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 |
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 |
|
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 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 |
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 |
|
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) |
|