Description of database fields

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field namecommentsdata typeallowed valuesrequiredmaximum length (characters)
idprimary key integer - yes 5
isolateisolate name text - yes 20
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
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 isolation integer min: 1900; max: 2021 no 4
regioncity/region inside country text - no 50
sourcebiological source of sample text
clinically acquired
experimental animal
unknown
yes -
clinical_sourcebiological source of clinically accuired sample, please put other sources in comments field text
amniotic fluid
anal swab
blood
CSF
genital swab
skin lesion
throat swab
tissue
unspecified ulcer
other
no -
rabbit_passagesnumber of rabbit passages integer min: 0; max: 1000 no -
age_yrage in years integer min: 0; max: 120 no -
age_mthmonth part of age (0-11) for patients under 1 year old integer min: 0; max: 11 no -
sexsex of patient text
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
MSMW
MSW
WSM
WSMW
WSW
no -
macrolidesprovide the data based on the 23S rDNA analyses text
sensitive
resistant
not done
yes -
resist_mutationsprovide the mutations leading to the macrolide resistance text
A2058G
A2059G
no -
stagestage of the disease, please put other diasease manifestation in other_disease field text
primary
secondary
primary/secondary
tertiary
latent
congenital
neurosyphilis
other
no -
other_disease text - no 30
serologyresults of the serological tests text
positive
negative
no -
RPRRapid Plasma Reagin test, provide titres text
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 titres text
0
1:1
1:2
1:4
1:8
1:16
1:32
1:64
1:128
higher
no -
USRUnheated Serum Reagin test, provide titres text
1:2
1:4
1:8
1:16
1:32
1:64
1:128
higher
no -
TRUSTToluidine Red Unheated Serum Test, provide titres text
1:2
1:4
1:8
1:16
1:32
1:64
1:128
higher
no -
TPHATreponema pallidum Hemagglutination Assay text
positive
negative
border
no -
TPPATreponema pallidum Particle Agglutination text
positive
negative
border
no -
FTA_ABSFluorescent Treponemal Antibody Absorption assay text
positive
negative
border
no -
EIA_IgMEnzyme Immunoassay for IgM text
positive
negative
border
no -
EIA_IgGEnzyme Immunoassay for IgG text
positive
negative
border
no -
WB_IgMWestern blot for IgM text
positive
negative
border
no -
WB_IgGWestern blot for IgG text
positive
negative
border
no -
DFMresults from Dark-Field Microscopy text
positive
negative
no -
sex_contactknown sexual contact, please put the sample ID of the contact in comments field text
yes
no
no -
treatmentprovide the antibiotic treatment text - no 30
treat_failure text
yes
no
no -
multiple_lesions text
yes
no
no -
bioproject_accessionENA/SRA bioproject accession number text (multiple) - no 20
biosample_accessionENA/SRA biosample accession number text (multiple) - no 20
ENA_run_accessionENA/SRA accession number to access short read data. This should start either ERR, SRR, or DRR. text - no 15
commentsany other comments text - no 1000
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