Description of database fields
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| field name | comments | data type | allowed values | required | maximum length (characters) |
|---|---|---|---|---|---|
| id | primary key | integer | - | yes | 5 |
| isolate | isolate name | 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 | - |
| country | country where strain was isolated | text | yes | - | |
| region | region inside country | text | - | no | 30 |
| town_or_city | this field is used in mapping so please try to ensure correct or most common spelling to facilitate GPS coordinates lookup. For US place names, please suffix 2-letter state code in square brackets, e.g. 'Dallas [TX]', to resolve ambiguities. | text | - | no | 50 |
| year | year of isolation | integer | min: 1900; max: 2023 | expected | 4 |
| date_sampled | date sample was taken | date | max: 2023-03-21 | 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: 2023-03-21 | no | 10 |
| non_culture | result comes from non-culture diagnosis | bool | - | no | - |
| age_yr | age in years if age over 12 months | integer | - | no | 4 |
| age_months | age in months if age less than 1 year | integer | min: 0; max: 11 | no | 2 |
| age_days | age in days where age is less than 4 months | integer | min: 0; max: 120 | no | 3 |
| sex | text |
male
female |
no | - | |
| disease | Add details to comments if 'other' is selected. | text (multiple) | no | - | |
| source | please put detail in comments field | text | no | - | |
| epidemiology | text |
hospital acquired
community acquired |
no | - | |
| capsular_serotype | serotype | text | no | - | |
| capsular_genotype | serotype | text | no | - | |
| erythromycin_disc_testing | Disc testing | text |
susceptible
intermediate resistant |
no | - |
| erythromycin_mic | MIC in microgram/ml | text | - | no | 6 |
| tetracycline_disc_testing | Disc testing | text |
susceptible
intermediate resistant |
no | - |
| tetracycline_mic | MIC in microgram/ml | text | - | no | 6 |
| clindamycin_disc_testing | Disc testing | text |
susceptible
intermediate resistant |
no | - |
| clindamycin_mic | MIC in microgram/ml | text | - | no | 6 |
| penicillin_disc_testing | Disc testing | text |
susceptible
intermediate resistant |
no | - |
| penicillin_mic | MIC in microgram/ml | text | - | no | 6 |
| comments | any other comments | text | - | no | 1000 |
| bioproject_accession | ENA/SRA bioproject accession number | text (multiple) | - | no | 20 |
| biosample_accession | ENA/SRA biosample accession number | text (multiple) | - | no | 20 |
| ENA_run_accession | ENA SRA accession number to access short read data | 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 |