Description of database fields

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field namecommentsdata typeallowed valuesrequiredmaximum length (characters)
idid - primary key integer - yes 6
isolateProvide the user-defined name for the sample. Every isolate name from a single user must be unique. Please, make it concise and avoid to use spaces (prefer the underscore instead) or special characters in the name text - yes 20
aliasesalternative names for isolatetext (multiple)-no-
referencesPubMed ids that link to publications that describe or include recordinteger (multiple)-no-
duplicate_numberTo be filled by curators only text - no 10
speciesProvide the species of the isolate from the pick list in the template text
B. ansorpii
B. avium
B. bronchialis
B. bronchiseptica
B. bronchiseptica I-1
B. bronchiseptica I-4
B. flabilis
B. hinzii
B. holmesii
B. muralis
B. parapertussis
B. pertussis
B. petrii
B. pseudohinzii
B. sputigena
B. trematum
B. tumbae
B. tumulicola
Genomic species 1
Genomic species 2
Genomic species 4
Genomic species 5
B. bronchiseptica II
Genomic species 7
Genomic species 8
Genomic species 9
Genomic species 10
Genomic species 11
Genomic species 12
Genomic species 13
Bordetella genogroup 16
Bordetella genogroup 17
Genomic species 18
Genomic species 19
Genomic species 20
Genomic species 21
Genomic species 22
Genomic species 23
Genomic species 24
Genomic species 25
Genomic species 26
Bordetella sp.
B. parapertussis (ovine)
yes -
siteProvide the anatomical site of isolation - if other please detail in comments text
bile
blood
cervix
ear
epiglottis
joint
lung
nasal cavity
nasopharynx
sinus
sputum
throat
tonsil
trachea
wound
other
unknown
no -
diseaseProvide disease state associated with isolate - if other please detail in comments text
cystic fibrosis
healthy
pertussis
pneumonia
septicemia
upper respiratory disease
other
no -
countryProvide the geographical of origin of the isolate as defined by the country or sea. If any doubt, please search terms here: http://insdc.org/country.html 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
Russia [Asia]
Russia [Europe]
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 -
regionProvide the administrative region (i.e. state, province, department, etc.) of origin of the isolate text - no 50
cityProvide the city/province/region of origine of the isolate. If any doubt, please search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz text - no 50
yearProvide the year on which the isolate was collected integer - no 4
source_typeProvide the source of origin of the isolate from the pick list in the template text
Human
Animal
Environment
Other
Unknown
yes -
hostProvide common name (e.g. human, dog, cow, ...) if there was a host. If the sample was environmental, put 'environment' text - no 30
other_source_infoPlease provide any other relevant details on the source text - no -
source_labProvide the name (full name) of the laboratory/agency that processed the strain, be consistent across multiple submissions text - no -
accession_numberENA/NCBI/DDBJ accession number to access short read data text - no 15
commentsAny comments from the user or curator text - no 1000
sequencing_technologyPlease provide the sequencing technology (Sanger, Illumina, PacBio, etc.) text - no -
senderuser who sent data, links to users table integer Click for list of sender ids yes 4
curatorcurator who entered data, links to user table integer Click for list of curator ids yes 4
date_entereddate first entered date - yes 10
datestampdate last modified date - yes 10