Omnivore 2.0 - midas-isg/data-format-repository GitHub Wiki
Omnivore 2.0 output format
Omnivore reads case count reports from health agencies and converts these files into a standard data format. The details of this specific output format are defined below.
Understanding the file format
The output file is a CSV file that has the following format:
| Variable | Description | Example |
|---|---|---|
| case_count_id | A numeric identifier that uniquely identifies the case count to a distinct location. | |
| interval_start_date_(ISO 8601) | The start date for a specific interval of the case count in ISO 8601 format. | 2014-01-05T12:00+0000 |
| interval_end_date_(ISO 8601) | The end date for a specific interval of the case count in ISO 8601 format. | 2014-01-06T12:00+0000 |
| admin_level_i_name | The name of the location at a variable administration level, i, that this case count reports on. The administration levels start at 0, which represents the country, and becomes more specific as the level increases. | Colombia |
| admin_level_i_id_(Apollo:ApolloLocationCode) | The Apollo Location Code that represents the location at a variable administration level, i, that this case count reports on. | 5076 |
| case_type_(Apollo:CaseTypeEnum) | The case definition for the case count. | FATAL_CASE, CONFIRMED_CASE, PROBABLE_CASE, SUSPECTED_CASE |
| case_count_type_(Apollo:CaseCountArrayTypeEnum) | The type of case count determined by the interval. | MUTUALLY_EXCLUSIVE_WITH_CONSTANT_LENGTH_INTERVALS, MUTUALLY_EXCLUSIVE_WITH_VARYING_LENGTH_INTERVALS, CUMULATIVE_WITH_RESETS, CUMULATIVE_WITHOUT_RESETS. A case count is determined to be mutually exclusive if the case count reports begin and end on an unique date. If the intervals span the same amount of time, e.g. 1 week, this would be a constant length interval, otherwise it would be of varying length. A case count is determined to be cumulative if the reports start on the same date but end on a different date. Some reports may reset counts back to 0 during the tracking period. |
| disease_name | The name of the disease for the case count. | Chikungunya fever |
| disease_id_(SNOMED) | The SNOMED code for the disease. | 111864006 |
| source_filename | The name of the case count report that this output was generated from. | |
| epidemic_week | The reporting week that this case count information from generated from. | |
| number_of_cases | The number of cases reported for this interval |
Sample Omnivore output
| case_count_id | interval_start_date_(ISO 8601) | interval_end_date_(ISO 8601) | admin_level_0_name | admin_level_0_id_(Apollo:ApolloLocationCode) | admin_level_1_name | admin_level_1_id_(Apollo:ApolloLocationCode) | admin_level_2_name | admin_level_2_id_(Apollo:ApolloLocationCode) | admin_level_3_name | admin_level_3_id_(Apollo:ApolloLocationCode) | admin_level_4_name | admin_level_4_id_(Apollo:ApolloLocationCode) | case_type_(Apollo:CaseDefinitionEnum) | case_count_type_(Apollo:CaseCountArrayTypeEnum) | disease_name | disease_id_(SNOMED) | source_filename | epidemic_week | number_of_cases |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2014-01-05T12:00+0000 | 2014-01-11T12:00+0000 | Colombia | 5076 | Putumayo | 5488 | Mocoa | 344829 | AUTOCHTHONOUS | MUTUALLY_EXCLUSIVE_WITH_CONSTANT_LENGTH_INTERVALS | Chikungunya fever | 111864006 | Vigilancia Rutinaria por evento Municipal 2014.xlsx | 1 | 6 | ||||
| 1 | 2014-01-12T12:00+0000 | 2014-01-18T12:00+0000 | Colombia | 5076 | Putumayo | 5488 | Mocoa | 344829 | AUTOCHTHONOUS | MUTUALLY_EXCLUSIVE_WITH_CONSTANT_LENGTH_INTERVALS | Chikungunya fever | 111864006 | Vigilancia Rutinaria por evento Municipal 2014.xlsx | 2 | 1 | ||||
| 1 | 2014-01-19T12:00+0000 | 2014-01-25T12:00+0000 | Colombia | 5076 | Putumayo | 5488 | Mocoa | 344829 | AUTOCHTHONOUS | MUTUALLY_EXCLUSIVE_WITH_CONSTANT_LENGTH_INTERVALS | Chikungunya fever | 111864006 | Vigilancia Rutinaria por evento Municipal 2014.xlsx | 3 | 5 | ||||
| 2 | 2016-01-03T12:00+0000 | 2016-01-09T12:00+0000 | Colombia | 5076 | Santander | 6907 | Matanza | 344905 | FATAL | MUTUALLY_EXCLUSIVE_WITH_CONSTANT_LENGTH_INTERVALS | Chikungunya fever | 111864006 | Vigilancia Rutinaria por evento Municipal a semana 28 2016.xlsx | 1 | 2 | ||||
| 2 | 2016-01-10T12:00+0000 | 2016-01-16T12:00+0000 | Colombia | 5076 | Santander | 6907 | Matanza | 344905 | FATAL | MUTUALLY_EXCLUSIVE_WITH_CONSTANT_LENGTH_INTERVALS | Chikungunya fever | 111864006 | Vigilancia Rutinaria por evento Municipal a semana 28 2016.xlsx | 2 | 0 | ||||
| 2 | 2016-01-17T12:00+0000 | 2016-01-23T12:00+0000 | Colombia | 5076 | Santander | 6907 | Matanza | 344905 | FATAL | MUTUALLY_EXCLUSIVE_WITH_CONSTANT_LENGTH_INTERVALS | Chikungunya fever | 111864006 | Vigilancia Rutinaria por evento Municipal a semana 28 2016.xlsx | 3 | 8 |