Description of database fields
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| field name | comments | data type | allowed values | required | maximum length (characters) |
|---|---|---|---|---|---|
| id | id - primary key | integer | - | yes | 6 |
| isolate | MANDATORY: Provide the user-defined name for the sample. Every isolate name from a single user must be unique. Please, make it concise and avoid to use spaces (prefer the underscore instead) or special characters in the name. Example: KPNIH2 | text | - | yes | 20 |
| aliases | alternative names for isolate | text (multiple) | - | no | - |
| references | PubMed ids that link to publications that describe or include record | integer (multiple) | - | no | - |
| sender | sender unique name, link to users | integer | Click for list of sender ids | yes | 4 |
| curator | curator who entered data,link to users | integer | Click for list of curator ids | yes | 4 |
| date_entered | date first entered | date | - | yes | 10 |
| datestamp | date last modified | date | - | yes | 10 |
| taxonomic_designation | MANDATORY: Provide the taxonomic designation of the isolate from the pick list in the template | text |
K. pneumoniae
K. quasipneumoniae subsp. quasipneumoniae K. variicola subsp. variicola K. quasipneumoniae subsp. similipneumoniae K. variicola subsp. tropica K. quasivariicola K. africana |
yes | - |
| phylogroup_from_ST | To be filled by curators only. Doubtful: at least one locus non-Kp (Outgroup); Mixed: at least 1 locus from different Kp phylogroup(s) than the majority of loci | text | - | no | 100 |
| QC_status | To be filled by curators only. State of genome's quality control | text | - | no | 100 |
| isolation_year | MANDATORY: Provide the year on which the isolate was collected | integer | - | yes | 4 |
| city | MANDATORY: Provide the city/province/region of origine of the isolate. If any doubt, please search for geography terms here:https://www.ebi.ac.uk/ols/ontologies/gaz | text | - | yes | 50 |
| country | MANDATORY: Provide the geographical of origin of the isolate from the pick list in the template. | text | yes | - | |
| source_type | MANDATORY: Provide the source of origin of the isolate from the pick list in the template | text |
Human
Food Feed Farm Animal Wild Animal Environment Other Unknown |
yes | - |
| host | MANDATORY: Provide common name (e.g. human, dog, cow, ...) if there was a host. If the sample was environmental, put 'environment' | text | - | yes | 30 |
| source_details | MANDATORY: Provide the detailed source of origin of the isolate (e.g. wound, urine, bood) | text | - | yes | 150 |
| infection | Provide the name of infection experienced by the host. Only required if there was a host. If the host was healthy, put 'carriage' or 'colonisation' | text | - | no | 30 |
| other_source_info | Please provide any other relevant details | text | - | no | 70 |
| source_lab | Provide the name (full name) of the laboratory/agency that processed the strain and be consistent across multiple submissions | text | - | no | 200 |
| resistance_info | Provide antimicrobial resistance pattern and/or mechanisms informations | text | - | no | 300 |
| virulence_info | Provide identified virulence genes | text | - | no | 150 |
| K_type | Provide the capsular (K) type | text | - | no | 12 |
| K_typing_method | Provide information on how the K type was determined from the pick-list in the template | text |
Antiserum
C-pattern K type-specific PCR (wzy, wzx...) wzi sequencing Full sequencing of CPS cluster Other |
no | - |
| duplicate_number | To be filled by curators only | text | - | no | 10 |
| comments | Any comments from the user or curator | text | - | no | 150 |
| accession_number | Provide assembly or run accession number. Example: ERR025479 | text | - | no | 50 |