A Database Scheme defines all epidemiological related database fields.

Category	Label	Examples	Description	Submission
Epi Basic	Sample ID		Unique name for the sample
Epi Basic	Alias ID(s)		Alternative unique laboratory or field identifier(s), separated by comma
Epi Basic	Collection Date		Date of sampling
Epi Basic	Receipt Date		Date of sample received
Epi Basic	Collected By		Name or address of the person or lab who collected the sample
Epi Basic	Comment		Comments related to the sample
Epi Source	Source Type	clinical/host-associated; environmental/food/other; unknown	Clinical/host-associated, environmental/food/other, or unknown
Epi Source	Source Subtype	human; environmental; food; animal; feed; plant	Sub-classification for the source type
Epi Source	Host	Homo sapiens	NCBI TaxID or organism name of the natural host
Epi Source	Host Age (years)		Age of the host in years at time of sampling
Epi Source	Host Sex	male; female	Gender or physical sex of the host
Epi Source	Host Disease		Healthy; specific disease afflicting the hostfrom which the sample is (vocabulary from NCBI MeSH)
Epi Source	Isolation Epi Source	stool; blood	Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived (e.g., blood, stool [human host] or sink, pork meat [enviromental/food])
Epi Source	Country of Isolation		Country geographical origin of the sample
Epi Source	State of Isolation		State or sub-region geographical origin of the sample (required for USA)
Epi Source	City of Isolation		City or county (preferred for USA) geographical origin of the sample
Epi Source	ZIP of Isolation		Postal code of geographical origin of the sample
Epi Source	Lat/Long of Isolation		Latitude and longitude of location of isolation in decimal degrees and in WGS84 system. Latitude and longitude must be separated by semicolon (e.g., "48.1711; 16.3778").
Epi Source	Lat/Long Resolution		Resolution level of the defined lat/long (e.g., City or Country)
Epi Source	Epi Info		Epidemilogical information (e.g., outbreak 1, carrier, ...)
Epi Source	Case ID		An identifier for the case related to this sample
Epi Source	ECDC Case ID		The ECDC identifier (TESSy) for the case related to this sample
Epi Characteristic	Genus		Genus name of the organism that provided the sequenced genetic material
Epi Characteristic	Species		Species name of the organism that provided the sequenced genetic material
Epi Characteristic	Subspecies		Supspecies name of the organism that provided the sequenced genetic material
Epi Characteristic	Strain		Taxonomy category in microorganisms equivalent to subspecies; also takes the place of species name in viruses.
Epi Characteristic	Genotype		Observed genotype of the sample.
Epi Characteristic	Serotype		Taxonomy below subspecies; a variety (in bacteria, fungi or virus) usually based on its antigenic properties. Same as serovar and serogroup. e.g. serotype="H1N1" in Influenza A virus CY098518.
Epi Characteristic	Pathotype		Bacterial species specific pathotypes (e.g., for Eschericia coli - STEC, UPEC, APEC)
Epi Characteristic	Identification Method		Speciation method for the sample (e.g., MALDI ToF, Vitek II, Phoenix)
Epi Characteristic	Identification Kit Vendor		Company producing speciation method (e.g., Bruker Daltonics, Biomerieux or Becton Dickinson)
Epi Characteristic	Culture Collection		The specific culture-collection identifier if the sample has been deposited at a culture collection (e.g., ATCC 12345 or DSM 12345)
Epi Characteristic	PubMed ID(s)		The specific PubMed identifier(s) if the sample has been used in publication(s), separated by comma
Epi Characteristic	Study		A study name or identifier
Epi Characteristic	Nucleotide Accession(s)		The specific NCBI/EMBL accessions if the genome data if downloaded from or deposited at NCBI/EMBL, separated by comma
Epi Characteristic	Experiment Accession		The specific NCBI/EMBL accessions if the genome data if downloaded from or deposited at NCBI/EMBL, separated by comma
Epi Characteristic	Sample Accession		The specific NCBI/EMBL accessions if the genome data if downloaded from or deposited at NCBI/EMBL, separated by comma
Epi Characteristic	Study Accession		The specific NCBI/EMBL accessions if the genome data if downloaded from or deposited at NCBI/EMBL, separated by comma
Report	Report Comment		A comment that is printed on a Sample report (PDF)

Submission Icons:

Potentially this field is submitted and published on cgMLST.org when the Sample is submitted.

This field is submitted and published on cgMLST.org when the Sample is submitted.

Potentially this field is submitted and published on EMBL-EBI ENA when the Sample is submitted.

This field is submitted (required) and published on EMBL-EBI ENA when the Sample is submitted.