Description of database fields
Provenance/primary metadata
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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 | 50 |
| 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 |
| month | month of isolation | integer | min: 1; max: 12 | no | 2 |
| isolation_date | date | - | no | 12 | |
| received_date | date | - | no | 12 | |
| age_yr | age in years | integer | max: 120 | no | 4 |
| age_mth | month part of age 0-11 when patient is less than 1 year old | integer | min: 0; max: 11 | no | 4 |
| sex | text |
male
female |
no | - | |
| disease | please put other diseases in comments field | text |
carrier
gastroenteritis systemic disease Guillain Barre Syndrome Miller Fisher Syndrome other neurological sequelae reactive arthritis other rheumatological sequelae |
no | - |
| source | please put detail in comments field | text | no | - | |
| epidemiology | human epidemiology | text |
carrier
sporadic case general outbreak family outbreak environmental isolate hospital inpatient |
no | - |
| species | species name | text | yes | - | |
| penner | Penner serotype | text | - | no | 20 |
| 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. This should start either ERR, SRR, or DRR. | text | - | no | 15 |
| private_project | Legacy field used to filter private data - do not use unless you have been explicitly told to put something here Leave this blank unless you know what you are doing - entering anything here will hide your data in the public interface |
text | - | no | 30 |
| comments | any other comments | text | - | no | 1000 |
| 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 |
Secondary metadata
| field name | comments | data type | allowed values | required | maximum length (characters) |
|---|---|---|---|---|---|
| aminoglycoside_genotypes_1 | - | text | no | - | |
| Anon_patient_ID | - | integer | - | no | 4 |
| ciprofloxacin_phenotype | - | text |
S
R |
no | - |
| erythromycin_phenotype | - | text |
S
R |
no | - |
| fluoroquinolone_genotypes_1 | - | text | no | - | |
| fluoroquinolone_genotypes_2 | - | text | no | - | |
| macrolide_genotypes_1 | - | text |
23s_CC[2075:A-G]
23s_CC[2075:A-G][c] 23s_CJ[2075:A-G] 23s_CJ[2075:A-G][c] 23s_CJ[2075:A-R] 23s_CC[2074:A-G] 23s_CC[2074:A-C][c] 23s_CC[2074:A-M][c] |
no | - |
| macrolide_genotypes_2 | - | text |
A737G
A736C A736G A736T |
no | - |
| tetracycline_genotypes_1 | - | text | no | - | |
| tetracycline_genotypes_2 | - | text |
tetO
tetO [incomplete] tetW tetO/32/O [incomplete] tetO [int stop] tetO / tetO/W/32/O [incomplete] tetM [incomplete] tetO/W/32/O [incomplete] |
no | - |
| tetracycline_phenotype | - | text |
S
R I |
no | - |