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Description of database fields

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field namecommentsdata typeallowed valuesrequiredmaximum length (characters)
idPrimary key integer - yes 5
isolateIsolate name text - yes 30
aliasesalternative names for isolatetext (multiple)-no-
referencesPubMed ids that link to publications that describe or include recordinteger (multiple)-no-
countrycountry where strain was isolated text
Afghanistan
Åland Islands
Albania
Algeria
American Samoa
Andorra
Angola
Anguilla
Antarctica
Antigua and Barbuda
Argentina
Armenia
Aruba
Australia
Austria
Azerbaijan
Bahamas
Bahrain
Bangladesh
Barbados
Belarus
Belgium
Belize
Benin
Bermuda
Bhutan
Bolivia
Bonaire, Sint Eustatius and Saba
Bosnia and Herzegovina
Botswana
Bouvet Island
Brazil
British Indian Ocean Territory
British Virgin Islands
Brunei
Bulgaria
Burkina Faso
Burundi
Cambodia
Cameroon
Canada
Cape Verde
Cayman Islands
Central African Republic
Chad
Chile
China
China [Hong Kong]
China [Macao]
Christmas Island
Cocos (Keeling) Islands
Colombia
Comoros
Congo [DRC]
Congo [Republic]
Cook Islands
Costa Rica
Croatia
Cuba
Curaçao
Cyprus
Czech Republic
Denmark
Djibouti
Dominica
Dominican Republic
East Timor
Ecuador
Egypt
El Salvador
Equatorial Guinea
Eritrea
Estonia
Ethiopia
Falkland Islands (Malvinas)
Faroe Islands
Fiji
Finland
France
French Guiana
French Polynesia
French Southern Territories
Gabon
Georgia
Germany
Ghana
Gibraltar
Greece
Greenland
Grenada
Guadeloupe
Guam
Guatemala
Guernsey
Guinea
Guinea-Bissau
Guyana
Haiti
Heard Island and McDonald Islands
Holy See
Honduras
Hungary
Iceland
India
Indonesia
Iran
Iraq
Ireland
Isle of Man
Israel
Italy
Ivory Coast
Jamaica
Japan
Jersey
Jordan
Kazakhstan
Kenya
Kiribati
Kuwait
Kyrgyzstan
Laos
Latvia
Lebanon
Lesotho
Liberia
Libya
Liechtenstein
Lithuania
Luxembourg
Madagascar
Malawi
Malaysia
Maldives
Mali
Malta
Marshall Islands
Martinique
Mauritania
Mauritius
Mayotte
Mexico
Micronesia
Moldova
Monaco
Mongolia
Montenegro
Montserrat
Morocco
Mozambique
Myanmar
Namibia
Nauru
Nepal
New Caledonia
New Zealand
Nicaragua
Niger
Nigeria
Niue
Norfolk Island
North Korea
North Macedonia
Northern Mariana Islands
Norway
Oman
Pakistan
Palau
Palestinian territories
Panama
Papua New Guinea
Paraguay
Peru
Philippines
Pitcairn
Poland
Portugal
Puerto Rico
Qatar
Réunion
Romania
Russia
Rwanda
Saint Barthélemy
Saint Helena
Saint Kitts and Nevis
Saint Lucia
Saint Martin (French Part)
Saint Pierre and Miquelon
Saint Vincent and the Grenadines
Samoa
San Marino
São Tomé and Príncipe
Sark
Saudi Arabia
Senegal
Serbia
Seychelles
Sierra Leone
Singapore
Sint Maarten (Dutch part)
Slovakia
Slovenia
Solomon Islands
Somalia
South Africa
South Georgia and the South Sandwich Islands
South Korea
South Sudan
Spain
Sri Lanka
Sudan
Suriname
Svalbard and Jan Mayen Islands
Swaziland
Sweden
Switzerland
Syria
Taiwan
Tajikistan
Tanzania
Thailand
The Gambia
The Netherlands
Togo
Tokelau
Tonga
Trinidad and Tobago
Tunisia
Turkey
Turkmenistan
Turks and Caicos Islands
Tuvalu
Uganda
UK
UK [England]
UK [Northern Ireland]
UK [Scotland]
UK [Wales]
Ukraine
United Arab Emirates
Uruguay
US Minor Outlying Islands
US Virgin Islands
USA
Uzbekistan
Vanuatu
Venezuela
Vietnam
Wallis and Futuna Islands
Western Sahara
Yemen
Zambia
Zimbabwe
Unknown
yes -
regionRegion/city etc inside country text - no 50
yearYear of isolation integer min: 1900; max: 2020 no 4
date_sampleddate sample was taken date max: 2020-06-04 no 10
isoyear_sampledISO 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_sampledweek of the year - value is determined automatically from the contents of the date_sampled field. This cannot be updated manually integer - no -
date_receiveddate received by laboratory (may be approximate) date max: 2020-06-04 no 10
non_cultureresult comes from non-culture diagnosis bool - no -
serotypeSerotype (or serogroup) designation text - no 20
age_yrAge of patient in years integer min: 0; max: 120 no 3
age_mthAge of patient in months if less than one year old integer min: 0; max: 11 no 3
sexPatient gender text
male
female
no -
diagnosisEnter further details in the comments field if 'other' selected. text (multiple)
bacteraemia
carriage
conjunctivitis
COVID-19
endocarditis
meningitis
otitis media
peritonitis
pharyngitis
pneumonia
septicaemia
sinusitis
other
no -
host text
cat
chimpanzee
cow
dog
dolphin
goat
gorilla
guinea pig
horse
human
llama
mouse
rat
sheep
unknown
yes -
sourceSource of isolate. Enter further details in the comments field if 'other' selected. text
blood
bronchi
bronchoalveolar lavage
cerebrospinal fluid
ear swab
eye swab
joint fluid
lung aspirate
middle ear fluid
nasopharynx
pharynx
pleural fluid
pus
sinus aspirate
sputum
other
no -
epidemiology1 text
hospital acquired
community acquired
no -
epidemiology2 text
outbreak
carriage
no -
penicillinPenicillin 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
erythromycinErythromycin 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
tetracyclineTetracycline 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
chloramphenicolChloramphenicol 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
cefotaximeCefotaxime 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
commentsAny other comments text - no 1000
ENA_accessionENA SRA accession number to access short read data text - no 30
rMLST_database_accessionAccession number in rMLST genome database integer - no 30
private_projectLeave this blank unless you know what you are doing - entering anything here will hide your data in the public interface text - no 30
senderSender unique name, link to users integer Click for list of sender ids yes 4
curatorCurator who entered data,link to users integer Click for list of curator ids yes 4
date_enteredDate first entered date - yes 10
datestampDate last modified date - yes 10