How to handle pooled samples

Although PHAROS is designed for granular (animal-level) data, pooled testing is still a welcome data source.

Researchers who are pooling samples from multiple animals can present that information one of two ways:

Option 1: One-to-many sample-animal relationship

Suppose a researcher swabs three marmosets, and pools the three swabs into a single test for herpesviruses---but still wants to record metadata on individual animals. They might represent the single positive test result as:

	Sample ID	Animal ID	Host species	Organism sex	Detection outcome	Pathogen	GenBank accession
1	CApool1	Calla01	Callithrix aurita	Female	Positive	Macacine alphaherpesvirus 1	GB8675309
2	CApool1	Calla002	Callithrix aurita	Male	Positive	Macacine alphaherpesvirus 1	GB8675309
3	CApool1	Calla003	Callithrix aurita	Female	Positive	Macacine alphaherpesvirus 1	GB8675309

In this format, the metadata for each animal is given on a separate row, but attached to the "Sample ID" and "GenBank accession".

Option 2: One-to-none sample-animal relationship

Suppose a researcher pools several dozen mosquitoes from a trap and tests that sample for West Nile virus.

Sample ID	Animal ID	Host species	Detection outcome	Pathogen	GenBank accession	Detection comments
Tuscon1		Aedes aegypti	Positive	West Nile virus	GB1738	Pooled mosquito traps

In this format, individual animals are not identified, and the finest resolution of the data is at the trap (= sample) level.