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 | 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 inside country | text | - | no | 50 |
| 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: 2023-02-07 | 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: 2023-02-07 | no | 10 |
| non_culture | result comes from non-culture diagnosis | bool | - | no | - |
| epidemiological_year | epidemiological year for study in format mm/yyyy-mm/yyyy | text | - | no | 15 |
| age_yr | age in years | integer | min: 0; max: 120 | no | - |
| age_range | age range - this will be populated automatically if you enter a value for age_yr | text |
<1
1-4 5-14 15-24 25-44 45-64 65+ |
no | - |
| age_mth | month part of age (0-11) for patients under 1 year old | integer | min: 0; max: 11 | no | - |
| sex | sex of patient/carrier | text |
male
female transgender male transgender female |
no | - |
| disease | please put other diseases in comments field | text | no | - | |
| source | biological source of sample - please put other sources in comments field | text | no | - | |
| epidemiology | text | no | - | ||
| species | text | yes | - | ||
| serogroup | group determined by serological means. If you select 'other' please provide further details in the comments field. Values in this field from legacy data may have been determined by genotypic means, but for new data this should only represent values determined by serology. | text | no | - | |
| genogroup | group determined by genotypic means | text | no | - | |
| genogroup_notes | details about genogroup prediction | text | - | no | 1000 |
| capsule_group | capsular group value is determined automatically from the contents of the serogroup and genogroup fields. This cannot be updated manually | text | - | no | - |
| serotype | text | - | no | 15 | |
| sero_subtype | text | - | no | 15 | |
| amoxicillin_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| amoxicillin_mic | MIC in mg/l | float | - | no | - |
| azithromycin_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| azithromycin_mic | MIC in mg/l | float | - | no | - |
| cefixime_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| cefixime_mic | MIC in mg/l | float | - | no | - |
| cefixime_SIR | S: susceptible, standard dose; I: susceptible, increased exposure; R: resistant. Based on EUCAST defined breakpoints: Ng (S: <=0.125; R: >0.125). Field value will be populated automatically if MIC value is provided. | text |
S
R |
no | - |
| cefotaxime_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| cefotaxime_mic | MIC in mg/l | float | - | no | - |
| cefotaxime_SIR | S: susceptible, standard dose; I: susceptible, increased exposure; R: resistant. Based on EUCAST defined breakpoints: Nm (S: <=0.125; R: >0.125); Ng (S: <=0.125; R: >0.125). Field value will be populated automatically if MIC value is provided. | text |
S
R |
no | - |
| ceftriaxone_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| ceftriaxone_mic | MIC in mg/l | float | - | no | - |
| ceftriaxone_SIR | S: susceptible, standard dose; I: susceptible, increased exposure; R: resistant. Based on EUCAST defined breakpoints: Nm (S: <=0.125; R: >0.125); Ng (S: <=0.125; R: >0.125). Field value will be populated automatically if MIC value is provided. | text |
S
R |
no | - |
| chloramphenicol_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| chloramphenicol_mic | MIC in mg/l | float | - | no | - |
| chloramphenicol_SIR | S: susceptible, standard dose; I: susceptible, increased exposure; R: resistant. Based on EUCAST defined breakpoints: Nm (S: <=2; R: >2). Field value will be populated automatically if MIC value is provided. | text |
S
R |
no | - |
| ciprofloxacin_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| ciprofloxacin_mic | MIC in mg/l | float | - | no | - |
| ciprofloxacin_SIR | S: susceptible, standard dose; I: susceptible, increased exposure; R: resistant. Based on EUCAST defined breakpoints: Nm (S: <=0.03; R: >0.03); Ng (S: <=0.03; I: >0.03-0.06; R: >0.06). Field value will be populated automatically if MIC value is provided. | text |
S
I R |
no | - |
| penicillin_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| penicillin_mic | MIC in mg/l | float | - | no | - |
| penicillin_SIR | S: susceptible, standard dose; I: susceptible, increased exposure; R: resistant. Based on EUCAST defined breakpoints: Nm (S: <=0.25; R: >0.25); Ng (S: <=0.06; I: >0.06-1; R: >1). Field value will be populated automatically if MIC value is provided. | text |
S
I R |
no | - |
| rifampicin_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| rifampicin_mic | MIC in mg/l | float | - | no | - |
| rifampicin_SIR | S: susceptible, standard dose; I: susceptible, increased exposure; R: resistant. Based on EUCAST defined breakpoints: Nm (S: <=0.25; R: >0.25). Field value will be populated automatically if MIC value is provided. | text |
S
R |
no | - |
| spectinomycin_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| spectinomycin_mic | MIC in mg/l | float | - | no | - |
| spectinomycin_SIR | S: susceptible, standard dose; I: susceptible, increased exposure; R: resistant. Based on EUCAST defined breakpoints: Ng (S: <=64; R: >64). Field value will be populated automatically if MIC value is provided. | text |
S
R |
no | - |
| sulphonamide_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| sulphonamide_mic | MIC in mg/l | float | - | no | - |
| tetracycline_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| tetracycline_mic | MIC in mg/l | float | - | no | - |
| tetracycline_SIR | S: susceptible, standard dose; I: susceptible, increased exposure; R: resistant. Based on EUCAST defined breakpoints: Nm (S: <=2; R: >2); Ng (S: <=0.5; I: >0.5-1; R: >1). Field value will be populated automatically if MIC value is provided. | text |
S
I R |
no | - |
| 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 (multiple) | - | no | 500 |
| 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
Deduced vaccine reactivity
| field name | comments | data type | allowed values | required | maximum length (characters) |
|---|---|---|---|---|---|
| Bexsero_reactivity | Prediction of Bexsero coverage. This field is automatically populated. | text |
exact match
cross-reactive none insufficient data |
no | - |
| Bexsero_notes | Explanation of Bexsero_reactivity result. This field is automatically populated. | text | - | no | - |
| Trumenba_reactivity | Prediction of Trumenba coverage. This field is automatically populated. | text |
exact match
cross-reactive none insufficient data |
no | - |
| Trumenba_notes | Explanation of Trumenba_reactivity result. This field is automatically populated. | text | - | no | - |
Risk factors
| field name | comments | data type | allowed values | required | maximum length (characters) |
|---|---|---|---|---|---|
| UK_school_year | School year that sample subject belonged to (UK) | text |
12
13 other not in full-time education |
no | - |
| persons_in_household | Number of people in the subject's household | integer | min: 1; max: 10 | no | - |
| antibiotic_use | Whether or not the subject recently took antibiotics | text |
yes [currently]
stopped [last month] stopped [last week] no |
no | - |
| current_URTI | current cold or sore throat | boolean | - | no | - |
| cigarettes_per_day | cigarettes smoked per day | text |
0
1-5 6-10 11-20 21+ |
no | - |
| ecigarettes_per_week | Number of e-cigarettes smoked per week | text |
0
1-2 3-6 7+ |
no | - |
| waterpipes_per_month | Number of water pipes (shisha) smoked per month | text |
0
1 2 3-4 5+ |
no | - |
| passive_smoking | exposure to passive smoking (inside or outside) | text |
yes [undefined]
no yes [inside] yes [outside] |
no | - |
| pubs_clubs_per_week | attendance at pubs or clubs per week | text |
0
1 2-3 4-5 6-7 |
no | - |
| persons_kissed_past_week | number of persons kissed in the past week | text |
0
1 2-3 4+ |
no | - |
| regular_partner | regular girlfriend or boyfriend | boolean | - | no | - |
| regular_partner_smokes | regular girlfriend or boyfriend who smokes | boolean | - | no | - |
| ethnicity | - | text |
white
asian black mixed other |
no | - |