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Alexander edited this page Dec 21, 2021 · 49 revisions

Additions to COVID-19 v2.0 Vocabulary Release (16 Dec, 2021)

1. COVID sequelae and related conditions.

In the recent vocabulary release we introduced a new temporary OMOP Extension concept in order to support the coding of the following clinical situations:

  • Sequelae of COVID-19.
  • Sequelae of COVID-19 treatment.
  • Chronic conditions that develops during or after acute COVID-19 (with or w/o ongoing persistence of virus).
  • Other conditions that develop during or after acute COVID-19 but where we don’t know the connection to the COVID-19.

Although the concept is named "Post-acute COVID-19", it's supposed to be an overarching one catch all bucket concept rather than a concept reflecting any of existing definitions. Therefore the synonyms of the concepts are:

  • Sequela of COVID-19
  • Chronic COVID-19
  • Long COVID
  • Ongoing symptomatic COVID-19
  • Post COVID-19
  • Post COVID-19 intensive care unit syndrome
  • Persistent COVID-19 symptoms
  • Long-term COVID-19 effects
  • Ongoing COVID-19
  • Post-acute sequelae of SARS CoV-2 infection (PASC)

This issue was discussed on the forums and the decision was done by the following inspirations:

  • There's a plenty of conflicting to each other and evolving definitions.
  • It's not yet investigated enough and not properly defined.
  • It's supposed to be not an input, but an output of the research, including the research in the OHDSI network.

Unless we have a better understanding of the issue, this new temporary concept will be used as the Standard target for the respective source codes. As well as emerging Standard SNOMED terms will be deStandardized and mapped over to it.

2. Long COVID clinic Visit.

In the recent vocabulary release we introduced a new "Ambulatory long COVID clinic" concept in the Visit Domain.

This is a subtype of outpatient Visit that is defined as follows: "confirmed presence of a clinical encounter that is specific to specialty care for those who are suspected to have long COVID. It, in itself, may have clinical noise in that there are different protocols for how people show in long COVID clinics depending on the clinical practice patterns of that specific medical center".

3. Alternate care site (ACS) Visit.

Alternate care sites are non-traditional environments (mobile field medical units, converted hotels, schools, stadiums) that may be established due to local surge in the need for medical care (e.g. disaster or public health emergency). ACSs provide medical care for injured or sick patients as well as continuing care for chronic conditions.

Because ACS can provide care of different levels (non-acute, hospital and acute care) an OMOP Extension "Alternate care site (ACS)" Visit concept is not rolled up to any of Visit concepts (inpatient, outpatient or emergency).

Even though patients with COVID-19 can remain in ACS and receive medical care for the duration of their isolation period, consider using respective quarantine/isolation Visit concepts properly.

COVID-19 v2.0 Vocabulary Release (19-25 May, 2020)

Following the initial v1.0 vocabulary release to support COVID-19 studies on 19-21 March 2020, several changes were implemented in subsequent releases. To summarize them, with the recent vocabulary releases v20200519 and v20200525, we announce v.2.0 COVID-19 vocabulary and describe here what has been changed.

Note: If you are involved in ETL or data analysis, please make sure to take a look at the changes 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. Also, after the first version of this instruction we updated some rules. It's highly recommended to re-run ETL with the recent version since the interim vocabulary versions are not supported by current or initial instructions.

1. Incorporation of novel Concepts

Most of the vocabularies keep adding Concepts around COVID-19. We incorporated them into non-standard Source Сoncepts (ICD10, ICD10CM, ICD10CN) and Standard Сoncepts (SNOMED, LOINC, RxNorm). Also we added new concepts into 'OMOP Extension' and 'RxNorm Extension' vocabularies with support of existing SNOMED and LOINC hierarchies.

Click to expand - New Concepts

Concept_id Concept_name domain_id vocabulary_id Concept_code
45756094 Emergency use of U07.2 | COVID-19, virus not identified Observation ICD10 U07.2
702953 Emergency use of U07.1 | COVID-19 Condition ICD10CM U07.1
702683 Emergency use of U07.2 | COVID-19, virus not identified Condition ICD10CN U07.2
723479 SARS coronavirus 2 IgG+IgM Ab [Presence] in Serum or Plasma by Immunoassay Measurement LOINC 94547-7
723477 SARS coronavirus 2 Ag [Presence] in Respiratory specimen by Rapid immunoassay Measurement LOINC 94558-4
723478 SARS coronavirus 2 ORF1ab region [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC 94559-2
723473 SARS coronavirus 2 IgA Ab [Presence] in Serum or Plasma by Immunoassay Measurement LOINC 94562-6
723474 SARS coronavirus 2 IgG Ab [Presence] in Serum or Plasma by Immunoassay Measurement LOINC 94563-4
723475 SARS coronavirus 2 IgM Ab [Presence] in Serum or Plasma by Immunoassay Measurement LOINC 94564-2
723476 SARS coronavirus 2 RNA [Presence] in Nasopharynx by NAA with non-probe detection Measurement LOINC 94565-9
723464 SARS coronavirus 2 ORF1ab region [Presence] in Unspecified specimen by NAA with probe detection Measurement LOINC 94639-2
723465 SARS coronavirus 2 S gene [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC 94640-0
723466 SARS coronavirus 2 S gene [Presence] in Unspecified specimen by NAA with probe detection Measurement LOINC 94641-8
723467 SARS coronavirus 2 S gene [Cycle Threshold #] in Respiratory specimen by NAA with probe detection Measurement LOINC 94642-6
723468 SARS coronavirus 2 S gene [Cycle Threshold #] in Unspecified specimen by NAA with probe detection Measurement LOINC 94643-4
723469 SARS coronavirus 2 ORF1ab region [Cycle Threshold #] in Respiratory specimen by NAA with probe detection Measurement LOINC 94644-2
723470 SARS coronavirus 2 RdRp gene [Cycle Threshold #] in Unspecified specimen by NAA with probe detection Measurement LOINC 94645-9
723471 SARS coronavirus 2 RdRp gene [Cycle Threshold #] in Respiratory specimen by NAA with probe detection Measurement LOINC 94646-7
723472 SARS-related coronavirus RNA [Presence] in Unspecified specimen by NAA with probe detection Measurement LOINC 94647-5
723481 Date contact confirmed as a case Measurement LOINC 94648-3
723483 Health department identifier Measurement LOINC 94649-1
723488 Contact identifier Contact Measurement LOINC 94650-9
723482 Country of travel [Location] Measurement LOINC 94651-7
723489 Known exposure date Measurement LOINC 94652-5
723484 City of travel [Location] Measurement LOINC 94653-3
723485 Known exposure panel Measurement LOINC 94654-1
723490 State of known exposure Measurement LOINC 94656-6
723486 Contact case identifier Measurement LOINC 94657-4
723491 City of known exposure Measurement LOINC 94658-2
723487 Case identifier Measurement LOINC 94659-0
723463 SARS coronavirus 2 RNA [Presence] in Serum or Plasma by NAA with probe detection Measurement LOINC 94660-8
723480 SARS coronavirus 2 Ab [Interpretation] in Serum or Plasma Measurement LOINC 94661-6
723459 SARS coronavirus 2 IgA Ab [Units/volume] in Serum or Plasma by Immunoassay Measurement LOINC 94720-0
723460 COVID-19 Evaluation note Measurement LOINC 94721-8
723462 COVID-19 Initial Evaluation form Measurement LOINC 94722-6
723461 Emergency department COVID-19 Initial Evaluation form Measurement LOINC 94723-4
586528 SARS coronavirus 2 RNA [Cycle Threshold #] in Respiratory specimen by NAA with probe detection Measurement LOINC 94745-7
586529 SARS coronavirus 2 RNA [Cycle Threshold #] in Unspecified specimen by NAA with probe detection Measurement LOINC 94746-5
586524 SARS coronavirus 2 N gene [Presence] in Respiratory specimen by Nucleic acid amplification using CDC primer-probe set N1 Measurement LOINC 94756-4
586525 SARS coronavirus 2 N gene [Presence] in Respiratory specimen by Nucleic acid amplification using CDC primer-probe set N2 Measurement LOINC 94757-2
586523 SARS coronavirus 2 E gene [Presence] in Respiratory specimen by NAA with probe detection Measurement LOINC 94758-0
586526 SARS coronavirus 2 RNA [Presence] in Nasopharynx by NAA with probe detection Measurement LOINC 94759-8
715272 SARS coronavirus 2 N gene [Presence] in Nasopharynx by NAA with probe detection Measurement LOINC 94760-6
586527 SARS coronavirus 2 IgG Ab [Presence] in DBS by Immunoassay Measurement LOINC 94761-4
586515 SARS coronavirus 2 Ab [Presence] in Serum or Plasma by Immunoassay Measurement LOINC 94762-2
586516 SARS coronavirus 2 [Presence] in Unspecified specimen by Organism specific culture Measurement LOINC 94763-0
586517 SARS coronavirus 2 whole genome [Nucleotide sequence] in Isolate by Sequencing Measurement LOINC 94764-8
586518 SARS coronavirus 2 E gene [Presence] in Serum or Plasma by NAA with probe detection Measurement LOINC 94765-5
586520 SARS coronavirus 2 N gene [Presence] in Serum or Plasma by NAA with probe detection Measurement LOINC 94766-3
586519 SARS coronavirus 2 S gene [Presence] in Serum or Plasma by NAA with probe detection Measurement LOINC 94767-1
586521 SARS coronavirus 2 IgA Ab [Presence] in Serum or Plasma by Rapid immunoassay Measurement LOINC 94768-9
586522 SARS coronavirus 2 Ab [Units/volume] in Serum or Plasma by Immunoassay Measurement LOINC 94769-7
715263 COVID-19 Intubation Consultation note Measurement LOINC 94806-7
715264 COVID-19 Intubation Consultation note Attending Measurement LOINC 94807-5
715265 COVID-19 Intubation Consultation note Resident Measurement LOINC 94808-3
715267 COVID-19 Intubation Progress note Measurement LOINC 94809-1
715268 COVID-19 Intubation Procedure note Measurement LOINC 94810-9
715266 COVID-19 Intubation Evaluation note Measurement LOINC 94811-7
715269 COVID-19 Intubation and Cardiopulmonary resuscitation note Measurement LOINC 94812-5
715270 COVID-19 Intubation Conference note Team Measurement LOINC 94813-3
715271 Critical care medicine COVID-19 Consultation note Measurement LOINC 94814-1
715262 SARS coronavirus 2 RNA [Log #/volume] (viral load) in Unspecified specimen by NAA with probe detection Measurement LOINC 94819-0
715261 SARS coronavirus 2 RNA [Presence] in Saliva (oral fluid) by Sequencing Measurement LOINC 94822-4
715260 SARS coronavirus 2 RNA [Presence] in Saliva (oral fluid) by NAA with probe detection Measurement LOINC 94845-5
704991 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Blood Measurement OMOP Extension OMOP4912972
705000 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using Nucleic acid amplification technique in Blood Measurement OMOP Extension OMOP4912973
704992 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using Culture method Measurement OMOP Extension OMOP4912974
704993 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using Sequencing Measurement OMOP Extension OMOP4912975
704994 COVID-19 Diagnostic criteria Observation OMOP Extension OMOP4912976
704995 Patient meets COVID-19 Clinical diagnostic criteria Observation OMOP Extension OMOP4912977
704996 Patient meets COVID-19 Laboratory diagnostic criteria Observation OMOP Extension OMOP4912978
704997 Patient meets COVID-19 Epidemiological diagnostic criteria Observation OMOP Extension OMOP4912979
704998 Patient meets COVID-19 Clinical and/or Epidemiological diagnostic criteria Observation OMOP Extension OMOP4912980
704999 Patient meets COVID-19 Clinical or Epidemiological diagnostic criteria Observation OMOP Extension OMOP4912981
705001 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using Nucleic acid amplification technique Measurement OMOP Extension OMOP4912982
586308 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using Nucleic acid amplification technique in Saliva Measurement OMOP Extension OMOP4912983
586307 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Saliva Measurement OMOP Extension OMOP4912984
586310 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Genetic material using Molecular method Measurement OMOP Extension OMOP4912985
586309 Measurement of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Specified specimen Measurement OMOP Extension OMOP4912986
700296 Patient meets COVID-19 Presumptive laboratory evidence criteria (Detection of specific antigen in a clinical specimen, OR detection of specific antibody in serum, plasma, or whole blood indicative of a new or recent infection) Observation OMOP Extension OMOP4912987
700297 Patient meets COVID-19 Laboratory confirmation criteria (Detection of specific RNA in a clinical specimen using a molecular amplification detection test) Observation OMOP Extension OMOP4912988
700298 Patient meets COVID-19 Vital records criteria Observation OMOP Extension OMOP4912989
37499271 remdesivir Drug RxNorm 2284718
32763 Remdesivir Drug RxNorm Extension OMOP4873974
32764 Umifenovir Drug RxNorm Extension OMOP4873975
32765 Favipiravir Drug RxNorm Extension OMOP4873976
32766 Middle East Respiratory Syndrome heterologous combined adenoviral-based vector vaccine Drug RxNorm Extension OMOP4873977
32767 Carrimycin Drug RxNorm Extension OMOP4873978
32768 CD24 Extracellular Domain-IgG1 Fc Domain Recombinant Fusion Protein CD24Fc Drug RxNorm Extension OMOP4873979
32769 Tetrandrine Drug RxNorm Extension OMOP4873980
32770 Xiyanping Drug RxNorm Extension OMOP4873981
703447 High risk category for developing complication from COVID-19 infection Condition SNOMED 1300561000000107
703446 Moderate risk category for developing complication from COVID-19 infection Condition SNOMED 1300571000000100
703445 Low risk category for developing complication from COVID-19 infection Condition SNOMED 1300591000000101
703444 COVID-19 severity score Observation SNOMED 1300631000000101
703443 COVID-19 severity scale Measurement SNOMED 1300671000000104
703442 Assessment using COVID-19 severity scale Procedure SNOMED 1300681000000102
703441 COVID-19 confirmed by laboratory test Condition SNOMED 1300721000000109
703440 Probable COVID-19 confirmed using clinical diagnostic criteria Condition SNOMED 1300731000000106
703439 Taking of swab for SARS-CoV-2 Procedure SNOMED 1320971000000102
703438 Self-taken swab for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) completed Observation SNOMED 1321031000000105
703437 Self-taken swab for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) offered Observation SNOMED 1321041000000101
703436 Swab for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) taken by healthcare professional Observation SNOMED 1321051000000103
703435 Signposting to NHS online isolation note service Procedure SNOMED 1321061000000100
703434 Has NHS digital isolation note Observation SNOMED 1321071000000107
703433 Self-isolation note issued to patient Observation SNOMED 1321081000000109
703432 Household isolation note issued to patient Observation SNOMED 1321091000000106
703431 COVID-19 excluded Observation SNOMED 1321101000000103
703430 COVID-19 excluded by laboratory test Observation SNOMED 1321111000000101
703429 COVID-19 excluded using clinical diagnostic criteria Observation SNOMED 1321121000000107
703428 Self quarantine to prevent exposure of community to contagion Visit SNOMED 1321131000000109
703427 Reverse isolation of household to prevent exposure of uninfected subject to contagion Visit SNOMED 1321141000000100
703426 Reverse self-isolation of uninfected subject to prevent exposure to contagion Visit SNOMED 1321151000000102
703425 Household quarantine to prevent exposure of community to contagion Visit SNOMED 1321161000000104
703424 Provision of advice, assessment or treatment limited due to COVID-19 pandemic Observation SNOMED 1321171000000106

2. Domain reassignment

Additional changes were done to provide the correct Domain assignment. In particular, 'Suspected diseases' hierarchy transition from Observation into Condition were rolled back. Note that the changes mentioned below affect the entire concept, their descendants, and the Source concepts mapped.

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

old_domain_id new_domain_id Concept_id Concept_name Vocabulary_id
Condition Observation 4219847 Disease suspected SNOMED
Observation Condition 4194404 Disorder confirmed SNOMED
Procedure Measurement 4035726 Immunohistochemistry procedure SNOMED
Observation Measurement 40218805 Testing for SARS-CoV-2 in CDC laboratory HCPCS
Observation Measurement 40218804 Testing for SARS-CoV-2 in non-CDC laboratory HCPCS
Procedure Measurement 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 CPT4
Observation Visit 703428 Self quarantine to prevent exposure of community to contagion SNOMED
Observation Visit 703427 Reverse isolation of household to prevent exposure of uninfected subject to contagion SNOMED
Observation Visit 703426 Reverse self-isolation of uninfected subject to prevent exposure to contagion SNOMED
Observation Visit 703425 Household quarantine to prevent exposure of community to contagion SNOMED

3. Status (probability) of COVID-19 diagnoses

By the definition, any record in the CONDITION_OCCURRENCE table implies the positive fact. Due to this reason, Condition_status_Concept_id field in the CONDITION_OCCURRENCE table is NOT longer supported and should NOT be used for this purpose.

Instead, we moved back to Observation Domain a 4219847 'Disease suspected' hierarchy and turned back to Standard 37311060 'Suspected disease caused by severe acute respiratory coronavirus 2' concept. This concept should be used for mapping of non-confirmed (suspected, probable) COVID-19 cases.

In the same way, 703431 'COVID-19 excluded' concept, placed into the Observation Domain, or any of its descendants might be used to capture negative COVID-19 information.

To support the coding of way/criteria the COVID-19 was confirmed, we introduced the following OMOP Extension concepts in Observation Domain that might be used in combination with COVID-19 Condition concepts.

Click to expand - COVID Diagnostic criteria Concepts

Concept_id Concept_name domain_id vocabulary_id Concept_code
704994 COVID-19 Diagnostic criteria Observation OMOP Extension OMOP4912976
704995 Patient meets COVID-19 Clinical diagnostic criteria Observation OMOP Extension OMOP4912977
704996 Patient meets COVID-19 Laboratory diagnostic criteria Observation OMOP Extension OMOP4912978
704997 Patient meets COVID-19 Epidemiological diagnostic criteria Observation OMOP Extension OMOP4912979
704998 Patient meets COVID-19 Clinical and/or Epidemiological diagnostic criteria Observation OMOP Extension OMOP4912980
704999 Patient meets COVID-19 Clinical or Epidemiological diagnostic criteria Observation OMOP Extension OMOP4912981
700296 Patient meets COVID-19 Presumptive laboratory evidence criteria (Detection of specific antigen in a clinical specimen, OR detection of specific antibody in serum, plasma, or whole blood indicative of a new or recent infection) Observation OMOP Extension OMOP4912987
700297 Patient meets COVID-19 Laboratory confirmation criteria (Detection of specific RNA in a clinical specimen using a molecular amplification detection test) Observation OMOP Extension OMOP4912988
700298 Patient meets COVID-19 Vital records criteria Observation OMOP Extension OMOP4912989

4. ICD10-like vocabularies Emergency Use Codes

ICD10 and ICD10CM introduced new and clarified the meaning of the recently added COVID-19 concepts. We pushed the actual mappings to the CONCEPT_RELATIONSHIP table based on the current coding guidelines of ICD10 and ICD10CM.

But this is still a responsibility of ETL to address the following issues:

5. Additional minor points

COVID-19 v1.0 Vocabulary Release (19-21 March, 2020)

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 interactions 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, before the reliable test result was 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 Domain. 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 different 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 Сoncept, 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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