diff --git a/web/templates/wastewater/export.js b/web/templates/wastewater/export.js index 592ad2d1..09a50485 100644 --- a/web/templates/wastewater/export.js +++ b/web/templates/wastewater/export.js @@ -1,2 +1,62 @@ // A dictionary of possible export formats -export default {}; +export default { + NCBI_SRA: { + fileType: 'xls', + status: 'published', + method: function(dh) { + const exportHeaders = new Map([ + ["sample_name", []], + ["library_ID", []], + ["title", []], + ["library_strategy", []], + ["library_source", []], + ["library_selection", []], + ["library_layout", []], + ["platform (click for details)", []], + ["instrument_model", []], + ["design_description", []], + ["filetype", []], + ["filename", []], + ["filename2", []], + ["filename3", []], + ["filename4", []], + ["assembly", []], + ["fasta_file", []], + ["enrichment_kit", []], + ["amplicon_PCR_primer_scheme", []], + ["library_preparation_kit", []], + ["amplicon_size", []], + ["quality_control_method", []], + ["quality_control_method_version", []], + ["quality_control_determination", []], + ["quality_control_issues", []], + ["quality_control_details", []], + ["dehosting_method", []], + ["sequence_submitter_contact_email", []], + ["raw_sequence_data_processing_method", []], + ]); + const outputMatrix = [[...exportHeaders.keys()]]; + const sourceFields = dh.getFields(dh.table); + const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); + dh.getHeaderMap(exportHeaders, sourceFields, 'NCBI_SRA'); + for (const inputRow of dh.getTrimmedData(dh.hot)) { + const outputRow = []; + let value; + for (const [headerName, sources] of exportHeaders) { + value = dh.getMappedField( + headerName, + inputRow, + sources, + sourceFields, + sourceFieldNameMap, + ':', + 'NCBI_SRA' + ); + outputRow.push(value); + } + outputMatrix.push(outputRow); + } + return outputMatrix; + }, + }, +}; diff --git a/web/templates/wastewater/schema.json b/web/templates/wastewater/schema.json index 721b4463..d7fd329c 100644 --- a/web/templates/wastewater/schema.json +++ b/web/templates/wastewater/schema.json @@ -8666,7 +8666,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample_collection_date}", + ">={sample_collection_start_date}", "<={today}" ], "comments": [ @@ -8790,7 +8790,7 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "NCBI_SRA:library_strategy", - "NCBI_SRA:%20library_source" + "NCBI_SRA:library_source" ], "slot_uri": "GENEPIO:0100997", "domain_of": [ @@ -8892,7 +8892,7 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "NCBI_SRA:library_selection", - "NCBI_SRA:%20design_description" + "NCBI_SRA:design_description" ], "slot_uri": "GENEPIO:0100966", "domain_of": [ @@ -15981,7 +15981,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample_collection_date}", + ">={sample_collection_start_date}", "<={today}" ], "comments": [ @@ -16121,7 +16121,7 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "NCBI_SRA:library_strategy", - "NCBI_SRA:%20library_source" + "NCBI_SRA:library_source" ], "rank": 152, "slot_uri": "GENEPIO:0100997", @@ -23214,7 +23214,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample_collection_date}", + ">={sample_collection_start_date}", "<={today}" ], "comments": [ @@ -23354,7 +23354,7 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "NCBI_SRA:library_strategy", - "NCBI_SRA:%20library_source" + "NCBI_SRA:library_source" ], "rank": 153, "slot_uri": "GENEPIO:0100997", @@ -23472,7 +23472,7 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "NCBI_SRA:library_selection", - "NCBI_SRA:%20design_description" + "NCBI_SRA:design_description" ], "rank": 157, "slot_uri": "GENEPIO:0100966", @@ -30919,7 +30919,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample_collection_date}", + ">={sample_collection_start_date}", "<={today}" ], "comments": [ @@ -31059,7 +31059,7 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "NCBI_SRA:library_strategy", - "NCBI_SRA:%20library_source" + "NCBI_SRA:library_source" ], "rank": 167, "slot_uri": "GENEPIO:0100997", @@ -31177,7 +31177,7 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "NCBI_SRA:library_selection", - "NCBI_SRA:%20design_description" + "NCBI_SRA:design_description" ], "rank": 171, "slot_uri": "GENEPIO:0100966", diff --git a/web/templates/wastewater/schema.yaml b/web/templates/wastewater/schema.yaml index d65e8b79..30ac3e1a 100644 --- a/web/templates/wastewater/schema.yaml +++ b/web/templates/wastewater/schema.yaml @@ -4730,7 +4730,7 @@ slots: slot_uri: GENEPIO:0001447 range: date todos: - - '>={sample_collection_date}' + - '>={sample_collection_start_date}' - <={today} examples: - value: '2020-06-22' @@ -4795,7 +4795,7 @@ slots: - value: whole genome sequencing assay exact_mappings: - NCBI_SRA:library_strategy - - NCBI_SRA:%20library_source + - NCBI_SRA:library_source library_preparation_kit: name: library_preparation_kit title: library preparation kit @@ -4847,7 +4847,7 @@ slots: - value: hybrid selection method exact_mappings: - NCBI_SRA:library_selection - - NCBI_SRA:%20design_description + - NCBI_SRA:design_description genomic_target_enrichment_method_details: name: genomic_target_enrichment_method_details title: genomic target enrichment method details diff --git a/web/templates/wastewater/schema_enums.tsv b/web/templates/wastewater/schema_enums.tsv index 39bf2aa1..2579e777 100644 --- a/web/templates/wastewater/schema_enums.tsv +++ b/web/templates/wastewater/schema_enums.tsv @@ -1,800 +1,799 @@ -title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_NCBI_SRA EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal - -null value menu NullValueMenu GENEPIO:0001619 Not Applicable [GENEPIO:0001619] A categorical choice recorded when a datum does not apply to a given context. not applicable - GENEPIO:0001618 Missing [GENEPIO:0001618] A categorical choice recorded when a datum is not included for an unknown reason. missing - GENEPIO:0001620 Not Collected [GENEPIO:0001620] A categorical choice recorded when a datum was not measured or collected. not collected - GENEPIO:0001668 Not Provided [GENEPIO:0001668] A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage. not provided - GENEPIO:0001810 Restricted Access [GENEPIO:0001810] A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns. restricted access - -geo_loc_name (country) menu GeoLocNameCountryMenu GAZ:00006882 Afghanistan [GAZ:00006882] A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ] - GAZ:00002953 Albania [GAZ:00002953] A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ] - GAZ:00000563 Algeria [GAZ:00000563] A country in North Africa. It is bordered by Tunisia in the northeast, Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, a few km of the Western Sahara in the west, Morocco in the northwest, and the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). [ url:http://en.wikipedia.org/wiki/Algeria ] - GAZ:00003957 American Samoa [GAZ:00003957] An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa ] - GAZ:00002948 Andorra [GAZ:00002948] A small landlocked country in western Europe, located in the eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. Andorra consists of seven communities known as parishes (Catalan: parroquies, singular - parroquia). Until relatively recently, it had only six parishes; the seventh, Escaldes-Engordany, was created in 1978. Some parishes have a further territorial subdivision. Ordino, La Massana and Sant Julia de Loria are subdivided into quarts (quarters), while Canillo is subdivided into veinats (neighborhoods). Those mostly coincide with villages, which are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ] - GAZ:00001095 Angola [GAZ:00001095] A country in south-central Africa bordering Namibia to the south, Democratic Republic of the Congo to the north, and Zambia to the east, and with a west coast along the Atlantic Ocean. The exclave province Cabinda has a border with the Republic of the Congo and the Democratic Republic of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ] - GAZ:00009159 Anguilla [GAZ:00009159] A British overseas territory in the Caribbean, one of the most northerly of the Leeward Islands in the Lesser Antilles. It consists of the main island of Anguilla itself, approximately 26 km long by 5 km wide at its widest point, together with a number of much smaller islands and cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila ] - GAZ:00000462 Antarctica [GAZ:00000462] The Earth's southernmost continent, overlying the South Pole. It is situated in the southern hemisphere, almost entirely south of the Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica ] - GAZ:00006883 Antigua and Barbuda [GAZ:00006883] An island nation located on the eastern boundary of the Caribbean Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda ] - GAZ:00002928 Argentina [GAZ:00002928] A South American country, constituted as a federation of twenty-three provinces and an autonomous city. It is bordered by Paraguay and Bolivia in the north, Brazil and Uruguay in the northeast, and Chile in the west and south. The country claims the British controlled territories of the Falkland Islands and South Georgia and the South Sandwich Islands. Argentina also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping other claims made by Chile and the United Kingdom. Argentina is subdivided into twenty-three provinces (Spanish: provincias, singular provincia) and one federal district (Capital de la Republica or Capital de la Nacion, informally the Capital Federal). The federal district and the provinces have their own constitutions, but exist under a federal system. Provinces are then divided into departments (Spanish: departamentos, singular departamento), except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina ] - GAZ:00004094 Armenia [GAZ:00004094] A landlocked mountainous country in Eurasia between the Black Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan exclave of Azerbaijan to the south. A transcontinental country at the juncture of Eastern Europe and Western Asia. A former republic of the Soviet Union. Armenia is divided into ten marzes (provinces, singular marz), with the city (kaghak) of Yerevan having special administrative status as the country's capital. [ url:http://en.wikipedia.org/wiki/Armenia ] - GAZ:00004025 Aruba [GAZ:00004025] An autonomous region within the Kingdom of the Netherlands, Aruba has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba ] - GAZ:00005901 Ashmore and Cartier Islands [GAZ:00005901] A Territory of Australia that includes two groups of small low-lying uninhabited tropical islands in the Indian Ocean situated on the edge of the continental shelf north-west of Australia and south of the Indonesian island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands ] - GAZ:00000463 Australia [GAZ:00000463] A country in the southern hemisphere comprising the mainland of the world's smallest continent, the major island of Tasmania, and a number of other islands in the Indian and Pacific Oceans. The neighbouring countries are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to the south-east. Australia has six states, two major mainland territories, and other minor territories. - GAZ:00002942 Austria [GAZ:00002942] A landlocked country in Central Europe. It borders both Germany and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia and Italy to the south, and Switzerland and Liechtenstein to the west. The capital is the city of Vienna on the Danube River. Austria is divided into nine states (Bundeslander). These states are then divided into districts (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities (Gemeinden). Cities have the competencies otherwise granted to both districts and municipalities. - GAZ:00004941 Azerbaijan [GAZ:00004941] A country in the he South Caucasus region of Eurasia, it is bounded by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan is bordered by Armenia to the north and east, Iran to the south and west, and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts in Azerbaijan's southwest, have been controlled by Armenia since the end of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons 11 city districts (saharlar), and one autonomous republic (muxtar respublika). - GAZ:00002733 Bahamas [GAZ:00002733] A country consisting of two thousand cays and seven hundred islands that form an archipelago. It is located in the Atlantic Ocean, southeast of Florida and the United States, north of Cuba, the island of Hispanola and the Caribbean, and northwest of the British overseas territory of the Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, whose affairs are handled directly by the central government. - GAZ:00005281 Bahrain [GAZ:00005281] A borderless island country in the Persian Gulf. Saudi Arabia lies to the west and is connected to Bahrain by the King Fahd Causeway, and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into five governorates. - GAZ:00007117 Baker Island [GAZ:00007117] An uninhabited atoll located just north of the equator in the central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island is an unincorporated and unorganized territory of the US. - GAZ:00003750 Bangladesh [GAZ:00003750] A country in South Asia. It is bordered by India on all sides except for a small border with Myanmar to the far southeast and by the Bay of Bengal to the south. Bangladesh is divided into six administrative divisions. Divisions are subdivided into districts (zila). There are 64 districts in Bangladesh, each further subdivided into upazila (subdistricts) or thana ("police stations"). - GAZ:00001251 Barbados [GAZ:00001251] An island country in the Lesser Antilles of the West Indies, in the Caribbean region of the Americas, and the most easterly of the Caribbean Islands. It is 34 kilometres (21 miles) in length and up to 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is in the western part of the North Atlantic, 100 km (62 mi) east of the Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards, part of the Lesser Antilles, at roughly 13°N of the equator. It is about 168 km (104 mi) east of both the countries of Saint Lucia and Saint Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside the principal Atlantic hurricane belt. Its capital and largest city is Bridgetown. - GAZ:00005810 Bassas da India [GAZ:00005810] A roughly circular atoll about 10 km in diameter, which corresponds to a total size (including lagoon) of 80 km2. It is located in the southern Mozambique Channel, about half-way between Madagascar (which is 385 km to the east) and Mozambique, and 110 km northwest of Europa Island. It rises steeply from the seabed 3000 m below. - GAZ:00006886 Belarus [GAZ:00006886] A landlocked country in Eastern Europe, that borders Russia to the north and east, Ukraine to the south, Poland to the west, and Lithuania and Latvia to the north. Its capital is Minsk. Belarus is divided into six voblasts, or provinces. Voblasts are further subdivided into raions (commonly translated as districts or regions). As of 2002, there are six voblasts, 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special status, due to the city serving as the national capital. - GAZ:00002938 Belgium [GAZ:00002938] A country in northwest Europe. Belgium shares borders with France (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each comprise five provinces; the third region, Brussels-Capital Region, is not a province, nor does it contain any Together, these comprise 589 municipalities, which in general consist of several sub-municipalities (which were independent municipalities before the municipal merger operation mainly in 1977). - GAZ:00002934 Belize [GAZ:00002934] A country in Central America. It is the only officially English speaking country in the region. Belize was a British colony for more than a century and was known as British Honduras until 1973. It became an independent nation within The Commonwealth in 1981. Belize is divided into 6 districts, which are further divided into 31 constituencies. - GAZ:00000904 Benin [GAZ:00000904] A country in Western Africa. It borders Togo to the west, Nigeria to the east and Burkina Faso and Niger to the north; its short coastline to the south leads to the Bight of Benin. Its capital is Porto Novo, but the seat of government is Cotonou. Benin is divided into 12 departments and subdivided into 77 communes. - GAZ:00001264 Bermuda [GAZ:00001264] A British overseas territory in the North Atlantic Ocean. Located off the east coast of the United States, it is situated around 1770 km NE of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately 138 islands. - GAZ:00003920 Bhutan [GAZ:00003920] A landlocked nation in South Asia. It is located amidst the eastern end of the Himalaya Mountains and is bordered to the south, east and west by India and to the north by Tibet. Bhutan is separated from Nepal by the Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative zones). Each dzongdey is further divided into dzongkhag (districts). There are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into subdistricts known as dungkhag. At the basic level, groups of villages form a constituency called gewog. - GAZ:00002511 Bolivia [GAZ:00002511] A landlocked country in central South America. It is bordered by Brazil on the north and east, Paraguay and Argentina on the south, and Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: departamentos). Each of the departments is subdivided into provinces (provincias), which are further subdivided into municipalities (municipios). - GAZ:00025355 Borneo [GAZ:00025355] An island at the grographic centre of Maritime Southeast Adia, in relation to major Indonesian islands, it is located north of Java, west of Sulawesi, and east of Sumatra. It is the third-largest island in the world and the larest in Asia. The island is politically divided among three countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] Approximately 73% of the island is Indonesian territory. In the north, the East Malaysian states of Sabah and Sarawak make up about 26% of the island. Additionally, the Malaysian federal territory of Labuan is situated on a small island just off the coast of Borneo. The sovereign state of Brunei, located on the north coast, comprises about 1% of Borneo's land area. A little more than half of the island is in the Northern Hemisphere, including Brunei and the Malaysian portion, while the Indonesian portion spans the Northern and Southern hemispheres. - GAZ:00006887 Bosnia and Herzegovina [GAZ:00006887] A country on the Balkan peninsula of Southern Europe. Bordered by Croatia to the north, west and south, Serbia to the east, and Montenegro to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided into three political regions of which one, the Brcko District is part of the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. All three have an equal constitutional status on the whole territory of Bosnia and Herzegovina. - GAZ:00001097 Botswana [GAZ:00001097] A landlocked nation in Southern Africa. It is bordered by South Africa to the south and southeast, Namibia to the west, Zambia to the north, and Zimbabwe to the northeast. Botswana is divided into nine districts, which are subdivided into a total twenty-eight subdistricts. - GAZ:00001453 Bouvet Island [GAZ:00001453] A sub-antarctic volcanic island in the South Atlantic Ocean, south-southwest of the Cape of Good Hope (South Africa). It is a dependent area of Norway and is not subject to the Antarctic Treaty, as it is north of the latitude south of which claims are suspended. - GAZ:00002828 Brazil [GAZ:00002828] A country in South America. Bordered by the Atlantic Ocean and by Venezuela, Suriname, Guyana and the department of French Guiana to the north, Colombia to the northwest, Bolivia and Peru to the west, Argentina and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six states (estados) and one federal district (Distrito Federal). The states are subdivided into municipalities. For statistical purposes, the States are grouped into five main regions: North, Northeast, Central-West, Southeast and South. - GAZ:00003961 British Virgin Islands [GAZ:00003961] A British overseas territory, located in the Caribbean to the east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, the remaining islands constituting the US Virgin Islands. The British Virgin Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately fifteen of the islands are inhabited. - GAZ:00003901 Brunei [GAZ:00003901] A country located on the north coast of the island of Borneo, in Southeast Asia. Apart from its coastline with the South China Sea it is completely surrounded by the State of Sarawak, Malaysia, and in fact it is separated into two parts by Limbang, which is part of Sarawak. Brunei is divided into four districts (daerah), the districts are subdivided into thirty-eight mukims, which are then divided into kampong (villages). - GAZ:00002950 Bulgaria [GAZ:00002950] A country in Southeastern Europe, borders five other countries; Romania to the north (mostly along the Danube), Serbia and the Republic of Macedonia to the west, and Greece and Turkey to the south. The Black Sea defines the extent of the country to the east. Since 1999, it has consisted of twenty-eight provinces. The provinces subdivide into 264 municipalities. - GAZ:00000905 Burkina Faso [GAZ:00000905] A landlocked nation in West Africa. It is surrounded by six countries: Mali to the north, Niger to the east, Benin to the south east, Togo and Ghana to the south, and Cote d'Ivoire to the south west. Burkina Faso is divided into thirteen regions, forty-five provinces, and 301 departments (communes). - GAZ:00001090 Burundi [GAZ:00001090] A small country in the Great Lakes region of Africa. It is bordered by Rwanda on the north, Tanzania on the south and east, and the Democratic Republic of the Congo on the west. Although the country is landlocked, much of its western border is adjacent to Lake Tanganyika. Burundi is divided into 17 provinces, 117 communes, and 2,638 collines. - GAZ:00006888 Cambodia [GAZ:00006888] A country in Southeast Asia. The country borders Thailand to its west and northwest, Laos to its northeast, and Vietnam to its east and southeast. In the south it faces the Gulf of Thailand. - GAZ:00001093 Cameroon [GAZ:00001093] A country of central and western Africa. It borders Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces and 58 divisions or departments. The divisions are further sub-divided into sub-divisions (arrondissements) and districts. - GAZ:00002560 Canada [GAZ:00002560] A country occupying most of northern North America, extending from the Atlantic Ocean in the east to the Pacific Ocean in the west and northward into the Arctic Ocean. Canada is a federation composed of ten provinces and three territories; in turn, these may be grouped into regions. Western Canada consists of British Columbia and the three Prairie provinces (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec and Ontario. Atlantic Canada consists of the three Maritime provinces (New Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada together. Three territories (Yukon, Northwest Territories, and Nunavut) make up Northern Canada. - GAZ:00001227 Cape Verde [GAZ:00001227] A republic located on an archipelago in the Macaronesia ecoregion of the North Atlantic Ocean, off the western coast of Africa. Cape Verde is divided into 22 municipalities (concelhos), and subdivided into 32 parishes (freguesias). - GAZ:00003986 Cayman Islands [GAZ:00003986] A British overseas territory located in the western Caribbean Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. The Cayman Islands are divided into seven districts. - GAZ:00001089 Central African Republic [GAZ:00001089] A landlocked country in Central Africa. It borders Chad in the north, Sudan in the east, the Republic of the Congo and the Democratic Republic of the Congo in the south, and Cameroon in the west. The Central African Republic is divided into 14 administrative prefectures (prefectures), along with 2 economic prefectures (prefectures economiques) and one autonomous commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures). - GAZ:00000586 Chad [GAZ:00000586] A landlocked country in central Africa. It is bordered by Libya to the north, Sudan to the east, the Central African Republic to the south, Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided into 18 regions. The departments are divided into 200 sub-prefectures, which are in turn composed of 446 cantons. This is due to change. - GAZ:00002825 Chile [GAZ:00002825] A country in South America occupying a long and narrow coastal strip wedged between the Andes mountains and the Pacific Ocean. The Pacific forms the country's entire western border, with Peru to the north, Bolivia to the northeast, Argentina to the east, and the Drake Passage at the country's southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. Chile is divided into 15 regions. Every region is further divided into provinces. Finally each province is divided into communes. Each region is designated by a name and a Roman numeral, assigned from north to south. The only exception is the region housing the nation's capital, which is designated RM, that stands for Region Metropolitana (Metropolitan Region). Two new regions were created in 2006: Arica-Parinacota in the north, and Los Rios in the south. Both became operative in 2007-10. - GAZ:00002845 China [GAZ:00002845] A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions. - GAZ:00005915 Christmas Island [GAZ:00005915] An island in the Indian Ocean, 500 km south of Indonesia and about 2600 km northwest of Perth. The island is the flat summit of a submarine mountain. - GAZ:00005838 Clipperton Island [GAZ:00005838] A nine-square km coral atoll in the North Pacific Ocean, southwest of Mexico and west of Costa Rica. - GAZ:00009721 Cocos Islands [GAZ:00009721] Islands that located in the Indian Ocean, about halfway between Australia and Sri Lanka. A territory of Australia. There are two atolls and twenty-seven coral islands in the group. - GAZ:00002929 Colombia [GAZ:00002929] A country located in the northwestern region of South America. Colombia is bordered to the east by Venezuela and Brazil; to the south by Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean Sea; to the north-west by Panama; and to the west by the Pacific Ocean. Besides the countries in South America, the Republic of Colombia is recognized to share maritime borders with the Caribbean countries of Jamaica, Haiti, the Dominican Republic and the Central American countries of Honduras, Nicaragua, and Costa Rica. Colombia is divided into 32 departments and one capital district which is treated as a department. There are in total 10 districts assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia is also subdivided into some municipalities which form departments, each with a municipal seat capital city assigned. Colombia is also subdivided into corregimientos which form municipalities. - GAZ:00005820 Comoros [GAZ:00005820] An island nation in the Indian Ocean, located off the eastern coast of Africa on the northern end of the Mozambique Channel between northern Madagascar and northeastern Mozambique. - GAZ:00053798 Cook Islands [GAZ:00053798] A self-governing parliamentary democracy in free association with New Zealand. The fifteen small islands in this South Pacific Ocean country have a total land area of 240 km2, but the Cook Islands Exclusive Economic Zone (EEZ) covers 1.8 million km2 of ocean. - GAZ:00005917 Coral Sea Islands [GAZ:00005917] A Territory of Australia which includes a group of small and mostly uninhabited tropical islands and reefs in the Coral Sea, northeast of Queensland, Australia. The only inhabited island is Willis Island. The territory covers 780,000 km2, extending east and south from the outer edge of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, the Willis Group, and fifteen other reef/island groups. - GAZ:00002901 Costa Rica [GAZ:00002901] A republic in Central America, bordered by Nicaragua to the north, Panama to the east-southeast, the Pacific Ocean to the west and south, and the Caribbean Sea to the east. Costa Rica is composed of seven provinces, which in turn are divided into 81 cantons. - GAZ:00000906 Cote d'Ivoire [GAZ:00000906] A country in West Africa. It borders Liberia and Guinea to the west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). The regions are further divided into 58 departments. - GAZ:00002719 Croatia [GAZ:00002719] A country at the crossroads of the Mediterranean, Central Europe, and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to the east, Montenegro to the far southeast, and the Adriatic Sea to the south. Croatia is divided into 21 counties (zupanija) and the capital Zagreb's city district. - GAZ:00003762 Cuba [GAZ:00003762] A country that consists of the island of Cuba (the largest and second-most populous island of the Greater Antilles), Isla de la Juventud and several adjacent small islands. Fourteen provinces and one special municipality (the Isla de la Juventud) now compose Cuba. - GAZ:00012582 Curacao [GAZ:00012582] One of five island areas of the Netherlands Antilles. - GAZ:00004006 Cyprus [GAZ:00004006] The third largest island in the Mediterranean Sea (after Sicily and Sardinia), Cyprus is situated in the eastern Mediterranean, just south of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, it is often included in the Middle East (see also Western Asia and Near East). Turkey is 75 km north; other neighbouring countries include Syria and Lebanon to the east, Israel to the southeast, Egypt to the south, and Greece to the west-north-west. - GAZ:00002954 Czech Republic [GAZ:00002954] A landlocked country in Central Europe. It has borders with Poland to the north, Germany to the northwest and southwest, Austria to the south, and Slovakia to the east. The capital and largest city is Prague. The country is composed of the historic regions of Bohemia and Moravia, as well as parts of Silesia. Since 2000, the Czech Republic is divided into thirteen regions (kraje, singular kraj) and the capital city of Prague. The older seventy-six districts (okresy, singular okres) including three 'statutory cities' (without Prague, which had special status) were disbanded in 1999 in an administrative reform; they remain as territorial division and seats of various branches of state administration. Since 2003-01-01, the regions have been divided into around 203 Municipalities with Extended Competence (unofficially named "Little Districts" (Czech: 'male okresy') which took over most of the administration of the former District Authorities. Some of these are further divided into Municipalities with Commissioned Local Authority. However, the old districts still exist as territorial units and remain as seats of some of the offices. - GAZ:00001086 Democratic Republic of the Congo [GAZ:00001086] A country of central Africa. It borders the Central African Republic and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia and Angola on the south, the Republic of the Congo on the west, and is separated from Tanzania by Lake Tanganyika on the east. The country enjoys access to the ocean through a 40 km stretch of Atlantic coastline at Muanda and the roughly 9 km wide mouth of the Congo river which opens into the Gulf of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed into 25 Provinces from 2.2009. Each Province is divided into Zones. - GAZ:00005852 Denmark [GAZ:00005852] That part of the Kingdom of Denmark located in continental Europe. The mainland is bordered to the south by Germany; Denmark is located to the southwest of Sweden and the south of Norway. Denmark borders both the Baltic and the North Sea. The country consists of a large peninsula, Jutland (Jylland) and a large number of islands, most notably Zealand (Sjaelland), Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds of minor islands often referred to as the Danish Archipelago. - GAZ:00000582 Djibouti [GAZ:00000582] A country in eastern Africa. Djibouti is bordered by Eritrea in the north, Ethiopia in the west and south, and Somalia in the southeast. The remainder of the border is formed by the Red Sea and the Gulf of Aden. On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. Djibouti is divided into 5 regions and one city. It is further subdivided into 11 districts. - GAZ:00006890 Dominica [GAZ:00006890] An island nation in the Caribbean Sea. Dominica is divided into ten parishes. - GAZ:00003952 Dominican Republic [GAZ:00003952] A country in the West Indies that occupies the E two-thirds of the Hispaniola island. The Dominican Republic's shores are washed by the Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona Passage, a channel about 130 km wide, separates the country (and the Hispaniola) from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, the national capital, Santo Domingo, is contained within its own Distrito Nacional (National District). The provinces are divided into municipalities (municipios; singular municipio). - GAZ:00002912 Ecuador [GAZ:00002912] A country in South America, bordered by Colombia on the north, by Peru on the east and south, and by the Pacific Ocean to the west. The country also includes the Galapagos Islands (Archipelago de Colon) in the Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, divided into 199 cantons and subdivided into parishes (or parroquias). - GAZ:00003934 Egypt [GAZ:00003934] A country in North Africa that includes the Sinai Peninsula, a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, and the Gaza Strip and Israel to the east. The northern coast borders the Mediterranean Sea and the island of Cyprus; the eastern coast borders the Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, singular muhafazah). The governorates are further divided into regions (markazes). - GAZ:00002935 El Salvador [GAZ:00002935] A country in Central America, bordering the Pacific Ocean between Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), which, in turn, are subdivided into 267 municipalities (municipios). - GAZ:00001091 Equatorial Guinea [GAZ:00001091] A country in Central Africa. It is one of the smallest countries in continental Africa, and comprises two regions: Rio Muni, continental region including several offshore islands; and Insular Region containing Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando Po) that contains the capital, Malabo. Equatorial Guinea is divided into seven provinces which are divided into districts. - GAZ:00000581 Eritrea [GAZ:00000581] A country situated in northern East Africa. It is bordered by Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. The east and northeast of the country have an extensive coastline on the Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago and several of the Hanish Islands are part of Eritrea. Eritrea is divided into six regions (zobas) and subdivided into districts ("sub-zobas"). - GAZ:00002959 Estonia [GAZ:00002959] A country in Northern Europe. Estonia has land borders to the south with Latvia and to the east with Russia. It is separated from Finland in the north by the Gulf of Finland and from Sweden in the west by the Baltic Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). Estonian counties are divided into rural (vallad, singular vald) and urban (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) municipalities. The municipalities comprise populated places (asula or asustusuksus) - various settlements and territorial units that have no administrative function. A group of populated places form a rural municipality with local administration. Most towns constitute separate urban municipalities, while some have joined with surrounding rural municipalities. - GAZ:00001099 Eswatini [GAZ:00001099] A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla). - GAZ:00000567 Ethiopia [GAZ:00000567] A country situated in the Horn of Africa that has been landlocked since the independence of its northern neighbor Eritrea in 1993. Apart from Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to the south, Djibouti to the northeast, and Somalia to the east. Since 1996 Ethiopia has had a tiered government system consisting of a federal government overseeing ethnically-based regional states, zones, districts (woredas), and neighborhoods (kebele). It is divided into nine ethnically-based administrative states (kililoch, singular kilil) and subdivided into sixty-eight zones and two chartered cities (astedader akababiwoch, singular astedader akababi): Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and six special woredas. - GAZ:00005811 Europa Island [GAZ:00005811] A 28 km2 low-lying tropical island in the Mozambique Channel, about a third of the way from southern Madagascar to southern Mozambique. - GAZ:00001412 Falkland Islands (Islas Malvinas) [GAZ:00001412] An archipelago in the South Atlantic Ocean, located 483 km from the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), and 940 km north of Antarctica (Elephant Island). They consist of two main islands, East Falkland and West Falkland, together with 776 smaller islands. - GAZ:00059206 Faroe Islands [GAZ:00059206] An autonomous province of the Kingdom of Denmark since 1948 located in the Faroes. Administratively, the islands are divided into 34 municipalities (kommunur) within which 120 or so cities and villages lie. - GAZ:00006891 Fiji [GAZ:00006891] An island nation in the South Pacific Ocean east of Vanuatu, west of Tonga and south of Tuvalu. The country occupies an archipelago of about 322 islands, of which 106 are permanently inhabited, and 522 islets. The two major islands, Viti Levu and Vanua Levu, account for 87% of the population. - GAZ:00002937 Finland [GAZ:00002937] A Nordic country situated in the Fennoscandian region of Northern Europe. It has borders with Sweden to the west, Russia to the east, and Norway to the north, while Estonia lies to its south across the Gulf of Finland. The capital city is Helsinki. Finland is divided into six administrative provinces (laani, plural laanit). These are divided into 20 regions (maakunt), 77 subregions (seutukunta) and then into municipalities (kunta). - GAZ:00003940 France [GAZ:00003940] A part of the country of France that extends from the Mediterranean Sea to the English Channel and the North Sea, and from the Rhine to the Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas departments. - GAZ:00002516 French Guiana [GAZ:00002516] An overseas department (departement d'outre-mer) of France, located on the northern coast of South America. It is bordered by Suriname, to the E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. French Guiana is divided into 2 departmental arrondissements, 19 cantons and 22 communes. - GAZ:00002918 French Polynesia [GAZ:00002918] A French overseas collectivity in the southern Pacific Ocean. It is made up of several groups of Polynesian islands. French Polynesia has five administrative subdivisions (French: subdivisions administratives). - GAZ:00003753 French Southern and Antarctic Lands [GAZ:00003753] The French Southern and Antarctic Lands have formed a territoire d'outre-mer (an overseas territory) of France since 1955. The territory is divided into five districts. - GAZ:00001092 Gabon [GAZ:00001092] A country in west central Africa sharing borders with Equatorial Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital and largest city is Libreville. Gabon is divided into 9 provinces and further divided into 37 departments. - GAZ:00000907 Gambia [GAZ:00000907] A country in Western Africa. It is the smallest country on the African continental mainland and is bordered to the north, east, and south by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing through the centre of the country and discharging to the Atlantic Ocean is the Gambia River. The Gambia is divided into five divisions and one city (Banjul). The divisions are further subdivided into 37 districts. - GAZ:00009571 Gaza Strip [GAZ:00009571] A Palestinian enclave on the eastern coast of the Mediterranean Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel on the east and north along a 51 km (32 mi) border. Gaza and the West Bank are claimed by the de jure sovereign State of Palestine. - GAZ:00004942 Georgia [GAZ:00004942] A Eurasian country in the Caucasus located at the east coast of the Black Sea. In the north, Georgia has a 723 km common border with Russia, specifically with the Northern Caucasus federal district. The following Russian republics/subdivisions: from west to east: border Georgia: Krasnodar Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to the south-west. It is a transcontinental country, located at the juncture of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 autonomous republics (avtonomiuri respublika), and 1 city (k'alak'i). The regions are further subdivided into 69 districts (raioni). - GAZ:00002646 Germany [GAZ:00002646] A country in Central Europe. It is bordered to the north by the North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech Republic; to the south by Austria and Switzerland; and to the west by France, Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) and cities (kreisfreie Stadte). - GAZ:00000908 Ghana [GAZ:00000908] A country in West Africa. It borders Cote d'Ivoire to the west, Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the south. Ghana is a divided into 10 regions, subdivided into a total of 138 districts. - GAZ:00003987 Gibraltar [GAZ:00003987] A British overseas territory located near the southernmost tip of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory shares a border with Spain to the north. - GAZ:00005808 Glorioso Islands [GAZ:00005808] A group of islands and rocks totalling 5 km2, in the northern Mozambique channel, about 160 km northwest of Madagascar. - GAZ:00002945 Greece [GAZ:00002945] A country in southeastern Europe, situated on the southern end of the Balkan Peninsula. It has borders with Albania, the former Yugoslav Republic of Macedonia and Bulgaria to the north, and Turkey to the east. The Aegean Sea lies to the east and south of mainland Greece, while the Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin feature a vast number of islands. Greece consists of thirteen peripheries subdivided into a total of fifty-one prefectures (nomoi, singular nomos). There is also one autonomous area, Mount Athos, which borders the periphery of Central Macedonia. - GAZ:00001507 Greenland [GAZ:00001507] A self-governing Danish province located between the Arctic and Atlantic Oceans, east of the Canadian Arctic Archipelago. - GAZ:02000573 Grenada [GAZ:02000573] An island country in the West Indies in the Caribbean Sea at the southern end of the Grenadines island chain. Grenada consists of the island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, and several small islands which lie to the north of the main island and are a part of the Grenadines. It is located northwest of Trinidad and Tobago, northeast of Venezuela and southwest of Saint Vincent and the Grenadines. Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated population of 112,523 in July 2020. - GAZ:00067142 Guadeloupe [GAZ:00067142] An archipelago and overseas department and region of France in the Caribbean. It consists of six inhabited islands—Basse-Terre, Grande-Terre, Marie-Galante, La Désirade, and the two inhabited Îles des Saintes—as well as many uninhabited islands and outcroppings. It is south of Antigua and Barbuda and Montserrat, and north of Dominica. - GAZ:00003706 Guam [GAZ:00003706] An organized, unincorporated territory of the United States in the Micronesia subregion of the western Pacific Ocean. It is the westernmost point and territory of the United States (reckoned from the geographic center of the U.S.); in Oceania, it is the largest and southernmost of the Mariana Islands and the largest island in Micronesia. - GAZ:00002936 Guatemala [GAZ:00002936] A country in Central America bordered by Mexico to the northwest, the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the northeast, and Honduras and El Salvador to the southeast. Guatemala is divided into 22 departments (departamentos) and sub-divided into about 332 municipalities (municipios). - GAZ:00001550 Guernsey [GAZ:00001550] A British Crown Dependency in the English Channel off the coast of Normandy. - GAZ:00000909 Guinea [GAZ:00000909] A nation in West Africa, formerly known as French Guinea. Guinea's territory has a curved shape, with its base at the Atlantic Ocean, inland to the east, and turning south. The base borders Guinea-Bissau and Senegal to the north, and Mali to the north and north-east; the inland part borders Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone to the west of the southern tip. - GAZ:00000910 Guinea-Bissau [GAZ:00000910] A country in western Africa, and one of the smallest nations in continental Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west. Formerly the Portuguese colony of Portuguese Guinea, upon independence, the name of its capital, Bissau, was added to the country's name in order to prevent confusion between itself and the Republic of Guinea. - GAZ:00002522 Guyana [GAZ:00002522] A country in the N of South America. Guyana lies north of the equator, in the tropics, and is located on the Atlantic Ocean. Guyana is bordered to the east by Suriname, to the south and southwest by Brazil and to the west by Venezuela. Guyana is divided into 10 regions. The regions of Guyana are divided into 27 neighborhood councils. - GAZ:00003953 Haiti [GAZ:00003953] A country located in the Greater Antilles archipelago on the Caribbean island of Hispaniola, which it shares with the Dominican Republic. Haiti is divided into 10 departments. The departments are further divided into 41 arrondissements, and 133 communes which serve as second and third level administrative divisions. - GAZ:00009718 Heard Island and McDonald Islands [GAZ:00009718] An Australian external territory comprising a volcanic group of mostly barren Antarctic islands, about two-thirds of the way from Madagascar to Antarctica. - GAZ:00002894 Honduras [GAZ:00002894] A republic in Central America. The country is bordered to the west by Guatemala, to the southwest by El Salvador, to the southeast by Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. Honduras is divided into 18 departments. The capital city is Tegucigalpa Central District of the department of Francisco Morazan. - GAZ:00003203 Hong Kong [GAZ:00003203] A special administrative region of the People's Republic of China (PRC). The territory lies on the eastern side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east, west and south. Hong Kong was a crown colony of the United Kingdom from 1842 until the transfer of its sovereignty to the People's Republic of China in 1997. - GAZ:00007120 Howland Island [GAZ:00007120] An uninhabited coral island located just north of the equator in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. The island is almost half way between Hawaii and Australia and is an unincorporated, unorganized territory of the United States, and is often included as one of the Phoenix Islands. For statistical purposes, Howland is grouped as one of the United States Minor Outlying Islands. - GAZ:00002952 Hungary [GAZ:00002952] A landlocked country in the Carpathian Basin of Central Europe, bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: megye). In addition, the capital city (fovaros), Budapest, is independent of any county government. The counties are further subdivided into 173 subregions (kistersegek), and Budapest is comprised of its own subregion. Since 1996, the counties and City of Budapest have been grouped into 7 regions for statistical and development purposes. These seven regions constitute NUTS second-level units of Hungary. - GAZ:00000843 Iceland [GAZ:00000843] A country in northern Europe, comprising the island of Iceland and its outlying islands in the North Atlantic Ocean between the rest of Europe and Greenland. - GAZ:00002839 India [GAZ:00002839] A country in South Asia. Bounded by the Indian Ocean on the south, the Arabian Sea on the west, and the Bay of Bengal on the east, India has a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, and Bhutan to the north-east; and Bangladesh and Burma to the east. India is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian Ocean. India is a federal republic of twenty-eight states and seven Union Territories. Each state or union territory is divided into basic units of government and administration called districts. There are nearly 600 districts in India. The districts in turn are further divided into tehsils and eventually into villages. - GAZ:00003727 Indonesia [GAZ:00003727] An archipelagic state in Southeast Asia. The country shares land borders with Papua New Guinea, East Timor and Malaysia. Other neighboring countries include Singapore, the Philippines, Australia, and the Indian territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, five of which have special status. The provinces are subdivided into regencies (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), which are further subdivided into subdistricts (kecamatan), and again into village groupings (either desa or kelurahan). - GAZ:00004474 Iran [GAZ:00004474] A country in Central Eurasia. Iran is bounded by the Gulf of Oman and the Persian Gulf to the south and the Caspian Sea to its north. It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into 30 provinces (ostan). The provinces are divided into counties (shahrestan), and subdivided into districts (bakhsh) and sub-districts (dehestan). - GAZ:00004483 Iraq [GAZ:00004483] A country in the Middle East spanning most of the northwestern end of the Zagros mountain range, the eastern part of the Syrian Desert and the northern part of the Arabian Desert. It shares borders with Kuwait and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, Turkey to the north, and Iran to the east. It has a very narrow section of coastline at Umm Qasr on the Persian Gulf. There are two major flowing rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates (or provinces) (muhafazah). The governorates are divided into qadhas (or districts). - GAZ:00002943 Ireland [GAZ:00002943] A country in north-western Europe. The modern sovereign state occupies five-sixths of the island of Ireland, which was partitioned in 1921. It is bordered by Northern Ireland (part of the United Kingdom) to the north, by the Atlantic Ocean to the west and by the Irish Sea to the east. Administration follows the 34 "county-level" counties and cities of Ireland. Of these twenty-nine are counties, governed by county councils while the five cities of Dublin, Cork, Limerick, Galway and Waterford have city councils, (previously known as corporations), and are administered separately from the counties bearing those names. The City of Kilkenny is the only city in the republic which does not have a "city council"; it is still a borough but not a county borough and is administered as part of County Kilkenny. Ireland is split into eight regions for NUTS statistical purposes. These are not related to the four traditional provinces but are based on the administrative counties. - GAZ:00052477 Isle of Man [GAZ:00052477] A Crown dependency of the United Kingdom in the centre of the Irish Sea. It is not part of the United Kingdom, European Union or United Nations. - GAZ:00002476 Israel [GAZ:00002476] A country in Western Asia located on the eastern edge of the Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, which are partially administrated by the Palestinian National Authority, are also adjacent. The State of Israel is divided into six main administrative districts, known as mehozot (singular mahoz). Districts are further divided into fifteen sub-districts known as nafot (singular: nafa), which are themselves partitioned into fifty natural regions. - GAZ:00002650 Italy [GAZ:00002650] A country located on the Italian Peninsula in Southern Europe, and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. Italy shares its northern Alpine boundary with France, Switzerland, Austria and Slovenia. The independent states of San Marino and the Vatican City are enclaves within the Italian Peninsula, while Campione d'Italia is an Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, singular regione). Five of these regions have a special autonomous status that enables them to enact legislation on some of their local matters. It is further divided into 109 provinces (province) and 8,101 municipalities (comuni). - GAZ:00003781 Jamaica [GAZ:00003781] A nation of the Greater Antilles. Jamaica is divided into 14 parishes, which are grouped into three historic counties that have no administrative relevance. - GAZ:00005853 Jan Mayen [GAZ:00005853] A volcanic island that is part of the Kingdom of Norway, It has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and 1,000 km west of the Norwegian mainland. The island is mountainous, the highest summit being the Beerenberg volcano in the north. The isthmus is the location of the two largest lakes of the island, Sorlaguna (South Lagoon), and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng Lagoon). Jan Mayen was formed by the Jan Mayen hotspot. - GAZ:00002747 Japan [GAZ:00002747] An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south. - GAZ:00007118 Jarvis Island [GAZ:00007118] An uninhabited 4.5 km2 coral atoll located in the South Pacific Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated territory of the United States administered from Washington, DC by the United States Fish and Wildlife Service of the United States Department of the Interior as part of the National Wildlife Refuge system. Jarvis is one of the southern Line Islands and for statistical purposes is also grouped as one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount. - GAZ:00001551 Jersey [GAZ:00001551] A British Crown Dependency[6] off the coast of Normandy, France. As well as the island of Jersey itself, the bailiwick includes two groups of small islands that are no longer permanently inhabited, the Minquiers and Ecrehous, and the Pierres de Lecq. - GAZ:00007114 Johnston Atoll [GAZ:00007114] A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 nm) west of Hawaii. There are four islands located on the coral reef platform, two natural islands, Johnston Island and Sand Island, which have been expanded by coral dredging, as well as North Island (Akau) and East Island (Hikina), artificial islands formed from coral dredging. Johnston is an unincorporated territory of the United States, administered by the US Fish and Wildlife Service of the Department of the Interior as part of the United States Pacific Island Wildlife Refuges. Sits atop Johnston Seamount. - GAZ:00002473 Jordan [GAZ:00002473] A country in Southwest Asia, bordered by Syria to the north, Iraq to the north-east, Israel and the West Bank to the west, and Saudi Arabia to the east and south. It shares the coastlines of the Dead Sea, and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided into 12 provinces called governorates. The Governorates are subdivided into approximately fifty-two nahias. - GAZ:00005809 Juan de Nova Island [GAZ:00005809] A 4.4 km2 low, flat, tropical island in the narrowest part of the Mozambique Channel, about one-third of the way between Madagascar and Mozambique. - GAZ:00004999 Kazakhstan [GAZ:00004999] A country in Central Asia and Europe. It is bordered by Russia, Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders on a significant part of the Caspian Sea. Kazakhstan is divided into 14 provinces and two municipal districts. The provinces of Kazakhstan are divided into raions. - GAZ:00001101 Kenya [GAZ:00001101] A country in Eastern Africa. It is bordered by Ethiopia to the north, Somalia to the east, Tanzania to the south, Uganda to the west, and Sudan to the northwest, with the Indian Ocean running along the southeast border. Kenya comprises eight provinces each headed by a Provincial Commissioner (centrally appointed by the president). The provinces (mkoa singular mikoa plural in Swahili) are subdivided into districts (wilaya). There were 69 districts as of 1999 census. Districts are then subdivided into 497 divisions (taarafa). The divisions are then subdivided into 2,427 locations (kata) and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the status of a full administrative province. - GAZ:00005682 Kerguelen Archipelago [GAZ:00005682] A group of islands in the southern Indian Ocean. It is a territory of France. They are composed primarily of Tertiary flood basalts and a complex of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano at the southern end was active during the late Pleistocene. The Rallier du Baty Peninsula on the SW tip of the island contains two youthful subglacial eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active fumarole field is related to a series of Holocene trachytic lava flows and lahars that extend beyond the icecap. - GAZ:00007116 Kingman Reef [GAZ:00007116] A largely submerged, uninhabited tropical atoll located in the North Pacific Ocean, roughly half way between Hawaiian Islands and American Samoa. It is the northernmost of the Northern Line Islands and lies 65 km NNW of Palmyra Atoll, the next closest island, and has the status of an unincorporated territory of the United States, administered from Washington, DC by the US Navy. Sits atop Kingman Reef Seamount. - GAZ:00006894 Kiribati [GAZ:00006894] An island nation located in the central tropical Pacific Ocean. It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 km2 straddling the equator and bordering the International Date Line to the east. It is divided into three island groups which have no administrative function, including a group which unites the Line Islands and the Phoenix Islands (ministry at London, Christmas). Each inhabited island has its own council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two councils on Tabiteuea). - GAZ:00011337 Kosovo [GAZ:00011337] A country on the Balkan Peninsula. Kosovo borders Central Serbia to the north and east, Montenegro to the northwest, Albania to the west and the Republic of Macedonia to the south. Kosovo is divided into 7 districts (Rreth) and 30 municipalities. Serbia does not recognise the unilateral secession of Kosovo[8] and considers it a United Nations-governed entity within its sovereign territory, the Autonomous Province of Kosovo and Metohija. - GAZ:00005285 Kuwait [GAZ:00005285] A sovereign emirate on the coast of the Persian Gulf, enclosed by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided into six governorates (muhafazat, singular muhafadhah). - GAZ:00006893 Kyrgyzstan [GAZ:00006893] A country in Central Asia. Landlocked and mountainous, it is bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan to the southwest and China to the east. Kyrgyzstan is divided into seven provinces (oblast. The capital, Bishkek, and the second large city Osh are administratively the independent cities (shaar) with a status equal to a province. Each province comprises a number of districts (raions). - GAZ:00006889 Laos [GAZ:00006889] A landlocked country in southeast Asia, bordered by Burma (Myanmar) and China to the northwest, Vietnam to the east, Cambodia to the south, and Thailand to the west. Laos is divided into sixteen provinces (qwang) and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided into districts (muang). - GAZ:00002958 Latvia [GAZ:00002958] A country in Northern Europe. Latvia shares land borders with Estonia to the north and Lithuania to the south, and both Russia and Belarus to the east. It is separated from Sweden in the west by the Baltic Sea. The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). There are also seven cities (lielpilsetas) that have a separate status. Latvia is also historically, culturally and constitutionally divided in four or more distinct regions. - GAZ:00002478 Lebanon [GAZ:00002478] A small, mostly mountainous country in Western Asia, on the eastern shore of the Mediterranean Sea. It is bordered by Syria to the north and east, and Israel to the south. Lebanon is divided into six governorates (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, singular: qadaa). - GAZ:00001098 Lesotho [GAZ:00001098] A land-locked country, entirely surrounded by the Republic of South Africa. Lesotho is divided into ten districts; these are further subdivided into 80 constituencies, which consists of 129 local community councils. - GAZ:00000911 Liberia [GAZ:00000911] A country on the west coast of Africa, bordered by Sierra Leone, Guinea, Cote d'Ivoire, and the Atlantic Ocean. - GAZ:00000566 Libya [GAZ:00000566] A country in North Africa. Bordering the Mediterranean Sea to the north, Libya lies between Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west. There are thirty-four municipalities of Libya, known by the Arabic term sha'biyat (singular sha'biyah). These came recently (in the 1990s to replaced old Baladiyat systam. The Baladiyat system in turn was introduced to replace the system of muhafazah (governorates or provinces) that existed from the 1960s to the 1970s. - GAZ:00003858 Liechtenstein [GAZ:00003858] A tiny, doubly landlocked alpine country in Western Europe, bordered by Switzerland to its west and by Austria to its east. The principality of Liechtenstein is divided into 11 municipalities called Gemeinden (singular Gemeinde). The Gemeinden mostly consist only of a single town. Five of them fall within the electoral district Unterland (the lower county), and the remainder within Oberland (the upper county). - GAZ:00007144 Line Islands [GAZ:00007144] A group of eleven atolls and low coral islands in the central Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, while three are United States territories that are grouped with the United States Minor Outlying Islands. - GAZ:00002960 Lithuania [GAZ:00002960] A country located along the south-eastern shore of the Baltic Sea, sharing borders with Latvia to the north, Belarus to the southeast, Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. Lithuania has a three-tier administrative division: the country is divided into 10 counties (singular apskritis, plural, apskritys) that are further subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) which consist of over 500 elderates (singular seniunija, plural seniunijos). - GAZ:00002947 Luxembourg [GAZ:00002947] A small landlocked country in western Europe, bordered by Belgium, France, and Germany. Luxembourg is divided into 3 districts, which are further divided into 12 cantons and then 116 communes. Twelve of the communes have city status, of which the city of Luxembourg is the largest. - GAZ:00003202 Macau [GAZ:00003202] One of the two special administrative regions of the People's Republic of China, the other being Hong Kong. Macau lies on the western side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east and south. Macau is situated 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang (West River) on the west. It borders the Zhuhai Special Economic Zone in mainland China. - GAZ:00001108 Madagascar [GAZ:00001108] An island nation in the Indian Ocean off the southeastern coast of Africa. The main island, also called Madagascar, is the fourth largest island in the world, and is home to 5% of the world's plant and animal species, of which more than 80% are endemic to Madagascar. Most notable are the lemur infraorder of primates, the carnivorous fossa, three endemic bird families and six endemic baobab species. Madagascar is divided into six autonomous provinces (faritany mizakatena), and 22 regions. The regions are further subdivided into 116 districts, 1,548 communes, and 16,969 fokontany. - GAZ:00001105 Malawi [GAZ:00001105] A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. - GAZ:00003902 Malaysia [GAZ:00003902] A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. - GAZ:00006924 Maldives [GAZ:00006924] An archipelago which consists of approximately 1,196 coral islands grouped in a double chain of 27 atolls, spread over roughly 90,000 km2. - GAZ:00000584 Mali [GAZ:00000584] A landlocked country in northern Africa. It borders Algeria on the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the south, Guinea on the south-west, and Senegal and Mauritania on the west. Mali is divided into 8 regions (regions) and 1 district, and subdivided into 49 cercles, totalling 288 arrondissements. - GAZ:00004017 Malta [GAZ:00004017] A Southern European country and consists of an archipelago situated centrally in the Mediterranean. - GAZ:00007161 Marshall Islands [GAZ:00007161] An archipelago that consists of twenty-nine atolls and five isolated islands. The most important atolls and islands form two groups: the Ratak Chain and the Ralik Chain (meaning "sunrise" and "sunset" chains). Two-thirds of the nation's population lives on Majuro (which is also the capital) and Ebeye. The outer islands are sparsely populated. - GAZ:00067143 Martinique [GAZ:00067143] An island and an overseas department/region and single territorial collectivity of France. - GAZ:00000583 Mauritania [GAZ:00000583] A country in North-West Africa. It is bordered by the Atlantic Ocean on the west, by Senegal on the southwest, by Mali on the east and southeast, by Algeria on the northeast, and by Western Sahara on the northwest (most of which is occupied by Morocco). The capital and largest city is Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 regions (regions) and one capital district, which in turn are subdivided into 44 departments (departements). - GAZ:00003745 Mauritius [GAZ:00003745] An island nation off the coast of the African continent in the southwest Indian Ocean, about 900 km east of Madagascar. In addition to the island of Mauritius, the republic includes the islands of St. Brandon, Rodrigues and the Agalega Islands. - GAZ:00003943 Mayotte [GAZ:00003943] An overseas collectivity of France consisting of a main island, Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and several islets around these two. - GAZ:00002852 Mexico [GAZ:00002852] A federal constitutional republic in North America. It is bounded on the north by the United States; on the south and west by the North Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of Mexico. The United Mexican States comprise a federation of thirty-one states and a federal district, the capital Mexico City. - GAZ:00005862 Micronesia [GAZ:00005862] A subregion of Oceania, comprising hundreds of small islands in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua New Guinea and Melanesia to the west and southwest, and Polynesia to the east. - GAZ:00007112 Midway Islands [GAZ:00007112] A 6.2 km2 atoll located in the North Pacific Ocean (near the northwestern end of the Hawaiian archipelago). It is an unincorporated territory of the United States, designated an insular area under the authority of the US Department of the Interior. - GAZ:00003897 Moldova [GAZ:00003897] A landlocked country in Eastern Europe, located between Romania to the west and Ukraine to the north, east and south. Moldova is divided into thirty-two districts (raioane, singular raion); three municipalities (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). The cities of Comrat and Tiraspol also have municipality status, however not as first-tier subdivisions of Moldova, but as parts of the regions of Gagauzia and Transnistria, respectively. The status of Transnistria is however under dispute. Although it is de jure part of Moldova and is recognized as such by the international community, Transnistria is not de facto under the control of the central government of Moldova. It is administered by an unrecognized breakaway authority under the name Pridnestrovian Moldovan Republic. - GAZ:00003857 Monaco [GAZ:00003857] A small country that is completely bordered by France to the north, west, and south; to the east it is bordered by the Mediterranean Sea. It consists of a single municipality (commune) currently divided into 4 quartiers and 10 wards. - GAZ:00008744 Mongolia [GAZ:00008744] A country in East-Central Asia. The landlocked country borders Russia to the north and China to the south. The capital and largest city is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are in turn divided into 315 sums (districts). The capital Ulan Bator is administrated separately as a khot (municipality) with provincial status. - GAZ:00006898 Montenegro [GAZ:00006898] A country located in Southeastern Europe. It has a coast on the Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina to the northwest, Serbia and its partially recognized breakaway southern province of Kosovo to the northeast and Albania to the southeast. Its capital and largest city is Podgorica. Montenegro is divided into twenty-one municipalities (opstina), and two urban municipalities, subdivisions of Podgorica municipality. - GAZ:00003988 Montserrat [GAZ:00003988] A British overseas territory located in the Leeward Islands. Montserrat is divided into three parishes. - GAZ:00000565 Morocco [GAZ:00000565] A country in North Africa. It has a coast on the Atlantic Ocean that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco has international borders with Algeria to the east, Spain to the north (a water border through the Strait and land borders with two small Spanish autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco is divided into 16 regions, and subdivided into 62 prefectures and provinces. Because of the conflict over Western Sahara, the status of both regions of "Saguia el-Hamra" and "Rio de Oro" is disputed. - GAZ:00001100 Mozambique [GAZ:00001100] A country in southeastern Africa bordered by the Indian Ocean to the east, Tanzania to the north, Malawi and Zambia to the northwest, Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique is divided into ten provinces (provincias) and one capital city (cidade capital) with provincial status. The provinces are subdivided into 129 districts (distritos). Districts are further divided in "Postos Administrativos" (Administrative Posts) and these in Localidades (Localities) the lowest geographical level of central state administration. - GAZ:00006899 Myanmar [GAZ:00006899] A country in SE Asia that is bordered by China on the north, Laos on the east, Thailand on the southeast, Bangladesh on the west, and India on the northwest, with the Bay of Bengal to the southwest. Myanmar is divided into seven states and seven divisions. The administrative divisions are further subdivided into districts, which are further subdivided into townships, wards, and villages. - GAZ:00001096 Namibia [GAZ:00001096] A country in southern Africa on the Atlantic coast. It shares borders with Angola and Zambia to the north, Botswana to the east, and South Africa to the south. Namibia is divided into 13 regions and subdivided into 102 constituencies. - GAZ:00006900 Nauru [GAZ:00006900] An island nation in the Micronesian South Pacific. The nearest neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. Nauru is divided into fourteen administrative districts which are grouped into eight electoral constituencies. - GAZ:00007119 Navassa Island [GAZ:00007119] A small, uninhabited island in the Caribbean Sea, and is an unorganized unincorporated territory of the United States, which administers it through the US Fish and Wildlife Service. The island is also claimed by Haiti. - GAZ:00004399 Nepal [GAZ:00004399] A landlocked nation in South Asia. It is bordered by the Tibet Autonomous Region of the People's Republic of China to the northeast and India to the south and west; it is separated from Bhutan by the Indian State of Sikkim and from Bangladesh by a small strip of the Indian State of West Bengal, known as the "Chicken's Neck". The Himalaya mountain range runs across Nepal's north and western parts, and eight of the world's ten highest mountains, including the highest, Mount Everest are situated within its territory. Nepal is divided into 14 zones and 75 districts, grouped into 5 development regions. - GAZ:00002946 Netherlands [GAZ:00002946] The European part of the Kingdom of the Netherlands. It is bordered by the North Sea to the north and west, Belgium to the south, and Germany to the east. The Netherlands is divided into twelve administrative regions, called provinces. All provinces of the Netherlands are divided into municipalities (gemeenten), together 443 (2007). - GAZ:00005206 New Caledonia [GAZ:00005206] A "sui generis collectivity" (in practice an overseas territory) of France, made up of a main island (Grande Terre), the Loyalty Islands, and several smaller islands. It is located in the region of Melanesia in the southwest Pacific. Administratively, the archipelago is divided into three provinces, and then into 33 communes. - GAZ:00000469 New Zealand [GAZ:00000469] A nation in the south-western Pacific Ocean comprising two large islands (the North Island and the South Island) and numerous smaller islands, most notably Stewart Island/Rakiura and the Chatham Islands. - GAZ:00002978 Nicaragua [GAZ:00002978] A republic in Central America. It is also the least densely populated with a demographic similar in size to its smaller neighbors. The country is bordered by Honduras to the north and by Costa Rica to the south. The Pacific Ocean lies to the west of the country, while the Caribbean Sea lies to the east. For administrative purposes it is divided into 15 departments (departamentos) and two self-governing regions (autonomous communities) based on the Spanish model. The departments are then subdivided into 153 municipios (municipalities). The two autonomous regions are Region Autonoma del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 they formed the single department of Zelaya. - GAZ:00000585 Niger [GAZ:00000585] A landlocked country in Western Africa, named after the Niger River. It borders Nigeria and Benin to the south, Burkina Faso and Mali to the west, Algeria and Libya to the north and Chad to the east. The capital city is Niamey. Niger is divided into 7 departments and one capital district. The departments are subdivided into 36 arrondissements and further subdivided into 129 communes. - GAZ:00000912 Nigeria [GAZ:00000912] A federal constitutional republic comprising thirty-six states and one Federal Capital Territory. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in the north. Its coast lies on the Gulf of Guinea, part of the Atlantic Ocean, in the south. The capital city is Abuja. Nigeria is divided into thirty-six states and one Federal Capital Territory, which are further sub-divided into 774 Local Government Areas (LGAs). - GAZ:00006902 Niue [GAZ:00006902] An island nation located in the South Pacific Ocean. Although self-governing, Niue is in free association with New Zealand, meaning that the Sovereign in Right of New Zealand is also Niue's head of state. - GAZ:00005908 Norfolk Island [GAZ:00005908] A Territory of Australia that includes Norfolk Island and neighboring islands. - GAZ:00002801 North Korea [GAZ:00002801] A state in East Asia in the northern half of the Korean Peninsula, with its capital in the city of Pyongyang. To the south and separated by the Korean Demilitarized Zone is South Korea, with which it formed one nation until division following World War II. At its northern Amnok River border are China and, separated by the Tumen River in the extreme north-east, Russia. - GAZ:00006895 North Macedonia [GAZ:00006895] A landlocked country on the Balkan peninsula in southeastern Europe. It is bordered by Serbia and Kosovo to the north, Albania to the west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), 10 of which comprise Greater Skopje. This is reduced from the previous 123 municipalities established in 1996-09. Prior to this, local government was organised into 34 administrative districts. - GAZ:00002284 North Sea [GAZ:00002284] A sea situated between the eastern coasts of the British Isles and the western coast of Europe. - GAZ:00003958 Northern Mariana Islands [GAZ:00003958] A group of 15 islands about three-quarters of the way from Hawaii to the Philippines. - GAZ:00002699 Norway [GAZ:00002699] A country and constitutional monarchy in Northern Europe that occupies the western portion of the Scandinavian Peninsula. It is bordered by Sweden, Finland, and Russia. The Kingdom of Norway also includes the Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty over Svalbard is based upon the Svalbard Treaty, but that treaty does not apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter I Island and Queen Maud Land in Antarctica are external dependencies, but those three entities do not form part of the kingdom. - GAZ:00005283 Oman [GAZ:00005283] A country in southwest Asia, on the southeast coast of the Arabian Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia on the west, and Yemen on the southwest. The coast is formed by the Arabian Sea on the south and east, and the Gulf of Oman on the northeast. The country also contains Madha, an exclave enclosed by the United Arab Emirates, and Musandam, an exclave also separated by Emirati territory. Oman is divided into four governorates (muhafazah) and five regions (mintaqat). The regions are subdivided into provinces (wilayat). - GAZ:00005246 Pakistan [GAZ:00005246] A country in Middle East which lies on the Iranian Plateau and some parts of South Asia. It is located in the region where South Asia converges with Central Asia and the Middle East. It has a 1,046 km coastline along the Arabian Sea in the south, and is bordered by Afghanistan and Iran in the west, India in the east and China in the far northeast. Pakistan is subdivided into four provinces and two territories. In addition, the portion of Kashmir that is administered by the Pakistani government is divided into two separate administrative units. The provinces are divided into a total of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly equivalent to counties). Tehsils may contain villages or municipalities. There are over five thousand local governments in Pakistan. - GAZ:00006905 Palau [GAZ:00006905] A nation that consists of eight principal islands and more than 250 smaller ones lying roughly 500 miles southeast of the Philippines. - GAZ:00002892 Panama [GAZ:00002892] The southernmost country of Central America. Situated on an isthmus, some categorize it as a transcontinental nation connecting the north and south part of America. It borders Costa Rica to the north-west, Colombia to the south-east, the Caribbean Sea to the north and the Pacific Ocean to the south. Panama's major divisions are nine provinces and five indigenous territories (comarcas indigenas). The provincial borders have not changed since they were determined at independence in 1903. The provinces are divided into districts, which in turn are subdivided into sections called corregimientos. Configurations of the corregimientos are changed periodically to accommodate population changes as revealed in the census reports. - GAZ:00003922 Papua New Guinea [GAZ:00003922] A country in Oceania that comprises the eastern half of the island of New Guinea and its offshore islands in Melanesia (a region of the southwestern Pacific Ocean north of Australia). - GAZ:00010832 Paracel Islands [GAZ:00010832] A group of small islands and reefs in the South China Sea, about one-third of the way from Vietnam to the Philippines. - GAZ:00002933 Paraguay [GAZ:00002933] A landlocked country in South America. It lies on both banks of the Paraguay River, bordering Argentina to the south and southwest, Brazil to the east and northeast, and Bolivia to the northwest, and is located in the very heart of South America. Paraguay consists of seventeen departments and one capital district (distrito capital). Each department is divided into districts. - GAZ:00002932 Peru [GAZ:00002932] A country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean. Peru is divided into 25 regions and the province of Lima. These regions are subdivided into provinces, which are composed of districts (provincias and distritos). There are 195 provinces and 1833 districts in Peru. The Lima Province, located in the central coast of the country, is unique in that it doesn't belong to any of the twenty-five regions. The city of Lima, which is the nation's capital, is located in this province. Callao is its own region, even though it only contains one province, the Constitutional Province of Callao. - GAZ:00004525 Philippines [GAZ:00004525] An archipelagic nation located in Southeast Asia. The Philippine archipelago comprises 7,107 islands in the western Pacific Ocean, bordering countries such as Indonesia, Malaysia, Palau and the Republic of China, although it is the only Southeast Asian country to share no land borders with its neighbors. The Philippines is divided into three island groups: Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, 136 cities, 1,494 municipalities and 41,995 barangays. - GAZ:00005867 Pitcairn Islands [GAZ:00005867] A group of four islands in the southern Pacific Ocean. The Pitcairn Islands form the southeasternmost extension of the geological archipelago of the Tuamotus of French Polynesia. - GAZ:00002939 Poland [GAZ:00002939] A country in Central Europe. Poland is bordered by Germany to the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a Russian exclave, to the north. The administrative division of Poland since 1999 has been based on three levels of subdivision. The territory of Poland is divided into voivodeships (provinces); these are further divided into powiats (counties), and these in turn are divided into gminas (communes or municipalities). Major cities normally have the status of both gmina and powiat. Poland currently has 16 voivodeships, 379 powiats (including 65 cities with powiat status), and 2,478 gminas. - GAZ:00004126 Portugal [GAZ:00004126] That part of the Portugese Republic that occupies the W part of the Iberian Peninsula, and immediately adjacent islands. - GAZ:00006935 Puerto Rico [GAZ:00006935] A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States). - GAZ:00005286 Qatar [GAZ:00005286] An Arab emirate in Southwest Asia, occupying the small Qatar Peninsula on the northeasterly coast of the larger Arabian Peninsula. It is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds the state. Qatar is divided into ten municipalities (Arabic: baladiyah), which are further divided into zones (districts). - GAZ:00001088 Republic of the Congo [GAZ:00001088] A country in Central Africa. It is bordered by Gabon, Cameroon, the Central African Republic, the Democratic Republic of the Congo, the Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic of the Congo is divided into 10 regions (regions) and one commune, the capital Brazzaville. The regions are subdivided into forty-six districts. - GAZ:00003945 Reunion [GAZ:00003945] An island, located in the Indian Ocean east of Madagascar, about 200 km south west of Mauritius, the nearest island. - GAZ:00002951 Romania [GAZ:00002951] A country in Southeastern Europe. It shares a border with Hungary and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, and Bulgaria to the south. Romania has a stretch of sea coast along the Black Sea. It is located roughly in the lower basin of the Danube and almost all of the Danube Delta is located within its territory. Romania is divided into forty-one counties (judete), as well as the municipality of Bucharest (Bucuresti) - which is its own administrative unit. The country is further subdivided into 319 cities and 2686 communes (rural localities). - GAZ:00023304 Ross Sea [GAZ:00023304] A large embayment of the Southern Ocean, extending deeply into Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck on the east, at 158degW. - GAZ:00002721 Russia [GAZ:00002721] A transcontinental country extending over much of northern Eurasia. Russia shares land borders with the following countries (counter-clockwise from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais (territories), 4 autonomous okrugs (autonomous districts), one autonomous oblast, and two federal cities. The federal subjects are grouped into seven federal districts. These subjects are divided into districts (raions), cities/towns and urban-type settlements, and, at level 4, selsovets (rural councils), towns and urban-type settlements under the jurisdiction of the district and city districts. - GAZ:00001087 Rwanda [GAZ:00001087] A small landlocked country in the Great Lakes region of east-central Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo and Tanzania. Rwanda is divided into five provinces (intara) and subdivided into thirty districts (akarere). The districts are divided into sectors (imirenge). - GAZ:00000849 Saint Helena [GAZ:00000849] An island of volcanic origin and a British overseas territory in the South Atlantic Ocean. - GAZ:00006906 Saint Kitts and Nevis [GAZ:00006906] A federal two-island nation in the West Indies. Located in the Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast are Antigua and Barbuda, and to the southeast is the small uninhabited island of Redonda, and the island of Montserrat. The federation of Saint Kitts and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts and five on Nevis. - GAZ:00006909 Saint Lucia [GAZ:00006909] An island nation in the eastern Caribbean Sea on the boundary with the Atlantic Ocean. - GAZ:00003942 Saint Pierre and Miquelon [GAZ:00003942] An Overseas Collectivity of France located in a group of small islands in the North Atlantic Ocean, the main ones being Saint Pierre and Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and Miquelon became an overseas department in 1976, but its status changed to that of an Overseas collectivity in 1985. - GAZ:00005841 Saint Martin [GAZ:00005841] An overseas collectivity of France that came into being on 2007-02-22, encompassing the northern parts of the island of Saint Martin and neighboring islets. The southern part of the island, Sint Maarten, is part of the Netherlands Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe. - GAZ:02000565 Saint Vincent and the Grenadines [GAZ:02000565] An island nation in the Lesser Antilles chain of the Caribbean Sea. - GAZ:00006910 Samoa [GAZ:00006910] A country governing the western part of the Samoan Islands archipelago in the South Pacific Ocean. Samoa is made up of eleven itumalo (political districts). - GAZ:00003102 San Marino [GAZ:00003102] A country in the Apennine Mountains. It is a landlocked enclave, completely surrounded by Italy. San Marino is an enclave in Italy, on the border between the regioni of Emilia Romagna and Marche. Its topography is dominated by the Apennines mountain range. San Marino is divided into nine municipalities, known locally as Castelli (singular castello). - GAZ:00006927 Sao Tome and Principe [GAZ:00006927] An island nation in the Gulf of Guinea, off the western equatorial coast of Africa. It consists of two islands: Sao Tome and Principe, located about 140 km apart and about 250 and 225 km respectively, off of the northwestern coast of Gabon. Both islands are part of an extinct volcanic mountain range. Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The provinces are further divided into seven districts, six on Sao Tome and one on Principe (with Principe having self-government since 1995-04-29). - GAZ:00005279 Saudi Arabia [GAZ:00005279] A country on the Arabian Peninsula. It is bordered by Jordan on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, and the United Arab Emirates on the east, Oman on the southeast, and Yemen on the south. The Persian Gulf lies to the northeast and the Red Sea to its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; singular mintaqah). Each is then divided into Governorates. - GAZ:00000913 Senegal [GAZ:00000913] A country south of the Senegal River in western Africa. Senegal is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies almost entirely within Senegal, surrounded on the north, east and south; from its western coast Gambia's territory follows the Gambia River more than 300 km inland. Dakar is the capital city of Senegal, located on the Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided into 11 regions and further subdivided into 34 Departements, 103 Arrondissements (neither of which have administrative function) and by Collectivites Locales. - GAZ:00002957 Serbia [GAZ:00002957] A landlocked country in Central and Southeastern Europe, covering the southern part of the Pannonian Plain and the central part of the Balkan Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria to the east; Republic of Macedonia, Montenegro to the south; Croatia and Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided into 29 districts plus the City of Belgrade. The districts and the city of Belgrade are further divided into municipalities. Serbia has two autonomous provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), and Vojvodina in the north (7 districts, 46 municipalities). - GAZ:00006922 Seychelles [GAZ:00006922] An archipelagic island country in the Indian Ocean at the eastern edge of the Somali Sea. It consists of 115 islands. - GAZ:00000914 Sierra Leone [GAZ:00000914] A country in West Africa. It is bordered by Guinea in the north and east, Liberia in the southeast, and the Atlantic Ocean in the southwest and west. The Republic of Sierra Leone is composed of 3 provinces and one area called the Western Area; the provinces are further divided into 12 districts. The Western Area is also divided into 2 districts. - GAZ:00003923 Singapore [GAZ:00003923] An island nation located at the southern tip of the Malay Peninsula. It lies 137 km north of the Equator, south of the Malaysian State of Johor and north of Indonesia's Riau Islands. Singapore consists of 63 islands, including mainland Singapore. There are two man-made connections to Johor, Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in the west. Since 2001-11-24, Singapore has had an administrative subdivision into 5 districts. It is also divided into five Regions, urban planning subdivisions with no administrative role. - GAZ:00012579 Sint Maarten [GAZ:00012579] One of five island areas (Eilandgebieden) of the Netherlands Antilles, encompassing the southern half of the island of Saint Martin/Sint Maarten. - GAZ:00002956 Slovakia [GAZ:00002956] A landlocked country in Central Europe. The Slovak Republic borders the Czech Republic and Austria to the west, Poland to the north, Ukraine to the east and Hungary to the south. The largest city is its capital, Bratislava. Slovakia is subdivided into 8 kraje (singular - kraj, usually translated as regions. The kraje are subdivided into many okresy (singular okres, usually translated as districts). Slovakia currently has 79 districts. - GAZ:00002955 Slovenia [GAZ:00002955] A country in southern Central Europe bordering Italy to the west, the Adriatic Sea to the southwest, Croatia to the south and east, Hungary to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. As of 2005-05 Slovenia is divided into 12 statistical regions for legal and statistical purposes. Slovenia is divided into 210 local municipalities, eleven of which have urban status. - GAZ:00005275 Solomon Islands [GAZ:00005275] A nation in Melanesia, east of Papua New Guinea, consisting of nearly one thousand islands. Together they cover a land mass of 28,400 km2. The capital is Honiara, located on the island of Guadalcanal. - GAZ:00001104 Somalia [GAZ:00001104] A country located in the Horn of Africa. It is bordered by Djibouti to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on its north, the Indian Ocean at its east, and Ethiopia to the west. Prior to the civil war, Somalia was divided into eighteen regions (gobollada, singular gobol), which were in turn subdivided into districts. On a de facto basis, northern Somalia is now divided up among the quasi-independent states of Puntland, Somaliland, Galmudug and Maakhir. - GAZ:00001094 South Africa [GAZ:00001094] A country located at the southern tip of Africa. It borders the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, Swaziland, and Lesotho, an independent enclave surrounded by South African territory. It is divided into nine provinces which are further subdivided into 52 districts: 6 metropolitan and 46 district municipalities. The 46 district municipalities are further subdivided into 231 local municipalities. The district municipalities also contain 20 district management areas (mostly game parks) that are directly governed by the district municipalities. The six metropolitan municipalities perform the functions of both district and local municipalities. - GAZ:00003990 South Georgia and the South Sandwich Islands [GAZ:00003990] A British overseas territory in the southern Atlantic Ocean. It iconsists of South Georgia and the Sandwich Islands, some 640 km to the SE. - GAZ:00002802 South Korea [GAZ:00002802] A republic in East Asia, occupying the southern half of the Korean Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 special city (teukbyeolsi). These are further subdivided into a variety of smaller entities, including cities (si), counties (gun), districts (gu), towns (eup), townships (myeon), neighborhoods (dong) and villages (ri). - GAZ:00233439 South Sudan [GAZ:00233439] A state located in Africa with Juba as its capital city. It's bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic of the Congo to the south, and the Central African Republic to the west and Sudan to the North. Southern Sudan includes the vast swamp region of the Sudd formed by the White Nile, locally called the Bahr el Jebel. - GAZ:00000591 Spain [GAZ:00000591] That part of the Kingdom of Spain that occupies the Iberian Peninsula plus the Balaeric Islands. The Spanish mainland is bordered to the south and east almost entirely by the Mediterranean Sea (except for a small land boundary with Gibraltar); to the north by France, Andorra, and the Bay of Biscay; and to the west by the Atlantic Ocean and Portugal. - GAZ:00010831 Spratly Islands [GAZ:00010831] A group of >100 islands located in the Southeastern Asian group of reefs and islands in the South China Sea, about two-thirds of the way from southern Vietnam to the southern Philippines. - GAZ:00003924 Sri Lanka [GAZ:00003924] An island nation in South Asia, located about 31 km off the southern coast of India. Sri Lanka is divided into 9 provinces and 25 districts. Districts are divided into Divisional Secretariats. - GAZ:00002475 State of Palestine [GAZ:00002475] The territory under the administration of the Palestine National Authority, as established by the Oslo Accords. The PNA divides the Palestinian territories into 16 governorates. - GAZ:00000560 Sudan [GAZ:00000560] A country in North Africa. It is bordered by Egypt to the north, the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and Uganda to the southeast, Democratic Republic of the Congo and the Central African Republic to the southwest, Chad to the west and Libya to the northwest. Sudan is divided into twenty-six states (wilayat, singular wilayah) which in turn are subdivided into 133 districts. - GAZ:00002525 Suriname [GAZ:00002525] A country in northern South America. It is situated between French Guiana to the east and Guyana to the west. The southern border is shared with Brazil and the northern border is the Atlantic coast. The southernmost border with French Guiana is disputed along the Marowijne river. Suriname is divided into 10 districts, each of which is divided into Ressorten. - GAZ:00005396 Svalbard [GAZ:00005396] An archipelago of continental islands lying in the Arctic Ocean north of mainland Europe, about midway between Norway and the North Pole. - GAZ:00002729 Sweden [GAZ:00002729] A Nordic country on the Scandinavian Peninsula in Northern Europe. It has borders with Norway (west and north) and Finland (northeast). Sweden is a unitary state, currently divided into twenty-one counties (lan). Each county further divides into a number of municipalities or kommuner, with a total of 290 municipalities in 2004. - GAZ:00002941 Switzerland [GAZ:00002941] A federal republic in Europe. Switzerland is bordered by Germany, France, Italy, Austria and Liechtenstein. The Swiss Confederation consists of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within Switzerland there are two enclaves: Busingen belongs to Germany, Campione d'Italia belongs to Italy. - GAZ:00002474 Syria [GAZ:00002474] A country in Southwest Asia, bordering Lebanon, the Mediterranean Sea and the island of Cyprus to the west, Israel to the southwest, Jordan to the south, Iraq to the east, and Turkey to the north. Syria has fourteen governorates, or muhafazat (singular: muhafazah). The governorates are divided into sixty districts, or manatiq (singular: mintaqah), which are further divided into sub-districts, or nawahi (singular: nahia). - GAZ:00005341 Taiwan [GAZ:00005341] A state in East Asia with de facto rule of the island of Tawain and adjacent territory. The Republic of China currently administers two historical provinces of China (one completely and a small part of another one) and centrally administers two direct-controlled municipalities. - GAZ:00006912 Tajikistan [GAZ:00006912] A mountainous landlocked country in Central Asia. Afghanistan borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and People's Republic of China to the east. Tajikistan consists of 4 administrative divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly known as Karotegin Province). Each region is divided into several districts (nohiya or raion). - GAZ:00001103 Tanzania [GAZ:00001103] A country in East Africa bordered by Kenya and Uganda on the north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, and Zambia, Malawi and Mozambique on the south. To the east it borders the Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight districts (wilaya), each with at least one council, have been created to further increase local authority; the councils are also known as local government authorities. Currently there are 114 councils operating in 99 districts; 22 are urban and 92 are rural. The 22 urban units are further classified as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) or town councils (the remaining eleven communities). - GAZ:00003744 Thailand [GAZ:00003744] A country in Southeast Asia. To its east lie Laos and Cambodia; to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided into 75 provinces (changwat), which are gathered into 5 groups of provinces by location. There are also 2 special governed districts: the capital Bangkok (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial level and thus often counted as a 76th province. - GAZ:00006913 Timor-Leste [GAZ:00006913] A country in Southeast Asia. It comprises the eastern half of the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, an exclave on the northwestern side of the island, within Indonesian West Timor. The small country of 15,410 km2 is located about 640 km northwest of Darwin, Australia. East Timor is divided into thirteen administrative districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, villages and hamlets. - GAZ:00000915 Togo [GAZ:00000915] A country in West Africa bordering Ghana in the west, Benin in the east and Burkina Faso in the north. In the south, it has a short Gulf of Guinea coast, on which the capital Lome is located. - GAZ:00260188 Tokelau [GAZ:00260188] A dependent territory of New Zealand in the southern Pacific Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and Fakaofo. They have a combined land area of 10 km2 (4 sq mi). - GAZ:00006916 Tonga [GAZ:00006916] A Polynesian country, and also an archipelago comprising 169 islands, of which 36 are inhabited. The archipelago's total surface area is about 750 square kilometres (290 sq mi) scattered over 700,000 square kilometres (270,000 sq mi) of the southern Pacific Ocean. - GAZ:00003767 Trinidad and Tobago [GAZ:00003767] An archipelagic state in the southern Caribbean, lying northeast of the South American nation of Venezuela and south of Grenada in the Lesser Antilles. It also shares maritime boundaries with Barbados to the northeast and Guyana to the southeast. The country covers an area of 5,128 km2and consists of two main islands, Trinidad and Tobago, and 21 smaller islands. - GAZ:00005812 Tromelin Island [GAZ:00005812] A low, flat 0.8 km2 island in the Indian Ocean, about 350 km east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 m long and 700 m wide, surrounded by coral reefs. The island is 7 m high at its highest point. - GAZ:00000562 Tunisia [GAZ:00000562] A country situated on the Mediterranean coast of North Africa. It is bordered by Algeria to the west and Libya to the southeast. Tunisia is subdivided into 24 governorates, divided into 262 "delegations" or "districts" (mutamadiyat), and further subdivided into municipalities (shaykhats). - GAZ:00000558 Turkey [GAZ:00000558] A Eurasian country that stretches across the Anatolian peninsula in western Asia and Thrace (Rumelia) in the Balkan region of southeastern Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago are to the west; and the Black Sea is to the north. Separating Anatolia and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus and the Dardanelles), which are commonly reckoned to delineate the border between Asia and Europe, thereby making Turkey transcontinental. The territory of Turkey is subdivided into 81 provinces for administrative purposes. The provinces are organized into 7 regions for census purposes; however, they do not represent an administrative structure. Each province is divided into districts, for a total of 923 districts. - GAZ:00005018 Turkmenistan [GAZ:00005018] A country in Central Asia. It is bordered by Afghanistan to the southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan to the northwest, and the Caspian Sea to the west. It was a constituent republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan is divided into five provinces or welayatlar (singular - welayat) and one independent city. - GAZ:00003955 Turks and Caicos Islands [GAZ:00003955] A British Overseas Territory consisting of two groups of tropical islands in the West Indies. The Turks and Caicos Islands are divided into six administrative districts (two in the Turks Islands and four in the Caicos Islands. - GAZ:00009715 Tuvalu [GAZ:00009715] A Polynesian island nation located in the Pacific Ocean midway between Hawaii and Australia. - GAZ:00002459 United States of America [GAZ:00002459] A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into "census areas"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a "charter township", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county. - GAZ:00001102 Uganda [GAZ:00001102] A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties. - GAZ:00002724 Ukraine [GAZ:00002724] A country in Eastern Europe. It borders Russia to the east, Belarus to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine is subdivided into twenty-four oblasts (provinces) and one autonomous republic (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, and Sevastopol, both have a special legal status. The 24 oblasts and Crimea are subdivided into 490 raions (districts), or second-level administrative units. - GAZ:00005282 United Arab Emirates [GAZ:00005282] A Middle Eastern federation of seven states situated in the southeast of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain. - GAZ:00002637 United Kingdom [GAZ:00002637] A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel. - GAZ:00002930 Uruguay [GAZ:00002930] A country located in the southeastern part of South America. It is bordered by Brazil to the north, by Argentina across the bank of both the Uruguay River to the west and the estuary of Rio de la Plata to the southwest, and the South Atlantic Ocean to the southeast. Uraguay consists of 19 departments (departamentos, singular - departamento). - GAZ:00004979 Uzbekistan [GAZ:00004979] A doubly landlocked country in Central Asia, formerly part of the Soviet Union. It shares borders with Kazakhstan to the west and to the north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one autonomous republic (respublika and one independent city (shahar). - GAZ:00006918 Vanuatu [GAZ:00006918] An island country located in the South Pacific Ocean. The archipelago, which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New Guinea, southeast of the Solomon Islands, and west of Fiji. - GAZ:00002931 Venezuela [GAZ:00002931] A country on the northern coast of South America. The country comprises a continental mainland and numerous islands located off the Venezuelan coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses borders with Guyana to the east, Brazil to the south, and Colombia to the west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just north, off the Venezuelan coast. Venezuela is divided into twenty-three states (Estados), a capital district (distrito capital) corresponding to the city of Caracas, the Federal Dependencies (Dependencias Federales, a special territory), and Guayana Esequiba (claimed in a border dispute with Guyana). Venezuela is further subdivided into 335 municipalities (municipios); these are subdivided into over one thousand parishes (parroquias). - GAZ:00003756 Viet Nam [GAZ:00003756] The easternmost country on the Indochina Peninsula in Southeast Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, alongside China, Laos, and Cambodia. - GAZ:00003959 Virgin Islands [GAZ:00003959] A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts. - GAZ:00007111 Wake Island [GAZ:00007111] A coral atoll (despite its name) having a coastline of 19 km in the North Pacific Ocean, located about two-thirds of the way from Honolulu (3,700 km west) to Guam (2,430 km east). - GAZ:00007191 Wallis and Futuna [GAZ:00007191] A Polynesian French island territory (but not part of, or even contiguous with, French Polynesia) in the South Pacific between Fiji and Samoa. It is made up of three main volcanic tropical islands and a number of tiny islets. - GAZ:00009572 West Bank [GAZ:00009572] A landlocked territory near the Mediterranean coast of Western Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the south, west and north.[2] Under Israeli occupation since 1967, the area is split into 167 Palestinian "islands" under partial Palestinian National Authority civil rule, and 230 Israeli settlements into which Israeli law is "pipelined". - GAZ:00000564 Western Sahara [GAZ:00000564] A territory of northwestern Africa, bordered by Morocco to the north, Algeria in the northeast, Mauritania to the east and south, and the Atlantic Ocean on the west. Western Sahara is administratively divided into four regions. - GAZ:00005284 Yemen [GAZ:00005284] A country located on the Arabian Peninsula in Southwest Asia. Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's territory includes over 200 islands, the largest of which is Socotra, about 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen is divided into twenty governorates (muhafazah) and one municipality. The population of each governorate is listed in the table below. The governorates of Yemen are divided into 333 districts (muderiah). The districts are subdivided into 2,210 sub-districts, and then into 38,284 villages (as of 2001). - GAZ:00001107 Zambia [GAZ:00001107] A landlocked country in Southern Africa. The neighbouring countries are the Democratic Republic of the Congo to the north, Tanzania to the north-east, Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, and Angola to the west. The capital city is Lusaka. Zambia is divided into nine provinces. Each province is subdivided into several districts with a total of 73 districts. - GAZ:00001106 Zimbabwe [GAZ:00001106] A landlocked country in the southern part of the continent of Africa, between the Zambezi and Limpopo rivers. It is bordered by South Africa to the south, Botswana to the southwest, Zambia to the northwest, and Mozambique to the east. Zimbabwe is divided into eight provinces and two cities with provincial status. The provinces are subdivided into 59 districts and 1,200 municipalities. - - - -watershed shapefile availability menu WatershedShapefileAvailabilityMenu GENEPIO:0100993 Available [GENEPIO:0100993] A datum status in which the required datum is able to be used, obtained or selected. - GENEPIO:0100995 Unknown [GENEPIO:0100995] A datum status in which the availabilty or presence of the required datum is not known. - -organism menu OrganismMenu NCBITaxon:2697049 Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] A strain of the species Betacoronavirus pandemicum, a coronavirus that causes COVID-19, the respiratory illness responsible for the COVID-19 pandemic. - -purpose of sampling menu PurposeOfSamplingMenu GENEPIO:0100869 Wastewater treatment efficiency assessment [GENEPIO:0100869] An environmental sampling strategy in which wastewater effluent is collected to assess the efficiency of wastewater treatment. - GENEPIO:0100870 Wastewater chemical surveillance [GENEPIO:0100870] An environmental sampling strategy in which wastewater samples are collected to monitor for chemical contamination. - GENEPIO:0100871 Wastewater drug surveillance [GENEPIO:0100871] An environmental sampling strategy in which wastewater samples are collected to monitor for community drug use. - GENEPIO:0100872 Wastewater pathogen surveillance [GENEPIO:0100872] An environmental sampling strategy in which samples are collected to identify and/or monitor the presence of pathogens. - GENEPIO:0100003 Research [GENEPIO:0100003] A sampling strategy in which samples are collected in order to perform research. - GENEPIO:0100873 Environmental survey (profiling) [GENEPIO:0100873] A research sampling strategy in which samples are collected in order to survey/profile entities in, or characteristics of, an environment. - GENEPIO:0100024 Protocol testing [GENEPIO:0100024] A research sampling strategy in which samples are collected in order to test a method or protocol. - -scale of sampling menu ScaleOfSamplingMenu GENEPIO:0100874 Community-level surveillance [GENEPIO:0100874] A surveillance strategy in which sites are sampled at the community level. - GENEPIO:0100875 Institution-level surveillance [GENEPIO:0100875] A surveillance strategy in which sites are sampled at the institution level. - GENEPIO:0100876 Building-level surveillance [GENEPIO:0100876] A surveillance strategy in which sites are sampled at the building level. - -sample collection time of day menu SampleCollectionTimeOfDayMenu NCIT:C64934 Morning [NCIT:C64934] The time period between dawn and noon. - NCIT:C64935 Afternoon [NCIT:C64935] The time period between noon and sunset. - NCIT:C64936 Evening [NCIT:C64936] The time period between late afternoon and bedtime. - NCIT:C65001 Night [NCIT:C65001] The time in every 24 hour period when it is dark. - -sample collection duration unit menu SampleCollectionDurationUnitMenu UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. - UO:0000031 Minute [UO:0000031] A time unit which is equal to 60 seconds. - UO:0000032 Hour [UO:0000032] A time unit which is equal to 60 minutes. - UO:0000033 Day [UO:0000033] A time unit which is equal to 24 hours. - UO:0000034 Week [UO:0000034] A time unit which is equal to 7 days. - UO:0000035 Month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. - UO:0000036 Year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. - -presampling activity menu PresamplingActivityMenu ENVO:01001442 Agricultural activity [ENVO:01001442] A land use process during which terrestrial environments are modified such that they can grow crop plants or allow the rearing of animals to provide food, fiber, medicines, or other products used by humans. - ENVO:01001248 Animal husbandry [ENVO:01001248] An agricultural process during which humans rear animals on land for harvest and consumption. - ENVO:01001450 Industrial activity [ENVO:01001450] A process that leads to the production of goods. - NCIT:C16205 Healthcare activity [NCIT:C16205] A process that includes the prevention, treatment, and management of physical and mental illness. - ENVO:06105300 Wastewater treatment [ENVO:06105300] A recycling process during which wastewater is treated. - GENEPIO:0101198 Wastewater screening process [GENEPIO:0101198] A wastewater treatment process which removes large objects such as rags, paper, plastics, and metals to prevent damage and clogging of downstream equipment, piping, and appurtenances. - GENEPIO:0101719 wastewater comminution process [GENEPIO:0101719] A wastewater treatment process which involves the mechanical reduction of solid materials in wastewater into smaller, more manageable particles through devices like comminutors or grinders to shred debris. - ENVO:03501445 Wastewater filtration [ENVO:03501445] A wastewater treatment process which removes solid particles from wastewater by means of filtration. - ENVO:03501446 Wastewater grit removal [ENVO:03501446] A wastewater treatment process which removes sand, silt, and grit from wastewater. - ENVO:03501448 Wastewater primary sedimentation [ENVO:03501448] A wastewater treatment process which removes solids and large particles from influent through gravitational force. - ENVO:03501447 Wastewater microbial treatment [ENVO:03501447] A wastewater treatment process in which microbes are used to degrade the biological material in wastewater. - GENEPIO:0101199 Wastewater aerobic digestion [GENEPIO:0101199] A wastewater microbial treatment process in which organic material is broken down in the presence of oxygen. - GENEPIO:0101200 Wastewater anaerobic digestion [GENEPIO:0101200] A wastewater microbial treatment process in which organic material is broken down in the absence of oxygen by anaerobic bacteria. - ENVO:03501449 Wastewater secondary sedimentation [ENVO:03501449] A wastewater treatment process which removes biomass produced in aeration from influent through gravitational force. - GENEPIO:0101201 Wastewater sludge removal [GENEPIO:0101201] A wastewater treatment process which removes large objects such as rags, paper, plastics, and metals to prevent damage and clogging of downstream equipment, piping, and appurtenances. - GENEPIO:0101202 Wastewater sludge dewatering [GENEPIO:0101202] A wastewater treatment process which mechanically reduces the water content of wastewater sludge using equipment like centrifuges or belt presses, resulting in a semi-solid material that is easier to handle and transport - GENEPIO:0101718 Wastewater sludge drying [GENEPIO:0101718] A wastewater treatment process which further reduces the moisture content of dewatered sludge, typically through thermal or air drying methods, producing a dry, stable material for easier disposal or use. - - -sample volume measurement unit menu SampleVolumeMeasurementUnitMenu UO:0000101 microliter (uL) [UO:0000101] A metric unit of volume equivalent to one thousandth of a cubic centimeter or one millionth of a liter. - UO:0000098 milliliter (mL) [UO:0000098] A metric unit of volume equivalent to one cubic centimeter or one thousandth of a liter. - UO:0000099 liter (L) [UO:0000099] A metric unit of volume equivalent to 1000 cubic centimeters - -sample storage duration unit menu SampleStorageDurationUnitMenu UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. - UO:0000031 Minute [UO:0000031] A time unit which is equal to 60 seconds. - UO:0000032 Hour [UO:0000032] A time unit which is equal to 60 minutes. - UO:0000033 Day [UO:0000033] A time unit which is equal to 24 hours. - UO:0000034 Week [UO:0000034] A time unit which is equal to 7 days. - UO:0000035 Month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. - UO:0000036 Year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. - -specimen processing menu SpecimenProcessingMenu OBI:0600041 Concentration [OBI:0600041] A process used to increase the density of a material of interest by removing other materials in the entity containing the material of interest. - OBI:0302886 Centrifugation [OBI:0302886] A process separating molecules by size or density using centrifugal forces generated by a spinning rotor. - OBI:0302885 Filtration [OBI:0302885] A process which separates components suspended in a fluid based on granularity properties relying on a filter device. - NCIT:C154798 Flocculation [NCIT:C154798] A process in which microscopic particles in suspension aggregate to form loosely clumped masses that are often macroscopically observable. - GENEPIO:0100886 Magnetic nanobead binding [GENEPIO:0100886] A process that uses nanobeads to bind to particles or microbes of interest. - OBI:0600034 Precipitation [OBI:0600034] A protocol application to cause a material to precipitate (becoming a solid) out of solution. - GENEPIO:0101011 Gravity separation [GENEPIO:0101011] A process through which solids are separated from a liquid by allowing the solids to settle by gravity. - IDO:0100170 Pasteurization [IDO:0100170] A planned process of heating a liquid entity, to a specific temperature of a defined length of time span, and then cooling it immediately. It has an objective of prevent the microbial's growth in the liquid entity, which is a specific input of this planned process. - GENEPIO:0101012 Growth in enrichment broth [GENEPIO:0101012] A process in which microorganisms, present in a collected sample, undergo cultivation within a nutrient-rich liquid medium, that facilitates growth. - OBI:0600016 Pooling specimens [OBI:0600016] Physical combination of several instances of like material. - GENEPIO:0101021 Technical replicate process [GENEPIO:0101021] A specimen collection process in which a replicate(s) is collected to assess technical variation within an experiment. For technical replicates the same BioSample is used e.g. the same pool of RNA is used to assess technical (as opposed to biological) variation. - GENEPIO:0101022 Biological replicate process [GENEPIO:0101022] A specimen collection process in which a replicate(s) is collected in parallel to assess for biological variation within an experiment. Biological replicates would have distinct BioSamples records. - -environmental site menu EnvironmentalSiteMenu ENVO:01001481 Correctional facility [ENVO:01001481] A prison facility which is owned and operated by a state. - ENVO:03501134 Healthcare facility [ENVO:03501134] A human construction in which healthcare is provided. - ENVO:00002173 Hospital [ENVO:00002173] A building in which health care services are provided by specialized staff and equipment. - ENVO:03501182 Clinic [ENVO:03501182] A facility which is used to provide treatment, remedial work, and/or instruction. - ENVO:03501129 Educational facility [ENVO:03501129] A human construction in which people are educated. - ENVO:03501335 Daycare facility [ENVO:03501335] A child care facility in which day care services are provided, by specialized staff and equipment, to a human child during the working day. - ENVO:03501130 School [ENVO:03501130] An institutional building in which students are educated. - ENVO:03501131 College or university [ENVO:03501131] An institutional building in which university services are performed. - ENVO:01001222 Commercial building [ENVO:01001222] A building which is primarily used to facilitate the buying or selling of goods or services. "Commerce includes legal, economic, political, social, cultural and technological systems that are in operation in any country or internationally." - ENVO:01001221 Office [ENVO:01001221] A commercial building which contains parts used as workplaces primarily for administrative and managerial workers. "An office building will be divided into sections for different companies or may be dedicated to one company. In either case, each company will typically have a reception area, one or several meeting rooms, singular or open-plan offices, as well as toilets." - ENVO:01000934 Restaurant [ENVO:01000934] A building within which food and drink are prepared and served to customers in exchange for money or other goods and/or services. - ENVO:03501207 Shopping mall [ENVO:03501207] A shopping center in which a large indoor pedestrian promenade provides access to stores and other facilities. - ENVO:01000933 Residential building [ENVO:01000933] A human house which serves as a long-term shelter for its inhabitants and within which they store personal property. - ENVO:03501133 Homeless shelter [ENVO:03501133] An institutional building which temporarily houses homeless people. - ENVO:01000932 Long-term care facility [ENVO:01000932] A building in which nursing aides and skilled nurses provide care and treatment to residents who have significant difficulty coping with the required activities of daily living. - ENVO:03501117 Transport hub [ENVO:03501117] A place where passengers and cargo are exchanged between vehicles or/and between transport modes. - ENVO:03501122 Airport [ENVO:03501122] A human construction with extended facilities from which aircraft flight operations take place. - ENVO:00000078 Farm [ENVO:00000078] An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein. - NCIT:C85867 Refugee camp [NCIT:C85867] A temporary, often makeshift shelter for persons displaced by war, political oppression, or for religious beliefs. - ENVO:00000064 Road [ENVO:00000064] An open way for the passage of vehicles, persons, or animals on land. - ENVO:01000447 Roadside [ENVO:01000447] An environmental zone of varying area which is adjacent to a road. - ENVO:00003861 Industrial plant [ENVO:00003861] A building within which goods are produced and, optionally, stored or within which services are rendered. - ENVO:03501297 Meat processing plant [ENVO:03501297] A processing plant for slaughtering, processing, packaging, labelling, handling, and storing of food animal carcasses, parts of carcasses, and meat products. - ENVO:03501450 Pharmaceutical manufacturing plant [ENVO:03501450] An industrial building in which pharamceutical drugs are synthesised and processed on an industrial scale. - ENVO:00000063 Body of water [ENVO:00000063] An accumulation of water of varying size. - ENVO:00002042 Surface water [ENVO:00002042] Water that is found on the surface of an astronomical object. - ENVO:00000020 Lake [ENVO:00000020] A body of water or other liquid of considerable size contained in a depression on a landmass. - ENVO:00000023 Stream [ENVO:00000023] A watercourse which is linear and flows across the solid portion of a planetary surface. - ENVO:00000022 River [ENVO:00000022] A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply. - ENVO:00000015 Ocean [ENVO:00000015] A marine water body which is constitutes the majority of an astronomical body's hydrosphere. - ENVO:00000016 Sea [ENVO:00000016] A large expanse of saline water usually connected with an ocean. - ENVO:00000014 Canal [ENVO:00000014] Artificial watercourse with no flow or a controlled flow used for navigation, drainage or irrigation. - ENVO:00000025 Reservoir [ENVO:00000025] An artificial body of water, often contained by a dam, constructed for the purpose of water storage. - ENVO:01001004 Ground water [ENVO:01001004] Underground water which is located in pore spaces found in rock or unconsolidated deposits such as soil, clay, or gravel. - ENVO:00000026 Well [ENVO:00000026] A cylindrical hole, pit, or tunnel drilled or dug down to a depth from which water, oil, or gas can be pumped or brought to the surface. - ENVO:00000027 Spring [ENVO:00000027] A surface landform which provides an egress for groundwater or steam to flow out of the ground. - ENVO:00002272 Wastewater treatment plant [ENVO:00002272] A plant in which wastewater is treated. - ENVO:03501465 Influent pump station [ENVO:03501465] A facility within a wastewater treatment plant designed to receive and lift incoming wastewater (influent) to a higher elevation for subsequent treatment processes. The influent pump station typically houses pumps, controls, and associated equipment necessary to move wastewater through the treatment process. - ENVO:03501467 Grit chamber [ENVO:03501467] A physical structure or equipment within a wastewater treatment plant where grit and other heavy inorganic particles are removed from the influent through sedimentation. The grit chamber helps protect downstream equipment from abrasion and reduces the accumulation of grit in subsequent treatment processes. - ENVO:03501472 Communitor [ENVO:03501472] A mechanical device designed to reduce the size of solid materials in wastewater. It uses rotating drums or cutting blades to shred large debris into smaller pieces, protecting downstream equipment and enhancing the efficiency of subsequent treatment processes. - ENVO:03501468 Primary clarifer [ENVO:03501468] A large, sedimentation tank in a wastewater treatment plant where the primary stage of solids separation occurs. In the primary clarifier, suspended solids settle to the bottom as sludge, while lighter materials, such as oils and greases, rise to the surface for removal. - ENVO:03501469 Aeration tank [ENVO:03501469] A tank or basin in a wastewater treatment plant where oxygen is introduced into the wastewater to promote the growth of aerobic microorganisms. These microorganisms break down organic pollutants in the water, facilitating the biological treatment process. The aeration tank is essential for reducing the organic load before the water moves to subsequent treatment stages. - ENVO:03501471 Secondary clarifer [ENVO:03501471] A sedimentation tank in a wastewater treatment plant used in the secondary treatment process. The secondary clarifier allows for the settling and removal of biological floc or sludge produced in the aeration tank, further clarifying the treated wastewater before discharge or further treatment. - ENVO:03501473 Sludge dryer [ENVO:03501473] A device designed to remove moisture from sludge through thermal drying methods, resulting in a dry, granular material that is easier to handle, store, or utilize in other applications. - ENVO:03600076 Waste stabilization pond (lagoon) [ENVO:03600076] A human construction which confines wastewater in a depression enclosed by earthen structures. - ENVO:01000924 Sewer [ENVO:01000924] An artificial channel which transports unwanted water or waste liquids away from their source, either to a more useful area, a receptacle, or into sewers or stormwater mains as waste discharge to be released or processed. - ENVO:01000604 Transportation vehicle [ENVO:01000604] A vehicle is a mobile machine which transports people or cargo. - ENVO:01000608 Boat [ENVO:01000608] A boat is a watercraft of any size which is able to float or plane on water. - ENVO:03501349 Airplane [ENVO:03501349] An aircraft which 1) has fixed wings and 2) is propelled by a thrust from a jet engine, propeller, or rocket engine. - -environmental material menu EnvironmentalMaterialMenu ENVO:03501474 Bar screen [ENVO:03501474] A mechanical filter used to remove large objects, such as rags and plastics, from wastewater - ENVO:00002042 Surface water [ENVO:00002042] Water that is found on the surface of an astronomical object. - ENVO:00002001 Wastewater [ENVO:00002001] Water that has been adversely affected in quality by anthropogenic influence - ENVO:03501456 Wastewater sediment [ENVO:03501456] A sediment which is removed from waste water during a waste water treatment process. - ENVO:00002044 Sludge [ENVO:00002044] The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes. - ENVO:00002057 Primary sludge [ENVO:00002057] Sludge generated from the initial processes (i.e., precipitation, sedimentation) of wastewater treatment. - ENVO:00002058 Secondary sludge [ENVO:00002058] Activated waste biomass generated during wastewater treatment. - ENVO:03501457 Wastewater effluent [ENVO:03501457] A wastewater which has been discharged from any item of equipment at a stage of a wastewater treatment process. - GENEPIO:0100892 Primary wastewater effluent [GENEPIO:0100892] A wastewater effluent which has been discharged from a primary clarifier after the first stage of sedimentation. - GENEPIO:0100893 Secondary wastewater effluent [GENEPIO:0100893] A wastewater effluent which has been discharged from a secondary clarifier after the second stage of sedimentation. - -environmental material properties menu EnvironmentalMaterialPropertiesMenu GENEPIO:0101004 Fluid (stagnant) [GENEPIO:0101004] A quality of a body of water wherein it has no current or flow. - GENEPIO:0101005 Fluid (slow) [GENEPIO:0101005] A quality of a body of water wherein there is a slow flow. - GENEPIO:0101006 Fluid (fast) [GENEPIO:0101006] A quality of a body of water wherein there is a fast flow. - PATO:0015031 Contamination [PATO:0015031] The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity. - GENEPIO:0101010 Fecal-contaminated [GENEPIO:0101010] A contamination quality in which fecal matter is a key component of the contamination. - PATO:0001735 Liquid [PATO:0001735] A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids. - GENEPIO:0101007 Slurry-like [GENEPIO:0101007] An quality in which the fluid like material is more viscous due to the suspension of insoluble solid particles. - NCIT:C149895 Semi-solid [NCIT:C149895] A state of matter consisting of molecules in a non-rigid structure that can retain its shape and volume but that is not resistant to such change. - PATO:0001736 Solid [PATO:0001736] A quality in which an object or material exhibits characteristics of solids, lacking movement or flow. - GENEPIO:0101008 Treated [GENEPIO:0101008] A quality which denotes an altered state of an item resulting from purposeful interventions or processes. - GENEPIO:0101009 Untreated [GENEPIO:0101009] A quality which denotes an absence of purposeful intervention or processes on an item. - -wastewater system type menu WastewaterSystemTypeMenu ENVO:03501453 Combined sewer system [ENVO:03501453] A sewered sanitation system that collects rainwater runoff, domestic sewage, and industrial wastewater. - ENVO:03501454 Sanitary sewer system [ENVO:03501454] A sewered sanitation system that collects only domestic sewage. - ENVO:03600076 Waste stabilization pond [ENVO:03600076] A human construction which confines wastewater in a depression enclosed by earthen structures. - ENVO:01000519 Latrine [ENVO:01000519] A latrine is a toilet which is of simple construction (relative to a flush or chemical toilet) and typically intended for communal use. - ENVO:03501451 Septic tank [ENVO:03501451] An underground holding and treatment site for domestic wastewater. - ENVO:03501452 Cesspit [ENVO:03501452] A pit for the disposal and storage of sewage. - ENVO:01000550 Composting toilet [ENVO:01000550] A composting toilet fixture is a dry toilet fixture in which managed, aerobic decomposition converts human excreta into organic matter suitable for the fertilisation or amendment of soils. - ENVO:01000924 Sewer drain [ENVO:01000924] An artificial channel which transports unwanted water or waste liquids away from their source, either to a more useful area, a receptacle, or into sewers or stormwater mains as waste discharge to be released or processed. - - - -experimental specimen role type menu ExperimentalSpecimenRoleTypeMenu GENEPIO:0101018 Positive experimental control [GENEPIO:0101018] A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment. - GENEPIO:0101019 Negative experimental control [GENEPIO:0101019] A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment - EFO:0002090 Technical replicate [EFO:0002090] A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment. - EFO:0002091 Biological replicate [EFO:0002091] A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples. - -collection device menu CollectionDeviceMenu GENEPIO:0100941 Grab sampler [GENEPIO:0100941] A specimen collection device which is used to collect discrete, instantaneous samples of water, soil, or other substances from a specific point in a body of water or at a specific location. - GENEPIO:0102027 Bag filtration device [GENEPIO:0102027] - GENEPIO:0100943 Core sampling device [GENEPIO:0100943] A grab sampler that captures a vertical section of the substrate matrix of fecal sludge. - GENEPIO:0100944 Vacuum sludge sampling device [GENEPIO:0100944] A grab sampler that takes a sample at a designated depth with minimal disturbance to surrounding layers. - GENEPIO:0100945 Cone-shaped sampling device [GENEPIO:0100945] A grab sample that has a controlled valve that opens to take a sample from a specific depth, then closes to bring the sample out. - GENEPIO:0100946 Horizontal grab sampling device [GENEPIO:0100946] A grab sampler in which the container for the sample is mounted on the end of a rod, which is suitable for collecting discharge from a pipe or truck. - GENEPIO:0100947 Vertical grab sampling device [GENEPIO:0100947] A grab sampler in which the container for the sample is mounted on the end of a rod, which is suitable for collecting waste from a tank. - GENEPIO:0100942 Composite sampler [GENEPIO:0100942] A specimen collection device that collects material over different times or locations. - GENEPIO:0100948 Passive (trap) sampler [GENEPIO:0100948] A composite sampler that passively collects a sample without use of electricity or a battery. - GENEPIO:0100949 Moore swab [GENEPIO:0100949] A composite sampler which consists of gauze pad tied with string, suspended in flowing water or wastewater, in order to collect a wastewater sample. - GENEPIO:0100950 Automatic composite sampler [GENEPIO:0100950] A composite sampler which is automated to collect and store multiple wastewater samples across multiple time points. - GENEPIO:0100951 Automatic flow-proportional sampler [GENEPIO:0100951] A composite sampler which is automated to collect and store multiple wastewater samples in a manner proportional to flow. - GENEPIO:0100952 Automatic sequential (time-proportional) sampler [GENEPIO:0100952] A composite sampler which is automated to collect and combine multiple samples of equal volume taken at a set time interval. - -collection method menu CollectionMethodMenu GENEPIO:0100953 Grab sampling [GENEPIO:0100953] An environmental material collection process in which a water or soil sample is taken at a single point of time using a container type known as a grab sampler. - GENEPIO:0102028 Bag Mediated Filtration [GENEPIO:0102028] - GENEPIO:0100954 Composite sampling [GENEPIO:0100954] An environmental material collection process in which mutliple water or soil samples are taken at different time points and combined to produce a composite. Samples can be collected continuously or at discrete time points. - GENEPIO:0100955 Passive composite sampling [GENEPIO:0100955] A method of composite sampling in which a continuous sample is collected passively without electrical input minimizing cost. - GENEPIO:0100956 Automatic composite sampling [GENEPIO:0100956] A method of composite sampling which utilizes an automated system to collect multiple samples, continuously or at discrete timepoints. - GENEPIO:0100957 Manual composite sampling [GENEPIO:0100957] A method of composite sampling in which multiple grab samples from discrete time points are taken and then combined to produce a single composite sample. - -water catchment area human population range menu WaterCatchmentAreaHumanPopulationRangeMenu <10 people An estimation of population size for a group smaller than 10 people. - 10 - 100 people An estimation of population size for a group smaller than 100 people and larger than 10 people. - 100 - 1,000 people An estimation of population size for a group smaller than 1,000 people and larger than 100 people. - 1,000 - 10,000 people An estimation of population size for a group smaller than 10,000 people and larger than 1,000 people. - 10,000 - 100,000 people An estimation of population size for a group smaller than 100,000 people and larger than 10,000 people. - 100,000 - 1,000,000 people An estimation of population size for a group smaller than 1,000,000 people and larger than 100,000 people. - 1,000,000+ people An estimation of population size for a group larger than 1,000,000 people. - -water catchment area human population density unit menu WaterCatchmentAreaHumanPopulationDensityUnitMenu GENEPIO:0100989 persons per square mile [GENEPIO:0100989] A unit of population density that describes the average number of people in a square mile of a given area. - GENEPIO:0100990 persons per square kilometer [GENEPIO:0100990] A unit of population density that describes the average number of people in a square kilometer of a given area. - GENEPIO:0100991 residents per square mile [GENEPIO:0100991] A unit of population density that describes the average number of registered residents in a square mile of a given area. - GENEPIO:0100992 residents per square kilometer [GENEPIO:0100992] A unit of population density that describes the average number of registered residents in a square kilometer of a given area. - -populated area type menu PopulatedAreaTypeMenu GSSO:011077 Suburban [GSSO:011077] A mixed-use or residential area, existing either as part of a city/urban area, or as a separate residential community within commuting distance of one. Suburbs might have their own political or legal jurisdiction, especially in the United States, but this is not always the case, especially in the United Kingdom where most suburbs are located within the administrative boundaries of cities. - GSSO:011078 Rural [GSSO:011078] A geographic area that is located outside towns and cities. Rural areas are primarily used for agriculture or pastoralism and may contain rural settlements. - GSSO:011080 Urban [GSSO:011080] A human settlement with a high population density and infrastructure of built environment. Urban areas are created through urbanization and are categorized by urban morphology as cities, towns, conurbations or suburbs. In urbanism, the term contrasts to rural areas such as villages and hamlets; in urban sociology or urban anthropology it contrasts with natural environment. - -sampling weather conditions menu SamplingWeatherConditionsMenu ENVO:03501418 Cloudy/Overcast [ENVO:03501418] Atmospheric weather in which the sky is mostly or completely obscured by clouds. - ENVO:03501419 Partially cloudy [ENVO:03501419] Atmospheric weather in which the sky is partially obscured by clouds. - ENVO:03501420 Drizzle [ENVO:03501420] An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process. - ENVO:01000844 Fog [ENVO:01000844] A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body. - ENVO:01001564 Rain [ENVO:01001564] An aggregate of raindrops falling to a planetary surface during a precipitation process. - ENVO:01000406 Snow [ENVO:01000406] Snow is an environmental material which is primarily composed of flakes of crystalline water ice. - ENVO:01000876 Storm [ENVO:01000876] A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates. - ENVO:03501421 Sunny/Clear [ENVO:03501421] Atmospheric weather in which the sun can be seen to shine brightly. - -presampling weather conditions menu PresamplingWeatherConditionsMenu ENVO:03501418 Cloudy/Overcast [ENVO:03501418] Atmospheric weather in which the sky is mostly or completely obscured by clouds. - ENVO:03501419 Partially cloudy [ENVO:03501419] Atmospheric weather in which the sky is partially obscured by clouds. - ENVO:03501420 Drizzle [ENVO:03501420] An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process. - ENVO:01000844 Fog [ENVO:01000844] A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body. - ENVO:01001564 Rain [ENVO:01001564] An aggregate of raindrops falling to a planetary surface during a precipitation process. - ENVO:01000406 Snow [ENVO:01000406] Snow is an environmental material which is primarily composed of flakes of crystalline water ice. - ENVO:01000876 Storm [ENVO:01000876] A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates. - ENVO:03501421 Sunny/Clear [ENVO:03501421] Atmospheric weather in which the sun can be seen to shine brightly. - -precipitation measurement unit menu PrecipitationMeasurementUnitMenu UO:0000016 millimeter (mm) [UO:0000016] A length unit which is defined as one thousandth of a meter. - UO:0000015 centimeter (cm) [UO:0000015] A length unit which is equal to one hundredth of a meter or 10^[-2] m - UO:0000008 meter (m) [UO:0000008] An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second. - UO:0010011 inch (in) [UO:0010011] A non-SI unit of length defined as one twelfth of a foot. - UO:0010013 foot (ft) [UO:0010013] A non-SI unit of length which is approximately 0.3048 meters. - -air pressure measurement unit menu AirPressureMeasurementUnitMenu EFO:0005212 atmosphere (atm) [EFO:0005212] A non-SI unit of pressure defined as 101,325 pascals (Pa). - bar - UO:0000110 pascal [UO:0000110] An SI unit of pressure defined as one newton per square meter (N/m^2). - -ambient temperature measurement unit menu AmbientTemperatureMeasurementUnitMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. - UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. - -total daily flow rate measurement unit menu TotalDailyFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second. - cubic meter per minute (m^3/min) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute. - cubic meter per hour (m^3/h) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour. - liter per second (L/s) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second. - liter per minute (L/min) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute. - liter per hour (L/h) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour. - liter per day (L/day) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day. - million gallons per day (MGD) A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day. - -instantaneous flow rate measurement unit menu InstantaneousFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second. - cubic meter per minute (m^3/min) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute. - cubic meter per hour (m^3/h) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour. - liter per second (L/s) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second. - liter per minute (L/min) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute. - liter per hour (L/h) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour. - liter per day (L/day) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day. - million gallons per day (MGD) A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day. - -turbidity measurement unit menu TurbidityMeasurementUnitMenu nephelometric turbidity unit (NTU) A measure of turbidity calculated by using a nephelometer to compare how white light is scattered in a water sample. - UO:0000318 formazin nephelometric unit (FNU) [UO:0000318] A measure of turbidity calculated by comparing how infrared light is scattered in a water sample against the amount of infrared light scattered in a reference solution containing formazin. - -dissolved oxygen measurement unit menu DissolvedOxygenMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. - UO:0000083 kilogram per cubic meter (kg/m^3) [UO:0000083] An SI unit of density that is one thousandth of the density of water. - UO:0000169 part per million (ppm) [UO:0000169] A unitless measure of density that represents one item out of a million. - -oxygen reduction potential (ORP) measurement unit menu OxygenReductionPotentialOrpMeasurementUnitMenu UO:0000247 milliVolt (mV) [UO:0000247] A non-SI unit of electromotive force that is one thousandth of a volt. - -chemical oxygen demand (COD) measurement unit menu ChemicalOxygenDemandCodMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. - -carbonaceous biochemical oxygen demand (CBOD) measurement unit menu CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. - -total suspended solids (TSS) measurement unit menu TotalSuspendedSolidsTssMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. - UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. - -total dissolved solids (TDS) measurement unit menu TotalDissolvedSolidsTdsMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. - UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. - -total solids (TS) measurement unit menu TotalSolidsTsMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. - UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. - -alkalinity measurement unit menu AlkalinityMeasurementUnitMenu milliequivalent per liter (meq/L) A unit of ion concentration that represents chemical activity per volume. - UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. - UO:0000169 parts per million [UO:0000169] A unitless measure of density that represents one item out of a million. - -conductivity measurement unit menu ConductivityMeasurementUnitMenu milliSiemen per centimeter (mS/cm) A non-SI unit of electrical conductivity that is equivalent to one tenth of a Siemen per meter (S/m). - microSiemen per centimeter (μS/cm) A non-SI unit of electrical conductivity that is equivalent to one ten thousandth of a Siemen per meter (S/m). - Siemen per meter (S/m) An SI unit of electrical conductivity that is equivalent to an ampere per volt per meter (A/v/m). - -salinity measurement unit menu SalinityMeasurementUnitMenu practical salinity unit (PSU) A unitless measure of salinity that is equivalent to per thousand. - weight for weight (% w/w) A unitless comparison based on weight rather than volume, which is equivalent to per hundred. - UO:0000168 parts per thousand [UO:0000168] A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same. - UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. - -total nitrogen (TN) measurement unit menu TotalNitrogenTnMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. - UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. - gram per total solids (g/gTS) A unitless comparison of the weight of a substance as a proportion to the weight of total solids. - -total phosphorpus (TP) measurement unit menu TotalPhosphorpusTpMeasurementUnitMenu gram per total solids (g/gTS) A unitless comparison of the weight of a substance as a proportion to the weight of total solids. - GENEPIO:0100998 orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998] A substance unit which describes the weight of orthophosphate as phosphorus (gPO4-P) within a sample to the weight of total solids. - UO:0000273 milligrams per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. - GENEPIO:0100999 milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999] A density unit comparing the weight of orthophosphate as phosphorus (PO4-P) in milligrams within a standard liter volume. - -fecal contamination indicator menu FecalContaminationIndicatorMenu NCBITaxon:1211417 crAssphage [NCBITaxon:1211417] CrAss-like phage, a bacteriophage discovered in 2014 in the human fecal metagenome. - NCBITaxon:12239 PMMoV / pepper mild mottle virus [NCBITaxon:12239] A plant RNA virus that is abundant in human feces. - GENEPIO:0101000 Bacteroides HF183 [GENEPIO:0101000] A fecal indicator which is the most commonly used sewage-associated marker gene, belonging to the Bacteroides genus. - GENEPIO:0101001 Lachnospiraceae Lachno3 [GENEPIO:0101001] A fecal indicator which is a human-associated genetic marker in the Lachnospiraceae family of bacteria. - GENEPIO:0101002 F+ (male specific) coliphages [GENEPIO:0101002] A fecal indicator which is a bacteriophage that infects coliform bacteria and is used in water assessment. - CHEBI:26756 Stercobilin [CHEBI:26756] Bile pigment found in fecal material. - -fecal contamination unit menu FecalContaminationUnitMenu log10 gene copies per 100 milliliter (log10 GC/100 mL) A unit that expresses on a logarithmic scale the number of copies of a given gene within one hundred milliliters of a biological material. - gene copies per liter (GC/L) A unit that measures the number of copies of a given gene within a liter of a biological material. - UO:0010077 PCR quantification cycle [UO:0010077] A count unit of how many Polymerase Chain Reaction (PCR) cycles it took to detect a real signal from a sample. Equivalent to the PCR cycle number at which a sample's reaction curve intersects the threshold line. - log10 gene copies per nanogram total DNA A unit that expresses on a logarithmic scale the number of copies within a nanogram of deoxyribonucleic acid genetic material. - -urinary contamination indicator menu UrinaryContaminationIndicatorMenu CHEBI:36378 Urobilin [CHEBI:36378] A tetrapyrroledicarboxylic acid that causes the yellow color in urine. Also known as urochrome. - -urinary contamination unit menu UrinaryContaminationUnitMenu EFO:0004382 nanograms per liter (ng/L) [EFO:0004382] A mass unit density which is equal to mass of an object in nanograms divided by the volume in liters. - -fecal coliform count unit menu FecalColiformCountUnitMenu UO:0000213 colony forming units per milliliter (CFU/mL) [UO:0000213] A unit of microbial density that describes the number of colony forming units within a milliliter of material. - colony forming units per 100 milliliter (CFU/100 mL) A unit of microbial density that describes the number of colony forming units within 100 milliliters of material. - colony forming units per grams total solids (CFU/gTS) A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material. - most probable number per milliliter (MPN/mL) A unit of microbial density that describes the most probable number of microbes within one milliliter of material. - most probable number per 100 milliliter (MPN/100 mL) A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material. - -sample temperature unit (at collection) menu SampleTemperatureUnitAtCollectionMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. - UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. - -sample temperature unit (when received) menu SampleTemperatureUnitWhenReceivedMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. - UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. - -purpose of sequencing menu PurposeOfSequencingMenu GENEPIO:0100005 Baseline surveillance (random sampling) [GENEPIO:0100005] A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling. - GENEPIO:0100006 Targeted surveillance (non-random sampling) [GENEPIO:0100006] A surveillance sampling strategy in which an aspired outcome is explicitly stated. - GENEPIO:0100007 Priority surveillance project [GENEPIO:0100007] A targeted surveillance strategy which is considered important and/or urgent. - GENEPIO:0100009 Longitudinal surveillance (repeat sampling) [GENEPIO:0100009] A surveillance strategy in which an individual or site is selected to undergo repeat sampling over a defined period of time. - GENEPIO:0100012 Travel-associated surveillance [GENEPIO:0100012] A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored. - GENEPIO:0100013 Domestic travel surveillance [GENEPIO:0100013] A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored, related to domestic travel. - GENEPIO:0100014 International travel surveillance [GENEPIO:0100014] A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored, related to international travel. - GENEPIO:0100022 Research [GENEPIO:0100022] A sampling strategy in which sites are sampled in order to perform research. - GENEPIO:0100023 Viral passage experiment [GENEPIO:0100023] A research sampling strategy in which samples are selected in order to perform a viral passage experiment. - GENEPIO:0100024 Protocol testing experiment [GENEPIO:0100024] A research sampling strategy in which samples are collected in order to test a method or protocol. - -sequencing platform menu SequencingPlatformMenu GENEPIO:0001923 Illumina [GENEPIO:0001923] A sequencing platform provided by the Illumina company. ILLUMINA - GENEPIO:0001927 Pacific Biosciences [GENEPIO:0001927] A sequencing platform provided by the Pacific Biosciences company. PACBIO_SMRT - GENEPIO:0002683 Ion Torrent [GENEPIO:0002683] A sequencing platform provided by the Ion Torrent company. ION_TORRENT - GENEPIO:0100986 Oxford Nanopore Technologies [GENEPIO:0100986] An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK. OXFORT_NANOPORE - GENEPIO:0004324 BGI Genomics [GENEPIO:0004324] A sequencing platform provided by the BGI Genomics company. BGISEQ - GENEPIO:0004325 MGI [GENEPIO:0004325] A sequencing platform provided by the MGI company. BGISEQ - GENEPIO:0001926 Roche LS454 [GENEPIO:0001926] A sequencing platform provided by the 454 Life Sciences company. _LS454 - GENEPIO:0002684 SOLiD sequencing [GENEPIO:0002684] A sequencing platform provided by Life Technologies Corporation. ABI_SOLID - GENEPIO:0001924 Complete Genomics [GENEPIO:0001924] An in-house sequencing platform provided by Complete Genomics. COMPLETE_GENOMICS - GENEPIO:0002682 Helicos [GENEPIO:0002682] A sequencing platform brand provided by Helicos corporation (now defunct). HELICOS - GENEPIO:0100985 Applied Biosystems [GENEPIO:0100985] A sequencing platform provided by ThermoFisher. CAPILLARY - -sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. #REF! - GENEPIO:0100106 Illumina Genome Analyzer [GENEPIO:0100106] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. - OBI:0000703 Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer manufactured by the Illumina (Solexa) corporation, which supports sequencing of single or paired end clone libraries relying on sequencing by synthesis technology. - OBI:0002000 Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. - GENEPIO:0100109 Illumina HiScanSQ [GENEPIO:0100109] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. - GENEPIO:0100110 Illumina HiSeq [GENEPIO:0100110] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. - GENEPIO:0100111 Illumina HiSeq X [GENEPIO:0100111] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that enables sufficient depth and coverage to produce the first 30x human genome for $1000. - GENEPIO:0100112 Illumina HiSeq X Five [GENEPIO:0100112] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. - GENEPIO:0100113 Illumina HiSeq X Ten [GENEPIO:0100113] A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. - OBI:0002022 Illumina HiSeq 1000 [OBI:0002022] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. - GENEPIO:0100115 Illumina HiSeq 1500 [GENEPIO:0100115] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day. - OBI:0002001 Illumina HiSeq 2000 [OBI:0002001] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. - OBI:0002002 Illumina HiSeq 2500 [OBI:0002002] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. - OBI:0002048 Illumina HiSeq 3000 [OBI:0002048] A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. - OBI:0002049 Illumina HiSeq 4000 [OBI:0002049] A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. - GENEPIO:0100120 Illumina iSeq [GENEPIO:0100120] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. - GENEPIO:0100121 Illumina iSeq 100 [GENEPIO:0100121] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. - GENEPIO:0100122 Illumina NovaSeq [GENEPIO:0100122] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that has an output capacity of 6 Tb and 20 billion reads in dual flow cell mode. - GENEPIO:0100123 Illumina NovaSeq 6000 [GENEPIO:0100123] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. - GENEPIO:0100124 Illumina MiniSeq [GENEPIO:0100124] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. - OBI:0002003 Illumina MiSeq [OBI:0002003] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. - GENEPIO:0100126 Illumina NextSeq [GENEPIO:0100126] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. - OBI:0002021 Illumina NextSeq 500 [OBI:0002021] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. - GENEPIO:0100128 Illumina NextSeq 550 [GENEPIO:0100128] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. - GENEPIO:0004432 Illumina NextSeq 1000 [GENEPIO:0004432] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. - GENEPIO:0100129 Illumina NextSeq 2000 [GENEPIO:0100129] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. - GENEPIO:0100130 PacBio [GENEPIO:0100130] A DNA sequencer manufactured by the Pacific Biosciences corporation. - GENEPIO:0100131 PacBio RS [GENEPIO:0100131] A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. - OBI:0002012 PacBio RS II [OBI:0002012] A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. - GENEPIO:0100133 PacBio Sequel [GENEPIO:0100133] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation - GENEPIO:0100134 PacBio Sequel II [GENEPIO:0100134] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. - GENEPIO:0100135 Ion Torrent [GENEPIO:0100135] A DNA sequencer manufactured by the Ion Torrent corporation. - GENEPIO:0100136 Ion Torrent PGM [GENEPIO:0100136] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. - GENEPIO:0100137 Ion Torrent Proton [GENEPIO:0100137] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. - GENEPIO:0100138 Ion Torrent S5 XL [GENEPIO:0100138] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. - GENEPIO:0100139 Ion Torrent S5 [GENEPIO:0100139] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. - GENEPIO:0100140 Oxford Nanopore [GENEPIO:0100140] A DNA sequencer manufactured by the Oxford Nanopore corporation. - GENEPIO:0004433 Oxford Nanopore Flongle [GENEPIO:0004433] An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. - GENEPIO:0100141 Oxford Nanopore GridION [GENEPIO:0100141] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual - GENEPIO:0100142 Oxford Nanopore MinION [GENEPIO:0100142] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. - GENEPIO:0100143 Oxford Nanopore PromethION [GENEPIO:0100143] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. - GENEPIO:0100144 BGI Genomics sequencing instrument [GENEPIO:0100144] A DNA sequencer manufactured by the BGI Genomics corporation. - GENEPIO:0100145 BGISEQ-500 [GENEPIO:0100145] A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". - GENEPIO:0100146 MGI sequencing instrument [GENEPIO:0100146] A DNA sequencer manufactured by the MGI corporation. - GENEPIO:0100971 MGISEQ-2000RS [GENEPIO:0100971] An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing ad which is capable of medium to high throughput sequencing. - GENEPIO:0100972 MGI DNBSEQ-G99 [GENEPIO:0100972] An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing and which adopts triangular matrix signal spots on sequencing flow cell, for low throughput at highspeeds. - GENEPIO:0100148 MGI DNBSEQ-G400 [GENEPIO:0100148] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run. - GENEPIO:0100149 MGI DNBSEQ-G400RS FAST [GENEPIO:0100149] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 330GB per run, which enables faster sequencing than the DNBSEQ-G400. - GENEPIO:0100147 MGI DNBSEQ-T7 [GENEPIO:0100147] A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day. - GENEPIO:0100973 MGI DNBSEQ-E25 [GENEPIO:0100973] An MGI sequencing instrument model that is a compact and lightweight standalone system which can bu used inside or outside the lab. - GENEPIO:0100150 MGI DNBSEQ-G50 [GENEPIO:0100150] A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. - GENEPIO:0001937 454 Genome Sequencer [GENEPIO:0001937] A DNA sequencer first manufactured by 454 Life Science Corporation that conducts pyrosequencing. - OBI:0000689 454 Genome Sequencer 20 [OBI:0000689] A DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. - OBI:0000702 454 Genome Sequencer FLX [OBI:0000702] A DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. - GENEPIO:0100982 454 Genome Sequencer FLX+ [GENEPIO:0100982] A 454 Genome Sequencer that performs pyrosequencing and comprises both optics and fluidics subsystems and can be used for longer reads when used with the long-read Sequencing Kit XL+. - GENEPIO:0001936 454 Genome Sequencer FLX Titanium [GENEPIO:0001936] A 454 Genome Sequencer that performs pyrosequencing and has enhanced capacity and generates longer reads. - GENEPIO:0001938 454 Genome Sequencer Junior [GENEPIO:0001938] A 454 Genome Sequencer that performs pyrosequencing and is more compact. - OBI:0000696 SOLiD System [OBI:0000696] A DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation. - GENEPIO:0001929 SOLiD 5500 [GENEPIO:0001929] A DNA sequencer which is manufactured by Applied Biosystems and utillizes sequencing by ligation technology and faster run times than the SOLiD 4 series. - GENEPIO:0001930 SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930] A DNA sequencer which is manufactured by Applied Biosystems and has two FlowChips for across 12 lanes and with a higher throughput than the 5500 model. - GENEPIO:0100984 SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology and with a higher throughput than SOLiD 5500xl Genetic Analyzer. - OBI:0002007 SOLiD 3 Plus System [OBI:0002007] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. - OBI:0002024 SOLiD 4 System [OBI:0002024] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 100 Gb mappable throughput. - GENEPIO:0001928 SOLiD 4hq System [GENEPIO:0001928] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 300 Gb mappable throughput. - GENEPIO:0001931 SOLiD PI System [GENEPIO:0001931] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine offers 50Gb mappable throughput. - GENEPIO:0001932 SOLiD System 2.0 [GENEPIO:0001932] A DNA sequencer which is manufactured by the Applied Biosystems corporation. - GENEPIO:0001933 SOLiD System 3.0 [GENEPIO:0001933] A DNA sequencer which is manufactured by the Applied Biosystems corporation. - OBI:0000717 HeliScope Single Molecule Sequencer [OBI:0000717] A DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry. - GENEPIO:0100974 Applied Biosystems sequencing instrument model [GENEPIO:0100974] A sequencing instrument model that is manufactured by Applied Biosystems and which performs Sanger sequencing and fragment analysis by capillary electrophoresis. - GENEPIO:0100975 AB 310 Genetic Analyzer [GENEPIO:0100975] An Applied Biosystems sequencing instrument model which utilises a single capillary electrophoresis system to perform Sanger sequencing and fragment analysis that is automated. - GENEPIO:0100976 AB 3130 Genetic Analyzer [GENEPIO:0100976] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 4 capillaries. - GENEPIO:0100977 AB 3130xL Genetic Analyzer [GENEPIO:0100977] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 16 capillaries. - GENEPIO:0100978 AB 3500 Genetic Analyzer [GENEPIO:0100978] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 8 capillaries, which can run 96 well plates. - GENEPIO:0100979 AB 3500xL Genetic Analyzer [GENEPIO:0100979] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 24 capillaries, which can run 384 well plates. - GENEPIO:0100980 AB 3730 Genetic Analyzer [GENEPIO:0100980] An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing. - GENEPIO:0100981 AB 3730xL Genetic Analyzer [GENEPIO:0100981] An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing. - -sequencing assay type menu SequencingAssayTypeMenu OBI:0002767 Amplicon sequencing assay [OBI:0002767] A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. AMPLICON - OBI:0002763 16S ribosomal gene sequencing assay [OBI:0002763] An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. AMPLICON - OBI:0002117 Whole genome sequencing assay [OBI:0002117] A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. WGS - OBI:0002623 Whole metagenome sequencing assay [OBI:0002623] A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. OTHER - OBI:0002768 Whole virome sequencing assay [OBI:0002768] A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. OTHER - -amplicon pcr primer scheme menu AmpliconPcrPrimerSchemeMenu GENEPIO:0100847 artic-v1 [GENEPIO:0100847] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 1.0.0. artic-v1 - GENEPIO:0100848 artic-v2 [GENEPIO:0100848] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 2.0.0. artic-v2 - GENEPIO:0100849 artic-v3 [GENEPIO:0100849] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 3.0.0. artic-v3 - GENEPIO:0100850 artic-v4 [GENEPIO:0100850] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.0.0. artic-v4 - GENEPIO:0100851 artic-v4.1 [GENEPIO:0100851] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.1.0. artic-v4.1 - GENEPIO:0100852 artic-v5.0.0_400 [GENEPIO:0100852] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons approximately 400bp in length. artic-v5.0.0_400 - GENEPIO:0100853 artic-v5.1.0_400 [GENEPIO:0100853] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons approximately 400bp in length. artic-v5.1.0_400 - GENEPIO:0100854 artic-v5.2.0_1200 [GENEPIO:0100854] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 1200bp in length. artic-v5.2.0_1200 - GENEPIO:0100855 artic-v5.2.0_400 [GENEPIO:0100855] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 400bp in length. artic-v5.2.0_400 - GENEPIO:0100856 artic-v5.3.2_400 [GENEPIO:0100856] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons approximately 400bp in length. artic-v5.3.2_400 - GENEPIO:0100857 eden-v1 [GENEPIO:0100857] An amplicon strategy which was developed by John-Sebastian Eden with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces amplicons approximately 2500bp in length. eden-v1 - GENEPIO:0100858 midnight-bccdc-v1 [GENEPIO:0100858] An amplicon strategy which is for SARS-CoV-2 and based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v1 - GENEPIO:0100859 midnight-bccdc-v2 [GENEPIO:0100859] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v2 - GENEPIO:0100860 midnight-bccdc-v3 [GENEPIO:0100860] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 3.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v3 - GENEPIO:0100861 midnight-bccdc-v4 [GENEPIO:0100861] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 4.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v4 - GENEPIO:0100862 midnight-ont-v3 [GENEPIO:0100862] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. midnight-ont-v3 - GENEPIO:0100863 midnight-v1 [GENEPIO:0100863] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. midnight-v1 - GENEPIO:0100864 midnight-v2 [GENEPIO:0100864] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. midnight-v2 - GENEPIO:0100865 varskip-vsl1a [GENEPIO:0100865] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a long. varskip-vsl1a - GENEPIO:0100866 varskip-vss1a [GENEPIO:0100866] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a short. varskip-vss1a - GENEPIO:0100867 varskip-vss2a [GENEPIO:0100867] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2a. varskip-vss2a - GENEPIO:0100868 varskip-vss2b [GENEPIO:0100868] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2b. varskip-vss2b - -genomic target enrichment method menu GenomicTargetEnrichmentMethodMenu GENEPIO:0001950 Hybridization capture [GENEPIO:0001950] Selection by hybridization in array or solution. Hybrid Selection - GENEPIO:0101020 rRNA depletion method [GENEPIO:0101020] Removal of background RNA for the purposes of enriching the genomic target. Other - -quality control determination menu QualityControlDeterminationMenu GENEPIO:0100562 No quality control issues identified [GENEPIO:0100562] A statement confirming that quality control processes were carried out and no quality issues were detected. no quality control issues identified - GENEPIO:0100563 Sequence passed quality control [GENEPIO:0100563] A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. Sequence passed quality control - GENEPIO:0100564 Sequence failed quality control [GENEPIO:0100564] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. Sequence failed quality control - GENEPIO:0100565 Minor quality control issues identified [GENEPIO:0100565] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. minor quality control issues identified - GENEPIO:0100566 Sequence flagged for potential quality control issues [GENEPIO:0100566] A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. sequence flagged for potential quality control issues - GENEPIO:0100567 Quality control not performed [GENEPIO:0100567] A statement confirming that quality control processes have not been carried out. not performed - -quality control issues menu QualityControlIssuesMenu GENEPIO:0100568 Low quality sequence [GENEPIO:0100568] Sequence data that does not meet quality control thresholds. low quality sequence - GENEPIO:0100569 Sequence contaminated [GENEPIO:0100569] Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. sequenced contaminated - GENEPIO:0100570 Low average genome coverage [GENEPIO:0100570] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage). low average genome coverage - GENEPIO:0100571 Low percent genome captured [GENEPIO:0100571] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). low % genome captured - GENEPIO:0100572 Read lengths shorter than expected [GENEPIO:0100572] Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. read lengths shorter than expected - GENEPIO:0100573 Sequence amplification artifacts [GENEPIO:0100573] Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). sequence amplification artifacts - GENEPIO:0100574 Low signal to noise ratio [GENEPIO:0100574] Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). low signal to noise ratio - GENEPIO:0100575 Low coverage of characteristic mutations [GENEPIO:0100575] Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. low coverage of characteristic mutations - -gene symbol menu GeneSymbolMenu GENEPIO:0100151 E gene (orf4) [GENEPIO:0100151] - GENEPIO:0100152 M gene (orf5) [GENEPIO:0100152] - GENEPIO:0100153 N gene (orf9) [GENEPIO:0100153] - GENEPIO:0100154 Spike gene (orf2) [GENEPIO:0100154] - GENEPIO:0100155 orf1ab (rep) [GENEPIO:0100155] - GENEPIO:0100156 orf1a (pp1a) [GENEPIO:0100156] - GENEPIO:0100157 nsp11 [GENEPIO:0100157] - GENEPIO:0100158 nsp1 [GENEPIO:0100158] - GENEPIO:0100159 nsp2 [GENEPIO:0100159] - GENEPIO:0100160 nsp3 [GENEPIO:0100160] - GENEPIO:0100161 nsp4 [GENEPIO:0100161] - GENEPIO:0100162 nsp5 [GENEPIO:0100162] - GENEPIO:0100163 nsp6 [GENEPIO:0100163] - GENEPIO:0100164 nsp7 [GENEPIO:0100164] - GENEPIO:0100165 nsp8 [GENEPIO:0100165] - GENEPIO:0100166 nsp9 [GENEPIO:0100166] - GENEPIO:0100167 nsp10 [GENEPIO:0100167] - GENEPIO:0100168 RdRp gene (nsp12) [GENEPIO:0100168] - GENEPIO:0100169 hel gene (nsp13) [GENEPIO:0100169] - GENEPIO:0100170 exoN gene (nsp14) [GENEPIO:0100170] - GENEPIO:0100171 nsp15 [GENEPIO:0100171] - GENEPIO:0100172 nsp16 [GENEPIO:0100172] - GENEPIO:0100173 orf3a [GENEPIO:0100173] - GENEPIO:0100174 orf3b [GENEPIO:0100174] - GENEPIO:0100175 orf6 (ns6) [GENEPIO:0100175] - GENEPIO:0100176 orf7a [GENEPIO:0100176] - GENEPIO:0100177 orf7b (ns7b) [GENEPIO:0100177] - GENEPIO:0100178 orf8 (ns8) [GENEPIO:0100178] - GENEPIO:0100179 orf9b [GENEPIO:0100179] - GENEPIO:0100180 orf9c [GENEPIO:0100180] - GENEPIO:0100181 orf10 [GENEPIO:0100181] - GENEPIO:0100182 orf14 [GENEPIO:0100182] - GENEPIO:0100183 SARS-COV-2 5' UTR [GENEPIO:0100183] - -diagnostic target presence menu DiagnosticTargetPresenceMenu GENEPIO:0100987 diagnostic target present [GENEPIO:0100987] A quality inhering in a bearer by virtue of the bearer's existence. - GENEPIO:0100988 diagnostic target absent [GENEPIO:0100988] Aquality denoting the lack of an entity. - -diagnostic measurement unit menu DiagnosticMeasurementUnitMenu gene copies per liter (GC/L) A unit that measures the number of copies of a given gene within a liter of a biological material. - GENEPIO:0100657 cycle threshold (Ct) [GENEPIO:0100657] A data field which describes the cycle threshold (Ct) value result from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) test. - UO:0000213 colony forming units per milliliter (CFU/mL) [UO:0000213] A unit of microbial density that describes the number of colony forming units within a milliliter of material. - colony forming units per 100 milliliter (CFU/100 mL) A unit of microbial density that describes the number of colony forming units within 100 milliliters of material. - colony forming units per grams total solids (CFU/gTS) A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material. - most probable number per milliliter (MPN/mL) A unit of microbial density that describes the most probable number of microbes within one milliliter of material. - most probable number per 100 milliliter (MPN/100 mL) A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material. - -diagnostic measurement method menu DiagnosticMeasurementMethodMenu OBI:0000893 Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893] An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. - Digital real time polymerase chain reaction (dPCR) A type of polymerase chain reaction technique in which the sample is fractionated, within which individual PCR reactions occur in each fraction - Bacteria culture test An assay to identify the presence of bacteria - \ No newline at end of file +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_NCBI_SRA EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal + +null value menu NullValueMenu GENEPIO:0001619 Not Applicable [GENEPIO:0001619] A categorical choice recorded when a datum does not apply to a given context. not applicable + GENEPIO:0001618 Missing [GENEPIO:0001618] A categorical choice recorded when a datum is not included for an unknown reason. missing + GENEPIO:0001620 Not Collected [GENEPIO:0001620] A categorical choice recorded when a datum was not measured or collected. not collected + GENEPIO:0001668 Not Provided [GENEPIO:0001668] A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage. not provided + GENEPIO:0001810 Restricted Access [GENEPIO:0001810] A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns. restricted access + +geo_loc_name (country) menu GeoLocNameCountryMenu GAZ:00006882 Afghanistan [GAZ:00006882] A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ] + GAZ:00002953 Albania [GAZ:00002953] A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ] + GAZ:00000563 Algeria [GAZ:00000563] A country in North Africa. It is bordered by Tunisia in the northeast, Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, a few km of the Western Sahara in the west, Morocco in the northwest, and the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). [ url:http://en.wikipedia.org/wiki/Algeria ] + GAZ:00003957 American Samoa [GAZ:00003957] An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa ] + GAZ:00002948 Andorra [GAZ:00002948] A small landlocked country in western Europe, located in the eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. Andorra consists of seven communities known as parishes (Catalan: parroquies, singular - parroquia). Until relatively recently, it had only six parishes; the seventh, Escaldes-Engordany, was created in 1978. Some parishes have a further territorial subdivision. Ordino, La Massana and Sant Julia de Loria are subdivided into quarts (quarters), while Canillo is subdivided into veinats (neighborhoods). Those mostly coincide with villages, which are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ] + GAZ:00001095 Angola [GAZ:00001095] A country in south-central Africa bordering Namibia to the south, Democratic Republic of the Congo to the north, and Zambia to the east, and with a west coast along the Atlantic Ocean. The exclave province Cabinda has a border with the Republic of the Congo and the Democratic Republic of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ] + GAZ:00009159 Anguilla [GAZ:00009159] A British overseas territory in the Caribbean, one of the most northerly of the Leeward Islands in the Lesser Antilles. It consists of the main island of Anguilla itself, approximately 26 km long by 5 km wide at its widest point, together with a number of much smaller islands and cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila ] + GAZ:00000462 Antarctica [GAZ:00000462] The Earth's southernmost continent, overlying the South Pole. It is situated in the southern hemisphere, almost entirely south of the Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica ] + GAZ:00006883 Antigua and Barbuda [GAZ:00006883] An island nation located on the eastern boundary of the Caribbean Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda ] + GAZ:00002928 Argentina [GAZ:00002928] A South American country, constituted as a federation of twenty-three provinces and an autonomous city. It is bordered by Paraguay and Bolivia in the north, Brazil and Uruguay in the northeast, and Chile in the west and south. The country claims the British controlled territories of the Falkland Islands and South Georgia and the South Sandwich Islands. Argentina also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping other claims made by Chile and the United Kingdom. Argentina is subdivided into twenty-three provinces (Spanish: provincias, singular provincia) and one federal district (Capital de la Republica or Capital de la Nacion, informally the Capital Federal). The federal district and the provinces have their own constitutions, but exist under a federal system. Provinces are then divided into departments (Spanish: departamentos, singular departamento), except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina ] + GAZ:00004094 Armenia [GAZ:00004094] A landlocked mountainous country in Eurasia between the Black Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan exclave of Azerbaijan to the south. A transcontinental country at the juncture of Eastern Europe and Western Asia. A former republic of the Soviet Union. Armenia is divided into ten marzes (provinces, singular marz), with the city (kaghak) of Yerevan having special administrative status as the country's capital. [ url:http://en.wikipedia.org/wiki/Armenia ] + GAZ:00004025 Aruba [GAZ:00004025] An autonomous region within the Kingdom of the Netherlands, Aruba has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba ] + GAZ:00005901 Ashmore and Cartier Islands [GAZ:00005901] A Territory of Australia that includes two groups of small low-lying uninhabited tropical islands in the Indian Ocean situated on the edge of the continental shelf north-west of Australia and south of the Indonesian island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands ] + GAZ:00000463 Australia [GAZ:00000463] A country in the southern hemisphere comprising the mainland of the world's smallest continent, the major island of Tasmania, and a number of other islands in the Indian and Pacific Oceans. The neighbouring countries are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to the south-east. Australia has six states, two major mainland territories, and other minor territories. + GAZ:00002942 Austria [GAZ:00002942] A landlocked country in Central Europe. It borders both Germany and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia and Italy to the south, and Switzerland and Liechtenstein to the west. The capital is the city of Vienna on the Danube River. Austria is divided into nine states (Bundeslander). These states are then divided into districts (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities (Gemeinden). Cities have the competencies otherwise granted to both districts and municipalities. + GAZ:00004941 Azerbaijan [GAZ:00004941] A country in the he South Caucasus region of Eurasia, it is bounded by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan is bordered by Armenia to the north and east, Iran to the south and west, and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts in Azerbaijan's southwest, have been controlled by Armenia since the end of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons 11 city districts (saharlar), and one autonomous republic (muxtar respublika). + GAZ:00002733 Bahamas [GAZ:00002733] A country consisting of two thousand cays and seven hundred islands that form an archipelago. It is located in the Atlantic Ocean, southeast of Florida and the United States, north of Cuba, the island of Hispanola and the Caribbean, and northwest of the British overseas territory of the Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, whose affairs are handled directly by the central government. + GAZ:00005281 Bahrain [GAZ:00005281] A borderless island country in the Persian Gulf. Saudi Arabia lies to the west and is connected to Bahrain by the King Fahd Causeway, and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into five governorates. + GAZ:00007117 Baker Island [GAZ:00007117] An uninhabited atoll located just north of the equator in the central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island is an unincorporated and unorganized territory of the US. + GAZ:00003750 Bangladesh [GAZ:00003750] A country in South Asia. It is bordered by India on all sides except for a small border with Myanmar to the far southeast and by the Bay of Bengal to the south. Bangladesh is divided into six administrative divisions. Divisions are subdivided into districts (zila). There are 64 districts in Bangladesh, each further subdivided into upazila (subdistricts) or thana ("police stations"). + GAZ:00001251 Barbados [GAZ:00001251] An island country in the Lesser Antilles of the West Indies, in the Caribbean region of the Americas, and the most easterly of the Caribbean Islands. It is 34 kilometres (21 miles) in length and up to 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is in the western part of the North Atlantic, 100 km (62 mi) east of the Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards, part of the Lesser Antilles, at roughly 13°N of the equator. It is about 168 km (104 mi) east of both the countries of Saint Lucia and Saint Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside the principal Atlantic hurricane belt. Its capital and largest city is Bridgetown. + GAZ:00005810 Bassas da India [GAZ:00005810] A roughly circular atoll about 10 km in diameter, which corresponds to a total size (including lagoon) of 80 km2. It is located in the southern Mozambique Channel, about half-way between Madagascar (which is 385 km to the east) and Mozambique, and 110 km northwest of Europa Island. It rises steeply from the seabed 3000 m below. + GAZ:00006886 Belarus [GAZ:00006886] A landlocked country in Eastern Europe, that borders Russia to the north and east, Ukraine to the south, Poland to the west, and Lithuania and Latvia to the north. Its capital is Minsk. Belarus is divided into six voblasts, or provinces. Voblasts are further subdivided into raions (commonly translated as districts or regions). As of 2002, there are six voblasts, 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special status, due to the city serving as the national capital. + GAZ:00002938 Belgium [GAZ:00002938] A country in northwest Europe. Belgium shares borders with France (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each comprise five provinces; the third region, Brussels-Capital Region, is not a province, nor does it contain any Together, these comprise 589 municipalities, which in general consist of several sub-municipalities (which were independent municipalities before the municipal merger operation mainly in 1977). + GAZ:00002934 Belize [GAZ:00002934] A country in Central America. It is the only officially English speaking country in the region. Belize was a British colony for more than a century and was known as British Honduras until 1973. It became an independent nation within The Commonwealth in 1981. Belize is divided into 6 districts, which are further divided into 31 constituencies. + GAZ:00000904 Benin [GAZ:00000904] A country in Western Africa. It borders Togo to the west, Nigeria to the east and Burkina Faso and Niger to the north; its short coastline to the south leads to the Bight of Benin. Its capital is Porto Novo, but the seat of government is Cotonou. Benin is divided into 12 departments and subdivided into 77 communes. + GAZ:00001264 Bermuda [GAZ:00001264] A British overseas territory in the North Atlantic Ocean. Located off the east coast of the United States, it is situated around 1770 km NE of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately 138 islands. + GAZ:00003920 Bhutan [GAZ:00003920] A landlocked nation in South Asia. It is located amidst the eastern end of the Himalaya Mountains and is bordered to the south, east and west by India and to the north by Tibet. Bhutan is separated from Nepal by the Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative zones). Each dzongdey is further divided into dzongkhag (districts). There are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into subdistricts known as dungkhag. At the basic level, groups of villages form a constituency called gewog. + GAZ:00002511 Bolivia [GAZ:00002511] A landlocked country in central South America. It is bordered by Brazil on the north and east, Paraguay and Argentina on the south, and Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: departamentos). Each of the departments is subdivided into provinces (provincias), which are further subdivided into municipalities (municipios). + GAZ:00025355 Borneo [GAZ:00025355] An island at the grographic centre of Maritime Southeast Adia, in relation to major Indonesian islands, it is located north of Java, west of Sulawesi, and east of Sumatra. It is the third-largest island in the world and the larest in Asia. The island is politically divided among three countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] Approximately 73% of the island is Indonesian territory. In the north, the East Malaysian states of Sabah and Sarawak make up about 26% of the island. Additionally, the Malaysian federal territory of Labuan is situated on a small island just off the coast of Borneo. The sovereign state of Brunei, located on the north coast, comprises about 1% of Borneo's land area. A little more than half of the island is in the Northern Hemisphere, including Brunei and the Malaysian portion, while the Indonesian portion spans the Northern and Southern hemispheres. + GAZ:00006887 Bosnia and Herzegovina [GAZ:00006887] A country on the Balkan peninsula of Southern Europe. Bordered by Croatia to the north, west and south, Serbia to the east, and Montenegro to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided into three political regions of which one, the Brcko District is part of the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. All three have an equal constitutional status on the whole territory of Bosnia and Herzegovina. + GAZ:00001097 Botswana [GAZ:00001097] A landlocked nation in Southern Africa. It is bordered by South Africa to the south and southeast, Namibia to the west, Zambia to the north, and Zimbabwe to the northeast. Botswana is divided into nine districts, which are subdivided into a total twenty-eight subdistricts. + GAZ:00001453 Bouvet Island [GAZ:00001453] A sub-antarctic volcanic island in the South Atlantic Ocean, south-southwest of the Cape of Good Hope (South Africa). It is a dependent area of Norway and is not subject to the Antarctic Treaty, as it is north of the latitude south of which claims are suspended. + GAZ:00002828 Brazil [GAZ:00002828] A country in South America. Bordered by the Atlantic Ocean and by Venezuela, Suriname, Guyana and the department of French Guiana to the north, Colombia to the northwest, Bolivia and Peru to the west, Argentina and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six states (estados) and one federal district (Distrito Federal). The states are subdivided into municipalities. For statistical purposes, the States are grouped into five main regions: North, Northeast, Central-West, Southeast and South. + GAZ:00003961 British Virgin Islands [GAZ:00003961] A British overseas territory, located in the Caribbean to the east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, the remaining islands constituting the US Virgin Islands. The British Virgin Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately fifteen of the islands are inhabited. + GAZ:00003901 Brunei [GAZ:00003901] A country located on the north coast of the island of Borneo, in Southeast Asia. Apart from its coastline with the South China Sea it is completely surrounded by the State of Sarawak, Malaysia, and in fact it is separated into two parts by Limbang, which is part of Sarawak. Brunei is divided into four districts (daerah), the districts are subdivided into thirty-eight mukims, which are then divided into kampong (villages). + GAZ:00002950 Bulgaria [GAZ:00002950] A country in Southeastern Europe, borders five other countries; Romania to the north (mostly along the Danube), Serbia and the Republic of Macedonia to the west, and Greece and Turkey to the south. The Black Sea defines the extent of the country to the east. Since 1999, it has consisted of twenty-eight provinces. The provinces subdivide into 264 municipalities. + GAZ:00000905 Burkina Faso [GAZ:00000905] A landlocked nation in West Africa. It is surrounded by six countries: Mali to the north, Niger to the east, Benin to the south east, Togo and Ghana to the south, and Cote d'Ivoire to the south west. Burkina Faso is divided into thirteen regions, forty-five provinces, and 301 departments (communes). + GAZ:00001090 Burundi [GAZ:00001090] A small country in the Great Lakes region of Africa. It is bordered by Rwanda on the north, Tanzania on the south and east, and the Democratic Republic of the Congo on the west. Although the country is landlocked, much of its western border is adjacent to Lake Tanganyika. Burundi is divided into 17 provinces, 117 communes, and 2,638 collines. + GAZ:00006888 Cambodia [GAZ:00006888] A country in Southeast Asia. The country borders Thailand to its west and northwest, Laos to its northeast, and Vietnam to its east and southeast. In the south it faces the Gulf of Thailand. + GAZ:00001093 Cameroon [GAZ:00001093] A country of central and western Africa. It borders Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces and 58 divisions or departments. The divisions are further sub-divided into sub-divisions (arrondissements) and districts. + GAZ:00002560 Canada [GAZ:00002560] A country occupying most of northern North America, extending from the Atlantic Ocean in the east to the Pacific Ocean in the west and northward into the Arctic Ocean. Canada is a federation composed of ten provinces and three territories; in turn, these may be grouped into regions. Western Canada consists of British Columbia and the three Prairie provinces (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec and Ontario. Atlantic Canada consists of the three Maritime provinces (New Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada together. Three territories (Yukon, Northwest Territories, and Nunavut) make up Northern Canada. + GAZ:00001227 Cape Verde [GAZ:00001227] A republic located on an archipelago in the Macaronesia ecoregion of the North Atlantic Ocean, off the western coast of Africa. Cape Verde is divided into 22 municipalities (concelhos), and subdivided into 32 parishes (freguesias). + GAZ:00003986 Cayman Islands [GAZ:00003986] A British overseas territory located in the western Caribbean Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. The Cayman Islands are divided into seven districts. + GAZ:00001089 Central African Republic [GAZ:00001089] A landlocked country in Central Africa. It borders Chad in the north, Sudan in the east, the Republic of the Congo and the Democratic Republic of the Congo in the south, and Cameroon in the west. The Central African Republic is divided into 14 administrative prefectures (prefectures), along with 2 economic prefectures (prefectures economiques) and one autonomous commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures). + GAZ:00000586 Chad [GAZ:00000586] A landlocked country in central Africa. It is bordered by Libya to the north, Sudan to the east, the Central African Republic to the south, Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided into 18 regions. The departments are divided into 200 sub-prefectures, which are in turn composed of 446 cantons. This is due to change. + GAZ:00002825 Chile [GAZ:00002825] A country in South America occupying a long and narrow coastal strip wedged between the Andes mountains and the Pacific Ocean. The Pacific forms the country's entire western border, with Peru to the north, Bolivia to the northeast, Argentina to the east, and the Drake Passage at the country's southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. Chile is divided into 15 regions. Every region is further divided into provinces. Finally each province is divided into communes. Each region is designated by a name and a Roman numeral, assigned from north to south. The only exception is the region housing the nation's capital, which is designated RM, that stands for Region Metropolitana (Metropolitan Region). Two new regions were created in 2006: Arica-Parinacota in the north, and Los Rios in the south. Both became operative in 2007-10. + GAZ:00002845 China [GAZ:00002845] A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions. + GAZ:00005915 Christmas Island [GAZ:00005915] An island in the Indian Ocean, 500 km south of Indonesia and about 2600 km northwest of Perth. The island is the flat summit of a submarine mountain. + GAZ:00005838 Clipperton Island [GAZ:00005838] A nine-square km coral atoll in the North Pacific Ocean, southwest of Mexico and west of Costa Rica. + GAZ:00009721 Cocos Islands [GAZ:00009721] Islands that located in the Indian Ocean, about halfway between Australia and Sri Lanka. A territory of Australia. There are two atolls and twenty-seven coral islands in the group. + GAZ:00002929 Colombia [GAZ:00002929] A country located in the northwestern region of South America. Colombia is bordered to the east by Venezuela and Brazil; to the south by Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean Sea; to the north-west by Panama; and to the west by the Pacific Ocean. Besides the countries in South America, the Republic of Colombia is recognized to share maritime borders with the Caribbean countries of Jamaica, Haiti, the Dominican Republic and the Central American countries of Honduras, Nicaragua, and Costa Rica. Colombia is divided into 32 departments and one capital district which is treated as a department. There are in total 10 districts assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia is also subdivided into some municipalities which form departments, each with a municipal seat capital city assigned. Colombia is also subdivided into corregimientos which form municipalities. + GAZ:00005820 Comoros [GAZ:00005820] An island nation in the Indian Ocean, located off the eastern coast of Africa on the northern end of the Mozambique Channel between northern Madagascar and northeastern Mozambique. + GAZ:00053798 Cook Islands [GAZ:00053798] A self-governing parliamentary democracy in free association with New Zealand. The fifteen small islands in this South Pacific Ocean country have a total land area of 240 km2, but the Cook Islands Exclusive Economic Zone (EEZ) covers 1.8 million km2 of ocean. + GAZ:00005917 Coral Sea Islands [GAZ:00005917] A Territory of Australia which includes a group of small and mostly uninhabited tropical islands and reefs in the Coral Sea, northeast of Queensland, Australia. The only inhabited island is Willis Island. The territory covers 780,000 km2, extending east and south from the outer edge of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, the Willis Group, and fifteen other reef/island groups. + GAZ:00002901 Costa Rica [GAZ:00002901] A republic in Central America, bordered by Nicaragua to the north, Panama to the east-southeast, the Pacific Ocean to the west and south, and the Caribbean Sea to the east. Costa Rica is composed of seven provinces, which in turn are divided into 81 cantons. + GAZ:00000906 Cote d'Ivoire [GAZ:00000906] A country in West Africa. It borders Liberia and Guinea to the west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). The regions are further divided into 58 departments. + GAZ:00002719 Croatia [GAZ:00002719] A country at the crossroads of the Mediterranean, Central Europe, and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to the east, Montenegro to the far southeast, and the Adriatic Sea to the south. Croatia is divided into 21 counties (zupanija) and the capital Zagreb's city district. + GAZ:00003762 Cuba [GAZ:00003762] A country that consists of the island of Cuba (the largest and second-most populous island of the Greater Antilles), Isla de la Juventud and several adjacent small islands. Fourteen provinces and one special municipality (the Isla de la Juventud) now compose Cuba. + GAZ:00012582 Curacao [GAZ:00012582] One of five island areas of the Netherlands Antilles. + GAZ:00004006 Cyprus [GAZ:00004006] The third largest island in the Mediterranean Sea (after Sicily and Sardinia), Cyprus is situated in the eastern Mediterranean, just south of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, it is often included in the Middle East (see also Western Asia and Near East). Turkey is 75 km north; other neighbouring countries include Syria and Lebanon to the east, Israel to the southeast, Egypt to the south, and Greece to the west-north-west. + GAZ:00002954 Czech Republic [GAZ:00002954] A landlocked country in Central Europe. It has borders with Poland to the north, Germany to the northwest and southwest, Austria to the south, and Slovakia to the east. The capital and largest city is Prague. The country is composed of the historic regions of Bohemia and Moravia, as well as parts of Silesia. Since 2000, the Czech Republic is divided into thirteen regions (kraje, singular kraj) and the capital city of Prague. The older seventy-six districts (okresy, singular okres) including three 'statutory cities' (without Prague, which had special status) were disbanded in 1999 in an administrative reform; they remain as territorial division and seats of various branches of state administration. Since 2003-01-01, the regions have been divided into around 203 Municipalities with Extended Competence (unofficially named "Little Districts" (Czech: 'male okresy') which took over most of the administration of the former District Authorities. Some of these are further divided into Municipalities with Commissioned Local Authority. However, the old districts still exist as territorial units and remain as seats of some of the offices. + GAZ:00001086 Democratic Republic of the Congo [GAZ:00001086] A country of central Africa. It borders the Central African Republic and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia and Angola on the south, the Republic of the Congo on the west, and is separated from Tanzania by Lake Tanganyika on the east. The country enjoys access to the ocean through a 40 km stretch of Atlantic coastline at Muanda and the roughly 9 km wide mouth of the Congo river which opens into the Gulf of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed into 25 Provinces from 2.2009. Each Province is divided into Zones. + GAZ:00005852 Denmark [GAZ:00005852] That part of the Kingdom of Denmark located in continental Europe. The mainland is bordered to the south by Germany; Denmark is located to the southwest of Sweden and the south of Norway. Denmark borders both the Baltic and the North Sea. The country consists of a large peninsula, Jutland (Jylland) and a large number of islands, most notably Zealand (Sjaelland), Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds of minor islands often referred to as the Danish Archipelago. + GAZ:00000582 Djibouti [GAZ:00000582] A country in eastern Africa. Djibouti is bordered by Eritrea in the north, Ethiopia in the west and south, and Somalia in the southeast. The remainder of the border is formed by the Red Sea and the Gulf of Aden. On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. Djibouti is divided into 5 regions and one city. It is further subdivided into 11 districts. + GAZ:00006890 Dominica [GAZ:00006890] An island nation in the Caribbean Sea. Dominica is divided into ten parishes. + GAZ:00003952 Dominican Republic [GAZ:00003952] A country in the West Indies that occupies the E two-thirds of the Hispaniola island. The Dominican Republic's shores are washed by the Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona Passage, a channel about 130 km wide, separates the country (and the Hispaniola) from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, the national capital, Santo Domingo, is contained within its own Distrito Nacional (National District). The provinces are divided into municipalities (municipios; singular municipio). + GAZ:00002912 Ecuador [GAZ:00002912] A country in South America, bordered by Colombia on the north, by Peru on the east and south, and by the Pacific Ocean to the west. The country also includes the Galapagos Islands (Archipelago de Colon) in the Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, divided into 199 cantons and subdivided into parishes (or parroquias). + GAZ:00003934 Egypt [GAZ:00003934] A country in North Africa that includes the Sinai Peninsula, a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, and the Gaza Strip and Israel to the east. The northern coast borders the Mediterranean Sea and the island of Cyprus; the eastern coast borders the Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, singular muhafazah). The governorates are further divided into regions (markazes). + GAZ:00002935 El Salvador [GAZ:00002935] A country in Central America, bordering the Pacific Ocean between Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), which, in turn, are subdivided into 267 municipalities (municipios). + GAZ:00001091 Equatorial Guinea [GAZ:00001091] A country in Central Africa. It is one of the smallest countries in continental Africa, and comprises two regions: Rio Muni, continental region including several offshore islands; and Insular Region containing Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando Po) that contains the capital, Malabo. Equatorial Guinea is divided into seven provinces which are divided into districts. + GAZ:00000581 Eritrea [GAZ:00000581] A country situated in northern East Africa. It is bordered by Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. The east and northeast of the country have an extensive coastline on the Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago and several of the Hanish Islands are part of Eritrea. Eritrea is divided into six regions (zobas) and subdivided into districts ("sub-zobas"). + GAZ:00002959 Estonia [GAZ:00002959] A country in Northern Europe. Estonia has land borders to the south with Latvia and to the east with Russia. It is separated from Finland in the north by the Gulf of Finland and from Sweden in the west by the Baltic Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). Estonian counties are divided into rural (vallad, singular vald) and urban (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) municipalities. The municipalities comprise populated places (asula or asustusuksus) - various settlements and territorial units that have no administrative function. A group of populated places form a rural municipality with local administration. Most towns constitute separate urban municipalities, while some have joined with surrounding rural municipalities. + GAZ:00001099 Eswatini [GAZ:00001099] A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla). + GAZ:00000567 Ethiopia [GAZ:00000567] A country situated in the Horn of Africa that has been landlocked since the independence of its northern neighbor Eritrea in 1993. Apart from Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to the south, Djibouti to the northeast, and Somalia to the east. Since 1996 Ethiopia has had a tiered government system consisting of a federal government overseeing ethnically-based regional states, zones, districts (woredas), and neighborhoods (kebele). It is divided into nine ethnically-based administrative states (kililoch, singular kilil) and subdivided into sixty-eight zones and two chartered cities (astedader akababiwoch, singular astedader akababi): Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and six special woredas. + GAZ:00005811 Europa Island [GAZ:00005811] A 28 km2 low-lying tropical island in the Mozambique Channel, about a third of the way from southern Madagascar to southern Mozambique. + GAZ:00001412 Falkland Islands (Islas Malvinas) [GAZ:00001412] An archipelago in the South Atlantic Ocean, located 483 km from the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), and 940 km north of Antarctica (Elephant Island). They consist of two main islands, East Falkland and West Falkland, together with 776 smaller islands. + GAZ:00059206 Faroe Islands [GAZ:00059206] An autonomous province of the Kingdom of Denmark since 1948 located in the Faroes. Administratively, the islands are divided into 34 municipalities (kommunur) within which 120 or so cities and villages lie. + GAZ:00006891 Fiji [GAZ:00006891] An island nation in the South Pacific Ocean east of Vanuatu, west of Tonga and south of Tuvalu. The country occupies an archipelago of about 322 islands, of which 106 are permanently inhabited, and 522 islets. The two major islands, Viti Levu and Vanua Levu, account for 87% of the population. + GAZ:00002937 Finland [GAZ:00002937] A Nordic country situated in the Fennoscandian region of Northern Europe. It has borders with Sweden to the west, Russia to the east, and Norway to the north, while Estonia lies to its south across the Gulf of Finland. The capital city is Helsinki. Finland is divided into six administrative provinces (laani, plural laanit). These are divided into 20 regions (maakunt), 77 subregions (seutukunta) and then into municipalities (kunta). + GAZ:00003940 France [GAZ:00003940] A part of the country of France that extends from the Mediterranean Sea to the English Channel and the North Sea, and from the Rhine to the Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas departments. + GAZ:00002516 French Guiana [GAZ:00002516] An overseas department (departement d'outre-mer) of France, located on the northern coast of South America. It is bordered by Suriname, to the E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. French Guiana is divided into 2 departmental arrondissements, 19 cantons and 22 communes. + GAZ:00002918 French Polynesia [GAZ:00002918] A French overseas collectivity in the southern Pacific Ocean. It is made up of several groups of Polynesian islands. French Polynesia has five administrative subdivisions (French: subdivisions administratives). + GAZ:00003753 French Southern and Antarctic Lands [GAZ:00003753] The French Southern and Antarctic Lands have formed a territoire d'outre-mer (an overseas territory) of France since 1955. The territory is divided into five districts. + GAZ:00001092 Gabon [GAZ:00001092] A country in west central Africa sharing borders with Equatorial Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital and largest city is Libreville. Gabon is divided into 9 provinces and further divided into 37 departments. + GAZ:00000907 Gambia [GAZ:00000907] A country in Western Africa. It is the smallest country on the African continental mainland and is bordered to the north, east, and south by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing through the centre of the country and discharging to the Atlantic Ocean is the Gambia River. The Gambia is divided into five divisions and one city (Banjul). The divisions are further subdivided into 37 districts. + GAZ:00009571 Gaza Strip [GAZ:00009571] A Palestinian enclave on the eastern coast of the Mediterranean Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel on the east and north along a 51 km (32 mi) border. Gaza and the West Bank are claimed by the de jure sovereign State of Palestine. + GAZ:00004942 Georgia [GAZ:00004942] A Eurasian country in the Caucasus located at the east coast of the Black Sea. In the north, Georgia has a 723 km common border with Russia, specifically with the Northern Caucasus federal district. The following Russian republics/subdivisions: from west to east: border Georgia: Krasnodar Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to the south-west. It is a transcontinental country, located at the juncture of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 autonomous republics (avtonomiuri respublika), and 1 city (k'alak'i). The regions are further subdivided into 69 districts (raioni). + GAZ:00002646 Germany [GAZ:00002646] A country in Central Europe. It is bordered to the north by the North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech Republic; to the south by Austria and Switzerland; and to the west by France, Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) and cities (kreisfreie Stadte). + GAZ:00000908 Ghana [GAZ:00000908] A country in West Africa. It borders Cote d'Ivoire to the west, Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the south. Ghana is a divided into 10 regions, subdivided into a total of 138 districts. + GAZ:00003987 Gibraltar [GAZ:00003987] A British overseas territory located near the southernmost tip of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory shares a border with Spain to the north. + GAZ:00005808 Glorioso Islands [GAZ:00005808] A group of islands and rocks totalling 5 km2, in the northern Mozambique channel, about 160 km northwest of Madagascar. + GAZ:00002945 Greece [GAZ:00002945] A country in southeastern Europe, situated on the southern end of the Balkan Peninsula. It has borders with Albania, the former Yugoslav Republic of Macedonia and Bulgaria to the north, and Turkey to the east. The Aegean Sea lies to the east and south of mainland Greece, while the Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin feature a vast number of islands. Greece consists of thirteen peripheries subdivided into a total of fifty-one prefectures (nomoi, singular nomos). There is also one autonomous area, Mount Athos, which borders the periphery of Central Macedonia. + GAZ:00001507 Greenland [GAZ:00001507] A self-governing Danish province located between the Arctic and Atlantic Oceans, east of the Canadian Arctic Archipelago. + GAZ:02000573 Grenada [GAZ:02000573] An island country in the West Indies in the Caribbean Sea at the southern end of the Grenadines island chain. Grenada consists of the island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, and several small islands which lie to the north of the main island and are a part of the Grenadines. It is located northwest of Trinidad and Tobago, northeast of Venezuela and southwest of Saint Vincent and the Grenadines. Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated population of 112,523 in July 2020. + GAZ:00067142 Guadeloupe [GAZ:00067142] An archipelago and overseas department and region of France in the Caribbean. It consists of six inhabited islands—Basse-Terre, Grande-Terre, Marie-Galante, La Désirade, and the two inhabited Îles des Saintes—as well as many uninhabited islands and outcroppings. It is south of Antigua and Barbuda and Montserrat, and north of Dominica. + GAZ:00003706 Guam [GAZ:00003706] An organized, unincorporated territory of the United States in the Micronesia subregion of the western Pacific Ocean. It is the westernmost point and territory of the United States (reckoned from the geographic center of the U.S.); in Oceania, it is the largest and southernmost of the Mariana Islands and the largest island in Micronesia. + GAZ:00002936 Guatemala [GAZ:00002936] A country in Central America bordered by Mexico to the northwest, the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the northeast, and Honduras and El Salvador to the southeast. Guatemala is divided into 22 departments (departamentos) and sub-divided into about 332 municipalities (municipios). + GAZ:00001550 Guernsey [GAZ:00001550] A British Crown Dependency in the English Channel off the coast of Normandy. + GAZ:00000909 Guinea [GAZ:00000909] A nation in West Africa, formerly known as French Guinea. Guinea's territory has a curved shape, with its base at the Atlantic Ocean, inland to the east, and turning south. The base borders Guinea-Bissau and Senegal to the north, and Mali to the north and north-east; the inland part borders Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone to the west of the southern tip. + GAZ:00000910 Guinea-Bissau [GAZ:00000910] A country in western Africa, and one of the smallest nations in continental Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west. Formerly the Portuguese colony of Portuguese Guinea, upon independence, the name of its capital, Bissau, was added to the country's name in order to prevent confusion between itself and the Republic of Guinea. + GAZ:00002522 Guyana [GAZ:00002522] A country in the N of South America. Guyana lies north of the equator, in the tropics, and is located on the Atlantic Ocean. Guyana is bordered to the east by Suriname, to the south and southwest by Brazil and to the west by Venezuela. Guyana is divided into 10 regions. The regions of Guyana are divided into 27 neighborhood councils. + GAZ:00003953 Haiti [GAZ:00003953] A country located in the Greater Antilles archipelago on the Caribbean island of Hispaniola, which it shares with the Dominican Republic. Haiti is divided into 10 departments. The departments are further divided into 41 arrondissements, and 133 communes which serve as second and third level administrative divisions. + GAZ:00009718 Heard Island and McDonald Islands [GAZ:00009718] An Australian external territory comprising a volcanic group of mostly barren Antarctic islands, about two-thirds of the way from Madagascar to Antarctica. + GAZ:00002894 Honduras [GAZ:00002894] A republic in Central America. The country is bordered to the west by Guatemala, to the southwest by El Salvador, to the southeast by Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. Honduras is divided into 18 departments. The capital city is Tegucigalpa Central District of the department of Francisco Morazan. + GAZ:00003203 Hong Kong [GAZ:00003203] A special administrative region of the People's Republic of China (PRC). The territory lies on the eastern side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east, west and south. Hong Kong was a crown colony of the United Kingdom from 1842 until the transfer of its sovereignty to the People's Republic of China in 1997. + GAZ:00007120 Howland Island [GAZ:00007120] An uninhabited coral island located just north of the equator in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. The island is almost half way between Hawaii and Australia and is an unincorporated, unorganized territory of the United States, and is often included as one of the Phoenix Islands. For statistical purposes, Howland is grouped as one of the United States Minor Outlying Islands. + GAZ:00002952 Hungary [GAZ:00002952] A landlocked country in the Carpathian Basin of Central Europe, bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: megye). In addition, the capital city (fovaros), Budapest, is independent of any county government. The counties are further subdivided into 173 subregions (kistersegek), and Budapest is comprised of its own subregion. Since 1996, the counties and City of Budapest have been grouped into 7 regions for statistical and development purposes. These seven regions constitute NUTS second-level units of Hungary. + GAZ:00000843 Iceland [GAZ:00000843] A country in northern Europe, comprising the island of Iceland and its outlying islands in the North Atlantic Ocean between the rest of Europe and Greenland. + GAZ:00002839 India [GAZ:00002839] A country in South Asia. Bounded by the Indian Ocean on the south, the Arabian Sea on the west, and the Bay of Bengal on the east, India has a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, and Bhutan to the north-east; and Bangladesh and Burma to the east. India is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian Ocean. India is a federal republic of twenty-eight states and seven Union Territories. Each state or union territory is divided into basic units of government and administration called districts. There are nearly 600 districts in India. The districts in turn are further divided into tehsils and eventually into villages. + GAZ:00003727 Indonesia [GAZ:00003727] An archipelagic state in Southeast Asia. The country shares land borders with Papua New Guinea, East Timor and Malaysia. Other neighboring countries include Singapore, the Philippines, Australia, and the Indian territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, five of which have special status. The provinces are subdivided into regencies (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), which are further subdivided into subdistricts (kecamatan), and again into village groupings (either desa or kelurahan). + GAZ:00004474 Iran [GAZ:00004474] A country in Central Eurasia. Iran is bounded by the Gulf of Oman and the Persian Gulf to the south and the Caspian Sea to its north. It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into 30 provinces (ostan). The provinces are divided into counties (shahrestan), and subdivided into districts (bakhsh) and sub-districts (dehestan). + GAZ:00004483 Iraq [GAZ:00004483] A country in the Middle East spanning most of the northwestern end of the Zagros mountain range, the eastern part of the Syrian Desert and the northern part of the Arabian Desert. It shares borders with Kuwait and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, Turkey to the north, and Iran to the east. It has a very narrow section of coastline at Umm Qasr on the Persian Gulf. There are two major flowing rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates (or provinces) (muhafazah). The governorates are divided into qadhas (or districts). + GAZ:00002943 Ireland [GAZ:00002943] A country in north-western Europe. The modern sovereign state occupies five-sixths of the island of Ireland, which was partitioned in 1921. It is bordered by Northern Ireland (part of the United Kingdom) to the north, by the Atlantic Ocean to the west and by the Irish Sea to the east. Administration follows the 34 "county-level" counties and cities of Ireland. Of these twenty-nine are counties, governed by county councils while the five cities of Dublin, Cork, Limerick, Galway and Waterford have city councils, (previously known as corporations), and are administered separately from the counties bearing those names. The City of Kilkenny is the only city in the republic which does not have a "city council"; it is still a borough but not a county borough and is administered as part of County Kilkenny. Ireland is split into eight regions for NUTS statistical purposes. These are not related to the four traditional provinces but are based on the administrative counties. + GAZ:00052477 Isle of Man [GAZ:00052477] A Crown dependency of the United Kingdom in the centre of the Irish Sea. It is not part of the United Kingdom, European Union or United Nations. + GAZ:00002476 Israel [GAZ:00002476] A country in Western Asia located on the eastern edge of the Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, which are partially administrated by the Palestinian National Authority, are also adjacent. The State of Israel is divided into six main administrative districts, known as mehozot (singular mahoz). Districts are further divided into fifteen sub-districts known as nafot (singular: nafa), which are themselves partitioned into fifty natural regions. + GAZ:00002650 Italy [GAZ:00002650] A country located on the Italian Peninsula in Southern Europe, and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. Italy shares its northern Alpine boundary with France, Switzerland, Austria and Slovenia. The independent states of San Marino and the Vatican City are enclaves within the Italian Peninsula, while Campione d'Italia is an Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, singular regione). Five of these regions have a special autonomous status that enables them to enact legislation on some of their local matters. It is further divided into 109 provinces (province) and 8,101 municipalities (comuni). + GAZ:00003781 Jamaica [GAZ:00003781] A nation of the Greater Antilles. Jamaica is divided into 14 parishes, which are grouped into three historic counties that have no administrative relevance. + GAZ:00005853 Jan Mayen [GAZ:00005853] A volcanic island that is part of the Kingdom of Norway, It has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and 1,000 km west of the Norwegian mainland. The island is mountainous, the highest summit being the Beerenberg volcano in the north. The isthmus is the location of the two largest lakes of the island, Sorlaguna (South Lagoon), and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng Lagoon). Jan Mayen was formed by the Jan Mayen hotspot. + GAZ:00002747 Japan [GAZ:00002747] An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south. + GAZ:00007118 Jarvis Island [GAZ:00007118] An uninhabited 4.5 km2 coral atoll located in the South Pacific Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated territory of the United States administered from Washington, DC by the United States Fish and Wildlife Service of the United States Department of the Interior as part of the National Wildlife Refuge system. Jarvis is one of the southern Line Islands and for statistical purposes is also grouped as one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount. + GAZ:00001551 Jersey [GAZ:00001551] A British Crown Dependency[6] off the coast of Normandy, France. As well as the island of Jersey itself, the bailiwick includes two groups of small islands that are no longer permanently inhabited, the Minquiers and Ecrehous, and the Pierres de Lecq. + GAZ:00007114 Johnston Atoll [GAZ:00007114] A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 nm) west of Hawaii. There are four islands located on the coral reef platform, two natural islands, Johnston Island and Sand Island, which have been expanded by coral dredging, as well as North Island (Akau) and East Island (Hikina), artificial islands formed from coral dredging. Johnston is an unincorporated territory of the United States, administered by the US Fish and Wildlife Service of the Department of the Interior as part of the United States Pacific Island Wildlife Refuges. Sits atop Johnston Seamount. + GAZ:00002473 Jordan [GAZ:00002473] A country in Southwest Asia, bordered by Syria to the north, Iraq to the north-east, Israel and the West Bank to the west, and Saudi Arabia to the east and south. It shares the coastlines of the Dead Sea, and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided into 12 provinces called governorates. The Governorates are subdivided into approximately fifty-two nahias. + GAZ:00005809 Juan de Nova Island [GAZ:00005809] A 4.4 km2 low, flat, tropical island in the narrowest part of the Mozambique Channel, about one-third of the way between Madagascar and Mozambique. + GAZ:00004999 Kazakhstan [GAZ:00004999] A country in Central Asia and Europe. It is bordered by Russia, Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders on a significant part of the Caspian Sea. Kazakhstan is divided into 14 provinces and two municipal districts. The provinces of Kazakhstan are divided into raions. + GAZ:00001101 Kenya [GAZ:00001101] A country in Eastern Africa. It is bordered by Ethiopia to the north, Somalia to the east, Tanzania to the south, Uganda to the west, and Sudan to the northwest, with the Indian Ocean running along the southeast border. Kenya comprises eight provinces each headed by a Provincial Commissioner (centrally appointed by the president). The provinces (mkoa singular mikoa plural in Swahili) are subdivided into districts (wilaya). There were 69 districts as of 1999 census. Districts are then subdivided into 497 divisions (taarafa). The divisions are then subdivided into 2,427 locations (kata) and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the status of a full administrative province. + GAZ:00005682 Kerguelen Archipelago [GAZ:00005682] A group of islands in the southern Indian Ocean. It is a territory of France. They are composed primarily of Tertiary flood basalts and a complex of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano at the southern end was active during the late Pleistocene. The Rallier du Baty Peninsula on the SW tip of the island contains two youthful subglacial eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active fumarole field is related to a series of Holocene trachytic lava flows and lahars that extend beyond the icecap. + GAZ:00007116 Kingman Reef [GAZ:00007116] A largely submerged, uninhabited tropical atoll located in the North Pacific Ocean, roughly half way between Hawaiian Islands and American Samoa. It is the northernmost of the Northern Line Islands and lies 65 km NNW of Palmyra Atoll, the next closest island, and has the status of an unincorporated territory of the United States, administered from Washington, DC by the US Navy. Sits atop Kingman Reef Seamount. + GAZ:00006894 Kiribati [GAZ:00006894] An island nation located in the central tropical Pacific Ocean. It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 km2 straddling the equator and bordering the International Date Line to the east. It is divided into three island groups which have no administrative function, including a group which unites the Line Islands and the Phoenix Islands (ministry at London, Christmas). Each inhabited island has its own council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two councils on Tabiteuea). + GAZ:00011337 Kosovo [GAZ:00011337] A country on the Balkan Peninsula. Kosovo borders Central Serbia to the north and east, Montenegro to the northwest, Albania to the west and the Republic of Macedonia to the south. Kosovo is divided into 7 districts (Rreth) and 30 municipalities. Serbia does not recognise the unilateral secession of Kosovo[8] and considers it a United Nations-governed entity within its sovereign territory, the Autonomous Province of Kosovo and Metohija. + GAZ:00005285 Kuwait [GAZ:00005285] A sovereign emirate on the coast of the Persian Gulf, enclosed by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided into six governorates (muhafazat, singular muhafadhah). + GAZ:00006893 Kyrgyzstan [GAZ:00006893] A country in Central Asia. Landlocked and mountainous, it is bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan to the southwest and China to the east. Kyrgyzstan is divided into seven provinces (oblast. The capital, Bishkek, and the second large city Osh are administratively the independent cities (shaar) with a status equal to a province. Each province comprises a number of districts (raions). + GAZ:00006889 Laos [GAZ:00006889] A landlocked country in southeast Asia, bordered by Burma (Myanmar) and China to the northwest, Vietnam to the east, Cambodia to the south, and Thailand to the west. Laos is divided into sixteen provinces (qwang) and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided into districts (muang). + GAZ:00002958 Latvia [GAZ:00002958] A country in Northern Europe. Latvia shares land borders with Estonia to the north and Lithuania to the south, and both Russia and Belarus to the east. It is separated from Sweden in the west by the Baltic Sea. The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). There are also seven cities (lielpilsetas) that have a separate status. Latvia is also historically, culturally and constitutionally divided in four or more distinct regions. + GAZ:00002478 Lebanon [GAZ:00002478] A small, mostly mountainous country in Western Asia, on the eastern shore of the Mediterranean Sea. It is bordered by Syria to the north and east, and Israel to the south. Lebanon is divided into six governorates (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, singular: qadaa). + GAZ:00001098 Lesotho [GAZ:00001098] A land-locked country, entirely surrounded by the Republic of South Africa. Lesotho is divided into ten districts; these are further subdivided into 80 constituencies, which consists of 129 local community councils. + GAZ:00000911 Liberia [GAZ:00000911] A country on the west coast of Africa, bordered by Sierra Leone, Guinea, Cote d'Ivoire, and the Atlantic Ocean. + GAZ:00000566 Libya [GAZ:00000566] A country in North Africa. Bordering the Mediterranean Sea to the north, Libya lies between Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west. There are thirty-four municipalities of Libya, known by the Arabic term sha'biyat (singular sha'biyah). These came recently (in the 1990s to replaced old Baladiyat systam. The Baladiyat system in turn was introduced to replace the system of muhafazah (governorates or provinces) that existed from the 1960s to the 1970s. + GAZ:00003858 Liechtenstein [GAZ:00003858] A tiny, doubly landlocked alpine country in Western Europe, bordered by Switzerland to its west and by Austria to its east. The principality of Liechtenstein is divided into 11 municipalities called Gemeinden (singular Gemeinde). The Gemeinden mostly consist only of a single town. Five of them fall within the electoral district Unterland (the lower county), and the remainder within Oberland (the upper county). + GAZ:00007144 Line Islands [GAZ:00007144] A group of eleven atolls and low coral islands in the central Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, while three are United States territories that are grouped with the United States Minor Outlying Islands. + GAZ:00002960 Lithuania [GAZ:00002960] A country located along the south-eastern shore of the Baltic Sea, sharing borders with Latvia to the north, Belarus to the southeast, Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. Lithuania has a three-tier administrative division: the country is divided into 10 counties (singular apskritis, plural, apskritys) that are further subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) which consist of over 500 elderates (singular seniunija, plural seniunijos). + GAZ:00002947 Luxembourg [GAZ:00002947] A small landlocked country in western Europe, bordered by Belgium, France, and Germany. Luxembourg is divided into 3 districts, which are further divided into 12 cantons and then 116 communes. Twelve of the communes have city status, of which the city of Luxembourg is the largest. + GAZ:00003202 Macau [GAZ:00003202] One of the two special administrative regions of the People's Republic of China, the other being Hong Kong. Macau lies on the western side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east and south. Macau is situated 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang (West River) on the west. It borders the Zhuhai Special Economic Zone in mainland China. + GAZ:00001108 Madagascar [GAZ:00001108] An island nation in the Indian Ocean off the southeastern coast of Africa. The main island, also called Madagascar, is the fourth largest island in the world, and is home to 5% of the world's plant and animal species, of which more than 80% are endemic to Madagascar. Most notable are the lemur infraorder of primates, the carnivorous fossa, three endemic bird families and six endemic baobab species. Madagascar is divided into six autonomous provinces (faritany mizakatena), and 22 regions. The regions are further subdivided into 116 districts, 1,548 communes, and 16,969 fokontany. + GAZ:00001105 Malawi [GAZ:00001105] A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. + GAZ:00003902 Malaysia [GAZ:00003902] A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. + GAZ:00006924 Maldives [GAZ:00006924] An archipelago which consists of approximately 1,196 coral islands grouped in a double chain of 27 atolls, spread over roughly 90,000 km2. + GAZ:00000584 Mali [GAZ:00000584] A landlocked country in northern Africa. It borders Algeria on the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the south, Guinea on the south-west, and Senegal and Mauritania on the west. Mali is divided into 8 regions (regions) and 1 district, and subdivided into 49 cercles, totalling 288 arrondissements. + GAZ:00004017 Malta [GAZ:00004017] A Southern European country and consists of an archipelago situated centrally in the Mediterranean. + GAZ:00007161 Marshall Islands [GAZ:00007161] An archipelago that consists of twenty-nine atolls and five isolated islands. The most important atolls and islands form two groups: the Ratak Chain and the Ralik Chain (meaning "sunrise" and "sunset" chains). Two-thirds of the nation's population lives on Majuro (which is also the capital) and Ebeye. The outer islands are sparsely populated. + GAZ:00067143 Martinique [GAZ:00067143] An island and an overseas department/region and single territorial collectivity of France. + GAZ:00000583 Mauritania [GAZ:00000583] A country in North-West Africa. It is bordered by the Atlantic Ocean on the west, by Senegal on the southwest, by Mali on the east and southeast, by Algeria on the northeast, and by Western Sahara on the northwest (most of which is occupied by Morocco). The capital and largest city is Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 regions (regions) and one capital district, which in turn are subdivided into 44 departments (departements). + GAZ:00003745 Mauritius [GAZ:00003745] An island nation off the coast of the African continent in the southwest Indian Ocean, about 900 km east of Madagascar. In addition to the island of Mauritius, the republic includes the islands of St. Brandon, Rodrigues and the Agalega Islands. + GAZ:00003943 Mayotte [GAZ:00003943] An overseas collectivity of France consisting of a main island, Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and several islets around these two. + GAZ:00002852 Mexico [GAZ:00002852] A federal constitutional republic in North America. It is bounded on the north by the United States; on the south and west by the North Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of Mexico. The United Mexican States comprise a federation of thirty-one states and a federal district, the capital Mexico City. + GAZ:00005862 Micronesia [GAZ:00005862] A subregion of Oceania, comprising hundreds of small islands in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua New Guinea and Melanesia to the west and southwest, and Polynesia to the east. + GAZ:00007112 Midway Islands [GAZ:00007112] A 6.2 km2 atoll located in the North Pacific Ocean (near the northwestern end of the Hawaiian archipelago). It is an unincorporated territory of the United States, designated an insular area under the authority of the US Department of the Interior. + GAZ:00003897 Moldova [GAZ:00003897] A landlocked country in Eastern Europe, located between Romania to the west and Ukraine to the north, east and south. Moldova is divided into thirty-two districts (raioane, singular raion); three municipalities (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). The cities of Comrat and Tiraspol also have municipality status, however not as first-tier subdivisions of Moldova, but as parts of the regions of Gagauzia and Transnistria, respectively. The status of Transnistria is however under dispute. Although it is de jure part of Moldova and is recognized as such by the international community, Transnistria is not de facto under the control of the central government of Moldova. It is administered by an unrecognized breakaway authority under the name Pridnestrovian Moldovan Republic. + GAZ:00003857 Monaco [GAZ:00003857] A small country that is completely bordered by France to the north, west, and south; to the east it is bordered by the Mediterranean Sea. It consists of a single municipality (commune) currently divided into 4 quartiers and 10 wards. + GAZ:00008744 Mongolia [GAZ:00008744] A country in East-Central Asia. The landlocked country borders Russia to the north and China to the south. The capital and largest city is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are in turn divided into 315 sums (districts). The capital Ulan Bator is administrated separately as a khot (municipality) with provincial status. + GAZ:00006898 Montenegro [GAZ:00006898] A country located in Southeastern Europe. It has a coast on the Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina to the northwest, Serbia and its partially recognized breakaway southern province of Kosovo to the northeast and Albania to the southeast. Its capital and largest city is Podgorica. Montenegro is divided into twenty-one municipalities (opstina), and two urban municipalities, subdivisions of Podgorica municipality. + GAZ:00003988 Montserrat [GAZ:00003988] A British overseas territory located in the Leeward Islands. Montserrat is divided into three parishes. + GAZ:00000565 Morocco [GAZ:00000565] A country in North Africa. It has a coast on the Atlantic Ocean that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco has international borders with Algeria to the east, Spain to the north (a water border through the Strait and land borders with two small Spanish autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco is divided into 16 regions, and subdivided into 62 prefectures and provinces. Because of the conflict over Western Sahara, the status of both regions of "Saguia el-Hamra" and "Rio de Oro" is disputed. + GAZ:00001100 Mozambique [GAZ:00001100] A country in southeastern Africa bordered by the Indian Ocean to the east, Tanzania to the north, Malawi and Zambia to the northwest, Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique is divided into ten provinces (provincias) and one capital city (cidade capital) with provincial status. The provinces are subdivided into 129 districts (distritos). Districts are further divided in "Postos Administrativos" (Administrative Posts) and these in Localidades (Localities) the lowest geographical level of central state administration. + GAZ:00006899 Myanmar [GAZ:00006899] A country in SE Asia that is bordered by China on the north, Laos on the east, Thailand on the southeast, Bangladesh on the west, and India on the northwest, with the Bay of Bengal to the southwest. Myanmar is divided into seven states and seven divisions. The administrative divisions are further subdivided into districts, which are further subdivided into townships, wards, and villages. + GAZ:00001096 Namibia [GAZ:00001096] A country in southern Africa on the Atlantic coast. It shares borders with Angola and Zambia to the north, Botswana to the east, and South Africa to the south. Namibia is divided into 13 regions and subdivided into 102 constituencies. + GAZ:00006900 Nauru [GAZ:00006900] An island nation in the Micronesian South Pacific. The nearest neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. Nauru is divided into fourteen administrative districts which are grouped into eight electoral constituencies. + GAZ:00007119 Navassa Island [GAZ:00007119] A small, uninhabited island in the Caribbean Sea, and is an unorganized unincorporated territory of the United States, which administers it through the US Fish and Wildlife Service. The island is also claimed by Haiti. + GAZ:00004399 Nepal [GAZ:00004399] A landlocked nation in South Asia. It is bordered by the Tibet Autonomous Region of the People's Republic of China to the northeast and India to the south and west; it is separated from Bhutan by the Indian State of Sikkim and from Bangladesh by a small strip of the Indian State of West Bengal, known as the "Chicken's Neck". The Himalaya mountain range runs across Nepal's north and western parts, and eight of the world's ten highest mountains, including the highest, Mount Everest are situated within its territory. Nepal is divided into 14 zones and 75 districts, grouped into 5 development regions. + GAZ:00002946 Netherlands [GAZ:00002946] The European part of the Kingdom of the Netherlands. It is bordered by the North Sea to the north and west, Belgium to the south, and Germany to the east. The Netherlands is divided into twelve administrative regions, called provinces. All provinces of the Netherlands are divided into municipalities (gemeenten), together 443 (2007). + GAZ:00005206 New Caledonia [GAZ:00005206] A "sui generis collectivity" (in practice an overseas territory) of France, made up of a main island (Grande Terre), the Loyalty Islands, and several smaller islands. It is located in the region of Melanesia in the southwest Pacific. Administratively, the archipelago is divided into three provinces, and then into 33 communes. + GAZ:00000469 New Zealand [GAZ:00000469] A nation in the south-western Pacific Ocean comprising two large islands (the North Island and the South Island) and numerous smaller islands, most notably Stewart Island/Rakiura and the Chatham Islands. + GAZ:00002978 Nicaragua [GAZ:00002978] A republic in Central America. It is also the least densely populated with a demographic similar in size to its smaller neighbors. The country is bordered by Honduras to the north and by Costa Rica to the south. The Pacific Ocean lies to the west of the country, while the Caribbean Sea lies to the east. For administrative purposes it is divided into 15 departments (departamentos) and two self-governing regions (autonomous communities) based on the Spanish model. The departments are then subdivided into 153 municipios (municipalities). The two autonomous regions are Region Autonoma del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 they formed the single department of Zelaya. + GAZ:00000585 Niger [GAZ:00000585] A landlocked country in Western Africa, named after the Niger River. It borders Nigeria and Benin to the south, Burkina Faso and Mali to the west, Algeria and Libya to the north and Chad to the east. The capital city is Niamey. Niger is divided into 7 departments and one capital district. The departments are subdivided into 36 arrondissements and further subdivided into 129 communes. + GAZ:00000912 Nigeria [GAZ:00000912] A federal constitutional republic comprising thirty-six states and one Federal Capital Territory. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in the north. Its coast lies on the Gulf of Guinea, part of the Atlantic Ocean, in the south. The capital city is Abuja. Nigeria is divided into thirty-six states and one Federal Capital Territory, which are further sub-divided into 774 Local Government Areas (LGAs). + GAZ:00006902 Niue [GAZ:00006902] An island nation located in the South Pacific Ocean. Although self-governing, Niue is in free association with New Zealand, meaning that the Sovereign in Right of New Zealand is also Niue's head of state. + GAZ:00005908 Norfolk Island [GAZ:00005908] A Territory of Australia that includes Norfolk Island and neighboring islands. + GAZ:00002801 North Korea [GAZ:00002801] A state in East Asia in the northern half of the Korean Peninsula, with its capital in the city of Pyongyang. To the south and separated by the Korean Demilitarized Zone is South Korea, with which it formed one nation until division following World War II. At its northern Amnok River border are China and, separated by the Tumen River in the extreme north-east, Russia. + GAZ:00006895 North Macedonia [GAZ:00006895] A landlocked country on the Balkan peninsula in southeastern Europe. It is bordered by Serbia and Kosovo to the north, Albania to the west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), 10 of which comprise Greater Skopje. This is reduced from the previous 123 municipalities established in 1996-09. Prior to this, local government was organised into 34 administrative districts. + GAZ:00002284 North Sea [GAZ:00002284] A sea situated between the eastern coasts of the British Isles and the western coast of Europe. + GAZ:00003958 Northern Mariana Islands [GAZ:00003958] A group of 15 islands about three-quarters of the way from Hawaii to the Philippines. + GAZ:00002699 Norway [GAZ:00002699] A country and constitutional monarchy in Northern Europe that occupies the western portion of the Scandinavian Peninsula. It is bordered by Sweden, Finland, and Russia. The Kingdom of Norway also includes the Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty over Svalbard is based upon the Svalbard Treaty, but that treaty does not apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter I Island and Queen Maud Land in Antarctica are external dependencies, but those three entities do not form part of the kingdom. + GAZ:00005283 Oman [GAZ:00005283] A country in southwest Asia, on the southeast coast of the Arabian Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia on the west, and Yemen on the southwest. The coast is formed by the Arabian Sea on the south and east, and the Gulf of Oman on the northeast. The country also contains Madha, an exclave enclosed by the United Arab Emirates, and Musandam, an exclave also separated by Emirati territory. Oman is divided into four governorates (muhafazah) and five regions (mintaqat). The regions are subdivided into provinces (wilayat). + GAZ:00005246 Pakistan [GAZ:00005246] A country in Middle East which lies on the Iranian Plateau and some parts of South Asia. It is located in the region where South Asia converges with Central Asia and the Middle East. It has a 1,046 km coastline along the Arabian Sea in the south, and is bordered by Afghanistan and Iran in the west, India in the east and China in the far northeast. Pakistan is subdivided into four provinces and two territories. In addition, the portion of Kashmir that is administered by the Pakistani government is divided into two separate administrative units. The provinces are divided into a total of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly equivalent to counties). Tehsils may contain villages or municipalities. There are over five thousand local governments in Pakistan. + GAZ:00006905 Palau [GAZ:00006905] A nation that consists of eight principal islands and more than 250 smaller ones lying roughly 500 miles southeast of the Philippines. + GAZ:00002892 Panama [GAZ:00002892] The southernmost country of Central America. Situated on an isthmus, some categorize it as a transcontinental nation connecting the north and south part of America. It borders Costa Rica to the north-west, Colombia to the south-east, the Caribbean Sea to the north and the Pacific Ocean to the south. Panama's major divisions are nine provinces and five indigenous territories (comarcas indigenas). The provincial borders have not changed since they were determined at independence in 1903. The provinces are divided into districts, which in turn are subdivided into sections called corregimientos. Configurations of the corregimientos are changed periodically to accommodate population changes as revealed in the census reports. + GAZ:00003922 Papua New Guinea [GAZ:00003922] A country in Oceania that comprises the eastern half of the island of New Guinea and its offshore islands in Melanesia (a region of the southwestern Pacific Ocean north of Australia). + GAZ:00010832 Paracel Islands [GAZ:00010832] A group of small islands and reefs in the South China Sea, about one-third of the way from Vietnam to the Philippines. + GAZ:00002933 Paraguay [GAZ:00002933] A landlocked country in South America. It lies on both banks of the Paraguay River, bordering Argentina to the south and southwest, Brazil to the east and northeast, and Bolivia to the northwest, and is located in the very heart of South America. Paraguay consists of seventeen departments and one capital district (distrito capital). Each department is divided into districts. + GAZ:00002932 Peru [GAZ:00002932] A country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean. Peru is divided into 25 regions and the province of Lima. These regions are subdivided into provinces, which are composed of districts (provincias and distritos). There are 195 provinces and 1833 districts in Peru. The Lima Province, located in the central coast of the country, is unique in that it doesn't belong to any of the twenty-five regions. The city of Lima, which is the nation's capital, is located in this province. Callao is its own region, even though it only contains one province, the Constitutional Province of Callao. + GAZ:00004525 Philippines [GAZ:00004525] An archipelagic nation located in Southeast Asia. The Philippine archipelago comprises 7,107 islands in the western Pacific Ocean, bordering countries such as Indonesia, Malaysia, Palau and the Republic of China, although it is the only Southeast Asian country to share no land borders with its neighbors. The Philippines is divided into three island groups: Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, 136 cities, 1,494 municipalities and 41,995 barangays. + GAZ:00005867 Pitcairn Islands [GAZ:00005867] A group of four islands in the southern Pacific Ocean. The Pitcairn Islands form the southeasternmost extension of the geological archipelago of the Tuamotus of French Polynesia. + GAZ:00002939 Poland [GAZ:00002939] A country in Central Europe. Poland is bordered by Germany to the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a Russian exclave, to the north. The administrative division of Poland since 1999 has been based on three levels of subdivision. The territory of Poland is divided into voivodeships (provinces); these are further divided into powiats (counties), and these in turn are divided into gminas (communes or municipalities). Major cities normally have the status of both gmina and powiat. Poland currently has 16 voivodeships, 379 powiats (including 65 cities with powiat status), and 2,478 gminas. + GAZ:00004126 Portugal [GAZ:00004126] That part of the Portugese Republic that occupies the W part of the Iberian Peninsula, and immediately adjacent islands. + GAZ:00006935 Puerto Rico [GAZ:00006935] A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States). + GAZ:00005286 Qatar [GAZ:00005286] An Arab emirate in Southwest Asia, occupying the small Qatar Peninsula on the northeasterly coast of the larger Arabian Peninsula. It is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds the state. Qatar is divided into ten municipalities (Arabic: baladiyah), which are further divided into zones (districts). + GAZ:00001088 Republic of the Congo [GAZ:00001088] A country in Central Africa. It is bordered by Gabon, Cameroon, the Central African Republic, the Democratic Republic of the Congo, the Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic of the Congo is divided into 10 regions (regions) and one commune, the capital Brazzaville. The regions are subdivided into forty-six districts. + GAZ:00003945 Reunion [GAZ:00003945] An island, located in the Indian Ocean east of Madagascar, about 200 km south west of Mauritius, the nearest island. + GAZ:00002951 Romania [GAZ:00002951] A country in Southeastern Europe. It shares a border with Hungary and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, and Bulgaria to the south. Romania has a stretch of sea coast along the Black Sea. It is located roughly in the lower basin of the Danube and almost all of the Danube Delta is located within its territory. Romania is divided into forty-one counties (judete), as well as the municipality of Bucharest (Bucuresti) - which is its own administrative unit. The country is further subdivided into 319 cities and 2686 communes (rural localities). + GAZ:00023304 Ross Sea [GAZ:00023304] A large embayment of the Southern Ocean, extending deeply into Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck on the east, at 158degW. + GAZ:00002721 Russia [GAZ:00002721] A transcontinental country extending over much of northern Eurasia. Russia shares land borders with the following countries (counter-clockwise from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais (territories), 4 autonomous okrugs (autonomous districts), one autonomous oblast, and two federal cities. The federal subjects are grouped into seven federal districts. These subjects are divided into districts (raions), cities/towns and urban-type settlements, and, at level 4, selsovets (rural councils), towns and urban-type settlements under the jurisdiction of the district and city districts. + GAZ:00001087 Rwanda [GAZ:00001087] A small landlocked country in the Great Lakes region of east-central Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo and Tanzania. Rwanda is divided into five provinces (intara) and subdivided into thirty districts (akarere). The districts are divided into sectors (imirenge). + GAZ:00000849 Saint Helena [GAZ:00000849] An island of volcanic origin and a British overseas territory in the South Atlantic Ocean. + GAZ:00006906 Saint Kitts and Nevis [GAZ:00006906] A federal two-island nation in the West Indies. Located in the Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast are Antigua and Barbuda, and to the southeast is the small uninhabited island of Redonda, and the island of Montserrat. The federation of Saint Kitts and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts and five on Nevis. + GAZ:00006909 Saint Lucia [GAZ:00006909] An island nation in the eastern Caribbean Sea on the boundary with the Atlantic Ocean. + GAZ:00003942 Saint Pierre and Miquelon [GAZ:00003942] An Overseas Collectivity of France located in a group of small islands in the North Atlantic Ocean, the main ones being Saint Pierre and Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and Miquelon became an overseas department in 1976, but its status changed to that of an Overseas collectivity in 1985. + GAZ:00005841 Saint Martin [GAZ:00005841] An overseas collectivity of France that came into being on 2007-02-22, encompassing the northern parts of the island of Saint Martin and neighboring islets. The southern part of the island, Sint Maarten, is part of the Netherlands Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe. + GAZ:02000565 Saint Vincent and the Grenadines [GAZ:02000565] An island nation in the Lesser Antilles chain of the Caribbean Sea. + GAZ:00006910 Samoa [GAZ:00006910] A country governing the western part of the Samoan Islands archipelago in the South Pacific Ocean. Samoa is made up of eleven itumalo (political districts). + GAZ:00003102 San Marino [GAZ:00003102] A country in the Apennine Mountains. It is a landlocked enclave, completely surrounded by Italy. San Marino is an enclave in Italy, on the border between the regioni of Emilia Romagna and Marche. Its topography is dominated by the Apennines mountain range. San Marino is divided into nine municipalities, known locally as Castelli (singular castello). + GAZ:00006927 Sao Tome and Principe [GAZ:00006927] An island nation in the Gulf of Guinea, off the western equatorial coast of Africa. It consists of two islands: Sao Tome and Principe, located about 140 km apart and about 250 and 225 km respectively, off of the northwestern coast of Gabon. Both islands are part of an extinct volcanic mountain range. Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The provinces are further divided into seven districts, six on Sao Tome and one on Principe (with Principe having self-government since 1995-04-29). + GAZ:00005279 Saudi Arabia [GAZ:00005279] A country on the Arabian Peninsula. It is bordered by Jordan on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, and the United Arab Emirates on the east, Oman on the southeast, and Yemen on the south. The Persian Gulf lies to the northeast and the Red Sea to its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; singular mintaqah). Each is then divided into Governorates. + GAZ:00000913 Senegal [GAZ:00000913] A country south of the Senegal River in western Africa. Senegal is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies almost entirely within Senegal, surrounded on the north, east and south; from its western coast Gambia's territory follows the Gambia River more than 300 km inland. Dakar is the capital city of Senegal, located on the Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided into 11 regions and further subdivided into 34 Departements, 103 Arrondissements (neither of which have administrative function) and by Collectivites Locales. + GAZ:00002957 Serbia [GAZ:00002957] A landlocked country in Central and Southeastern Europe, covering the southern part of the Pannonian Plain and the central part of the Balkan Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria to the east; Republic of Macedonia, Montenegro to the south; Croatia and Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided into 29 districts plus the City of Belgrade. The districts and the city of Belgrade are further divided into municipalities. Serbia has two autonomous provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), and Vojvodina in the north (7 districts, 46 municipalities). + GAZ:00006922 Seychelles [GAZ:00006922] An archipelagic island country in the Indian Ocean at the eastern edge of the Somali Sea. It consists of 115 islands. + GAZ:00000914 Sierra Leone [GAZ:00000914] A country in West Africa. It is bordered by Guinea in the north and east, Liberia in the southeast, and the Atlantic Ocean in the southwest and west. The Republic of Sierra Leone is composed of 3 provinces and one area called the Western Area; the provinces are further divided into 12 districts. The Western Area is also divided into 2 districts. + GAZ:00003923 Singapore [GAZ:00003923] An island nation located at the southern tip of the Malay Peninsula. It lies 137 km north of the Equator, south of the Malaysian State of Johor and north of Indonesia's Riau Islands. Singapore consists of 63 islands, including mainland Singapore. There are two man-made connections to Johor, Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in the west. Since 2001-11-24, Singapore has had an administrative subdivision into 5 districts. It is also divided into five Regions, urban planning subdivisions with no administrative role. + GAZ:00012579 Sint Maarten [GAZ:00012579] One of five island areas (Eilandgebieden) of the Netherlands Antilles, encompassing the southern half of the island of Saint Martin/Sint Maarten. + GAZ:00002956 Slovakia [GAZ:00002956] A landlocked country in Central Europe. The Slovak Republic borders the Czech Republic and Austria to the west, Poland to the north, Ukraine to the east and Hungary to the south. The largest city is its capital, Bratislava. Slovakia is subdivided into 8 kraje (singular - kraj, usually translated as regions. The kraje are subdivided into many okresy (singular okres, usually translated as districts). Slovakia currently has 79 districts. + GAZ:00002955 Slovenia [GAZ:00002955] A country in southern Central Europe bordering Italy to the west, the Adriatic Sea to the southwest, Croatia to the south and east, Hungary to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. As of 2005-05 Slovenia is divided into 12 statistical regions for legal and statistical purposes. Slovenia is divided into 210 local municipalities, eleven of which have urban status. + GAZ:00005275 Solomon Islands [GAZ:00005275] A nation in Melanesia, east of Papua New Guinea, consisting of nearly one thousand islands. Together they cover a land mass of 28,400 km2. The capital is Honiara, located on the island of Guadalcanal. + GAZ:00001104 Somalia [GAZ:00001104] A country located in the Horn of Africa. It is bordered by Djibouti to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on its north, the Indian Ocean at its east, and Ethiopia to the west. Prior to the civil war, Somalia was divided into eighteen regions (gobollada, singular gobol), which were in turn subdivided into districts. On a de facto basis, northern Somalia is now divided up among the quasi-independent states of Puntland, Somaliland, Galmudug and Maakhir. + GAZ:00001094 South Africa [GAZ:00001094] A country located at the southern tip of Africa. It borders the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, Swaziland, and Lesotho, an independent enclave surrounded by South African territory. It is divided into nine provinces which are further subdivided into 52 districts: 6 metropolitan and 46 district municipalities. The 46 district municipalities are further subdivided into 231 local municipalities. The district municipalities also contain 20 district management areas (mostly game parks) that are directly governed by the district municipalities. The six metropolitan municipalities perform the functions of both district and local municipalities. + GAZ:00003990 South Georgia and the South Sandwich Islands [GAZ:00003990] A British overseas territory in the southern Atlantic Ocean. It iconsists of South Georgia and the Sandwich Islands, some 640 km to the SE. + GAZ:00002802 South Korea [GAZ:00002802] A republic in East Asia, occupying the southern half of the Korean Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 special city (teukbyeolsi). These are further subdivided into a variety of smaller entities, including cities (si), counties (gun), districts (gu), towns (eup), townships (myeon), neighborhoods (dong) and villages (ri). + GAZ:00233439 South Sudan [GAZ:00233439] A state located in Africa with Juba as its capital city. It's bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic of the Congo to the south, and the Central African Republic to the west and Sudan to the North. Southern Sudan includes the vast swamp region of the Sudd formed by the White Nile, locally called the Bahr el Jebel. + GAZ:00000591 Spain [GAZ:00000591] That part of the Kingdom of Spain that occupies the Iberian Peninsula plus the Balaeric Islands. The Spanish mainland is bordered to the south and east almost entirely by the Mediterranean Sea (except for a small land boundary with Gibraltar); to the north by France, Andorra, and the Bay of Biscay; and to the west by the Atlantic Ocean and Portugal. + GAZ:00010831 Spratly Islands [GAZ:00010831] A group of >100 islands located in the Southeastern Asian group of reefs and islands in the South China Sea, about two-thirds of the way from southern Vietnam to the southern Philippines. + GAZ:00003924 Sri Lanka [GAZ:00003924] An island nation in South Asia, located about 31 km off the southern coast of India. Sri Lanka is divided into 9 provinces and 25 districts. Districts are divided into Divisional Secretariats. + GAZ:00002475 State of Palestine [GAZ:00002475] The territory under the administration of the Palestine National Authority, as established by the Oslo Accords. The PNA divides the Palestinian territories into 16 governorates. + GAZ:00000560 Sudan [GAZ:00000560] A country in North Africa. It is bordered by Egypt to the north, the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and Uganda to the southeast, Democratic Republic of the Congo and the Central African Republic to the southwest, Chad to the west and Libya to the northwest. Sudan is divided into twenty-six states (wilayat, singular wilayah) which in turn are subdivided into 133 districts. + GAZ:00002525 Suriname [GAZ:00002525] A country in northern South America. It is situated between French Guiana to the east and Guyana to the west. The southern border is shared with Brazil and the northern border is the Atlantic coast. The southernmost border with French Guiana is disputed along the Marowijne river. Suriname is divided into 10 districts, each of which is divided into Ressorten. + GAZ:00005396 Svalbard [GAZ:00005396] An archipelago of continental islands lying in the Arctic Ocean north of mainland Europe, about midway between Norway and the North Pole. + GAZ:00002729 Sweden [GAZ:00002729] A Nordic country on the Scandinavian Peninsula in Northern Europe. It has borders with Norway (west and north) and Finland (northeast). Sweden is a unitary state, currently divided into twenty-one counties (lan). Each county further divides into a number of municipalities or kommuner, with a total of 290 municipalities in 2004. + GAZ:00002941 Switzerland [GAZ:00002941] A federal republic in Europe. Switzerland is bordered by Germany, France, Italy, Austria and Liechtenstein. The Swiss Confederation consists of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within Switzerland there are two enclaves: Busingen belongs to Germany, Campione d'Italia belongs to Italy. + GAZ:00002474 Syria [GAZ:00002474] A country in Southwest Asia, bordering Lebanon, the Mediterranean Sea and the island of Cyprus to the west, Israel to the southwest, Jordan to the south, Iraq to the east, and Turkey to the north. Syria has fourteen governorates, or muhafazat (singular: muhafazah). The governorates are divided into sixty districts, or manatiq (singular: mintaqah), which are further divided into sub-districts, or nawahi (singular: nahia). + GAZ:00005341 Taiwan [GAZ:00005341] A state in East Asia with de facto rule of the island of Tawain and adjacent territory. The Republic of China currently administers two historical provinces of China (one completely and a small part of another one) and centrally administers two direct-controlled municipalities. + GAZ:00006912 Tajikistan [GAZ:00006912] A mountainous landlocked country in Central Asia. Afghanistan borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and People's Republic of China to the east. Tajikistan consists of 4 administrative divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly known as Karotegin Province). Each region is divided into several districts (nohiya or raion). + GAZ:00001103 Tanzania [GAZ:00001103] A country in East Africa bordered by Kenya and Uganda on the north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, and Zambia, Malawi and Mozambique on the south. To the east it borders the Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight districts (wilaya), each with at least one council, have been created to further increase local authority; the councils are also known as local government authorities. Currently there are 114 councils operating in 99 districts; 22 are urban and 92 are rural. The 22 urban units are further classified as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) or town councils (the remaining eleven communities). + GAZ:00003744 Thailand [GAZ:00003744] A country in Southeast Asia. To its east lie Laos and Cambodia; to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided into 75 provinces (changwat), which are gathered into 5 groups of provinces by location. There are also 2 special governed districts: the capital Bangkok (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial level and thus often counted as a 76th province. + GAZ:00006913 Timor-Leste [GAZ:00006913] A country in Southeast Asia. It comprises the eastern half of the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, an exclave on the northwestern side of the island, within Indonesian West Timor. The small country of 15,410 km2 is located about 640 km northwest of Darwin, Australia. East Timor is divided into thirteen administrative districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, villages and hamlets. + GAZ:00000915 Togo [GAZ:00000915] A country in West Africa bordering Ghana in the west, Benin in the east and Burkina Faso in the north. In the south, it has a short Gulf of Guinea coast, on which the capital Lome is located. + GAZ:00260188 Tokelau [GAZ:00260188] A dependent territory of New Zealand in the southern Pacific Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and Fakaofo. They have a combined land area of 10 km2 (4 sq mi). + GAZ:00006916 Tonga [GAZ:00006916] A Polynesian country, and also an archipelago comprising 169 islands, of which 36 are inhabited. The archipelago's total surface area is about 750 square kilometres (290 sq mi) scattered over 700,000 square kilometres (270,000 sq mi) of the southern Pacific Ocean. + GAZ:00003767 Trinidad and Tobago [GAZ:00003767] An archipelagic state in the southern Caribbean, lying northeast of the South American nation of Venezuela and south of Grenada in the Lesser Antilles. It also shares maritime boundaries with Barbados to the northeast and Guyana to the southeast. The country covers an area of 5,128 km2and consists of two main islands, Trinidad and Tobago, and 21 smaller islands. + GAZ:00005812 Tromelin Island [GAZ:00005812] A low, flat 0.8 km2 island in the Indian Ocean, about 350 km east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 m long and 700 m wide, surrounded by coral reefs. The island is 7 m high at its highest point. + GAZ:00000562 Tunisia [GAZ:00000562] A country situated on the Mediterranean coast of North Africa. It is bordered by Algeria to the west and Libya to the southeast. Tunisia is subdivided into 24 governorates, divided into 262 "delegations" or "districts" (mutamadiyat), and further subdivided into municipalities (shaykhats). + GAZ:00000558 Turkey [GAZ:00000558] A Eurasian country that stretches across the Anatolian peninsula in western Asia and Thrace (Rumelia) in the Balkan region of southeastern Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago are to the west; and the Black Sea is to the north. Separating Anatolia and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus and the Dardanelles), which are commonly reckoned to delineate the border between Asia and Europe, thereby making Turkey transcontinental. The territory of Turkey is subdivided into 81 provinces for administrative purposes. The provinces are organized into 7 regions for census purposes; however, they do not represent an administrative structure. Each province is divided into districts, for a total of 923 districts. + GAZ:00005018 Turkmenistan [GAZ:00005018] A country in Central Asia. It is bordered by Afghanistan to the southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan to the northwest, and the Caspian Sea to the west. It was a constituent republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan is divided into five provinces or welayatlar (singular - welayat) and one independent city. + GAZ:00003955 Turks and Caicos Islands [GAZ:00003955] A British Overseas Territory consisting of two groups of tropical islands in the West Indies. The Turks and Caicos Islands are divided into six administrative districts (two in the Turks Islands and four in the Caicos Islands. + GAZ:00009715 Tuvalu [GAZ:00009715] A Polynesian island nation located in the Pacific Ocean midway between Hawaii and Australia. + GAZ:00002459 United States of America [GAZ:00002459] A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into "census areas"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a "charter township", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county. + GAZ:00001102 Uganda [GAZ:00001102] A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties. + GAZ:00002724 Ukraine [GAZ:00002724] A country in Eastern Europe. It borders Russia to the east, Belarus to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine is subdivided into twenty-four oblasts (provinces) and one autonomous republic (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, and Sevastopol, both have a special legal status. The 24 oblasts and Crimea are subdivided into 490 raions (districts), or second-level administrative units. + GAZ:00005282 United Arab Emirates [GAZ:00005282] A Middle Eastern federation of seven states situated in the southeast of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain. + GAZ:00002637 United Kingdom [GAZ:00002637] A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel. + GAZ:00002930 Uruguay [GAZ:00002930] A country located in the southeastern part of South America. It is bordered by Brazil to the north, by Argentina across the bank of both the Uruguay River to the west and the estuary of Rio de la Plata to the southwest, and the South Atlantic Ocean to the southeast. Uraguay consists of 19 departments (departamentos, singular - departamento). + GAZ:00004979 Uzbekistan [GAZ:00004979] A doubly landlocked country in Central Asia, formerly part of the Soviet Union. It shares borders with Kazakhstan to the west and to the north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one autonomous republic (respublika and one independent city (shahar). + GAZ:00006918 Vanuatu [GAZ:00006918] An island country located in the South Pacific Ocean. The archipelago, which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New Guinea, southeast of the Solomon Islands, and west of Fiji. + GAZ:00002931 Venezuela [GAZ:00002931] A country on the northern coast of South America. The country comprises a continental mainland and numerous islands located off the Venezuelan coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses borders with Guyana to the east, Brazil to the south, and Colombia to the west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just north, off the Venezuelan coast. Venezuela is divided into twenty-three states (Estados), a capital district (distrito capital) corresponding to the city of Caracas, the Federal Dependencies (Dependencias Federales, a special territory), and Guayana Esequiba (claimed in a border dispute with Guyana). Venezuela is further subdivided into 335 municipalities (municipios); these are subdivided into over one thousand parishes (parroquias). + GAZ:00003756 Viet Nam [GAZ:00003756] The easternmost country on the Indochina Peninsula in Southeast Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, alongside China, Laos, and Cambodia. + GAZ:00003959 Virgin Islands [GAZ:00003959] A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts. + GAZ:00007111 Wake Island [GAZ:00007111] A coral atoll (despite its name) having a coastline of 19 km in the North Pacific Ocean, located about two-thirds of the way from Honolulu (3,700 km west) to Guam (2,430 km east). + GAZ:00007191 Wallis and Futuna [GAZ:00007191] A Polynesian French island territory (but not part of, or even contiguous with, French Polynesia) in the South Pacific between Fiji and Samoa. It is made up of three main volcanic tropical islands and a number of tiny islets. + GAZ:00009572 West Bank [GAZ:00009572] A landlocked territory near the Mediterranean coast of Western Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the south, west and north.[2] Under Israeli occupation since 1967, the area is split into 167 Palestinian "islands" under partial Palestinian National Authority civil rule, and 230 Israeli settlements into which Israeli law is "pipelined". + GAZ:00000564 Western Sahara [GAZ:00000564] A territory of northwestern Africa, bordered by Morocco to the north, Algeria in the northeast, Mauritania to the east and south, and the Atlantic Ocean on the west. Western Sahara is administratively divided into four regions. + GAZ:00005284 Yemen [GAZ:00005284] A country located on the Arabian Peninsula in Southwest Asia. Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's territory includes over 200 islands, the largest of which is Socotra, about 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen is divided into twenty governorates (muhafazah) and one municipality. The population of each governorate is listed in the table below. The governorates of Yemen are divided into 333 districts (muderiah). The districts are subdivided into 2,210 sub-districts, and then into 38,284 villages (as of 2001). + GAZ:00001107 Zambia [GAZ:00001107] A landlocked country in Southern Africa. The neighbouring countries are the Democratic Republic of the Congo to the north, Tanzania to the north-east, Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, and Angola to the west. The capital city is Lusaka. Zambia is divided into nine provinces. Each province is subdivided into several districts with a total of 73 districts. + GAZ:00001106 Zimbabwe [GAZ:00001106] A landlocked country in the southern part of the continent of Africa, between the Zambezi and Limpopo rivers. It is bordered by South Africa to the south, Botswana to the southwest, Zambia to the northwest, and Mozambique to the east. Zimbabwe is divided into eight provinces and two cities with provincial status. The provinces are subdivided into 59 districts and 1,200 municipalities. + + + +watershed shapefile availability menu WatershedShapefileAvailabilityMenu GENEPIO:0100993 Available [GENEPIO:0100993] A datum status in which the required datum is able to be used, obtained or selected. + GENEPIO:0100995 Unknown [GENEPIO:0100995] A datum status in which the availabilty or presence of the required datum is not known. + +organism menu OrganismMenu NCBITaxon:2697049 Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] A strain of the species Betacoronavirus pandemicum, a coronavirus that causes COVID-19, the respiratory illness responsible for the COVID-19 pandemic. + +purpose of sampling menu PurposeOfSamplingMenu GENEPIO:0100869 Wastewater treatment efficiency assessment [GENEPIO:0100869] An environmental sampling strategy in which wastewater effluent is collected to assess the efficiency of wastewater treatment. + GENEPIO:0100870 Wastewater chemical surveillance [GENEPIO:0100870] An environmental sampling strategy in which wastewater samples are collected to monitor for chemical contamination. + GENEPIO:0100871 Wastewater drug surveillance [GENEPIO:0100871] An environmental sampling strategy in which wastewater samples are collected to monitor for community drug use. + GENEPIO:0100872 Wastewater pathogen surveillance [GENEPIO:0100872] An environmental sampling strategy in which samples are collected to identify and/or monitor the presence of pathogens. + GENEPIO:0100003 Research [GENEPIO:0100003] A sampling strategy in which samples are collected in order to perform research. + GENEPIO:0100873 Environmental survey (profiling) [GENEPIO:0100873] A research sampling strategy in which samples are collected in order to survey/profile entities in, or characteristics of, an environment. + GENEPIO:0100024 Protocol testing [GENEPIO:0100024] A research sampling strategy in which samples are collected in order to test a method or protocol. + +scale of sampling menu ScaleOfSamplingMenu GENEPIO:0100874 Community-level surveillance [GENEPIO:0100874] A surveillance strategy in which sites are sampled at the community level. + GENEPIO:0100875 Institution-level surveillance [GENEPIO:0100875] A surveillance strategy in which sites are sampled at the institution level. + GENEPIO:0100876 Building-level surveillance [GENEPIO:0100876] A surveillance strategy in which sites are sampled at the building level. + +sample collection time of day menu SampleCollectionTimeOfDayMenu NCIT:C64934 Morning [NCIT:C64934] The time period between dawn and noon. + NCIT:C64935 Afternoon [NCIT:C64935] The time period between noon and sunset. + NCIT:C64936 Evening [NCIT:C64936] The time period between late afternoon and bedtime. + NCIT:C65001 Night [NCIT:C65001] The time in every 24 hour period when it is dark. + +sample collection duration unit menu SampleCollectionDurationUnitMenu UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + UO:0000031 Minute [UO:0000031] A time unit which is equal to 60 seconds. + UO:0000032 Hour [UO:0000032] A time unit which is equal to 60 minutes. + UO:0000033 Day [UO:0000033] A time unit which is equal to 24 hours. + UO:0000034 Week [UO:0000034] A time unit which is equal to 7 days. + UO:0000035 Month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. + UO:0000036 Year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. + +presampling activity menu PresamplingActivityMenu ENVO:01001442 Agricultural activity [ENVO:01001442] A land use process during which terrestrial environments are modified such that they can grow crop plants or allow the rearing of animals to provide food, fiber, medicines, or other products used by humans. + ENVO:01001248 Animal husbandry [ENVO:01001248] An agricultural process during which humans rear animals on land for harvest and consumption. + ENVO:01001450 Industrial activity [ENVO:01001450] A process that leads to the production of goods. + NCIT:C16205 Healthcare activity [NCIT:C16205] A process that includes the prevention, treatment, and management of physical and mental illness. + ENVO:06105300 Wastewater treatment [ENVO:06105300] A recycling process during which wastewater is treated. + GENEPIO:0101198 Wastewater screening process [GENEPIO:0101198] A wastewater treatment process which removes large objects such as rags, paper, plastics, and metals to prevent damage and clogging of downstream equipment, piping, and appurtenances. + GENEPIO:0101719 wastewater comminution process [GENEPIO:0101719] A wastewater treatment process which involves the mechanical reduction of solid materials in wastewater into smaller, more manageable particles through devices like comminutors or grinders to shred debris. + ENVO:03501445 Wastewater filtration [ENVO:03501445] A wastewater treatment process which removes solid particles from wastewater by means of filtration. + ENVO:03501446 Wastewater grit removal [ENVO:03501446] A wastewater treatment process which removes sand, silt, and grit from wastewater. + ENVO:03501448 Wastewater primary sedimentation [ENVO:03501448] A wastewater treatment process which removes solids and large particles from influent through gravitational force. + ENVO:03501447 Wastewater microbial treatment [ENVO:03501447] A wastewater treatment process in which microbes are used to degrade the biological material in wastewater. + GENEPIO:0101199 Wastewater aerobic digestion [GENEPIO:0101199] A wastewater microbial treatment process in which organic material is broken down in the presence of oxygen. + GENEPIO:0101200 Wastewater anaerobic digestion [GENEPIO:0101200] A wastewater microbial treatment process in which organic material is broken down in the absence of oxygen by anaerobic bacteria. + ENVO:03501449 Wastewater secondary sedimentation [ENVO:03501449] A wastewater treatment process which removes biomass produced in aeration from influent through gravitational force. + GENEPIO:0101201 Wastewater sludge removal [GENEPIO:0101201] A wastewater treatment process which removes large objects such as rags, paper, plastics, and metals to prevent damage and clogging of downstream equipment, piping, and appurtenances. + GENEPIO:0101202 Wastewater sludge dewatering [GENEPIO:0101202] A wastewater treatment process which mechanically reduces the water content of wastewater sludge using equipment like centrifuges or belt presses, resulting in a semi-solid material that is easier to handle and transport + GENEPIO:0101718 Wastewater sludge drying [GENEPIO:0101718] A wastewater treatment process which further reduces the moisture content of dewatered sludge, typically through thermal or air drying methods, producing a dry, stable material for easier disposal or use. + + +sample volume measurement unit menu SampleVolumeMeasurementUnitMenu UO:0000101 microliter (uL) [UO:0000101] A metric unit of volume equivalent to one thousandth of a cubic centimeter or one millionth of a liter. + UO:0000098 milliliter (mL) [UO:0000098] A metric unit of volume equivalent to one cubic centimeter or one thousandth of a liter. + UO:0000099 liter (L) [UO:0000099] A metric unit of volume equivalent to 1000 cubic centimeters + +sample storage duration unit menu SampleStorageDurationUnitMenu UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + UO:0000031 Minute [UO:0000031] A time unit which is equal to 60 seconds. + UO:0000032 Hour [UO:0000032] A time unit which is equal to 60 minutes. + UO:0000033 Day [UO:0000033] A time unit which is equal to 24 hours. + UO:0000034 Week [UO:0000034] A time unit which is equal to 7 days. + UO:0000035 Month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. + UO:0000036 Year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. + +specimen processing menu SpecimenProcessingMenu OBI:0600041 Concentration [OBI:0600041] A process used to increase the density of a material of interest by removing other materials in the entity containing the material of interest. + OBI:0302886 Centrifugation [OBI:0302886] A process separating molecules by size or density using centrifugal forces generated by a spinning rotor. + OBI:0302885 Filtration [OBI:0302885] A process which separates components suspended in a fluid based on granularity properties relying on a filter device. + NCIT:C154798 Flocculation [NCIT:C154798] A process in which microscopic particles in suspension aggregate to form loosely clumped masses that are often macroscopically observable. + GENEPIO:0100886 Magnetic nanobead binding [GENEPIO:0100886] A process that uses nanobeads to bind to particles or microbes of interest. + OBI:0600034 Precipitation [OBI:0600034] A protocol application to cause a material to precipitate (becoming a solid) out of solution. + GENEPIO:0101011 Gravity separation [GENEPIO:0101011] A process through which solids are separated from a liquid by allowing the solids to settle by gravity. + IDO:0100170 Pasteurization [IDO:0100170] A planned process of heating a liquid entity, to a specific temperature of a defined length of time span, and then cooling it immediately. It has an objective of prevent the microbial's growth in the liquid entity, which is a specific input of this planned process. + GENEPIO:0101012 Growth in enrichment broth [GENEPIO:0101012] A process in which microorganisms, present in a collected sample, undergo cultivation within a nutrient-rich liquid medium, that facilitates growth. + OBI:0600016 Pooling specimens [OBI:0600016] Physical combination of several instances of like material. + GENEPIO:0101021 Technical replicate process [GENEPIO:0101021] A specimen collection process in which a replicate(s) is collected to assess technical variation within an experiment. For technical replicates the same BioSample is used e.g. the same pool of RNA is used to assess technical (as opposed to biological) variation. + GENEPIO:0101022 Biological replicate process [GENEPIO:0101022] A specimen collection process in which a replicate(s) is collected in parallel to assess for biological variation within an experiment. Biological replicates would have distinct BioSamples records. + +environmental site menu EnvironmentalSiteMenu ENVO:01001481 Correctional facility [ENVO:01001481] A prison facility which is owned and operated by a state. + ENVO:03501134 Healthcare facility [ENVO:03501134] A human construction in which healthcare is provided. + ENVO:00002173 Hospital [ENVO:00002173] A building in which health care services are provided by specialized staff and equipment. + ENVO:03501182 Clinic [ENVO:03501182] A facility which is used to provide treatment, remedial work, and/or instruction. + ENVO:03501129 Educational facility [ENVO:03501129] A human construction in which people are educated. + ENVO:03501335 Daycare facility [ENVO:03501335] A child care facility in which day care services are provided, by specialized staff and equipment, to a human child during the working day. + ENVO:03501130 School [ENVO:03501130] An institutional building in which students are educated. + ENVO:03501131 College or university [ENVO:03501131] An institutional building in which university services are performed. + ENVO:01001222 Commercial building [ENVO:01001222] A building which is primarily used to facilitate the buying or selling of goods or services. "Commerce includes legal, economic, political, social, cultural and technological systems that are in operation in any country or internationally." + ENVO:01001221 Office [ENVO:01001221] A commercial building which contains parts used as workplaces primarily for administrative and managerial workers. "An office building will be divided into sections for different companies or may be dedicated to one company. In either case, each company will typically have a reception area, one or several meeting rooms, singular or open-plan offices, as well as toilets." + ENVO:01000934 Restaurant [ENVO:01000934] A building within which food and drink are prepared and served to customers in exchange for money or other goods and/or services. + ENVO:03501207 Shopping mall [ENVO:03501207] A shopping center in which a large indoor pedestrian promenade provides access to stores and other facilities. + ENVO:01000933 Residential building [ENVO:01000933] A human house which serves as a long-term shelter for its inhabitants and within which they store personal property. + ENVO:03501133 Homeless shelter [ENVO:03501133] An institutional building which temporarily houses homeless people. + ENVO:01000932 Long-term care facility [ENVO:01000932] A building in which nursing aides and skilled nurses provide care and treatment to residents who have significant difficulty coping with the required activities of daily living. + ENVO:03501117 Transport hub [ENVO:03501117] A place where passengers and cargo are exchanged between vehicles or/and between transport modes. + ENVO:03501122 Airport [ENVO:03501122] A human construction with extended facilities from which aircraft flight operations take place. + ENVO:00000078 Farm [ENVO:00000078] An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein. + NCIT:C85867 Refugee camp [NCIT:C85867] A temporary, often makeshift shelter for persons displaced by war, political oppression, or for religious beliefs. + ENVO:00000064 Road [ENVO:00000064] An open way for the passage of vehicles, persons, or animals on land. + ENVO:01000447 Roadside [ENVO:01000447] An environmental zone of varying area which is adjacent to a road. + ENVO:00003861 Industrial plant [ENVO:00003861] A building within which goods are produced and, optionally, stored or within which services are rendered. + ENVO:03501297 Meat processing plant [ENVO:03501297] A processing plant for slaughtering, processing, packaging, labelling, handling, and storing of food animal carcasses, parts of carcasses, and meat products. + ENVO:03501450 Pharmaceutical manufacturing plant [ENVO:03501450] An industrial building in which pharamceutical drugs are synthesised and processed on an industrial scale. + ENVO:00000063 Body of water [ENVO:00000063] An accumulation of water of varying size. + ENVO:00002042 Surface water [ENVO:00002042] Water that is found on the surface of an astronomical object. + ENVO:00000020 Lake [ENVO:00000020] A body of water or other liquid of considerable size contained in a depression on a landmass. + ENVO:00000023 Stream [ENVO:00000023] A watercourse which is linear and flows across the solid portion of a planetary surface. + ENVO:00000022 River [ENVO:00000022] A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply. + ENVO:00000015 Ocean [ENVO:00000015] A marine water body which is constitutes the majority of an astronomical body's hydrosphere. + ENVO:00000016 Sea [ENVO:00000016] A large expanse of saline water usually connected with an ocean. + ENVO:00000014 Canal [ENVO:00000014] Artificial watercourse with no flow or a controlled flow used for navigation, drainage or irrigation. + ENVO:00000025 Reservoir [ENVO:00000025] An artificial body of water, often contained by a dam, constructed for the purpose of water storage. + ENVO:01001004 Ground water [ENVO:01001004] Underground water which is located in pore spaces found in rock or unconsolidated deposits such as soil, clay, or gravel. + ENVO:00000026 Well [ENVO:00000026] A cylindrical hole, pit, or tunnel drilled or dug down to a depth from which water, oil, or gas can be pumped or brought to the surface. + ENVO:00000027 Spring [ENVO:00000027] A surface landform which provides an egress for groundwater or steam to flow out of the ground. + ENVO:00002272 Wastewater treatment plant [ENVO:00002272] A plant in which wastewater is treated. + ENVO:03501465 Influent pump station [ENVO:03501465] A facility within a wastewater treatment plant designed to receive and lift incoming wastewater (influent) to a higher elevation for subsequent treatment processes. The influent pump station typically houses pumps, controls, and associated equipment necessary to move wastewater through the treatment process. + ENVO:03501467 Grit chamber [ENVO:03501467] A physical structure or equipment within a wastewater treatment plant where grit and other heavy inorganic particles are removed from the influent through sedimentation. The grit chamber helps protect downstream equipment from abrasion and reduces the accumulation of grit in subsequent treatment processes. + ENVO:03501472 Communitor [ENVO:03501472] A mechanical device designed to reduce the size of solid materials in wastewater. It uses rotating drums or cutting blades to shred large debris into smaller pieces, protecting downstream equipment and enhancing the efficiency of subsequent treatment processes. + ENVO:03501468 Primary clarifer [ENVO:03501468] A large, sedimentation tank in a wastewater treatment plant where the primary stage of solids separation occurs. In the primary clarifier, suspended solids settle to the bottom as sludge, while lighter materials, such as oils and greases, rise to the surface for removal. + ENVO:03501469 Aeration tank [ENVO:03501469] A tank or basin in a wastewater treatment plant where oxygen is introduced into the wastewater to promote the growth of aerobic microorganisms. These microorganisms break down organic pollutants in the water, facilitating the biological treatment process. The aeration tank is essential for reducing the organic load before the water moves to subsequent treatment stages. + ENVO:03501471 Secondary clarifer [ENVO:03501471] A sedimentation tank in a wastewater treatment plant used in the secondary treatment process. The secondary clarifier allows for the settling and removal of biological floc or sludge produced in the aeration tank, further clarifying the treated wastewater before discharge or further treatment. + ENVO:03501473 Sludge dryer [ENVO:03501473] A device designed to remove moisture from sludge through thermal drying methods, resulting in a dry, granular material that is easier to handle, store, or utilize in other applications. + ENVO:03600076 Waste stabilization pond (lagoon) [ENVO:03600076] A human construction which confines wastewater in a depression enclosed by earthen structures. + ENVO:01000924 Sewer [ENVO:01000924] An artificial channel which transports unwanted water or waste liquids away from their source, either to a more useful area, a receptacle, or into sewers or stormwater mains as waste discharge to be released or processed. + ENVO:01000604 Transportation vehicle [ENVO:01000604] A vehicle is a mobile machine which transports people or cargo. + ENVO:01000608 Boat [ENVO:01000608] A boat is a watercraft of any size which is able to float or plane on water. + ENVO:03501349 Airplane [ENVO:03501349] An aircraft which 1) has fixed wings and 2) is propelled by a thrust from a jet engine, propeller, or rocket engine. + +environmental material menu EnvironmentalMaterialMenu ENVO:03501474 Bar screen [ENVO:03501474] A mechanical filter used to remove large objects, such as rags and plastics, from wastewater + ENVO:00002042 Surface water [ENVO:00002042] Water that is found on the surface of an astronomical object. + ENVO:00002001 Wastewater [ENVO:00002001] Water that has been adversely affected in quality by anthropogenic influence + ENVO:03501456 Wastewater sediment [ENVO:03501456] A sediment which is removed from waste water during a waste water treatment process. + ENVO:00002044 Sludge [ENVO:00002044] The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes. + ENVO:00002057 Primary sludge [ENVO:00002057] Sludge generated from the initial processes (i.e., precipitation, sedimentation) of wastewater treatment. + ENVO:00002058 Secondary sludge [ENVO:00002058] Activated waste biomass generated during wastewater treatment. + ENVO:03501457 Wastewater effluent [ENVO:03501457] A wastewater which has been discharged from any item of equipment at a stage of a wastewater treatment process. + GENEPIO:0100892 Primary wastewater effluent [GENEPIO:0100892] A wastewater effluent which has been discharged from a primary clarifier after the first stage of sedimentation. + GENEPIO:0100893 Secondary wastewater effluent [GENEPIO:0100893] A wastewater effluent which has been discharged from a secondary clarifier after the second stage of sedimentation. + +environmental material properties menu EnvironmentalMaterialPropertiesMenu GENEPIO:0101004 Fluid (stagnant) [GENEPIO:0101004] A quality of a body of water wherein it has no current or flow. + GENEPIO:0101005 Fluid (slow) [GENEPIO:0101005] A quality of a body of water wherein there is a slow flow. + GENEPIO:0101006 Fluid (fast) [GENEPIO:0101006] A quality of a body of water wherein there is a fast flow. + PATO:0015031 Contamination [PATO:0015031] The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity. + GENEPIO:0101010 Fecal-contaminated [GENEPIO:0101010] A contamination quality in which fecal matter is a key component of the contamination. + PATO:0001735 Liquid [PATO:0001735] A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids. + GENEPIO:0101007 Slurry-like [GENEPIO:0101007] An quality in which the fluid like material is more viscous due to the suspension of insoluble solid particles. + NCIT:C149895 Semi-solid [NCIT:C149895] A state of matter consisting of molecules in a non-rigid structure that can retain its shape and volume but that is not resistant to such change. + PATO:0001736 Solid [PATO:0001736] A quality in which an object or material exhibits characteristics of solids, lacking movement or flow. + GENEPIO:0101008 Treated [GENEPIO:0101008] A quality which denotes an altered state of an item resulting from purposeful interventions or processes. + GENEPIO:0101009 Untreated [GENEPIO:0101009] A quality which denotes an absence of purposeful intervention or processes on an item. + +wastewater system type menu WastewaterSystemTypeMenu ENVO:03501453 Combined sewer system [ENVO:03501453] A sewered sanitation system that collects rainwater runoff, domestic sewage, and industrial wastewater. + ENVO:03501454 Sanitary sewer system [ENVO:03501454] A sewered sanitation system that collects only domestic sewage. + ENVO:03600076 Waste stabilization pond [ENVO:03600076] A human construction which confines wastewater in a depression enclosed by earthen structures. + ENVO:01000519 Latrine [ENVO:01000519] A latrine is a toilet which is of simple construction (relative to a flush or chemical toilet) and typically intended for communal use. + ENVO:03501451 Septic tank [ENVO:03501451] An underground holding and treatment site for domestic wastewater. + ENVO:03501452 Cesspit [ENVO:03501452] A pit for the disposal and storage of sewage. + ENVO:01000550 Composting toilet [ENVO:01000550] A composting toilet fixture is a dry toilet fixture in which managed, aerobic decomposition converts human excreta into organic matter suitable for the fertilisation or amendment of soils. + ENVO:01000924 Sewer drain [ENVO:01000924] An artificial channel which transports unwanted water or waste liquids away from their source, either to a more useful area, a receptacle, or into sewers or stormwater mains as waste discharge to be released or processed. + + + +experimental specimen role type menu ExperimentalSpecimenRoleTypeMenu GENEPIO:0101018 Positive experimental control [GENEPIO:0101018] A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment. + GENEPIO:0101019 Negative experimental control [GENEPIO:0101019] A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment + EFO:0002090 Technical replicate [EFO:0002090] A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment. + EFO:0002091 Biological replicate [EFO:0002091] A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples. + +collection device menu CollectionDeviceMenu GENEPIO:0100941 Grab sampler [GENEPIO:0100941] A specimen collection device which is used to collect discrete, instantaneous samples of water, soil, or other substances from a specific point in a body of water or at a specific location. + GENEPIO:0102027 Bag filtration device [GENEPIO:0102027] + GENEPIO:0100943 Core sampling device [GENEPIO:0100943] A grab sampler that captures a vertical section of the substrate matrix of fecal sludge. + GENEPIO:0100944 Vacuum sludge sampling device [GENEPIO:0100944] A grab sampler that takes a sample at a designated depth with minimal disturbance to surrounding layers. + GENEPIO:0100945 Cone-shaped sampling device [GENEPIO:0100945] A grab sample that has a controlled valve that opens to take a sample from a specific depth, then closes to bring the sample out. + GENEPIO:0100946 Horizontal grab sampling device [GENEPIO:0100946] A grab sampler in which the container for the sample is mounted on the end of a rod, which is suitable for collecting discharge from a pipe or truck. + GENEPIO:0100947 Vertical grab sampling device [GENEPIO:0100947] A grab sampler in which the container for the sample is mounted on the end of a rod, which is suitable for collecting waste from a tank. + GENEPIO:0100942 Composite sampler [GENEPIO:0100942] A specimen collection device that collects material over different times or locations. + GENEPIO:0100948 Passive (trap) sampler [GENEPIO:0100948] A composite sampler that passively collects a sample without use of electricity or a battery. + GENEPIO:0100949 Moore swab [GENEPIO:0100949] A composite sampler which consists of gauze pad tied with string, suspended in flowing water or wastewater, in order to collect a wastewater sample. + GENEPIO:0100950 Automatic composite sampler [GENEPIO:0100950] A composite sampler which is automated to collect and store multiple wastewater samples across multiple time points. + GENEPIO:0100951 Automatic flow-proportional sampler [GENEPIO:0100951] A composite sampler which is automated to collect and store multiple wastewater samples in a manner proportional to flow. + GENEPIO:0100952 Automatic sequential (time-proportional) sampler [GENEPIO:0100952] A composite sampler which is automated to collect and combine multiple samples of equal volume taken at a set time interval. + +collection method menu CollectionMethodMenu GENEPIO:0100953 Grab sampling [GENEPIO:0100953] An environmental material collection process in which a water or soil sample is taken at a single point of time using a container type known as a grab sampler. + GENEPIO:0102028 Bag Mediated Filtration [GENEPIO:0102028] + GENEPIO:0100954 Composite sampling [GENEPIO:0100954] An environmental material collection process in which mutliple water or soil samples are taken at different time points and combined to produce a composite. Samples can be collected continuously or at discrete time points. + GENEPIO:0100955 Passive composite sampling [GENEPIO:0100955] A method of composite sampling in which a continuous sample is collected passively without electrical input minimizing cost. + GENEPIO:0100956 Automatic composite sampling [GENEPIO:0100956] A method of composite sampling which utilizes an automated system to collect multiple samples, continuously or at discrete timepoints. + GENEPIO:0100957 Manual composite sampling [GENEPIO:0100957] A method of composite sampling in which multiple grab samples from discrete time points are taken and then combined to produce a single composite sample. + +water catchment area human population range menu WaterCatchmentAreaHumanPopulationRangeMenu <10 people An estimation of population size for a group smaller than 10 people. + 10 - 100 people An estimation of population size for a group smaller than 100 people and larger than 10 people. + 100 - 1,000 people An estimation of population size for a group smaller than 1,000 people and larger than 100 people. + 1,000 - 10,000 people An estimation of population size for a group smaller than 10,000 people and larger than 1,000 people. + 10,000 - 100,000 people An estimation of population size for a group smaller than 100,000 people and larger than 10,000 people. + 100,000 - 1,000,000 people An estimation of population size for a group smaller than 1,000,000 people and larger than 100,000 people. + 1,000,000+ people An estimation of population size for a group larger than 1,000,000 people. + +water catchment area human population density unit menu WaterCatchmentAreaHumanPopulationDensityUnitMenu GENEPIO:0100989 persons per square mile [GENEPIO:0100989] A unit of population density that describes the average number of people in a square mile of a given area. + GENEPIO:0100990 persons per square kilometer [GENEPIO:0100990] A unit of population density that describes the average number of people in a square kilometer of a given area. + GENEPIO:0100991 residents per square mile [GENEPIO:0100991] A unit of population density that describes the average number of registered residents in a square mile of a given area. + GENEPIO:0100992 residents per square kilometer [GENEPIO:0100992] A unit of population density that describes the average number of registered residents in a square kilometer of a given area. + +populated area type menu PopulatedAreaTypeMenu GSSO:011077 Suburban [GSSO:011077] A mixed-use or residential area, existing either as part of a city/urban area, or as a separate residential community within commuting distance of one. Suburbs might have their own political or legal jurisdiction, especially in the United States, but this is not always the case, especially in the United Kingdom where most suburbs are located within the administrative boundaries of cities. + GSSO:011078 Rural [GSSO:011078] A geographic area that is located outside towns and cities. Rural areas are primarily used for agriculture or pastoralism and may contain rural settlements. + GSSO:011080 Urban [GSSO:011080] A human settlement with a high population density and infrastructure of built environment. Urban areas are created through urbanization and are categorized by urban morphology as cities, towns, conurbations or suburbs. In urbanism, the term contrasts to rural areas such as villages and hamlets; in urban sociology or urban anthropology it contrasts with natural environment. + +sampling weather conditions menu SamplingWeatherConditionsMenu ENVO:03501418 Cloudy/Overcast [ENVO:03501418] Atmospheric weather in which the sky is mostly or completely obscured by clouds. + ENVO:03501419 Partially cloudy [ENVO:03501419] Atmospheric weather in which the sky is partially obscured by clouds. + ENVO:03501420 Drizzle [ENVO:03501420] An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process. + ENVO:01000844 Fog [ENVO:01000844] A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body. + ENVO:01001564 Rain [ENVO:01001564] An aggregate of raindrops falling to a planetary surface during a precipitation process. + ENVO:01000406 Snow [ENVO:01000406] Snow is an environmental material which is primarily composed of flakes of crystalline water ice. + ENVO:01000876 Storm [ENVO:01000876] A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates. + ENVO:03501421 Sunny/Clear [ENVO:03501421] Atmospheric weather in which the sun can be seen to shine brightly. + +presampling weather conditions menu PresamplingWeatherConditionsMenu ENVO:03501418 Cloudy/Overcast [ENVO:03501418] Atmospheric weather in which the sky is mostly or completely obscured by clouds. + ENVO:03501419 Partially cloudy [ENVO:03501419] Atmospheric weather in which the sky is partially obscured by clouds. + ENVO:03501420 Drizzle [ENVO:03501420] An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process. + ENVO:01000844 Fog [ENVO:01000844] A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body. + ENVO:01001564 Rain [ENVO:01001564] An aggregate of raindrops falling to a planetary surface during a precipitation process. + ENVO:01000406 Snow [ENVO:01000406] Snow is an environmental material which is primarily composed of flakes of crystalline water ice. + ENVO:01000876 Storm [ENVO:01000876] A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates. + ENVO:03501421 Sunny/Clear [ENVO:03501421] Atmospheric weather in which the sun can be seen to shine brightly. + +precipitation measurement unit menu PrecipitationMeasurementUnitMenu UO:0000016 millimeter (mm) [UO:0000016] A length unit which is defined as one thousandth of a meter. + UO:0000015 centimeter (cm) [UO:0000015] A length unit which is equal to one hundredth of a meter or 10^[-2] m + UO:0000008 meter (m) [UO:0000008] An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second. + UO:0010011 inch (in) [UO:0010011] A non-SI unit of length defined as one twelfth of a foot. + UO:0010013 foot (ft) [UO:0010013] A non-SI unit of length which is approximately 0.3048 meters. + +air pressure measurement unit menu AirPressureMeasurementUnitMenu EFO:0005212 atmosphere (atm) [EFO:0005212] A non-SI unit of pressure defined as 101,325 pascals (Pa). + bar + UO:0000110 pascal [UO:0000110] An SI unit of pressure defined as one newton per square meter (N/m^2). + +ambient temperature measurement unit menu AmbientTemperatureMeasurementUnitMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +total daily flow rate measurement unit menu TotalDailyFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second. + cubic meter per minute (m^3/min) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute. + cubic meter per hour (m^3/h) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour. + liter per second (L/s) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second. + liter per minute (L/min) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute. + liter per hour (L/h) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour. + liter per day (L/day) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day. + million gallons per day (MGD) A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day. + +instantaneous flow rate measurement unit menu InstantaneousFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second. + cubic meter per minute (m^3/min) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute. + cubic meter per hour (m^3/h) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour. + liter per second (L/s) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second. + liter per minute (L/min) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute. + liter per hour (L/h) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour. + liter per day (L/day) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day. + million gallons per day (MGD) A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day. + +turbidity measurement unit menu TurbidityMeasurementUnitMenu nephelometric turbidity unit (NTU) A measure of turbidity calculated by using a nephelometer to compare how white light is scattered in a water sample. + UO:0000318 formazin nephelometric unit (FNU) [UO:0000318] A measure of turbidity calculated by comparing how infrared light is scattered in a water sample against the amount of infrared light scattered in a reference solution containing formazin. + +dissolved oxygen measurement unit menu DissolvedOxygenMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + UO:0000083 kilogram per cubic meter (kg/m^3) [UO:0000083] An SI unit of density that is one thousandth of the density of water. + UO:0000169 part per million (ppm) [UO:0000169] A unitless measure of density that represents one item out of a million. + +oxygen reduction potential (ORP) measurement unit menu OxygenReductionPotentialOrpMeasurementUnitMenu UO:0000247 milliVolt (mV) [UO:0000247] A non-SI unit of electromotive force that is one thousandth of a volt. + +chemical oxygen demand (COD) measurement unit menu ChemicalOxygenDemandCodMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + +carbonaceous biochemical oxygen demand (CBOD) measurement unit menu CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + +total suspended solids (TSS) measurement unit menu TotalSuspendedSolidsTssMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +total dissolved solids (TDS) measurement unit menu TotalDissolvedSolidsTdsMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +total solids (TS) measurement unit menu TotalSolidsTsMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +alkalinity measurement unit menu AlkalinityMeasurementUnitMenu milliequivalent per liter (meq/L) A unit of ion concentration that represents chemical activity per volume. + UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + UO:0000169 parts per million [UO:0000169] A unitless measure of density that represents one item out of a million. + +conductivity measurement unit menu ConductivityMeasurementUnitMenu milliSiemen per centimeter (mS/cm) A non-SI unit of electrical conductivity that is equivalent to one tenth of a Siemen per meter (S/m). + microSiemen per centimeter (μS/cm) A non-SI unit of electrical conductivity that is equivalent to one ten thousandth of a Siemen per meter (S/m). + Siemen per meter (S/m) An SI unit of electrical conductivity that is equivalent to an ampere per volt per meter (A/v/m). + +salinity measurement unit menu SalinityMeasurementUnitMenu practical salinity unit (PSU) A unitless measure of salinity that is equivalent to per thousand. + weight for weight (% w/w) A unitless comparison based on weight rather than volume, which is equivalent to per hundred. + UO:0000168 parts per thousand [UO:0000168] A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +total nitrogen (TN) measurement unit menu TotalNitrogenTnMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + gram per total solids (g/gTS) A unitless comparison of the weight of a substance as a proportion to the weight of total solids. + +total phosphorpus (TP) measurement unit menu TotalPhosphorpusTpMeasurementUnitMenu gram per total solids (g/gTS) A unitless comparison of the weight of a substance as a proportion to the weight of total solids. + GENEPIO:0100998 orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998] A substance unit which describes the weight of orthophosphate as phosphorus (gPO4-P) within a sample to the weight of total solids. + UO:0000273 milligrams per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + GENEPIO:0100999 milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999] A density unit comparing the weight of orthophosphate as phosphorus (PO4-P) in milligrams within a standard liter volume. + +fecal contamination indicator menu FecalContaminationIndicatorMenu NCBITaxon:1211417 crAssphage [NCBITaxon:1211417] CrAss-like phage, a bacteriophage discovered in 2014 in the human fecal metagenome. + NCBITaxon:12239 PMMoV / pepper mild mottle virus [NCBITaxon:12239] A plant RNA virus that is abundant in human feces. + GENEPIO:0101000 Bacteroides HF183 [GENEPIO:0101000] A fecal indicator which is the most commonly used sewage-associated marker gene, belonging to the Bacteroides genus. + GENEPIO:0101001 Lachnospiraceae Lachno3 [GENEPIO:0101001] A fecal indicator which is a human-associated genetic marker in the Lachnospiraceae family of bacteria. + GENEPIO:0101002 F+ (male specific) coliphages [GENEPIO:0101002] A fecal indicator which is a bacteriophage that infects coliform bacteria and is used in water assessment. + CHEBI:26756 Stercobilin [CHEBI:26756] Bile pigment found in fecal material. + +fecal contamination unit menu FecalContaminationUnitMenu log10 gene copies per 100 milliliter (log10 GC/100 mL) A unit that expresses on a logarithmic scale the number of copies of a given gene within one hundred milliliters of a biological material. + gene copies per liter (GC/L) A unit that measures the number of copies of a given gene within a liter of a biological material. + UO:0010077 PCR quantification cycle [UO:0010077] A count unit of how many Polymerase Chain Reaction (PCR) cycles it took to detect a real signal from a sample. Equivalent to the PCR cycle number at which a sample's reaction curve intersects the threshold line. + log10 gene copies per nanogram total DNA A unit that expresses on a logarithmic scale the number of copies within a nanogram of deoxyribonucleic acid genetic material. + +urinary contamination indicator menu UrinaryContaminationIndicatorMenu CHEBI:36378 Urobilin [CHEBI:36378] A tetrapyrroledicarboxylic acid that causes the yellow color in urine. Also known as urochrome. + +urinary contamination unit menu UrinaryContaminationUnitMenu EFO:0004382 nanograms per liter (ng/L) [EFO:0004382] A mass unit density which is equal to mass of an object in nanograms divided by the volume in liters. + +fecal coliform count unit menu FecalColiformCountUnitMenu UO:0000213 colony forming units per milliliter (CFU/mL) [UO:0000213] A unit of microbial density that describes the number of colony forming units within a milliliter of material. + colony forming units per 100 milliliter (CFU/100 mL) A unit of microbial density that describes the number of colony forming units within 100 milliliters of material. + colony forming units per grams total solids (CFU/gTS) A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material. + most probable number per milliliter (MPN/mL) A unit of microbial density that describes the most probable number of microbes within one milliliter of material. + most probable number per 100 milliliter (MPN/100 mL) A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material. + +sample temperature unit (at collection) menu SampleTemperatureUnitAtCollectionMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +sample temperature unit (when received) menu SampleTemperatureUnitWhenReceivedMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +purpose of sequencing menu PurposeOfSequencingMenu GENEPIO:0100005 Baseline surveillance (random sampling) [GENEPIO:0100005] A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling. + GENEPIO:0100006 Targeted surveillance (non-random sampling) [GENEPIO:0100006] A surveillance sampling strategy in which an aspired outcome is explicitly stated. + GENEPIO:0100007 Priority surveillance project [GENEPIO:0100007] A targeted surveillance strategy which is considered important and/or urgent. + GENEPIO:0100009 Longitudinal surveillance (repeat sampling) [GENEPIO:0100009] A surveillance strategy in which an individual or site is selected to undergo repeat sampling over a defined period of time. + GENEPIO:0100012 Travel-associated surveillance [GENEPIO:0100012] A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored. + GENEPIO:0100013 Domestic travel surveillance [GENEPIO:0100013] A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored, related to domestic travel. + GENEPIO:0100014 International travel surveillance [GENEPIO:0100014] A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored, related to international travel. + GENEPIO:0100022 Research [GENEPIO:0100022] A sampling strategy in which sites are sampled in order to perform research. + GENEPIO:0100023 Viral passage experiment [GENEPIO:0100023] A research sampling strategy in which samples are selected in order to perform a viral passage experiment. + GENEPIO:0100024 Protocol testing experiment [GENEPIO:0100024] A research sampling strategy in which samples are collected in order to test a method or protocol. + +sequencing platform menu SequencingPlatformMenu GENEPIO:0001923 Illumina [GENEPIO:0001923] A sequencing platform provided by the Illumina company. ILLUMINA + GENEPIO:0001927 Pacific Biosciences [GENEPIO:0001927] A sequencing platform provided by the Pacific Biosciences company. PACBIO_SMRT + GENEPIO:0002683 Ion Torrent [GENEPIO:0002683] A sequencing platform provided by the Ion Torrent company. ION_TORRENT + GENEPIO:0100986 Oxford Nanopore Technologies [GENEPIO:0100986] An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK. OXFORT_NANOPORE + GENEPIO:0004324 BGI Genomics [GENEPIO:0004324] A sequencing platform provided by the BGI Genomics company. BGISEQ + GENEPIO:0004325 MGI [GENEPIO:0004325] A sequencing platform provided by the MGI company. BGISEQ + GENEPIO:0001926 Roche LS454 [GENEPIO:0001926] A sequencing platform provided by the 454 Life Sciences company. _LS454 + GENEPIO:0002684 SOLiD sequencing [GENEPIO:0002684] A sequencing platform provided by Life Technologies Corporation. ABI_SOLID + GENEPIO:0001924 Complete Genomics [GENEPIO:0001924] An in-house sequencing platform provided by Complete Genomics. COMPLETE_GENOMICS + GENEPIO:0002682 Helicos [GENEPIO:0002682] A sequencing platform brand provided by Helicos corporation (now defunct). HELICOS + GENEPIO:0100985 Applied Biosystems [GENEPIO:0100985] A sequencing platform provided by ThermoFisher. CAPILLARY + +sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. #REF! + GENEPIO:0100106 Illumina Genome Analyzer [GENEPIO:0100106] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. + OBI:0000703 Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer manufactured by the Illumina (Solexa) corporation, which supports sequencing of single or paired end clone libraries relying on sequencing by synthesis technology. + OBI:0002000 Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. + GENEPIO:0100109 Illumina HiScanSQ [GENEPIO:0100109] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. + GENEPIO:0100110 Illumina HiSeq [GENEPIO:0100110] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. + GENEPIO:0100111 Illumina HiSeq X [GENEPIO:0100111] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that enables sufficient depth and coverage to produce the first 30x human genome for $1000. + GENEPIO:0100112 Illumina HiSeq X Five [GENEPIO:0100112] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. + GENEPIO:0100113 Illumina HiSeq X Ten [GENEPIO:0100113] A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + OBI:0002022 Illumina HiSeq 1000 [OBI:0002022] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + GENEPIO:0100115 Illumina HiSeq 1500 [GENEPIO:0100115] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day. + OBI:0002001 Illumina HiSeq 2000 [OBI:0002001] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. + OBI:0002002 Illumina HiSeq 2500 [OBI:0002002] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. + OBI:0002048 Illumina HiSeq 3000 [OBI:0002048] A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. + OBI:0002049 Illumina HiSeq 4000 [OBI:0002049] A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. + GENEPIO:0100120 Illumina iSeq [GENEPIO:0100120] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. + GENEPIO:0100121 Illumina iSeq 100 [GENEPIO:0100121] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. + GENEPIO:0100122 Illumina NovaSeq [GENEPIO:0100122] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that has an output capacity of 6 Tb and 20 billion reads in dual flow cell mode. + GENEPIO:0100123 Illumina NovaSeq 6000 [GENEPIO:0100123] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. + GENEPIO:0100124 Illumina MiniSeq [GENEPIO:0100124] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + OBI:0002003 Illumina MiSeq [OBI:0002003] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. + GENEPIO:0100126 Illumina NextSeq [GENEPIO:0100126] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + OBI:0002021 Illumina NextSeq 500 [OBI:0002021] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + GENEPIO:0100128 Illumina NextSeq 550 [GENEPIO:0100128] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. + GENEPIO:0004432 Illumina NextSeq 1000 [GENEPIO:0004432] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. + GENEPIO:0100129 Illumina NextSeq 2000 [GENEPIO:0100129] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. + GENEPIO:0100130 PacBio [GENEPIO:0100130] A DNA sequencer manufactured by the Pacific Biosciences corporation. + GENEPIO:0100131 PacBio RS [GENEPIO:0100131] A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. + OBI:0002012 PacBio RS II [OBI:0002012] A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. + GENEPIO:0100133 PacBio Sequel [GENEPIO:0100133] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation + GENEPIO:0100134 PacBio Sequel II [GENEPIO:0100134] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. + GENEPIO:0100135 Ion Torrent [GENEPIO:0100135] A DNA sequencer manufactured by the Ion Torrent corporation. + GENEPIO:0100136 Ion Torrent PGM [GENEPIO:0100136] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. + GENEPIO:0100137 Ion Torrent Proton [GENEPIO:0100137] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. + GENEPIO:0100138 Ion Torrent S5 XL [GENEPIO:0100138] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. + GENEPIO:0100139 Ion Torrent S5 [GENEPIO:0100139] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. + GENEPIO:0100140 Oxford Nanopore [GENEPIO:0100140] A DNA sequencer manufactured by the Oxford Nanopore corporation. + GENEPIO:0004433 Oxford Nanopore Flongle [GENEPIO:0004433] An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. + GENEPIO:0100141 Oxford Nanopore GridION [GENEPIO:0100141] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual + GENEPIO:0100142 Oxford Nanopore MinION [GENEPIO:0100142] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. + GENEPIO:0100143 Oxford Nanopore PromethION [GENEPIO:0100143] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. + GENEPIO:0100144 BGI Genomics sequencing instrument [GENEPIO:0100144] A DNA sequencer manufactured by the BGI Genomics corporation. + GENEPIO:0100145 BGISEQ-500 [GENEPIO:0100145] A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". + GENEPIO:0100146 MGI sequencing instrument [GENEPIO:0100146] A DNA sequencer manufactured by the MGI corporation. + GENEPIO:0100971 MGISEQ-2000RS [GENEPIO:0100971] An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing ad which is capable of medium to high throughput sequencing. + GENEPIO:0100972 MGI DNBSEQ-G99 [GENEPIO:0100972] An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing and which adopts triangular matrix signal spots on sequencing flow cell, for low throughput at highspeeds. + GENEPIO:0100148 MGI DNBSEQ-G400 [GENEPIO:0100148] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run. + GENEPIO:0100149 MGI DNBSEQ-G400RS FAST [GENEPIO:0100149] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 330GB per run, which enables faster sequencing than the DNBSEQ-G400. + GENEPIO:0100147 MGI DNBSEQ-T7 [GENEPIO:0100147] A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day. + GENEPIO:0100973 MGI DNBSEQ-E25 [GENEPIO:0100973] An MGI sequencing instrument model that is a compact and lightweight standalone system which can bu used inside or outside the lab. + GENEPIO:0100150 MGI DNBSEQ-G50 [GENEPIO:0100150] A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. + GENEPIO:0001937 454 Genome Sequencer [GENEPIO:0001937] A DNA sequencer first manufactured by 454 Life Science Corporation that conducts pyrosequencing. + OBI:0000689 454 Genome Sequencer 20 [OBI:0000689] A DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. + OBI:0000702 454 Genome Sequencer FLX [OBI:0000702] A DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. + GENEPIO:0100982 454 Genome Sequencer FLX+ [GENEPIO:0100982] A 454 Genome Sequencer that performs pyrosequencing and comprises both optics and fluidics subsystems and can be used for longer reads when used with the long-read Sequencing Kit XL+. + GENEPIO:0001936 454 Genome Sequencer FLX Titanium [GENEPIO:0001936] A 454 Genome Sequencer that performs pyrosequencing and has enhanced capacity and generates longer reads. + GENEPIO:0001938 454 Genome Sequencer Junior [GENEPIO:0001938] A 454 Genome Sequencer that performs pyrosequencing and is more compact. + OBI:0000696 SOLiD System [OBI:0000696] A DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation. + GENEPIO:0001929 SOLiD 5500 [GENEPIO:0001929] A DNA sequencer which is manufactured by Applied Biosystems and utillizes sequencing by ligation technology and faster run times than the SOLiD 4 series. + GENEPIO:0001930 SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930] A DNA sequencer which is manufactured by Applied Biosystems and has two FlowChips for across 12 lanes and with a higher throughput than the 5500 model. + GENEPIO:0100984 SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology and with a higher throughput than SOLiD 5500xl Genetic Analyzer. + OBI:0002007 SOLiD 3 Plus System [OBI:0002007] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. + OBI:0002024 SOLiD 4 System [OBI:0002024] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 100 Gb mappable throughput. + GENEPIO:0001928 SOLiD 4hq System [GENEPIO:0001928] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 300 Gb mappable throughput. + GENEPIO:0001931 SOLiD PI System [GENEPIO:0001931] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine offers 50Gb mappable throughput. + GENEPIO:0001932 SOLiD System 2.0 [GENEPIO:0001932] A DNA sequencer which is manufactured by the Applied Biosystems corporation. + GENEPIO:0001933 SOLiD System 3.0 [GENEPIO:0001933] A DNA sequencer which is manufactured by the Applied Biosystems corporation. + OBI:0000717 HeliScope Single Molecule Sequencer [OBI:0000717] A DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry. + GENEPIO:0100974 Applied Biosystems sequencing instrument model [GENEPIO:0100974] A sequencing instrument model that is manufactured by Applied Biosystems and which performs Sanger sequencing and fragment analysis by capillary electrophoresis. + GENEPIO:0100975 AB 310 Genetic Analyzer [GENEPIO:0100975] An Applied Biosystems sequencing instrument model which utilises a single capillary electrophoresis system to perform Sanger sequencing and fragment analysis that is automated. + GENEPIO:0100976 AB 3130 Genetic Analyzer [GENEPIO:0100976] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 4 capillaries. + GENEPIO:0100977 AB 3130xL Genetic Analyzer [GENEPIO:0100977] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 16 capillaries. + GENEPIO:0100978 AB 3500 Genetic Analyzer [GENEPIO:0100978] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 8 capillaries, which can run 96 well plates. + GENEPIO:0100979 AB 3500xL Genetic Analyzer [GENEPIO:0100979] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 24 capillaries, which can run 384 well plates. + GENEPIO:0100980 AB 3730 Genetic Analyzer [GENEPIO:0100980] An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing. + GENEPIO:0100981 AB 3730xL Genetic Analyzer [GENEPIO:0100981] An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing. + +sequencing assay type menu SequencingAssayTypeMenu OBI:0002767 Amplicon sequencing assay [OBI:0002767] A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. AMPLICON + OBI:0002763 16S ribosomal gene sequencing assay [OBI:0002763] An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. AMPLICON + OBI:0002117 Whole genome sequencing assay [OBI:0002117] A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. WGS + OBI:0002623 Whole metagenome sequencing assay [OBI:0002623] A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. OTHER + OBI:0002768 Whole virome sequencing assay [OBI:0002768] A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. OTHER + +amplicon pcr primer scheme menu AmpliconPcrPrimerSchemeMenu GENEPIO:0100847 artic-v1 [GENEPIO:0100847] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 1.0.0. artic-v1 + GENEPIO:0100848 artic-v2 [GENEPIO:0100848] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 2.0.0. artic-v2 + GENEPIO:0100849 artic-v3 [GENEPIO:0100849] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 3.0.0. artic-v3 + GENEPIO:0100850 artic-v4 [GENEPIO:0100850] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.0.0. artic-v4 + GENEPIO:0100851 artic-v4.1 [GENEPIO:0100851] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.1.0. artic-v4.1 + GENEPIO:0100852 artic-v5.0.0_400 [GENEPIO:0100852] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons approximately 400bp in length. artic-v5.0.0_400 + GENEPIO:0100853 artic-v5.1.0_400 [GENEPIO:0100853] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons approximately 400bp in length. artic-v5.1.0_400 + GENEPIO:0100854 artic-v5.2.0_1200 [GENEPIO:0100854] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 1200bp in length. artic-v5.2.0_1200 + GENEPIO:0100855 artic-v5.2.0_400 [GENEPIO:0100855] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 400bp in length. artic-v5.2.0_400 + GENEPIO:0100856 artic-v5.3.2_400 [GENEPIO:0100856] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons approximately 400bp in length. artic-v5.3.2_400 + GENEPIO:0100857 eden-v1 [GENEPIO:0100857] An amplicon strategy which was developed by John-Sebastian Eden with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces amplicons approximately 2500bp in length. eden-v1 + GENEPIO:0100858 midnight-bccdc-v1 [GENEPIO:0100858] An amplicon strategy which is for SARS-CoV-2 and based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v1 + GENEPIO:0100859 midnight-bccdc-v2 [GENEPIO:0100859] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v2 + GENEPIO:0100860 midnight-bccdc-v3 [GENEPIO:0100860] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 3.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v3 + GENEPIO:0100861 midnight-bccdc-v4 [GENEPIO:0100861] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 4.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v4 + GENEPIO:0100862 midnight-ont-v3 [GENEPIO:0100862] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. midnight-ont-v3 + GENEPIO:0100863 midnight-v1 [GENEPIO:0100863] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. midnight-v1 + GENEPIO:0100864 midnight-v2 [GENEPIO:0100864] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. midnight-v2 + GENEPIO:0100865 varskip-vsl1a [GENEPIO:0100865] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a long. varskip-vsl1a + GENEPIO:0100866 varskip-vss1a [GENEPIO:0100866] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a short. varskip-vss1a + GENEPIO:0100867 varskip-vss2a [GENEPIO:0100867] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2a. varskip-vss2a + GENEPIO:0100868 varskip-vss2b [GENEPIO:0100868] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2b. varskip-vss2b + +genomic target enrichment method menu GenomicTargetEnrichmentMethodMenu GENEPIO:0001950 Hybridization capture [GENEPIO:0001950] Selection by hybridization in array or solution. Hybrid Selection + GENEPIO:0101020 rRNA depletion method [GENEPIO:0101020] Removal of background RNA for the purposes of enriching the genomic target. Other + +quality control determination menu QualityControlDeterminationMenu GENEPIO:0100562 No quality control issues identified [GENEPIO:0100562] A statement confirming that quality control processes were carried out and no quality issues were detected. no quality control issues identified + GENEPIO:0100563 Sequence passed quality control [GENEPIO:0100563] A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. Sequence passed quality control + GENEPIO:0100564 Sequence failed quality control [GENEPIO:0100564] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. Sequence failed quality control + GENEPIO:0100565 Minor quality control issues identified [GENEPIO:0100565] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. minor quality control issues identified + GENEPIO:0100566 Sequence flagged for potential quality control issues [GENEPIO:0100566] A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. sequence flagged for potential quality control issues + GENEPIO:0100567 Quality control not performed [GENEPIO:0100567] A statement confirming that quality control processes have not been carried out. not performed + +quality control issues menu QualityControlIssuesMenu GENEPIO:0100568 Low quality sequence [GENEPIO:0100568] Sequence data that does not meet quality control thresholds. low quality sequence + GENEPIO:0100569 Sequence contaminated [GENEPIO:0100569] Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. sequenced contaminated + GENEPIO:0100570 Low average genome coverage [GENEPIO:0100570] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage). low average genome coverage + GENEPIO:0100571 Low percent genome captured [GENEPIO:0100571] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). low % genome captured + GENEPIO:0100572 Read lengths shorter than expected [GENEPIO:0100572] Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. read lengths shorter than expected + GENEPIO:0100573 Sequence amplification artifacts [GENEPIO:0100573] Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). sequence amplification artifacts + GENEPIO:0100574 Low signal to noise ratio [GENEPIO:0100574] Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). low signal to noise ratio + GENEPIO:0100575 Low coverage of characteristic mutations [GENEPIO:0100575] Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. low coverage of characteristic mutations + +gene symbol menu GeneSymbolMenu GENEPIO:0100151 E gene (orf4) [GENEPIO:0100151] + GENEPIO:0100152 M gene (orf5) [GENEPIO:0100152] + GENEPIO:0100153 N gene (orf9) [GENEPIO:0100153] + GENEPIO:0100154 Spike gene (orf2) [GENEPIO:0100154] + GENEPIO:0100155 orf1ab (rep) [GENEPIO:0100155] + GENEPIO:0100156 orf1a (pp1a) [GENEPIO:0100156] + GENEPIO:0100157 nsp11 [GENEPIO:0100157] + GENEPIO:0100158 nsp1 [GENEPIO:0100158] + GENEPIO:0100159 nsp2 [GENEPIO:0100159] + GENEPIO:0100160 nsp3 [GENEPIO:0100160] + GENEPIO:0100161 nsp4 [GENEPIO:0100161] + GENEPIO:0100162 nsp5 [GENEPIO:0100162] + GENEPIO:0100163 nsp6 [GENEPIO:0100163] + GENEPIO:0100164 nsp7 [GENEPIO:0100164] + GENEPIO:0100165 nsp8 [GENEPIO:0100165] + GENEPIO:0100166 nsp9 [GENEPIO:0100166] + GENEPIO:0100167 nsp10 [GENEPIO:0100167] + GENEPIO:0100168 RdRp gene (nsp12) [GENEPIO:0100168] + GENEPIO:0100169 hel gene (nsp13) [GENEPIO:0100169] + GENEPIO:0100170 exoN gene (nsp14) [GENEPIO:0100170] + GENEPIO:0100171 nsp15 [GENEPIO:0100171] + GENEPIO:0100172 nsp16 [GENEPIO:0100172] + GENEPIO:0100173 orf3a [GENEPIO:0100173] + GENEPIO:0100174 orf3b [GENEPIO:0100174] + GENEPIO:0100175 orf6 (ns6) [GENEPIO:0100175] + GENEPIO:0100176 orf7a [GENEPIO:0100176] + GENEPIO:0100177 orf7b (ns7b) [GENEPIO:0100177] + GENEPIO:0100178 orf8 (ns8) [GENEPIO:0100178] + GENEPIO:0100179 orf9b [GENEPIO:0100179] + GENEPIO:0100180 orf9c [GENEPIO:0100180] + GENEPIO:0100181 orf10 [GENEPIO:0100181] + GENEPIO:0100182 orf14 [GENEPIO:0100182] + GENEPIO:0100183 SARS-COV-2 5' UTR [GENEPIO:0100183] + +diagnostic target presence menu DiagnosticTargetPresenceMenu GENEPIO:0100987 diagnostic target present [GENEPIO:0100987] A quality inhering in a bearer by virtue of the bearer's existence. + GENEPIO:0100988 diagnostic target absent [GENEPIO:0100988] Aquality denoting the lack of an entity. + +diagnostic measurement unit menu DiagnosticMeasurementUnitMenu gene copies per liter (GC/L) A unit that measures the number of copies of a given gene within a liter of a biological material. + GENEPIO:0100657 cycle threshold (Ct) [GENEPIO:0100657] A data field which describes the cycle threshold (Ct) value result from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) test. + UO:0000213 colony forming units per milliliter (CFU/mL) [UO:0000213] A unit of microbial density that describes the number of colony forming units within a milliliter of material. + colony forming units per 100 milliliter (CFU/100 mL) A unit of microbial density that describes the number of colony forming units within 100 milliliters of material. + colony forming units per grams total solids (CFU/gTS) A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material. + most probable number per milliliter (MPN/mL) A unit of microbial density that describes the most probable number of microbes within one milliliter of material. + most probable number per 100 milliliter (MPN/100 mL) A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material. + +diagnostic measurement method menu DiagnosticMeasurementMethodMenu OBI:0000893 Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893] An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. + Digital real time polymerase chain reaction (dPCR) A type of polymerase chain reaction technique in which the sample is fractionated, within which individual PCR reactions occur in each fraction + Bacteria culture test An assay to identify the presence of bacteria \ No newline at end of file diff --git a/web/templates/wastewater/schema_slots.tsv b/web/templates/wastewater/schema_slots.tsv index 166a379a..0bc066c9 100644 --- a/web/templates/wastewater/schema_slots.tsv +++ b/web/templates/wastewater/schema_slots.tsv @@ -1,266 +1,266 @@ -class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_NCBI_BIOSAMPLE_SARS-COV-2_WWS EXPORT_NCBI_SRA EXPORT_VirusSeq_Portal -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001122 Database Identifiers -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. ASDFG123 sample_name sample_name -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100752 specimen collector subsample ID specimen_collector_subsample_id WhitespaceMinimizedString The user-defined identifier assigned to a portion of the original sample. Store the ID for the subsample/aliquot. ASDFG123_12 specimen_processing_id -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100996 pooled sample ID pooled_sample_id WhitespaceMinimizedString The user-defined identifier assigned to a combined (pooled) set of samples. If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID. 12345AYZ -WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100753 metagenome-assembled genome (MAG) ID metagenomeassembled_genome_mag_id WhitespaceMinimizedString The user-defined identifier assigned to a genome reconstructed from metagenomic data. Store the MAG ID. XYZ1234.1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100918 specimen collector project ID specimen_collector_project_id WhitespaceMinimizedString The user-defined project name assigned to a sequencing project. If the sample was collected or analyzed under the umbrella of a specific project, include the name of that project here. project_name -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001136 BioProject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 bioproject_accession -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001139 BioSample accession biosample_accession WhitespaceMinimizedString TRUE {UPPER_CASE} {UPPER_CASE} The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD SAMN14180202, SAMEA00000002, SAMD00000001 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. ERR123456, DRR123456, CRR123456 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100759 Enterobase accession enterobase_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in Enterobase archives. Store the barcode assigned to the submitted sequence. Enterobase barcodes start with different 3 letter codes depending on the organism. SAL_AA0019AA_ST -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives. Store the accession assigned to the submitted sequence. GISAID accessions start with EPI. EPI_ISL_402131 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100282 GISAID virus name gisaid_virus_name WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The user-defined GISAID virus name assigned to the sequence. GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". hCoV-19/Canada/prov_rona_99/2020 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100760 sampling site ID sampling_site_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific location from which samples are taken. Store the ID for the site from which a sample was taken. The "site" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID. Site 12A collection_site_id -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100761 sampling event ID sampling_event_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites. Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site. Event 120522.1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001150 Sample collection and processing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100762 sample collection data steward name sample_collection_data_steward_name WhitespaceMinimizedString The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the name of the sample collection data steward. Joe Bloggs -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100428 sample collected by laboratory name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada collected_by -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100432 sample collector contact name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca WaterTester@facility.ca -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001181 geo loc name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. If known, select a value from the pick list. Canada -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001185 geo loc name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga Western Cape -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100280 geo loc name (county/region) geo_loc_name_county_region WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001189 geo loc name (city) geo_loc_name_city WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100436 geo loc name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100309 geo loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100310 geo loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100919 watershed shapefile availability watershed_shapefile_availability WatershedShapefileAvailabilityMenu NullValueMenu The availability status of a shapefile descriping the catchment contributing to a watershed. Select a value from the picklist to describe whether or not a watershed shapefile would be available upon request. watershed shapefile available -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100920 watershed shapefile filename watershed_shapefile_filename WhitespaceMinimizedString The name of the watershed shapefile. Provide the shapefile filename corresponding to the watershed from which the sample was taken. If there are multiple files associated with the watershed, provide all names separated by commas. siteAD17.shp, siteAD17.kml -WastewaterSARS-CoV-2 Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism present in the sample. For SARS-CoV-2, use "Severe acute respiratory syndrome coronavirus 2" provided in the picklist. Severe acute respiratory syndrome coronavirus 2 ww_surv_target_1 -WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 -WastewaterAMR Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample if AMR profiles are assigned to organisms. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Public health surveillance purpose_of_ww_sampling -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100877 scale of sampling scale_of_sampling ScaleOfSamplingMenu NullValueMenu TRUE The range of locations or entities sampled expressed in general terms. Provide the scale of wastewater sampling by selecting a value from the picklist. Community-level surveillance purpose_of_ww_sampling -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu {today} The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001174 sample collection start date sample_collection_start_date date NullValueMenu TRUE {today} The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101071 sample collection end date sample_collection_end_date date NullValueMenu TRUE {sample_collection_start_date} {today} The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date NullValueMenu {today} The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101072 sample collection start time sample_collection_start_time time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101073 sample collection end time sample_collection_end_time time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100765 sample collection time of day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100766 sample collection time duration value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 4 ww_sample_duration -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100767 sample collection time duration unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour ww_sample_duration -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100433 presampling activity presampling_activity PresamplingActivityMenu NullValueMenu TRUE The activities or variables upstream of sample collection that may affect the sample. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Agricultural activity -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100434 presampling activity details presampling_activity_details WhitespaceMinimizedString NullValueMenu The details of the activities or variables that affected the sample collected. Briefly describe the presampling activities using free text. Agricultural waste from large farm contributes waste to the site sampled. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100768 sample volume measurement value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 collection_volume -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100769 sample volume measurement unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu NullValueMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. mL collection_volume -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100448 sample storage method sample_storage_method WhitespaceMinimizedString The process used to store the sample. Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here. The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100449 sample storage medium sample_storage_medium WhitespaceMinimizedString The medium in which a sample is stored. Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write "None". Cary-Blair transport medium -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101014 sample storage duration value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101015 sample storage duration unit sample_storage_duration_unit SampleStorageDurationUnitMenu NullValueMenu The units of a measured sample storage duration. Provide the units from the pick list. Day -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Select processes from the picklist that were applied to this sample. Centrifugation specimen_processing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. specimen_processing_details -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101029 experimental protocol field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001232 environmental site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor of the environmental site sampled. Use the picklist provided in the template. If not applicable, choose a null value. Meat processing plant ww_sample_site -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101205 proximal environmental site proximal_environmental_site EnvironmentalSiteMenu TRUE An environmental location in the natural or built environment, that is proximal to a sampling location and which can impact a sample. Provide a descriptor of the environmental site close to the sampling site. Use the picklist provided in the template. If not applicable, choose a null value. Farm -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor of the environmental material sampled. Use the picklist provided in the template. If not applicable, choose a null value. Raw wastewater ww_sample_matrix -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100770 environmental material properties environmental_material_properties EnvironmentalMaterialPropertiesMenu NullValueMenu TRUE TRUE The properties, characteristics and qualities of a substance obtained from the natural or man-made environment. Provide the environmental material properties by selecting descriptors from the pick list. Stagnant -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100771 wastewater system type wastewater_system_type WastewaterSystemTypeMenu NullValueMenu TRUE The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine Provide the classification of the wastewater system by selecting from the provided pick list. Sanitary sewer -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100922 experimental control details experimental_control_details WhitespaceMinimizedString The details regarding the experimental control contained in the sample. Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor. Human coronavirus 229E (HCoV-229E) spiked in sample as process control -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. grab sampler. Provide a descriptor of the device used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic flow-proportional sampler -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample. Provide a descriptor of the collection method used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic composite sampling ww_sample_type -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 extraction_method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. ww_endog_control_1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100924 extraction recovery efficiency measurement value extraction_recovery_efficiency_measurement_value WhitespaceMinimizedString The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the amount expected. Provide value as a percent. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100925 extraction recovery efficiency measurement method extraction_recovery_efficiency_measurement_method WhitespaceMinimizedString The method by which recovery efficiency of an extraction was calculated. Provide a brief description of how extraction recovery efficiency was measured or estimated. -WastewaterPathogenAgnostic GENEPIO:0100453 Strain and isolation information -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100454 microbiological method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100456 isolate ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100457 alternative isolate ID alternative_isolate_id WhitespaceMinimizedString TRUE TRUE An alternative isolate_ID assigned to the isolate by another organization. Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]. Multiple alternative isolate IDs can be provided, separated by semi-colons. GHIF3456[PHAC]; QWICK222[CFIA] -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100458 progeny isolate ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100461 isolated by isolated_by WhitespaceMinimizedString The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100462 isolated by laboratory name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100463 isolated by contact name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100464 isolated by contact email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100465 isolation date isolation_date date {today} The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100466 isolate received date isolate_received_date WhitespaceMinimizedString {today} The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100468 serotyping method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100773 water catchment area human population measurement value water_catchment_area_human_population_measurement_value integer NullValueMenu TRUE The numerical value of the human population measurement that contributes to the composition of water in a catchment area. Where known, provide the numerical value of population size, i.e. the number of people. 10,500 ww_population -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100774 water catchment area human population range water_catchment_area_human_population_range WaterCatchmentAreaHumanPopulationRangeMenu NullValueMenu The human population range of the water catchment that contributes effluent to a wastewater site. Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist. 1,000 - 10,000 people -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100775 water catchment area human population measurement method water_catchment_area_human_population_measurement_method WhitespaceMinimizedString The method by which a water catchment 's human population size was measured or estimated Provide a brief description of how catchment population size was measured or estimated. population of jurisdiction encompassing the wastewater service area ww_population_source -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100776 water catchment area human population density value water_catchment_area_human_population_density_value WhitespaceMinimizedString The numerical value describing the number of humans per geographical area in a water catchment. Provide the numerical value of the population density in the catchement area. 4 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water_catchment_area_human_population_density_unit WaterCatchmentAreaHumanPopulationDensityUnitMenu NullValueMenu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type PopulatedAreaTypeMenu NullValueMenu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling_weather_conditions PresamplingWeatherConditionsMenu NullValueMenu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString NullValueMenu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100913 precipitation measurement method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100935 ambient temperature measurement value ambient_temperature_measurement_value WhitespaceMinimizedString The numerical value of a measurement of the ambient temperature. Provide the numerical value of the measured temperature. 70 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100936 ambient temperature measurement unit ambient_temperature_measurement_unit AmbientTemperatureMeasurementUnitMenu NullValueMenu The units of a measurement of the ambient temperature. Provide the units of the measured temperature. degree Celsius (C) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0001736 pH measurement value ph_measurement_value WhitespaceMinimizedString The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution. Provide the numerical value of the measured pH. 7.4 ww_ph -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100781 pH measurement method ph_measurement_method WhitespaceMinimizedString The process used to measure pH value. Provide the name of the procedure or technology used to measure pH. pH test strip (litmus test) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100905 total daily flow rate measurement value total_daily_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured fluid flow rate over the course of a day. Provide the numerical value of the measured flow rate. 10 ww_flow -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100906 total daily flow rate measurement unit total_daily_flow_rate_measurement_unit TotalDailyFlowRateMeasurementUnitMenu NullValueMenu The units of a measured fluid flow rate over the course of a day. Provide the units of the measured flow rate by selecting a value from the pick list. million gallons per day (MGD) ww_flow -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100907 total daily flow rate measurement method total_daily_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure total daily fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100908 instantaneous flow rate measurement value instantaneous_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured instantaneous fluid flow rate. Provide the numerical value of the measured flow rate. 25 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100909 instantaneous flow rate measurement unit instantaneous_flow_rate_measurement_unit InstantaneousFlowRateMeasurementUnitMenu NullValueMenu The units of a measured instantaneous fluid flow rate. Provide the units of the measured flow rate by selecting a value from the pick list. cubic meter per hour (m^3/h) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100910 instantaneous flow rate measurement method instantaneous_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure instantaneous fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100783 turbidity measurement value turbidity_measurement_value WhitespaceMinimizedString TRUE The numerical value of a measurement of turbidity. Provide the numerical value of the measured turbidity. 0.02 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100914 turbidity measurement unit turbidity_measurement_unit TurbidityMeasurementUnitMenu NullValueMenu TRUE The units of a measurement of turbidity. Provide the units of the measured turbidity by selecting a value from the pick list. nephelometric turbidity unit (NTU) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0101013 turbidity measurement method turbidity_measurement_method WhitespaceMinimizedString The process used to measure turbidity. Provide the name of the procedure or technology used to measure turbidity. Nephelometric method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0000035 dissolved oxygen measurement value dissolved_oxygen_measurement_value WhitespaceMinimizedString The numerical value of a measurement of dissolved oxygen. Provide the numerical value of the measured dissolved oxygen. 5 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100784 dissolved oxygen measurement unit dissolved_oxygen_measurement_unit DissolvedOxygenMeasurementUnitMenu NullValueMenu The units of a measurement of dissolved oxygen. Provide the units of the measured dissolved oxygen by selecting a value from the pick list. part per million (ppm) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100785 dissolved oxygen measurement method dissolved_oxygen_measurement_method WhitespaceMinimizedString The method used to measure dissolved oxygen. Provide the name of the procedure or technology used to measure dissolved oxygen. Dissolved oxygen meter in vertical direction -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements FIX:0000278 oxygen reduction potential (ORP) measurement value oxygen_reduction_potential_orp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of oxygen reduction potential (ORP). Provide the numerical value of the measured oxygen reduction potential. -50 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100786 oxygen reduction potential (ORP) measurement unit oxygen_reduction_potential_orp_measurement_unit OxygenReductionPotentialOrpMeasurementUnitMenu NullValueMenu The units of a measurement of oxygen reduction potential (ORP). Provide the units of the measured oxygen reduction potential by selecting a value from the pick list. milliVolt (mV) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100787 oxygen reduction potential (ORP) measurement method oxygen_reduction_potential_orp_measurement_method WhitespaceMinimizedString The method used to measure oxygen reduction potential (ORP). Provide the name of the procedure or technology used to measure oxygen reduction potential. ORP sensor -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100788 chemical oxygen demand (COD) measurement value chemical_oxygen_demand_cod_measurement_value WhitespaceMinimizedString The measured value from a chemical oxygen demand (COD) test. Provide the numerical value of the COD test result. 26 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100789 chemical oxygen demand (COD) measurement unit chemical_oxygen_demand_cod_measurement_unit ChemicalOxygenDemandCodMeasurementUnitMenu NullValueMenu The units associated with a value from a chemical oxygen demand (COD) test. Provide the units of the COD test result. milligram per liter (mg/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100790 chemical oxygen demand (COD) measurement method chemical_oxygen_demand_cod_measurement_method WhitespaceMinimizedString The method used to measure chemical oxygen demand (COD). Provide the name of the procedure or technology used to measure COD. Hach LCK test kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100791 carbonaceous biochemical oxygen demand (CBOD) measurement value carbonaceous_biochemical_oxygen_demand_cbod_measurement_value WhitespaceMinimizedString The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the numerical value of the measured CBOD. 20 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100792 carbonaceous biochemical oxygen demand (CBOD) measurement unit carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu NullValueMenu The units of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the units of the measured CBOD by selecting a value from the pick list. milligram per liter (mg/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100793 carbonaceous biochemical oxygen demand (CBOD) measurement method carbonaceous_biochemical_oxygen_demand_cbod_measurement_method WhitespaceMinimizedString The method used to measure carbonaceous biochemical oxygen demand (CBOD). Provide the name of the procedure or technology used to measure CBOD. CBOD measurement by optical probe -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100794 total suspended solids (TSS) measurement value total_suspended_solids_tss_measurement_value WhitespaceMinimizedString The numerical value from a total suspended solids (TSS) test. Provide the numerical value of the measured TSS. 8 ww_total_suspended_solids -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100795 total suspended solids (TSS) measurement unit total_suspended_solids_tss_measurement_unit TotalSuspendedSolidsTssMeasurementUnitMenu NullValueMenu The units associated with a value from a total suspended solids (TSS) test. Provide the units of the measured TSS. percent (%) ww_total_suspended_solids -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100796 total suspended solids (TSS) measurement method total_suspended_solids_tss_measurement_method WhitespaceMinimizedString The method used to measure total suspended solids (TSS). Provide the name of the procedure or technology used to measure TSS. Vacuum filter through a 2-micron filter, then oven-dried and weighed sample -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100797 total dissolved solids (TDS) measurement value total_dissolved_solids_tds_measurement_value WhitespaceMinimizedString The numerical value from a total dissolved solids (TDS) test. Provide the numerical value of the measured TDS. 2 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100798 total dissolved solids (TDS) measurement unit total_dissolved_solids_tds_measurement_unit TotalDissolvedSolidsTdsMeasurementUnitMenu NullValueMenu The units associated with a value from a total dissolved solids (TDS) test. Provide the units of the measured TDS. percent (%) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100799 total dissolved solids (TDS) measurement method total_dissolved_solids_tds_measurement_method WhitespaceMinimizedString The method used to measure total dissolved solids (TDS). Provide the name of the procedure or technology used to measure TDS. Subtract calculated TSS from calculated TS -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100800 total solids (TS) measurement value total_solids_ts_measurement_value WhitespaceMinimizedString The numerical value from a total solids (TS) test. Provide the numerical value of the measured TS. 10 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100801 total solids (TS) measurement unit total_solids_ts_measurement_unit TotalSolidsTsMeasurementUnitMenu NullValueMenu The units associated with a value from a total solids (TS) test. Provide the units of the measured TS. percent (%) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100802 total solids (TS) measurement method total_solids_ts_measurement_method WhitespaceMinimizedString The method used to measure total solids (TS). Provide the name of the procedure or technology used to measure TS. Gravimetric method by oven drying, then weighing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100878 alkalinity measurement value alkalinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of alkalinity. Provide the numerical value of the measured alkalinity. 3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100879 alkalinity measurement unit alkalinity_measurement_unit AlkalinityMeasurementUnitMenu NullValueMenu The units of a measurement of alkalinity. Provide the units of the measured alkalinity. milligram per liter of calcium carbonate (mg/L CaCO3) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100880 alkalinity measurement method alkalinity_measurement_method WhitespaceMinimizedString The process used to measure alkalinity. Provide the name of the procedure or technology used to measure alkalinity. Titration method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100916 conductivity measurement value conductivity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of conductivity. Provide the numerical value of the measured conductivity. 1412 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100803 conductivity measurement unit conductivity_measurement_unit ConductivityMeasurementUnitMenu NullValueMenu The units of a measurement of conductivity. Provide the units of the measured conductivity. microSiemen per centimeter (μS/cm) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100804 conductivity measurement method conductivity_measurement_method WhitespaceMinimizedString The method used to measure conductivity. Provide the name of the procedure or technology used to measure conductivity. Conductivity electrode and meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100805 salinity measurement value salinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of salinity. Provide the numerical value of the measured salinity. 35 ww_sample_salinity -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100806 salinity measurement unit salinity_measurement_unit SalinityMeasurementUnitMenu NullValueMenu The units of a measurement of salinity. Provide the units of the measured salinity. practical salinity unit (PSU) ww_sample_salinity -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100807 salinity measurement method salinity_measurement_method WhitespaceMinimizedString The method used to measure salinity. Provide the name of the procedure or technology used to measure salinity. conductivity meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100808 total nitrogen (TN) measurement value total_nitrogen_tn_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total nitrogen (TN). Provide the numerical value of the measured TN. 120 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total_nitrogen_tn_measurement_unit TotalNitrogenTnMeasurementUnitMenu NullValueMenu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100810 total nitrogen (TN) measurement method total_nitrogen_tn_measurement_method WhitespaceMinimizedString The method used to measure total nitrogen (TN). Provide the name of the procedure or technology used to measure TN. Hach total nitrogen spectrophotometric test -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100811 total phosphorus (TP) measurement value total_phosphorus_tp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total phosphorus (TP). Provide the numerical value of the measured TP. 2 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit TotalPhosphorpusTpMeasurementUnitMenu NullValueMenu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100813 total phosphorus (TP) measurement method total_phosphorus_tp_measurement_method WhitespaceMinimizedString The method used to measure total phosphorus (TP). Provide the name of the procedure or technology used to measure TP. Merck phosphate spectrophotometric test kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal_contamination_indicator FecalContaminationIndicatorMenu NullValueMenu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100815 fecal contamination value fecal_contamination_value WhitespaceMinimizedString TRUE The numerical value of a measurement of fecal contamination. Provide the numerical value of the measured fecal contamination. 10 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100816 fecal contamination unit fecal_contamination_unit FecalContaminationUnitMenu NullValueMenu TRUE The units of a measurement of fecal contamination. Provide the units of the measured fecal contamination. cycle threshold (Ct) / quantification cycle (Cq) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100817 fecal contamination method fecal_contamination_method WhitespaceMinimizedString The method used to measure fecal contamination. Provide the name of the procedure or technology used to measure fecal contamination. quantitative PCR assay -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100818 fecal coliform count value fecal_coliform_count_value WhitespaceMinimizedString The numerical value of a measurement of fecal coliforms within a sample. Provide the numerical value of the measured fecal coliforms. 3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100819 fecal coliform count unit fecal_coliform_count_unit FecalColiformCountUnitMenu NullValueMenu The units of a measurement of fecal coliforms. Provide the units of the measured fecal coliforms. most probable number per milliliter (MPN/mL) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100820 fecal coliform count method fecal_coliform_count_method WhitespaceMinimizedString The method used to measure fecal coliforms. Provide the name of the procedure or technology used to measure fecal coliforms. MPN method via serial dilutions until lack of growth -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100837 urinary contamination indicator urinary_contamination_indicator UrinaryContaminationIndicatorMenu NullValueMenu A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination. If a urinary contamination indicator was measured, select it from the picklist. urobilin -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100838 urinary contamination value urinary_contamination_value WhitespaceMinimizedString The numerical value of a measurement of urinary contamination. Provide the numerical value of the measured urinary contamination. 3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100839 urinary contamination unit urinary_contamination_unit UrinaryContaminationUnitMenu NullValueMenu The units of a measurement of urinary contamination. Provide the units of the measured urinary contamination. nanograms per liter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100840 urinary contamination method urinary_contamination_method WhitespaceMinimizedString The method used to measure urinary contamination. Provide the name of the procedure or technology used to measure urinary contamination. Urobilin Concentration Test -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100821 sample temperature value (at collection) sample_temperature_value_at_collection WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample at collection. Provide the numerical value of the measured temperature. 20 ww_temperature -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100822 sample temperature unit (at collection) sample_temperature_unit_at_collection SampleTemperatureUnitAtCollectionMenu NullValueMenu The units of a measurement of temperature of a sample at the time of collection. Provide the units of the measured temperature. degree Celsius (C) ww_temperature -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100823 sample temperature value (when received) sample_temperature_value_when_received WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample upon receipt. Provide the numerical value of the measured temperature. 22 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100824 sample temperature unit (when received) sample_temperature_unit_when_received SampleTemperatureUnitWhenReceivedMenu NullValueMenu The units of a measurement of temperature of a sample at the time upon receipt. Provide the units of the measured temperature. degree Celsius (C) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001441 Sequence Information -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance purpose_of_ww_sequencing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100416 sequenced by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) sequenced_by -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString NullValueMenu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca sequence_submitter_contact_email -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001447 sequencing date sequencing_date date {sample_collection_date} {today} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001448 library ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100473 sequencing platform sequencing_platform SequencingPlatformMenu NullValueMenu TRUE The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] platform -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] instrument_model -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeMenu NullValueMenu TRUE The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay library_strategy; library_source -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT library_preparation_kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001454 sequencing protocol sequencing_protocol WhitespaceMinimizedString TRUE The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no design_description -WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100843 DNA fragment length dna_fragment_length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 -WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method library_selection; design_description -WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme AmpliconPcrPrimerSchemeMenu NullValueMenu TRUE The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 amplicon_PCR_primer_scheme -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001449 amplicon size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 amplicon_size -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001457 Bioinformatics and QC metrics -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools quality_control_method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 quality_control_method_version -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control quality_control_determination -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage quality_control_issues -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. quality_control_details -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version or a link to the github protocol e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 raw_sequence_data_processing_method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper dehosting_method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString NullValueMenu The name of the consensus sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta filename -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101716 genome sequence file path genome_sequence_file_path WhitespaceMinimizedString NullValueMenu The filepath of the consensus sequence file. Provide the filepath of the genome sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta -WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet -WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 -WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 assembly -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf -WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0101082 Taxonomic identification information -WastewaterAMR Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat -WastewaterAMR Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 -WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat -WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date {today} The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 -WastewaterAMR GENEPIO:0100479 AMR detection information -WastewaterAMR AMR detection information GENEPIO:0101076 AMR analysis software name amr_analysis_software_name WhitespaceMinimizedString TRUE The name of the software used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the software used for AMR analysis. Resistance Gene Identifier -WastewaterAMR AMR detection information GENEPIO:0101077 AMR analysis software version amr_analysis_software_version WhitespaceMinimizedString TRUE The version number of the software used to perform an in silico antimicrobial resistance determinant idenrtification/analysis. Provide the version number of the software used for AMR analysis. 6.0.3 -WastewaterAMR AMR detection information GENEPIO:0101078 AMR reference database name amr_reference_database_name WhitespaceMinimizedString TRUE Thr name of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the reference database used for AMR analysis. Comprehensive Antibiotic Resistance Database (CARD) -WastewaterAMR AMR detection information GENEPIO:0101079 AMR reference database version amr_reference_database_version WhitespaceMinimizedString TRUE The version number of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the version number of the reference database used for AMR analysis. 3.2.9 -WastewaterAMR AMR detection information GENEPIO:0101080 AMR analysis report filename amr_analysis_report_filename WhitespaceMinimizedString TRUE The filename of the report containing the results of an in silico antimicrobial resistance analysis. Provide the filename of the report containing the results of the AMR analysis. WWAMR_report_Feb1_2024.doc -WastewaterSARS-CoV-2 GENEPIO:0001498 Lineage/clade information -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001500 lineage/clade name lineage_clade_name WhitespaceMinimizedString The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. Multiple lineages/clades can be provided, separated by a semicolon. B.1.1.7 -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001501 lineage/clade analysis software name lineage_clade_analysis_software_name WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Freyja -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001502 lineage/clade analysis software version lineage_clade_analysis_software_version WhitespaceMinimizedString The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 1.5.0 -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0101081 lineage/clade analysis report filename lineage_clade_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a lineage/clade analysis. Provide the filename of the report containing the results of the lineage/clade analysis. aggregated-WWSC2-ABC-b_1234.tsv -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001506 Pathogen diagnostic testing -WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102049 target taxonomic name 1 target_taxonomic_name_1 WhitespaceMinimizedString The scientific name of the organism or taxon that is the focus of the study, assay, or diagnostic test. The target taxonomic name refers to the specific species, genus, or other taxonomic classification that the assay or diagnostic test is designed to identify, detect, or characterize. This may include the full binomial name (Genus species) or a higher taxonomic rank (e.g., genus, family) when species-level identification is not applicable. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. ww_surv_target_1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102052 assay target name 1 assay_target_name_1 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102040 assay target details assay_target_details WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -WastewaterSARS-CoV-2 Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) -WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100962 diagnostic target presence 1 diagnostic_target_presence_1 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_1_known_present -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100963 diagnostic measurement value 1 diagnostic_measurement_value_1 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_1_conc -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100964 diagnostic measurement unit 1 diagnostic_measurement_unit_1 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_1_conc_unit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100965 diagnostic measurement method 1 diagnostic_measurement_method_1 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR ww_surv_target_1_protocol -WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102050 target taxonomic name 2 The scientific name of the organism or taxon that is the focus of the study, assay, or diagnostic test. The target taxonomic name refers to the specific species, genus, or other taxonomic classification that the assay or diagnostic test is designed to identify, detect, or characterize. This may include the full binomial name (Genus species) or a higher taxonomic rank (e.g., genus, family) when species-level identification is not applicable. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. ww_surv_target_2 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102038 assay target name 2 assay_target_name_2 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102046 assay target details 2 assay_target_details_2 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -WastewaterSARS-CoV-2 Pathogen diagnostic testing GENEPIO:0102042 gene symbol 2 gene_symbol_2 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) ww_surv_target_2_gene -WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102042 gene symbol 2 gene_symbol_2 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A ww_surv_target_2_gene -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 2 diagnostic_target_presence_2 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_2_known_present -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 2 diagnostic_measurement_value_2 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_2_conc -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 2 diagnostic_measurement_unit_2 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_2_conc_unit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 2 diagnostic_measurement_method_2 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR -WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102051 target taxonomic name 3 The scientific name of the organism or taxon that is the focus of the study, assay, or diagnostic test. The target taxonomic name refers to the specific species, genus, or other taxonomic classification that the assay or diagnostic test is designed to identify, detect, or characterize. This may include the full binomial name (Genus species) or a higher taxonomic rank (e.g., genus, family) when species-level identification is not applicable. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102039 assay target name 3 assay_target_name_3 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102047 assay target details 3 assay_target_details_3 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -WastewaterSARS-CoV-2 Pathogen diagnostic testing GENEPIO:0102043 gene symbol 3 gene_symbol_3 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) -WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102043 gene symbol 3 gene_symbol_3 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 3 diagnostic_target_presence_3 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 3 diagnostic_measurement_value_3 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 3 diagnostic_measurement_unit_3 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 3 diagnostic_measurement_method_3 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001516 Contributor acknowledgement -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001517 authors authors TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a semicolon. Tejinder Singh; Fei Hu; Joe Blogs Authors -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v3.3.3, Influenza v1.0.0 DataHarmonizer provenance \ No newline at end of file +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_NCBI_BIOSAMPLE_SARS-COV-2_WWS EXPORT_NCBI_SRA EXPORT_VirusSeq_Portal +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001122 Database Identifiers +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. ASDFG123 sample_name sample_name +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100752 specimen collector subsample ID specimen_collector_subsample_id WhitespaceMinimizedString The user-defined identifier assigned to a portion of the original sample. Store the ID for the subsample/aliquot. ASDFG123_12 specimen_processing_id +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100996 pooled sample ID pooled_sample_id WhitespaceMinimizedString The user-defined identifier assigned to a combined (pooled) set of samples. If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID. 12345AYZ +WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100753 metagenome-assembled genome (MAG) ID metagenomeassembled_genome_mag_id WhitespaceMinimizedString The user-defined identifier assigned to a genome reconstructed from metagenomic data. Store the MAG ID. XYZ1234.1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100918 specimen collector project ID specimen_collector_project_id WhitespaceMinimizedString The user-defined project name assigned to a sequencing project. If the sample was collected or analyzed under the umbrella of a specific project, include the name of that project here. project_name +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001136 BioProject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 bioproject_accession +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001139 BioSample accession biosample_accession WhitespaceMinimizedString TRUE {UPPER_CASE} {UPPER_CASE} The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD SAMN14180202, SAMEA00000002, SAMD00000001 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. ERR123456, DRR123456, CRR123456 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100759 Enterobase accession enterobase_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in Enterobase archives. Store the barcode assigned to the submitted sequence. Enterobase barcodes start with different 3 letter codes depending on the organism. SAL_AA0019AA_ST +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives. Store the accession assigned to the submitted sequence. GISAID accessions start with EPI. EPI_ISL_402131 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100282 GISAID virus name gisaid_virus_name WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The user-defined GISAID virus name assigned to the sequence. GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". hCoV-19/Canada/prov_rona_99/2020 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100760 sampling site ID sampling_site_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific location from which samples are taken. Store the ID for the site from which a sample was taken. The "site" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID. Site 12A collection_site_id +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100761 sampling event ID sampling_event_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites. Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site. Event 120522.1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001150 Sample collection and processing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100762 sample collection data steward name sample_collection_data_steward_name WhitespaceMinimizedString The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the name of the sample collection data steward. Joe Bloggs +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100428 sample collected by laboratory name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada collected_by +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100432 sample collector contact name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca WaterTester@facility.ca +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001181 geo loc name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. If known, select a value from the pick list. Canada +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001185 geo loc name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga Western Cape +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100280 geo loc name (county/region) geo_loc_name_county_region WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001189 geo loc name (city) geo_loc_name_city WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100436 geo loc name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100309 geo loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100310 geo loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100919 watershed shapefile availability watershed_shapefile_availability WatershedShapefileAvailabilityMenu NullValueMenu The availability status of a shapefile descriping the catchment contributing to a watershed. Select a value from the picklist to describe whether or not a watershed shapefile would be available upon request. watershed shapefile available +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100920 watershed shapefile filename watershed_shapefile_filename WhitespaceMinimizedString The name of the watershed shapefile. Provide the shapefile filename corresponding to the watershed from which the sample was taken. If there are multiple files associated with the watershed, provide all names separated by commas. siteAD17.shp, siteAD17.kml +WastewaterSARS-CoV-2 Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism present in the sample. For SARS-CoV-2, use "Severe acute respiratory syndrome coronavirus 2" provided in the picklist. Severe acute respiratory syndrome coronavirus 2 ww_surv_target_1 +WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 +WastewaterAMR Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample if AMR profiles are assigned to organisms. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Public health surveillance purpose_of_ww_sampling +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100877 scale of sampling scale_of_sampling ScaleOfSamplingMenu NullValueMenu TRUE The range of locations or entities sampled expressed in general terms. Provide the scale of wastewater sampling by selecting a value from the picklist. Community-level surveillance purpose_of_ww_sampling +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu {today} The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001174 sample collection start date sample_collection_start_date date NullValueMenu TRUE {today} The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101071 sample collection end date sample_collection_end_date date NullValueMenu TRUE {sample_collection_start_date} {today} The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date NullValueMenu {today} The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101072 sample collection start time sample_collection_start_time time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101073 sample collection end time sample_collection_end_time time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100765 sample collection time of day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100766 sample collection time duration value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 4 ww_sample_duration +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100767 sample collection time duration unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour ww_sample_duration +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100433 presampling activity presampling_activity PresamplingActivityMenu NullValueMenu TRUE The activities or variables upstream of sample collection that may affect the sample. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Agricultural activity +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100434 presampling activity details presampling_activity_details WhitespaceMinimizedString NullValueMenu The details of the activities or variables that affected the sample collected. Briefly describe the presampling activities using free text. Agricultural waste from large farm contributes waste to the site sampled. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100768 sample volume measurement value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 collection_volume +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100769 sample volume measurement unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu NullValueMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. mL collection_volume +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100448 sample storage method sample_storage_method WhitespaceMinimizedString The process used to store the sample. Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here. The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100449 sample storage medium sample_storage_medium WhitespaceMinimizedString The medium in which a sample is stored. Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write "None". Cary-Blair transport medium +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101014 sample storage duration value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101015 sample storage duration unit sample_storage_duration_unit SampleStorageDurationUnitMenu NullValueMenu The units of a measured sample storage duration. Provide the units from the pick list. Day +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Select processes from the picklist that were applied to this sample. Centrifugation specimen_processing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. specimen_processing_details +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101029 experimental protocol field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001232 environmental site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor of the environmental site sampled. Use the picklist provided in the template. If not applicable, choose a null value. Meat processing plant ww_sample_site +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101205 proximal environmental site proximal_environmental_site EnvironmentalSiteMenu TRUE An environmental location in the natural or built environment, that is proximal to a sampling location and which can impact a sample. Provide a descriptor of the environmental site close to the sampling site. Use the picklist provided in the template. If not applicable, choose a null value. Farm +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor of the environmental material sampled. Use the picklist provided in the template. If not applicable, choose a null value. Raw wastewater ww_sample_matrix +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100770 environmental material properties environmental_material_properties EnvironmentalMaterialPropertiesMenu NullValueMenu TRUE TRUE The properties, characteristics and qualities of a substance obtained from the natural or man-made environment. Provide the environmental material properties by selecting descriptors from the pick list. Stagnant +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100771 wastewater system type wastewater_system_type WastewaterSystemTypeMenu NullValueMenu TRUE The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine Provide the classification of the wastewater system by selecting from the provided pick list. Sanitary sewer +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100922 experimental control details experimental_control_details WhitespaceMinimizedString The details regarding the experimental control contained in the sample. Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor. Human coronavirus 229E (HCoV-229E) spiked in sample as process control +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. grab sampler. Provide a descriptor of the device used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic flow-proportional sampler +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample. Provide a descriptor of the collection method used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic composite sampling ww_sample_type +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 extraction_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. ww_endog_control_1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100924 extraction recovery efficiency measurement value extraction_recovery_efficiency_measurement_value WhitespaceMinimizedString The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the amount expected. Provide value as a percent. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100925 extraction recovery efficiency measurement method extraction_recovery_efficiency_measurement_method WhitespaceMinimizedString The method by which recovery efficiency of an extraction was calculated. Provide a brief description of how extraction recovery efficiency was measured or estimated. +WastewaterPathogenAgnostic GENEPIO:0100453 Strain and isolation information +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100454 microbiological method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100456 isolate ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100457 alternative isolate ID alternative_isolate_id WhitespaceMinimizedString TRUE TRUE An alternative isolate_ID assigned to the isolate by another organization. Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]. Multiple alternative isolate IDs can be provided, separated by semi-colons. GHIF3456[PHAC]; QWICK222[CFIA] +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100458 progeny isolate ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100461 isolated by isolated_by WhitespaceMinimizedString The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100462 isolated by laboratory name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100463 isolated by contact name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100464 isolated by contact email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100465 isolation date isolation_date date {today} The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100466 isolate received date isolate_received_date WhitespaceMinimizedString {today} The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100468 serotyping method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100773 water catchment area human population measurement value water_catchment_area_human_population_measurement_value integer NullValueMenu TRUE The numerical value of the human population measurement that contributes to the composition of water in a catchment area. Where known, provide the numerical value of population size, i.e. the number of people. 10,500 ww_population +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100774 water catchment area human population range water_catchment_area_human_population_range WaterCatchmentAreaHumanPopulationRangeMenu NullValueMenu The human population range of the water catchment that contributes effluent to a wastewater site. Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist. 1,000 - 10,000 people +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100775 water catchment area human population measurement method water_catchment_area_human_population_measurement_method WhitespaceMinimizedString The method by which a water catchment 's human population size was measured or estimated Provide a brief description of how catchment population size was measured or estimated. population of jurisdiction encompassing the wastewater service area ww_population_source +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100776 water catchment area human population density value water_catchment_area_human_population_density_value WhitespaceMinimizedString The numerical value describing the number of humans per geographical area in a water catchment. Provide the numerical value of the population density in the catchement area. 4 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water_catchment_area_human_population_density_unit WaterCatchmentAreaHumanPopulationDensityUnitMenu NullValueMenu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type PopulatedAreaTypeMenu NullValueMenu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling_weather_conditions PresamplingWeatherConditionsMenu NullValueMenu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString NullValueMenu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100913 precipitation measurement method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100935 ambient temperature measurement value ambient_temperature_measurement_value WhitespaceMinimizedString The numerical value of a measurement of the ambient temperature. Provide the numerical value of the measured temperature. 70 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100936 ambient temperature measurement unit ambient_temperature_measurement_unit AmbientTemperatureMeasurementUnitMenu NullValueMenu The units of a measurement of the ambient temperature. Provide the units of the measured temperature. degree Celsius (C) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0001736 pH measurement value ph_measurement_value WhitespaceMinimizedString The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution. Provide the numerical value of the measured pH. 7.4 ww_ph +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100781 pH measurement method ph_measurement_method WhitespaceMinimizedString The process used to measure pH value. Provide the name of the procedure or technology used to measure pH. pH test strip (litmus test) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100905 total daily flow rate measurement value total_daily_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured fluid flow rate over the course of a day. Provide the numerical value of the measured flow rate. 10 ww_flow +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100906 total daily flow rate measurement unit total_daily_flow_rate_measurement_unit TotalDailyFlowRateMeasurementUnitMenu NullValueMenu The units of a measured fluid flow rate over the course of a day. Provide the units of the measured flow rate by selecting a value from the pick list. million gallons per day (MGD) ww_flow +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100907 total daily flow rate measurement method total_daily_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure total daily fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100908 instantaneous flow rate measurement value instantaneous_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured instantaneous fluid flow rate. Provide the numerical value of the measured flow rate. 25 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100909 instantaneous flow rate measurement unit instantaneous_flow_rate_measurement_unit InstantaneousFlowRateMeasurementUnitMenu NullValueMenu The units of a measured instantaneous fluid flow rate. Provide the units of the measured flow rate by selecting a value from the pick list. cubic meter per hour (m^3/h) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100910 instantaneous flow rate measurement method instantaneous_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure instantaneous fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100783 turbidity measurement value turbidity_measurement_value WhitespaceMinimizedString TRUE The numerical value of a measurement of turbidity. Provide the numerical value of the measured turbidity. 0.02 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100914 turbidity measurement unit turbidity_measurement_unit TurbidityMeasurementUnitMenu NullValueMenu TRUE The units of a measurement of turbidity. Provide the units of the measured turbidity by selecting a value from the pick list. nephelometric turbidity unit (NTU) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0101013 turbidity measurement method turbidity_measurement_method WhitespaceMinimizedString The process used to measure turbidity. Provide the name of the procedure or technology used to measure turbidity. Nephelometric method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0000035 dissolved oxygen measurement value dissolved_oxygen_measurement_value WhitespaceMinimizedString The numerical value of a measurement of dissolved oxygen. Provide the numerical value of the measured dissolved oxygen. 5 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100784 dissolved oxygen measurement unit dissolved_oxygen_measurement_unit DissolvedOxygenMeasurementUnitMenu NullValueMenu The units of a measurement of dissolved oxygen. Provide the units of the measured dissolved oxygen by selecting a value from the pick list. part per million (ppm) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100785 dissolved oxygen measurement method dissolved_oxygen_measurement_method WhitespaceMinimizedString The method used to measure dissolved oxygen. Provide the name of the procedure or technology used to measure dissolved oxygen. Dissolved oxygen meter in vertical direction +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements FIX:0000278 oxygen reduction potential (ORP) measurement value oxygen_reduction_potential_orp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of oxygen reduction potential (ORP). Provide the numerical value of the measured oxygen reduction potential. -50 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100786 oxygen reduction potential (ORP) measurement unit oxygen_reduction_potential_orp_measurement_unit OxygenReductionPotentialOrpMeasurementUnitMenu NullValueMenu The units of a measurement of oxygen reduction potential (ORP). Provide the units of the measured oxygen reduction potential by selecting a value from the pick list. milliVolt (mV) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100787 oxygen reduction potential (ORP) measurement method oxygen_reduction_potential_orp_measurement_method WhitespaceMinimizedString The method used to measure oxygen reduction potential (ORP). Provide the name of the procedure or technology used to measure oxygen reduction potential. ORP sensor +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100788 chemical oxygen demand (COD) measurement value chemical_oxygen_demand_cod_measurement_value WhitespaceMinimizedString The measured value from a chemical oxygen demand (COD) test. Provide the numerical value of the COD test result. 26 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100789 chemical oxygen demand (COD) measurement unit chemical_oxygen_demand_cod_measurement_unit ChemicalOxygenDemandCodMeasurementUnitMenu NullValueMenu The units associated with a value from a chemical oxygen demand (COD) test. Provide the units of the COD test result. milligram per liter (mg/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100790 chemical oxygen demand (COD) measurement method chemical_oxygen_demand_cod_measurement_method WhitespaceMinimizedString The method used to measure chemical oxygen demand (COD). Provide the name of the procedure or technology used to measure COD. Hach LCK test kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100791 carbonaceous biochemical oxygen demand (CBOD) measurement value carbonaceous_biochemical_oxygen_demand_cbod_measurement_value WhitespaceMinimizedString The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the numerical value of the measured CBOD. 20 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100792 carbonaceous biochemical oxygen demand (CBOD) measurement unit carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu NullValueMenu The units of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the units of the measured CBOD by selecting a value from the pick list. milligram per liter (mg/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100793 carbonaceous biochemical oxygen demand (CBOD) measurement method carbonaceous_biochemical_oxygen_demand_cbod_measurement_method WhitespaceMinimizedString The method used to measure carbonaceous biochemical oxygen demand (CBOD). Provide the name of the procedure or technology used to measure CBOD. CBOD measurement by optical probe +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100794 total suspended solids (TSS) measurement value total_suspended_solids_tss_measurement_value WhitespaceMinimizedString The numerical value from a total suspended solids (TSS) test. Provide the numerical value of the measured TSS. 8 ww_total_suspended_solids +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100795 total suspended solids (TSS) measurement unit total_suspended_solids_tss_measurement_unit TotalSuspendedSolidsTssMeasurementUnitMenu NullValueMenu The units associated with a value from a total suspended solids (TSS) test. Provide the units of the measured TSS. percent (%) ww_total_suspended_solids +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100796 total suspended solids (TSS) measurement method total_suspended_solids_tss_measurement_method WhitespaceMinimizedString The method used to measure total suspended solids (TSS). Provide the name of the procedure or technology used to measure TSS. Vacuum filter through a 2-micron filter, then oven-dried and weighed sample +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100797 total dissolved solids (TDS) measurement value total_dissolved_solids_tds_measurement_value WhitespaceMinimizedString The numerical value from a total dissolved solids (TDS) test. Provide the numerical value of the measured TDS. 2 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100798 total dissolved solids (TDS) measurement unit total_dissolved_solids_tds_measurement_unit TotalDissolvedSolidsTdsMeasurementUnitMenu NullValueMenu The units associated with a value from a total dissolved solids (TDS) test. Provide the units of the measured TDS. percent (%) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100799 total dissolved solids (TDS) measurement method total_dissolved_solids_tds_measurement_method WhitespaceMinimizedString The method used to measure total dissolved solids (TDS). Provide the name of the procedure or technology used to measure TDS. Subtract calculated TSS from calculated TS +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100800 total solids (TS) measurement value total_solids_ts_measurement_value WhitespaceMinimizedString The numerical value from a total solids (TS) test. Provide the numerical value of the measured TS. 10 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100801 total solids (TS) measurement unit total_solids_ts_measurement_unit TotalSolidsTsMeasurementUnitMenu NullValueMenu The units associated with a value from a total solids (TS) test. Provide the units of the measured TS. percent (%) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100802 total solids (TS) measurement method total_solids_ts_measurement_method WhitespaceMinimizedString The method used to measure total solids (TS). Provide the name of the procedure or technology used to measure TS. Gravimetric method by oven drying, then weighing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100878 alkalinity measurement value alkalinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of alkalinity. Provide the numerical value of the measured alkalinity. 3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100879 alkalinity measurement unit alkalinity_measurement_unit AlkalinityMeasurementUnitMenu NullValueMenu The units of a measurement of alkalinity. Provide the units of the measured alkalinity. milligram per liter of calcium carbonate (mg/L CaCO3) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100880 alkalinity measurement method alkalinity_measurement_method WhitespaceMinimizedString The process used to measure alkalinity. Provide the name of the procedure or technology used to measure alkalinity. Titration method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100916 conductivity measurement value conductivity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of conductivity. Provide the numerical value of the measured conductivity. 1412 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100803 conductivity measurement unit conductivity_measurement_unit ConductivityMeasurementUnitMenu NullValueMenu The units of a measurement of conductivity. Provide the units of the measured conductivity. microSiemen per centimeter (μS/cm) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100804 conductivity measurement method conductivity_measurement_method WhitespaceMinimizedString The method used to measure conductivity. Provide the name of the procedure or technology used to measure conductivity. Conductivity electrode and meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100805 salinity measurement value salinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of salinity. Provide the numerical value of the measured salinity. 35 ww_sample_salinity +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100806 salinity measurement unit salinity_measurement_unit SalinityMeasurementUnitMenu NullValueMenu The units of a measurement of salinity. Provide the units of the measured salinity. practical salinity unit (PSU) ww_sample_salinity +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100807 salinity measurement method salinity_measurement_method WhitespaceMinimizedString The method used to measure salinity. Provide the name of the procedure or technology used to measure salinity. conductivity meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100808 total nitrogen (TN) measurement value total_nitrogen_tn_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total nitrogen (TN). Provide the numerical value of the measured TN. 120 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total_nitrogen_tn_measurement_unit TotalNitrogenTnMeasurementUnitMenu NullValueMenu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100810 total nitrogen (TN) measurement method total_nitrogen_tn_measurement_method WhitespaceMinimizedString The method used to measure total nitrogen (TN). Provide the name of the procedure or technology used to measure TN. Hach total nitrogen spectrophotometric test +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100811 total phosphorus (TP) measurement value total_phosphorus_tp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total phosphorus (TP). Provide the numerical value of the measured TP. 2 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit TotalPhosphorpusTpMeasurementUnitMenu NullValueMenu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100813 total phosphorus (TP) measurement method total_phosphorus_tp_measurement_method WhitespaceMinimizedString The method used to measure total phosphorus (TP). Provide the name of the procedure or technology used to measure TP. Merck phosphate spectrophotometric test kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal_contamination_indicator FecalContaminationIndicatorMenu NullValueMenu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100815 fecal contamination value fecal_contamination_value WhitespaceMinimizedString TRUE The numerical value of a measurement of fecal contamination. Provide the numerical value of the measured fecal contamination. 10 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100816 fecal contamination unit fecal_contamination_unit FecalContaminationUnitMenu NullValueMenu TRUE The units of a measurement of fecal contamination. Provide the units of the measured fecal contamination. cycle threshold (Ct) / quantification cycle (Cq) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100817 fecal contamination method fecal_contamination_method WhitespaceMinimizedString The method used to measure fecal contamination. Provide the name of the procedure or technology used to measure fecal contamination. quantitative PCR assay +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100818 fecal coliform count value fecal_coliform_count_value WhitespaceMinimizedString The numerical value of a measurement of fecal coliforms within a sample. Provide the numerical value of the measured fecal coliforms. 3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100819 fecal coliform count unit fecal_coliform_count_unit FecalColiformCountUnitMenu NullValueMenu The units of a measurement of fecal coliforms. Provide the units of the measured fecal coliforms. most probable number per milliliter (MPN/mL) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100820 fecal coliform count method fecal_coliform_count_method WhitespaceMinimizedString The method used to measure fecal coliforms. Provide the name of the procedure or technology used to measure fecal coliforms. MPN method via serial dilutions until lack of growth +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100837 urinary contamination indicator urinary_contamination_indicator UrinaryContaminationIndicatorMenu NullValueMenu A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination. If a urinary contamination indicator was measured, select it from the picklist. urobilin +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100838 urinary contamination value urinary_contamination_value WhitespaceMinimizedString The numerical value of a measurement of urinary contamination. Provide the numerical value of the measured urinary contamination. 3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100839 urinary contamination unit urinary_contamination_unit UrinaryContaminationUnitMenu NullValueMenu The units of a measurement of urinary contamination. Provide the units of the measured urinary contamination. nanograms per liter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100840 urinary contamination method urinary_contamination_method WhitespaceMinimizedString The method used to measure urinary contamination. Provide the name of the procedure or technology used to measure urinary contamination. Urobilin Concentration Test +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100821 sample temperature value (at collection) sample_temperature_value_at_collection WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample at collection. Provide the numerical value of the measured temperature. 20 ww_temperature +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100822 sample temperature unit (at collection) sample_temperature_unit_at_collection SampleTemperatureUnitAtCollectionMenu NullValueMenu The units of a measurement of temperature of a sample at the time of collection. Provide the units of the measured temperature. degree Celsius (C) ww_temperature +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100823 sample temperature value (when received) sample_temperature_value_when_received WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample upon receipt. Provide the numerical value of the measured temperature. 22 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100824 sample temperature unit (when received) sample_temperature_unit_when_received SampleTemperatureUnitWhenReceivedMenu NullValueMenu The units of a measurement of temperature of a sample at the time upon receipt. Provide the units of the measured temperature. degree Celsius (C) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001441 Sequence Information +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance purpose_of_ww_sequencing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100416 sequenced by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) sequenced_by +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString NullValueMenu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca sequence_submitter_contact_email +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001447 sequencing date sequencing_date date {sample_collection_start_date} {today} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001448 library ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100473 sequencing platform sequencing_platform SequencingPlatformMenu NullValueMenu TRUE The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] platform +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] instrument_model +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeMenu NullValueMenu TRUE The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay library_strategy;library_source +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT library_preparation_kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001454 sequencing protocol sequencing_protocol WhitespaceMinimizedString TRUE The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no design_description +WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100843 DNA fragment length dna_fragment_length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 +WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method library_selection;design_description +WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme AmpliconPcrPrimerSchemeMenu NullValueMenu TRUE The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 amplicon_PCR_primer_scheme +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001449 amplicon size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 amplicon_size +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001457 Bioinformatics and QC metrics +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools quality_control_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 quality_control_method_version +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control quality_control_determination +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage quality_control_issues +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. quality_control_details +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version or a link to the github protocol e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 raw_sequence_data_processing_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper dehosting_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString NullValueMenu The name of the consensus sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta filename +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101716 genome sequence file path genome_sequence_file_path WhitespaceMinimizedString NullValueMenu The filepath of the consensus sequence file. Provide the filepath of the genome sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta +WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet +WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 +WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 assembly +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf +WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0101082 Taxonomic identification information +WastewaterAMR Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat +WastewaterAMR Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 +WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat +WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date {today} The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 +WastewaterAMR GENEPIO:0100479 AMR detection information +WastewaterAMR AMR detection information GENEPIO:0101076 AMR analysis software name amr_analysis_software_name WhitespaceMinimizedString TRUE The name of the software used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the software used for AMR analysis. Resistance Gene Identifier +WastewaterAMR AMR detection information GENEPIO:0101077 AMR analysis software version amr_analysis_software_version WhitespaceMinimizedString TRUE The version number of the software used to perform an in silico antimicrobial resistance determinant idenrtification/analysis. Provide the version number of the software used for AMR analysis. 6.0.3 +WastewaterAMR AMR detection information GENEPIO:0101078 AMR reference database name amr_reference_database_name WhitespaceMinimizedString TRUE Thr name of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the reference database used for AMR analysis. Comprehensive Antibiotic Resistance Database (CARD) +WastewaterAMR AMR detection information GENEPIO:0101079 AMR reference database version amr_reference_database_version WhitespaceMinimizedString TRUE The version number of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the version number of the reference database used for AMR analysis. 3.2.9 +WastewaterAMR AMR detection information GENEPIO:0101080 AMR analysis report filename amr_analysis_report_filename WhitespaceMinimizedString TRUE The filename of the report containing the results of an in silico antimicrobial resistance analysis. Provide the filename of the report containing the results of the AMR analysis. WWAMR_report_Feb1_2024.doc +WastewaterSARS-CoV-2 GENEPIO:0001498 Lineage/clade information +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001500 lineage/clade name lineage_clade_name WhitespaceMinimizedString The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. Multiple lineages/clades can be provided, separated by a semicolon. B.1.1.7 +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001501 lineage/clade analysis software name lineage_clade_analysis_software_name WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Freyja +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001502 lineage/clade analysis software version lineage_clade_analysis_software_version WhitespaceMinimizedString The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 1.5.0 +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0101081 lineage/clade analysis report filename lineage_clade_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a lineage/clade analysis. Provide the filename of the report containing the results of the lineage/clade analysis. aggregated-WWSC2-ABC-b_1234.tsv +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001506 Pathogen diagnostic testing +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102049 target taxonomic name 1 target_taxonomic_name_1 WhitespaceMinimizedString The scientific name of the organism or taxon that is the focus of the study, assay, or diagnostic test. The target taxonomic name refers to the specific species, genus, or other taxonomic classification that the assay or diagnostic test is designed to identify, detect, or characterize. This may include the full binomial name (Genus species) or a higher taxonomic rank (e.g., genus, family) when species-level identification is not applicable. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. ww_surv_target_1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102052 assay target name 1 assay_target_name_1 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102040 assay target details assay_target_details WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +WastewaterSARS-CoV-2 Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100962 diagnostic target presence 1 diagnostic_target_presence_1 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_1_known_present +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100963 diagnostic measurement value 1 diagnostic_measurement_value_1 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_1_conc +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100964 diagnostic measurement unit 1 diagnostic_measurement_unit_1 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_1_conc_unit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100965 diagnostic measurement method 1 diagnostic_measurement_method_1 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR ww_surv_target_1_protocol +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102050 target taxonomic name 2 The scientific name of the organism or taxon that is the focus of the study, assay, or diagnostic test. The target taxonomic name refers to the specific species, genus, or other taxonomic classification that the assay or diagnostic test is designed to identify, detect, or characterize. This may include the full binomial name (Genus species) or a higher taxonomic rank (e.g., genus, family) when species-level identification is not applicable. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. ww_surv_target_2 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102038 assay target name 2 assay_target_name_2 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102046 assay target details 2 assay_target_details_2 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +WastewaterSARS-CoV-2 Pathogen diagnostic testing GENEPIO:0102042 gene symbol 2 gene_symbol_2 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) ww_surv_target_2_gene +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102042 gene symbol 2 gene_symbol_2 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A ww_surv_target_2_gene +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 2 diagnostic_target_presence_2 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_2_known_present +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 2 diagnostic_measurement_value_2 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_2_conc +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 2 diagnostic_measurement_unit_2 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_2_conc_unit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 2 diagnostic_measurement_method_2 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102051 target taxonomic name 3 The scientific name of the organism or taxon that is the focus of the study, assay, or diagnostic test. The target taxonomic name refers to the specific species, genus, or other taxonomic classification that the assay or diagnostic test is designed to identify, detect, or characterize. This may include the full binomial name (Genus species) or a higher taxonomic rank (e.g., genus, family) when species-level identification is not applicable. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102039 assay target name 3 assay_target_name_3 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102047 assay target details 3 assay_target_details_3 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +WastewaterSARS-CoV-2 Pathogen diagnostic testing GENEPIO:0102043 gene symbol 3 gene_symbol_3 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102043 gene symbol 3 gene_symbol_3 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 3 diagnostic_target_presence_3 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 3 diagnostic_measurement_value_3 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 3 diagnostic_measurement_unit_3 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 3 diagnostic_measurement_method_3 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001516 Contributor acknowledgement +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001517 authors authors TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a semicolon. Tejinder Singh; Fei Hu; Joe Blogs Authors +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v3.3.3, Influenza v1.0.0 DataHarmonizer provenance \ No newline at end of file