A Database Scheme defines all epidemiological related database fields.
| Category | Label | Examples | Description | Submission |
|---|---|---|---|---|
| Epi Basic | Sample ID | Unique name for the sample | 
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| Epi Basic | Alias ID(s) | Alternative unique laboratory or field identifier(s), separated by comma |
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| Epi Basic | Collection Date | Date of sampling |
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| 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 |
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| Epi Source | Source Subtype | human; animal; plant; environmental; food; feed |
Sub-classification for the source type | |
| Epi Source | Host | Homo sapiens | NCBI TaxID or organism name of the natural host |
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| Epi Source | Host Age (years) | Age of the host in years at time of sampling |
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| Epi Source | Host Sex | male; female | Gender or physical sex of the host |
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| Epi Source | Host Disease | Healthy; specific disease afflicting the hostfrom which the sample is (vocabulary from NCBI MeSH) |
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| 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]) |
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| Epi Source | Country of Isolation | Country geographical origin of the sample |
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| Epi Source | State of Isolation | State or sub-region geographical origin of the sample (required for USA) |
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| Epi Source | City of Isolation | City or county (preferred for USA) geographical origin of the sample |
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| 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").
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| 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 | 
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| Epi Characteristic | Species | Species name of the organism that provided the sequenced genetic material |
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| Epi Characteristic | Subspecies | Supspecies name of the organism that provided the sequenced genetic material |
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| Epi Characteristic | Strain | Taxonomy category in microorganisms equivalent to subspecies; also takes the place of species name in viruses. |
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| Epi Characteristic | Genotype | Observed genotype of the sample. |
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| 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. |
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| Epi Characteristic | Pathotype | Bacterial species specific pathotypes (e.g., for Eschericia coli - STEC, UPEC, APEC) |
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| 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) |
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| 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 EMBL-EBI ENA when the Sample is submitted.
This field is submitted (required) and published on EMBL-EBI ENA when the Sample is submitted.
FOR RESEARCH USE ONLY. NOT FOR USE IN CLINICAL DIAGNOSTIC PROCEDURES.