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Christian Reich edited this page Mar 21, 2020 · 49 revisions

This is an ad-hoc release for the purpose of creating harmonized data assets for our COVID-19 Study-a-thon on the 26-Mar-2020. This documentation has two parts: 1. The changes made to the vocabularies and 2. Instructions for folks ETLing data assets into the OMOP CDM.

Note: If you are involved in ETL please make sure to take a look at the instructions below. The reason is that there will be exceptions from the standard mapping rules applied during normal ETL, which are due to the provisional nature of some of the vocabulary artifacts.

1. Vocabulary changes

We identified relevant clinical entities that will potentially be used in definitions of COVID-19 study-a-thon cohorts and subsequent research. These were prioritized and processed accordingly. For each, we performed the following tasks:

1.1. Incorporation of novel Concepts

A number of vocabularies issued updated and newly added Concepts around COVID-19. We incorporated them into Standard Сoncepts (SNOMED, LOINC, CPT4, HCPCS) and non-standard Source Сoncepts (ICD10, KCD7, ICD10CN):

Click to expand - New Concepts

Concept_id Concept_name domain_id vocabulary_id Concept_code
700360 Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), amplified probe technique Procedure CPT4 87635
40218805 Testing for SARS-CoV-2 in CDC laboratory Observation HCPCS U0001
40218804 Testing for SARS-CoV-2 in non-CDC laboratory Observation HCPCS U0002
45756093 Emergency use of U07.1 | Disease caused by severe acute respiratory syndrome coronavirus 2 Condition ICD10 U07.1
710159 Confirmed COVID-19, excluding pneumonia (machine translation) Observation ICD10CN U07.100x002
710158 COVID-19 (machine translation) Observation ICD10CN U07.100
710155 COVID-19 pneumonia (machine translation) Observation ICD10CN U07.100x003
710156 COVID-19 pneumonia (machine translation) Observation ICD10CN U07.100x001
710160 Emergency use of U07.1 | Disease caused by severe acute respiratory syndrome coronavirus 2 Observation ICD10CN U07.1
710157 Suspected case of COVID-19 (machine translation) Procedure ICD10CN Z03.800x001
42501115 Emergency use of U07.1 | Disease caused by severe acute respiratory syndrome coronavirus 2 Condition KCD7 U07.1
586414 Novel coronavirus infection Condition KCD7 U18.1
586415 Provisional assignment of new diseases or emergency use Condition KCD7 U18
706164 Middle East respiratory syndrome coronavirus (MERS-CoV) RNA [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC 94501-4
706162 Respiratory viral pathogens DNA and RNA panel - Respiratory specimen Qualitative by NAA with probe detection Measurement LOINC 94499-1
706166 SARS coronavirus 2 E gene [Cycle Threshold #] in Unspecified specimen by NAA with probe detection Measurement LOINC 94509-7
706174 SARS coronavirus 2 E gene [Presence] in Unspecified specimen by NAA with probe detection Measurement LOINC 94315-9
706181 SARS coronavirus 2 IgG Ab [Presence] in Serum or Plasma by Immunoassay Measurement LOINC 94507-1
706177 SARS coronavirus 2 IgG Ab [Units/volume] in Serum or Plasma by Immunoassay Measurement LOINC 94505-5
706179 SARS coronavirus 2 IgG and IgM panel - Serum or Plasma by Immunoassay Measurement LOINC 94504-8
706176 SARS coronavirus 2 IgG and IgM panel - Serum or Plasma Qualitative by Immunoassay Measurement LOINC 94503-0
706180 SARS coronavirus 2 IgM Ab [Presence] in Serum or Plasma by Immunoassay Measurement LOINC 94508-9
706178 SARS coronavirus 2 IgM Ab [Units/volume] in Serum or Plasma by Immunoassay Measurement LOINC 94506-3
706167 SARS coronavirus 2 N gene [Cycle Threshold #] in Unspecified specimen by NAA with probe detection Measurement LOINC 94510-5
706157 SARS coronavirus 2 N gene [Cycle Threshold #] in Unspecified specimen by Nucleic acid amplification using primer-probe set N1 Measurement LOINC 94311-8
706155 SARS coronavirus 2 N gene [Cycle Threshold #] in Unspecified specimen by Nucleic acid amplification using primer-probe set N2 Measurement LOINC 94312-6
706161 SARS coronavirus 2 N gene [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC 94533-7
706175 SARS coronavirus 2 N gene [Presence] in Unspecified specimen by NAA with probe detection Measurement LOINC 94316-7
706156 SARS coronavirus 2 N gene [Presence] in Unspecified specimen by Nucleic acid amplification using primer-probe set N1 Measurement LOINC 94307-6
706154 SARS coronavirus 2 N gene [Presence] in Unspecified specimen by Nucleic acid amplification using primer-probe set N2 Measurement LOINC 94308-4
706168 SARS coronavirus 2 ORF1ab region [Cycle Threshold #] in Unspecified specimen by NAA with probe detection Measurement LOINC 94511-3
706160 SARS coronavirus 2 RdRp gene [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC 94534-5
706173 SARS coronavirus 2 RdRp gene [Presence] in Unspecified specimen by NAA with probe detection Measurement LOINC 94314-2
706158 SARS Coronavirus 2 RNA panel - Respiratory specimen by NAA with probe detection Measurement LOINC 94531-1
706169 SARS Coronavirus 2 RNA panel - Unspecified specimen by NAA with probe detection Measurement LOINC 94306-8
706163 SARS coronavirus 2 RNA [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC 94500-6
706170 SARS coronavirus 2 RNA [Presence] in Unspecified specimen by NAA with probe detection Measurement LOINC 94309-2
706159 SARS coronavirus+SARS-like coronavirus+SARS coronavirus 2+MERS coronavirus RNA [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC 94532-9
706165 SARS coronavirus+SARS-like coronavirus+SARS coronavirus 2 RNA [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC 94502-2
706172 SARS-like Coronavirus N gene [Cycle Threshold #] in Unspecified specimen by NAA with probe detection Measurement LOINC 94313-4
706171 SARS-like Coronavirus N gene [Presence] in Unspecified specimen by NAA with probe detection Measurement LOINC 94310-0
37310269 Disease caused by 2019 novel coronavirus Condition SNOMED 1240751000000100
37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 Condition SNOMED 840539006
37310284 Encephalopathy caused by 2019 novel coronavirus Condition SNOMED 1240561000000108
37310283 Gastroenteritis caused by 2019 novel coronavirus Condition SNOMED 1240571000000101
37310286 Infection of upper respiratory tract caused by 2019 novel coronavirus Condition SNOMED 1240541000000107
37310287 Myocarditis caused by 2019 novel coronavirus Condition SNOMED 1240531000000103
37310254 Otitis media caused by 2019 novel coronavirus Condition SNOMED 1240521000000100
37310285 Pneumonia caused by 2019 novel coronavirus Condition SNOMED 1240551000000105
37310268 Suspected disease caused by 2019 novel coronavirus Condition SNOMED 1240761000000102
37311060 Suspected disease caused by severe acute respiratory coronavirus 2 Condition SNOMED 840544004
37310282 2019 novel coronavirus detected Measurement SNOMED 1240581000000104
37310281 2019 novel coronavirus not detected Measurement SNOMED 1240591000000102
37310255 Detection of 2019 novel coronavirus using polymerase chain reaction technique Measurement SNOMED 1240511000000106
37310258 Measurement of 2019 novel coronavirus antibody Measurement SNOMED 1240461000000109
37310257 Measurement of 2019 novel coronavirus antigen Measurement SNOMED 1240471000000102
37310266 2019 novel coronavirus Observation SNOMED 1240381000000105
37310270 2019 novel coronavirus serology Observation SNOMED 1240741000000103
37310277 2019 novel coronavirus vaccination contraindicated Observation SNOMED 1240661000000107
37310278 2019 novel coronavirus vaccination declined Observation SNOMED 1240651000000109
37310267 2019 novel coronavirus vaccination invitation short message service text message sent Observation SNOMED 1240781000000106
37310275 2019 novel coronavirus vaccination not done Observation SNOMED 1240681000000103
37310276 2019 novel coronavirus vaccination not indicated Observation SNOMED 1240671000000100
37310274 2019 novel coronavirus vaccine not available Observation SNOMED 1240701000000101
37310271 Advice given about 2019 novel coronavirus by telephone Observation SNOMED 1240731000000107
37310272 Advice given about 2019 novel coronavirus infection Observation SNOMED 1240721000000105
37310264 Antibody to 2019 novel coronavirus Observation SNOMED 1240401000000105
37311063 Antibody to severe acute respiratory syndrome coronavirus 2 Observation SNOMED 840535000
37310265 Antigen of 2019 novel coronavirus Observation SNOMED 1240391000000107
37311062 Antigen of severe acute respiratory syndrome coronavirus 2 Observation SNOMED 840536004
37310260 Close exposure to 2019 novel coronavirus infection Observation SNOMED 1240441000000108
37310279 Did not attend 2019 novel coronavirus vaccination Observation SNOMED 1240631000000102
37310273 Educated about 2019 novel coronavirus infection Observation SNOMED 1240711000000104
37310261 Exposure to 2019 novel coronavirus infection Observation SNOMED 1240431000000104
37311059 Exposure to severe acute respiratory syndrome coronavirus 2 Observation SNOMED 840546002
37310280 High priority for 2019 novel coronavirus vaccination Observation SNOMED 1240601000000108
37310263 Ribonucleic acid of 2019 novel coronavirus Observation SNOMED 1240411000000107
37310262 Serotype 2019 novel coronavirus Observation SNOMED 1240421000000101
37311065 Severe acute respiratory syndrome coronavirus 2 Observation SNOMED 840533007
37310259 Telephone consultation for suspected 2019 novel coronavirus Observation SNOMED 1240451000000106
37310256 2019 novel coronavirus vaccination Procedure SNOMED 1240491000000103
37311064 Severe acute respiratory syndrome coronavirus 2 vaccination Procedure SNOMED 840534001

1.2. De-duplication of Concepts

Amongst new and existing Concepts, a few duplicates with identical or near identical semantic content were identified. One of these twins became non-Standard and was remapped to the other Standard equivalent.

Click to expand - Remapped duplicates

Concept_id Concept_name vocabulary_id relationship_id target_Concept_id target_Concept_name target_vocabulary_id
37310256 2019 novel coronavirus vaccination SNOMED Maps to 37311064 Severe acute respiratory syndrome coronavirus 2 vaccination SNOMED
37310261 Exposure to 2019 novel coronavirus infection SNOMED Maps to 37311059 Exposure to severe acute respiratory syndrome coronavirus 2 SNOMED
37310264 Antibody to 2019 novel coronavirus SNOMED Maps to 37311063 Antibody to severe acute respiratory syndrome coronavirus 2 SNOMED
37310265 Antigen of 2019 novel coronavirus SNOMED Maps to 37311062 Antigen of severe acute respiratory syndrome coronavirus 2 SNOMED
37310266 2019 novel coronavirus SNOMED Maps to 37311065 Severe acute respiratory syndrome coronavirus 2 SNOMED
37310268 Suspected disease caused by 2019 novel coronavirus SNOMED Maps to 37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 SNOMED
37310269 Disease caused by 2019 novel coronavirus SNOMED Maps to 37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 SNOMED
37311060 Suspected disease caused by severe acute respiratory coronavirus 2 SNOMED Maps to 37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 SNOMED

1.3. Domain reassignment

We also reviewed the Concepts for their correct Domain assignment and made necessary fixes. In particular, we moved test results from Condition into Measurement and suspected diseases from Observation into Condition.

Click to expand - Concepts (and descendents, not shown) with Domain update

old_domain_id new_domain_id Concept_id Concept_name
Observation Condition 4219847 Disease suspected
Condition Measurement 764933 Virus not detected
Condition Measurement 4038778 O/E -skin temperature abnormal
Condition Measurement 4039791 O/E - rectal temperature
Condition Measurement 4039792 O/E - core temperature
Condition Measurement 4039794 O/E - temperature normal
Condition Measurement 4039795 O/E - temperature elevated
Condition Measurement 4039796 O/E - hyperpyrexia - greater than 40.5 degrees Celsius
Condition Measurement 4040104 O/E - groin temperature
Condition Measurement 4040106 O/E - temperature low
Condition Measurement 4040267 O/E - fever - general
Condition Measurement 4040474 O/E - method fever registered
Condition Measurement 4040476 O/E - axillary temperature
Condition Measurement 4061901 O/E - rate of respiration
Condition Measurement 4077057 O/E - oral temperature
Condition Measurement 4141062 Fever greater than 100.4 Fahrenheit
Condition Measurement 4151775 O/E - tympanic temperature
Condition Measurement 4164378 O/E - hyperpyrexia
Condition Measurement 4231947 Virus present
Condition Measurement 4276586 Finding of HIV status
Condition Measurement 37310281 2019 novel coronavirus not detected
Condition Measurement 46272568 Bacteria present

1.4. Creation of de novo Concepts

To cover the entire semantic space we looked at various CRFs from prospective COVID-19 studies, we created 64 new Concepts of an ‘OMOP Extension’ placeholder vocabulary with various Domain assignments. These Concepts were mostly pre-coordinated Concepts between COVID-19 and its complications as well as various scenarios of exposure to the disease. All Concepts were placed into existing SNOMED and LOINC hierarchies. We expect some of them to be overwritten by the authoritative vocabularies at a later point in time, and we will deprecate and upgrade them appropriately if and when that happens.

Click to expand - Newly created Concepts

Concept_id Concept_name domain_id vocabulary_id
756023 Acute bronchitis caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
756044 Acute respiratory distress syndrome (ARDS) caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
756061 Asymptomatic infection caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
756031 Bronchitis caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
756081 Infection of lower respiratory tract caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
756039 Respiratory infection caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
756029 Detection of severe acute respiratory syndrome coronavirus 2 in Respiratory specimen Measurement OMOP Extension
756065 Detection of severe acute respiratory syndrome coronavirus 2 in Unspecified specimen Measurement OMOP Extension
756085 Detection of severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction technique in Respiratory specimen Measurement OMOP Extension
756084 Detection of severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction technique in Unspecified specimen Measurement OMOP Extension
756055 Measurement of severe acute respiratory syndrome coronavirus 2 Measurement OMOP Extension
756063 History of Animal exposure in the 14 days prior to illness onset Observation OMOP Extension
756060 History of Close contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756036 History of Close contact with patient with confirmed or presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756078 History of Close contact with patient with presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756024 History of Close contact with patient with presumptive/probable (then not confirmed) case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756028 History of Close contact with symptomatic patient with confirmed or presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756040 History of Close exposure to severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756042 History of Community contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756030 History of Contact with live/dead animals, raw meat or insect bites in the 14 days prior to illness onset Observation OMOP Extension
756070 History of Direct contact with animals in countries where COVID-19 is known to be circulating in animal populations or where human infections have occurred as a result of presumed zoonotic transmission in the 14 days prior to illness onset Observation OMOP Extension
756052 History of Exposure to patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756038 History of Exposure to patient with presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756025 History of Exposure to patient with presumptive/probable (then not confirmed) case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756034 History of Exposure to patient with severe acute lower respiratory distress (SARS) of unknown etiology in the 14 days prior to illness onset Observation OMOP Extension
756066 History of Exposure to severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756073 History of Healthcare contact of Healthcare worker with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756058 History of Healthcare contact of Patient with another patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756033 History of Healthcare contact of Visitor with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756067 History of Healthcare contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756080 History of Household contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756071 History of Presence in a healthcare facility where disease caused by severe acute respiratory syndrome coronavirus 2 has been managed in the 14 days prior to illness onset Observation OMOP Extension
756054 History of Presence in a laboratory handling suspected or confirmed cases samples of disease caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756049 History of Suspected exposure (but ruled out after evaluation) to severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756048 History of Suspected exposure to severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756043 History of travel to an area with documented cases of infection caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756074 History of travel to China in the 14 days prior to illness onset Observation OMOP Extension
756032 History of travel to Hubei in the 14 days prior to illness onset Observation OMOP Extension
756059 History of travel to Iran in the 14 days prior to illness onset Observation OMOP Extension
756053 History of travel to Italy in the 14 days prior to illness onset Observation OMOP Extension
756056 History of travel to South Korea in the 14 days prior to illness onset Observation OMOP Extension
756026 History of travel to Wuhan in the 14 days prior to illness onset Observation OMOP Extension
756046 Person Employed as a Healthcare Worker Observation OMOP Extension
756051 Person Employed in a Microbiology laboratory Observation OMOP Extension
756057 Travel in the 14 days prior to illness onset Observation OMOP Extension
756077 Close contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756069 Close contact with patient with confirmed or presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756076 Close contact with patient with presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756068 Close contact with patient with presumptive/probable (then not confirmed) case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756041 Close contact with symptomatic patient with confirmed or presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756062 Community contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756022 Exposure to patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756075 Exposure to patient with presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756082 Exposure to patient with presumptive/probable (then not confirmed) case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756050 Exposure to patient with severe acute lower respiratory distress (SARS) of unknown etiology Observation OMOP Extension
756047 Healthcare contact of Healthcare worker with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756035 Healthcare contact of Patient with another patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756079 Healthcare contact of Visitor with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756027 Healthcare contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756045 Household contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756072 Presence in a healthcare facility where disease caused by severe acute respiratory syndrome coronavirus 2 has been managed Observation OMOP Extension
756037 Presence in a laboratory handling suspected or confirmed cases samples of disease caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756064 Suspected exposure (but ruled out after evaluation) to severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756083 Suspected exposure to severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension

1.5. Revision of mapping for new and existing Concepts

All mappings between Source and Standard Concepts were reviewed and revised, and de-novo mapping of unmapped Concepts (ICD10, ICD10CM, ICD10CN, KCD7, Read, EDI, LOINC) created.

2. Instructions for ETL

2.1. ICD10 Emergency Use Codes

Emergency use codes U07.1 in ICD10 and related vocabularies (U18.1 in KCD7, U07.100 in ICD10CN) are reserved for situations, where the vocabulary contained in an EHR or other electronic system cannot be updated quickly enough. These codes can be temporary placeholders until a new proper code is assigned and percolated to the applications. This mechanism has been employed for COVID-19. We therefore added a 'Maps to' record to the CONCEPT_RELATIONSHIP table cross-linking these Emergency Use Codes to SNOMED ‘Disease caused by severe acute respiratory syndrome coronavirus 2’.

However, if these codes are used in predefined code combinations like in the case of ICD10CM (see below), it is the responsibility of the ETL to apply appropriate mappings. The CONCEPT_RELATIONSHIP table is not designed to support mapping of code combinations to pre-coordinated Concepts.

Click to expand - Emergency use codes and mapping

Concept_id Concept_name Concept_code vocabulary_id relationship_id target_Concept_id target_Concept_name target_vocabulary_id
586414 Novel coronavirus infection U18.1 KCD7 Maps to 37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 SNOMED
586415 Provisional assignment of new diseases or emergency use U18 KCD7 Maps to 37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 SNOMED
710155 COVID-19 pneumonia (machine translation) U07.100x003 ICD10CN Maps to 37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 SNOMED
710156 COVID-19 pneumonia (machine translation) U07.100x001 ICD10CN Maps to 37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 SNOMED
710157 Suspected case of COVID-19 (machine translation) Z03.800x001 ICD10CN Maps to 37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 SNOMED
710158 COVID-19 (machine translation) U07.100 ICD10CN Maps to 37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 SNOMED
710159 Confirmed COVID-19, excluding pneumonia (machine translation) U07.100x002 ICD10CN Maps to 37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 SNOMED
710160 Emergency use of U07.1 | Disease caused by severe acute respiratory syndrome coronavirus 2 U07.1 ICD10CN Maps to 37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 SNOMED
42501115 Emergency use of U07.1 | Disease caused by severe acute respiratory syndrome coronavirus 2 U07.1 KCD7 Maps to 37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 SNOMED
45756093 Emergency use of U07.1 | Disease caused by severe acute respiratory syndrome coronavirus 2 U07.1 ICD10 Maps to 37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 SNOMED

2.2. ICD10CM codes

For ICD10CM, instead of adding COVID-19 directly, the CDC introduced coding guidelines based on post-coordination of existing codes. It is the responsibility of the ETL to detect these combinations (both corresponding records on the same day) and map them according to the table below. **Note **that the CONCEPT_RELATIONSHIP table cannot support the mapping of post-coordinated to pre-coordinated Concepts and therefore does not contain this mapping information.

Click to expand - ICD10CM combination mapping

source_vocabulary_id source_code combo target_Concept_id target_Concept_name target_domain_id target_vocabulary_id
ICD10CM B97.29+J98.8 756039 Respiratory infection caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
ICD10CM B97.29+J22 756081 Infection of lower respiratory tract caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
ICD10CM B97.29+J40 756031 Bronchitis caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
ICD10CM B97.29+J20.8 756023 Acute bronchitis caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
ICD10CM B97.29+J12.89 37310285 Pneumonia caused by 2019 novel coronavirus Condition SNOMED
ICD10CM B97.29+J80 756044 Acute respiratory distress syndrome (ARDS) caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension

2.3. Other situations where generic codes are temporarily used

When COVID-19 appeared, coding systems around the world were not prepared for the rapidly spreading condition. As a result, preexisting non-specific codes or combination thereof started to appear in data or were instructed to be used. Since the use of these generic codes is temporary and differs from before the outbreak, we did not create mappings to COVID-19-related Concepts. It is therefore the task of the ETL to asses such codes in the context of the COVID-19 timing and to map them properly:

  • Use the old mappings from the CONCEPT_RELATIONSHIP table for records from the pre-pandemic period
  • Map codes recorded during the pandemic period to Standard Concepts below

The main Concept for the COVID-19 Condition should be SNOMED ‘Disease caused by severe acute respiratory syndrome coronavirus 2’. However, there is a number of more granular Condition Concepts from which you can select. **Note **that the selection of the right target Concept is the responsibility of the ETL script. The CONCEPT_RELATIONSHIP table does not offer any of these mappings.

Click to expand - Standard Concepts for COVID-19

Concept_id Concept_name domain_id vocabulary_id
756023 Acute bronchitis caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
756044 Acute respiratory distress syndrome (ARDS) caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
756061 Asymptomatic infection caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
756031 Bronchitis caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
756081 Infection of lower respiratory tract caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
756039 Respiratory infection caused by severe acute respiratory syndrome coronavirus 2 Condition OMOP Extension
37311061 Disease caused by severe acute respiratory syndrome coronavirus 2 Condition SNOMED
37310284 Encephalopathy caused by 2019 novel coronavirus Condition SNOMED
37310283 Gastroenteritis caused by 2019 novel coronavirus Condition SNOMED
37310286 Infection of upper respiratory tract caused by 2019 novel coronavirus Condition SNOMED
37310287 Myocarditis caused by 2019 novel coronavirus Condition SNOMED
37310254 Otitis media caused by 2019 novel coronavirus Condition SNOMED
37310285 Pneumonia caused by 2019 novel coronavirus Condition SNOMED

2.4. Patients quarantined or investigated

After exposure to SARS-CoV-2, patients are routinely put into isolation or quarantine. Likewise, explicit investigation are carried out to track the infection chain and localize all other exposed people. For these healthcare interactiosn specific to COVID-19, new Visit Concepts were added. Note that it is the responsibility of the ETL to identify these situations. **Note **that the CONCEPT_RELATIONSHIP table does not contain these default mappings.

Click to expand - New Visit Concepts

source_vocabulary_id source_code target_Concept_id target_Concept_name target_domain_id target_vocabulary_id
CDC case definition Person under investigation 32761 Person Under Investigation (PUI) Visit Visit
- - 32759 Home isolation Visit Visit
- - 32760 Isolation in inpatient setting Visit Visit

2.5. Status of COVID-19 diagnoses

Many people are being tested for COVID-19 infection, requiring several days. During this period, if inconclusive test results were obtained, the diagnosis of the patient is preliminary. This fact is not to be part of a pre-coordinated Condition, but should be declared through a record in the condition_status_Concept_id field in the CONDITION_OCCURRENCE table. Note that these mappings are NOT incorporated into the CONCEPT_RELATIONSHIP table:

Click to expand - Condition Status Concepts

source_vocabulary_id source_code target_Concept_id target_Concept_name target_domain_id target_vocabulary_id
WHO/ECDC case definition Suspected case 4217851 Suspected Observation SNOMED
ICD10CM Z20.828 4217851 Suspected Observation SNOMED
WHO/ECDC case definition Probable case 764222 Probable Observation SNOMED
CDC case definition Presumptive positive case 36715206 Presumptive positive Meas Value SNOMED
CDC case definition Laboratory-confirmed case 4194404 Disorder confirmed Observation SNOMED
WHO/ECDC case definition Confirmed case 4194404 Disorder confirmed Observation SNOMED
ICD10CM B97.29 4194404 Disorder confirmed Observation SNOMED

2.6. Oxygen therapy

Source codes related to oxygen therapy were mapped to RxNorm Oxygen ingredient in addition to existing mapping to Procedure Domainю. It is therefore expected that these will create records in both the DRUG_EXPOSURE and PROCEDURE_OCCURRENCE tables.

2.7. Testing laboratory

COVID-19 testing is performed by diferent labs at different levels of quality. In order to represent the laboratory that performed testing, the measurement_type_Concept_id field in the table below should be used. **Note ** that these mappings are NOT incorporated to the CONCEPT_RELATIONSHIP table and just demonstrate the example of how the source data should be converted during ETL.

Click to expand - Testing Lab Measurement Type Concepts

source_vocabulary_id source_code target_Concept_id target_Concept_name target_domain_id target_vocabulary_id
HCPCS U0001 32762 Reference Lab result Type Concept Meas Type
HCPCS U0002 44818702 Lab result Type Concept Meas Type

2.8. SARS-CoV-2 testing

OMOP Extension ‘Measurement of severe acute respiratory syndrome coronavirus 2’ is the main representative Сщncept, with a mixed pool (SNOMED, OMOP Extension, LOINC, CPT4, HCPCS) of Concepts hierarchically under this Concept. It is the responsibility of the ETL to find the appropriate mapping, if supported vocabularies are not used. **Note ** that there are two Concepts that comprise the result of the measurement by itself ('2019 novel coronavirus detected' and '2019 novel coronavirus not detected'), instead of splitting into Measurement Concept and Value Concept. All other Concepts are designed correctly.

Click to expand - SARS-CoV-2 testing Concepts

Concept_id Concept_name domain_id vocabulary_id
700360 Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), amplified probe technique Procedure CPT4
40218805 Testing for SARS-CoV-2 in CDC laboratory Observation HCPCS
40218804 Testing for SARS-CoV-2 in non-CDC laboratory Observation HCPCS
706164 Middle East respiratory syndrome coronavirus (MERS-CoV) RNA [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC
706162 Respiratory viral pathogens DNA and RNA panel - Respiratory specimen Qualitative by NAA with probe detection Measurement LOINC
706166 SARS coronavirus 2 E gene [Cycle Threshold #] in Unspecified specimen by NAA with probe detection Measurement LOINC
706174 SARS coronavirus 2 E gene [Presence] in Unspecified specimen by NAA with probe detection Measurement LOINC
706181 SARS coronavirus 2 IgG Ab [Presence] in Serum or Plasma by Immunoassay Measurement LOINC
706177 SARS coronavirus 2 IgG Ab [Units/volume] in Serum or Plasma by Immunoassay Measurement LOINC
706179 SARS coronavirus 2 IgG and IgM panel - Serum or Plasma by Immunoassay Measurement LOINC
706176 SARS coronavirus 2 IgG and IgM panel - Serum or Plasma Qualitative by Immunoassay Measurement LOINC
706180 SARS coronavirus 2 IgM Ab [Presence] in Serum or Plasma by Immunoassay Measurement LOINC
706178 SARS coronavirus 2 IgM Ab [Units/volume] in Serum or Plasma by Immunoassay Measurement LOINC
706167 SARS coronavirus 2 N gene [Cycle Threshold #] in Unspecified specimen by NAA with probe detection Measurement LOINC
706157 SARS coronavirus 2 N gene [Cycle Threshold #] in Unspecified specimen by Nucleic acid amplification using primer-probe set N1 Measurement LOINC
706155 SARS coronavirus 2 N gene [Cycle Threshold #] in Unspecified specimen by Nucleic acid amplification using primer-probe set N2 Measurement LOINC
706161 SARS coronavirus 2 N gene [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC
706175 SARS coronavirus 2 N gene [Presence] in Unspecified specimen by NAA with probe detection Measurement LOINC
706156 SARS coronavirus 2 N gene [Presence] in Unspecified specimen by Nucleic acid amplification using primer-probe set N1 Measurement LOINC
706154 SARS coronavirus 2 N gene [Presence] in Unspecified specimen by Nucleic acid amplification using primer-probe set N2 Measurement LOINC
706168 SARS coronavirus 2 ORF1ab region [Cycle Threshold #] in Unspecified specimen by NAA with probe detection Measurement LOINC
706160 SARS coronavirus 2 RdRp gene [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC
706173 SARS coronavirus 2 RdRp gene [Presence] in Unspecified specimen by NAA with probe detection Measurement LOINC
706158 SARS Coronavirus 2 RNA panel - Respiratory specimen by NAA with probe detection Measurement LOINC
706169 SARS Coronavirus 2 RNA panel - Unspecified specimen by NAA with probe detection Measurement LOINC
706163 SARS coronavirus 2 RNA [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC
706170 SARS coronavirus 2 RNA [Presence] in Unspecified specimen by NAA with probe detection Measurement LOINC
706159 SARS coronavirus+SARS-like coronavirus+SARS coronavirus 2+MERS coronavirus RNA [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC
706165 SARS coronavirus+SARS-like coronavirus+SARS coronavirus 2 RNA [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC
706172 SARS-like Coronavirus N gene [Cycle Threshold #] in Unspecified specimen by NAA with probe detection Measurement LOINC
706171 SARS-like Coronavirus N gene [Presence] in Unspecified specimen by NAA with probe detection Measurement LOINC
756029 Detection of severe acute respiratory syndrome coronavirus 2 in Respiratory specimen Measurement OMOP Extension
756065 Detection of severe acute respiratory syndrome coronavirus 2 in Unspecified specimen Measurement OMOP Extension
756085 Detection of severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction technique in Respiratory specimen Measurement OMOP Extension
756084 Detection of severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction technique in Unspecified specimen Measurement OMOP Extension
756055 Measurement of severe acute respiratory syndrome coronavirus 2 Measurement OMOP Extension
37310282 2019 novel coronavirus detected Measurement SNOMED
37310281 2019 novel coronavirus not detected Measurement SNOMED
37310255 Detection of 2019 novel coronavirus using polymerase chain reaction technique Measurement SNOMED
37310258 Measurement of 2019 novel coronavirus antibody Measurement SNOMED
37310257 Measurement of 2019 novel coronavirus antigen Measurement SNOMED

2.9. SARS-CoV-2 exposure/suspected exposure

SNOMED ‘Exposure to severe acute respiratory syndrome coronavirus 2’ is the main representative Concept, with a mixed pool (SNOMED, OMOP Extension) of Concepts placed hierarchically under this Concept. It is the responsibility of the ETL to select the right Concept with the appropriate granularity, if supported vocabularies are not used in the source data. This hierarchy includes both confirmed and suspected exposures placed under the OMOP Extension 'Suspected exposure to severe acute respiratory syndrome coronavirus 2' Concept. There is no split like for Conditions between fact and suspicion.

Use these Concepts if the date of the exposure is known and can be recorded as the time stamp of the Observation. If not, use the History of exposure (see below).

Click to expand - SARS-CoV-2 exposure Concepts

Concept_id Concept_name domain_id vocabulary_id
756046 Person Employed as a Healthcare Worker Observation OMOP Extension
756051 Person Employed in a Microbiology laboratory Observation OMOP Extension
756077 Close contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756069 Close contact with patient with confirmed or presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756076 Close contact with patient with presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756068 Close contact with patient with presumptive/probable (then not confirmed) case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756041 Close contact with symptomatic patient with confirmed or presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756062 Community contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756022 Exposure to patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756075 Exposure to patient with presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756082 Exposure to patient with presumptive/probable (then not confirmed) case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756050 Exposure to patient with severe acute lower respiratory distress (SARS) of unknown etiology Observation OMOP Extension
756047 Healthcare contact of Healthcare worker with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756035 Healthcare contact of Patient with another patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756079 Healthcare contact of Visitor with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756027 Healthcare contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756045 Household contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756072 Presence in a healthcare facility where disease caused by severe acute respiratory syndrome coronavirus 2 has been managed Observation OMOP Extension
756037 Presence in a laboratory handling suspected or confirmed cases samples of disease caused by severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756064 Suspected exposure (but ruled out after evaluation) to severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
756083 Suspected exposure to severe acute respiratory syndrome coronavirus 2 Observation OMOP Extension
37310260 Close exposure to 2019 novel coronavirus infection Observation SNOMED
37311059 Exposure to severe acute respiratory syndrome coronavirus 2 Observation SNOMED

2.10. History of SARS-CoV-2 exposure/suspected exposure

OMOP Extension ‘History of Exposure to severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset’ is the main representative Concept, with a mixed pool (SNOMED, OMOP Extension) of Concepts placed hierarchically under this Concept. It is the responsibility of the ETL to select the right Concept with the appropriate granularity, if supported vocabularies are not used in the source data. This hierarchy includes both confirmed and suspected histories of exposures in the OMOP Extension 'History of Suspected exposure to severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset' Concept.

Use these Concepts if the date of the actual exposure is unknown. The time stamp of the Observation refers to the date of recording of the fact, not the exposure. If the date is known, use exposure Concepts (see above)

Click to expand - SARS-CoV-2 History of exposure Concepts

Concept_id Concept_name domain_id vocabulary_id
756060 History of Close contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756036 History of Close contact with patient with confirmed or presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756078 History of Close contact with patient with presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756024 History of Close contact with patient with presumptive/probable (then not confirmed) case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756028 History of Close contact with symptomatic patient with confirmed or presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756040 History of Close exposure to severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756042 History of Community contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756052 History of Exposure to patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756038 History of Exposure to patient with presumptive/probable case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756025 History of Exposure to patient with presumptive/probable (then not confirmed) case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756034 History of Exposure to patient with severe acute lower respiratory distress (SARS) of unknown etiology in the 14 days prior to illness onset Observation OMOP Extension
756066 History of Exposure to severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756073 History of Healthcare contact of Healthcare worker with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756058 History of Healthcare contact of Patient with another patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756033 History of Healthcare contact of Visitor with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756067 History of Healthcare contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756080 History of Household contact with patient with confirmed case caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756071 History of Presence in a healthcare facility where disease caused by severe acute respiratory syndrome coronavirus 2 has been managed in the 14 days prior to illness onset Observation OMOP Extension
756054 History of Presence in a laboratory handling suspected or confirmed cases samples of disease caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756049 History of Suspected exposure (but ruled out after evaluation) to severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756048 History of Suspected exposure to severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension

2.11. History of travelling

OMOP Extension ‘Travel in the 14 days prior to illness onset’ is the main representative Concept, with a pool of OMOP Extension Concepts placed hierarchically under this Concept. It is the responsibility of the ETL to select the right Concept with the appropriate granularity, if supported vocabularies are not used in the source data. **Note ** that these Concepts should be recorded with the date of collecting the fact, not the actual travel date.

Click to expand - History of travelling Concepts

Concept_id Concept_name domain_id vocabulary_id
756043 History of travel to an area with documented cases of infection caused by severe acute respiratory syndrome coronavirus 2 in the 14 days prior to illness onset Observation OMOP Extension
756074 History of travel to China in the 14 days prior to illness onset Observation OMOP Extension
756032 History of travel to Hubei in the 14 days prior to illness onset Observation OMOP Extension
756059 History of travel to Iran in the 14 days prior to illness onset Observation OMOP Extension
756053 History of travel to Italy in the 14 days prior to illness onset Observation OMOP Extension
756056 History of travel to South Korea in the 14 days prior to illness onset Observation OMOP Extension
756026 History of travel to Wuhan in the 14 days prior to illness onset Observation OMOP Extension
756057 Travel in the 14 days prior to illness onset Observation OMOP Extension

2.12. History of animal exposure

OMOP Extension ‘History of Animal exposure in the 14 days prior to illness onset’ is the main representative Concept, with a pool of OMOP Extension Concepts hierarchically under this Concept. It is the responsibility of the ETL to select the right Concept with the appropriate granularity, if supported vocabularies are not used in the source data. **Note ** that these Concepts should be recorded with the date of collecting the fact, not the actual exposure date.

Click to expand - History of animal exposure Concepts

Concept_id Concept_name domain_id vocabulary_id
756063 History of Animal exposure in the 14 days prior to illness onset Observation OMOP Extension
756030 History of Contact with live/dead animals, raw meat or insect bites in the 14 days prior to illness onset Observation OMOP Extension
756070 History of Direct contact with animals in countries where COVID-19 is known to be circulating in animal populations or where human infections have occurred as a result of presumed zoonotic transmission in the 14 days prior to illness onset Observation OMOP Extension
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