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 | |||
| Epi Source | Source Type | clinical/host-associated; environmental/food/other; unknown | Clinical/host-associated, environmental/food/other, or unknown |
|
| 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 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.