diff --git a/templates/ERC000011/ERC000011.json b/templates/ERC000011/ERC000011.json index 4ca7728..50ccd5c 100644 --- a/templates/ERC000011/ERC000011.json +++ b/templates/ERC000011/ERC000011.json @@ -637,8 +637,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000011/README.md b/templates/ERC000011/README.md index e741730..6962b54 100644 --- a/templates/ERC000011/README.md +++ b/templates/ERC000011/README.md @@ -65,7 +65,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | lat_lon | optional | Geographical coordinates of the location where the specimen was collected | | | collected_by | optional | Name of persons or institute who collected the specimen | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | | identified_by | optional | Name of the expert who identified the specimen taxonomically | | | environmental_sample | optional | Identifies sequences derived by direct molecular isolation from a bulk environmental dna sample (by pcr with or without subsequent cloning of the product, dgge, or other anonymous methods) with no reliable identification of the source organism | No, Yes | diff --git a/templates/ERC000011/metadata_template_ERC000011.xlsx b/templates/ERC000011/metadata_template_ERC000011.xlsx index da43618..8e651de 100644 Binary files a/templates/ERC000011/metadata_template_ERC000011.xlsx and b/templates/ERC000011/metadata_template_ERC000011.xlsx differ diff --git a/templates/ERC000012/ERC000012.json b/templates/ERC000012/ERC000012.json index c5c74e5..0067a3d 100644 --- a/templates/ERC000012/ERC000012.json +++ b/templates/ERC000012/ERC000012.json @@ -824,8 +824,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1516,15 +1516,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "chemical administration", "cardinality": "optional", diff --git a/templates/ERC000012/README.md b/templates/ERC000012/README.md index fa97d5f..3309069 100644 --- a/templates/ERC000012/README.md +++ b/templates/ERC000012/README.md @@ -80,7 +80,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | mandatory | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -132,6 +132,5 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | chemical administration | optional | List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, n fertilizer, air filter); can include multiple compounds. for chemical entities of biological interest ontology (chebi) (v111), please see http://purl.bioontology.org/ontology/chebi | | diff --git a/templates/ERC000012/metadata_template_ERC000012.xlsx b/templates/ERC000012/metadata_template_ERC000012.xlsx index 09bb31f..1d52c22 100644 Binary files a/templates/ERC000012/metadata_template_ERC000012.xlsx and b/templates/ERC000012/metadata_template_ERC000012.xlsx differ diff --git a/templates/ERC000012/sample.tsv b/templates/ERC000012/sample.tsv index 37ff4e5..6640093 100644 --- a/templates/ERC000012/sample.tsv +++ b/templates/ERC000012/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "ventilation rate" "ventilation type" "amount or size of sample collected" "organism count" "sample storage duration" "host disease status" "host scientific name" "barometric pressure" "humidity" "pollutants" "solar irradiance" "wind direction" "wind speed" "temperature" "carbon dioxide" "carbon monoxide" "oxygen" "air particulate matter concentration" "volatile organic compounds" "methane" "salinity" "source material identifiers" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "chemical administration" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "ventilation rate" "ventilation type" "amount or size of sample collected" "organism count" "sample storage duration" "host disease status" "host scientific name" "barometric pressure" "humidity" "pollutants" "solar irradiance" "wind direction" "wind speed" "temperature" "carbon dioxide" "carbon monoxide" "oxygen" "air particulate matter concentration" "volatile organic compounds" "methane" "salinity" "source material identifiers" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "chemical administration" diff --git a/templates/ERC000013/ERC000013.json b/templates/ERC000013/ERC000013.json index 34b7519..58243c5 100644 --- a/templates/ERC000013/ERC000013.json +++ b/templates/ERC000013/ERC000013.json @@ -860,8 +860,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1727,15 +1727,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "depth", "cardinality": "optional", diff --git a/templates/ERC000013/README.md b/templates/ERC000013/README.md index 5303e76..62269ad 100644 --- a/templates/ERC000013/README.md +++ b/templates/ERC000013/README.md @@ -84,7 +84,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -153,7 +153,6 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | depth | optional | The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. depth can be reported as an interval for subsurface samples. (Units: mm) | | | chemical administration | optional | List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, n fertilizer, air filter); can include multiple compounds. for chemical entities of biological interest ontology (chebi) (v111), please see http://purl.bioontology.org/ontology/chebi | | diff --git a/templates/ERC000013/metadata_template_ERC000013.xlsx b/templates/ERC000013/metadata_template_ERC000013.xlsx index 44c04e3..f7ec9c5 100644 Binary files a/templates/ERC000013/metadata_template_ERC000013.xlsx and b/templates/ERC000013/metadata_template_ERC000013.xlsx differ diff --git a/templates/ERC000013/sample.tsv b/templates/ERC000013/sample.tsv index 345e9b0..fee01fc 100644 --- a/templates/ERC000013/sample.tsv +++ b/templates/ERC000013/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "sample disease stage" "oxygenation status of sample" "sample disease status" "sample derived from" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample capture status" "biological status" "sample storage duration" "host disease status" "host common name" "host subject id" "host age" "host taxid" "host body habitat" "host body site" "host life stage" "host height" "host length" "host growth conditions" "host substrate" "host total mass" "host phenotype" "host body temperature" "host color" "host shape" "host sex" "host scientific name" "host subspecific genetic lineage" "temperature" "salinity" "source material identifiers" "host blood pressure diastolic" "host blood pressure systolic" "host diet" "host last meal" "host family relationship" "host genotype" "gravidity" "host dry mass" "host body product" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "genetic modification" "subspecific genetic lineage" "ancestral data" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "depth" "chemical administration" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "sample disease stage" "oxygenation status of sample" "sample disease status" "sample derived from" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample capture status" "biological status" "sample storage duration" "host disease status" "host common name" "host subject id" "host age" "host taxid" "host body habitat" "host body site" "host life stage" "host height" "host length" "host growth conditions" "host substrate" "host total mass" "host phenotype" "host body temperature" "host color" "host shape" "host sex" "host scientific name" "host subspecific genetic lineage" "temperature" "salinity" "source material identifiers" "host blood pressure diastolic" "host blood pressure systolic" "host diet" "host last meal" "host family relationship" "host genotype" "gravidity" "host dry mass" "host body product" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "genetic modification" "subspecific genetic lineage" "ancestral data" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "depth" "chemical administration" diff --git a/templates/ERC000014/ERC000014.json b/templates/ERC000014/ERC000014.json index 9f0dd5f..f5989d2 100644 --- a/templates/ERC000014/ERC000014.json +++ b/templates/ERC000014/ERC000014.json @@ -872,8 +872,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1855,15 +1855,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "chemical administration", "cardinality": "optional", diff --git a/templates/ERC000014/README.md b/templates/ERC000014/README.md index 211ecc0..8ecdd36 100644 --- a/templates/ERC000014/README.md +++ b/templates/ERC000014/README.md @@ -84,7 +84,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -158,6 +158,5 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | chemical administration | optional | List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, n fertilizer, air filter); can include multiple compounds. for chemical entities of biological interest ontology (chebi) (v111), please see http://purl.bioontology.org/ontology/chebi | | diff --git a/templates/ERC000014/metadata_template_ERC000014.xlsx b/templates/ERC000014/metadata_template_ERC000014.xlsx index 1bc197d..d452120 100644 Binary files a/templates/ERC000014/metadata_template_ERC000014.xlsx and b/templates/ERC000014/metadata_template_ERC000014.xlsx differ diff --git a/templates/ERC000014/sample.tsv b/templates/ERC000014/sample.tsv index 0c183e0..1c9351f 100644 --- a/templates/ERC000014/sample.tsv +++ b/templates/ERC000014/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "urine/collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "medical history performed" "study completion status" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample storage duration" "nose/mouth/teeth/throat disorder" "host HIV status" "host disease status" "lung/pulmonary disorder" "lung/nose-throat disorder" "blood/blood disorder" "urine/kidney disorder" "urine/urogenital tract disorder" "host subject id" "IHMC medication code" "host age" "host body site" "drug usage" "host height" "host body-mass index" "ethnicity" "host occupation" "host total mass" "host phenotype" "host body temperature" "host sex" "host scientific name" "presence of pets, animals, or insects" "temperature" "salinity" "source material identifiers" "smoker" "major diet change in last six months" "weight loss in last three months" "travel outside the country in last six months" "host diet" "twin sibling presence" "host last meal" "amniotic fluid/gestation state" "host family relationship" "amniotic fluid/maternal health status" "host genotype" "amniotic fluid/foetal health status" "host pulse" "amniotic fluid/color" "host body product" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "chemical administration" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "urine/collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "medical history performed" "study completion status" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample storage duration" "nose/mouth/teeth/throat disorder" "host HIV status" "host disease status" "lung/pulmonary disorder" "lung/nose-throat disorder" "blood/blood disorder" "urine/kidney disorder" "urine/urogenital tract disorder" "host subject id" "IHMC medication code" "host age" "host body site" "drug usage" "host height" "host body-mass index" "ethnicity" "host occupation" "host total mass" "host phenotype" "host body temperature" "host sex" "host scientific name" "presence of pets, animals, or insects" "temperature" "salinity" "source material identifiers" "smoker" "major diet change in last six months" "weight loss in last three months" "travel outside the country in last six months" "host diet" "twin sibling presence" "host last meal" "amniotic fluid/gestation state" "host family relationship" "amniotic fluid/maternal health status" "host genotype" "amniotic fluid/foetal health status" "host pulse" "amniotic fluid/color" "host body product" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "chemical administration" diff --git a/templates/ERC000015/ERC000015.json b/templates/ERC000015/ERC000015.json index f3b4591..3b6bc3b 100644 --- a/templates/ERC000015/ERC000015.json +++ b/templates/ERC000015/ERC000015.json @@ -845,8 +845,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1686,15 +1686,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "chemical administration", "cardinality": "optional", diff --git a/templates/ERC000015/README.md b/templates/ERC000015/README.md index a8e2f7f..9debaae 100644 --- a/templates/ERC000015/README.md +++ b/templates/ERC000015/README.md @@ -82,7 +82,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -141,6 +141,5 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | chemical administration | optional | List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, n fertilizer, air filter); can include multiple compounds. for chemical entities of biological interest ontology (chebi) (v111), please see http://purl.bioontology.org/ontology/chebi | | diff --git a/templates/ERC000015/metadata_template_ERC000015.xlsx b/templates/ERC000015/metadata_template_ERC000015.xlsx index be82e2b..4308794 100644 Binary files a/templates/ERC000015/metadata_template_ERC000015.xlsx and b/templates/ERC000015/metadata_template_ERC000015.xlsx differ diff --git a/templates/ERC000015/sample.tsv b/templates/ERC000015/sample.tsv index 6a7b76a..ce638f4 100644 --- a/templates/ERC000015/sample.tsv +++ b/templates/ERC000015/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "medical history performed" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample storage duration" "gastrointestinal tract disorder" "liver disorder" "host disease status" "host subject id" "IHMC medication code" "host age" "host body site" "host height" "host body-mass index" "ethnicity" "host occupation" "host total mass" "host phenotype" "host body temperature" "host sex" "host scientific name" "temperature" "salinity" "source material identifiers" "special diet" "host diet" "host last meal" "host family relationship" "host genotype" "host pulse" "host body product" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "chemical administration" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "medical history performed" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample storage duration" "gastrointestinal tract disorder" "liver disorder" "host disease status" "host subject id" "IHMC medication code" "host age" "host body site" "host height" "host body-mass index" "ethnicity" "host occupation" "host total mass" "host phenotype" "host body temperature" "host sex" "host scientific name" "temperature" "salinity" "source material identifiers" "special diet" "host diet" "host last meal" "host family relationship" "host genotype" "host pulse" "host body product" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "chemical administration" diff --git a/templates/ERC000016/ERC000016.json b/templates/ERC000016/ERC000016.json index c3f9e3e..1ce9c7f 100644 --- a/templates/ERC000016/ERC000016.json +++ b/templates/ERC000016/ERC000016.json @@ -854,8 +854,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1686,15 +1686,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "chemical administration", "cardinality": "optional", diff --git a/templates/ERC000016/README.md b/templates/ERC000016/README.md index f360824..e3a2656 100644 --- a/templates/ERC000016/README.md +++ b/templates/ERC000016/README.md @@ -83,7 +83,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | lat_lon | optional | Geographical coordinates of the location where the specimen was collected | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -141,6 +141,5 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | chemical administration | optional | List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, n fertilizer, air filter); can include multiple compounds. for chemical entities of biological interest ontology (chebi) (v111), please see http://purl.bioontology.org/ontology/chebi | | diff --git a/templates/ERC000016/metadata_template_ERC000016.xlsx b/templates/ERC000016/metadata_template_ERC000016.xlsx index 511d17a..ef76577 100644 Binary files a/templates/ERC000016/metadata_template_ERC000016.xlsx and b/templates/ERC000016/metadata_template_ERC000016.xlsx differ diff --git a/templates/ERC000016/sample.tsv b/templates/ERC000016/sample.tsv index cc4a10e..0186197 100644 --- a/templates/ERC000016/sample.tsv +++ b/templates/ERC000016/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "medical history performed" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "lat_lon" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample storage duration" "nose/mouth/teeth/throat disorder" "host disease status" "host subject id" "IHMC medication code" "host age" "host body site" "host height" "host body-mass index" "ethnicity" "host occupation" "host total mass" "host phenotype" "host body temperature" "host sex" "host scientific name" "temperature" "salinity" "source material identifiers" "time since last toothbrushing" "host diet" "host last meal" "host family relationship" "host genotype" "host pulse" "host body product" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "chemical administration" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "medical history performed" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "lat_lon" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample storage duration" "nose/mouth/teeth/throat disorder" "host disease status" "host subject id" "IHMC medication code" "host age" "host body site" "host height" "host body-mass index" "ethnicity" "host occupation" "host total mass" "host phenotype" "host body temperature" "host sex" "host scientific name" "temperature" "salinity" "source material identifiers" "time since last toothbrushing" "host diet" "host last meal" "host family relationship" "host genotype" "host pulse" "host body product" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "chemical administration" diff --git a/templates/ERC000017/ERC000017.json b/templates/ERC000017/ERC000017.json index a4569a3..64e5231 100644 --- a/templates/ERC000017/ERC000017.json +++ b/templates/ERC000017/ERC000017.json @@ -845,8 +845,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1690,15 +1690,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "chemical administration", "cardinality": "optional", diff --git a/templates/ERC000017/README.md b/templates/ERC000017/README.md index 7829d6d..fa34e9f 100644 --- a/templates/ERC000017/README.md +++ b/templates/ERC000017/README.md @@ -82,7 +82,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -141,6 +141,5 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | chemical administration | optional | List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, n fertilizer, air filter); can include multiple compounds. for chemical entities of biological interest ontology (chebi) (v111), please see http://purl.bioontology.org/ontology/chebi | | diff --git a/templates/ERC000017/metadata_template_ERC000017.xlsx b/templates/ERC000017/metadata_template_ERC000017.xlsx index c808339..8e9fd4c 100644 Binary files a/templates/ERC000017/metadata_template_ERC000017.xlsx and b/templates/ERC000017/metadata_template_ERC000017.xlsx differ diff --git a/templates/ERC000017/sample.tsv b/templates/ERC000017/sample.tsv index 5ad9077..7b0d763 100644 --- a/templates/ERC000017/sample.tsv +++ b/templates/ERC000017/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "medical history performed" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample storage duration" "dermatology disorder" "host disease status" "host subject id" "IHMC medication code" "host age" "host body site" "host height" "host body-mass index" "ethnicity" "host occupation" "host total mass" "host phenotype" "host body temperature" "host sex" "host scientific name" "temperature" "salinity" "source material identifiers" "time since last wash" "dominant hand" "host diet" "host last meal" "host family relationship" "host genotype" "host pulse" "host body product" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "chemical administration" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "medical history performed" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample storage duration" "dermatology disorder" "host disease status" "host subject id" "IHMC medication code" "host age" "host body site" "host height" "host body-mass index" "ethnicity" "host occupation" "host total mass" "host phenotype" "host body temperature" "host sex" "host scientific name" "temperature" "salinity" "source material identifiers" "time since last wash" "dominant hand" "host diet" "host last meal" "host family relationship" "host genotype" "host pulse" "host body product" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "chemical administration" diff --git a/templates/ERC000018/ERC000018.json b/templates/ERC000018/ERC000018.json index 62ea953..44ad4f6 100644 --- a/templates/ERC000018/ERC000018.json +++ b/templates/ERC000018/ERC000018.json @@ -845,8 +845,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1761,15 +1761,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "chemical administration", "cardinality": "optional", diff --git a/templates/ERC000018/README.md b/templates/ERC000018/README.md index 971cba3..6e8fba2 100644 --- a/templates/ERC000018/README.md +++ b/templates/ERC000018/README.md @@ -82,7 +82,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -149,6 +149,5 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | chemical administration | optional | List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, n fertilizer, air filter); can include multiple compounds. for chemical entities of biological interest ontology (chebi) (v111), please see http://purl.bioontology.org/ontology/chebi | | diff --git a/templates/ERC000018/metadata_template_ERC000018.xlsx b/templates/ERC000018/metadata_template_ERC000018.xlsx index c05130f..7db9866 100644 Binary files a/templates/ERC000018/metadata_template_ERC000018.xlsx and b/templates/ERC000018/metadata_template_ERC000018.xlsx differ diff --git a/templates/ERC000018/sample.tsv b/templates/ERC000018/sample.tsv index e2ed522..4dd86af 100644 --- a/templates/ERC000018/sample.tsv +++ b/templates/ERC000018/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "medical history performed" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample storage duration" "gynecological disorder" "urogenital disorder" "host disease status" "host subject id" "IHMC medication code" "host age" "host body site" "host height" "host body-mass index" "ethnicity" "host occupation" "host total mass" "host phenotype" "host body temperature" "host sex" "host scientific name" "temperature" "sample salinity" "salinity" "source material identifiers" "menarche" "sexual activity" "pregnancy" "douche" "birth control" "menopause" "HRT" "hysterectomy" "host diet" "host last meal" "host family relationship" "host genotype" "host pulse" "host body product" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "chemical administration" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "medical history performed" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample storage duration" "gynecological disorder" "urogenital disorder" "host disease status" "host subject id" "IHMC medication code" "host age" "host body site" "host height" "host body-mass index" "ethnicity" "host occupation" "host total mass" "host phenotype" "host body temperature" "host sex" "host scientific name" "temperature" "sample salinity" "salinity" "source material identifiers" "menarche" "sexual activity" "pregnancy" "douche" "birth control" "menopause" "HRT" "hysterectomy" "host diet" "host last meal" "host family relationship" "host genotype" "host pulse" "host body product" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "chemical administration" diff --git a/templates/ERC000019/ERC000019.json b/templates/ERC000019/ERC000019.json index c40a18d..26263be 100644 --- a/templates/ERC000019/ERC000019.json +++ b/templates/ERC000019/ERC000019.json @@ -824,8 +824,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1827,15 +1827,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "depth", "cardinality": "mandatory", diff --git a/templates/ERC000019/README.md b/templates/ERC000019/README.md index fc73e7f..e0c68ba 100644 --- a/templates/ERC000019/README.md +++ b/templates/ERC000019/README.md @@ -80,7 +80,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -167,7 +167,6 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | depth | mandatory | The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. depth can be reported as an interval for subsurface samples. (Units: mm) | | | chemical administration | optional | List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, n fertilizer, air filter); can include multiple compounds. for chemical entities of biological interest ontology (chebi) (v111), please see http://purl.bioontology.org/ontology/chebi | | diff --git a/templates/ERC000019/metadata_template_ERC000019.xlsx b/templates/ERC000019/metadata_template_ERC000019.xlsx index 53604fb..bfd9efa 100644 Binary files a/templates/ERC000019/metadata_template_ERC000019.xlsx and b/templates/ERC000019/metadata_template_ERC000019.xlsx differ diff --git a/templates/ERC000019/sample.tsv b/templates/ERC000019/sample.tsv index 5fd7ac8..a0de107 100644 --- a/templates/ERC000019/sample.tsv +++ b/templates/ERC000019/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "biomass" "organism count" "sample storage duration" "host disease status" "host scientific name" "mean friction velocity" "mean peak friction velocity" "pressure" "temperature" "turbidity" "pH" "water content" "alkyl diethers" "aminopeptidase activity" "ammonium" "bacterial carbon production" "bishomohopanol" "bromide" "calcium" "carbon/nitrogen ratio" "chloride" "chlorophyll" "diether lipids" "dissolved carbon dioxide" "dissolved hydrogen" "dissolved inorganic carbon" "dissolved organic carbon" "dissolved organic nitrogen" "methane" "dissolved oxygen" "glucosidase activity" "magnesium" "n-alkanes" "nitrate" "nitrite" "total nitrogen concentration" "organic carbon" "organic matter" "organic nitrogen" "particulate organic carbon" "petroleum hydrocarbon" "phaeopigments" "phosphate" "phospholipid fatty acid" "potassium" "redox potential" "salinity" "total carbon" "silicate" "sodium" "total organic carbon" "sulfate" "sulfide" "total nitrogen content" "alkalinity" "source material identifiers" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "depth" "chemical administration" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "biomass" "organism count" "sample storage duration" "host disease status" "host scientific name" "mean friction velocity" "mean peak friction velocity" "pressure" "temperature" "turbidity" "pH" "water content" "alkyl diethers" "aminopeptidase activity" "ammonium" "bacterial carbon production" "bishomohopanol" "bromide" "calcium" "carbon/nitrogen ratio" "chloride" "chlorophyll" "diether lipids" "dissolved carbon dioxide" "dissolved hydrogen" "dissolved inorganic carbon" "dissolved organic carbon" "dissolved organic nitrogen" "methane" "dissolved oxygen" "glucosidase activity" "magnesium" "n-alkanes" "nitrate" "nitrite" "total nitrogen concentration" "organic carbon" "organic matter" "organic nitrogen" "particulate organic carbon" "petroleum hydrocarbon" "phaeopigments" "phosphate" "phospholipid fatty acid" "potassium" "redox potential" "salinity" "total carbon" "silicate" "sodium" "total organic carbon" "sulfate" "sulfide" "total nitrogen content" "alkalinity" "source material identifiers" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "depth" "chemical administration" diff --git a/templates/ERC000020/ERC000020.json b/templates/ERC000020/ERC000020.json index e151e1c..a6f1e6e 100644 --- a/templates/ERC000020/ERC000020.json +++ b/templates/ERC000020/ERC000020.json @@ -867,8 +867,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1730,15 +1730,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "plant product", "cardinality": "optional", diff --git a/templates/ERC000020/README.md b/templates/ERC000020/README.md index f7f888e..becda71 100644 --- a/templates/ERC000020/README.md +++ b/templates/ERC000020/README.md @@ -84,7 +84,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -154,7 +154,6 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | plant product | optional | Substance produced by the plant, where the sample was obtained from | | | depth | optional | The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. depth can be reported as an interval for subsurface samples. (Units: mm) | | | air temperature regimen | optional | Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment duration, interval and total experimental duration; can include different temperature regimens | | diff --git a/templates/ERC000020/metadata_template_ERC000020.xlsx b/templates/ERC000020/metadata_template_ERC000020.xlsx index 8df7c99..ca43048 100644 Binary files a/templates/ERC000020/metadata_template_ERC000020.xlsx and b/templates/ERC000020/metadata_template_ERC000020.xlsx differ diff --git a/templates/ERC000020/sample.tsv b/templates/ERC000020/sample.tsv index 27a27ba..d39f6f0 100644 --- a/templates/ERC000020/sample.tsv +++ b/templates/ERC000020/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "growth facility" "sample disease stage" "oxygenation status of sample" "sample disease status" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample capture status" "growth habit" "plant sex" "plant structure" "sample storage duration" "host disease status" "host common name" "host age" "host taxid" "host life stage" "host height" "host length" "plant body site" "host total mass" "host phenotype" "host scientific name" "host subspecific genetic lineage" "climate environment" "gaseous environment" "seasonal environment" "temperature" "salinity" "source material identifiers" "host genotype" "host dry mass" "host wet mass" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "genetic modification" "subspecific genetic lineage" "ancestral data" "taxonomic classification" "plant growth medium" "rooting conditions" "culture rooting medium" "rooting medium macronutrients" "rooting medium micronutrients" "rooting medium organic supplements" "rooting medium carbon" "rooting medium regulators" "rooting medium solidifier" "rooting medium pH" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "plant product" "depth" "air temperature regimen" "antibiotic regimen" "chemical mutagen" "fertilizer administration" "fungicide regimen" "gravity" "growth hormone regimen" "growth media" "herbicide regimen" "humidity regimen" "mineral nutrient regimen" "non-mineral nutrient regimen" "pesticide regimen" "pH regimen" "radiation regimen" "rainfall regimen" "salt regimen" "standing water regimen" "tissue culture growth media" "watering regimen" "water temperature regimen" "light regimen" "biotic regimen" "mechanical damage" "chemical administration" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "observed host symbionts" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "growth facility" "sample disease stage" "oxygenation status of sample" "sample disease status" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample capture status" "growth habit" "plant sex" "plant structure" "sample storage duration" "host disease status" "host common name" "host age" "host taxid" "host life stage" "host height" "host length" "plant body site" "host total mass" "host phenotype" "host scientific name" "host subspecific genetic lineage" "climate environment" "gaseous environment" "seasonal environment" "temperature" "salinity" "source material identifiers" "host genotype" "host dry mass" "host wet mass" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "genetic modification" "subspecific genetic lineage" "ancestral data" "taxonomic classification" "plant growth medium" "rooting conditions" "culture rooting medium" "rooting medium macronutrients" "rooting medium micronutrients" "rooting medium organic supplements" "rooting medium carbon" "rooting medium regulators" "rooting medium solidifier" "rooting medium pH" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "plant product" "depth" "air temperature regimen" "antibiotic regimen" "chemical mutagen" "fertilizer administration" "fungicide regimen" "gravity" "growth hormone regimen" "growth media" "herbicide regimen" "humidity regimen" "mineral nutrient regimen" "non-mineral nutrient regimen" "pesticide regimen" "pH regimen" "radiation regimen" "rainfall regimen" "salt regimen" "standing water regimen" "tissue culture growth media" "watering regimen" "water temperature regimen" "light regimen" "biotic regimen" "mechanical damage" "chemical administration" diff --git a/templates/ERC000021/ERC000021.json b/templates/ERC000021/ERC000021.json index d7c591f..4d03562 100644 --- a/templates/ERC000021/ERC000021.json +++ b/templates/ERC000021/ERC000021.json @@ -851,8 +851,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1875,15 +1875,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "porosity", "cardinality": "optional", diff --git a/templates/ERC000021/README.md b/templates/ERC000021/README.md index d4bffb3..92a09d9 100644 --- a/templates/ERC000021/README.md +++ b/templates/ERC000021/README.md @@ -83,7 +83,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -172,7 +172,6 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | porosity | optional | Porosity of deposited sediment is volume of voids divided by the total volume of sample | | | depth | mandatory | The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. depth can be reported as an interval for subsurface samples. (Units: mm) | | | chemical administration | optional | List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, n fertilizer, air filter); can include multiple compounds. for chemical entities of biological interest ontology (chebi) (v111), please see http://purl.bioontology.org/ontology/chebi | | diff --git a/templates/ERC000021/metadata_template_ERC000021.xlsx b/templates/ERC000021/metadata_template_ERC000021.xlsx index 4312575..548d3ad 100644 Binary files a/templates/ERC000021/metadata_template_ERC000021.xlsx and b/templates/ERC000021/metadata_template_ERC000021.xlsx differ diff --git a/templates/ERC000021/sample.tsv b/templates/ERC000021/sample.tsv index 7824636..b77ea83 100644 --- a/templates/ERC000021/sample.tsv +++ b/templates/ERC000021/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "particle classification" "sediment type" "oxygenation status of sample" "density" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "biomass" "organism count" "sample storage duration" "host disease status" "host scientific name" "mean friction velocity" "mean peak friction velocity" "pressure" "temperature" "tidal stage" "turbidity" "pH" "total depth of water column" "water content" "alkyl diethers" "aminopeptidase activity" "ammonium" "bacterial carbon production" "bishomohopanol" "bromide" "calcium" "carbon/nitrogen ratio" "chloride" "chlorophyll" "diether lipids" "dissolved carbon dioxide" "dissolved hydrogen" "dissolved inorganic carbon" "dissolved organic carbon" "dissolved organic nitrogen" "methane" "dissolved oxygen" "glucosidase activity" "magnesium" "n-alkanes" "nitrate" "nitrite" "total nitrogen concentration" "organic carbon" "organic matter" "organic nitrogen" "particulate organic carbon" "petroleum hydrocarbon" "phaeopigments" "phosphate" "phospholipid fatty acid" "potassium" "redox potential" "salinity" "total carbon" "silicate" "sodium" "total organic carbon" "sulfate" "sulfide" "total nitrogen content" "alkalinity" "source material identifiers" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "porosity" "depth" "chemical administration" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "particle classification" "sediment type" "oxygenation status of sample" "density" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "biomass" "organism count" "sample storage duration" "host disease status" "host scientific name" "mean friction velocity" "mean peak friction velocity" "pressure" "temperature" "tidal stage" "turbidity" "pH" "total depth of water column" "water content" "alkyl diethers" "aminopeptidase activity" "ammonium" "bacterial carbon production" "bishomohopanol" "bromide" "calcium" "carbon/nitrogen ratio" "chloride" "chlorophyll" "diether lipids" "dissolved carbon dioxide" "dissolved hydrogen" "dissolved inorganic carbon" "dissolved organic carbon" "dissolved organic nitrogen" "methane" "dissolved oxygen" "glucosidase activity" "magnesium" "n-alkanes" "nitrate" "nitrite" "total nitrogen concentration" "organic carbon" "organic matter" "organic nitrogen" "particulate organic carbon" "petroleum hydrocarbon" "phaeopigments" "phosphate" "phospholipid fatty acid" "potassium" "redox potential" "salinity" "total carbon" "silicate" "sodium" "total organic carbon" "sulfate" "sulfide" "total nitrogen content" "alkalinity" "source material identifiers" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "porosity" "depth" "chemical administration" diff --git a/templates/ERC000022/ERC000022.json b/templates/ERC000022/ERC000022.json index e6c3d3b..4f8e33c 100644 --- a/templates/ERC000022/ERC000022.json +++ b/templates/ERC000022/ERC000022.json @@ -908,8 +908,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1860,15 +1860,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "depth", "cardinality": "mandatory", diff --git a/templates/ERC000022/README.md b/templates/ERC000022/README.md index 7e6b934..d355d0f 100644 --- a/templates/ERC000022/README.md +++ b/templates/ERC000022/README.md @@ -86,7 +86,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -164,6 +164,5 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | depth | mandatory | The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. depth can be reported as an interval for subsurface samples. (Units: mm) | | diff --git a/templates/ERC000022/metadata_template_ERC000022.xlsx b/templates/ERC000022/metadata_template_ERC000022.xlsx index 22f36a8..6b0a637 100644 Binary files a/templates/ERC000022/metadata_template_ERC000022.xlsx and b/templates/ERC000022/metadata_template_ERC000022.xlsx differ diff --git a/templates/ERC000022/sample.tsv b/templates/ERC000022/sample.tsv index b8651c0..b9176d8 100644 --- a/templates/ERC000022/sample.tsv +++ b/templates/ERC000022/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage conditions" "soil_taxonomic/FAO classification" "soil_taxonomic/local classification" "soil_taxonomic/local classification method" "soil type" "soil type method" "soil texture measurement" "soil texture method" "microbial biomass" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "sieving" "microbial biomass method" "horizon method" "extreme_unusual_properties/heavy metals" "extreme_unusual_properties/heavy metals method" "extreme_unusual_properties/Al saturation" "extreme_unusual_properties/Al saturation method" "host disease status" "host scientific name" "link to climate information" "link to classification information" "links to additional analysis" "current land use" "current vegetation" "current vegetation method" "soil horizon" "drainage classification" "temperature" "pH" "pH method" "water content" "slope gradient" "slope aspect" "profile position" "water content method" "total organic carbon method" "total nitrogen content method" "organic matter" "organic nitrogen" "total organic carbon" "total nitrogen content" "salinity method" "source material identifiers" "history/previous land use" "previous land use method" "history/crop rotation" "history/agrochemical additions" "history/tillage" "history/fire" "history/flooding" "history/extreme events" "mean seasonal temperature" "mean seasonal precipitation" "mean annual precipitation" "mean annual temperature" "host specificity or range" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample pooling" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "depth" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage conditions" "soil_taxonomic/FAO classification" "soil_taxonomic/local classification" "soil_taxonomic/local classification method" "soil type" "soil type method" "soil texture measurement" "soil texture method" "microbial biomass" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "sieving" "microbial biomass method" "horizon method" "extreme_unusual_properties/heavy metals" "extreme_unusual_properties/heavy metals method" "extreme_unusual_properties/Al saturation" "extreme_unusual_properties/Al saturation method" "host disease status" "host scientific name" "link to climate information" "link to classification information" "links to additional analysis" "current land use" "current vegetation" "current vegetation method" "soil horizon" "drainage classification" "temperature" "pH" "pH method" "water content" "slope gradient" "slope aspect" "profile position" "water content method" "total organic carbon method" "total nitrogen content method" "organic matter" "organic nitrogen" "total organic carbon" "total nitrogen content" "salinity method" "source material identifiers" "history/previous land use" "previous land use method" "history/crop rotation" "history/agrochemical additions" "history/tillage" "history/fire" "history/flooding" "history/extreme events" "mean seasonal temperature" "mean seasonal precipitation" "mean annual precipitation" "mean annual temperature" "host specificity or range" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample pooling" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "depth" diff --git a/templates/ERC000023/ERC000023.json b/templates/ERC000023/ERC000023.json index 2f0dff5..75f3d08 100644 --- a/templates/ERC000023/ERC000023.json +++ b/templates/ERC000023/ERC000023.json @@ -824,8 +824,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1629,15 +1629,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "depth", "cardinality": "optional", diff --git a/templates/ERC000023/README.md b/templates/ERC000023/README.md index b17733b..1f67134 100644 --- a/templates/ERC000023/README.md +++ b/templates/ERC000023/README.md @@ -80,7 +80,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -145,7 +145,6 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | depth | optional | The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. depth can be reported as an interval for subsurface samples. (Units: mm) | | | chemical administration | optional | List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, n fertilizer, air filter); can include multiple compounds. for chemical entities of biological interest ontology (chebi) (v111), please see http://purl.bioontology.org/ontology/chebi | | diff --git a/templates/ERC000023/metadata_template_ERC000023.xlsx b/templates/ERC000023/metadata_template_ERC000023.xlsx index 15474f4..241a1a4 100644 Binary files a/templates/ERC000023/metadata_template_ERC000023.xlsx and b/templates/ERC000023/metadata_template_ERC000023.xlsx differ diff --git a/templates/ERC000023/sample.tsv b/templates/ERC000023/sample.tsv index 0099c8e..42556d2 100644 --- a/templates/ERC000023/sample.tsv +++ b/templates/ERC000023/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample storage duration" "biochemical oxygen demand" "chemical oxygen demand" "pre-treatment" "primary treatment" "reactor type" "secondary treatment" "sludge retention time" "tertiary treatment" "host disease status" "host scientific name" "industrial effluent percent" "sewage type" "wastewater type" "temperature" "pH" "efficiency percent" "emulsions" "gaseous substances" "inorganic particles" "organic particles" "soluble inorganic material" "soluble organic material" "suspended solids" "total phosphate" "nitrate" "total nitrogen concentration" "phosphate" "salinity" "sodium" "total nitrogen content" "alkalinity" "source material identifiers" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "depth" "chemical administration" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "organism count" "sample storage duration" "biochemical oxygen demand" "chemical oxygen demand" "pre-treatment" "primary treatment" "reactor type" "secondary treatment" "sludge retention time" "tertiary treatment" "host disease status" "host scientific name" "industrial effluent percent" "sewage type" "wastewater type" "temperature" "pH" "efficiency percent" "emulsions" "gaseous substances" "inorganic particles" "organic particles" "soluble inorganic material" "soluble organic material" "suspended solids" "total phosphate" "nitrate" "total nitrogen concentration" "phosphate" "salinity" "sodium" "total nitrogen content" "alkalinity" "source material identifiers" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "depth" "chemical administration" diff --git a/templates/ERC000024/ERC000024.json b/templates/ERC000024/ERC000024.json index 8541933..4d3563a 100644 --- a/templates/ERC000024/ERC000024.json +++ b/templates/ERC000024/ERC000024.json @@ -851,8 +851,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -2019,15 +2019,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "depth", "cardinality": "mandatory", diff --git a/templates/ERC000024/README.md b/templates/ERC000024/README.md index 7ec1eff..8e37bfb 100644 --- a/templates/ERC000024/README.md +++ b/templates/ERC000024/README.md @@ -83,7 +83,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -188,7 +188,6 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | depth | mandatory | The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. depth can be reported as an interval for subsurface samples. (Units: mm) | | | chemical administration | optional | List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, n fertilizer, air filter); can include multiple compounds. for chemical entities of biological interest ontology (chebi) (v111), please see http://purl.bioontology.org/ontology/chebi | | diff --git a/templates/ERC000024/metadata_template_ERC000024.xlsx b/templates/ERC000024/metadata_template_ERC000024.xlsx index 7f7abec..03dafe5 100644 Binary files a/templates/ERC000024/metadata_template_ERC000024.xlsx and b/templates/ERC000024/metadata_template_ERC000024.xlsx differ diff --git a/templates/ERC000024/sample.tsv b/templates/ERC000024/sample.tsv index 540c6d0..edcd1e2 100644 --- a/templates/ERC000024/sample.tsv +++ b/templates/ERC000024/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "size-fraction lower threshold" "size-fraction upper threshold" "oxygenation status of sample" "density" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "biomass" "organism count" "sample storage duration" "host disease status" "host scientific name" "atmospheric data" "conductivity" "water current" "fluorescence" "light intensity" "mean friction velocity" "mean peak friction velocity" "downward PAR" "photon flux" "pressure" "temperature" "tidal stage" "turbidity" "pH" "total depth of water column" "alkyl diethers" "aminopeptidase activity" "ammonium" "bacterial carbon production" "bacterial production" "bacterial respiration" "bishomohopanol" "bromide" "calcium" "carbon/nitrogen ratio" "chloride" "chlorophyll" "diether lipids" "dissolved carbon dioxide" "dissolved hydrogen" "dissolved inorganic carbon" "dissolved inorganic nitrogen" "dissolved inorganic phosphorus" "dissolved organic carbon" "dissolved organic nitrogen" "dissolved oxygen" "glucosidase activity" "magnesium" "n-alkanes" "nitrate" "nitrite" "total nitrogen concentration" "organic carbon" "organic matter" "organic nitrogen" "particulate organic carbon" "particulate organic nitrogen" "petroleum hydrocarbon" "phaeopigments" "phosphate" "phospholipid fatty acid" "potassium" "primary production" "redox potential" "salinity" "silicate" "sodium" "soluble reactive phosphorus" "sulfate" "sulfide" "suspended particulate matter" "total dissolved nitrogen" "total inorganic nitrogen" "total nitrogen content" "total particulate carbon" "total phosphorus" "alkalinity method" "alkalinity" "source material identifiers" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "depth" "chemical administration" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "size-fraction lower threshold" "size-fraction upper threshold" "oxygenation status of sample" "density" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "biomass" "organism count" "sample storage duration" "host disease status" "host scientific name" "atmospheric data" "conductivity" "water current" "fluorescence" "light intensity" "mean friction velocity" "mean peak friction velocity" "downward PAR" "photon flux" "pressure" "temperature" "tidal stage" "turbidity" "pH" "total depth of water column" "alkyl diethers" "aminopeptidase activity" "ammonium" "bacterial carbon production" "bacterial production" "bacterial respiration" "bishomohopanol" "bromide" "calcium" "carbon/nitrogen ratio" "chloride" "chlorophyll" "diether lipids" "dissolved carbon dioxide" "dissolved hydrogen" "dissolved inorganic carbon" "dissolved inorganic nitrogen" "dissolved inorganic phosphorus" "dissolved organic carbon" "dissolved organic nitrogen" "dissolved oxygen" "glucosidase activity" "magnesium" "n-alkanes" "nitrate" "nitrite" "total nitrogen concentration" "organic carbon" "organic matter" "organic nitrogen" "particulate organic carbon" "particulate organic nitrogen" "petroleum hydrocarbon" "phaeopigments" "phosphate" "phospholipid fatty acid" "potassium" "primary production" "redox potential" "salinity" "silicate" "sodium" "soluble reactive phosphorus" "sulfate" "sulfide" "suspended particulate matter" "total dissolved nitrogen" "total inorganic nitrogen" "total nitrogen content" "total particulate carbon" "total phosphorus" "alkalinity method" "alkalinity" "source material identifiers" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "depth" "chemical administration" diff --git a/templates/ERC000025/ERC000025.json b/templates/ERC000025/ERC000025.json index 015a9fe..5d01a7f 100644 --- a/templates/ERC000025/ERC000025.json +++ b/templates/ERC000025/ERC000025.json @@ -833,8 +833,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1656,15 +1656,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "depth", "cardinality": "optional", diff --git a/templates/ERC000025/README.md b/templates/ERC000025/README.md index 6bac312..1e19739 100644 --- a/templates/ERC000025/README.md +++ b/templates/ERC000025/README.md @@ -81,7 +81,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -148,7 +148,6 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | depth | optional | The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. depth can be reported as an interval for subsurface samples. (Units: mm) | | | chemical administration | optional | List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, n fertilizer, air filter); can include multiple compounds. for chemical entities of biological interest ontology (chebi) (v111), please see http://purl.bioontology.org/ontology/chebi | | diff --git a/templates/ERC000025/metadata_template_ERC000025.xlsx b/templates/ERC000025/metadata_template_ERC000025.xlsx index 3c7ff44..4322615 100644 Binary files a/templates/ERC000025/metadata_template_ERC000025.xlsx and b/templates/ERC000025/metadata_template_ERC000025.xlsx differ diff --git a/templates/ERC000025/sample.tsv b/templates/ERC000025/sample.tsv index 7e2b314..9eb3b4d 100644 --- a/templates/ERC000025/sample.tsv +++ b/templates/ERC000025/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "density" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "biomass" "organism count" "sample storage duration" "host disease status" "host scientific name" "water current" "pressure" "temperature" "pH" "ammonium" "bromide" "calcium" "chloride" "chlorophyll" "diether lipids" "dissolved carbon dioxide" "dissolved hydrogen" "dissolved inorganic carbon" "dissolved organic nitrogen" "dissolved oxygen" "nitrate" "nitrite" "total nitrogen concentration" "organic carbon" "organic matter" "organic nitrogen" "phosphate" "phospholipid fatty acid" "potassium" "salinity" "silicate" "sodium" "sulfate" "sulfide" "alkalinity" "source material identifiers" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "depth" "chemical administration" +"alias" "title" "taxon_id" "sample_description" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "sample storage temperature" "sample storage location" "oxygenation status of sample" "density" "project name" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "biomass" "organism count" "sample storage duration" "host disease status" "host scientific name" "water current" "pressure" "temperature" "pH" "ammonium" "bromide" "calcium" "chloride" "chlorophyll" "diether lipids" "dissolved carbon dioxide" "dissolved hydrogen" "dissolved inorganic carbon" "dissolved organic nitrogen" "dissolved oxygen" "nitrate" "nitrite" "total nitrogen concentration" "organic carbon" "organic matter" "organic nitrogen" "phosphate" "phospholipid fatty acid" "potassium" "salinity" "silicate" "sodium" "sulfate" "sulfide" "alkalinity" "source material identifiers" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "depth" "chemical administration" diff --git a/templates/ERC000027/ERC000027.json b/templates/ERC000027/ERC000027.json index 4328427..c37485f 100644 --- a/templates/ERC000027/ERC000027.json +++ b/templates/ERC000027/ERC000027.json @@ -880,8 +880,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000027/README.md b/templates/ERC000027/README.md index 0a5ff1b..2b7cf9b 100644 --- a/templates/ERC000027/README.md +++ b/templates/ERC000027/README.md @@ -86,7 +86,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | environmental package | mandatory | Migs/mims/mimarks extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. all environmental packages listed here are further defined in separate subtables. by giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported | water | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | broad-scale environmental context | mandatory | Report the major environmental system the sample or specimen came from. the system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). we recommend using subclasses of envo’s biome class: http://purl.obolibrary.org/obo/envo_00000428. envo documentation about how to use the field: https://github.com/environmentontology/envo/wiki/using-envo-with-mixs. | | | local environmental context | mandatory | Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. we recommend using envo terms which are of smaller spatial grain than your entry for "broad-scale environmental context". terms, such as anatomical sites, from other obo library ontologies which interoperate with envo (e.g. uberon) are accepted in this field. envo documentation about how to use the field: https://github.com/environmentontology/envo/wiki/using-envo-with-mixs. | | | environmental medium | mandatory | Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. we recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/envo_00010483). envo documentation about how to use the field: https://github.com/environmentontology/envo/wiki/using-envo-with-mixs . terms from other obo ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top). | | diff --git a/templates/ERC000027/metadata_template_ERC000027.xlsx b/templates/ERC000027/metadata_template_ERC000027.xlsx index 214c289..e3979d6 100644 Binary files a/templates/ERC000027/metadata_template_ERC000027.xlsx and b/templates/ERC000027/metadata_template_ERC000027.xlsx differ diff --git a/templates/ERC000028/ERC000028.json b/templates/ERC000028/ERC000028.json index 8c018df..d5b8635 100644 --- a/templates/ERC000028/ERC000028.json +++ b/templates/ERC000028/ERC000028.json @@ -592,8 +592,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000028/README.md b/templates/ERC000028/README.md index 4d034f9..667961b 100644 --- a/templates/ERC000028/README.md +++ b/templates/ERC000028/README.md @@ -60,7 +60,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | lat_lon | recommended | Geographical coordinates of the location where the specimen was collected | | | collected_by | optional | Name of persons or institute who collected the specimen | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | | identified_by | optional | Name of the expert who identified the specimen taxonomically | | | environmental_sample | optional | Identifies sequences derived by direct molecular isolation from a bulk environmental dna sample (by pcr with or without subsequent cloning of the product, dgge, or other anonymous methods) with no reliable identification of the source organism | No, Yes | diff --git a/templates/ERC000028/metadata_template_ERC000028.xlsx b/templates/ERC000028/metadata_template_ERC000028.xlsx index 57495bc..5fa9f53 100644 Binary files a/templates/ERC000028/metadata_template_ERC000028.xlsx and b/templates/ERC000028/metadata_template_ERC000028.xlsx differ diff --git a/templates/ERC000029/ERC000029.json b/templates/ERC000029/ERC000029.json index 230d356..95489f4 100644 --- a/templates/ERC000029/ERC000029.json +++ b/templates/ERC000029/ERC000029.json @@ -909,8 +909,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000029/README.md b/templates/ERC000029/README.md index 097473f..31dc343 100644 --- a/templates/ERC000029/README.md +++ b/templates/ERC000029/README.md @@ -64,7 +64,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | collected_by | mandatory | Name of persons or institute who collected the specimen | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | diff --git a/templates/ERC000029/metadata_template_ERC000029.xlsx b/templates/ERC000029/metadata_template_ERC000029.xlsx index 759324d..de61e4e 100644 Binary files a/templates/ERC000029/metadata_template_ERC000029.xlsx and b/templates/ERC000029/metadata_template_ERC000029.xlsx differ diff --git a/templates/ERC000030/ERC000030.json b/templates/ERC000030/ERC000030.json index 319cd49..ea7e90d 100644 --- a/templates/ERC000030/ERC000030.json +++ b/templates/ERC000030/ERC000030.json @@ -711,8 +711,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000030/README.md b/templates/ERC000030/README.md index 073549f..eb45917 100644 --- a/templates/ERC000030/README.md +++ b/templates/ERC000030/README.md @@ -73,7 +73,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | project name | mandatory | Name of the project within which the sequencing was organized | | | environmental package | mandatory | Migs/mims/mimarks extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. all environmental packages listed here are further defined in separate subtables. by giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported | water | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | broad-scale environmental context | mandatory | Report the major environmental system the sample or specimen came from. the system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). we recommend using subclasses of envo’s biome class: http://purl.obolibrary.org/obo/envo_00000428. envo documentation about how to use the field: https://github.com/environmentontology/envo/wiki/using-envo-with-mixs. | | | local environmental context | mandatory | Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. we recommend using envo terms which are of smaller spatial grain than your entry for "broad-scale environmental context". terms, such as anatomical sites, from other obo library ontologies which interoperate with envo (e.g. uberon) are accepted in this field. envo documentation about how to use the field: https://github.com/environmentontology/envo/wiki/using-envo-with-mixs. | | | environmental medium | mandatory | Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. we recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/envo_00010483). envo documentation about how to use the field: https://github.com/environmentontology/envo/wiki/using-envo-with-mixs . terms from other obo ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top). | | diff --git a/templates/ERC000030/metadata_template_ERC000030.xlsx b/templates/ERC000030/metadata_template_ERC000030.xlsx index 6beabb0..f759e8d 100644 Binary files a/templates/ERC000030/metadata_template_ERC000030.xlsx and b/templates/ERC000030/metadata_template_ERC000030.xlsx differ diff --git a/templates/ERC000031/ERC000031.json b/templates/ERC000031/ERC000031.json index fb7167b..6820805 100644 --- a/templates/ERC000031/ERC000031.json +++ b/templates/ERC000031/ERC000031.json @@ -812,8 +812,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -2631,15 +2631,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "date last rain", "cardinality": "optional", diff --git a/templates/ERC000031/README.md b/templates/ERC000031/README.md index f9ed6ca..5c2c6c5 100644 --- a/templates/ERC000031/README.md +++ b/templates/ERC000031/README.md @@ -79,7 +79,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -245,7 +245,6 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | pcr conditions | optional | Description of reaction conditions and components for pcr in the form of 'initial denaturation:94degc_1.5min; annealing=...' | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | date last rain | optional | The date of the last time it rained | | | sampling day weather | optional | The weather on the sampling day (Units: g/m3) | | | amount of light | optional | The unit of illuminance and luminous emittance, measuring luminous flux per unit area (Units: W/m2) | | diff --git a/templates/ERC000031/metadata_template_ERC000031.xlsx b/templates/ERC000031/metadata_template_ERC000031.xlsx index eda4ece..f49e7b9 100644 Binary files a/templates/ERC000031/metadata_template_ERC000031.xlsx and b/templates/ERC000031/metadata_template_ERC000031.xlsx differ diff --git a/templates/ERC000031/sample.tsv b/templates/ERC000031/sample.tsv index 27ce29f..9abedee 100644 --- a/templates/ERC000031/sample.tsv +++ b/templates/ERC000031/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "number of inoculated individuals" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "project name" "frequency of cooking" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "sampling time outside" "temperature outside house" "train station collection location" "train stop collection location" "surface material" "surface-air contaminant" "indoor surface" "indoor space" "filter type" "heating and cooling system type" "substructure type" "light type" "building setting" "building occupancy type" "space typical state" "typical occupant density" "occupancy at sampling" "occupant density at sampling" "ventilation type" "rooms that are on the same hallway" "wall surface treatment" "wall area" "elevator count" "floor area" "furniture" "water feature type" "room door distance" "room type" "window location" "ceiling type" "door direction of opening" "exposed pipes" "wall height" "door type, metal" "inside lux light" "exposed ductwork" "door material" "adjacent rooms" "wall thermal mass" "ceiling signs of water/mold" "window status" "door location" "window signs of water/mold" "window type" "window material" "window horizontal position" "room condition" "window area/size" "sampling floor" "room count" "average daily occupancy" "floor condition" "door type, wood" "door condition" "door movement" "interior wall condition" "floor signs of water/mold" "ceiling structure" "wall texture" "floor thermal mass" "room air exchange rate" "bathroom count" "shading device signs of water/mold" "window covering" "ceiling texture" "maximum occupancy" "gender of restroom" "ceiling condition" "floor structure" "rooms that share a wall with sampling room" "wall finish material" "room occupancy" "room location in building" "floor finish material" "room window count" "sampling room id or name" "height carpet fiber mat" "ceiling area" "heating system delivery method" "room sampling position" "room moisture damage or mold history" "door signs of water/mold" "room net area" "ceiling thermal mass" "rooms that share a door with sampling room" "orientations of exterior window" "wall location" "room volume" "door type, composite" "bedroom count" "wall construction type" "wall signs of water/mold" "window condition" "escalator count" "cooling system identifier" "quadrant position" "number of pets" "window vertical position" "fireplace type" "heating delivery locations" "ceiling finish material" "door type" "number of houseplants" "floor age" "rooms connected by a doorway" "specifications" "specific humidity" "window open frequency" "room dimensions" "water feature size" "amount or size of sample collected" "sample size sorting method" "organism count" "mechanical structure" "handidness" "host disease status" "host scientific name" "relative air humidity" "absolute air humidity" "surface humidity" "air temperature" "surface temperature" "surface moisture" "surface moisture pH" "dew point" "temperature" "last time swept/mopped/vacuumed" "number of residents" "average dew point" "frequency of cleaning" "carbon dioxide" "source material identifiers" "seasonal use" "season" "average temperature" "host specificity or range" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "sequencing method" "date last rain" "sampling day weather" "amount of light" "train line" "outside relative humidity" "depth" "door area or size" "visual media" "built structure setting" "built structure type" "exterior door count" "design, construction, and operation documents" "shading device condition" "occupancy documentation" "floor count" "shading device material" "built structure age" "hallway/corridor count" "architectural structure" "shading device type" "shading device location" "drawings" "address" "room architectural elements" "aerospace structure" +"alias" "title" "taxon_id" "sample_description" "number of inoculated individuals" "trophic level" "observed biotic relationship" "known pathogenicity" "relationship to oxygen" "propagation" "sample collection device" "sample collection method" "project name" "frequency of cooking" "ploidy" "number of replicons" "extrachromosomal elements" "estimated size" "target gene" "target subfragment" "multiplex identifiers" "sequence quality check" "chimera check software" "relevant electronic resources" "relevant standard operating procedures" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "sampling time outside" "temperature outside house" "train station collection location" "train stop collection location" "surface material" "surface-air contaminant" "indoor surface" "indoor space" "filter type" "heating and cooling system type" "substructure type" "light type" "building setting" "building occupancy type" "space typical state" "typical occupant density" "occupancy at sampling" "occupant density at sampling" "ventilation type" "rooms that are on the same hallway" "wall surface treatment" "wall area" "elevator count" "floor area" "furniture" "water feature type" "room door distance" "room type" "window location" "ceiling type" "door direction of opening" "exposed pipes" "wall height" "door type, metal" "inside lux light" "exposed ductwork" "door material" "adjacent rooms" "wall thermal mass" "ceiling signs of water/mold" "window status" "door location" "window signs of water/mold" "window type" "window material" "window horizontal position" "room condition" "window area/size" "sampling floor" "room count" "average daily occupancy" "floor condition" "door type, wood" "door condition" "door movement" "interior wall condition" "floor signs of water/mold" "ceiling structure" "wall texture" "floor thermal mass" "room air exchange rate" "bathroom count" "shading device signs of water/mold" "window covering" "ceiling texture" "maximum occupancy" "gender of restroom" "ceiling condition" "floor structure" "rooms that share a wall with sampling room" "wall finish material" "room occupancy" "room location in building" "floor finish material" "room window count" "sampling room id or name" "height carpet fiber mat" "ceiling area" "heating system delivery method" "room sampling position" "room moisture damage or mold history" "door signs of water/mold" "room net area" "ceiling thermal mass" "rooms that share a door with sampling room" "orientations of exterior window" "wall location" "room volume" "door type, composite" "bedroom count" "wall construction type" "wall signs of water/mold" "window condition" "escalator count" "cooling system identifier" "quadrant position" "number of pets" "window vertical position" "fireplace type" "heating delivery locations" "ceiling finish material" "door type" "number of houseplants" "floor age" "rooms connected by a doorway" "specifications" "specific humidity" "window open frequency" "room dimensions" "water feature size" "amount or size of sample collected" "sample size sorting method" "organism count" "mechanical structure" "handidness" "host disease status" "host scientific name" "relative air humidity" "absolute air humidity" "surface humidity" "air temperature" "surface temperature" "surface moisture" "surface moisture pH" "dew point" "temperature" "last time swept/mopped/vacuumed" "number of residents" "average dew point" "frequency of cleaning" "carbon dioxide" "source material identifiers" "seasonal use" "season" "average temperature" "host specificity or range" "perturbation" "negative control type" "positive control type" "experimental factor" "encoded traits" "subspecific genetic lineage" "taxonomic classification" "isolation and growth condition" "annotation source" "reference for biomaterial" "sample material processing" "sample volume or weight for DNA extraction" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library construction method" "library vector" "library screening strategy" "pcr conditions" "pcr primers" "adapters" "date last rain" "sampling day weather" "amount of light" "train line" "outside relative humidity" "depth" "door area or size" "visual media" "built structure setting" "built structure type" "exterior door count" "design, construction, and operation documents" "shading device condition" "occupancy documentation" "floor count" "shading device material" "built structure age" "hallway/corridor count" "architectural structure" "shading device type" "shading device location" "drawings" "address" "room architectural elements" "aerospace structure" diff --git a/templates/ERC000032/ERC000032.json b/templates/ERC000032/ERC000032.json index 0c2dae5..8078d72 100644 --- a/templates/ERC000032/ERC000032.json +++ b/templates/ERC000032/ERC000032.json @@ -784,8 +784,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000032/README.md b/templates/ERC000032/README.md index 8ca781c..6e95a85 100644 --- a/templates/ERC000032/README.md +++ b/templates/ERC000032/README.md @@ -80,7 +80,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | illness duration | optional | The number of days the illness lasted. example: 4 | | | illness symptoms | optional | The symptoms that have been reported in relation to the illness, such as cough, diarrhea, fever, headache, malaise, myalgia, nausea, runny_nose, shortness_of_breath, sore_throat. if multiple exposures are applicable, please state them separated by semicolon. | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | recommended | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | recommended | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | recommended | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | diff --git a/templates/ERC000032/metadata_template_ERC000032.xlsx b/templates/ERC000032/metadata_template_ERC000032.xlsx index 6e1d108..7756551 100644 Binary files a/templates/ERC000032/metadata_template_ERC000032.xlsx and b/templates/ERC000032/metadata_template_ERC000032.xlsx differ diff --git a/templates/ERC000033/ERC000033.json b/templates/ERC000033/ERC000033.json index da45e9b..ab25371 100644 --- a/templates/ERC000033/ERC000033.json +++ b/templates/ERC000033/ERC000033.json @@ -631,8 +631,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000033/README.md b/templates/ERC000033/README.md index a49e595..9caae01 100644 --- a/templates/ERC000033/README.md +++ b/templates/ERC000033/README.md @@ -64,7 +64,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | illness duration | optional | The number of days the illness lasted. example: 4 | | | illness symptoms | optional | The symptoms that have been reported in relation to the illness, such as cough, diarrhea, fever, headache, malaise, myalgia, nausea, runny_nose, shortness_of_breath, sore_throat. if multiple exposures are applicable, please state them separated by semicolon. | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | recommended | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | recommended | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | recommended | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | diff --git a/templates/ERC000033/metadata_template_ERC000033.xlsx b/templates/ERC000033/metadata_template_ERC000033.xlsx index 309742b..06e2cf8 100644 Binary files a/templates/ERC000033/metadata_template_ERC000033.xlsx and b/templates/ERC000033/metadata_template_ERC000033.xlsx differ diff --git a/templates/ERC000034/ERC000034.json b/templates/ERC000034/ERC000034.json index aa1d070..1a747eb 100644 --- a/templates/ERC000034/ERC000034.json +++ b/templates/ERC000034/ERC000034.json @@ -574,8 +574,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000034/README.md b/templates/ERC000034/README.md index f86b6d7..052a051 100644 --- a/templates/ERC000034/README.md +++ b/templates/ERC000034/README.md @@ -58,7 +58,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | sample_description | optional | Free-form text describing the sample, its origin, and its method of isolation. | | | tissue_type | mandatory | Tissue type from which the sample was obtained | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | sex | mandatory | Sex of the organism from which the sample was obtained | | | date of birth | recommended | Date of birth of subject the sample was derived from. | | | date of death | recommended | Date of death of subject the sample was derived from. | | diff --git a/templates/ERC000034/metadata_template_ERC000034.xlsx b/templates/ERC000034/metadata_template_ERC000034.xlsx index 893bff0..1ffdd17 100644 Binary files a/templates/ERC000034/metadata_template_ERC000034.xlsx and b/templates/ERC000034/metadata_template_ERC000034.xlsx differ diff --git a/templates/ERC000035/ERC000035.json b/templates/ERC000035/ERC000035.json index 4868952..fb5e43a 100644 --- a/templates/ERC000035/ERC000035.json +++ b/templates/ERC000035/ERC000035.json @@ -610,8 +610,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000035/README.md b/templates/ERC000035/README.md index c15de78..57b7b22 100644 --- a/templates/ERC000035/README.md +++ b/templates/ERC000035/README.md @@ -62,7 +62,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | ploidy | optional | The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). it has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). for terms, please select terms listed under class ploidy (pato:001374) of phenotypic quality ontology (pato), and for a browser of pato (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/pato | | | infect | optional | The name of the disease causing/contaminating organism; the value can also be ‘control’. | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | sampling time point | optional | Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point. indicate the timepoint written in iso 8601 format. | | | initial time point | optional | The first time point measured at the start of some process. | | | sex | optional | Sex of the organism from which the sample was obtained | | diff --git a/templates/ERC000035/metadata_template_ERC000035.xlsx b/templates/ERC000035/metadata_template_ERC000035.xlsx index 7544d87..11d822f 100644 Binary files a/templates/ERC000035/metadata_template_ERC000035.xlsx and b/templates/ERC000035/metadata_template_ERC000035.xlsx differ diff --git a/templates/ERC000036/ERC000036.json b/templates/ERC000036/ERC000036.json index f90dad0..8ff5d35 100644 --- a/templates/ERC000036/ERC000036.json +++ b/templates/ERC000036/ERC000036.json @@ -659,8 +659,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000036/README.md b/templates/ERC000036/README.md index b218fe5..e7f2ca3 100644 --- a/templates/ERC000036/README.md +++ b/templates/ERC000036/README.md @@ -66,7 +66,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | investigation type | mandatory | Nucleic acid sequence report is the root element of all mixs compliant reports as standardised by genomic standards consortium | bacteria_archaea, eukaryote, metagenome, metagenome-assembled genome, metatranscriptome, mimarks-specimen, mimarks-survey, organelle, plasmid, single amplified genome, uncultivated viral genomes, virus | | surveillance target | recommended | Valid species level ncbi taxon id of the organism being surveyed for (if any) e.g. for escherichia coli enter 562. | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | recommended | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | recommended | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | diff --git a/templates/ERC000036/metadata_template_ERC000036.xlsx b/templates/ERC000036/metadata_template_ERC000036.xlsx index a0f61d5..c5ace35 100644 Binary files a/templates/ERC000036/metadata_template_ERC000036.xlsx and b/templates/ERC000036/metadata_template_ERC000036.xlsx differ diff --git a/templates/ERC000037/ERC000037.json b/templates/ERC000037/ERC000037.json index 6dc6f48..0d2da27 100644 --- a/templates/ERC000037/ERC000037.json +++ b/templates/ERC000037/ERC000037.json @@ -884,8 +884,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000037/README.md b/templates/ERC000037/README.md index ed87141..d4dd8e7 100644 --- a/templates/ERC000037/README.md +++ b/templates/ERC000037/README.md @@ -87,7 +87,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | collected_by | optional | Name of persons or institute who collected the specimen | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | diff --git a/templates/ERC000037/metadata_template_ERC000037.xlsx b/templates/ERC000037/metadata_template_ERC000037.xlsx index c1587a3..cd6d737 100644 Binary files a/templates/ERC000037/metadata_template_ERC000037.xlsx and b/templates/ERC000037/metadata_template_ERC000037.xlsx differ diff --git a/templates/ERC000038/ERC000038.json b/templates/ERC000038/ERC000038.json index d79b36b..98e8520 100644 --- a/templates/ERC000038/ERC000038.json +++ b/templates/ERC000038/ERC000038.json @@ -680,8 +680,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000038/README.md b/templates/ERC000038/README.md index 04eac6c..38f9b86 100644 --- a/templates/ERC000038/README.md +++ b/templates/ERC000038/README.md @@ -69,7 +69,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | sample health state | optional | Health status of the subject at the time of sample collection | diseased, healthy | | sample disease status | optional | List of diseases with which the subject has been diagnosed at the time of sample collection; can include multiple diagnoses; the value of the field depends on subject; e.g. charcoal rot (macrophomina phaseolina), late wilt (cephalosporium maydis) | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | broad-scale environmental context | mandatory | Report the major environmental system the sample or specimen came from. the system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). we recommend using subclasses of envo’s biome class: http://purl.obolibrary.org/obo/envo_00000428. envo documentation about how to use the field: https://github.com/environmentontology/envo/wiki/using-envo-with-mixs. | | | local environmental context | mandatory | Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. we recommend using envo terms which are of smaller spatial grain than your entry for "broad-scale environmental context". terms, such as anatomical sites, from other obo library ontologies which interoperate with envo (e.g. uberon) are accepted in this field. envo documentation about how to use the field: https://github.com/environmentontology/envo/wiki/using-envo-with-mixs. | | | environmental medium | mandatory | Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. we recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/envo_00010483). envo documentation about how to use the field: https://github.com/environmentontology/envo/wiki/using-envo-with-mixs . terms from other obo ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top). | | diff --git a/templates/ERC000038/metadata_template_ERC000038.xlsx b/templates/ERC000038/metadata_template_ERC000038.xlsx index 87c28f1..db73185 100644 Binary files a/templates/ERC000038/metadata_template_ERC000038.xlsx and b/templates/ERC000038/metadata_template_ERC000038.xlsx differ diff --git a/templates/ERC000039/ERC000039.json b/templates/ERC000039/ERC000039.json index f178e05..da3ae6a 100644 --- a/templates/ERC000039/ERC000039.json +++ b/templates/ERC000039/ERC000039.json @@ -909,8 +909,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000039/README.md b/templates/ERC000039/README.md index 099a528..b2286a1 100644 --- a/templates/ERC000039/README.md +++ b/templates/ERC000039/README.md @@ -64,7 +64,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | clinical setting | optional | The timing of the clinic visit in relation to travel. | after travel, during travel | | country of travel | optional | The name of the country of patient's travel. | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burma, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Cyprus, Czech Republic, Czechoslovakia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands, Faroe Islands, Federal Republic of Germany, Fiji, Finland, Former Yugoslav Republic of Macedonia, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, GDR, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kingman Reef, Kiribati, Korea, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Namibia, Nauru, Navassa Island, Nepal, Netherlands, Netherlands Antilles, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, Northern Mariana Islands, Norway, Oman, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Russia, Rwanda, Saint Barthelemy, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Martin, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Serbia and Montenegro, Seychelles, Sierra Leone, Singapore, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, South Sudan, Spain, Spratly Islands, Sri Lanka, State of Palestine, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Thailand, Timor-Leste, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, USSR, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | recommended | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | recommended | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | diff --git a/templates/ERC000039/metadata_template_ERC000039.xlsx b/templates/ERC000039/metadata_template_ERC000039.xlsx index 0312abb..1c9bdc4 100644 Binary files a/templates/ERC000039/metadata_template_ERC000039.xlsx and b/templates/ERC000039/metadata_template_ERC000039.xlsx differ diff --git a/templates/ERC000040/ERC000040.json b/templates/ERC000040/ERC000040.json index 73e293c..9b73772 100644 --- a/templates/ERC000040/ERC000040.json +++ b/templates/ERC000040/ERC000040.json @@ -637,8 +637,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000040/README.md b/templates/ERC000040/README.md index 123bc07..8b7854a 100644 --- a/templates/ERC000040/README.md +++ b/templates/ERC000040/README.md @@ -65,7 +65,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | collected_by | optional | Name of persons or institute who collected the specimen | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | diff --git a/templates/ERC000040/metadata_template_ERC000040.xlsx b/templates/ERC000040/metadata_template_ERC000040.xlsx index 63bb785..ce3ad28 100644 Binary files a/templates/ERC000040/metadata_template_ERC000040.xlsx and b/templates/ERC000040/metadata_template_ERC000040.xlsx differ diff --git a/templates/ERC000041/ERC000041.json b/templates/ERC000041/ERC000041.json index 6433fa9..26c250c 100644 --- a/templates/ERC000041/ERC000041.json +++ b/templates/ERC000041/ERC000041.json @@ -646,8 +646,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000041/README.md b/templates/ERC000041/README.md index 71bef89..2e59c83 100644 --- a/templates/ERC000041/README.md +++ b/templates/ERC000041/README.md @@ -66,7 +66,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | DNA concentration | optional | Dna concentration used for sequencing in ng/µl (Units: ng/µl) | | | isolation_source | optional | Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (region and locality) | recommended | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | | amount or size of sample collected | optional | The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. (Units: m3) | | | sampling time point | optional | Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point. indicate the timepoint written in iso 8601 format. | | diff --git a/templates/ERC000041/metadata_template_ERC000041.xlsx b/templates/ERC000041/metadata_template_ERC000041.xlsx index 738de78..1b8c096 100644 Binary files a/templates/ERC000041/metadata_template_ERC000041.xlsx and b/templates/ERC000041/metadata_template_ERC000041.xlsx differ diff --git a/templates/ERC000043/ERC000043.json b/templates/ERC000043/ERC000043.json index 01d0ebe..b9d929e 100644 --- a/templates/ERC000043/ERC000043.json +++ b/templates/ERC000043/ERC000043.json @@ -601,8 +601,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000043/README.md b/templates/ERC000043/README.md index b804e45..ae8c960 100644 --- a/templates/ERC000043/README.md +++ b/templates/ERC000043/README.md @@ -61,7 +61,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | sample storage temperature | optional | Temperature at which sample was stored, e.g. -80 (Units: °C) | | | collected_by | recommended | Name of persons or institute who collected the specimen | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | recommended | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | recommended | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | amount or size of sample collected | optional | The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. (Units: m3) | | diff --git a/templates/ERC000043/metadata_template_ERC000043.xlsx b/templates/ERC000043/metadata_template_ERC000043.xlsx index 1c8e0a5..44f3f32 100644 Binary files a/templates/ERC000043/metadata_template_ERC000043.xlsx and b/templates/ERC000043/metadata_template_ERC000043.xlsx differ diff --git a/templates/ERC000044/ERC000044.json b/templates/ERC000044/ERC000044.json index d23cdf5..121361f 100644 --- a/templates/ERC000044/ERC000044.json +++ b/templates/ERC000044/ERC000044.json @@ -891,8 +891,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000044/README.md b/templates/ERC000044/README.md index 501f05d..8a65210 100644 --- a/templates/ERC000044/README.md +++ b/templates/ERC000044/README.md @@ -62,7 +62,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | country of travel | optional | The name of the country of patient's travel. | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burma, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Cyprus, Czech Republic, Czechoslovakia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands, Faroe Islands, Federal Republic of Germany, Fiji, Finland, Former Yugoslav Republic of Macedonia, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, GDR, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kingman Reef, Kiribati, Korea, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Namibia, Nauru, Navassa Island, Nepal, Netherlands, Netherlands Antilles, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, Northern Mariana Islands, Norway, Oman, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Russia, Rwanda, Saint Barthelemy, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Martin, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Serbia and Montenegro, Seychelles, Sierra Leone, Singapore, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, South Sudan, Spain, Spratly Islands, Sri Lanka, State of Palestine, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Thailand, Timor-Leste, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, USSR, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe | | collected_by | mandatory | Name of persons or institute who collected the specimen | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | | subject exposure duration | optional | Duration of the exposure of the subject to an infected human or animal. if multiple exposures are applicable, please state their duration in the same order in which you reported the exposure in the field 'subject exposure'. example: 1 day; 0.33 days (Units: year) | | | host disease status | optional | List of diseases with which the host has been diagnosed; can include multiple diagnoses. the value of the field depends on host; for humans the terms should be chosen from do (disease ontology) at http://www.disease-ontology.org, other hosts are free text | | diff --git a/templates/ERC000044/metadata_template_ERC000044.xlsx b/templates/ERC000044/metadata_template_ERC000044.xlsx index a7ca000..d98a5b4 100644 Binary files a/templates/ERC000044/metadata_template_ERC000044.xlsx and b/templates/ERC000044/metadata_template_ERC000044.xlsx differ diff --git a/templates/ERC000045/ERC000045.json b/templates/ERC000045/ERC000045.json index e51c834..3766362 100644 --- a/templates/ERC000045/ERC000045.json +++ b/templates/ERC000045/ERC000045.json @@ -583,8 +583,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000045/README.md b/templates/ERC000045/README.md index feeaaf0..42657d7 100644 --- a/templates/ERC000045/README.md +++ b/templates/ERC000045/README.md @@ -59,7 +59,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | isolation_source | mandatory | Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived | | | collected_by | optional | Name of persons or institute who collected the specimen | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | | receipt date | recommended | Date on which the sample was received. format:yyyy-mm-dd. please provide the highest precision possible. if the sample was received by the institution and not collected, the 'receipt date' must be provided instead. either the 'collection date' or 'receipt date' must be provided. if available, provide both dates. | | | isolate | mandatory | Individual isolate from which the sample was obtained | | diff --git a/templates/ERC000045/metadata_template_ERC000045.xlsx b/templates/ERC000045/metadata_template_ERC000045.xlsx index 96a5c62..979f914 100644 Binary files a/templates/ERC000045/metadata_template_ERC000045.xlsx and b/templates/ERC000045/metadata_template_ERC000045.xlsx differ diff --git a/templates/ERC000047/ERC000047.json b/templates/ERC000047/ERC000047.json index 8454f91..f519bdb 100644 --- a/templates/ERC000047/ERC000047.json +++ b/templates/ERC000047/ERC000047.json @@ -856,8 +856,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1301,15 +1301,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "depth", "cardinality": "optional", diff --git a/templates/ERC000047/README.md b/templates/ERC000047/README.md index bbd7e5c..8df0a5e 100644 --- a/templates/ERC000047/README.md +++ b/templates/ERC000047/README.md @@ -87,7 +87,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | isolation_source | mandatory | Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -112,6 +112,5 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | library screening strategy | optional | Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences | | | assembly software | recommended | Tool(s) used for assembly, including version number and parameters in the format {software};{version};{parameters} e.g. metaspades;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | depth | optional | The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. depth can be reported as an interval for subsurface samples. (Units: mm) | | diff --git a/templates/ERC000047/metadata_template_ERC000047.xlsx b/templates/ERC000047/metadata_template_ERC000047.xlsx index 470bf2c..c42b8e8 100644 Binary files a/templates/ERC000047/metadata_template_ERC000047.xlsx and b/templates/ERC000047/metadata_template_ERC000047.xlsx differ diff --git a/templates/ERC000047/sample.tsv b/templates/ERC000047/sample.tsv index 5073d30..56e9442 100644 --- a/templates/ERC000047/sample.tsv +++ b/templates/ERC000047/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "relationship to oxygen" "sample collection device" "sample collection method" "metagenomic source" "sample derived from" "project name" "multiplex identifiers" "relevant electronic resources" "relevant standard operating procedures" "number of standard tRNAs extracted" "feature prediction" "similarity search method" "16s recovered" "16S recovery software" "tRNA extraction software" "completeness score" "completeness software" "completeness approach" "contamination score" "contamination screening input" "contamination screening parameters" "decontamination software" "binning software" "reassembly post binning" "MAG coverage software" "assembly quality" "binning parameters" "taxonomic identity marker" "isolation_source" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "size fraction selected" "source material identifiers" "experimental factor" "taxonomic classification" "annotation source" "reference for biomaterial" "reference database(s)" "sample material processing" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library vector" "library screening strategy" "assembly software" "adapters" "sequencing method" "depth" +"alias" "title" "taxon_id" "sample_description" "relationship to oxygen" "sample collection device" "sample collection method" "metagenomic source" "sample derived from" "project name" "multiplex identifiers" "relevant electronic resources" "relevant standard operating procedures" "number of standard tRNAs extracted" "feature prediction" "similarity search method" "16s recovered" "16S recovery software" "tRNA extraction software" "completeness score" "completeness software" "completeness approach" "contamination score" "contamination screening input" "contamination screening parameters" "decontamination software" "binning software" "reassembly post binning" "MAG coverage software" "assembly quality" "binning parameters" "taxonomic identity marker" "isolation_source" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "size fraction selected" "source material identifiers" "experimental factor" "taxonomic classification" "annotation source" "reference for biomaterial" "reference database(s)" "sample material processing" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library vector" "library screening strategy" "assembly software" "adapters" "depth" diff --git a/templates/ERC000048/ERC000048.json b/templates/ERC000048/ERC000048.json index 6bf1195..d73d8f4 100644 --- a/templates/ERC000048/ERC000048.json +++ b/templates/ERC000048/ERC000048.json @@ -817,8 +817,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1322,15 +1322,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "depth", "cardinality": "optional", diff --git a/templates/ERC000048/README.md b/templates/ERC000048/README.md index 46c6704..7398f93 100644 --- a/templates/ERC000048/README.md +++ b/templates/ERC000048/README.md @@ -83,7 +83,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | isolation_source | mandatory | Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -113,6 +113,5 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | WGA amplification kit | optional | Kit used to amplify genomic dna in preparation for sequencing | | | sorting technology | mandatory | Method used to sort/isolate cells or particles of interest | flow cytometric cell sorting, lazer-tweezing, microfluidics, micromanipulation, optical manipulation, other | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | depth | optional | The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. depth can be reported as an interval for subsurface samples. (Units: mm) | | diff --git a/templates/ERC000048/metadata_template_ERC000048.xlsx b/templates/ERC000048/metadata_template_ERC000048.xlsx index f8b903e..1d85dd8 100644 Binary files a/templates/ERC000048/metadata_template_ERC000048.xlsx and b/templates/ERC000048/metadata_template_ERC000048.xlsx differ diff --git a/templates/ERC000048/sample.tsv b/templates/ERC000048/sample.tsv index 51afa7d..d9c0422 100644 --- a/templates/ERC000048/sample.tsv +++ b/templates/ERC000048/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "relationship to oxygen" "sample collection device" "sample collection method" "metagenomic source" "sample derived from" "project name" "multiplex identifiers" "relevant electronic resources" "relevant standard operating procedures" "number of standard tRNAs extracted" "feature prediction" "similarity search method" "16s recovered" "16S recovery software" "tRNA extraction software" "completeness score" "completeness software" "completeness approach" "contamination score" "contamination screening input" "contamination screening parameters" "decontamination software" "assembly quality" "taxonomic identity marker" "isolation_source" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "size fraction selected" "source material identifiers" "experimental factor" "taxonomic classification" "annotation source" "reference for biomaterial" "reference database(s)" "single cell or viral particle lysis approach" "single cell or viral particle lysis kit protocol" "sample material processing" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library vector" "library screening strategy" "assembly software" "WGA amplification approach" "WGA amplification kit" "sorting technology" "adapters" "sequencing method" "depth" +"alias" "title" "taxon_id" "sample_description" "relationship to oxygen" "sample collection device" "sample collection method" "metagenomic source" "sample derived from" "project name" "multiplex identifiers" "relevant electronic resources" "relevant standard operating procedures" "number of standard tRNAs extracted" "feature prediction" "similarity search method" "16s recovered" "16S recovery software" "tRNA extraction software" "completeness score" "completeness software" "completeness approach" "contamination score" "contamination screening input" "contamination screening parameters" "decontamination software" "assembly quality" "taxonomic identity marker" "isolation_source" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "size fraction selected" "source material identifiers" "experimental factor" "taxonomic classification" "annotation source" "reference for biomaterial" "reference database(s)" "single cell or viral particle lysis approach" "single cell or viral particle lysis kit protocol" "sample material processing" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library vector" "library screening strategy" "assembly software" "WGA amplification approach" "WGA amplification kit" "sorting technology" "adapters" "depth" diff --git a/templates/ERC000049/ERC000049.json b/templates/ERC000049/ERC000049.json index 6a46576..7b2608d 100644 --- a/templates/ERC000049/ERC000049.json +++ b/templates/ERC000049/ERC000049.json @@ -913,8 +913,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1475,15 +1475,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "optional", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "depth", "cardinality": "optional", diff --git a/templates/ERC000049/README.md b/templates/ERC000049/README.md index 73982f9..9dcc2a7 100644 --- a/templates/ERC000049/README.md +++ b/templates/ERC000049/README.md @@ -91,7 +91,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | isolation_source | mandatory | Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -125,6 +125,5 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | sorting technology | optional | Method used to sort/isolate cells or particles of interest | flow cytometric cell sorting, lazer-tweezing, microfluidics, micromanipulation, optical manipulation, other | | virus enrichment approach | mandatory | List of approaches used to enrich the sample for viruses, if any | CsCl density gradient, DNAse, FeCl Precipitation, PEG Precipitation, RNAse, centrifugation, filtration, none, other, targeted sequence capture, ultracentrifugation, ultrafiltration | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | optional | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | depth | optional | The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. depth can be reported as an interval for subsurface samples. (Units: mm) | | diff --git a/templates/ERC000049/metadata_template_ERC000049.xlsx b/templates/ERC000049/metadata_template_ERC000049.xlsx index 82236f4..3f80145 100644 Binary files a/templates/ERC000049/metadata_template_ERC000049.xlsx and b/templates/ERC000049/metadata_template_ERC000049.xlsx differ diff --git a/templates/ERC000049/sample.tsv b/templates/ERC000049/sample.tsv index e30d21a..f4e02ae 100644 --- a/templates/ERC000049/sample.tsv +++ b/templates/ERC000049/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "observed biotic relationship" "known pathogenicity" "sample collection device" "sample collection method" "metagenomic source" "sample derived from" "project name" "estimated size" "multiplex identifiers" "relevant electronic resources" "relevant standard operating procedures" "number of standard tRNAs extracted" "feature prediction" "similarity search method" "tRNA extraction software" "completeness score" "completeness software" "completeness approach" "binning software" "reassembly post binning" "MAG coverage software" "binning parameters" "taxonomic identity marker" "source of UViGs" "predicted genome type" "predicted genome structure" "detection type" "viral identification software" "OTU classification approach" "OTU sequence comparison approach" "OTU database" "UViG assembly quality" "isolation_source" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "size fraction selected" "host scientific name" "source material identifiers" "host prediction approach" "host prediction estimated accuracy" "experimental factor" "taxonomic classification" "annotation source" "reference for biomaterial" "reference database(s)" "single cell or viral particle lysis approach" "single cell or viral particle lysis kit protocol" "sample material processing" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library vector" "library screening strategy" "assembly software" "WGA amplification approach" "WGA amplification kit" "sorting technology" "virus enrichment approach" "adapters" "sequencing method" "depth" +"alias" "title" "taxon_id" "sample_description" "observed biotic relationship" "known pathogenicity" "sample collection device" "sample collection method" "metagenomic source" "sample derived from" "project name" "estimated size" "multiplex identifiers" "relevant electronic resources" "relevant standard operating procedures" "number of standard tRNAs extracted" "feature prediction" "similarity search method" "tRNA extraction software" "completeness score" "completeness software" "completeness approach" "binning software" "reassembly post binning" "MAG coverage software" "binning parameters" "taxonomic identity marker" "source of UViGs" "predicted genome type" "predicted genome structure" "detection type" "viral identification software" "OTU classification approach" "OTU sequence comparison approach" "OTU database" "UViG assembly quality" "isolation_source" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "size fraction selected" "host scientific name" "source material identifiers" "host prediction approach" "host prediction estimated accuracy" "experimental factor" "taxonomic classification" "annotation source" "reference for biomaterial" "reference database(s)" "single cell or viral particle lysis approach" "single cell or viral particle lysis kit protocol" "sample material processing" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library vector" "library screening strategy" "assembly software" "WGA amplification approach" "WGA amplification kit" "sorting technology" "virus enrichment approach" "adapters" "depth" diff --git a/templates/ERC000050/ERC000050.json b/templates/ERC000050/ERC000050.json index f68dc74..c6899a4 100644 --- a/templates/ERC000050/ERC000050.json +++ b/templates/ERC000050/ERC000050.json @@ -717,7 +717,7 @@ }, { "name": "investigation type", - "cardinality": "mandatory", + "cardinality": "optional", "description": "Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardised by Genomic Standards Consortium", "cv": [ "bacteria_archaea", @@ -851,8 +851,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1269,15 +1269,6 @@ "field_type": "TEXT_FIELD", "regex": "" }, - { - "name": "sequencing method", - "cardinality": "mandatory", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" - }, { "name": "depth", "cardinality": "optional", diff --git a/templates/ERC000050/README.md b/templates/ERC000050/README.md index ca82b8c..6beae16 100644 --- a/templates/ERC000050/README.md +++ b/templates/ERC000050/README.md @@ -79,13 +79,13 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | reassembly post binning | optional | Has an assembly been performed on a genome bin extracted from a metagenomic assembly? (Units: Yes) | No, Yes | | MAG coverage software | optional | Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets e.g. bwa, bbmap, bowtie, other | | | assembly quality | recommended | The assembly quality category is based on sets of criteria outlined for each assembly quality category. for misag/mimag; finished: single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to q50 or better. high quality draft:multiple fragments where gaps span repetitive regions. presence of the 23s, 16s and 5s rrna genes and at least 18 trnas. medium quality draft:many fragments with little to no review of assembly other than reporting of standard assembly statistics. low quality draft:many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly statistics include, but are not limited to total assembly size, number of contigs, contig n50/l50, and maximum contig length. for miuvig; finished: single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. high-quality draft genome: one or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. genome fragment(s): one or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated. | Many fragments with little to no review of assembly other than reporting of standard assembly statistics, Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs, Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better | -| investigation type | mandatory | Nucleic acid sequence report is the root element of all mixs compliant reports as standardised by genomic standards consortium | bacteria_archaea, eukaryote, metagenome, metagenome-assembled genome, metatranscriptome, mimarks-specimen, mimarks-survey, organelle, plasmid, single amplified genome, uncultivated viral genomes, virus | +| investigation type | optional | Nucleic acid sequence report is the root element of all mixs compliant reports as standardised by genomic standards consortium | bacteria_archaea, eukaryote, metagenome, metagenome-assembled genome, metatranscriptome, mimarks-specimen, mimarks-survey, organelle, plasmid, single amplified genome, uncultivated viral genomes, virus | | binning parameters | mandatory | The parameters that have been applied during the extraction of genomes from metagenomic datasets e.g. coverage and kmer | | | taxonomic identity marker | recommended | The phylogenetic marker(s) used to assign an organism name to the bin, sag or mag. examples are 16s gene, multi-marker approach or other e.g. rpob gene. mandatory for all samples directly linked with sags or mags. | | | isolation_source | mandatory | Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | | altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | mandatory | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | mandatory | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | broad-scale environmental context | mandatory | Report the major environmental system the sample or specimen came from. the system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). we recommend using subclasses of envo’s biome class: http://purl.obolibrary.org/obo/envo_00000428. envo documentation about how to use the field: https://github.com/environmentontology/envo/wiki/using-envo-with-mixs. | | @@ -107,6 +107,5 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | library screening strategy | optional | Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences | | | assembly software | mandatory | Tool(s) used for assembly, including version number and parameters in the format {software};{version};{parameters} e.g. metaspades;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise | | | adapters | optional | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | mandatory | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | | depth | optional | The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. depth can be reported as an interval for subsurface samples. (Units: mm) | | diff --git a/templates/ERC000050/metadata_template_ERC000050.xlsx b/templates/ERC000050/metadata_template_ERC000050.xlsx index 24490e0..2291fd7 100644 Binary files a/templates/ERC000050/metadata_template_ERC000050.xlsx and b/templates/ERC000050/metadata_template_ERC000050.xlsx differ diff --git a/templates/ERC000050/sample.tsv b/templates/ERC000050/sample.tsv index c69307b..7f11231 100644 --- a/templates/ERC000050/sample.tsv +++ b/templates/ERC000050/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "relationship to oxygen" "sample collection method" "metagenomic source" "sample derived from" "project name" "multiplex identifiers" "relevant electronic resources" "relevant standard operating procedures" "number of standard tRNAs extracted" "16s recovered" "16S recovery software" "tRNA extraction software" "completeness score" "completeness software" "completeness approach" "contamination score" "contamination screening input" "contamination screening parameters" "decontamination software" "binning software" "reassembly post binning" "MAG coverage software" "assembly quality" "investigation type" "binning parameters" "taxonomic identity marker" "isolation_source" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "size fraction selected" "source material identifiers" "experimental factor" "taxonomic classification" "reference for biomaterial" "sample material processing" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library vector" "library screening strategy" "assembly software" "adapters" "sequencing method" "depth" +"alias" "title" "taxon_id" "sample_description" "relationship to oxygen" "sample collection method" "metagenomic source" "sample derived from" "project name" "multiplex identifiers" "relevant electronic resources" "relevant standard operating procedures" "number of standard tRNAs extracted" "16s recovered" "16S recovery software" "tRNA extraction software" "completeness score" "completeness software" "completeness approach" "contamination score" "contamination screening input" "contamination screening parameters" "decontamination software" "binning software" "reassembly post binning" "MAG coverage software" "assembly quality" "investigation type" "binning parameters" "taxonomic identity marker" "isolation_source" "collection date" "altitude" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "broad-scale environmental context" "local environmental context" "environmental medium" "elevation" "amount or size of sample collected" "size fraction selected" "source material identifiers" "experimental factor" "taxonomic classification" "reference for biomaterial" "sample material processing" "nucleic acid extraction" "nucleic acid amplification" "library size" "library reads sequenced" "library vector" "library screening strategy" "assembly software" "adapters" "depth" diff --git a/templates/ERC000051/ERC000051.json b/templates/ERC000051/ERC000051.json index e086aa5..edce513 100644 --- a/templates/ERC000051/ERC000051.json +++ b/templates/ERC000051/ERC000051.json @@ -634,8 +634,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000051/README.md b/templates/ERC000051/README.md index 59f4a7c..232668d 100644 --- a/templates/ERC000051/README.md +++ b/templates/ERC000051/README.md @@ -62,7 +62,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | sample unique ID | mandatory | Unique identifier of the pdx or tumor sample, e.g. crc00003 | | | patient tumor type | mandatory | For a primary sample (a tumor at the original site of origin), please select “primary neoplasm” . for a metastatic sample (a tumor that has spread from its original (primary) site of growth to another site, close to or distant from the primary site), please select “metastatic neoplasm” . for a recurring neoplasm sample (neoplasm returning after a period of remission at the same location), please select “recurrent neoplasm” . if unknown tumor type, please select “not provided”. | Metastatic Neoplasm, Primary Neoplasm, Recurrent Neoplasm, not provided | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | engrafted tumor sample passage | mandatory | If engrafted tumor sample, please indicate the passage from which the engrafted tumor sample was harvested (passage 0 must be the first engraftment in the mouse). please ensure you add a non-negative number greater than 0. if the sample origin is “patient tumor” please enter "not applicable". if passage number is unknown please enter "not provided”. | | | engrafted tumor collection site | recommended | If the sample origin is “engrafted tumor”, please indicate the collection site from which the engrafted tumor sample was extracted (e.g. liver). please use terminology from ncit ontology: https://www.ebi.ac.uk/ols/ontologies/ncit. if unknown please select ncit term: “not available” ( http://purl.obolibrary.org/obo/ncit_c126101)”. if the sample origin is “patient tumor” please do not use this attribute. | | | patient tumor site of collection | mandatory | Site of collection of the patient tissue sample which was extracted (can be different to primary site if it is a metastatic sample). please use ncit ontology, e.g. liver (http://purl.obolibrary.org/obo/ncit_c12392). if unknown please select ncit term: “not available” (http://purl.obolibrary.org/obo/ncit_c126101) | | diff --git a/templates/ERC000051/metadata_template_ERC000051.xlsx b/templates/ERC000051/metadata_template_ERC000051.xlsx index 5f70c80..99a02ce 100644 Binary files a/templates/ERC000051/metadata_template_ERC000051.xlsx and b/templates/ERC000051/metadata_template_ERC000051.xlsx differ diff --git a/templates/ERC000052/ERC000052.json b/templates/ERC000052/ERC000052.json index acb7c35..af704c4 100644 --- a/templates/ERC000052/ERC000052.json +++ b/templates/ERC000052/ERC000052.json @@ -619,8 +619,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", @@ -1099,15 +1099,6 @@ "units": "", "field_type": "TEXT_FIELD", "regex": "" - }, - { - "name": "sequencing method", - "cardinality": "mandatory", - "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", - "cv": [], - "units": "", - "field_type": "TEXT_FIELD", - "regex": "" } ] } diff --git a/templates/ERC000052/README.md b/templates/ERC000052/README.md index 221a561..96b2fb7 100644 --- a/templates/ERC000052/README.md +++ b/templates/ERC000052/README.md @@ -63,7 +63,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | project name | mandatory | Name of the project within which the sequencing was organized | | | reference host genome for decontamination | mandatory | Reference host genome that was mapped against for host decontamination (in the form of a valid assembly accession - e.g. in the format gca_xxxxxxx.x) | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | optional | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | optional | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | @@ -90,5 +90,4 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | nucleic acid extraction | optional | A link to a literature reference, electronic resource or a standard operating procedure (sop), that describes the material separation to recover the nucleic acid fraction from a sample | | | pcr primers | optional | Pcr primers that were used to amplify the sequence of the targeted gene, locus or subfragment. this field should contain all the primers used for a single pcr reaction if multiple forward or reverse primers are present in a single pcr reaction. the primer sequence should be reported in uppercase letters | | | adapters | recommended | Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. both adapters should be reported; in uppercase letters | | -| sequencing method | mandatory | Sequencing machine used. where possible the term should be taken from the obi list of dna sequencers (http://purl.obolibrary.org/obo/obi_0400103). | | diff --git a/templates/ERC000052/metadata_template_ERC000052.xlsx b/templates/ERC000052/metadata_template_ERC000052.xlsx index f187e7e..c015b34 100644 Binary files a/templates/ERC000052/metadata_template_ERC000052.xlsx and b/templates/ERC000052/metadata_template_ERC000052.xlsx differ diff --git a/templates/ERC000052/sample.tsv b/templates/ERC000052/sample.tsv index 5648766..3a616a2 100644 --- a/templates/ERC000052/sample.tsv +++ b/templates/ERC000052/sample.tsv @@ -1 +1 @@ -"alias" "title" "taxon_id" "sample_description" "sample storage temperature" "sample storage buffer" "sample storage device" "sample storage location" "project name" "reference host genome for decontamination" "collection date" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "trial length" "trial timepoint" "host disease status" "host common name" "host subject id" "host taxid" "host body site" "host length" "host total mass" "host sex" "host scientific name" "host breed" "host gutted mass" "host diet" "host diet treatment" "host diet treatment concentration" "host storage container" "host storage container pH" "host storage container temperature" "sample volume or weight for DNA extraction" "nucleic acid extraction" "pcr primers" "adapters" "sequencing method" +"alias" "title" "taxon_id" "sample_description" "sample storage temperature" "sample storage buffer" "sample storage device" "sample storage location" "project name" "reference host genome for decontamination" "collection date" "geographic location (country and/or sea)" "geographic location (latitude)" "geographic location (longitude)" "geographic location (region and locality)" "trial length" "trial timepoint" "host disease status" "host common name" "host subject id" "host taxid" "host body site" "host length" "host total mass" "host sex" "host scientific name" "host breed" "host gutted mass" "host diet" "host diet treatment" "host diet treatment concentration" "host storage container" "host storage container pH" "host storage container temperature" "sample volume or weight for DNA extraction" "nucleic acid extraction" "pcr primers" "adapters" diff --git a/templates/ERC000053/ERC000053.json b/templates/ERC000053/ERC000053.json index 692445a..394bee4 100644 --- a/templates/ERC000053/ERC000053.json +++ b/templates/ERC000053/ERC000053.json @@ -745,8 +745,8 @@ "Cuba", "Curacao", "Cyprus", - "Czech Republic", "Czechia", + "Czech Republic", "Democratic Republic of the Congo", "Denmark", "Djibouti", diff --git a/templates/ERC000053/README.md b/templates/ERC000053/README.md index feb4d87..c333d23 100644 --- a/templates/ERC000053/README.md +++ b/templates/ERC000053/README.md @@ -74,7 +74,7 @@ A Sample defines an isolate of sequenceable material upon which sequencing exper | tolid | optional | A tolid (tree of life id) is a unique and easy to communicate sample identifier that provides species recognition, differentiates between specimen of the same species and adds taxonomic context. tolids are issued by id.tol.sanger.ac.uk. they are endorsed by the earthbiogenome project (ebp) and should be assigned to any sample with association to the ebp. | | | collected_by | mandatory | Name of persons or institute who collected the specimen | | | collection date | mandatory | The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | | -| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czech Republic, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | +| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access | | geographic location (latitude) | recommended | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (longitude) | recommended | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | | | geographic location (region and locality) | mandatory | The geographical origin of the sample as defined by the specific region name followed by the locality name. | | diff --git a/templates/ERC000053/metadata_template_ERC000053.xlsx b/templates/ERC000053/metadata_template_ERC000053.xlsx index c58ca81..4ffb046 100644 Binary files a/templates/ERC000053/metadata_template_ERC000053.xlsx and b/templates/ERC000053/metadata_template_ERC000053.xlsx differ