32 master descriptions | 5046 |
| CDT | Current Dental Terminology (ADA) | http://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html | 2019 Release | 581438 |
| PPI | AllOfUs_PPI (Columbia) | http://terminology.pmi-ops.org/CodeSystem/ppi | Codebook Version 0.3.34 | 581404 |
| ICD9Proc | International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 3 (NCHS) | http://www.cms.gov/Medicare/Coding/ICD9ProviderDiagnosticCodes/codes.html | ICD9CM v32 master descriptions | 44819099 |
| Sponsor | Sponsor - institution or individual financing healthcare transactions | OMOP generated | 32472 | |
| NUCC | National Uniform Claim Committee Health Care Provider Taxonomy Code Set (NUCC) | http://www.nucc.org/index.php?option=com_content&view=article&id=107&Itemid=132 | 2018-06-26 NUCC | 44819137 |
| UB04 Point of Origin | UB04 Claim Source Inpatient Admission Code (CMS) | https://www.resdac.org/cms-data/variables/Claim-Source-Inpatient-Admission-Code | 32045 | |
| UB04 Pt dis status | UB04 Patient Discharge Status Code (CMS) | https://www.resdac.org/cms-data/variables/patient-discharge-status-code | 32047 | |
| CMS Place of Service | Place of Service Codes for Professional Claims (CMS) | http://www.cms.gov/Medicare/Medicare-Fee-for-Service-Payment/PhysicianFeeSched/downloads//Website_POS_database.pdf | 2009-01-11 | 44819110 |
| DPD | Drug Product Database (Health Canada) | http://open.canada.ca/data/en/dataset/bf55e42a-63cb-4556-bfd8-44f26e5a36fe | DPD 25-JUN-17 | 231 |
| Observation Type | OMOP Observation Type | OMOP generated | 44819129 | |
| CIEL | Columbia International eHealth Laboratory (Columbia University) | https://wiki.openmrs.org/display/docs/Getting+and+Using+the+MVP-CIEL+Concept+Dictionary | Openmrs 1.11.0 20150227 | 45905710 |
| Gender | OMOP Gender | OMOP generated | 44819108 | |
| SNOMED Veterinary | SNOMED Veterinary | https://vtsl.vetmed.vt.edu/extension/ | SNOMED Veterinary 20190401 | 32549 |
| HES Specialty | Hospital Episode Statistics Specialty (NHS) | http://www.datadictionary.nhs.uk/data_dictionary/attributes/m/main_specialty_code_de.asp?shownav=0 | 2018-06-26 HES Specialty | 44819145 |
| GCN_SEQNO | Clinical Formulation ID (FDB) | FDB US distribution package | 20151119 Release | 44819141 |
| NDC | National Drug Code (FDA and manufacturers) | http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html, http://www.fda.gov/downloads/Drugs/DevelopmentApprovalProcess/UCM070838.zip | NDC 20190707 | 44819105 |
| SPL | Structured Product Labeling (FDA) | http://www.fda.gov/Drugs/InformationOnDrugs/ucm142438.htm | NDC 20190707 | 44819140 |
| LOINC | Logical Observation Identifiers Names and Codes (Regenstrief Institute) | http://loinc.org/downloads/loinc | 2.66 | 44819102 |
#deprecated with no successor in LOINC and RxNorm
search_by_invalid_reason(invalid_reason_value = 'D',vocabulary = c('LOINC','RxNorm')) %>% head()## concept_id concept_name vocabulary_id
## 1 3023253 Deprecated Skilled nursing treatmen LOINC
## 2 3003626 Deprecated Alcohol-substance abuse LOINC
## 3 3010062 Deprecated Respiratory therapy trea LOINC
## 4 3038461 Deprecated Psychiatric rehabilitati LOINC
## 5 3038465 Deprecated Physical therapy treatme LOINC
## 6 3037178 Deprecated Cardiac rehabilitation t LOINCcid=1710316
search_concept_id(cid)## concept_id concept_name vocabulary_id
## 1 1710316 emtricitabine 200 MG / Tenofovir di RxNormsearch_relationships(cid,vocabulary = 'RxNorm',full_output = TRUE) %>% datatable(rownames = FALSE)#dummy#
#translate-dx.csv
tset<-c('ICD10CM','ICD9CM','ICD10')
#start<-concept %>% filter(vocabulary_id %in% tset)
#only taking certain relationship
mt<-concept_relationship %>% filter(relationship_id=='Maps to')
#more info on the concept 1 (from)
mt %<>% left_join(concept, by=c('concept_id_1'='concept_id'))
names(mt)## [1] "concept_id_1" "concept_id_2" "relationship_id"
## [4] "valid_start_date.x" "valid_end_date.x" "invalid_reason.x"
## [7] "concept_name" "domain_id" "vocabulary_id"
## [10] "concept_class_id" "standard_concept" "concept_code"
## [13] "valid_start_date.y" "valid_end_date.y" "invalid_reason.y"#restrict to our starting terminologies
mt2<-mt %>% filter(vocabulary_id %in% tset)
mt2 %<>% left_join(concept, by=c('concept_id_2'='concept_id'))
names(mt2)## [1] "concept_id_1" "concept_id_2" "relationship_id"
## [4] "valid_start_date.x" "valid_end_date.x" "invalid_reason.x"
## [7] "concept_name.x" "domain_id.x" "vocabulary_id.x"
## [10] "concept_class_id.x" "standard_concept.x" "concept_code.x"
## [13] "valid_start_date.y" "valid_end_date.y" "invalid_reason.y"
## [16] "concept_name.y" "domain_id.y" "vocabulary_id.y"
## [19] "concept_class_id.y" "standard_concept.y" "concept_code.y"
## [22] "valid_start_date" "valid_end_date" "invalid_reason"#all relationships are valid
mt2 %>% count(invalid_reason.x)## # A tibble: 1 x 2
## invalid_reason.x n
## <lgl> <int>
## 1 NA 158237#export
oname='local/translate_dx'
mt2 %>% write_csv(paste0(oname,'-all.csv'))
mt3<-mt2 %>% select(vocabulary_id=vocabulary_id.x,concept_code=concept_code.x,target_concept_id=concept_id_2)
mt3 %>% write_csv(paste0(oname,'.csv'))Small analysis
i10<-concept %>% filter(vocabulary_id=='ICD10' & invalid_reason=='')
i10cm<-concept %>% filter(vocabulary_id=='ICD10CM' & invalid_reason=='')
#inner_join(i10$concept_code,i10cm$concept_code)
#length(intersect(i10$concept_code,i10cm$concept_code) )
nrow(i10)## [1] 15297inInotCM<-setdiff(i10$concept_code,i10cm$concept_code)
nrow(i10cm)## [1] 94444#that many concepts are in Int and not in US version ( ICD10CM)
length(inInotCM)## [1] 3236d<-i10 %>% filter(concept_code %in% inInotCM)
d %>% datatable(rownames = FALSE)d %>% write_csv('local/inInotCM.csv')cid=37395835 #familial prostate cancer
#brief output
get_ancestors(cid) %>% datatable(rownames = FALSE)#full output (use full output parameter)