Description of database fields
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| field name | comments | data type | allowed values | required | maximum length (characters) |
|---|---|---|---|---|---|
| id | Primary key | integer | - | yes | 6 |
| isolate | Isolate name | text | - | yes | 30 |
| aliases | alternative names for isolate | text (multiple) | - | no | - |
| references | PubMed ids that link to publications that describe or include record | integer (multiple) | - | no | - |
| country | country where strain was isolated | text | yes | - | |
| region | Region/city etc inside country | text | - | no | 50 |
| year | Year of isolation | integer | min: 1900; max: 2022 | expected | 4 |
| date_sampled | date sample was taken | date | max: 2022-05-18 | no | 10 |
| isoyear_sampled | ISO year (this may be different from the Gregorian year recorded in the year field) - value is determined automatically from the contents of the date_sampled field. This cannot be updated manually | integer | - | no | - |
| week_sampled | week of the year - value is determined automatically from the contents of the date_sampled field. This cannot be updated manually | integer | - | no | - |
| date_received | date received by laboratory (may be approximate) | date | max: 2022-05-18 | no | 10 |
| non_culture | result comes from non-culture diagnosis | bool | - | no | - |
| serotype | text | yes | - | ||
| serotyping_method | text (multiple) |
Latex
PCR PneumoCAT Quellung SeroBA other unknown |
yes | - | |
| serotype_comments | text | - | no | 128 | |
| submitted_serotype | serotype (or serogroup) designation as submitted by user. This is a legacy field that can help indicate why a serotype value is listed as inconclusive. | text | - | no | 20 |
| age_yr | Age of patient in years | integer | min: 0; max: 120 | no | 3 |
| age_mth | Age of patient in months if less than one year old | integer | min: 0; max: 11 | no | 3 |
| age_range | age range (values based on whole years) - this will be populated automatically if you enter a value for age_yr | text | no | - | |
| sex | Patient gender | text |
male
female |
no | - |
| diagnosis | Enter further details in the comments field if 'other' selected. | text (multiple) | no | - | |
| host | text | yes | - | ||
| source | Source of isolate. Enter further details in the comments field if 'other' selected. | text | no | - | |
| epidemiology1 | text |
hospital acquired
community acquired |
no | - | |
| epidemiology2 | text |
outbreak
carriage |
no | - | |
| penicillin | Penicillin susceptibility. Enter MIC value (if only S, I, or R is known, that is acceptable also). Please enter the susceptibility test method in the comments section. | text | - | no | 10 |
| erythromycin | Erythromycin susceptibility. Enter MIC value (if only S, I, or R is known, that is acceptable also). Please enter the susceptibility test method in the comments section. | text | - | no | 10 |
| tetracycline | Tetracycline susceptibility. Enter MIC value (if only S, I, or R is known, that is acceptable also). Please enter the susceptibility test method in the comments section. | text | - | no | 10 |
| chloramphenicol | Chloramphenicol susceptibility. Enter MIC value (if only S, I, or R is known, that is acceptable also). Please enter the susceptibility test method in the comments section. | text | - | no | 10 |
| cefotaxime | Cefotaxime susceptibility. Enter MIC value (if only S, I, or R is known, that is acceptable also). Please enter the susceptibility test method in the comments section. | text | - | no | 10 |
| comments | Any other comments | text | - | no | 1000 |
| QC_override | text (multiple) |
Fail - rMLST species id
Fail - rMLST multiple alleles Fail - MLST multiple alleles Warning - rMLST species id |
no | - | |
| ENA_accession | ENA SRA accession number to access short read data | text | - | no | 30 |
| rMLST_database_accession | Accession number in rMLST genome database | integer | - | no | 30 |
| private_project | Leave this blank unless you know what you are doing - entering anything here will hide your data in the public interface | text | - | no | 30 |
| 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 |