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.