merging Covid-19 data together the repository contains folders per datasets. Each folder's name is a copy of the dataset name. Additionally, each folder has a config files for mapping the ontologies according to panmap view protocol. Each folder will contain a column mapping in which all variables with the provided names will appear as rows under provided column. The provided column names will be 'recoded' to ontological name - a universal name. This is done for the purpose of interoperability and working with universal names,where possible, in the process of merging the datasets into one.
provided variable for Sex -> gender
provided categories for gender if M -> male
F -> female
NA -> unknown
provided variable Date -> date
provided AGEGROUP -> agegroup
provided variable for number tested -> sample_count
provided variable latitude -> GPS_latitude provided vartiable longitude -> GPS_longitude
provided State -> state
provided County -> county
provided Deaths -> deaths ontology term: life-death temporal boundary UBERON_0035944
Aggregate data -> pool Individual data -> individual
Add a column that provides the name of the country the data was collected from Column to be named -> location_country
Two columns needed standard -> Aggregate data -> pool -> Individual data -> individual additional column -> OBI_0302716 -> OBI_0002648 ontologies can be found here : https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/blob/master/src/ontology/eupath_dev.owl
git clone this onto your computer and view using protege which can be downloaded here: https://protege.stanford.edu/
Two columns needed -> case count and case type case count -> 25 case type -> deaths -> positive cases -> negative cases -> clinical diagnosis -> self reporting -> symptom report