Genomic Epidemiology Ontology

The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.

  Afghanistan
  Africa
  Albania
  Algeria
  American Samoa
  Anatolia
  Andorra
  Angola
  Anguilla
  Antarctica
  Antigua and Barbuda
  Applied Biosystems
  Arabian Peninsula
  Arctic Ocean
  Arctic Ocean region
  Argentina
  Armenia
  Aruba
  Asia
  Atlantic Ocean
  Atlantic Ocean region
  Australasia
  Australasian Mediterranean Sea
  Australia
  Australian Antarctic Territory
  Australian Capital Territory
  Austria
  Autonomous Province (Serbia)
  Autonomous Region (China)
  Autonomous Region (Portugal)
  Azerbaijan
  Azores
  Bahama Banks
  Bahrain
  Bahrain Archipelago
  Baker Island
  Bali
  Bali Province
  Bali Sea
  Bangladesh
  Barbados
  Barents Sea
  Belarus
  Belgium
  Belize
  Benin
  Bermuda
  Bhutan
  Bjornoya [Svalbard]
  Bolivia
  Borneo
  Borneo group
  Bosnia and Herzegovina
  Botswana
  Bouvet Island
  Bouvet Islands
  Brazil
  British Indian Ocean Territory
  British Isles
  British Isles
  British Overseas Territory
  British Virgin Islands
  Brunei Darussalam
  Bulgaria
  Burkina Faso
  Burundi
  Cambodia
  Cameroon
  Canada
  Canary Islands
  Cape Verde
  Cape Verde Islands
  Capital Territory (Nigeria)
  Caribbean Region
  Caribbean Sea
  Caroline Islands
  Caucasian Russia
  Caucasus
  Caucasus Mountains
  Cayman Islands
  Central Africa
  Central African Republic
  Central America
  Central Asia
  Chad
  Channel Islands
  Chile
  China
  Christmas Island
  Clipperton Island
  Cocos Island
  Cocos Islands
  Collectivite d'outre-mer
  Colombia
  Commonwealth of Kentucky
  Commonwealth of Massachusetts
  Commonwealth of Pennsylvania
  Commonwealth of Puerto Rico
  Commonwealth of Virginia
  Comoro Islands
  Comoros
  Cook Archipelago
  Cook Islands
  Coral Sea
  Coral Sea Islands Territory
  Costa Rica
  Cote d'Ivoire
  Country of Curacao
  Croatia
  Cuba
  Cuban Archipelago
  Curacao Island
  Czech Republic
  DataHarmonizer provenance
  DataHarmonizer provenance example
  Delmarva Peninsula
  Democratic Republic of the Congo
  Department of Guadeloupe
  Dependancy (Grenada)
  Directly Governed City
  District (Palestinian Territories)
  District of Columbia
  Djibouti
  Dominica
  Dominican Republic
  East Africa
  East Asia
  East Midlands Region
  East North Central Division
  East Region
  East South Central Division
  Eastern Indian Ocean
  Ecuador
  Egypt
  El Salvador
  England
  English Channel
  Equatorial Guinea
  Equatorial Pacific Ocean
  Eritrea
  Estonia
  Ethiopia
  Eurasia
  Europe
  European Seas
  Falkland Islands
  Faroe Islands
  Faroes
  Federal District (Mexico)
  Fiji
  Fiji islands
  Finland
  French Guiana Region
  French Polynesia
  French Republic
  GAZ_00000373
  GAZ_00005925
  GAZ_00006932
  GAZ_00007145
  GAZ_00007149
  GAZ_00008907
  GAZ_00009605
  GAZ_00012749
  GAZ_00048661
  GAZ_00093896
  GAZ_00114678
  GAZ_00142926
  GAZ_00144775
  GAZ_00156610
  GENEPIO_0001367
  GENEPIO_0001368
  GENEPIO_0001369
  GENEPIO_0001370
  GENEPIO_0001372
  GENEPIO_0001373
  GISAID accession
  GISAID accession example
  GISAID virus name
  GISAID virus name example
  Gabon
  Gambia
  Gaza Strip
  GenBank accession example
  GenBank accession local name
  GenBank/ENA/DDBJ accession
  Georgia
  Germany
  Ghana
  Gibraltar
  Glorioso Islands
  Great Britain
  Greater Antilles
  Greater London Region
  Greater Sunda Islands
  Greece
  Greenland
  Grenada
  Grenadines
  Guadeloupe Archipelago
  Guadeloupe Region
  Guatemala
  Guernsey
  Guinea
  Guinea-Bissau
  Gulf of Guinea
  Gulf of Saint Lawrence
  Guyana
  Guyane
  Haiti
  Hawaiian Islands
  Heard Island and McDonald Islands Territory
  Heard and McDonald islands
  Helicos
  Hispaniola
  Honduras
  Hong Kong
  Howland Island
  Hungary
  IRIDA sample name
  IRIDA sample name example
  IRIDA sample name local name
  ISO_23418.organization_contact.service
  Iberian Peninsula
  Iceland
  Ile Bassas da India
  Ile Europa
  Ile Tromelin
  Illumina
  India
  Indian Ocean
  Indian Ocean region
  Indian subcontinent
  Indonesia
  Iran
  Iranian Plateau
  Iraq
  Ireland
  Irish Sea
  Island of Cuba
  Island of Cyprus
  Island of Dominica
  Island of Sri Lanka
  Islands of Mauritius
  Isle of Man
  Isles of Man
  Israel
  Italian Peninsula
  Italy
  JIle uan de Nova
  Jamaica
  Jan Mayen
  Japan
  Jarvis Island
  Java
  Java group
  Jersey
  Jervis Bay Territory
  Johnston Atoll
  Jordan
  Kazakhstan
  Kenya
  Kerguelen Archipelago
  Kingdom of Denmark
  Kingdom of Norway
  Kingdom of Spain
  Kingdom of the Netherlands
  Kingman Reef
  Kiribati
  Kiribati islands
  Korean Peninsula
  Kosovo
  Kurdistan
  Kuwait
  Kyrgyzstan
  Laccadive Sea
  Laos
  Latvia
  Lebanon
  Leeward Antilles
  Leeward Islands
  Lesotho
  Lesser Antilles
  Lesser Sunda Islands
  Levant
  Liberia
  Libya
  Liechtenstein
  Line Islands
  Lithuania
  Lucayan Archipelago
  Luxembourg
  MSH
  Macaronesian Islands
  Macau
  Macedonia
  Madagascar
  Madagascar Island
  Malacca and Singapore Straits
  Malawi
  Malay Peninsula
  Malaysia
  Maldives Archipelago
  Mali
  Malta
  Manchuria
  Marianas Islands
  Marshall Islands
  Martinique Region
  Mascarene Islands
  Mauritania
  Mauritius
  Mayotte
  Mediterranean Sea
  Mediterranean Sea, Eastern Basin
  Melanesia
  Metropolitan City (Republic of Korea)
  Metropolitan Denmark
  Metropolitan France
  Metropolitan Norway
  Metropolitan Portugal
  Metropolitan Spain
  Mexico
  Micronesia
  Middle Atlantic Division
  Midway Atoll
  Midwest Region
  Moldova
  Monaco
  Mongolia
  Montenegro
  Montserrat
  Morocco
  Mountain Division
  Mozambique
  Mozambique Channel
  Municipality (China)
  Myanmar
  NCI_Thesaurus
  NIFSTD
  NML submitted specimen type
  NML submitted specimen type example
  Namibia
  Nanumanga Atoll
  Nanumanga District
  Nanumanga Island
  Nauru
  Nauru Island
  Navassa Island
  Neotropical Kingdom
  Nepal
  Netherlands Antilles
  New Caledonia
  New England Division
  New Guinea
  New Zealand
  Nicaragua
  Niger
  Nigeria
  Niue Fekai
  Niue Islands
  North Africa
  North America
  North Atlantic Ocean
  North East Pacific Ocean
  North East Pacific Ocean coastal waters of Central America and Columbia
  North East Region
  North Korea
  North Pacific Ocean
  North Sea
  North West Pacific Ocean
  North West Region
  Northeast Asia
  Northeast Atlantic Ocean
  Northeast Atlantic Ocean coastal waters of Africa
  Northeast Region
  Northern Ireland
  Northern Mariana Islands
  Northern Territory
  Northwest Atlantic Ocean
  Northwest Atlantic Ocean coastal waters of Barbados
  Northwest Atlantic Ocean coastal waters of Bermuda
  Northwest Atlantic Ocean coastal waters of Canada
  Northwest Atlantic Ocean coastal waters of Greenland
  Northwest Territories
  Ns per 100 kbp
  Ns per 100 kbp example
  Nunavut
  Oceania
  Oceans and Seas
  Oman
  Pacific Biosciences
  Pacific Division
  Pacific Ocean
  Pacific Ocean region
  Pakistan
  Palau
  Palestinian Territories
  Panama
  Papua New Guinea
  Papua Province
  Paracel Islands
  Paraguay
  Paulu Archipelago
  Persian Gulf
  Peru
  Pitcairn Island
  Pitcairn, Henderson, Ducie and Oeno Islands
  Poland
  Polynesia
  Portuguese Republic
  Prince Edward Island
  Province (Afghanistan)
  Province (Algeria)
  Province (Angola)
  Province (Argentina)
  Province (Armenia)
  Province (Burundi)
  Province (Cambodia)
  Province (Canada)
  Province (China)
  Province (Costa Rica)
  Province (Cuba)
  Province (Democratic Republic of Congo)
  Province (Dominican Republic)
  Province (Ecuador)
  Province (Gabon)
  Province (Greenland)
  Province (Indonesia)
  Province (Iran)
  Province (Kazakhstan)
  Province (Kenya)
  Province (Laos)
  Province (Madagascar)
  Province (Mongolia)
  Province (Mozambique)
  Province (New Caledonia)
  Province (North Korea)
  Province (Oman)
  Province (Pakistan)
  Province (Panama)
  Province (Poland)
  Province (Republic of China)
  Province (Republic of Korea)
  Province (Republic of South Africa)
  Province (Rwanda)
  Province (Saudi Arabia)
  Province (Sierra Leone)
  Province (Solomon Islands)
  Province (Sri Lanka)
  Province (Tajikistan)
  Province (The Netherlands)
  Province (Turkmenistan)
  Province (Uzbekistan)
  Province (Vanuatu)
  Province (Zambia)
  Province (Zimbabwe)
  Province of Alberta
  Province of British Columbia
  Province of Manitoba
  Province of New Brunswick
  Province of Newfoundland and Labrador
  Province of Nova Scotia
  Province of Ontario
  Province of Prince Edward Island
  Province of Quebec
  Province of Saskatchewan
  PulseNet:AntigenForm
  PulseNet:FoodNet
  PulseNet:IsolatDate
  PulseNet:LabID
  PulseNet:ListMember
  PulseNet:NARMS-EB
  PulseNet:OGroup
  PulseNet:OtherStateIsolate
  PulseNet:Outbreak
  PulseNet:PFGE-BlnI-file
  PulseNet:PFGE-BlnI-pattern
  PulseNet:PFGE-BlnI-rundate
  PulseNet:PFGE-BlnI-status
  PulseNet:PFGE-SpeI-file
  PulseNet:PFGE-SpeI-pattern
  PulseNet:PFGE-SpeI-rundate
  PulseNet:PFGE-SpeI-status
  PulseNet:PFGE-XbaI-file
  PulseNet:PFGE-XbaI-pattern
  PulseNet:PFGE-XbaI-rundate
  PulseNet:PFGE-XbaI-status
  PulseNet:PatientAge
  PulseNet:PatientSex
  PulseNet:Phagetype
  PulseNet:ReceivedDate
  PulseNet:Serotype
  PulseNet:SourceCity
  PulseNet:SourceCountry
  PulseNet:SourceSite
  PulseNet:SourceState
  PulseNet:SourceType
  PulseNet:Status
  PulseNet:SubmittedNumber
  PulseNet:Subspecies
  PulseNet:TEMP
  PulseNet:Traveled_To
  PulseNet:TypeDetails
  PulseNet:UploadDate
  PulseNet:UploadModifiedDate
  PulseNet:cdc_id
  Puntarenas Canton
  Puntarenas Province
  Qatar
  Qatari Peninsula
  Region (Azerbaijan)
  Region (New Zealand)
  Region (contiguous United States of America)
  Region d'outre-mer
  Related specimen relationship type
  Related specimen relationship type example
  Republic of China
  Republic of Congo
  Republic of Ireland
  Republic of South Africa
  Reunion Island
  Reunion Region
  Roche
  Romania
  Ross Sea
  Russia
  Rwanda
  SRA accession
  SRA accession example
  SRA accession local name
  Saint Helena
  Saint Kitts-Nevis
  Saint Lucia
  Saint Martin
  Saint Vincent and the Grenadines
  Saint-Martin Island
  Saint-Pierre and Miquelon
  Samoa
  Samoan Archipelago
  San Marino
  Sao Tome and Principe
  Saudi Arabia
  Scandinavian Peninsula
  Scotland
  Senegal
  Serbia
  Sierra Leone
  Singapore
  Singapore Island
  Sint Maarten
  Slovak Republic
  Slovenia
  Society Islands
  Solomon Archipelago
  Solomon Islands
  Somalia
  SourceCountry
  South Africa
  South America
  South Asia
  South Atlantic Division
  South Atlantic Ocean
  South Caucasus
  South China Sea
  South East Region
  South Georgia and South Sandwich Islands
  South Korea
  South Pacific Ocean
  South Region
  South Sudan
  South West Region
  Southeast Asia
  Southeast Atlantic Ocean
  Southeast Pacific Ocean
  Southern Marianas Islands
  Southwest Asia
  Southwest Atlantic Ocean
  Southwest Pacific Ocean
  Special Adminstrative Region (China)
  Special Territory (Indonesia)
  Spratly Islands
  Sri Lanka
  State (Australia)
  State (India)
  State (Myanmar)
  State (Nigeria)
  State (United States of Mexico)
  State (Venezuela)
  State of Alabama
  State of Alaska
  State of Arizona
  State of Arkansas
  State of California
  State of Colorado
  State of Connecticut
  State of Delaware
  State of Florida
  State of Georgia
  State of Hawaii
  State of Idaho
  State of Illinois
  State of Indiana
  State of Iowa
  State of Kansas
  State of Louisiana
  State of Maine
  State of Maryland
  State of Michigan
  State of Minnesota
  State of Mississippi
  State of Missouri
  State of Montana
  State of Nebraska
  State of Nevada
  State of New Hampshire
  State of New Jersey
  State of New Mexico
  State of New York
  State of North Carolina
  State of North Dakota
  State of Ohio
  State of Oklahoma
  State of Oregon
  State of Rhode Island
  State of South Carolina
  State of South Dakota
  State of Tennessee
  State of Texas
  State of Utah
  State of Vermont
  State of Washington
  State of West Virginia
  State of Wisconsin
  State of Wyoming
  Sub-Saharan Africa
  Sudan
  Sulawesi
  Sulawesi group
  Sumatra
  Sumatra group
  Sunda Islands
  Suriname
  Svalbard Archipelago
  Swaziland
  Sweden
  Switzerland
  Syria
  Tahiti
  Tajikistan
  Takhtajan's floristic provinces
  Tanzania
  Territoire des Terres australes et antarctiques francaises
  Territory (Australia)
  Territory (Canada)
  Territory (Pakistan)
  Territory of Ashmore and Cartier Islands
  Territory of Christmas Island
  Territory of Guam
  Territory of Norfolk Island
  Territory of the Cocos (Keeling) Islands
  Territory, Antarctica
  Thailand
  The Bahamas
  The Netherlands
  The Philippines
  The Seychelles
  Thermo
  Timor
  Timor-Leste
  Togo
  Tokelau
  Tonga
  Tonga Archipelago
  Trinidad and Tobago
  Tunisia
  Turkey
  Turkmenistan
  Turks and Caicos Islands
  Tuvalu
  Tuvalu Islands
  Uganda
  Ukraine
  Ulster
  Unincorporated Territory (USA)
  Union Territory (India)
  United Arab Emirates
  United Kingdom
  United Nations
  United States Minor Outlying Islands
  United States Virgin Islands
  United States of America
  Uruguay
  Uzbekistan
  Vanuatu
  Vanuatu Islands
  Vatican City
  Venezuela
  Viet Nam
  Virgin Islands Archipelago
  Wake Island
  Wales
  Wallis and Futuna Islands
  Wallis and Futuna islands
  West Africa
  West Bank
  West Indies
  West Midlands Region
  West North Central Division
  West Region
  West South Central Division
  Western Indian Ocean
  Western Indian Ocean coastal waters of Southern Africa and Madagascar
  Western Sahara
  Windward Islands
  Windward islands
  Yemen
  Yorkshire and the Humber
  Yukon
  Zambia
  Zimbabwe
  [Former] Yugoslavia
  _test_individual
  amplicon pcr primer scheme
  amplicon pcr primer scheme example
  amplicon size
  amplicon size example
  anatomical material
  anatomical material example
  anatomical part
  anatomical part example
  angstrom
  authors
  authors example
  base pair
  biogeographic location
  bioinformatics protocol
  bioinformatics protocol example
  biomaterial extracted
  biomaterial extracted example
  bioproject accession
  bioproject accession example
  bioproject accession local name
  biosample accession
  biosample accession example
  biosample accession local name
  body product
  body product example
  breadth of coverage value
  breadth of coverage value example
  cable
  case ID
  case ID example
  centiMorgan
  centiRay
  centimeter
  century
  chain
  collection device
  collection device example
  collection method
  collection method example
  collection protocol
  collection protocol example
  colony forming unit
  colony forming unit per milliliter
  complications
  complications example
  confluence percentage
  consensus genome length
  consensus genome length example
  consensus sequence filename
  consensus sequence filename example
  consensus sequence filepath
  consensus sequence filepath example
  consensus sequence name
  consensus sequence name example
  consensus sequence software name
  consensus sequence software name example
  consensus sequence software version
  consensus sequence software version example
  contiguous United States of America
  continent
  core
  cubic centimeter
  cubic centimeter per mole
  cubic decimeter
  cubic meter
  cubic meter per kilogram
  cubic meter per mole
  culture collection
  culture collection example
  data abstraction details
  data abstraction details example
  day
  deciliter
  degree
  degree Celsius
  degree Fahrenheit
  dehosting method
  dehosting method example
  depth of coverage threshold
  depth of coverage threshold example
  depth of coverage value
  depth of coverage value example
  destination of most recent travel (city)
  destination of most recent travel (city) example
  destination of most recent travel (country)
  destination of most recent travel (country) example
  destination of most recent travel (state/province/territory)
  destination of most recent travel (state/province/territory) example
  diagnostic pcr Ct value 1
  diagnostic pcr Ct value 1 example
  diagnostic pcr Ct value 2
  diagnostic pcr Ct value 2 example
  diagnostic pcr Ct value 3
  diagnostic pcr Ct value 3 example
  diagnostic pcr protocol 1
  diagnostic pcr protocol 1 example
  diagnostic pcr protocol 2
  diagnostic pcr protocol 2 example
  diagnostic pcr protocol 3
  diagnostic pcr protocol 3 example
  environmental material
  environmental material example
  environmental site
  environmental site example
  example to be eventually removed
  exposure contact level
  exposure contact level example
  exposure details
  exposure details example
  exposure event
  exposure event example
  exposure setting
  exposure setting example
  failed exploratory term
  fast5 filename
  fast5 filename example
  fast5 filepath
  fast5 filepath example
  fathom
  femtoliter
  floristic kingdom
  flow cell barcode
  flow cell barcode example
  fluid ounce
  foot
  furlong
  gallon
  gender modality
  gender variance
  gene name 1
  gene name 1 example
  gene name 2
  gene name 2 example
  gene name 3
  gene name 3 example
  geographic location
  giga base pair
  gill
  gram per cubic centimeter
  gram per deciliter
  gram per liter
  gram per milliliter
  half life
  host (common name)
  host (common name) example
  host (scientific name)
  host (scientific name) example
  host age
  host age bin
  host age bin example
  host age example
  host age unit
  host age unit example
  host disease
  host disease example
  host ethnicity
  host ethnicity example
  host gender
  host gender example
  host health outcome
  host health outcome example
  host health state
  host health state example
  host health status details
  host health status details example
  host residence geo_loc name (country)
  host residence geo_loc name (country) example
  host residence geo_loc name (state/province/territory)
  host residence geo_loc name (state/province/territory) example
  host role
  host role example
  host specimen voucher
  host specimen voucher example
  host subject ID
  host subject ID example
  host vaccination status
  host vaccination status example
  hour
  inch
  isolate example
  kelvin
  kilogram per cubic meter
  kilogram per liter
  lab host
  lab host example
  league
  library ID
  library ID example
  library preparation kit
  library preparation kit example
  lineage/clade analysis software name
  lineage/clade analysis software name example
  lineage/clade analysis software version
  lineage/clade analysis software version example
  lineage/clade name
  lineage/clade name example
  liter
  liter per kilogram
  location of exposure geo_loc name (country)
  location of exposure geo_loc name (country) example
  maritime length unit
  mass percentage
  mass volume percentage
  mega base pair
  metadata complete
  metadata incomplete
  meter
  meter per second
  microgram per liter
  microgram per milliliter
  micrograms per wheaton bottle
  microliter
  microliter per kilogram
  micrometer
  micromole
  micromole per kilogram
  micromole per litre
  microsecond
  mile
  milligram per liter
  milligram per milliliter
  milliliter
  milliliter per kilogram
  millimeter
  millisecond
  millisiemens
  millivolt
  minute
  mole fraction
  month
  most recent travel departure date
  most recent travel departure date example
  most recent travel return date
  most recent travel return date example
  named class expression
  nanogram per microliter
  nanogram per milliliter
  nanoliter
  nanometer
  nanosecond
  nautical mile
  number of base pairs sequenced
  number of base pairs sequenced example
  number of vaccine doses received
  number of vaccine doses received example
  organizational term
  pH
  passage method
  passage method example
  passage number
  passage number example
  pending final vetting
  phone type - home
  picoliter
  picometer
  picosecond
  pint
  placeholder removed
  populated place, Alaska
  populated place, Algeria
  populated place, American Samoa
  populated place, Andorra
  populated place, Angola
  populated place, Antigua and Barbuda
  populated place, Argentina
  populated place, Armenia
  populated place, Australia
  populated place, Azerbaijan
  populated place, Azores
  populated place, Bahamas
  populated place, Bangladesh
  populated place, Benin
  populated place, Bhutan
  populated place, Bolivia
  populated place, Botswana
  populated place, Brazil
  populated place, Burkina Faso
  populated place, Burundi

Ontology information

Ontology ID: genepio
Version: 2022-02-06
Number of terms: 6680
Last loaded: Tue Feb 15 19:26:38 GMT 2022

date

2022-02-06

license

http://creativecommons.org/licenses/by/3.0/

description

The Genomic Epidemiology Ontology aims to provide a comprehensive controlled vocabulary for infectious disease surveillance and outbreak investigations. It is an application ontology that draws on many other ontologies including anatomy, taxonomy, disease, symptoms, environment and food types for foodborn pathogen metadata.

title

Genomic Epidemiology Ontology