data_dictionary.txt

DATA DICTIONARY
2022-01-06

CHANGELOG

2022-01-06 Removed empty genomeSequences.*
2021-12-01 Added SGTF field

Unless mentioned all fields are text strings.

[] next to a field indicates that it is a comma separated
array.

* marks mandatory fields

METADATA

 1. _id *

    Internal ID used by Global.health database.
    This is not expected to be stable.

 2. caseReference.additionalSources []

    Additional sources (URLs) for this case

 3. caseReference.sourceId *

    Unique source ID for this case. Each case is ingested from
    a specific source URL, which has an unique ID. This is
    stable for a particular source.

 4. caseReference.sourceUrl *

    Data URL from which this case was ingested.

 5. caseReference.uploadIds [] *

    Subsequent uploads following the initial upload of a case can
    change the data of a case (only in sources that provide an
    unique ID in caseReference.sourceEntryId). This field records
    the unique upload IDs that updated this case.

 6. caseReference.verificationStatus *

    Case verification status
    Values: VERIFIED | UNVERIFIED | EXCLUDED

      VERIFIED: Case was verified by a curator after ingestion
    UNVERIFIED: Case was automatically ingested without verification
      EXCLUDED: Case has been excluded from the line list

    Most of our automated data ingestion is from authoritative
    government datasets, with a few from volunteer-operated datasets.

DEMOGRAPHICS

Generally, we prefer to ingest demographic information over
location, if they are not available in the same dataset.

 7. demographics.ageRange.end

    Upper age range of individual (0 - 120)

 8. demographics.ageRange.start

    Lower age range of individual (0 - 120)

9. demographics.ethnicity

    Ethnicity of individual

10. demographics.gender

    Gender of individual (Male | Female | Non-binary/Third gender | Other)

11. demographics.nationalities []

    All the nationalities of the individual

12. demographics.occupation

    Occupation of the individual

EVENTS

All .date values are dates in YYYY-MM-DD format.

13. events.confirmed.date *
14. events.confirmed.value

    Confirmed date. If value is present, indicates
    method of confirmation.

15. events.firstClinicalConsultation.date

    First clinical consultation date

16. events.hospitalAdmission.date
17. events.hospitalAdmission.value

    Hospital admission date, value (Yes | No)

18. events.icuAdmission.date
19. events.icuAdmission.value

    Intensive Care Unit admission date, value (Yes | No)

20. events.onsetSymptoms.date

    Date of onset of symptoms

21. events.outcome.date
22. events.outcome.value

    Outcome date, values are
      Death | Recovered | hospitalAdmission | icuAdmission | Unknown

23. events.selfIsolation.date

    Date that individual started self-isolating

LOCATION

24. location.administrativeAreaLevel1

    Admin1 level location of individual (usually state or province)

25. location.administrativeAreaLevel2

    Admin2 level location of individual (usually district)

26. location.administrativeAreaLevel3

    Admin3 level location of individual (usually city)

27. location.country *

    Country that case was reported in.

28. location.geoResolution *

    Geo-resolution of location (how coarse the location is)
      Country | Admin1 | Admin2 | Admin3 | Point

29. location.geometry.latitude *

    Geolocated latitude (-90 to 90)
    Positive values are North, negative values are South

30. location.geometry.longitude *

    Geolocated longitude (-180 to 180)
    Positive values are East, negative values are West

31. location.name

    Full name of location
    (example: Lyon, Auvergne-Rhône-Alpes, France)

32. location.place

    Name of the place this location refers to
    (example: Boston Children's Hospital)

PATHOGENS

33. pathogens []

    Pathogens other than SARS-CoV-2


PRE-EXISTING CONDITIONS

34. preexistingConditions.hasPreexistingConditions

    Whether the patient has pre-existing conditions
    Boolean: True | False

35. preexistingConditions.values []

    List of pre-existing conditions

REVISION METADATA

36. revisionMetadata.creationMetadata.date

    Date this case was first created

37. revisionMetadata.creationMetadata.notes

    Notes added by the curator for this case

38. revisionMetadata.editMetadata.date

    Date this case was last edited
    
39. revisionMetadata.editMetadata.notes

    Notes added by the curator for last edit
    
40. revisionMetadata.revisionNumber

    Revision number of the case (positive integer)

SGTF

41. SGTF

    S-Gene Target failure (0 = no deletion, 1 = deletion (S-))

SYMPTOMS

42. symptoms.status

    Symptom status (Asymptomatic | Symptomatic | Presymptomatic | null)

43. symptoms.values []

    List of symptoms

TRANSMISSION

How this case got infected and by who if known

44. transmission.linkedCaseIds []

    UUID of a related case in the system

45. transmission.places []

    Places where transmission occurred

46. transmission.routes []

    Routes of transmission

TRAVEL HISTORY

47. travelHistory.travel.dateRange.end
48. travelHistory.travel.dateRange.start

    Start and end dates for travel history

49. travelHistory.travel.location.administrativeAreaLevel1 []
50. travelHistory.travel.location.administrativeAreaLevel2 []
51. travelHistory.travel.location.administrativeAreaLevel3 []
52. travelHistory.travel.location.country []
53. travelHistory.travel.location.geoResolution []

    These have the same meaning as in LOCATION, except that these
    pertain to travel history of the individual. Unlike the fields in
    location, the fields here are all comma-separated arrays, with each
    item corresponding to a travel location in the last 30 days.

54. travelHistory.travel.location.geometry.coordinates []

    Comma-separated tuples of latitude and longitude. If the individual
    visited latitude m1 and longitude n1 this would be represented as
    "(m1, n1)". If there was another travel coordinate (m2, n2), then
    this would be represented as "(m1, n1),(m2, n2)"

55. travelHistory.travel.location.name []
56. travelHistory.travel.location.place []
    
    Same as LOCATION, except these are arrays

57. travelHistory.travel.methods []

    Corresponding travel methods (such as air, ship, rail ...)

58. travelHistory.travel.purpose []

    Purpose of travel

59. travelHistory.traveledPrior30Days

    Whether the patient has travelled in the past 30 days
    Boolean: True | False

VACCINES

60. vaccines.0.batch

    First vaccine batch

61. vaccines.0.date

    Date of first vaccine

62. vaccines.0.name

    Name of first vaccine

63. vaccines.0.sideEffects []

    List of side-effects experienced after vaccine

64. vaccines.1.batch
65. vaccines.1.date
66. vaccines.1.name
67. vaccines.1.sideEffects
68. vaccines.2.batch
69. vaccines.2.date
70. vaccines.2.name
71. vaccines.2.sideEffects
72. vaccines.3.batch
73. vaccines.3.date
74. vaccines.3.name
75. vaccines.3.sideEffects

    Same as before, for subsequent vaccines taken by the same individual

VARIANT OF CONCERN

76. variantOfConcern

    Variant of concern that was detected. This uses the Pango lineage.