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Description of database fields

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field namecommentsdata typeallowed valuesrequired
idprimary keyint - yes
isolateisolate nametext - yes
countrycountry where strain was isolatedtext Afghanistan
Albania
Algeria
Andorra
Angola
Antigua & Barbuda
Argentina
Armenia
Australia
Austria
Azerbaijan
Bahamas
Bahrain
Bangladesh
Barbados
Belarus
Belgium
Belize
Benin
Bhutan
Bolivia
Bosnia & Herzegovina
Botswana
Brazil
Brunei
Bulgaria
Burkina Faso
Burma
Burundi
Cambodia
Cameroon
Canada
Cape Verde
Central African Republic
Chad
Chile
China
Colombia
Comoros
Congo [DRC]
Costa Rica
Croatia
Cuba
Cyprus
Czech Republic
Denmark
Djibouti
Dominica
Dominican Republic
East Timor
Ecuador
Egypt
El Salvador
Equatorial Guinea
Eritrea
Estonia
Ethiopia
Fiji
Finland
France
Gabon
Georgia
Germany
Ghana
Greece
Grenada
Guadeloupe
Guatemala
Guinea
Guinea Bissau
Guyana
Haiti
Honduras
Hungary
Iceland
India
Indonesia
Iran
Iraq
Ireland
Isle of Man
Israel
Italy
Ivory Coast
Jamaica
Japan
Jordan
Kazakhstan
Kenya
Kiribati
Kuwait
Kyrgyzstan
Laos
Latvia
Lebanon
Lesotho
Liberia
Libya
Liechtenstein
Lithuania
Luxembourg
Macedonia
Madagascar
Malawi
Malaysia
Maldives
Mali
Malta
Marshall Islands
Martinique
Mauritania
Mauritius
Mayotte
Mexico
Micronesia
Moldavia
Moldova
Monaco
Mongolia
Montenegro
Morocco
Mozambique
Namibia
Nauru
Nepal
New Caledonia
New Zealand
Nicaragua
Niger
Nigeria
None
North Korea
Norway
Oman
Pakistan
Palau
Palestinian territories
Panama
Papua New Guinea
Paraguay
Peru
Philippines
Poland
Portugal
Qatar
Reunion
Romania
Russia
Rwanda
Samoa
San Marino
São Tomé and Príncipe
Saudi Arabia
Senegal
Serbia
Seychelles
Sierra Leone
Singapore
Slovakia
Slovenia
Solomon Islands
Somalia
South Africa
South Korea
Spain
Sri Lanka
St. Kitts & Nevis
St. Lucia
Sudan
Suriname
Swaziland
Sweden
Switzerland
Syria
Tahiti
Taiwan
Tajikistan
Tanzania
Thailand
The Gambia
The Netherlands
Togo
Tonga
Trinidad & Tobago
Tunisia
Turkey
Turkmenistan
Tuvalu
UK
USA
Uganda
Ukraine
United Arab Emirates
Uruguay
Uzbekistan
Vanuatu
Vatican City
Venezuela
Vietnam
Yemen
Zambia
Zimbabwe
Unknown
yes
yearyear of isolationint min: 1900; max: 2019 no
regioncity/region inside countrytext - no
sourcebiological source of sampletext clinically acquired
experimental animal
unknown
yes
clinical_sourcebiological source of clinically accuired sample, please put other sources in comments fieldtext amniotic fluid
anal swab
blood
CSF
genital swab
skin lesion
throat swab
tissue
unspecified ulcer
other
no
rabbit_passagesnumber of rabbit passagesint min: 0; max: 1000 no
age_yrage in yearsint min: 0; max: 120 no
age_mthmonth part of age (0-11) for patients under 1 year oldint min: 0; max: 11 no
sexsex of patienttext male
female
no
sex_orientationsexual orientation of patient - MSM (Men who have Sex with Men), MSW (Men who have Sex with Women), WSM (Women who have Sex with Men), WSW (Women who have Sex with Women)text MSM
MSMSW
MSW
WSM
WSMW
WSW
no
macrolidesprovide the data based on the 23S rDNA analysestext sensitive
resistant
not done
yes
resist_mutationsprovide the mutations leading to the macrolide resistancetext A2058G
A2059G
no
stagestage of the disease, please put other diasease manifestation in other_disease fieldtext primary
secondary
primary/secondary
tertiary
latent
congenital
neurosyphilis
other
no
other_diseasetext - no
serologyresults of the serological teststext positive
negative
no
RPRRapid Plasma Reagin test, provide titrestext 0
1:1
1:2
1:4
1:8
1:16
1:32
1:64
1:128
higher
no
VDRLVenereal Disease Research Laboratory test, provide titrestext 0
1:1
1:2
1:4
1:8
1:16
1:32
1:64
1:128
higher
no
USRUnheated Serum Reagin test, provide titrestext 1:2
1:4
1:8
1:16
1:32
1:64
1:128
higher
no
TRUSTToluidine Red Unheated Serum Test, provide titrestext 1:2
1:4
1:8
1:16
1:32
1:64
1:128
higher
no
TPHATreponema pallidum Hemagglutination Assaytext positive
negative
border
no
TPPATreponema pallidum Particle Agglutinationtext positive
negative
border
no
FTA_ABSFluorescent Treponemal Antibody Absorption assaytext positive
negative
border
no
EIA_IgMEnzyme Immunoassay for IgMtext positive
negative
border
no
EIA_IgGEnzyme Immunoassay for IgGtext positive
negative
border
no
WB_IgMWestern blot for IgMtext positive
negative
border
no
WB_IgGWestern blot for IgGtext positive
negative
border
no
DFMresults from Dark-Field Microscopytext positive
negative
no
sex_contactknown sexual contact, please put the sample ID of the contact in comments fieldtext yes
no
no
treatmentprovide the antibiotic treatmenttext - no
treat_failuretext yes
no
no
multiple_lesionstext yes
no
no
ENA_accessionENA SRA accession number to access short read datatext - no
commentsany other commentstext - no
sendersender unique name, link to usersint Click for list of sender ids yes
curatorcurator who entered data,link to usersint Click for list of curator ids yes
date_entereddate first entereddate - yes
datestampdate last modifieddate - yes