A Database Scheme defines all epidemiological related database fields.


Category Label Examples Description Submission
Epi Basic Sample ID Unique name for the sample Button16-ENA grey.png
Epi Basic Alias ID(s) Alternative unique laboratory or field identifier(s), separated by comma Button16-ENA grey.png
Epi Basic Collection Date Date of sampling Button16-ENA grey.png
Epi Basic Receipt Date Date of sample received
Epi Basic Sample ID of Collector Sample ID given by the sample provider
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 Button16-ENA grey.png
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 Button16-ENA grey.png
Epi Source Host Age (years) Age of the host in years at time of sampling Button16-ENA grey.png
Epi Source Host Sex male; female Gender or physical sex of the host Button16-ENA grey.png
Epi Source Host Disease Healthy; specific disease afflicting the hostfrom which the sample is (vocabulary from NCBI MeSH) Button16-ENA grey.png
Epi Source Isolation 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]) Button16-ENA grey.png
Epi Source Country of Isolation Country geographical origin of the sample Button16-ENA grey.png
Epi Source State of Isolation State or sub-region geographical origin of the sample (required for USA) Button16-ENA grey.png
Epi Source City of Isolation City or county (preferred for USA) geographical origin of the sample Button16-ENA grey.png
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 Cluster/Outbreak Name or number of the Cluster or the Outbreak
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 Button16-ENA.png
Epi Characteristic Species Species name of the organism that provided the sequenced genetic material Button16-ENA.png
Epi Characteristic Subspecies Supspecies name of the organism that provided the sequenced genetic material Button16-ENA grey.png
Epi Characteristic Strain Taxonomy category in microorganisms equivalent to subspecies; also takes the place of species name in viruses. Button16-ENA grey.png
Epi Characteristic Genotype Observed genotype of the sample. Button16-ENA grey.png
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. Button16-ENA grey.png
Epi Characteristic Pathotype Bacterial species specific pathotypes (e.g., for Eschericia coli - STEC, UPEC, APEC) Button16-ENA grey.png
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) Button16-ENA grey.png
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:

Button16-ENA grey.png Potentially this field is submitted and published on EMBL-EBI ENA when the Sample is submitted.

Button16-ENA.png This field is submitted (required) and published on EMBL-EBI ENA when the Sample is submitted.