{ "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://github.com/BU-ISCIII/relecov-tools/blob/main/relecov_tools/schema/relecov_schema.json", "title": "relecov-tools Schema.", "description": "Json Schema that specifies the structure, content, and validation rules for relecov-tools", "version": "3.2.0", "type": "object", "properties": { "organism": { "enum": [ "Severe acute respiratory syndrome coronavirus 2 [LOINC:LA31065-8]", "Respiratory syncytial virus [SNOMED:6415009]", "Influenza virus [SNOMED:725894000]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]" ], "ontology": "SNOMED:410607006", "type": "string", "description": "Taxonomic species name of the organism.", "classification": "Sample collection and processing", "label": "Organism", "fill_mode": "batch", "header": "Y" }, "public_health_sample_id": { "examples": [ "2022CEU03926" ], "ontology": "0", "type": "string", "description": "Identificator provided by the Public Health system", "classification": "Sample collection and processing", "label": "Public Health sample id (SIVIRA)", "fill_mode": "sample", "header": "Y" }, "collecting_lab_sample_id": { "examples": [ "1197677" ], "ontology": "GENEPIO:0001123", "type": "string", "description": "Sample ID provided by the laboratory that collects the sample, the collecting institution is requested in column L of this file", "classification": "Database Identifiers", "label": "Sample ID given by originating laboratory", "fill_mode": "sample", "header": "Y" }, "submitting_lab_sample_id": { "examples": [ "202203144" ], "ontology": "GENEPIO:0001148", "type": "string", "description": "Sample ID provided by the submitting laboratory that delivers the sample. The submitting laboratory is requested in column M", "classification": "Sequencing", "label": "Sample ID given by the submitting laboratory", "fill_mode": "sample", "header": "Y" }, "microbiology_lab_sample_id": { "examples": [ "220624" ], "ontology": "0", "type": "string", "description": "Sample identification provided by the microbiology laboratory", "classification": "Sample collection and processing", "label": "Sample ID given in the microbiology lab", "fill_mode": "sample", "header": "Y" }, "isolate_sample_id": { "examples": [ "220624.1" ], "ontology": "GENEPIO:0001644", "type": "string", "description": "Sample identification provided if multiple rna-extraction or passages", "classification": "Database Identifiers", "label": "Sample ID given if multiple rna-extraction or passages", "fill_mode": "sample", "header": "Y" }, "sequencing_sample_id": { "examples": [ "SEQ_220624 (SEQ_220624.2)" ], "ontology": "GENEPIO:0000079", "type": "string", "description": "ID assigned to the sample for sequencing. It must be a unique identifier. If the sample is re-sequenced, the run number should be included, preceded by a dot.", "classification": "Database Identifiers", "label": "Sample ID given for sequencing", "fill_mode": "sample", "header": "Y" }, "ena_sample_accession": { "examples": [ "ERS123456" ], "ontology": "GENEPIO:0001139", "type": "string", "description": "ID generated when uploading the sample to ENA", "classification": "Public databases", "label": "ENA Sample ID", "fill_mode": "batch", "header": "Y" }, "gisaid_virus_name": { "examples": [ "hCoV-19/Spain/CT-HUJT-RB31776/2022" ], "ontology": "GENEPIO:0100282", "type": "string", "description": "The user-defined GISAID virus name assigned to the sequence.", "classification": "Public databases", "label": "GISAID Virus Name", "fill_mode": "sample", "header": "Y" }, "gisaid_accession_id": { "examples": [ "EPI_ISL_11222687" ], "ontology": "NCIT:C180324", "type": "string", "description": "GISAID sequence ID.", "classification": "Public databases", "label": "GISAID id", "fill_mode": "sample", "header": "Y" }, "collecting_institution": { "enum": [ "Adinfa, Sociedad Cooperativa Andaluza", "Alm Univass S.L.", "Antic Hospital De Sant Jaume I Santa Magdalena", "Aptima Centre Clinic - Mutua De Terrassa", "Area Psiquiatrica San Juan De Dios", "Avances Medicos S.A.", "Avantmedic", "Banc de Sang i Teixits Catalunya", "Benito Menni Complex Assistencial En Salut Mental", "Benito Menni, Complex Assistencial En Salut Mental", "Cap La Salut", "Cap Mataro Centre", "Cap Montmelo", "Cap Montornes", "Casal De Curacio", "Casaverde Centro De Rehabilitacion Neurologico De Extremadura S.L.", "Casta Guadarrama", "Castell D'Oliana Residencial,S.L", "Catlab-Centre Analitiques Terrassa, Aie", "Centre Collserola Mutual", "Centre D'Hospitalitzacio I Hospital De Dia Trastorns De La Conducta", "Centre D'Oftalmologia Barraquer", "Centre De Prevencio I Rehabilitacio Asepeyo", "Centre De Salut Doctor Vilaseca-Can Mariner", "Centre Forum", "Centre Geriatric Del Maresme", "Centre Hospitalari Policlinica Barcelona", "Centre Integral De Serveis En Salut Mental Comunitaria", "Centre La Creueta", "Centre Medic Molins, Sl", "Centre Mq Reus", "Centre Palamos Gent Gran", "Centre Polivalent Can Fosc", "Centre Sanitari Del Solsones, Fpc", "Centre Social I Sanitari Frederica Montseny", "Centre Sociosanitari Bernat Jaume", "Centre Sociosanitari Blauclinic Dolors Aleu", "Centre Sociosanitari Can Torras", "Centre Sociosanitari Ciutat De Reus", "Centre Sociosanitari D'Esplugues", "Centre Sociosanitari De L'Hospitalet - Consorci Sanitari Integral", "Centre Sociosanitari De Puigcerda", "Centre Sociosanitari Del Centre Integral De Salut Cotxeres", "Centre Sociosanitari El Carme", "Centre Sociosanitari I Residencia Assistida Salou", "Centre Sociosanitari Isabel Roig", "Centre Sociosanitari Llevant", "Centre Sociosanitari Parc Hospitalari Marti I Julia", "Centre Sociosanitari Ricard Fortuny", "Centre Sociosanitari Sant Jordi De La Vall D'Hebron", "Centre Sociosanitari Sarquavitae Sant Jordi", "Centre Sociosanitari Verge Del Puig", "Centres Assistencials Dr. Emili Mira I Lopez (Recinte Torribera).", "Centro Asistencial Albelda De Iregua", "Centro Asistencial Hnas. Hospitalarias Del Sagrado Corazon De Jesus", "Centro Asistencial San Juan De Dios", "Centro De Atencion A La Salud Mental, La Milagrosa", "Centro De Rehabilitacion Neurologica Casaverde", "Centro De Rehabilitacion Psicosocial Nuestra Señora Del Pilar", "Centro De Rehabilitacion Psicosocial San Juan De Dios", "Centro De Rehabilitacion Psicosocial Santo Cristo De Los Milagros", "Centro De Tratamiento De Drogodependientes El Alba", "Centro De Tratamiento Integral Montevil", "Centro Habilitado Ernest Lluch", "Centro Hospitalario Benito Menni", "Centro Hospitalario De Alta Resolucion De Cazorla", "Centro Hospitalario Padre Menni", "Centro Medico De Asturias", "Centro Medico El Carmen", "Centro Medico Pintado", "Centro Medico Teknon, Grupo Quironsalud", "Centro Neuropsiquiatrico Nuestra Señora Del Carmen", "Centro Oncoloxico De Galicia", "Centro Residencial Domusvi La Salut Josep Servat.", "Centro Salud Mental Perez Espinosa", "Centro San Francisco Javier", "Centro San Juan De Dios Ciempozuelos", "Centro Sanitario Bajo Cinca-Baix Cinca", "Centro Sanitario Cinco Villas", "Centro Sanitario Residencial Las Palmas (Cesar Las Palmas)", "Centro Sociosanitario De Convalecencia Nuestra Señora Virgen Del Carmen", "Centro Sociosanitario De Convalencencia Los Jazmines", "Centro Sociosanitario De Merida", "Centro Sociosanitario De Plasencia", "Centro Terapeutico Vista Alegre", "Centro de Investigación Biomédica de Aragón", "Clinica Activa Mutua 2008", "Clinica Arcangel San Miguel - Pamplona", "Clinica Asturias", "Clinica Bandama", "Clinica Bofill", "Clinica Cajal", "Clinica Cemtro", "Clinica Corachan", "Clinica Coroleu - Ssr Hestia.", "Clinica Creu Blanca", "Clinica Cristo Rey", "Clinica De Salud Mental Miguel De Mañara", "Clinica Diagonal", "Clinica Doctor Sanz Vazquez", "Clinica Dr. Leon", "Clinica El Seranil", "Clinica Ercilla Mutualia", "Clinica Galatea", "Clinica Girona", "Clinica Guimon, S.A.", "Clinica Imq Zorrotzaurre", "Clinica Imske", "Clinica Indautxu, S.A.", "Clinica Isadora S.A.", "Clinica Jorgani", "Clinica Juaneda", "Clinica Juaneda Mahon", "Clinica Juaneda Menorca", "Clinica La Luz, S.L.", "Clinica Lluria", "Clinica Lopez Ibor", "Clinica Los Alamos", "Clinica Los Manzanos", "Clinica Los Naranjos", "Clinica Luz De Palma", "Clinica Mc Copernic", "Clinica Mc Londres", "Clinica Mi Nova Aliança", "Clinica Montpellier, Grupo Hla, S.A.U", "Clinica Nostra Senyora De Guadalupe", "Clinica Nostra Senyora Del Remei", "Clinica Nuestra Se?Ora De Aranzazu", "Clinica Nuestra Señora De La Paz", "Clinica Perpetuo Socorro De Lerida, Grupo Hla, Slu", "Clinica Planas", "Clinica Ponferrada Recoletas", "Clinica Psicogeriatrica Josefina Arregui", "Clinica Psiquiatrica Bellavista", "Clinica Psiquiatrica Padre Menni", "Clinica Psiquiatrica Somio", "Clinica Quirurgica Onyar", "Clinica Residencia El Pinar", "Clinica Rotger", "Clinica Sagrada Familia", "Clinica Salus Infirmorum", "Clinica San Felipe", "Clinica San Miguel", "Clinica San Rafael", "Clinica Sant Antoni", "Clinica Sant Josep", "Clinica Santa Creu", "Clinica Santa Isabel", "Clinica Santa Maria De La Asuncion (Inviza S. A.)", "Clinica Santa Teresa", "Clinica Soquimex", "Clinica Tara", "Clinica Terres De L'Ebre", "Clinica Tres Torres", "Clinica Universidad De Navarra", "Clinica Virgen Blanca", "Clinica Vistahermosa Grupo Hla", "Clinicas Del Sur Slu", "Complejo Asistencial Benito Menni", "Complejo Asistencial De Soria", "Complejo Asistencial De Zamora", "Complejo Asistencial De Ávila", "Complejo Asistencial Universitario De Burgos", "Complejo Asistencial Universitario De León", "Complejo Asistencial Universitario De Palencia", "Complejo Asistencial Universitario De Salamanca", "Complejo Hospitalario De Albacete", "Complejo Hospitalario De Cartagena Chc", "Complejo Hospitalario De Cáceres", "Complejo Hospitalario De Don Benito-Villanueva De La Serena", "Complejo Hospitalario De Toledo", "Complejo Hospitalario Del Área De Salud De Mérida", "Complejo Hospitalario Gregorio Marañón", "Complejo Hospitalario Infanta Leonor", "Complejo Hospitalario La Paz", "Complejo Hospitalario Llerena-Zafra", "Complejo Hospitalario San Pedro Hospital De La Rioja", "Complejo Hospitalario Universitario De Badajoz", "Complejo Hospitalario Universitario De Canarias", "Complejo Hospitalario Universitario De Gran Canaria Dr. Negrín", "Complejo Hospitalario Universitario Insular Materno Infantil", "Complejo Hospitalario Universitario Nuestra Señora De Candelaria", "Complexo Hospitalario Universitario A Coruña", "Complexo Hospitalario Universitario De Ferrol", "Complexo Hospitalario Universitario De Lugo", "Complexo Hospitalario Universitario De Ourense", "Complexo Hospitalario Universitario De Pontevedra", "Complexo Hospitalario Universitario De Santiago", "Complexo Hospitalario Universitario De Vigo", "Comunitat Terapeutica Arenys De Munt", "Concheiro Centro Medico Quirurgico", "Consejería de Sanidad", "Consorcio Hospital General Universitario De Valencia", "Consorcio Hospitalario Provincial De Castellon", "Consorcio LUCIA (SACYL,ITACYL UBU,UVa)", "Cqm Clinic Maresme, Sl", "Cti De La Corredoria", "Eatica", "Espitau Val D'Aran", "Fraternidad Muprespa, Mutua Colaboradora Con La Seguridad Social Nº 275", "Fremap Hospital Majadahonda", "Fremap, Hospital De Barcelona", "Fremap, Hospital De Vigo", "Fremap_Hospital Y Centro De Rehabilitacion De Sevilla", "Fundacio Hospital De L'Esperit Sant", "Fundacio Hospital Sant Joan De Deu (Martorell)", "Fundacio Puigvert - Iuna", "Fundacio Sanitaria Sant Josep", "Fundacio Sant Hospital.", "Fundacion Cudeca. Centro De Cuidados Paliativos", "Fundacion Hospital De Aviles", "Fundacion Instituto San Jose", "Fundacion Instituto Valenciano De Oncologia", "Fundacion Sanatorio Adaro", "Fundació Althaia-Manresa", "Fundació Fisabio", "Gerencia de Atención Primaria Pontevedra Sur", "Germanes Hospitalaries. Hospital Sagrat Cor", "Grupo Quironsalud Pontevedra", "Hc Marbella International Hospital", "Helicopteros Sanitarios Hospital", "Hestia Balaguer.", "Hestia Duran I Reynals", "Hestia Gracia", "Hestia La Robleda", "Hestia Palau.", "Hestia San Jose", "Hm El Pilar", "Hm Galvez", "Hm Hospitales 1.989, S.A.", "Hm Malaga", "Hm Modelo-Belen", "Hm Nou Delfos", "Hm Regla", "Hospital 9 De Octubre", "Hospital Aita Menni", "Hospital Alto Guadalquivir", "Hospital Arnau De Vilanova", "Hospital Asepeyo Madrid", "Hospital Asilo De La Real Piedad De Cehegin", "Hospital Asociado Universitario Guadarrama", "Hospital Asociado Universitario Virgen De La Poveda", "Hospital Beata Maria Ana", "Hospital Begoña", "Hospital Bidasoa (Osi Bidasoa)", "Hospital C. M. Virgen De La Caridad Cartagena", "Hospital Campo Arañuelo", "Hospital Can Misses", "Hospital Carlos Iii", "Hospital Carmen Y Severo Ochoa", "Hospital Casaverde Valladolid", "Hospital Catolico Casa De Salud", "Hospital Central De La Cruz Roja, San Jose Y Santa Adela", "Hospital Central De La Defensa Gomez Ulla", "Hospital Centro De Andalucia", "Hospital Centro De Cuidados Laguna", "Hospital Centro Medico Virgen De La Caridad Caravaca", "Hospital Ciudad De Coria", "Hospital Ciudad De Telde", "Hospital Civil", "Hospital Clinic De Barcelona", "Hospital Clinic De Barcelona, Seu Plato", "Hospital Clinic De Barcelona, Seu Sabino De Arana", "Hospital Clinica Benidorm", "Hospital Clinico Universitario De Valencia", "Hospital Clinico Universitario De Valladolid", "Hospital Clinico Universitario Lozano Blesa", "Hospital Clinico Universitario Virgen De La Arrixaca", "Hospital Comarcal", "Hospital Comarcal D'Amposta", "Hospital Comarcal De Blanes", "Hospital Comarcal De L'Alt Penedes", "Hospital Comarcal De Laredo", "Hospital Comarcal De Vinaros", "Hospital Comarcal Del Noroeste", "Hospital Comarcal Del Pallars", "Hospital Comarcal D´Inca", "Hospital Comarcal Mora D'Ebre", "Hospital Comarcal Sant Jaume De Calella", "Hospital Costa Del Sol", "Hospital Cruz Roja De Bilbao - Victoria Eugenia", "Hospital Cruz Roja De Cordoba", "Hospital Cruz Roja Gijon", "Hospital D'Igualada", "Hospital D'Olot I Comarcal De La Garrotxa", "Hospital De Alcañiz", "Hospital De Alta Resolucion De Alcala La Real", "Hospital De Alta Resolucion De Alcaudete", "Hospital De Alta Resolucion De Benalmadena", "Hospital De Alta Resolucion De Ecija", "Hospital De Alta Resolucion De Especialidades De La Janda", "Hospital De Alta Resolucion De Estepona", "Hospital De Alta Resolucion De Guadix", "Hospital De Alta Resolucion De Lebrija", "Hospital De Alta Resolucion De Loja", "Hospital De Alta Resolucion De Moron De La Frontera", "Hospital De Alta Resolucion De Puente Genil", "Hospital De Alta Resolucion De Utrera", "Hospital De Alta Resolucion Eltoyo", "Hospital De Alta Resolucion Sierra De Segura", "Hospital De Alta Resolucion Sierra Norte", "Hospital De Alta Resolucion Valle Del Guadiato", "Hospital De Antequera", "Hospital De Barbastro", "Hospital De Barcelona", "Hospital De Baza", "Hospital De Benavente Complejo Asistencial De Zamora", "Hospital De Berga", "Hospital De Bermeo", "Hospital De Calahorra", "Hospital De Campdevanol", "Hospital De Cantoblanco", "Hospital De Cerdanya / Hopital De Cerdagne", "Hospital De Cronicos De Mislata (Antiguo Hospital Militar De Valencia)", "Hospital De Cuidados Medios Villademar", "Hospital De Denia", "Hospital De Emergencia Covid 19", "Hospital De Figueres", "Hospital De Formentera", "Hospital De Gorliz", "Hospital De Hellin", "Hospital De Jaca Salud", "Hospital De Jarrio", "Hospital De Jove", "Hospital De L'Esperança.", "Hospital De La Axarquia", "Hospital De La Creu Roja Espanyola", "Hospital De La Fuenfria", "Hospital De La Inmaculada Concepcion", "Hospital De La Malva-Rosa", "Hospital De La Mujer", "Hospital De La Reina", "Hospital De La Rioja", "Hospital De La Santa Creu", "Hospital De La Santa Creu I Sant Pau", "Hospital De La Serrania", "Hospital De La V.O.T. De San Francisco De Asis", "Hospital De La Vega Lorenzo Guirao", "Hospital De Leon Complejo Asistencial Universitario De Leon", "Hospital De Leza", "Hospital De Llevant", "Hospital De Lliria", "Hospital De Luarca", "Hospital De Manacor", "Hospital De Manises", "Hospital De Mataro", "Hospital De Mendaro (Osi Bajo Deba)", "Hospital De Merida", "Hospital De Mollet", "Hospital De Montilla", "Hospital De Neurotraumatologia Y Rehabilitacion Del H.U. Virgen De Las Nieves", "Hospital De Ofra", "Hospital De Palamos", "Hospital De Rehabilitacion Psiquiatrica Prisma", "Hospital De Rehabilitacion Y Traumatologia Del H.U. Virgen Del Rocio", "Hospital De Riotinto", "Hospital De Sabadell", "Hospital De Sagunto", "Hospital De Salud Mental Casta Salud Arevalo", "Hospital De Salud Mental Provincial", "Hospital De San Antonio", "Hospital De San Jose", "Hospital De San Rafael", "Hospital De Sant Andreu", "Hospital De Sant Celoni.", "Hospital De Sant Jaume", "Hospital De Sant Joan De Deu (Manresa)", "Hospital De Sant Joan De Deu.", "Hospital De Sant Joan Despi Moises Broggi", "Hospital De Sant Llatzer", "Hospital De Sant Pau I Santa Tecla", "Hospital De Terrassa.", "Hospital De Tortosa Verge De La Cinta", "Hospital De Viladecans", "Hospital De Zafra", "Hospital De Zaldibar", "Hospital De Zamudio", "Hospital De Zumarraga (Osi Goierri - Alto Urola)", "Hospital Del Mar", "Hospital Del Norte", "Hospital Del Oriente De Asturias Francisco Grande Covian", "Hospital Del Sur", "Hospital Del Vendrell", "Hospital Doctor Moliner", "Hospital Doctor Oloriz", "Hospital Doctor Sagaz", "Hospital Don Benito-Villanueva De La Serena", "Hospital Dos De Maig", "Hospital Egarsat Sant Honorat", "Hospital El Angel", "Hospital El Bierzo", "Hospital El Escorial", "Hospital El Pilar", "Hospital El Tomillar", "Hospital Ernest Lluch Martin", "Hospital Fatima", "Hospital Francesc De Borja De Gandia", "Hospital Fuensanta", "Hospital Fuente Bermeja- Complejo Asistencial Universitario De Burgos-", "Hospital G. Universitario J.M. Morales Meseguer", "Hospital Galdakao-Usansolo Asociado A La Upv/Ehu", "Hospital Garcia Orcoyen", "Hospital General De Almansa", "Hospital General De Fuerteventura", "Hospital General De Granollers.", "Hospital General De L'Hospitalet", "Hospital General De La Defensa En Zaragoza", "Hospital General De La Santisima Trinidad", "Hospital General De Llerena", "Hospital General De Mallorca", "Hospital General De Ontinyent", "Hospital General De Requena", "Hospital General De Segovia Complejo Asistencial De Segovia", "Hospital General De Tomelloso", "Hospital General De Valdepeñas", "Hospital General De Villalba", "Hospital General De Villarrobledo", "Hospital General La Mancha Centro", "Hospital General Nuestra Señora Del Prado", "Hospital General Penitenciari", "Hospital General Santa Maria Del Puerto", "Hospital General Universitario De Albacete", "Hospital General Universitario De Castellon", "Hospital General Universitario De Ciudad Real", "Hospital General Universitario De Elche", "Hospital General Universitario De Elda-Virgen De La Salud", "Hospital General Universitario Dr. Balmis", "Hospital General Universitario Gregorio Marañon", "Hospital General Universitario Los Arcos Del Mar Menor", "Hospital General Universitario Reina Sofia", "Hospital General Universitario Santa Lucia", "Hospital Geriatrico Virgen Del Valle", "Hospital Gijon", "Hospital Hernan Cortes Miraflores", "Hospital Hestia Madrid", "Hospital Hla Universitario Moncloa", "Hospital Hm Nuevo Belen", "Hospital Hm Rosaleda-Hm La Esperanza", "Hospital Hm San Francisco", "Hospital Hm Valles", "Hospital Ibermutuamur - Patologia Laboral", "Hospital Imed Elche", "Hospital Imed Gandia", "Hospital Imed Levante", "Hospital Imed San Jorge", "Hospital Infanta Elena", "Hospital Infanta Margarita", "Hospital Infantil", "Hospital Infantil Universitario Niño Jesus", "Hospital Insular De Lanzarote", "Hospital Insular Nuestra Señora De Los Reyes", "Hospital Intermutual De Euskadi", "Hospital Intermutual De Levante", "Hospital Internacional Hcb Denia", "Hospital Internacional Hm Santa Elena", "Hospital Jaume Nadal Meroles", "Hospital Jerez Puerta Del Sur", "Hospital Joan March", "Hospital Juaneda Muro", "Hospital La Antigua", "Hospital La Inmaculada", "Hospital La Magdalena", "Hospital La Merced", "Hospital La Milagrosa S.A.", "Hospital La Paloma", "Hospital La Pedrera", "Hospital La Vega Grupo Hla", "Hospital Latorre", "Hospital Lluis Alcanyis De Xativa", "Hospital Los Madroños", "Hospital Los Montalvos (Complejo Asistencial Universitario De Salamanca)", "Hospital Los Morales", "Hospital Mare De Deu De La Merce", "Hospital Marina Baixa De La Vila Joiosa", "Hospital Maritimo De Torremolinos", "Hospital Materno - Infantil Del H.U. Reina Sofia", "Hospital Materno Infantil", "Hospital Materno Infantil Del H.U.R. De Malaga", "Hospital Materno-Infantil", "Hospital Materno-Infantil Del H.U. De Jaen", "Hospital Materno-Infantil Del H.U. Virgen De Las Nieves", "Hospital Mateu Orfila", "Hospital Maz", "Hospital Md Anderson Cancer Center Madrid", "Hospital Medimar Internacional", "Hospital Medina Del Campo", "Hospital Mediterraneo", "Hospital Mesa Del Castillo", "Hospital Metropolitano De Jaen", "Hospital Mompia", "Hospital Monte Naranco", "Hospital Monte San Isidro Complejo Asistencial Universitario De Leon", "Hospital Municipal De Badalona", "Hospital Mutua Montañesa", "Hospital Nacional De Paraplejicos", "Hospital Neurotraumatologico Del H.U. De Jaen", "Hospital Nisa Aguas Vivas", "Hospital Ntra. Sra. Del Perpetuo Socorro", "Hospital Nuestra Señora De America", "Hospital Nuestra Señora De Gracia", "Hospital Nuestra Señora De Guadalupe", "Hospital Nuestra Señora De La Salud Hla Sl", "Hospital Nuestra Señora De Sonsoles", "Hospital Obispo Polanco", "Hospital Ochoa", "Hospital Palma Del Rio", "Hospital Pardo De Aravaca", "Hospital Pare Jofre", "Hospital Parque", "Hospital Parque Fuerteventura", "Hospital Parque Marazuela", "Hospital Parque San Francisco", "Hospital Parque Vegas Altas", "Hospital Perpetuo Socorro", "Hospital Perpetuo Socorro Alameda", "Hospital Polivalente Anexo Juan Carlos I", "Hospital Provincial", "Hospital Provincial De Avila", "Hospital Provincial De Zamora Complejo Asistencial De Zamora", "Hospital Provincial Ntra.Sra.De La Misericordia", "Hospital Psiquiatric", "Hospital Psiquiatrico Doctor Rodriguez Lafora", "Hospital Psiquiatrico Penitenciario", "Hospital Psiquiatrico Penitenciario De Fontcalent", "Hospital Psiquiatrico Roman Alberca", "Hospital Psiquiatrico San Francisco De Asis", "Hospital Psiquiatrico San Juan De Dios", "Hospital Psiquiatrico San Luis", "Hospital Publico Da Barbanza", "Hospital Publico Da Mariña", "Hospital Publico De Monforte", "Hospital Publico De Valdeorras", "Hospital Publico De Verin", "Hospital Publico Do Salnes", "Hospital Publico Virxe Da Xunqueira", "Hospital Puerta De Andalucia", "Hospital Punta De Europa", "Hospital Quiron Campo De Gibraltar", "Hospital Quiron Salud Costa Adeje", "Hospital Quiron Salud Del Valles - Clinica Del Valles", "Hospital Quiron Salud Lugo", "Hospital Quiron Salud Tenerife", "Hospital Quiron Salud Valle Del Henares", "Hospital Quironsalud A Coruña", "Hospital Quironsalud Albacete", "Hospital Quironsalud Barcelona", "Hospital Quironsalud Bizkaia", "Hospital Quironsalud Caceres", "Hospital Quironsalud Ciudad Real", "Hospital Quironsalud Clideba", "Hospital Quironsalud Cordoba", "Hospital Quironsalud Huelva", "Hospital Quironsalud Infanta Luisa", "Hospital Quironsalud Malaga", "Hospital Quironsalud Marbella", "Hospital Quironsalud Murcia", "Hospital Quironsalud Palmaplanas", "Hospital Quironsalud Sagrado Corazon", "Hospital Quironsalud San Jose", "Hospital Quironsalud Santa Cristina", "Hospital Quironsalud Son Veri", "Hospital Quironsalud Sur", "Hospital Quironsalud Toledo", "Hospital Quironsalud Torrevieja", "Hospital Quironsalud Valencia", "Hospital Quironsalud Vida", "Hospital Quironsalud Vitoria", "Hospital Quironsalud Zaragoza", "Hospital Rafael Mendez", "Hospital Recoletas Cuenca, S.L.U.", "Hospital Recoletas De Burgos", "Hospital Recoletas De Palencia", "Hospital Recoletas De Zamora", "Hospital Recoletas Marbella Slu", "Hospital Recoletas Salud Campo Grande", "Hospital Recoletas Salud Felipe Ii", "Hospital Recoletas Segovia Nuestra Señora De La Misericordia", "Hospital Reina Sofia", "Hospital Residencia Sant Camil - Consorci Sanitari De L'Alt Penedes I Garraf", "Hospital Ribera Almendralejo", "Hospital Ribera Badajoz", "Hospital Ribera Covadonga", "Hospital Ribera Juan Cardona", "Hospital Ribera Polusa", "Hospital Ribera Povisa", "Hospital Ricardo Bermingham", "Hospital Rio Carrion Complejo Asistencial Universitario De Palencia", "Hospital Royo Villanova", "Hospital Ruber Internacional", "Hospital Ruber Juan Bravo", "Hospital Sagrado Corazon De Jesus", "Hospital San Agustin", "Hospital San Camilo", "Hospital San Carlos De Denia Grupo Hla", "Hospital San Carlos De San Fernando", "Hospital San Eloy", "Hospital San Francisco De Asis", "Hospital San Jose", "Hospital San Jose Solimat", "Hospital San Juan De Dios", "Hospital San Juan De Dios Burgos", "Hospital San Juan De Dios De Cordoba", "Hospital San Juan De Dios De Sevilla", "Hospital San Juan De Dios Del Aljarafe", "Hospital San Juan De Dios Donostia", "Hospital San Juan De Dios Leon", "Hospital San Juan De Dios Tenerife", "Hospital San Juan De La Cruz", "Hospital San Juan Grande", "Hospital San Lazaro", "Hospital San Pedro De Alcantara", "Hospital San Rafael", "Hospital San Roque De Guia", "Hospital San Telmo ,Complejo Asistencial Universitario De Palencia", "Hospital Sanitas Cima", "Hospital Sant Antoni Abat - Consorci Sanitari Del Garraf.", "Hospital Sant Joan De Deu", "Hospital Sant Joan De Deu Inca", "Hospital Sant Joan De Deu Lleida", "Hospital Sant Vicent Del Raspeig", "Hospital Santa Ana", "Hospital Santa Barbara", "Hospital Santa Barbara ,Complejo Asistencial De Soria", "Hospital Santa Caterina-Ias", "Hospital Santa Clotilde", "Hospital Santa Isabel Complejo Asistencial Universitario De Leon", "Hospital Santa Maria", "Hospital Santa Maria Del Rosell", "Hospital Santa Marina", "Hospital Santa Teresa", "Hospital Santiago Apostol", "Hospital Santos Reyes", "Hospital Siberia-Serena", "Hospital Sierrallana", "Hospital Sociosanitari De Lloret De Mar", "Hospital Sociosanitari De Mollet", "Hospital Sociosanitari Francoli", "Hospital Sociosanitari Mutuam Girona", "Hospital Sociosanitari Mutuam Guell", "Hospital Sociosanitari Pere Virgili", "Hospital Son Llatzer", "Hospital Tierra De Barros", "Hospital Universitari Arnau De Vilanova De Lleida", "Hospital Universitari De Bellvitge", "Hospital Universitari De Girona Dr. Josep Trueta", "Hospital Universitari De Sant Joan De Reus", "Hospital Universitari De Vic", "Hospital Universitari General De Catalunya", "Hospital Universitari Germans Trias I Pujol De Badalona", "Hospital Universitari Joan Xxiii De Tarragona", "Hospital Universitari Mutua De Terrassa", "Hospital Universitari Quir¿N Dexeus", "Hospital Universitari Sagrat Cor", "Hospital Universitari Son Espases", "Hospital Universitari Vall D'Hebron", "Hospital Universitario 12 De Octubre", "Hospital Universitario Araba (Sede Txagorritxu Y Sede Santiago)", "Hospital Universitario Basurto", "Hospital Universitario Central De Asturias", "Hospital Universitario Clinico San Carlos", "Hospital Universitario Clinico San Cecilio", "Hospital Universitario Clínico San Cecilio", "Hospital Universitario Costa Del Sol", "Hospital Universitario Cruces", "Hospital Universitario De Badajoz", "Hospital Universitario De Burgos Complejo Asistencial Univer. De Burgos", "Hospital Universitario De Cabueñes", "Hospital Universitario De Caceres", "Hospital Universitario De Canarias", "Hospital Universitario De Ceuta", "Hospital Universitario De Fuenlabrada", "Hospital Universitario De Getafe", "Hospital Universitario De Gran Canaria Dr. Negrin", "Hospital Universitario De Guadalajara", "Hospital Universitario De Jaen", "Hospital Universitario De Jaén", "Hospital Universitario De Jerez De La Frontera", "Hospital Universitario De La Linea De La Concepcion", "Hospital Universitario De La Plana", "Hospital Universitario De La Princesa", "Hospital Universitario De La Ribera", "Hospital Universitario De Mostoles", "Hospital Universitario De Navarra", "Hospital Universitario De Poniente", "Hospital Universitario De Puerto Real", "Hospital Universitario De Salamanca ,Complejo Asistencial Universitario De", "Hospital Universitario De Salud Mental Juan Carlos I", "Hospital Universitario De Toledo (Hut)", "Hospital Universitario De Torrejon", "Hospital Universitario De Torrevieja", "Hospital Universitario Del Henares", "Hospital Universitario Del Sureste", "Hospital Universitario Del Tajo", "Hospital Universitario Donostia", "Hospital Universitario Dr. Jose Molina Orosa", "Hospital Universitario Dr. Peset Aleixandre", "Hospital Universitario Fundacion Alcorcon", "Hospital Universitario Fundacion Jimenez Diaz", "Hospital Universitario General De La Palma", "Hospital Universitario Hm Madrid", "Hospital Universitario Hm Monteprincipe", "Hospital Universitario Hm Puerta Del Sur", "Hospital Universitario Hm Sanchinarro", "Hospital Universitario Hm Torrelodones", "Hospital Universitario Hospiten Bellevue", "Hospital Universitario Hospiten Rambla", "Hospital Universitario Hospiten Sur", "Hospital Universitario Infanta Cristina", "Hospital Universitario Infanta Elena", "Hospital Universitario Infanta Leonor", "Hospital Universitario Infanta Sofia", "Hospital Universitario Jose Germain", "Hospital Universitario Juan Ramon Jimenez", "Hospital Universitario Juan Ramón Jiménez", "Hospital Universitario La Moraleja", "Hospital Universitario La Paz", "Hospital Universitario La Zarzuela", "Hospital Universitario Marques De Valdecilla", "Hospital Universitario Miguel Servet", "Hospital Universitario Nuestra Señora De Candelaria", "Hospital Universitario Nuestra Señora Del Perpetuo Socorro", "Hospital Universitario Principe De Asturias", "Hospital Universitario Puerta De Hierro Majadahonda", "Hospital Universitario Puerta Del Mar", "Hospital Universitario Quironsalud Madrid", "Hospital Universitario Ramon Y Cajal", "Hospital Universitario Regional De Malaga", "Hospital Universitario Regional De Málaga", "Hospital Universitario Reina Sofia", "Hospital Universitario Reina Sofía", "Hospital Universitario Rio Hortega", "Hospital Universitario San Agustin", "Hospital Universitario San Jorge", "Hospital Universitario San Juan De Alicante", "Hospital Universitario San Pedro", "Hospital Universitario San Roque Las Palmas", "Hospital Universitario San Roque Maspalomas", "Hospital Universitario Santa Cristina", "Hospital Universitario Severo Ochoa", "Hospital Universitario Torrecardenas", "Hospital Universitario Torrecárdenas", "Hospital Universitario Vinalopo", "Hospital Universitario Virgen De La Victoria", "Hospital Universitario Virgen De Las Nieves", "Hospital Universitario Virgen De Valme", "Hospital Universitario Virgen Del Rocio", "Hospital Universitario Virgen Del Rocío", "Hospital Universitario Virgen Macarena", "Hospital Universitario Vithas Las Palmas", "Hospital Universitario Y Politecnico La Fe", "Hospital Urduliz Ospitalea", "Hospital Valle De Guadalhorce De Cartama", "Hospital Valle De Laciana", "Hospital Valle De Los Pedroches", "Hospital Valle Del Nalon", "Hospital Vazquez Diaz", "Hospital Vega Baja De Orihuela", "Hospital Viamed Bahia De Cadiz", "Hospital Viamed Montecanal", "Hospital Viamed Novo Sancti Petri", "Hospital Viamed San Jose", "Hospital Viamed Santa Angela De La Cruz", "Hospital Viamed Santa Elena, S.L", "Hospital Viamed Santiago", "Hospital Viamed Tarragona", "Hospital Victoria Eugenia De La Cruz Roja Española", "Hospital Virgen De Altagracia", "Hospital Virgen De La Bella", "Hospital Virgen De La Concha Complejo Asistencial De Zamora", "Hospital Virgen De La Luz", "Hospital Virgen De La Torre", "Hospital Virgen De Las Montañas", "Hospital Virgen De Los Lirios", "Hospital Virgen Del Alcazar De Lorca", "Hospital Virgen Del Camino", "Hospital Virgen Del Castillo", "Hospital Virgen Del Mar", "Hospital Virgen Del Miron ,Complejo Asistencial De Soria", "Hospital Virgen Del Puerto", "Hospital Vital Alvarez Buylla", "Hospital Vithas Castellon", "Hospital Vithas Granada", "Hospital Vithas Parque San Antonio", "Hospital Vithas Sevilla", "Hospital Vithas Valencia Consuelo", "Hospital Vithas Vitoria", "Hospital Vithas Xanit Estepona", "Hospital Vithas Xanit Internacional", "Hospiten Clinica Roca San Agustin", "Hospiten Lanzarote", "Idcsalud Mostoles Sa", "Imed Valencia", "Institut Catala D'Oncologia - Hospital Duran I Reynals", "Institut Catala D'Oncologia - Hospital Germans Trias I Pujol", "Institut Catala D'Oncologia Girona - Hospital Josep Trueta", "Institut Guttmann", "Institut Pere Mata, S.A", "Instituto De Enfermedades Neurologicas De Castilla-La Mancha", "Instituto De Salud Carlos Iii - Centro Nacional De Microbiologia", "Instituto De Traumatologia De Union De Mutuas (Matepss Nº 267)", "Instituto Oftalmologico Fernandez-Vega", "Instituto Provincial De Rehabilitacion", "Instituto Psiquiátrico Servicios De Salud Mental José Germain", "Instituto Tecnológico y de Energías Renovables, S.A. (ITER, S.A.)", "Ita Canet", "Ita Clinic Bcn", "Ita Godella", "Ita Maresme", "Ivan Mañero Clinic", "Juaneda Miramar", "Lab Clínic ICS Camp de Tarragona-Terres de l'Ebre. Hospital Joan XXIII", "Laboratori De Referencia De Catalunya", "Laboratorio Echevarne, Sa", "Lepant Residencial Qgg, Sl", "Microbiología HUC San Cecilio", "Microbiología. Hospital Universitario Virgen del Rocio", "Ministerio Sanidad", "Mutua Balear", "Mutua De Granollers, Mutua De Previsio Social A Prima Fixa", "Mutualia Clinica Pakea", "Nou Hospital Evangelic", "Organizacion Sanitaria Integrada Debagoiena", "Parc Sanitari Sant Joan De Deu - Numancia", "Parc Sanitari Sant Joan De Deu - Recinte Sant Boi.", "Parc Sanitari Sant Joan De Deu - Til·Lers", "Parc Sanitari Sant Joan De Deu - Uhpp - 1", "Parc Sanitari Sant Joan De Deu - Uhpp - 2", "Pius Hospital De Valls", "Plataforma de Genómica y Bioinformática", "Plataforma de Medicina Computacional, Fundación Progreso y Salud", "Policlinica Comarcal Del Vendrell.", "Policlinica Gipuzkoa", "Policlinica Nuestra Sra. Del Rosario", "Policlinico Riojano Nuestra Señora De Valvanera", "Presidencia del Gobierno", "Prytanis Hospitalet Centre Sociosanitari", "Prytanis Sant Boi Centre Sociosanitari", "Quinta Medica De Reposo", "Red De Salud Mental De Araba (Hospital Psiquiatrico De Araba)", "Residencia Alt Camp", "Residencia De Gent Gran Puig D'En Roca", "Residencia De Salud Mental Nuestra Se?Ora Del Carmen", "Residencia Geriatrica Maria Gay", "Residencia L'Estada", "Residencia Puig-Reig", "Residencia Santa Susanna", "Residencia Santa Tecla Ponent", "Residencia Terraferma", "Residencia Vila-Seca", "Ribera Hospital De Molina", "Ronda De Dalt, Centre Sociosanitari", "Sanatorio Bilbaino", "Sanatorio Dr. Muñoz", "Sanatorio Esquerdo, S.A.", "Sanatorio Nuestra Señora Del Rosario", "Sanatorio Sagrado Corazon", "Sanatorio San Francisco De Borja Fontilles", "Sanatorio Usurbil, S. L.", "Santo Y Real Hospital De Caridad", "Sar Mont Marti", "Serveis Clinics, S.A.", "Servicio Madrileño De Salud", "Servicio de Microbiologia HU Son Espases", "Servicios Sanitarios Y Asistenciales", "U.R.R. De Enfermos Psiquicos Alcohete", "Unidad De Rehabilitacion De Larga Estancia", "Unidad Rehabilitadora De Media Estancia Profesor Rey Ardid", "Unidades Clinicas Y De Rehabilitacion De Salud Mental", "Unitat Polivalent Benito Menni En Salut Mental De L'Hospitalet-El Prat De Llobregat", "Unitat Polivalent En Salut Mental D'Amposta", "Unitat Polivalent Salut Mental Barcelona-Nord", "Unitat Terapeutica-Educativa Acompanya'M", "Villablanca Serveis Assistencials, Sa", "Vithas Hospital Montserrat", "Vithas Hospital Nosa Señora De Fatima", "Vithas Hospital Perpetuo Internacional", "Vithas Hospital Santa Cruz" ], "examples": [ "Hospital Universitario de Ceuta" ], "ontology": "GENEPIO:0001153", "type": "string", "description": "The name of the agency/institution that collected the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory", "fill_mode": "sample", "header": "Y" }, "submitting_institution": { "enum": [ "Adinfa, Sociedad Cooperativa Andaluza", "Alm Univass S.L.", "Antic Hospital De Sant Jaume I Santa Magdalena", "Aptima Centre Clinic - Mutua De Terrassa", "Area Psiquiatrica San Juan De Dios", "Avances Medicos S.A.", "Avantmedic", "Banc de Sang i Teixits Catalunya", "Benito Menni Complex Assistencial En Salut Mental", "Benito Menni, Complex Assistencial En Salut Mental", "Cap La Salut", "Cap Mataro Centre", "Cap Montmelo", "Cap Montornes", "Casal De Curacio", "Casaverde Centro De Rehabilitacion Neurologico De Extremadura S.L.", "Casta Guadarrama", "Castell D'Oliana Residencial,S.L", "Catlab-Centre Analitiques Terrassa, Aie", "Centre Collserola Mutual", "Centre D'Hospitalitzacio I Hospital De Dia Trastorns De La Conducta", "Centre D'Oftalmologia Barraquer", "Centre De Prevencio I Rehabilitacio Asepeyo", "Centre De Salut Doctor Vilaseca-Can Mariner", "Centre Forum", "Centre Geriatric Del Maresme", "Centre Hospitalari Policlinica Barcelona", "Centre Integral De Serveis En Salut Mental Comunitaria", "Centre La Creueta", "Centre Medic Molins, Sl", "Centre Mq Reus", "Centre Palamos Gent Gran", "Centre Polivalent Can Fosc", "Centre Sanitari Del Solsones, Fpc", "Centre Social I Sanitari Frederica Montseny", "Centre Sociosanitari Bernat Jaume", "Centre Sociosanitari Blauclinic Dolors Aleu", "Centre Sociosanitari Can Torras", "Centre Sociosanitari Ciutat De Reus", "Centre Sociosanitari D'Esplugues", "Centre Sociosanitari De L'Hospitalet - Consorci Sanitari Integral", "Centre Sociosanitari De Puigcerda", "Centre Sociosanitari Del Centre Integral De Salut Cotxeres", "Centre Sociosanitari El Carme", "Centre Sociosanitari I Residencia Assistida Salou", "Centre Sociosanitari Isabel Roig", "Centre Sociosanitari Llevant", "Centre Sociosanitari Parc Hospitalari Marti I Julia", "Centre Sociosanitari Ricard Fortuny", "Centre Sociosanitari Sant Jordi De La Vall D'Hebron", "Centre Sociosanitari Sarquavitae Sant Jordi", "Centre Sociosanitari Verge Del Puig", "Centres Assistencials Dr. Emili Mira I Lopez (Recinte Torribera).", "Centro Asistencial Albelda De Iregua", "Centro Asistencial Hnas. Hospitalarias Del Sagrado Corazon De Jesus", "Centro Asistencial San Juan De Dios", "Centro De Atencion A La Salud Mental, La Milagrosa", "Centro De Rehabilitacion Neurologica Casaverde", "Centro De Rehabilitacion Psicosocial Nuestra Señora Del Pilar", "Centro De Rehabilitacion Psicosocial San Juan De Dios", "Centro De Rehabilitacion Psicosocial Santo Cristo De Los Milagros", "Centro De Tratamiento De Drogodependientes El Alba", "Centro De Tratamiento Integral Montevil", "Centro Habilitado Ernest Lluch", "Centro Hospitalario Benito Menni", "Centro Hospitalario De Alta Resolucion De Cazorla", "Centro Hospitalario Padre Menni", "Centro Medico De Asturias", "Centro Medico El Carmen", "Centro Medico Pintado", "Centro Medico Teknon, Grupo Quironsalud", "Centro Neuropsiquiatrico Nuestra Señora Del Carmen", "Centro Oncoloxico De Galicia", "Centro Residencial Domusvi La Salut Josep Servat.", "Centro Salud Mental Perez Espinosa", "Centro San Francisco Javier", "Centro San Juan De Dios Ciempozuelos", "Centro Sanitario Bajo Cinca-Baix Cinca", "Centro Sanitario Cinco Villas", "Centro Sanitario Residencial Las Palmas (Cesar Las Palmas)", "Centro Sociosanitario De Convalecencia Nuestra Señora Virgen Del Carmen", "Centro Sociosanitario De Convalencencia Los Jazmines", "Centro Sociosanitario De Merida", "Centro Sociosanitario De Plasencia", "Centro Terapeutico Vista Alegre", "Centro de Investigación Biomédica de Aragón", "Clinica Activa Mutua 2008", "Clinica Arcangel San Miguel - Pamplona", "Clinica Asturias", "Clinica Bandama", "Clinica Bofill", "Clinica Cajal", "Clinica Cemtro", "Clinica Corachan", "Clinica Coroleu - Ssr Hestia.", "Clinica Creu Blanca", "Clinica Cristo Rey", "Clinica De Salud Mental Miguel De Mañara", "Clinica Diagonal", "Clinica Doctor Sanz Vazquez", "Clinica Dr. Leon", "Clinica El Seranil", "Clinica Ercilla Mutualia", "Clinica Galatea", "Clinica Girona", "Clinica Guimon, S.A.", "Clinica Imq Zorrotzaurre", "Clinica Imske", "Clinica Indautxu, S.A.", "Clinica Isadora S.A.", "Clinica Jorgani", "Clinica Juaneda", "Clinica Juaneda Mahon", "Clinica Juaneda Menorca", "Clinica La Luz, S.L.", "Clinica Lluria", "Clinica Lopez Ibor", "Clinica Los Alamos", "Clinica Los Manzanos", "Clinica Los Naranjos", "Clinica Luz De Palma", "Clinica Mc Copernic", "Clinica Mc Londres", "Clinica Mi Nova Aliança", "Clinica Montpellier, Grupo Hla, S.A.U", "Clinica Nostra Senyora De Guadalupe", "Clinica Nostra Senyora Del Remei", "Clinica Nuestra Se?Ora De Aranzazu", "Clinica Nuestra Señora De La Paz", "Clinica Perpetuo Socorro De Lerida, Grupo Hla, Slu", "Clinica Planas", "Clinica Ponferrada Recoletas", "Clinica Psicogeriatrica Josefina Arregui", "Clinica Psiquiatrica Bellavista", "Clinica Psiquiatrica Padre Menni", "Clinica Psiquiatrica Somio", "Clinica Quirurgica Onyar", "Clinica Residencia El Pinar", "Clinica Rotger", "Clinica Sagrada Familia", "Clinica Salus Infirmorum", "Clinica San Felipe", "Clinica San Miguel", "Clinica San Rafael", "Clinica Sant Antoni", "Clinica Sant Josep", "Clinica Santa Creu", "Clinica Santa Isabel", "Clinica Santa Maria De La Asuncion (Inviza S. A.)", "Clinica Santa Teresa", "Clinica Soquimex", "Clinica Tara", "Clinica Terres De L'Ebre", "Clinica Tres Torres", "Clinica Universidad De Navarra", "Clinica Virgen Blanca", "Clinica Vistahermosa Grupo Hla", "Clinicas Del Sur Slu", "Complejo Asistencial Benito Menni", "Complejo Asistencial De Soria", "Complejo Asistencial De Zamora", "Complejo Asistencial De Ávila", "Complejo Asistencial Universitario De Burgos", "Complejo Asistencial Universitario De León", "Complejo Asistencial Universitario De Palencia", "Complejo Asistencial Universitario De Salamanca", "Complejo Hospitalario De Albacete", "Complejo Hospitalario De Cartagena Chc", "Complejo Hospitalario De Cáceres", "Complejo Hospitalario De Don Benito-Villanueva De La Serena", "Complejo Hospitalario De Toledo", "Complejo Hospitalario Del Área De Salud De Mérida", "Complejo Hospitalario Gregorio Marañón", "Complejo Hospitalario Infanta Leonor", "Complejo Hospitalario La Paz", "Complejo Hospitalario Llerena-Zafra", "Complejo Hospitalario San Pedro Hospital De La Rioja", "Complejo Hospitalario Universitario De Badajoz", "Complejo Hospitalario Universitario De Canarias", "Complejo Hospitalario Universitario De Gran Canaria Dr. Negrín", "Complejo Hospitalario Universitario Insular Materno Infantil", "Complejo Hospitalario Universitario Nuestra Señora De Candelaria", "Complexo Hospitalario Universitario A Coruña", "Complexo Hospitalario Universitario De Ferrol", "Complexo Hospitalario Universitario De Lugo", "Complexo Hospitalario Universitario De Ourense", "Complexo Hospitalario Universitario De Pontevedra", "Complexo Hospitalario Universitario De Santiago", "Complexo Hospitalario Universitario De Vigo", "Comunitat Terapeutica Arenys De Munt", "Concheiro Centro Medico Quirurgico", "Consejería de Sanidad", "Consorcio Hospital General Universitario De Valencia", "Consorcio Hospitalario Provincial De Castellon", "Consorcio LUCIA (SACYL,ITACYL UBU,UVa)", "Cqm Clinic Maresme, Sl", "Cti De La Corredoria", "Eatica", "Espitau Val D'Aran", "Fraternidad Muprespa, Mutua Colaboradora Con La Seguridad Social Nº 275", "Fremap Hospital Majadahonda", "Fremap, Hospital De Barcelona", "Fremap, Hospital De Vigo", "Fremap_Hospital Y Centro De Rehabilitacion De Sevilla", "Fundacio Hospital De L'Esperit Sant", "Fundacio Hospital Sant Joan De Deu (Martorell)", "Fundacio Puigvert - Iuna", "Fundacio Sanitaria Sant Josep", "Fundacio Sant Hospital.", "Fundacion Cudeca. Centro De Cuidados Paliativos", "Fundacion Hospital De Aviles", "Fundacion Instituto San Jose", "Fundacion Instituto Valenciano De Oncologia", "Fundacion Sanatorio Adaro", "Fundació Althaia-Manresa", "Fundació Fisabio", "Gerencia de Atención Primaria Pontevedra Sur", "Germanes Hospitalaries. Hospital Sagrat Cor", "Grupo Quironsalud Pontevedra", "Hc Marbella International Hospital", "Helicopteros Sanitarios Hospital", "Hestia Balaguer.", "Hestia Duran I Reynals", "Hestia Gracia", "Hestia La Robleda", "Hestia Palau.", "Hestia San Jose", "Hm El Pilar", "Hm Galvez", "Hm Hospitales 1.989, S.A.", "Hm Malaga", "Hm Modelo-Belen", "Hm Nou Delfos", "Hm Regla", "Hospital 9 De Octubre", "Hospital Aita Menni", "Hospital Alto Guadalquivir", "Hospital Arnau De Vilanova", "Hospital Asepeyo Madrid", "Hospital Asilo De La Real Piedad De Cehegin", "Hospital Asociado Universitario Guadarrama", "Hospital Asociado Universitario Virgen De La Poveda", "Hospital Beata Maria Ana", "Hospital Begoña", "Hospital Bidasoa (Osi Bidasoa)", "Hospital C. M. Virgen De La Caridad Cartagena", "Hospital Campo Arañuelo", "Hospital Can Misses", "Hospital Carlos Iii", "Hospital Carmen Y Severo Ochoa", "Hospital Casaverde Valladolid", "Hospital Catolico Casa De Salud", "Hospital Central De La Cruz Roja, San Jose Y Santa Adela", "Hospital Central De La Defensa Gomez Ulla", "Hospital Centro De Andalucia", "Hospital Centro De Cuidados Laguna", "Hospital Centro Medico Virgen De La Caridad Caravaca", "Hospital Ciudad De Coria", "Hospital Ciudad De Telde", "Hospital Civil", "Hospital Clinic De Barcelona", "Hospital Clinic De Barcelona, Seu Plato", "Hospital Clinic De Barcelona, Seu Sabino De Arana", "Hospital Clinica Benidorm", "Hospital Clinico Universitario De Valencia", "Hospital Clinico Universitario De Valladolid", "Hospital Clinico Universitario Lozano Blesa", "Hospital Clinico Universitario Virgen De La Arrixaca", "Hospital Comarcal", "Hospital Comarcal D'Amposta", "Hospital Comarcal De Blanes", "Hospital Comarcal De L'Alt Penedes", "Hospital Comarcal De Laredo", "Hospital Comarcal De Vinaros", "Hospital Comarcal Del Noroeste", "Hospital Comarcal Del Pallars", "Hospital Comarcal D´Inca", "Hospital Comarcal Mora D'Ebre", "Hospital Comarcal Sant Jaume De Calella", "Hospital Costa Del Sol", "Hospital Cruz Roja De Bilbao - Victoria Eugenia", "Hospital Cruz Roja De Cordoba", "Hospital Cruz Roja Gijon", "Hospital D'Igualada", "Hospital D'Olot I Comarcal De La Garrotxa", "Hospital De Alcañiz", "Hospital De Alta Resolucion De Alcala La Real", "Hospital De Alta Resolucion De Alcaudete", "Hospital De Alta Resolucion De Benalmadena", "Hospital De Alta Resolucion De Ecija", "Hospital De Alta Resolucion De Especialidades De La Janda", "Hospital De Alta Resolucion De Estepona", "Hospital De Alta Resolucion De Guadix", "Hospital De Alta Resolucion De Lebrija", "Hospital De Alta Resolucion De Loja", "Hospital De Alta Resolucion De Moron De La Frontera", "Hospital De Alta Resolucion De Puente Genil", "Hospital De Alta Resolucion De Utrera", "Hospital De Alta Resolucion Eltoyo", "Hospital De Alta Resolucion Sierra De Segura", "Hospital De Alta Resolucion Sierra Norte", "Hospital De Alta Resolucion Valle Del Guadiato", "Hospital De Antequera", "Hospital De Barbastro", "Hospital De Barcelona", "Hospital De Baza", "Hospital De Benavente Complejo Asistencial De Zamora", "Hospital De Berga", "Hospital De Bermeo", "Hospital De Calahorra", "Hospital De Campdevanol", "Hospital De Cantoblanco", "Hospital De Cerdanya / Hopital De Cerdagne", "Hospital De Cronicos De Mislata (Antiguo Hospital Militar De Valencia)", "Hospital De Cuidados Medios Villademar", "Hospital De Denia", "Hospital De Emergencia Covid 19", "Hospital De Figueres", "Hospital De Formentera", "Hospital De Gorliz", "Hospital De Hellin", "Hospital De Jaca Salud", "Hospital De Jarrio", "Hospital De Jove", "Hospital De L'Esperança.", "Hospital De La Axarquia", "Hospital De La Creu Roja Espanyola", "Hospital De La Fuenfria", "Hospital De La Inmaculada Concepcion", "Hospital De La Malva-Rosa", "Hospital De La Mujer", "Hospital De La Reina", "Hospital De La Rioja", "Hospital De La Santa Creu", "Hospital De La Santa Creu I Sant Pau", "Hospital De La Serrania", "Hospital De La V.O.T. De San Francisco De Asis", "Hospital De La Vega Lorenzo Guirao", "Hospital De Leon Complejo Asistencial Universitario De Leon", "Hospital De Leza", "Hospital De Llevant", "Hospital De Lliria", "Hospital De Luarca", "Hospital De Manacor", "Hospital De Manises", "Hospital De Mataro", "Hospital De Mendaro (Osi Bajo Deba)", "Hospital De Merida", "Hospital De Mollet", "Hospital De Montilla", "Hospital De Neurotraumatologia Y Rehabilitacion Del H.U. Virgen De Las Nieves", "Hospital De Ofra", "Hospital De Palamos", "Hospital De Rehabilitacion Psiquiatrica Prisma", "Hospital De Rehabilitacion Y Traumatologia Del H.U. Virgen Del Rocio", "Hospital De Riotinto", "Hospital De Sabadell", "Hospital De Sagunto", "Hospital De Salud Mental Casta Salud Arevalo", "Hospital De Salud Mental Provincial", "Hospital De San Antonio", "Hospital De San Jose", "Hospital De San Rafael", "Hospital De Sant Andreu", "Hospital De Sant Celoni.", "Hospital De Sant Jaume", "Hospital De Sant Joan De Deu (Manresa)", "Hospital De Sant Joan De Deu.", "Hospital De Sant Joan Despi Moises Broggi", "Hospital De Sant Llatzer", "Hospital De Sant Pau I Santa Tecla", "Hospital De Terrassa.", "Hospital De Tortosa Verge De La Cinta", "Hospital De Viladecans", "Hospital De Zafra", "Hospital De Zaldibar", "Hospital De Zamudio", "Hospital De Zumarraga (Osi Goierri - Alto Urola)", "Hospital Del Mar", "Hospital Del Norte", "Hospital Del Oriente De Asturias Francisco Grande Covian", "Hospital Del Sur", "Hospital Del Vendrell", "Hospital Doctor Moliner", "Hospital Doctor Oloriz", "Hospital Doctor Sagaz", "Hospital Don Benito-Villanueva De La Serena", "Hospital Dos De Maig", "Hospital Egarsat Sant Honorat", "Hospital El Angel", "Hospital El Bierzo", "Hospital El Escorial", "Hospital El Pilar", "Hospital El Tomillar", "Hospital Ernest Lluch Martin", "Hospital Fatima", "Hospital Francesc De Borja De Gandia", "Hospital Fuensanta", "Hospital Fuente Bermeja- Complejo Asistencial Universitario De Burgos-", "Hospital G. Universitario J.M. Morales Meseguer", "Hospital Galdakao-Usansolo Asociado A La Upv/Ehu", "Hospital Garcia Orcoyen", "Hospital General De Almansa", "Hospital General De Fuerteventura", "Hospital General De Granollers.", "Hospital General De L'Hospitalet", "Hospital General De La Defensa En Zaragoza", "Hospital General De La Santisima Trinidad", "Hospital General De Llerena", "Hospital General De Mallorca", "Hospital General De Ontinyent", "Hospital General De Requena", "Hospital General De Segovia Complejo Asistencial De Segovia", "Hospital General De Tomelloso", "Hospital General De Valdepeñas", "Hospital General De Villalba", "Hospital General De Villarrobledo", "Hospital General La Mancha Centro", "Hospital General Nuestra Señora Del Prado", "Hospital General Penitenciari", "Hospital General Santa Maria Del Puerto", "Hospital General Universitario De Albacete", "Hospital General Universitario De Castellon", "Hospital General Universitario De Ciudad Real", "Hospital General Universitario De Elche", "Hospital General Universitario De Elda-Virgen De La Salud", "Hospital General Universitario Dr. Balmis", "Hospital General Universitario Gregorio Marañon", "Hospital General Universitario Los Arcos Del Mar Menor", "Hospital General Universitario Reina Sofia", "Hospital General Universitario Santa Lucia", "Hospital Geriatrico Virgen Del Valle", "Hospital Gijon", "Hospital Hernan Cortes Miraflores", "Hospital Hestia Madrid", "Hospital Hla Universitario Moncloa", "Hospital Hm Nuevo Belen", "Hospital Hm Rosaleda-Hm La Esperanza", "Hospital Hm San Francisco", "Hospital Hm Valles", "Hospital Ibermutuamur - Patologia Laboral", "Hospital Imed Elche", "Hospital Imed Gandia", "Hospital Imed Levante", "Hospital Imed San Jorge", "Hospital Infanta Elena", "Hospital Infanta Margarita", "Hospital Infantil", "Hospital Infantil Universitario Niño Jesus", "Hospital Insular De Lanzarote", "Hospital Insular Nuestra Señora De Los Reyes", "Hospital Intermutual De Euskadi", "Hospital Intermutual De Levante", "Hospital Internacional Hcb Denia", "Hospital Internacional Hm Santa Elena", "Hospital Jaume Nadal Meroles", "Hospital Jerez Puerta Del Sur", "Hospital Joan March", "Hospital Juaneda Muro", "Hospital La Antigua", "Hospital La Inmaculada", "Hospital La Magdalena", "Hospital La Merced", "Hospital La Milagrosa S.A.", "Hospital La Paloma", "Hospital La Pedrera", "Hospital La Vega Grupo Hla", "Hospital Latorre", "Hospital Lluis Alcanyis De Xativa", "Hospital Los Madroños", "Hospital Los Montalvos (Complejo Asistencial Universitario De Salamanca)", "Hospital Los Morales", "Hospital Mare De Deu De La Merce", "Hospital Marina Baixa De La Vila Joiosa", "Hospital Maritimo De Torremolinos", "Hospital Materno - Infantil Del H.U. Reina Sofia", "Hospital Materno Infantil", "Hospital Materno Infantil Del H.U.R. De Malaga", "Hospital Materno-Infantil", "Hospital Materno-Infantil Del H.U. De Jaen", "Hospital Materno-Infantil Del H.U. Virgen De Las Nieves", "Hospital Mateu Orfila", "Hospital Maz", "Hospital Md Anderson Cancer Center Madrid", "Hospital Medimar Internacional", "Hospital Medina Del Campo", "Hospital Mediterraneo", "Hospital Mesa Del Castillo", "Hospital Metropolitano De Jaen", "Hospital Mompia", "Hospital Monte Naranco", "Hospital Monte San Isidro Complejo Asistencial Universitario De Leon", "Hospital Municipal De Badalona", "Hospital Mutua Montañesa", "Hospital Nacional De Paraplejicos", "Hospital Neurotraumatologico Del H.U. De Jaen", "Hospital Nisa Aguas Vivas", "Hospital Ntra. Sra. Del Perpetuo Socorro", "Hospital Nuestra Señora De America", "Hospital Nuestra Señora De Gracia", "Hospital Nuestra Señora De Guadalupe", "Hospital Nuestra Señora De La Salud Hla Sl", "Hospital Nuestra Señora De Sonsoles", "Hospital Obispo Polanco", "Hospital Ochoa", "Hospital Palma Del Rio", "Hospital Pardo De Aravaca", "Hospital Pare Jofre", "Hospital Parque", "Hospital Parque Fuerteventura", "Hospital Parque Marazuela", "Hospital Parque San Francisco", "Hospital Parque Vegas Altas", "Hospital Perpetuo Socorro", "Hospital Perpetuo Socorro Alameda", "Hospital Polivalente Anexo Juan Carlos I", "Hospital Provincial", "Hospital Provincial De Avila", "Hospital Provincial De Zamora Complejo Asistencial De Zamora", "Hospital Provincial Ntra.Sra.De La Misericordia", "Hospital Psiquiatric", "Hospital Psiquiatrico Doctor Rodriguez Lafora", "Hospital Psiquiatrico Penitenciario", "Hospital Psiquiatrico Penitenciario De Fontcalent", "Hospital Psiquiatrico Roman Alberca", "Hospital Psiquiatrico San Francisco De Asis", "Hospital Psiquiatrico San Juan De Dios", "Hospital Psiquiatrico San Luis", "Hospital Publico Da Barbanza", "Hospital Publico Da Mariña", "Hospital Publico De Monforte", "Hospital Publico De Valdeorras", "Hospital Publico De Verin", "Hospital Publico Do Salnes", "Hospital Publico Virxe Da Xunqueira", "Hospital Puerta De Andalucia", "Hospital Punta De Europa", "Hospital Quiron Campo De Gibraltar", "Hospital Quiron Salud Costa Adeje", "Hospital Quiron Salud Del Valles - Clinica Del Valles", "Hospital Quiron Salud Lugo", "Hospital Quiron Salud Tenerife", "Hospital Quiron Salud Valle Del Henares", "Hospital Quironsalud A Coruña", "Hospital Quironsalud Albacete", "Hospital Quironsalud Barcelona", "Hospital Quironsalud Bizkaia", "Hospital Quironsalud Caceres", "Hospital Quironsalud Ciudad Real", "Hospital Quironsalud Clideba", "Hospital Quironsalud Cordoba", "Hospital Quironsalud Huelva", "Hospital Quironsalud Infanta Luisa", "Hospital Quironsalud Malaga", "Hospital Quironsalud Marbella", "Hospital Quironsalud Murcia", "Hospital Quironsalud Palmaplanas", "Hospital Quironsalud Sagrado Corazon", "Hospital Quironsalud San Jose", "Hospital Quironsalud Santa Cristina", "Hospital Quironsalud Son Veri", "Hospital Quironsalud Sur", "Hospital Quironsalud Toledo", "Hospital Quironsalud Torrevieja", "Hospital Quironsalud Valencia", "Hospital Quironsalud Vida", "Hospital Quironsalud Vitoria", "Hospital Quironsalud Zaragoza", "Hospital Rafael Mendez", "Hospital Recoletas Cuenca, S.L.U.", "Hospital Recoletas De Burgos", "Hospital Recoletas De Palencia", "Hospital Recoletas De Zamora", "Hospital Recoletas Marbella Slu", "Hospital Recoletas Salud Campo Grande", "Hospital Recoletas Salud Felipe Ii", "Hospital Recoletas Segovia Nuestra Señora De La Misericordia", "Hospital Reina Sofia", "Hospital Residencia Sant Camil - Consorci Sanitari De L'Alt Penedes I Garraf", "Hospital Ribera Almendralejo", "Hospital Ribera Badajoz", "Hospital Ribera Covadonga", "Hospital Ribera Juan Cardona", "Hospital Ribera Polusa", "Hospital Ribera Povisa", "Hospital Ricardo Bermingham", "Hospital Rio Carrion Complejo Asistencial Universitario De Palencia", "Hospital Royo Villanova", "Hospital Ruber Internacional", "Hospital Ruber Juan Bravo", "Hospital Sagrado Corazon De Jesus", "Hospital San Agustin", "Hospital San Camilo", "Hospital San Carlos De Denia Grupo Hla", "Hospital San Carlos De San Fernando", "Hospital San Eloy", "Hospital San Francisco De Asis", "Hospital San Jose", "Hospital San Jose Solimat", "Hospital San Juan De Dios", "Hospital San Juan De Dios Burgos", "Hospital San Juan De Dios De Cordoba", "Hospital San Juan De Dios De Sevilla", "Hospital San Juan De Dios Del Aljarafe", "Hospital San Juan De Dios Donostia", "Hospital San Juan De Dios Leon", "Hospital San Juan De Dios Tenerife", "Hospital San Juan De La Cruz", "Hospital San Juan Grande", "Hospital San Lazaro", "Hospital San Pedro De Alcantara", "Hospital San Rafael", "Hospital San Roque De Guia", "Hospital San Telmo ,Complejo Asistencial Universitario De Palencia", "Hospital Sanitas Cima", "Hospital Sant Antoni Abat - Consorci Sanitari Del Garraf.", "Hospital Sant Joan De Deu", "Hospital Sant Joan De Deu Inca", "Hospital Sant Joan De Deu Lleida", "Hospital Sant Vicent Del Raspeig", "Hospital Santa Ana", "Hospital Santa Barbara", "Hospital Santa Barbara ,Complejo Asistencial De Soria", "Hospital Santa Caterina-Ias", "Hospital Santa Clotilde", "Hospital Santa Isabel Complejo Asistencial Universitario De Leon", "Hospital Santa Maria", "Hospital Santa Maria Del Rosell", "Hospital Santa Marina", "Hospital Santa Teresa", "Hospital Santiago Apostol", "Hospital Santos Reyes", "Hospital Siberia-Serena", "Hospital Sierrallana", "Hospital Sociosanitari De Lloret De Mar", "Hospital Sociosanitari De Mollet", "Hospital Sociosanitari Francoli", "Hospital Sociosanitari Mutuam Girona", "Hospital Sociosanitari Mutuam Guell", "Hospital Sociosanitari Pere Virgili", "Hospital Son Llatzer", "Hospital Tierra De Barros", "Hospital Universitari Arnau De Vilanova De Lleida", "Hospital Universitari De Bellvitge", "Hospital Universitari De Girona Dr. Josep Trueta", "Hospital Universitari De Sant Joan De Reus", "Hospital Universitari De Vic", "Hospital Universitari General De Catalunya", "Hospital Universitari Germans Trias I Pujol De Badalona", "Hospital Universitari Joan Xxiii De Tarragona", "Hospital Universitari Mutua De Terrassa", "Hospital Universitari Quir¿N Dexeus", "Hospital Universitari Sagrat Cor", "Hospital Universitari Son Espases", "Hospital Universitari Vall D'Hebron", "Hospital Universitario 12 De Octubre", "Hospital Universitario Araba (Sede Txagorritxu Y Sede Santiago)", "Hospital Universitario Basurto", "Hospital Universitario Central De Asturias", "Hospital Universitario Clinico San Carlos", "Hospital Universitario Clinico San Cecilio", "Hospital Universitario Clínico San Cecilio", "Hospital Universitario Costa Del Sol", "Hospital Universitario Cruces", "Hospital Universitario De Badajoz", "Hospital Universitario De Burgos Complejo Asistencial Univer. De Burgos", "Hospital Universitario De Cabueñes", "Hospital Universitario De Caceres", "Hospital Universitario De Canarias", "Hospital Universitario De Ceuta", "Hospital Universitario De Fuenlabrada", "Hospital Universitario De Getafe", "Hospital Universitario De Gran Canaria Dr. Negrin", "Hospital Universitario De Guadalajara", "Hospital Universitario De Jaen", "Hospital Universitario De Jaén", "Hospital Universitario De Jerez De La Frontera", "Hospital Universitario De La Linea De La Concepcion", "Hospital Universitario De La Plana", "Hospital Universitario De La Princesa", "Hospital Universitario De La Ribera", "Hospital Universitario De Mostoles", "Hospital Universitario De Navarra", "Hospital Universitario De Poniente", "Hospital Universitario De Puerto Real", "Hospital Universitario De Salamanca ,Complejo Asistencial Universitario De", "Hospital Universitario De Salud Mental Juan Carlos I", "Hospital Universitario De Toledo (Hut)", "Hospital Universitario De Torrejon", "Hospital Universitario De Torrevieja", "Hospital Universitario Del Henares", "Hospital Universitario Del Sureste", "Hospital Universitario Del Tajo", "Hospital Universitario Donostia", "Hospital Universitario Dr. Jose Molina Orosa", "Hospital Universitario Dr. Peset Aleixandre", "Hospital Universitario Fundacion Alcorcon", "Hospital Universitario Fundacion Jimenez Diaz", "Hospital Universitario General De La Palma", "Hospital Universitario Hm Madrid", "Hospital Universitario Hm Monteprincipe", "Hospital Universitario Hm Puerta Del Sur", "Hospital Universitario Hm Sanchinarro", "Hospital Universitario Hm Torrelodones", "Hospital Universitario Hospiten Bellevue", "Hospital Universitario Hospiten Rambla", "Hospital Universitario Hospiten Sur", "Hospital Universitario Infanta Cristina", "Hospital Universitario Infanta Elena", "Hospital Universitario Infanta Leonor", "Hospital Universitario Infanta Sofia", "Hospital Universitario Jose Germain", "Hospital Universitario Juan Ramon Jimenez", "Hospital Universitario Juan Ramón Jiménez", "Hospital Universitario La Moraleja", "Hospital Universitario La Paz", "Hospital Universitario La Zarzuela", "Hospital Universitario Marques De Valdecilla", "Hospital Universitario Miguel Servet", "Hospital Universitario Nuestra Señora De Candelaria", "Hospital Universitario Nuestra Señora Del Perpetuo Socorro", "Hospital Universitario Principe De Asturias", "Hospital Universitario Puerta De Hierro Majadahonda", "Hospital Universitario Puerta Del Mar", "Hospital Universitario Quironsalud Madrid", "Hospital Universitario Ramon Y Cajal", "Hospital Universitario Regional De Malaga", "Hospital Universitario Regional De Málaga", "Hospital Universitario Reina Sofia", "Hospital Universitario Reina Sofía", "Hospital Universitario Rio Hortega", "Hospital Universitario San Agustin", "Hospital Universitario San Jorge", "Hospital Universitario San Juan De Alicante", "Hospital Universitario San Pedro", "Hospital Universitario San Roque Las Palmas", "Hospital Universitario San Roque Maspalomas", "Hospital Universitario Santa Cristina", "Hospital Universitario Severo Ochoa", "Hospital Universitario Torrecardenas", "Hospital Universitario Torrecárdenas", "Hospital Universitario Vinalopo", "Hospital Universitario Virgen De La Victoria", "Hospital Universitario Virgen De Las Nieves", "Hospital Universitario Virgen De Valme", "Hospital Universitario Virgen Del Rocio", "Hospital Universitario Virgen Del Rocío", "Hospital Universitario Virgen Macarena", "Hospital Universitario Vithas Las Palmas", "Hospital Universitario Y Politecnico La Fe", "Hospital Urduliz Ospitalea", "Hospital Valle De Guadalhorce De Cartama", "Hospital Valle De Laciana", "Hospital Valle De Los Pedroches", "Hospital Valle Del Nalon", "Hospital Vazquez Diaz", "Hospital Vega Baja De Orihuela", "Hospital Viamed Bahia De Cadiz", "Hospital Viamed Montecanal", "Hospital Viamed Novo Sancti Petri", "Hospital Viamed San Jose", "Hospital Viamed Santa Angela De La Cruz", "Hospital Viamed Santa Elena, S.L", "Hospital Viamed Santiago", "Hospital Viamed Tarragona", "Hospital Victoria Eugenia De La Cruz Roja Española", "Hospital Virgen De Altagracia", "Hospital Virgen De La Bella", "Hospital Virgen De La Concha Complejo Asistencial De Zamora", "Hospital Virgen De La Luz", "Hospital Virgen De La Torre", "Hospital Virgen De Las Montañas", "Hospital Virgen De Los Lirios", "Hospital Virgen Del Alcazar De Lorca", "Hospital Virgen Del Camino", "Hospital Virgen Del Castillo", "Hospital Virgen Del Mar", "Hospital Virgen Del Miron ,Complejo Asistencial De Soria", "Hospital Virgen Del Puerto", "Hospital Vital Alvarez Buylla", "Hospital Vithas Castellon", "Hospital Vithas Granada", "Hospital Vithas Parque San Antonio", "Hospital Vithas Sevilla", "Hospital Vithas Valencia Consuelo", "Hospital Vithas Vitoria", "Hospital Vithas Xanit Estepona", "Hospital Vithas Xanit Internacional", "Hospiten Clinica Roca San Agustin", "Hospiten Lanzarote", "Idcsalud Mostoles Sa", "Imed Valencia", "Institut Catala D'Oncologia - Hospital Duran I Reynals", "Institut Catala D'Oncologia - Hospital Germans Trias I Pujol", "Institut Catala D'Oncologia Girona - Hospital Josep Trueta", "Institut Guttmann", "Institut Pere Mata, S.A", "Instituto De Enfermedades Neurologicas De Castilla-La Mancha", "Instituto De Salud Carlos Iii - Centro Nacional De Microbiologia", "Instituto De Traumatologia De Union De Mutuas (Matepss Nº 267)", "Instituto Oftalmologico Fernandez-Vega", "Instituto Provincial De Rehabilitacion", "Instituto Psiquiátrico Servicios De Salud Mental José Germain", "Instituto Tecnológico y de Energías Renovables, S.A. (ITER, S.A.)", "Ita Canet", "Ita Clinic Bcn", "Ita Godella", "Ita Maresme", "Ivan Mañero Clinic", "Juaneda Miramar", "Lab Clínic ICS Camp de Tarragona-Terres de l'Ebre. Hospital Joan XXIII", "Laboratori De Referencia De Catalunya", "Laboratorio Echevarne, Sa", "Lepant Residencial Qgg, Sl", "Microbiología HUC San Cecilio", "Microbiología. Hospital Universitario Virgen del Rocio", "Ministerio Sanidad", "Mutua Balear", "Mutua De Granollers, Mutua De Previsio Social A Prima Fixa", "Mutualia Clinica Pakea", "Nou Hospital Evangelic", "Organizacion Sanitaria Integrada Debagoiena", "Parc Sanitari Sant Joan De Deu - Numancia", "Parc Sanitari Sant Joan De Deu - Recinte Sant Boi.", "Parc Sanitari Sant Joan De Deu - Til·Lers", "Parc Sanitari Sant Joan De Deu - Uhpp - 1", "Parc Sanitari Sant Joan De Deu - Uhpp - 2", "Pius Hospital De Valls", "Plataforma de Genómica y Bioinformática", "Plataforma de Medicina Computacional, Fundación Progreso y Salud", "Policlinica Comarcal Del Vendrell.", "Policlinica Gipuzkoa", "Policlinica Nuestra Sra. Del Rosario", "Policlinico Riojano Nuestra Señora De Valvanera", "Presidencia del Gobierno", "Prytanis Hospitalet Centre Sociosanitari", "Prytanis Sant Boi Centre Sociosanitari", "Quinta Medica De Reposo", "Red De Salud Mental De Araba (Hospital Psiquiatrico De Araba)", "Residencia Alt Camp", "Residencia De Gent Gran Puig D'En Roca", "Residencia De Salud Mental Nuestra Se?Ora Del Carmen", "Residencia Geriatrica Maria Gay", "Residencia L'Estada", "Residencia Puig-Reig", "Residencia Santa Susanna", "Residencia Santa Tecla Ponent", "Residencia Terraferma", "Residencia Vila-Seca", "Ribera Hospital De Molina", "Ronda De Dalt, Centre Sociosanitari", "Sanatorio Bilbaino", "Sanatorio Dr. Muñoz", "Sanatorio Esquerdo, S.A.", "Sanatorio Nuestra Señora Del Rosario", "Sanatorio Sagrado Corazon", "Sanatorio San Francisco De Borja Fontilles", "Sanatorio Usurbil, S. L.", "Santo Y Real Hospital De Caridad", "Sar Mont Marti", "Serveis Clinics, S.A.", "Servicio Madrileño De Salud", "Servicio de Microbiologia HU Son Espases", "Servicios Sanitarios Y Asistenciales", "U.R.R. De Enfermos Psiquicos Alcohete", "Unidad De Rehabilitacion De Larga Estancia", "Unidad Rehabilitadora De Media Estancia Profesor Rey Ardid", "Unidades Clinicas Y De Rehabilitacion De Salud Mental", "Unitat Polivalent Benito Menni En Salut Mental De L'Hospitalet-El Prat De Llobregat", "Unitat Polivalent En Salut Mental D'Amposta", "Unitat Polivalent Salut Mental Barcelona-Nord", "Unitat Terapeutica-Educativa Acompanya'M", "Villablanca Serveis Assistencials, Sa", "Vithas Hospital Montserrat", "Vithas Hospital Nosa Señora De Fatima", "Vithas Hospital Perpetuo Internacional", "Vithas Hospital Santa Cruz" ], "examples": [ "Instituto de Salud Carlos III " ], "ontology": "GENEPIO:0001159", "type": "string", "description": "The name of the agency that submitted the sequence to the platform.", "classification": "Sample collection and processing", "label": "Submitting Institution", "fill_mode": "sample", "header": "Y" }, "sequencing_institution": { "enum": [ "Adinfa, Sociedad Cooperativa Andaluza", "Alm Univass S.L.", "Antic Hospital De Sant Jaume I Santa Magdalena", "Aptima Centre Clinic - Mutua De Terrassa", "Area Psiquiatrica San Juan De Dios", "Avances Medicos S.A.", "Avantmedic", "Banc de Sang i Teixits Catalunya", "Benito Menni Complex Assistencial En Salut Mental", "Benito Menni, Complex Assistencial En Salut Mental", "Cap La Salut", "Cap Mataro Centre", "Cap Montmelo", "Cap Montornes", "Casal De Curacio", "Casaverde Centro De Rehabilitacion Neurologico De Extremadura S.L.", "Casta Guadarrama", "Castell D'Oliana Residencial,S.L", "Catlab-Centre Analitiques Terrassa, Aie", "Centre Collserola Mutual", "Centre D'Hospitalitzacio I Hospital De Dia Trastorns De La Conducta", "Centre D'Oftalmologia Barraquer", "Centre De Prevencio I Rehabilitacio Asepeyo", "Centre De Salut Doctor Vilaseca-Can Mariner", "Centre Forum", "Centre Geriatric Del Maresme", "Centre Hospitalari Policlinica Barcelona", "Centre Integral De Serveis En Salut Mental Comunitaria", "Centre La Creueta", "Centre Medic Molins, Sl", "Centre Mq Reus", "Centre Palamos Gent Gran", "Centre Polivalent Can Fosc", "Centre Sanitari Del Solsones, Fpc", "Centre Social I Sanitari Frederica Montseny", "Centre Sociosanitari Bernat Jaume", "Centre Sociosanitari Blauclinic Dolors Aleu", "Centre Sociosanitari Can Torras", "Centre Sociosanitari Ciutat De Reus", "Centre Sociosanitari D'Esplugues", "Centre Sociosanitari De L'Hospitalet - Consorci Sanitari Integral", "Centre Sociosanitari De Puigcerda", "Centre Sociosanitari Del Centre Integral De Salut Cotxeres", "Centre Sociosanitari El Carme", "Centre Sociosanitari I Residencia Assistida Salou", "Centre Sociosanitari Isabel Roig", "Centre Sociosanitari Llevant", "Centre Sociosanitari Parc Hospitalari Marti I Julia", "Centre Sociosanitari Ricard Fortuny", "Centre Sociosanitari Sant Jordi De La Vall D'Hebron", "Centre Sociosanitari Sarquavitae Sant Jordi", "Centre Sociosanitari Verge Del Puig", "Centres Assistencials Dr. Emili Mira I Lopez (Recinte Torribera).", "Centro Asistencial Albelda De Iregua", "Centro Asistencial Hnas. Hospitalarias Del Sagrado Corazon De Jesus", "Centro Asistencial San Juan De Dios", "Centro De Atencion A La Salud Mental, La Milagrosa", "Centro De Rehabilitacion Neurologica Casaverde", "Centro De Rehabilitacion Psicosocial Nuestra Señora Del Pilar", "Centro De Rehabilitacion Psicosocial San Juan De Dios", "Centro De Rehabilitacion Psicosocial Santo Cristo De Los Milagros", "Centro De Tratamiento De Drogodependientes El Alba", "Centro De Tratamiento Integral Montevil", "Centro Habilitado Ernest Lluch", "Centro Hospitalario Benito Menni", "Centro Hospitalario De Alta Resolucion De Cazorla", "Centro Hospitalario Padre Menni", "Centro Medico De Asturias", "Centro Medico El Carmen", "Centro Medico Pintado", "Centro Medico Teknon, Grupo Quironsalud", "Centro Neuropsiquiatrico Nuestra Señora Del Carmen", "Centro Oncoloxico De Galicia", "Centro Residencial Domusvi La Salut Josep Servat.", "Centro Salud Mental Perez Espinosa", "Centro San Francisco Javier", "Centro San Juan De Dios Ciempozuelos", "Centro Sanitario Bajo Cinca-Baix Cinca", "Centro Sanitario Cinco Villas", "Centro Sanitario Residencial Las Palmas (Cesar Las Palmas)", "Centro Sociosanitario De Convalecencia Nuestra Señora Virgen Del Carmen", "Centro Sociosanitario De Convalencencia Los Jazmines", "Centro Sociosanitario De Merida", "Centro Sociosanitario De Plasencia", "Centro Terapeutico Vista Alegre", "Centro de Investigación Biomédica de Aragón", "Clinica Activa Mutua 2008", "Clinica Arcangel San Miguel - Pamplona", "Clinica Asturias", "Clinica Bandama", "Clinica Bofill", "Clinica Cajal", "Clinica Cemtro", "Clinica Corachan", "Clinica Coroleu - Ssr Hestia.", "Clinica Creu Blanca", "Clinica Cristo Rey", "Clinica De Salud Mental Miguel De Mañara", "Clinica Diagonal", "Clinica Doctor Sanz Vazquez", "Clinica Dr. Leon", "Clinica El Seranil", "Clinica Ercilla Mutualia", "Clinica Galatea", "Clinica Girona", "Clinica Guimon, S.A.", "Clinica Imq Zorrotzaurre", "Clinica Imske", "Clinica Indautxu, S.A.", "Clinica Isadora S.A.", "Clinica Jorgani", "Clinica Juaneda", "Clinica Juaneda Mahon", "Clinica Juaneda Menorca", "Clinica La Luz, S.L.", "Clinica Lluria", "Clinica Lopez Ibor", "Clinica Los Alamos", "Clinica Los Manzanos", "Clinica Los Naranjos", "Clinica Luz De Palma", "Clinica Mc Copernic", "Clinica Mc Londres", "Clinica Mi Nova Aliança", "Clinica Montpellier, Grupo Hla, S.A.U", "Clinica Nostra Senyora De Guadalupe", "Clinica Nostra Senyora Del Remei", "Clinica Nuestra Se?Ora De Aranzazu", "Clinica Nuestra Señora De La Paz", "Clinica Perpetuo Socorro De Lerida, Grupo Hla, Slu", "Clinica Planas", "Clinica Ponferrada Recoletas", "Clinica Psicogeriatrica Josefina Arregui", "Clinica Psiquiatrica Bellavista", "Clinica Psiquiatrica Padre Menni", "Clinica Psiquiatrica Somio", "Clinica Quirurgica Onyar", "Clinica Residencia El Pinar", "Clinica Rotger", "Clinica Sagrada Familia", "Clinica Salus Infirmorum", "Clinica San Felipe", "Clinica San Miguel", "Clinica San Rafael", "Clinica Sant Antoni", "Clinica Sant Josep", "Clinica Santa Creu", "Clinica Santa Isabel", "Clinica Santa Maria De La Asuncion (Inviza S. A.)", "Clinica Santa Teresa", "Clinica Soquimex", "Clinica Tara", "Clinica Terres De L'Ebre", "Clinica Tres Torres", "Clinica Universidad De Navarra", "Clinica Virgen Blanca", "Clinica Vistahermosa Grupo Hla", "Clinicas Del Sur Slu", "Complejo Asistencial Benito Menni", "Complejo Asistencial De Soria", "Complejo Asistencial De Zamora", "Complejo Asistencial De Ávila", "Complejo Asistencial Universitario De Burgos", "Complejo Asistencial Universitario De León", "Complejo Asistencial Universitario De Palencia", "Complejo Asistencial Universitario De Salamanca", "Complejo Hospitalario De Albacete", "Complejo Hospitalario De Cartagena Chc", "Complejo Hospitalario De Cáceres", "Complejo Hospitalario De Don Benito-Villanueva De La Serena", "Complejo Hospitalario De Toledo", "Complejo Hospitalario Del Área De Salud De Mérida", "Complejo Hospitalario Gregorio Marañón", "Complejo Hospitalario Infanta Leonor", "Complejo Hospitalario La Paz", "Complejo Hospitalario Llerena-Zafra", "Complejo Hospitalario San Pedro Hospital De La Rioja", "Complejo Hospitalario Universitario De Badajoz", "Complejo Hospitalario Universitario De Canarias", "Complejo Hospitalario Universitario De Gran Canaria Dr. Negrín", "Complejo Hospitalario Universitario Insular Materno Infantil", "Complejo Hospitalario Universitario Nuestra Señora De Candelaria", "Complexo Hospitalario Universitario A Coruña", "Complexo Hospitalario Universitario De Ferrol", "Complexo Hospitalario Universitario De Lugo", "Complexo Hospitalario Universitario De Ourense", "Complexo Hospitalario Universitario De Pontevedra", "Complexo Hospitalario Universitario De Santiago", "Complexo Hospitalario Universitario De Vigo", "Comunitat Terapeutica Arenys De Munt", "Concheiro Centro Medico Quirurgico", "Consejería de Sanidad", "Consorcio Hospital General Universitario De Valencia", "Consorcio Hospitalario Provincial De Castellon", "Consorcio LUCIA (SACYL,ITACYL UBU,UVa)", "Cqm Clinic Maresme, Sl", "Cti De La Corredoria", "Eatica", "Espitau Val D'Aran", "Fraternidad Muprespa, Mutua Colaboradora Con La Seguridad Social Nº 275", "Fremap Hospital Majadahonda", "Fremap, Hospital De Barcelona", "Fremap, Hospital De Vigo", "Fremap_Hospital Y Centro De Rehabilitacion De Sevilla", "Fundacio Hospital De L'Esperit Sant", "Fundacio Hospital Sant Joan De Deu (Martorell)", "Fundacio Puigvert - Iuna", "Fundacio Sanitaria Sant Josep", "Fundacio Sant Hospital.", "Fundacion Cudeca. Centro De Cuidados Paliativos", "Fundacion Hospital De Aviles", "Fundacion Instituto San Jose", "Fundacion Instituto Valenciano De Oncologia", "Fundacion Sanatorio Adaro", "Fundació Althaia-Manresa", "Fundació Fisabio", "Gerencia de Atención Primaria Pontevedra Sur", "Germanes Hospitalaries. Hospital Sagrat Cor", "Grupo Quironsalud Pontevedra", "Hc Marbella International Hospital", "Helicopteros Sanitarios Hospital", "Hestia Balaguer.", "Hestia Duran I Reynals", "Hestia Gracia", "Hestia La Robleda", "Hestia Palau.", "Hestia San Jose", "Hm El Pilar", "Hm Galvez", "Hm Hospitales 1.989, S.A.", "Hm Malaga", "Hm Modelo-Belen", "Hm Nou Delfos", "Hm Regla", "Hospital 9 De Octubre", "Hospital Aita Menni", "Hospital Alto Guadalquivir", "Hospital Arnau De Vilanova", "Hospital Asepeyo Madrid", "Hospital Asilo De La Real Piedad De Cehegin", "Hospital Asociado Universitario Guadarrama", "Hospital Asociado Universitario Virgen De La Poveda", "Hospital Beata Maria Ana", "Hospital Begoña", "Hospital Bidasoa (Osi Bidasoa)", "Hospital C. M. Virgen De La Caridad Cartagena", "Hospital Campo Arañuelo", "Hospital Can Misses", "Hospital Carlos Iii", "Hospital Carmen Y Severo Ochoa", "Hospital Casaverde Valladolid", "Hospital Catolico Casa De Salud", "Hospital Central De La Cruz Roja, San Jose Y Santa Adela", "Hospital Central De La Defensa Gomez Ulla", "Hospital Centro De Andalucia", "Hospital Centro De Cuidados Laguna", "Hospital Centro Medico Virgen De La Caridad Caravaca", "Hospital Ciudad De Coria", "Hospital Ciudad De Telde", "Hospital Civil", "Hospital Clinic De Barcelona", "Hospital Clinic De Barcelona, Seu Plato", "Hospital Clinic De Barcelona, Seu Sabino De Arana", "Hospital Clinica Benidorm", "Hospital Clinico Universitario De Valencia", "Hospital Clinico Universitario De Valladolid", "Hospital Clinico Universitario Lozano Blesa", "Hospital Clinico Universitario Virgen De La Arrixaca", "Hospital Comarcal", "Hospital Comarcal D'Amposta", "Hospital Comarcal De Blanes", "Hospital Comarcal De L'Alt Penedes", "Hospital Comarcal De Laredo", "Hospital Comarcal De Vinaros", "Hospital Comarcal Del Noroeste", "Hospital Comarcal Del Pallars", "Hospital Comarcal D´Inca", "Hospital Comarcal Mora D'Ebre", "Hospital Comarcal Sant Jaume De Calella", "Hospital Costa Del Sol", "Hospital Cruz Roja De Bilbao - Victoria Eugenia", "Hospital Cruz Roja De Cordoba", "Hospital Cruz Roja Gijon", "Hospital D'Igualada", "Hospital D'Olot I Comarcal De La Garrotxa", "Hospital De Alcañiz", "Hospital De Alta Resolucion De Alcala La Real", "Hospital De Alta Resolucion De Alcaudete", "Hospital De Alta Resolucion De Benalmadena", "Hospital De Alta Resolucion De Ecija", "Hospital De Alta Resolucion De Especialidades De La Janda", "Hospital De Alta Resolucion De Estepona", "Hospital De Alta Resolucion De Guadix", "Hospital De Alta Resolucion De Lebrija", "Hospital De Alta Resolucion De Loja", "Hospital De Alta Resolucion De Moron De La Frontera", "Hospital De Alta Resolucion De Puente Genil", "Hospital De Alta Resolucion De Utrera", "Hospital De Alta Resolucion Eltoyo", "Hospital De Alta Resolucion Sierra De Segura", "Hospital De Alta Resolucion Sierra Norte", "Hospital De Alta Resolucion Valle Del Guadiato", "Hospital De Antequera", "Hospital De Barbastro", "Hospital De Barcelona", "Hospital De Baza", "Hospital De Benavente Complejo Asistencial De Zamora", "Hospital De Berga", "Hospital De Bermeo", "Hospital De Calahorra", "Hospital De Campdevanol", "Hospital De Cantoblanco", "Hospital De Cerdanya / Hopital De Cerdagne", "Hospital De Cronicos De Mislata (Antiguo Hospital Militar De Valencia)", "Hospital De Cuidados Medios Villademar", "Hospital De Denia", "Hospital De Emergencia Covid 19", "Hospital De Figueres", "Hospital De Formentera", "Hospital De Gorliz", "Hospital De Hellin", "Hospital De Jaca Salud", "Hospital De Jarrio", "Hospital De Jove", "Hospital De L'Esperança.", "Hospital De La Axarquia", "Hospital De La Creu Roja Espanyola", "Hospital De La Fuenfria", "Hospital De La Inmaculada Concepcion", "Hospital De La Malva-Rosa", "Hospital De La Mujer", "Hospital De La Reina", "Hospital De La Rioja", "Hospital De La Santa Creu", "Hospital De La Santa Creu I Sant Pau", "Hospital De La Serrania", "Hospital De La V.O.T. De San Francisco De Asis", "Hospital De La Vega Lorenzo Guirao", "Hospital De Leon Complejo Asistencial Universitario De Leon", "Hospital De Leza", "Hospital De Llevant", "Hospital De Lliria", "Hospital De Luarca", "Hospital De Manacor", "Hospital De Manises", "Hospital De Mataro", "Hospital De Mendaro (Osi Bajo Deba)", "Hospital De Merida", "Hospital De Mollet", "Hospital De Montilla", "Hospital De Neurotraumatologia Y Rehabilitacion Del H.U. Virgen De Las Nieves", "Hospital De Ofra", "Hospital De Palamos", "Hospital De Rehabilitacion Psiquiatrica Prisma", "Hospital De Rehabilitacion Y Traumatologia Del H.U. Virgen Del Rocio", "Hospital De Riotinto", "Hospital De Sabadell", "Hospital De Sagunto", "Hospital De Salud Mental Casta Salud Arevalo", "Hospital De Salud Mental Provincial", "Hospital De San Antonio", "Hospital De San Jose", "Hospital De San Rafael", "Hospital De Sant Andreu", "Hospital De Sant Celoni.", "Hospital De Sant Jaume", "Hospital De Sant Joan De Deu (Manresa)", "Hospital De Sant Joan De Deu.", "Hospital De Sant Joan Despi Moises Broggi", "Hospital De Sant Llatzer", "Hospital De Sant Pau I Santa Tecla", "Hospital De Terrassa.", "Hospital De Tortosa Verge De La Cinta", "Hospital De Viladecans", "Hospital De Zafra", "Hospital De Zaldibar", "Hospital De Zamudio", "Hospital De Zumarraga (Osi Goierri - Alto Urola)", "Hospital Del Mar", "Hospital Del Norte", "Hospital Del Oriente De Asturias Francisco Grande Covian", "Hospital Del Sur", "Hospital Del Vendrell", "Hospital Doctor Moliner", "Hospital Doctor Oloriz", "Hospital Doctor Sagaz", "Hospital Don Benito-Villanueva De La Serena", "Hospital Dos De Maig", "Hospital Egarsat Sant Honorat", "Hospital El Angel", "Hospital El Bierzo", "Hospital El Escorial", "Hospital El Pilar", "Hospital El Tomillar", "Hospital Ernest Lluch Martin", "Hospital Fatima", "Hospital Francesc De Borja De Gandia", "Hospital Fuensanta", "Hospital Fuente Bermeja- Complejo Asistencial Universitario De Burgos-", "Hospital G. Universitario J.M. Morales Meseguer", "Hospital Galdakao-Usansolo Asociado A La Upv/Ehu", "Hospital Garcia Orcoyen", "Hospital General De Almansa", "Hospital General De Fuerteventura", "Hospital General De Granollers.", "Hospital General De L'Hospitalet", "Hospital General De La Defensa En Zaragoza", "Hospital General De La Santisima Trinidad", "Hospital General De Llerena", "Hospital General De Mallorca", "Hospital General De Ontinyent", "Hospital General De Requena", "Hospital General De Segovia Complejo Asistencial De Segovia", "Hospital General De Tomelloso", "Hospital General De Valdepeñas", "Hospital General De Villalba", "Hospital General De Villarrobledo", "Hospital General La Mancha Centro", "Hospital General Nuestra Señora Del Prado", "Hospital General Penitenciari", "Hospital General Santa Maria Del Puerto", "Hospital General Universitario De Albacete", "Hospital General Universitario De Castellon", "Hospital General Universitario De Ciudad Real", "Hospital General Universitario De Elche", "Hospital General Universitario De Elda-Virgen De La Salud", "Hospital General Universitario Dr. Balmis", "Hospital General Universitario Gregorio Marañon", "Hospital General Universitario Los Arcos Del Mar Menor", "Hospital General Universitario Reina Sofia", "Hospital General Universitario Santa Lucia", "Hospital Geriatrico Virgen Del Valle", "Hospital Gijon", "Hospital Hernan Cortes Miraflores", "Hospital Hestia Madrid", "Hospital Hla Universitario Moncloa", "Hospital Hm Nuevo Belen", "Hospital Hm Rosaleda-Hm La Esperanza", "Hospital Hm San Francisco", "Hospital Hm Valles", "Hospital Ibermutuamur - Patologia Laboral", "Hospital Imed Elche", "Hospital Imed Gandia", "Hospital Imed Levante", "Hospital Imed San Jorge", "Hospital Infanta Elena", "Hospital Infanta Margarita", "Hospital Infantil", "Hospital Infantil Universitario Niño Jesus", "Hospital Insular De Lanzarote", "Hospital Insular Nuestra Señora De Los Reyes", "Hospital Intermutual De Euskadi", "Hospital Intermutual De Levante", "Hospital Internacional Hcb Denia", "Hospital Internacional Hm Santa Elena", "Hospital Jaume Nadal Meroles", "Hospital Jerez Puerta Del Sur", "Hospital Joan March", "Hospital Juaneda Muro", "Hospital La Antigua", "Hospital La Inmaculada", "Hospital La Magdalena", "Hospital La Merced", "Hospital La Milagrosa S.A.", "Hospital La Paloma", "Hospital La Pedrera", "Hospital La Vega Grupo Hla", "Hospital Latorre", "Hospital Lluis Alcanyis De Xativa", "Hospital Los Madroños", "Hospital Los Montalvos (Complejo Asistencial Universitario De Salamanca)", "Hospital Los Morales", "Hospital Mare De Deu De La Merce", "Hospital Marina Baixa De La Vila Joiosa", "Hospital Maritimo De Torremolinos", "Hospital Materno - Infantil Del H.U. Reina Sofia", "Hospital Materno Infantil", "Hospital Materno Infantil Del H.U.R. De Malaga", "Hospital Materno-Infantil", "Hospital Materno-Infantil Del H.U. De Jaen", "Hospital Materno-Infantil Del H.U. Virgen De Las Nieves", "Hospital Mateu Orfila", "Hospital Maz", "Hospital Md Anderson Cancer Center Madrid", "Hospital Medimar Internacional", "Hospital Medina Del Campo", "Hospital Mediterraneo", "Hospital Mesa Del Castillo", "Hospital Metropolitano De Jaen", "Hospital Mompia", "Hospital Monte Naranco", "Hospital Monte San Isidro Complejo Asistencial Universitario De Leon", "Hospital Municipal De Badalona", "Hospital Mutua Montañesa", "Hospital Nacional De Paraplejicos", "Hospital Neurotraumatologico Del H.U. De Jaen", "Hospital Nisa Aguas Vivas", "Hospital Ntra. Sra. Del Perpetuo Socorro", "Hospital Nuestra Señora De America", "Hospital Nuestra Señora De Gracia", "Hospital Nuestra Señora De Guadalupe", "Hospital Nuestra Señora De La Salud Hla Sl", "Hospital Nuestra Señora De Sonsoles", "Hospital Obispo Polanco", "Hospital Ochoa", "Hospital Palma Del Rio", "Hospital Pardo De Aravaca", "Hospital Pare Jofre", "Hospital Parque", "Hospital Parque Fuerteventura", "Hospital Parque Marazuela", "Hospital Parque San Francisco", "Hospital Parque Vegas Altas", "Hospital Perpetuo Socorro", "Hospital Perpetuo Socorro Alameda", "Hospital Polivalente Anexo Juan Carlos I", "Hospital Provincial", "Hospital Provincial De Avila", "Hospital Provincial De Zamora Complejo Asistencial De Zamora", "Hospital Provincial Ntra.Sra.De La Misericordia", "Hospital Psiquiatric", "Hospital Psiquiatrico Doctor Rodriguez Lafora", "Hospital Psiquiatrico Penitenciario", "Hospital Psiquiatrico Penitenciario De Fontcalent", "Hospital Psiquiatrico Roman Alberca", "Hospital Psiquiatrico San Francisco De Asis", "Hospital Psiquiatrico San Juan De Dios", "Hospital Psiquiatrico San Luis", "Hospital Publico Da Barbanza", "Hospital Publico Da Mariña", "Hospital Publico De Monforte", "Hospital Publico De Valdeorras", "Hospital Publico De Verin", "Hospital Publico Do Salnes", "Hospital Publico Virxe Da Xunqueira", "Hospital Puerta De Andalucia", "Hospital Punta De Europa", "Hospital Quiron Campo De Gibraltar", "Hospital Quiron Salud Costa Adeje", "Hospital Quiron Salud Del Valles - Clinica Del Valles", "Hospital Quiron Salud Lugo", "Hospital Quiron Salud Tenerife", "Hospital Quiron Salud Valle Del Henares", "Hospital Quironsalud A Coruña", "Hospital Quironsalud Albacete", "Hospital Quironsalud Barcelona", "Hospital Quironsalud Bizkaia", "Hospital Quironsalud Caceres", "Hospital Quironsalud Ciudad Real", "Hospital Quironsalud Clideba", "Hospital Quironsalud Cordoba", "Hospital Quironsalud Huelva", "Hospital Quironsalud Infanta Luisa", "Hospital Quironsalud Malaga", "Hospital Quironsalud Marbella", "Hospital Quironsalud Murcia", "Hospital Quironsalud Palmaplanas", "Hospital Quironsalud Sagrado Corazon", "Hospital Quironsalud San Jose", "Hospital Quironsalud Santa Cristina", "Hospital Quironsalud Son Veri", "Hospital Quironsalud Sur", "Hospital Quironsalud Toledo", "Hospital Quironsalud Torrevieja", "Hospital Quironsalud Valencia", "Hospital Quironsalud Vida", "Hospital Quironsalud Vitoria", "Hospital Quironsalud Zaragoza", "Hospital Rafael Mendez", "Hospital Recoletas Cuenca, S.L.U.", "Hospital Recoletas De Burgos", "Hospital Recoletas De Palencia", "Hospital Recoletas De Zamora", "Hospital Recoletas Marbella Slu", "Hospital Recoletas Salud Campo Grande", "Hospital Recoletas Salud Felipe Ii", "Hospital Recoletas Segovia Nuestra Señora De La Misericordia", "Hospital Reina Sofia", "Hospital Residencia Sant Camil - Consorci Sanitari De L'Alt Penedes I Garraf", "Hospital Ribera Almendralejo", "Hospital Ribera Badajoz", "Hospital Ribera Covadonga", "Hospital Ribera Juan Cardona", "Hospital Ribera Polusa", "Hospital Ribera Povisa", "Hospital Ricardo Bermingham", "Hospital Rio Carrion Complejo Asistencial Universitario De Palencia", "Hospital Royo Villanova", "Hospital Ruber Internacional", "Hospital Ruber Juan Bravo", "Hospital Sagrado Corazon De Jesus", "Hospital San Agustin", "Hospital San Camilo", "Hospital San Carlos De Denia Grupo Hla", "Hospital San Carlos De San Fernando", "Hospital San Eloy", "Hospital San Francisco De Asis", "Hospital San Jose", "Hospital San Jose Solimat", "Hospital San Juan De Dios", "Hospital San Juan De Dios Burgos", "Hospital San Juan De Dios De Cordoba", "Hospital San Juan De Dios De Sevilla", "Hospital San Juan De Dios Del Aljarafe", "Hospital San Juan De Dios Donostia", "Hospital San Juan De Dios Leon", "Hospital San Juan De Dios Tenerife", "Hospital San Juan De La Cruz", "Hospital San Juan Grande", "Hospital San Lazaro", "Hospital San Pedro De Alcantara", "Hospital San Rafael", "Hospital San Roque De Guia", "Hospital San Telmo ,Complejo Asistencial Universitario De Palencia", "Hospital Sanitas Cima", "Hospital Sant Antoni Abat - Consorci Sanitari Del Garraf.", "Hospital Sant Joan De Deu", "Hospital Sant Joan De Deu Inca", "Hospital Sant Joan De Deu Lleida", "Hospital Sant Vicent Del Raspeig", "Hospital Santa Ana", "Hospital Santa Barbara", "Hospital Santa Barbara ,Complejo Asistencial De Soria", "Hospital Santa Caterina-Ias", "Hospital Santa Clotilde", "Hospital Santa Isabel Complejo Asistencial Universitario De Leon", "Hospital Santa Maria", "Hospital Santa Maria Del Rosell", "Hospital Santa Marina", "Hospital Santa Teresa", "Hospital Santiago Apostol", "Hospital Santos Reyes", "Hospital Siberia-Serena", "Hospital Sierrallana", "Hospital Sociosanitari De Lloret De Mar", "Hospital Sociosanitari De Mollet", "Hospital Sociosanitari Francoli", "Hospital Sociosanitari Mutuam Girona", "Hospital Sociosanitari Mutuam Guell", "Hospital Sociosanitari Pere Virgili", "Hospital Son Llatzer", "Hospital Tierra De Barros", "Hospital Universitari Arnau De Vilanova De Lleida", "Hospital Universitari De Bellvitge", "Hospital Universitari De Girona Dr. Josep Trueta", "Hospital Universitari De Sant Joan De Reus", "Hospital Universitari De Vic", "Hospital Universitari General De Catalunya", "Hospital Universitari Germans Trias I Pujol De Badalona", "Hospital Universitari Joan Xxiii De Tarragona", "Hospital Universitari Mutua De Terrassa", "Hospital Universitari Quir¿N Dexeus", "Hospital Universitari Sagrat Cor", "Hospital Universitari Son Espases", "Hospital Universitari Vall D'Hebron", "Hospital Universitario 12 De Octubre", "Hospital Universitario Araba (Sede Txagorritxu Y Sede Santiago)", "Hospital Universitario Basurto", "Hospital Universitario Central De Asturias", "Hospital Universitario Clinico San Carlos", "Hospital Universitario Clinico San Cecilio", "Hospital Universitario Clínico San Cecilio", "Hospital Universitario Costa Del Sol", "Hospital Universitario Cruces", "Hospital Universitario De Badajoz", "Hospital Universitario De Burgos Complejo Asistencial Univer. De Burgos", "Hospital Universitario De Cabueñes", "Hospital Universitario De Caceres", "Hospital Universitario De Canarias", "Hospital Universitario De Ceuta", "Hospital Universitario De Fuenlabrada", "Hospital Universitario De Getafe", "Hospital Universitario De Gran Canaria Dr. Negrin", "Hospital Universitario De Guadalajara", "Hospital Universitario De Jaen", "Hospital Universitario De Jaén", "Hospital Universitario De Jerez De La Frontera", "Hospital Universitario De La Linea De La Concepcion", "Hospital Universitario De La Plana", "Hospital Universitario De La Princesa", "Hospital Universitario De La Ribera", "Hospital Universitario De Mostoles", "Hospital Universitario De Navarra", "Hospital Universitario De Poniente", "Hospital Universitario De Puerto Real", "Hospital Universitario De Salamanca ,Complejo Asistencial Universitario De", "Hospital Universitario De Salud Mental Juan Carlos I", "Hospital Universitario De Toledo (Hut)", "Hospital Universitario De Torrejon", "Hospital Universitario De Torrevieja", "Hospital Universitario Del Henares", "Hospital Universitario Del Sureste", "Hospital Universitario Del Tajo", "Hospital Universitario Donostia", "Hospital Universitario Dr. Jose Molina Orosa", "Hospital Universitario Dr. Peset Aleixandre", "Hospital Universitario Fundacion Alcorcon", "Hospital Universitario Fundacion Jimenez Diaz", "Hospital Universitario General De La Palma", "Hospital Universitario Hm Madrid", "Hospital Universitario Hm Monteprincipe", "Hospital Universitario Hm Puerta Del Sur", "Hospital Universitario Hm Sanchinarro", "Hospital Universitario Hm Torrelodones", "Hospital Universitario Hospiten Bellevue", "Hospital Universitario Hospiten Rambla", "Hospital Universitario Hospiten Sur", "Hospital Universitario Infanta Cristina", "Hospital Universitario Infanta Elena", "Hospital Universitario Infanta Leonor", "Hospital Universitario Infanta Sofia", "Hospital Universitario Jose Germain", "Hospital Universitario Juan Ramon Jimenez", "Hospital Universitario Juan Ramón Jiménez", "Hospital Universitario La Moraleja", "Hospital Universitario La Paz", "Hospital Universitario La Zarzuela", "Hospital Universitario Marques De Valdecilla", "Hospital Universitario Miguel Servet", "Hospital Universitario Nuestra Señora De Candelaria", "Hospital Universitario Nuestra Señora Del Perpetuo Socorro", "Hospital Universitario Principe De Asturias", "Hospital Universitario Puerta De Hierro Majadahonda", "Hospital Universitario Puerta Del Mar", "Hospital Universitario Quironsalud Madrid", "Hospital Universitario Ramon Y Cajal", "Hospital Universitario Regional De Malaga", "Hospital Universitario Regional De Málaga", "Hospital Universitario Reina Sofia", "Hospital Universitario Reina Sofía", "Hospital Universitario Rio Hortega", "Hospital Universitario San Agustin", "Hospital Universitario San Jorge", "Hospital Universitario San Juan De Alicante", "Hospital Universitario San Pedro", "Hospital Universitario San Roque Las Palmas", "Hospital Universitario San Roque Maspalomas", "Hospital Universitario Santa Cristina", "Hospital Universitario Severo Ochoa", "Hospital Universitario Torrecardenas", "Hospital Universitario Torrecárdenas", "Hospital Universitario Vinalopo", "Hospital Universitario Virgen De La Victoria", "Hospital Universitario Virgen De Las Nieves", "Hospital Universitario Virgen De Valme", "Hospital Universitario Virgen Del Rocio", "Hospital Universitario Virgen Del Rocío", "Hospital Universitario Virgen Macarena", "Hospital Universitario Vithas Las Palmas", "Hospital Universitario Y Politecnico La Fe", "Hospital Urduliz Ospitalea", "Hospital Valle De Guadalhorce De Cartama", "Hospital Valle De Laciana", "Hospital Valle De Los Pedroches", "Hospital Valle Del Nalon", "Hospital Vazquez Diaz", "Hospital Vega Baja De Orihuela", "Hospital Viamed Bahia De Cadiz", "Hospital Viamed Montecanal", "Hospital Viamed Novo Sancti Petri", "Hospital Viamed San Jose", "Hospital Viamed Santa Angela De La Cruz", "Hospital Viamed Santa Elena, S.L", "Hospital Viamed Santiago", "Hospital Viamed Tarragona", "Hospital Victoria Eugenia De La Cruz Roja Española", "Hospital Virgen De Altagracia", "Hospital Virgen De La Bella", "Hospital Virgen De La Concha Complejo Asistencial De Zamora", "Hospital Virgen De La Luz", "Hospital Virgen De La Torre", "Hospital Virgen De Las Montañas", "Hospital Virgen De Los Lirios", "Hospital Virgen Del Alcazar De Lorca", "Hospital Virgen Del Camino", "Hospital Virgen Del Castillo", "Hospital Virgen Del Mar", "Hospital Virgen Del Miron ,Complejo Asistencial De Soria", "Hospital Virgen Del Puerto", "Hospital Vital Alvarez Buylla", "Hospital Vithas Castellon", "Hospital Vithas Granada", "Hospital Vithas Parque San Antonio", "Hospital Vithas Sevilla", "Hospital Vithas Valencia Consuelo", "Hospital Vithas Vitoria", "Hospital Vithas Xanit Estepona", "Hospital Vithas Xanit Internacional", "Hospiten Clinica Roca San Agustin", "Hospiten Lanzarote", "Idcsalud Mostoles Sa", "Imed Valencia", "Institut Catala D'Oncologia - Hospital Duran I Reynals", "Institut Catala D'Oncologia - Hospital Germans Trias I Pujol", "Institut Catala D'Oncologia Girona - Hospital Josep Trueta", "Institut Guttmann", "Institut Pere Mata, S.A", "Instituto De Enfermedades Neurologicas De Castilla-La Mancha", "Instituto De Salud Carlos Iii - Centro Nacional De Microbiologia", "Instituto De Traumatologia De Union De Mutuas (Matepss Nº 267)", "Instituto Oftalmologico Fernandez-Vega", "Instituto Provincial De Rehabilitacion", "Instituto Psiquiátrico Servicios De Salud Mental José Germain", "Instituto Tecnológico y de Energías Renovables, S.A. (ITER, S.A.)", "Ita Canet", "Ita Clinic Bcn", "Ita Godella", "Ita Maresme", "Ivan Mañero Clinic", "Juaneda Miramar", "Lab Clínic ICS Camp de Tarragona-Terres de l'Ebre. Hospital Joan XXIII", "Laboratori De Referencia De Catalunya", "Laboratorio Echevarne, Sa", "Lepant Residencial Qgg, Sl", "Microbiología HUC San Cecilio", "Microbiología. Hospital Universitario Virgen del Rocio", "Ministerio Sanidad", "Mutua Balear", "Mutua De Granollers, Mutua De Previsio Social A Prima Fixa", "Mutualia Clinica Pakea", "Nou Hospital Evangelic", "Organizacion Sanitaria Integrada Debagoiena", "Parc Sanitari Sant Joan De Deu - Numancia", "Parc Sanitari Sant Joan De Deu - Recinte Sant Boi.", "Parc Sanitari Sant Joan De Deu - Til·Lers", "Parc Sanitari Sant Joan De Deu - Uhpp - 1", "Parc Sanitari Sant Joan De Deu - Uhpp - 2", "Pius Hospital De Valls", "Plataforma de Genómica y Bioinformática", "Plataforma de Medicina Computacional, Fundación Progreso y Salud", "Policlinica Comarcal Del Vendrell.", "Policlinica Gipuzkoa", "Policlinica Nuestra Sra. Del Rosario", "Policlinico Riojano Nuestra Señora De Valvanera", "Presidencia del Gobierno", "Prytanis Hospitalet Centre Sociosanitari", "Prytanis Sant Boi Centre Sociosanitari", "Quinta Medica De Reposo", "Red De Salud Mental De Araba (Hospital Psiquiatrico De Araba)", "Residencia Alt Camp", "Residencia De Gent Gran Puig D'En Roca", "Residencia De Salud Mental Nuestra Se?Ora Del Carmen", "Residencia Geriatrica Maria Gay", "Residencia L'Estada", "Residencia Puig-Reig", "Residencia Santa Susanna", "Residencia Santa Tecla Ponent", "Residencia Terraferma", "Residencia Vila-Seca", "Ribera Hospital De Molina", "Ronda De Dalt, Centre Sociosanitari", "Sanatorio Bilbaino", "Sanatorio Dr. Muñoz", "Sanatorio Esquerdo, S.A.", "Sanatorio Nuestra Señora Del Rosario", "Sanatorio Sagrado Corazon", "Sanatorio San Francisco De Borja Fontilles", "Sanatorio Usurbil, S. L.", "Santo Y Real Hospital De Caridad", "Sar Mont Marti", "Serveis Clinics, S.A.", "Servicio Madrileño De Salud", "Servicio de Microbiologia HU Son Espases", "Servicios Sanitarios Y Asistenciales", "U.R.R. De Enfermos Psiquicos Alcohete", "Unidad De Rehabilitacion De Larga Estancia", "Unidad Rehabilitadora De Media Estancia Profesor Rey Ardid", "Unidades Clinicas Y De Rehabilitacion De Salud Mental", "Unitat Polivalent Benito Menni En Salut Mental De L'Hospitalet-El Prat De Llobregat", "Unitat Polivalent En Salut Mental D'Amposta", "Unitat Polivalent Salut Mental Barcelona-Nord", "Unitat Terapeutica-Educativa Acompanya'M", "Villablanca Serveis Assistencials, Sa", "Vithas Hospital Montserrat", "Vithas Hospital Nosa Señora De Fatima", "Vithas Hospital Perpetuo Internacional", "Vithas Hospital Santa Cruz" ], "examples": [ "Instituto de Salud Carlos III " ], "ontology": "GENEPIO:0100416", "type": "string", "description": "The name of the agency that generated the sequence", "classification": "Sequencing", "label": "Sequencing Institution", "fill_mode": "sample", "header": "Y" }, "sample_collection_date": { "examples": [ "2021-04-13" ], "ontology": "SNOMED:399445004", "type": "string", "format": "date", "description": "The date on which the sample was collected. YYYY-MM-DD", "classification": "Sample collection and processing", "label": "Sample Collection Date", "fill_mode": "sample", "header": "Y" }, "sample_received_date": { "examples": [ "2021-05-13" ], "ontology": "SNOMED:281271004", "type": "string", "format": "date", "description": "The date on which the sample was received. YYYY-MM-DD", "classification": "Sample collection and processing", "label": "Sample Received Date", "fill_mode": "sample", "header": "Y" }, "purpose_sampling": { "enum": [ "Cluster/Outbreak Investigation [GENEPIO:0100001]", "Diagnostic Testing [GENEPIO:0100002]", "Research [LOINC:LP173021-9]", "Protocol Testing [GENEPIO:0100024]", "Surveillance [GENEPIO:0100004]", "Other [NCIT:C124261]", "Not Collected [LOINC:LA4700-6]", "Not Applicable [SNOMED:385432009]", "Missing [LOINC:LA14698-7]", "Not Provided [SNOMED:434941000124101]" ], "examples": [ "Surveillance" ], "ontology": "GENEPIO:0001198", "type": "string", "description": "The reason that the sample was collected.", "classification": "Sample collection and processing", "label": "Purpose of sampling", "fill_mode": "batch", "header": "Y" }, "sample_storage_conditions": { "examples": [ "-80ºC" ], "ontology": "NCIT:C115535", "type": "string", "description": "Conditions under which the sample is stored", "classification": "Sample collection and processing", "label": "Biological Sample Storage Condition", "fill_mode": "batch", "header": "Y" }, "specimen_source": { "enum": [ "Specimen from abscess [SNOMED:119371008]", "Specimen from intra-abdominal abscess [SNOMED:16211211000119102]", "Fluid specimen from Bartholin gland cyst [SNOMED:446128003]", "Specimen from abscess of brain [SNOMED:446774006]", "Specimen from head and neck structure [SNOMED:430220009]", "Specimen of neck abscess [SNOMED:1023721000122100]", "Fluid specimen from epidural space [SNOMED:444965000]", "Specimen from abscess of liver [SNOMED:446674003]", "Specimen from breast [SNOMED:127456000]", "Specimen from abscess of tooth [SNOMED:29021000087108]", "Oropharyngeal aspirate [SNOMED:258412000]", "Soft tissue specimen [SNOMED:309072003]", "Specimen from abscess of lung [SNOMED:29011000087100]", "Specimen of fluid from cyst of kidney [SNOMED:16220971000119101]", "Specimen from a subphrenic abscess [SNOMED:75981000122101]", "Nucleic acid specimen [SNOMED:448789008]", "Water specimen [SNOMED:119318008]", "Air specimen [SNOMED:446302006]", "Specimen obtained by bronchial aspiration [SNOMED:441903006]", "Gastric aspirate specimen [SNOMED:168137004]", "Specimen from nasopharyngeal structure [SNOMED:430248009]", "Nasopharyngeal aspirate [SNOMED:258411007]", "Specimen from endotracheal tube [SNOMED:119307008]", "Bile specimen [SNOMED:119341000]", "Articular tissue specimen [SNOMED:309126004]", "Specimen from brain obtained by biopsy [SNOMED:432139004]", "Skin biopsy specimen [SNOMED:309066003]", "Mouth biopsy specimen [SNOMED:309188000]", "Tissue specimen from uterine cervix [SNOMED:127481002]", "Duodenal biopsy specimen [SNOMED:309216003]", "Specimen from endometrium obtained by biopsy [SNOMED:122704003]", "Specimen from intervertebral disc [SNOMED:438960000]", "Specimen obtained from skin of the scapular region biopsy [SNOMED:76011000122104]", "Esophageal biopsy specimen [SNOMED:309209004]", "Fascia biopsy specimen [SNOMED:309118007]", "Lymph node biopsy specimen [SNOMED:309079007]", "Gastric biopsy specimen [SNOMED:309211008]", "Liver biopsy specimen [SNOMED:309203003]", "Tissue specimen from gastrointestinal tract [SNOMED:127466008]", "Tissue specimen from large intestine [SNOMED:122643008]", "Muscle biopsy specimen [SNOMED:309507001]", "Soft tissue biopsy specimen [SNOMED:309074002]", "Specimen from pericardium obtained by biopsy [SNOMED:434250007]", "Pleura biopsy specimen [SNOMED:309172000]", "Specimen from lung obtained by biopsy [SNOMED:122610009]", "Prostate biopsy specimen [SNOMED:309132009]", "Rectal biopsy specimen [SNOMED:309262006]", "Synovium biopsy specimen [SNOMED:309122002]", "Tendon biopsy specimen [SNOMED:309113003]", "Tissue specimen from small intestine [SNOMED:122638001]", "Erythrocyte specimen from blood product [SNOMED:122582004]", "Platelet specimen [SNOMED:119358005]", "Specimen from plasma bag [SNOMED:119305000]", "Specimen from blood bag [SNOMED:119304001]", "Specimen from bronchoscope [SNOMED:76081000122109]", "Gallstone specimen [SNOMED:258492001]", "Renal stone specimen [SNOMED:258495004]", "Specimen of implantable venous access port [SNOMED:76091000122107]", "Catheter tip submitted as specimen [SNOMED:119312009]", "Calculus specimen [SNOMED:119350003]", "Bronchial brushings specimen [SNOMED:309176002]", "Scotch tape slide specimen [SNOMED:258664003]", "Specimen of cystoscope [SNOMED:76031000122108]", "Blood clot specimen [SNOMED:258582006]", "Serum specimen from blood product [SNOMED:122591000]", "Specimen of a sent Colonoscope [SNOMED:76041000122100]", "Specimen from cornea [SNOMED:119400006]", "Conjunctival swab [SNOMED:258498002]", "Intrauterine contraceptive device submitted as specimen [SNOMED:473415003]", "Abdominal cavity fluid specimen [SNOMED:8761000122107]", "Body fluid specimen obtained via chest tube [SNOMED:447375004]", "Specimen of a sent duodenoscope [SNOMED:76051000122103]", "Swab of endocervix [SNOMED:444787003]", "Specimen of a sent endoscope [SNOMED:76061000122101]", "Coughed sputum specimen [SNOMED:119335007]", "Sputum specimen obtained by sputum induction [SNOMED:258610001]", "Drainage fluid specimen [SNOMED:258455001]", "Specimen from endometrium [SNOMED:119396006]", "Glans penis swab [SNOMED:258512002]", "Specimen from mediastinum [SNOMED:433326001]", "Ear swab specimen [SNOMED:309166000]", "Middle ear fluid specimen [SNOMED:258466008]", "Swab from gastrostomy stoma [SNOMED:472886009]", "Specimen of diabetic foot ulcer exudate [SNOMED:75991000122103]", "Swab from external stoma wound [SNOMED:29001000087102]", "Swab from tracheostomy wound [SNOMED:472870002]", "Specimen obtained by swabbing ureterostomy wound [SNOMED:1023731000122102]", "Specimen obtained by vesicostomy wound swabbing [SNOMED:1023741000122105]", "specimen obtained by colostomy wound swabbing [SNOMED:1023751000122107]", "Specimen obtained by swabbing ileostomy wound[SNOMED:1023761000122109]", "Swab of umbilicus [SNOMED:445367006]", "Swab from placenta [SNOMED:472879001]", "Urethral swab [SNOMED:258530009]", "Vaginal swab [SNOMED:258520000]", "Rectal swab [SNOMED:258528007]", "Oropharyngeal swab [SNOMED:461911000124106]", "Skin swab [SNOMED:258503004]", "Swab from tonsil [SNOMED:472867001]", "Specimen from graft [SNOMED:29031000087105]", "Swab from larynx [SNOMED:472888005]", "Swab of internal nose [SNOMED:445297001]", "Nasopharyngeal swab [SNOMED:258500001]", "Swab of vascular catheter insertion site [SNOMED:735950000]", "Vulval swab [SNOMED:258523003]", "Specimen of sent gastroscope [SNOMED:76071000122106]", "Stool specimen [SNOMED:119339001]", "Hematoma specimen [SNOMED:258588005]", "Blood specimen obtained for blood culture [SNOMED:446131002]", "Specimen from surgical wound [SNOMED:734380008]", "Specimen from bone [SNOMED: 430268003]", "Aqueous humor specimen [SNOMED:258444001]", "Vitreous humor specimen [SNOMED:258438000]", "Graft specimen from patient [SNOMED:440493002]", "Allogeneic bone graft material submitted as specimen [SNOMED:33631000087102]", "Bronchoalveolar lavage fluid specimen [SNOMED:258607008]", "Specimen of bone graft obtained through lavage [SNOMED:1023771000122104]", "Mediastinal specimen obtained by lavage [SNOMED:76021000122105]", "Nasopharyngeal washings [SNOMED:258467004]", "Breast fluid specimen [SNOMED:309055005]", "Contact lens submitted as specimen [SNOMED:440473005]", "Intraocular lens specimen [SNOMED:258602002]", "Leukocyte specimen from patient [SNOMED:122584003]", "Lymphocyte specimen [SNOMED:119353001]", "Fluid specimen [SNOMED:258442002]", "Amniotic fluid specimen [SNOMED:119373006]", "Joint fluid specimen [SNOMED:431361003]", "Peritoneal fluid specimen [SNOMED:168139001]", "Cerebrospinal fluid specimen obtained via ventriculoperitoneal shunt [SNOMED:446861007]", "Cerebrospinal fluid specimen [SNOMED:258450006]", "Pericardial fluid specimen [SNOMED:122571007]", "Pleural fluid specimen [SNOMED:418564007]", "Cyst fluid specimen [SNOMED:258453008]", "Genital lochia specimen [SNOMED:122579009]", "Device submitted as specimen [SNOMED:472919007]", "Meconium specimen [SNOMED:119340004]", "Bone marrow specimen [SNOMED:119359002]", "Tissue specimen from amniotic membrane [SNOMED:446837000]", "Microbial isolate [SNOMED:119303007]", "Specimen from environment [SNOMED:440229008]", "Intravenous lipid infusion fluid specimen [SNOMED:258650003]", "Urine specimen obtained by single catheterization of urinary bladder [SNOMED:447589008]", "Urine specimen obtained from urinary collection bag [SNOMED:446306009]", "Urine specimen [SNOMED:122575003]", "Mid-stream urine specimen [SNOMED:258574006]", "Urine specimen from nephrostomy tube [SNOMED:442173007]", "Urine specimen obtained via indwelling urinary catheter [SNOMED:446846006]", "Postejaculation urine specimen [SNOMED:445743000]", "Urine specimen obtained from kidney [SNOMED:446907008]", "Suprapubic urine specimen [SNOMED:447488002]", "Parasite specimen [SNOMED:258617003]", "Hair specimen [SNOMED:119326000]", "Tissue specimen from placenta [SNOMED:122736005]", "Specimen from prosthetic device [SNOMED:438660002]", "Cardiac pacemaker lead submitted as specimen [SNOMED:473417006]", "Specimen of sent vascular catheter puncture [SNOMED:8561000122101]", "Peritoneal catheter submitted as specimen [SNOMED:472944004]", "Intracranial ventricular catheter submitted as specimen [SNOMED:472940008]", "Corneal scraping specimen [SNOMED:258485006]", "Serum specimen [SNOMED:119364003]", "Prostatic fluid specimen [SNOMED:258470000]", "Seminal fluid specimen [SNOMED:119347001]", "Specimen from nasal sinus [SNOMED:430238007]", "Pharmaceutical product submitted as specimen [SNOMED:446137003]", "Surface swab [SNOMED:258537007]", "Skin ulcer swab [SNOMED:258505006]", "Specimen obtained from genital ulcer [SNOMED:76001000122102 ]", "Nail specimen [SNOMED:119327009]", "Heart valve specimen [SNOMED:258542004]", "Native heart valve specimen [SNOMED:258544003]", "Specimen from prosthetic heart valve [SNOMED:1003714002]", "Vegetation from heart valve [SNOMED:258437005]", "Skin cyst specimen [SNOMED:309075001]", "Cardiac pacemaker submitted as specimen [SNOMED:33491000087103]", "Blood specimen [SNOMED: 119297000]", "Plasma specimen [SNOMED:119361006]", "Biopsy specimen [SNOMED:258415003]", "Peritoneal dialysate specimen [SNOMED:168140004]", "Dialysate specimen [SNOMED:258454002]", "Not Collected [LOINC:LA4700-6]", "Not Applicable [SNOMED:385432009]", "Missing [LOINC:LA14698-7]", "Not Provided [SNOMED:434941000124101]" ], "examples": [ "Nasopharynx exudate" ], "ontology": "SNOMED:703065002", "type": "string", "description": "Source of the specimen, merge of anatomical_part, anatomical_material, body_product and collection method.", "classification": "Sample collection and processing", "label": "Specimen source", "fill_mode": "batch", "header": "Y" }, "environmental_material": { "enum": [ "Air vent [ENVO:03501208]", "Banknote [ENVO:00003896]", "Bed rail [ENVO:03501209]", "Building Floor [SNOMED:258535004]", "Cloth [SNOMED:81293006]", "Control Panel [ENVO:03501210]", "Door [SNOMED:224751004]", "Door Handle [ENVO:03501211]", "Face Mask [SNOMED:261352009]", "Face Shield [SNOMED:706724001]", "Food [SNOMED:255620007]", "Food Packaging [MeSH:D018857]", "Glass [SNOMED:32039001]", "Handrail [ENVO:03501212]", "Hospital Gown [OBI:0002796]", "Light Switch [ENVO:03501213]", "Locker [ENVO:03501214]", "N95 Mask [OBI:0002790]", "Nurse Call Button [ENVO:03501215]", "Paper [LOINC:LA26662-9]", "Particulate matter [ENVO:01000060]", "Plastic [SNOMED:61088005]", "PPE Gown [GENEPIO:0100025]", "Sewage [SNOMED:224939005]", "Sink [SNOMED:705607007]", "Soil [SNOMED:415555003]", "Stainless Steel material [SNOMED:256506002]", "Tissue Paper [ENVO:03501217]", "Toilet Bowl [ENVO:03501218]", "Water [SNOMED:11713004]", "Wastewater [ENVO:00002001]", "Window [SNOMED:224755008]", "Wood [SNOMED:14402002]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Food isolate" ], "ontology": "GENEPIO:0001223", "type": "string", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", "classification": "Sample collection and processing", "label": "Environmental Material", "fill_mode": "batch", "header": "Y" }, "environmental_system": { "enum": [ "Acute care facility [ENVO:03501135]", "Animal house [ENVO:00003040]", "Bathroom [SNOMED:223359008]", "Clinical assessment centre [ENVO:03501136]", "Conference venue [ENVO:03501127]", "Corridor [SNOMED:224720006]", "Daycare [LOINC:LA26176-0]", "Emergency room (ER) [LOINC:LA7172-]", "Family practice clinic [ENVO:03501186]", "Group home [ENVO:03501196]", "Homeless shelter [NCIT:C204034]", "Hospital [SNOMED:22232009]", "Intensive Care Unit (ICU) [ENVO:03501152]", "Long Term Care Facility [LOINC:LP173046-6]", "Patient room [SNOMED:462598009]", "Prison [LOINC:LA18820-3]", "Production Facility [SNOMED:257605002]", "School [SNOMED:257698009]", "Sewage Plant [ENVO:00003043]", "Subway train [ENVO:03501109]", "Wet market [ENVO:03501198]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Earth surface" ], "ontology": "GENEPIO:0001232", "type": "string", "description": "A data field which describes an environmental location as a site in the natural or built environment.", "classification": "Sample collection and processing", "label": "Environmental System", "fill_mode": "batch", "header": "Y" }, "collection_device": { "enum": [ "Air filter [SNOMED:972002]", "Blood Collection Tube [NCIT:C113122]", "Bronchoscope [SNOMED:706028009]", "Collection Container [NCIT:C43446] [NCIT:C43446]", "Collection Cup [GENEPIO:0100026] [GENEPIO:0100026]", "Filter [SNOMED:116250002]", "Needle [SNOMED:79068005]", "Serum Collection Tube [NCIT:C113675]", "Sputum Collection Tube [GENEPIO:0002115]", "Suction Catheter [SNOMED:58253008]", "Swab [SNOMED:257261003]", "Other [NCIT:C17649]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Swab" ], "ontology": "GENEPIO:0001234", "type": "string", "description": "A data field which describes the instrument or container used to collect the sample. ", "classification": "Sample collection and processing", "label": "Collection Device", "fill_mode": "batch", "header": "Y" }, "host_common_name": { "enum": [ "Human [LOINC:LA19711-3]", "Bat [LOINC:LA31034-4]", "Cat [SNOMED:257528009]", "Chicken [SNOMED:2022008]", "Civet [SNOMED:75427002]", "Cow [LOINC:LA31041-9]", "Dog [LOINC:LA14178-0]", "Lion [SNOMED:112507006]", "Mink [SNOMED:57418000]", "Pangolin [SNOMED:106948007]", "Pig [LOINC:LA31036-9]", "Pigeon [LOINC:LP31646-0]", "Tiger [SNOMED:79047009]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Human" ], "ontology": "GENEPIO:0001386", "type": "string", "description": "The commonly used name of the host.", "classification": "Host information", "label": "Host", "fill_mode": "batch", "header": "Y" }, "host_age_years": { "examples": [ "55" ], "ontology": "SNOMED:424144002", "type": "integer", "minimum": 3, "maximum": 120, "description": "Age of host at the time of sampling. Age between 3 and 110 years old. Recommended", "classification": "Host information", "label": "Host Age Years", "fill_mode": "sample", "header": "Y" }, "host_age_months": { "examples": [ "14" ], "ontology": "LOINC:LA33639-8", "type": "integer", "minimum": 0, "maximum": 36, "description": "ONLY when [Host Age years] < 3. Age of host at the time of sampling. If the age is less than three years indicate in months between 0 and 36. Recommended", "classification": "Host information", "label": "Host Age Months", "fill_mode": "sample", "header": "Y" }, "host_gender": { "enum": [ "Female [LOINC:LA3-6]", "Male [LOINC:LA2-8]", "Non-binary Gender [SNOMED:772004004]", "Transgender (assigned male at birth) [GSSO:004004]", "Transgender (assigned female at birth) [GSSO:004005]", "Undeclared [GSSO:000131]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Female" ], "ontology": "SNOMED:263495000", "type": "string", "description": "The gender of the host at the time of sample collection. Recomended", "classification": "Host information", "label": "Host Gender", "fill_mode": "sample", "header": "Y" }, "vaccinated": { "enum": [ "Yes [SNOMED:373066001]", "No [SNOMED:373067005]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Yes" ], "ontology": "NCIT:C28385", "type": "string", "description": "A status indicating that an individual has received a vaccination.", "classification": "Host information", "label": "Vaccinated", "fill_mode": "sample", "header": "Y" }, "medicated": { "enum": [ "Yes [SNOMED:373066001]", "No [SNOMED:373067005]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Yes" ], "ontology": "SNOMED:18629005", "type": "string", "description": "Has received medication for the identified treatment or prophylaxis", "classification": "Host information", "label": "Specific medication for treatment or prophylaxis", "fill_mode": "sample", "header": "Y" }, "hospitalized": { "enum": [ "Yes [SNOMED:373066001]", "No [SNOMED:373067005]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Yes" ], "ontology": "LOINC:LA15417-1", "type": "string", "description": "Whether the patient was admitted to a hospital", "classification": "Host information", "label": "Hospitalization", "fill_mode": "sample", "header": "Y" }, "icu_admission": { "enum": [ "Yes [SNOMED:373066001]", "No [SNOMED:373067005]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Yes" ], "ontology": "SNOMED:305351004", "type": "string", "description": "Whether the patient required ICU care during the illness.", "classification": "Host information", "label": "Admission to intensive care unit", "fill_mode": "sample", "header": "Y" }, "death": { "enum": [ "Yes [SNOMED:373066001]", "No [SNOMED:373067005]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "No" ], "ontology": "LOINC:LA7424-0", "type": "string", "description": "Whether the patient died as a result of the infection.", "classification": "Host information", "label": "Death", "fill_mode": "sample", "header": "Y" }, "immunosuppressed": { "enum": [ "Yes [SNOMED:373066001]", "No [SNOMED:373067005]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "No" ], "ontology": "SNOMED:38013005", "type": "string", "description": "Whether the patient has a weakened immune system.", "classification": "Host information", "label": "Immunosuppression", "fill_mode": "sample", "header": "Y" }, "sequencing_date": { "examples": [ "2022-02-22" ], "ontology": "GENEPIO:0001447", "type": "string", "format": "date", "description": "The date the sample was sequenced. YYYY-MM-DD", "classification": "Sequencing", "label": "Sequencing Date", "fill_mode": "batch", "header": "Y" }, "nucleic_acid_extraction_protocol": { "examples": [ "RT-PCR" ], "ontology": "OBI_0302884", "type": "string", "description": "DNA/RNA extraction protocol", "classification": "Sequencing", "label": "Nucleic acid extraction protocol", "fill_mode": "batch", "header": "Y" }, "all_in_one_library_kit": { "enum": [ "Ion Xpress", "ABL_DeepChek NGS", "Ion AmpliSeq Kit for Chef DL8", "NEBNext Fast DNA Library Prep Set for Ion Torrent", "NEBNext ARTIC SARS-CoV-2 FS", "Illumina COVIDSeq Test [CIDO:0020172]", "Illumina COVIDSeq Assay", "ABL DeepChek® Assay WG SC2 V1", "ABL DeepChek® Assay WG SC2 V4", "Not Provided [SNOMED:434941000124101]", "Other [NCIT:C17649]" ], "examples": [ "Ion Xpress" ], "ontology": "GENEPIO:0000085", "type": "string", "description": "Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids.", "classification": "Sequencing", "label": "Commercial All-in-one library kit", "fill_mode": "batch", "header": "Y" }, "library_preparation_kit": { "enum": [ "Illumina DNA PCR-Free Prep", "Illumina DNA Prep", "Illumina FFPE DNA Prep", "Illumina Stranded mRNA Prep", "Nextera XT DNA Library Preparation Kit", "TrueSeq ChIP Library Preparation Kit", "TruSeq DNA Nano", "TruSeq DNA Nano Library Prep Kit for NeoPrep", "TruSeq DNA PCR-Free", "TruSeq RNA Library Prep Kit v2", "TruSeq Stranded Total RNA", "TruSeq Stranded mRNA", "Nextera XT", "NEBNex Fast DNA Library Prep Set for Ion Torrent", "Nextera DNA Flex", "Ion AmpliSeq Kit Library Kit Plus", "Ion AmpliSeq Library Kit 2.0", "Ion Xpress Plus Fragment Library Kit", "Oxford Nanopore Sequencing Kit", "SQK-RBK110-96", "SQK-RBK114-96", "Nanopore COVID Maxi: 9216 samples", "Nanopore COVID Midi: 2304 samples", "Nanopore COVID Mini: 576 samples", "Vela Diagnostics:ViroKey SQ FLEX Library Prep Reagents", "Not Provided [SNOMED:434941000124101]", "Other [NCIT:C17649]" ], "examples": [ "Illumina DNA Prep Tagmentation" ], "ontology": "NCIT:C182085", "type": "string", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "classification": "Sequencing", "label": "Library Preparation Kit", "fill_mode": "batch", "header": "Y" }, "enrichment_protocol": { "enum": [ "Amplicon [GENEPIO:0001974]", "Probes [OMIT:0016121]", "Custom probes [OMIT:0016112]", "Custom amplicon [OMIT:0016112]", "No enrichment [NCIT:C154307]", "Other [NCIT:C17649]", "Not Provided [SNOMED:434941000124101]" ], "examples": [ "Amplicon" ], "ontology": "EFO_0009089", "type": "string", "description": "Type of enrichment protocol", "classification": "Sequencing", "label": "Enrichment Protocol", "fill_mode": "batch", "header": "Y" }, "if_enrichment_protocol_is_other_specify": { "examples": [ "Ultracentrifugation-based viral particle enrichment" ], "ontology": "0", "type": "string", "description": "Specify if you have used another enrichment protocol", "classification": "Sequencing", "label": "If Enrichment Protocol Is Other, Specify", "fill_mode": "batch", "header": "Y" }, "enrichment_panel": { "enum": [ "ARTIC", "Exome 2.5", "Illumina respiratory Virus Oligo Panel", "Illumina AmpliSeq Community panel", "Illumina AmpliSeq SARS-CoV-2 Research Panel for Illumina", "Ion AmpliSeq SARS-CoV-2 Research Panel", "xGen SC2 Midnight1200 Amplicon Panel", "ViroKey SQ FLEX SARS-CoV-2 Primer Set", "NEBNext VarSkip Short SARS-CoV-2 primers", "Illumina Microbial Amplicon Prep-Influenza A/B", "Illumina Respiratory Pathogen ID/AMR Enrichment Panel", "Illumina Viral Surveillance Panel v2", "Twist Bioscience Respiratory Virus Research Panel", "Other [NCIT:C17649]" ], "examples": [ "ARTIC" ], "ontology": "NGBO:6000323", "type": "string", "description": "Commercial or custom panel/assay used for enrichment.", "classification": "Sequencing", "label": "Enrichment panel/assay", "fill_mode": "batch", "header": "Y" }, "if_enrichment_panel_assay_is_other_specify": { "examples": [ "Swift Normalase Amplicon SARS-CoV-2 Panel" ], "ontology": "0", "type": "string", "description": "Specify if you have used another enrichment panel/assay", "classification": "Sequencing", "label": "If Enrichment panel/assay Is Other, Specify", "fill_mode": "batch", "header": "Y" }, "enrichment_panel_version": { "enum": [ "ARTIC v1", "ARTIC v2", "ARTIC v3", "ARTIC v4", "ARTIC v4.1", "ARTIC v5", "ARTIC v5.1", "ARTIC v5.2", "ARTIC v5.3", "ARTIC v5.3.2", "Illumina AmpliSeq Community panel", "Illumina AmpliSeq SARS-CoV-2 Research Panel for Illumina", "Illumina Respiratory Virus Oligos Panel V1", "Illumina Respiratory Virus Oligos Panel V2", "Ion AmpliSeq SARS-CoV-2 Insight", "xGen SC2 Midnight1200 Amplicon Panel", "Midnight Amplicon Panel v2", "ViroKey SQ FLEX SARS-CoV-2 Primer Set", "NEBNext VarSkip Short SARS-CoV-2 primers", "Illumina Viral Surveillance Panel v2", "Other [NCIT:C17649]" ], "examples": [ "ARTIC v4" ], "ontology": "0", "type": "string", "description": "Version fo the enrichment panel", "classification": "Sequencing", "label": "Enrichment panel/assay version", "fill_mode": "batch", "header": "Y" }, "number_of_samples_in_run": { "examples": [ "96" ], "ontology": "KISAO_0000326", "type": "integer", "minimum": 1, "maximum": 10000, "description": "Total count of samples included in the sequencing run.", "classification": "Sequencing", "label": "Number Of Samples In Run", "fill_mode": "batch", "header": "Y" }, "runID": { "examples": [ "MiSeq_GEN_267_20220208_ICasas" ], "ontology": "NCIT:C117058", "type": "string", "description": "Unique sequencing run identifier.", "classification": "Sequencing", "label": "Runid", "fill_mode": "batch", "header": "Y" }, "sequencing_instrument_model": { "enum": [ "Illumina sequencing instrument [GENEPIO:0100105]", "Illumina Genome Analyzer [GENEPIO:0100106]", "Illumina Genome Analyzer II [OBI:0000703]", "Illumina Genome Analyzer IIx [OBI:0002000]", "Illumina HiScanSQ [GENEPIO:0100109]", "Illumina HiSeq [GENEPIO:0100110]", "Illumina HiSeq X [GENEPIO:0100111]", "Illumina HiSeq X Five [GENEPIO:0100112]", "Illumina HiSeq X Ten [GENEPIO:0100113]", "Illumina HiSeq 1000 [OBI:0002022]", "Illumina HiSeq 1500 [GENEPIO:0100115]", "Illumina HiSeq 2000 [OBI:0002001]", "Illumina HiSeq 2500 [OBI:0002002]", "Illumina HiSeq 3000 [OBI:0002048]", "Illumina HiSeq 4000 [OBI:0002049]", "Illumina iSeq [GENEPIO:0100120]", "Illumina iSeq 100 [GENEPIO:0100121]", "Illumina NovaSeq [GENEPIO:0100122]", "Illumina NovaSeq 6000 [GENEPIO:0100123]", "Illumina MiniSeq [GENEPIO:0100124]", "Illumina MiSeq [OBI:0002003]", "Illumina NextSeq [GENEPIO:0100126]", "Illumina NextSeq 500 [OBI:0002021]", "Illumina NextSeq 550 [GENEPIO:0100128]", "Illumina NextSeq 1000 [OBI:0003606]", "Illumina NextSeq 2000 [GENEPIO:0100129]", "Illumina NextSeq 6000", "Ion GeneStudio S5 Prime", "Ion GeneStudio S5 Plus", "Ion GeneStudio S5", "Ion Torrent sequencing instrument [GENEPIO:0100135]", "Ion Torrent Genexus", "Ion Torrent PGM [GENEPIO:0100136]", "Ion Torrent Proton [GENEPIO:0100137]", "Ion Torrent S5 [GENEPIO:0100139]", "Ion Torrent S5 XL [GENEPIO:0100138]", "MinION [GENEPIO:0100142]", "GridION [GENEPIO:0100141]", "PromethION [GENEPIO:0100143]", "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", "PacBio RS [GENEPIO:0100131]", "PacBio RS II [OBI:0002012]", "PacBio Sequel [GENEPIO:0100133]", "PacBio Sequel II [GENEPIO:0100134]", "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", "Oxford Nanopore GridION [GENEPIO:0100141]", "Oxford Nanopore MinION [GENEPIO:0100142]", "Oxford Nanopore PromethION [GENEPIO:0100143]", "AB 310 Genetic Analyzer", "AB 3130 Genetic Analyzer", "AB 3130xL Genetic Analyzer", "AB 3500 Genetic Analyzer", "AB 3500xL Genetic Analyzer", "AB 3730 Genetic Analyzer", "AB 3730xL Genetic Analyzer", "AB SOLID System [OBI:0000696]", "AB SOLID System 2.0 [EFO:0004442]", "AB SOLID System 3.0 [EFO:0004439]", "AB SOLID 3 Plus System [OBI:0002007]", "AB SOLID 4 System [EFO:0004438]", "AB SOLID 4hq System [AB SOLID 4hq System]", "AB SOLID PI System [EFO:0004437]", "AB. 5500 Genetic Analyzer", "AB 5500xl Genetic Analyzer", "AB 5500xl-W Genetic Analysis System", "BGI Genomics sequencing instrument [GENEPIO:0100144]", "BGISEQ-500 [GENEPIO:0100145]", "BGISEQ-50", "DNBSEQ-T7 [GENEPIO:0100147]", "DNBSEQ-G400 [GENEPIO:0100148]", "DNBSEQ-G400 FAST [GENEPIO:0100149]", "MGI sequencing instrument [GENEPIO:0100146]", "MGISEQ-2000RS", "MGI DNBSEQ-T7 [GENEPIO:0100147]", "MGI DNBSEQ-G400 [GENEPIO:0100148]", "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", "MGI DNBSEQ-G50 [GENEPIO:0100150]", "454 GS [EFO:0004431]", "454 GS 20 [EFO:0004206]", "454 GS FLX + [EFO:0004432]", "454 GS FLX Titanium [EFO:0004433]", "454 GS FLX Junior [GENEPIO:0001938]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Illumina NextSeq 550" ], "ontology": "GENEPIO:0001452", "type": "string", "description": "The model of the sequencing instrument used.", "classification": "Sequencing", "label": "Sequencing Instrument Model", "fill_mode": "batch", "header": "Y" }, "flowcell_kit": { "enum": [ "HiSeq 3000/4000 PE Cluster Kit", "HiSeq 3000/4000 SBS Kit (50 cycles)", "HiSeq 3000/4000 SBS Kit (150 cycles)", "HiSeq 3000/4000 SBS Kit (300 cycles)", "HiSeq 3000/4000 SBS Kit", "HiSeq 3000/4000 SR Cluster Kit", "TG HiSeq 3000/4000 SBS Kit (50 cycles)", "TG HiSeq 3000/4000 SBS Kit (150 cycles)", "TG HiSeq 3000/4000 SBS Kit (300 cycles)", "TG HiSeq 3000/4000 PE ClusterKit", "TG HiSeq 3000/4000 SR ClusterKit", "HiSeq PE Cluster Kit v4 cBot", "HiSeq SR Rapid Cluster Kit v2", "HiSeq PE Rapid Cluster Kit v2", "TG HiSeq Rapid PE Cluster Kit v2", "HiSeq Rapid Duo cBot Sample Loading Kit", "TG TruSeq Rapid Duo cBot Sample Loading Kit", "HiSeq Rapid SBS Kit v2 (50 cycles)", "HiSeq Rapid SBS Kit v2 (200 cycles)", "HiSeq Rapid SBS Kit v2 (500 cycles)", "TG HiSeq Rapid SBS Kit v2 (200 Cycle)", "TG HiSeq Rapid SBS Kit v2 (50 Cycle)", "HiSeq SR Cluster Kit v4 cBot", "TG HiSeq SR Cluster Kit v4 – cBot", "TG HiSeq PE Cluster Kit v4 – cBot", "HiSeq X Ten Reagent Kit v2.5", "HiSeq X Ten Reagent Kit v2.5 – 10 pack", "HiSeq X Five Reagent Kit v2.5", "MiSeq Reagent Kit v3 (150-cycle)", "MiSeq Reagent Kit v3 (600-cycle)", "TG MiSeq Reagent Kit v3 (600 cycle)", "TG MiSeq Reagent Kit v3 (150 cycle)", "MiSeq Reagent Kit v2 (50-cycles)", "MiSeq Reagent Kit v2 (300-cycles)", "MiSeq Reagent Kit v2 (500-cycles)", "MiniSeq Rapid Reagent Kit (100 cycles)", "MiniSeq High Output Reagent Kit (75-cycles)", "MiniSeq High Output Reagent Kit (150-cycles)", "NextSeq 1000/2000 P1 Reagents (300 Cycles)", "NextSeq 1000/2000 P2 Reagents (100 Cycles) v3", "NextSeq 1000/2000 P2 Reagents (200 Cycles) v3", "NextSeq 1000/2000 P2 Reagents (300 Cycles) v3", "NextSeq 2000 P3 Reagents (50 Cycles)", "NextSeq 2000 P3 Reagents (100 Cycles)", "NextSeq 2000 P3 Reagents (200 Cycles)", "NextSeq 2000 P3 Reagents (300 Cycles)", "NextSeq 1000/2000 Read and Index Primers", "NextSeq 1000/2000 Index Primer Kit", "NextSeq 1000/2000 Read Primer Kit", "NextSeq 500/550 High Output Kit v2.5 (75 Cycles)", "NextSeq 500/550 High Output Kit v2.5 (150 Cycles)", "NextSeq 500/550 High Output Kit v2.5 (300 Cycles)", "NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles)", "NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles)", "TG NextSeq 500/550 High Output Kit v2.5 (75 Cycles)", "TG NextSeq 500/550 High Output Kit v2.5 (150 Cycles)", "TG NextSeq 500/550 High Output Kit v2.5 (300 Cycles)", "TG NextSeq 500/550 Mid Output Kit v2.5 (150 Cycles)", "TG NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles)", "NovaSeq 6000 S4 Reagent Kit v1.5 (300 cycles)", "NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles)", "NovaSeq 6000 S4 Reagent Kit v1.5 (35 cycles)", "NovaSeq 6000 S2 Reagent Kit v1.5 (300 cycles)", "NovaSeq 6000 S2 Reagent Kit v1.5 (200 cycles)", "NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles)", "NovaSeq 6000 S1 Reagent Kit v1.5 (300 cycles)", "NovaSeq 6000 S1 Reagent Kit v1.5 (200 cycles)", "NovaSeq 6000 S1 Reagent Kit v1.5 (100 cycles)", "NovaSeq 6000 SP Reagent Kit v1.5 (500 cycles)", "NovaSeq 6000 SP Reagent Kit v1.5 (300 cycles)", "NovaSeq 6000 SP Reagent Kit v1.5 (200 cycles)", "NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles)", "NovaSeq 6000 SP Reagent Kit (100 cycles)", "NovaSeq 6000 SP Reagent Kit (200 cycles)", "NovaSeq 6000 SP Reagent Kit (300 cycles)", "NovaSeq 6000 SP Reagent Kit (500 cycles)", "NovaSeq 6000 S1 Reagent Kit (100 cycles)", "NovaSeq 6000 S1 Reagent Kit (200 cycles)", "NovaSeq 6000 S1 Reagent Kit (300 cycles)", "NovaSeq 6000 S2 Reagent Kit (100 cycles)", "NovaSeq 6000 S2 Reagent Kit (200 cycles)", "NovaSeq 6000 S2 Reagent Kit (300 cycles)", "NovaSeq 6000 S4 Reagent Kit (200 cycles)", "NovaSeq 6000 S4 Reagent Kit (300 cycles)", "NovaSeq 6000 S4 Reagent Kit (300 Cycles) – 10 pack", "NovaSeq 6000 S4 Reagent Kit (300 Cycles) – 20 pack", "NovaSeq 6000 S4 Reagent Kit (300 Cycles) – 40 pack", "NovaSeq Library Tubes Accessory Pack (24 tubes)", "NovaSeq XP 4-Lane Kit v1.5", "NovaSeq XP 2-Lane Kit v1.5", "NovaSeq XP 2-Lane Kit", "NovaSeq Xp 4-Lane Kit", "NovaSeq Xp Flow Cell Dock", "NovaSeq Xp 2-Lane Manifold Pack", "NovaSeq Xp 4-Lane Manifold Pack", "PhiX Control v3", "TG PhiX Control Kit v3", "NextSeq PhiX Control Kit", "Single-Read", "TruSeq Dual Index Sequencing Primer Box", "Paired-End", "TruSeq PE Cluster Kit v3-cBot-HS", "TruSeq PE Cluster Kit v5-CS-GA", "TruSeq SBS Kit v3-HS (200 cycles)", "TruSeq SBS Kit v3-HS (50 cycles)", "TG TruSeq SBS Kit v3 - HS (200-cycles)", "TruSeq SBS Kit v5-GA", "TruSeq SR Cluster Kit v3-cBot-HS", "TG TruSeq SR Cluster Kit v1-cBot – HS", "iSeq 100 i1 Reagent v2 (300-cycle)", "iSeq 100 i1 Reagent v2 (300-cycle) 4 pack", "iSeq 100 i1 Reagent v2 (300-cycle) 8 pack", "Ion 540 Chip Kit", "Not Provided [SNOMED:434941000124101]", "Other [NCIT:C17649]" ], "examples": [ "NextSeq 500/550 High Output Kit v2.5 (75 Cycles)" ], "ontology": "0", "type": "string", "description": "Flowcell sequencer used for sequencing the sample", "classification": "Sequencing", "label": "Flowcell Kit", "fill_mode": "batch", "header": "Y" }, "library_source": { "enum": [ "Genomic single cell [EDAM:4028]", "Transcriptomic [NCIT:C153189]", "Metagenomic [NCIT:C201925]", "Metatranscriptomic [NCIT:C201926]", "Synthetic [BAO:0003073]", "Viral rna [NCIT:C204811]", "Other [NCIT:C17649]", "Not Provided [SNOMED:434941000124101]" ], "examples": [ "viral RNA source" ], "ontology": "GENEPIO:0001965", "type": "string", "description": "Molecule type used to make the library.", "classification": "Sequencing", "label": "Source material", "fill_mode": "batch", "header": "Y" }, "library_selection": { "enum": [ "RANDOM [LOINC:LA29504-0]", "PCR [LOINC:LA26418-6]", "RANDOM PCR [GENEPIO:0001957]", "RT-PCR [LOINC:LP435370-4]", "HMPR [GENEPIO:0001949]", "MF [GENEPIO:0001952]", "repeat fractionation", "size fractionation [GENEPIO:0001963]", "MSLL [GENEPIO:0001954]", "cDNA [NCIT:C324]", "ChIP [GENEPIO:0001947]", "MNase [GENEPIO:0001953]", "DNase [GENEPIO:0001948]", "Hybrid Selection [GENEPIO:0001950]", "Reduced Representation [GENEPIO:0001960]", "Restriction Digest [GENEPIO:0001961]", "5-methylcytidine antibody [GENEPIO:0001941]", "MBD2 protein methyl-CpG binding domain [GENEPIO:0001951]", "CAGE [GENEPIO:0001942]", "RACE [GENEPIO:0001956]", "MDA [EFO:0008800]", "padlock probes capture method", "Oligo-dT [NCIT:C18685]", "Inverse rRNA selection", "ChIP-Seq [NCIT:C106049]", "Other [NCIT:C17649]", "Not Provided [SNOMED:434941000124101]" ], "examples": [ "PCR method" ], "ontology": "GENEPIO:0001940", "type": "string", "description": "Library capture method.", "classification": "Sequencing", "label": "Capture method", "fill_mode": "batch", "header": "Y" }, "library_strategy": { "enum": [ "Bisultife-Seq strategy [GENEPIO:0001975]", "CTS strategy [GENEPIO:0001978]", "ChIP-Seq strategy [GENEPIO:0001979]", "DNase-Hypersensitivity strategy [GENEPIO:0001980]", "EST strategy [GENEPIO:0001981]", "FL-cDNA strategy [GENEPIO:0001983]", "MB-Seq strategy [GENEPIO:0001984]", "MNase-Seq strategy [GENEPIO:0001985]", "MRE-Seq strategy [GENEPIO:0001986]", "MeDIP-Seq strategy [GENEPIO:0001987]", "RNA-Seq strategy [GENEPIO:0001990]", "WCS strategy [GENEPIO:0001991]", "WGS strategy [GENEPIO:0001992]", "WXS strategy [GENEPIO:0001993]", "Amplicon [GENEPIO:0001974]", "Clone end strategy [GENEPIO:0001976]", "Clone strategy [GENEPIO:0001977]", "Finishing strategy [GENEPIO:0001982]", "Other library strategy [GENEPIO:0001988]", "Pool clone strategy [GENEPIO:0001989]", "Not Provided [SNOMED:434941000124101]" ], "examples": [ "WGS strategy" ], "ontology": "GENEPIO:0001973", "type": "string", "description": "Overall sequencing strategy or approach.", "classification": "Sequencing", "label": "Sequencing technique", "fill_mode": "batch", "header": "Y" }, "library_layout": { "enum": [ "Single-end [OBI:0002481]", "Paired-end [OBI:0001852]" ], "examples": [ "Single-end" ], "ontology": "NCIT:C175894", "type": "string", "description": "Single or paired sequencing configuration", "classification": "Sequencing", "label": "Library Layout", "fill_mode": "batch", "header": "Y" }, "gene_name_1": { "enum": [ "E gene [LOINC:LP422409-5]", "M gene [LOINC:LP422882-3]", "N gene [LOINC:LP417599-0]", "Spike gene [GENEPIO:0100154]", "orf1ab (rep) [LOINC:LP437152-4]", "orf1a (pp1a) [LP428394-3]", "nsp11 [GENEPIO:0100157]", "nsp1 [GENEPIO:0100158]", "nsp2 [GENEPIO:0100159]", "nsp3 [GENEPIO:0100160]", "nsp4 [GENEPIO:0100161]", "nsp5 [GENEPIO:0100162]", "nsp6 [GENEPIO:0100163]", "nsp7 [GENEPIO:0100164]", "nsp8 [GENEPIO:0100165]", "nsp9 [GENEPIO:0100166]", "nsp10 [GENEPIO:0100167]", "RdRp gene (nsp12) [GENEPIO:0100168]", "hel gene (nsp13) [GENEPIO:0100169]", "exoN gene (nsp14) [GENEPIO:0100170]", "nsp15 [GENEPIO:0100171]", "nsp16 [GENEPIO:0100172]", "orf3a [GENEPIO:0100173]", "orf3b [GENEPIO:0100174]", "orf6 (ns6) [GENEPIO:0100175]", "orf7a [GENEPIO:0100176]", "orf7b (ns7b) [GENEPIO:0100177]", "orf8 (ns8) [GENEPIO:0100178]", "orf9b [GENEPIO:0100179]", "orf9c [GENEPIO:0100180]", "orf10 [GENEPIO:0100181]", "orf14 [GENEPIO:0100182]", "SARS-COV-2 5' UTR [GENEPIO:0100183]", "Other [NCIT:C124261]", "Not Applicable [LOINC:LA4720-4]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "ORF1ab" ], "ontology": "GENEPIO:0001507", "type": "string", "description": "The name of the gene used in the diagnostic RT-PCR test.", "classification": "Pathogen diagnostic testing", "label": "Gene Name 1", "fill_mode": "batch", "header": "Y" }, "diagnostic_pcr_Ct_value_1": { "examples": [ "40" ], "ontology": "GENEPIO:0001509", "type": "number", "minimum": 0, "maximum": 40, "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "classification": "Pathogen diagnostic testing", "label": "Diagnostic Pcr Ct Value 1", "fill_mode": "batch", "header": "Y" }, "gene_name_2": { "enum": [ "E gene [LOINC:LP422409-5]", "M gene [LOINC:LP422882-3]", "N gene [LOINC:LP417599-0]", "Spike gene [GENEPIO:0100154]", "orf1ab (rep) [LOINC:LP437152-4]", "orf1a (pp1a) [LOINC:LP428394-3]", "nsp11 [GENEPIO:0100157]", "nsp1 [GENEPIO:0100158]", "nsp2 [GENEPIO:0100159]", "nsp3 [GENEPIO:0100160]", "nsp4 [GENEPIO:0100161]", "nsp5 [GENEPIO:0100162]", "nsp6 [GENEPIO:0100163]", "nsp7 [GENEPIO:0100164]", "nsp8 [GENEPIO:0100165]", "nsp9 [GENEPIO:0100166]", "nsp10 [GENEPIO:0100167]", "RdRp gene (nsp12) [GENEPIO:0100168]", "hel gene (nsp13) [GENEPIO:0100169]", "exoN gene (nsp14) [GENEPIO:0100170]", "nsp15 [GENEPIO:0100171]", "nsp16 [GENEPIO:0100172]", "orf3a [GENEPIO:0100173]", "orf3b [GENEPIO:0100174]", "orf6 (ns6) [GENEPIO:0100175]", "orf7a [GENEPIO:0100176]", "orf7b (ns7b) [GENEPIO:0100177]", "orf8 (ns8) [GENEPIO:0100178]", "orf9b [GENEPIO:0100179]", "orf9c [GENEPIO:0100180]", "orf10 [GENEPIO:0100181]", "orf14 [GENEPIO:0100182]", "SARS-COV-2 5' UTR [GENEPIO:0100183]", "Other [NCIT:C124261]", "Not Applicable [LOINC:LA4720-4]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "S" ], "ontology": "GENEPIO:0001510", "type": "string", "description": "The name of the gene used in the diagnostic RT-PCR test.", "classification": "Pathogen diagnostic testing", "label": "Gene Name 2", "fill_mode": "batch", "header": "Y" }, "diagnostic_pcr_Ct_value_2": { "examples": [ "40" ], "ontology": "GENEPIO:0001512", "type": "string", "minimum": 0, "maximum": 40, "description": "The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.", "classification": "Pathogen diagnostic testing", "label": "Diagnostic Pcr Ct Value-2", "fill_mode": "batch", "header": "Y" }, "authors": { "examples": [ "Sánchez P" ], "ontology": "NCIT:C183329", "type": "string", "description": "A data field which describes the names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", "classification": "Public databases", "label": "Authors", "fill_mode": "batch", "header": "Y" }, "sequence_file_R1": { "examples": [ "ABC123_S1_L001_R1_001.fastq.gz" ], "ontology": "GENEPIO:0001476", "type": "string", "description": "A data field which describes the user-specified filename of the read 1 (r1) file.", "classification": "Bioinformatics and QC metrics fields", "label": "Sequence file R1", "fill_mode": "sample", "header": "Y" }, "sequence_file_R2": { "examples": [ "ABC123_S1_L001_R2_002.fastq.gz" ], "ontology": "GENEPIO:0001477", "type": "string", "description": "A data field which describes the user-specified filename of the read 2 (r2) file. ", "classification": "Bioinformatics and QC metrics fields", "label": "Sequence file R2", "fill_mode": "sample", "header": "Y" }, "unique_sample_id": { "examples": [ "AXM1456" ], "ontology": "NCIT:C70663", "type": "string", "description": "Unique identifier for each sample", "classification": "Sample collection and processing", "label": "Unique identifier", "fill_mode": "batch", "header": "N" }, "batch_id": { "examples": [ "20250506140633" ], "ontology": "NCIT:C104504", "type": "string", "description": "Unique identifier for each analysis batch", "classification": "Sample collection and processing", "label": "Batch identifier", "fill_mode": "batch", "header": "N" }, "submitting_institution_id": { "examples": [ "COD-1111-BU" ], "ontology": "NCIT:C81294", "type": "string", "description": "The Institution identifier that is submitting data or information.", "classification": "Sample collection and processing", "label": "Submitting Institution Identifier", "fill_mode": "batch", "header": "N" }, "collecting_institution_code_1": { "examples": [ "1328021542" ], "ontology": "SNOMED:423901009", "type": "string", "description": "CCN code from the agency/institution that collected the sample.", "classification": "Sample collection and processing", "label": "CCN", "fill_mode": "sample", "header": "N" }, "collecting_institution_code_2": { "examples": [ "40059" ], "ontology": "SNOMED:423901009", "type": "string", "description": "CODCNH code from the agency/institution that collected the sample.", "classification": "Sample collection and processing", "label": "CODCNH", "fill_mode": "batch", "header": "N" }, "collecting_institution_email": { "examples": [ "johnnyblogs@lab.ca" ], "ontology": "OBI:0001890", "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory Email", "fill_mode": "batch", "header": "N" }, "collecting_institution_address": { "examples": [ "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" ], "ontology": "GENEPIO:0001158", "type": "string", "description": "The mailing address of the agency collecting the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory Address", "fill_mode": "batch", "header": "N" }, "autonom_cod": { "examples": [ "11380" ], "ontology": "", "type": "string", "description": "Código de Centro Autonómico", "classification": "Sample collection and processing", "label": "Código de Centro Autonómico", "fill_mode": "batch", "header": "N" }, "submitting_institution_email": { "examples": [ "RespLab@lab.ca" ], "ontology": "GENEPIO:0001165", "type": "string", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "classification": "Sample collection and processing", "label": "Submitting Institution Email", "fill_mode": "batch", "header": "N" }, "submitting_institution_address": { "examples": [ "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" ], "ontology": "GENEPIO:0001167", "type": "string", "description": "The mailing address of the agency submitting the sequence.", "classification": "Sample collection and processing", "label": "Submitting Institution Address", "fill_mode": "batch", "header": "N" }, "geo_loc_country": { "enum": [ "Afghanistan [GAZ:00006882]", "Albania [GAZ:00002953]", "Algeria [GAZ:00000563]", "American Samoa [GAZ:00003957]", "Andorra [GAZ:00002948]", "Angola [GAZ:00001095]", "Anguilla [GAZ:00009159]", "Antarctica [GAZ:00000462]", "Antigua and Barbuda [GAZ:00006883]", "Argentina [GAZ:00002928]", "Armenia [GAZ:00004094]", "Aruba [GAZ:00004025]", "Ashmore and Cartier Islands [GAZ:00005901]", "Australia [GAZ:00000463]", "Austria [GAZ:00002942]", "Azerbaijan [GAZ:00004941]", "Bahamas [GAZ:00002733]", "Bahrain [GAZ:00005281]", "Baker Island [GAZ:00007117]", "Bangladesh [GAZ:00003750]", "Barbados [GAZ:00001251]", "Bassas da India [GAZ:00005810]", "Belarus [GAZ:00006886]", "Belgium [GAZ:00002938]", "Belize [GAZ:00002934]", "Benin [GAZ:00000904]", "Bermuda [GAZ:00001264]", "Bhutan [GAZ:00003920]", "Bolivia [GAZ:00002511]", "Borneo [GAZ:00025355]", "Bosnia and Herzegovina [GAZ:00006887]", "Botswana [GAZ:00001097]", "Bouvet Island [GAZ:00001453]", "Brazil [GAZ:00002828]", "British Virgin Islands [GAZ:00003961]", "Brunei [GAZ:00003901]", "Bulgaria [GAZ:00002950]", "Burkina Faso [GAZ:00000905]", "Burundi [GAZ:00001090]", "Cambodia [GAZ:00006888]", "Cameroon [GAZ:00001093]", "Canada [GAZ:00002560]", "Cape Verde [GAZ:00001227]", "Cayman Islands [GAZ:00003986]", "Central African Republic [GAZ:00001089]", "Chad [GAZ:00000586]", "Chile [GAZ:00002825]", "China [GAZ:00002845]", "Christmas Island [GAZ:00005915]", "Clipperton Island [GAZ:00005838]", "Cocos Islands [GAZ:00009721]", "Colombia [GAZ:00002929]", "Comoros [GAZ:00005820]", "Cook Islands [GAZ:00053798]", "Coral Sea Islands [GAZ:00005917]", "Costa Rica [GAZ:00002901]", "Cote d'Ivoire [GAZ:00000906]", "Croatia [GAZ:00002719]", "Cuba [GAZ:00003762]", "Curacao [GAZ:00012582]", "Cyprus [GAZ:00004006]", "Czech Republic [GAZ:00002954]", "Democratic Republic of the Congo [GAZ:00001086]", "Denmark [GAZ:00005852]", "Djibouti [GAZ:00000582]", "Dominica [GAZ:00006890]", "Dominican Republic [GAZ:00003952]", "Ecuador [GAZ:00002912]", "Egypt [GAZ:00003934]", "El Salvador [GAZ:00002935]", "Equatorial Guinea [GAZ:00001091]", "Eritrea [GAZ:00000581]", "Estonia [GAZ:00002959]", "Eswatini [GAZ:00001099]", "Ethiopia [GAZ:00000567]", "Europa Island [GAZ:00005811]", "Falkland Islands [GAZ:00001412]", "Faroe Islands [GAZ:00059206]", "Fiji [GAZ:00006891]", "Finland [GAZ:00002937]", "France [GAZ:00003940]", "French Guiana [GAZ:00002516]", "French Polynesia [GAZ:00002918]", "French Southern and Antarctic Lands [GAZ:00003753]", "Gabon [GAZ:00001092]", "Gambia [GAZ:00000907]", "Gaza Strip [GAZ:00009571]", "Georgia [GAZ:00004942]", "Germany [GAZ:00002646]", "Ghana [GAZ:00000908]", "Gibraltar [GAZ:00003987]", "Glorioso Islands [GAZ:00005808]", "Greece [GAZ:00002945]", "Greenland [GAZ:00001507]", "Grenada [GAZ:02000573]", "Guadeloupe [GAZ:00067142]", "Guam [GAZ:00003706]", "Guatemala [GAZ:00002936]", "Guernsey [GAZ:00001550]", "Guinea [GAZ:00000909]", "Guinea-Bissau [GAZ:00000910]", "Guyana [GAZ:00002522]", "Haiti [GAZ:00003953]", "Heard Island and McDonald Islands [GAZ:00009718]", "Honduras [GAZ:00002894]", "Hong Kong [GAZ:00003203]", "Howland Island [GAZ:00007120]", "Hungary [GAZ:00002952]", "Iceland [GAZ:00000843]", "India [GAZ:00002839]", "Indonesia [GAZ:00003727]", "Iran [GAZ:00004474]", "Iraq [GAZ:00004483]", "Ireland [GAZ:00002943]", "Isle of Man [GAZ:00052477]", "Israel [GAZ:00002476]", "Italy [GAZ:00002650]", "Jamaica [GAZ:00003781]", "Jan Mayen [GAZ:00005853]", "Japan [GAZ:00002747]", "Jarvis Island [GAZ:00007118]", "Jersey [GAZ:00001551]", "Johnston Atoll [GAZ:00007114]", "Jordan [GAZ:00002473]", "Juan de Nova Island [GAZ:00005809]", "Kazakhstan [GAZ:00004999]", "Kenya [GAZ:00001101]", "Kerguelen Archipelago [GAZ:00005682]", "Kingman Reef [GAZ:00007116]", "Kiribati [GAZ:00006894]", "Kosovo [GAZ:00011337]", "Kuwait [GAZ:00005285]", "Kyrgyzstan [GAZ:00006893]", "Laos [GAZ:00006889]", "Latvia [GAZ:00002958]", "Lebanon [GAZ:00002478]", "Lesotho [GAZ:00001098]", "Liberia [GAZ:00000911]", "Libya [GAZ:00000566]", "Liechtenstein [GAZ:00003858]", "Line Islands [GAZ:00007144]", "Lithuania [GAZ:00002960]", "Luxembourg [GAZ:00002947]", "Macau [GAZ:00003202]", "Madagascar [GAZ:00001108]", "Malawi [GAZ:00001105]", "Malaysia [GAZ:00003902]", "Maldives [GAZ:00006924]", "Mali [GAZ:00000584]", "Malta [GAZ:00004017]", "Marshall Islands [GAZ:00007161]", "Martinique [GAZ:00067143]", "Mauritania [GAZ:00000583]", "Mauritius [GAZ:00003745]", "Mayotte [GAZ:00003943]", "Mexico [GAZ:00002852]", "Micronesia [GAZ:00005862]", "Midway Islands [GAZ:00007112]", "Moldova [GAZ:00003897]", "Monaco [GAZ:00003857]", "Mongolia [GAZ:00008744]", "Montenegro [GAZ:00006898]", "Montserrat [GAZ:00003988]", "Morocco [GAZ:00000565]", "Mozambique [GAZ:00001100]", "Myanmar [GAZ:00006899]", "Namibia [GAZ:00001096]", "Nauru [GAZ:00006900]", "Navassa Island [GAZ:00007119]", "Nepal [GAZ:00004399]", "Netherlands [GAZ:00002946]", "New Caledonia [GAZ:00005206]", "New Zealand [GAZ:00000469]", "Nicaragua [GAZ:00002978]", "Niger [GAZ:00000585]", "Nigeria [GAZ:00000912]", "Niue [GAZ:00006902]", "Norfolk Island [GAZ:00005908]", "North Korea [GAZ:00002801]", "North Macedonia [GAZ:00006895]", "North Sea [GAZ:00002284]", "Northern Mariana Islands [GAZ:00003958]", "Norway [GAZ:00002699]", "Oman [GAZ:00005283]", "Pakistan [GAZ:00005246]", "Palau [GAZ:00006905]", "Panama [GAZ:00002892]", "Papua New Guinea [GAZ:00003922]", "Paracel Islands [GAZ:00010832]", "Paraguay [GAZ:00002933]", "Peru [GAZ:00002932]", "Philippines [GAZ:00004525]", "Pitcairn Islands [GAZ:00005867]", "Poland [GAZ:00002939]", "Portugal [GAZ:00004126]", "Puerto Rico [GAZ:00006935]", "Qatar [GAZ:00005286]", "Republic of the Congo [GAZ:00001088]", "Reunion [GAZ:00003945]", "Romania [GAZ:00002951]", "Ross Sea [GAZ:00023304]", "Russia [GAZ:00002721]", "Rwanda [GAZ:00001087]", "Saint Helena [GAZ:00000849]", "Saint Kitts and Nevis [GAZ:00006906]", "Saint Lucia [GAZ:00006909]", "Saint Pierre and Miquelon [GAZ:00003942]", "Saint Martin [GAZ:00005841]", "Saint Vincent and the Grenadines [GAZ:02000565]", "Samoa [GAZ:00006910]", "San Marino [GAZ:00003102]", "Sao Tome and Principe [GAZ:00006927]", "Saudi Arabia [GAZ:00005279]", "Senegal [GAZ:00000913]", "Serbia [GAZ:00002957]", "Seychelles [GAZ:00006922]", "Sierra Leone [GAZ:00000914]", "Singapore [GAZ:00003923]", "Sint Maarten [GAZ:00012579]", "Slovakia [GAZ:00002956]", "Slovenia [GAZ:00002955]", "Solomon Islands [GAZ:00005275]", "Somalia [GAZ:00001104]", "South Africa [GAZ:00001094]", "South Georgia and the South Sandwich Islands [GAZ:00003990]", "South Korea [GAZ:00002802]", "South Sudan [GAZ:00233439]", "Spain [GAZ:00003936]", "Spratly Islands [GAZ:00010831]", "Sri Lanka [GAZ:00003924]", "State of Palestine [GAZ:00002475]", "Sudan [GAZ:00000560]", "Suriname [GAZ:00002525]", "Svalbard [GAZ:00005396]", "Swaziland [GAZ:00001099]", "Sweden [GAZ:00002729]", "Switzerland [GAZ:00002941]", "Syria [GAZ:00002474]", "Taiwan [GAZ:00005341]", "Tajikistan [GAZ:00006912]", "Tanzania [GAZ:00001103]", "Thailand [GAZ:00003744]", "Timor-Leste [GAZ:00006913]", "Togo [GAZ:00000915]", "Tokelau [GAZ:00260188]", "Tonga [GAZ:00006916]", "Trinidad and Tobago [GAZ:00003767]", "Tromelin Island [GAZ:00005812]", "Tunisia [GAZ:00000562]", "Turkey [GAZ:00000558]", "Turkmenistan [GAZ:00005018]", "Turks and Caicos Islands [GAZ:00003955]", "Tuvalu [GAZ:00009715]", "USA [GAZ:00002459]", "Uganda [GAZ:00001102]", "Ukraine [GAZ:00002724]", "United Arab Emirates [GAZ:00005282]", "United Kingdom [GAZ:00002637]", "Uruguay [GAZ:00002930]", "Uzbekistan [GAZ:00004979]", "Vanuatu [GAZ:00006918]", "Venezuela [GAZ:00002931]", "Viet Nam [GAZ:00003756]", "Virgin Islands [GAZ:00003959]", "Wake Island [GAZ:00007111]", "Wallis and Futuna [GAZ:00007191]", "West Bank [GAZ:00009572]", "Western Sahara [GAZ:00000564]", "Yemen [GAZ:00005284]", "Zambia [GAZ:00001107]", "Zimbabwe [GAZ:00001106]", "Not Applicable [GENEPIO:0001619]", "Not Collected [GENEPIO:0001620]", "Missing [GENEPIO:0001618]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "South Africa [GAZ:00001094]" ], "ontology": "GENEPIO:0001181", "type": "string", "description": "The country of origin of the sample.", "classification": "Sample collection and processing", "label": "Country", "fill_mode": "batch", "header": "N" }, "geo_loc_state": { "enum": [ "Andalucía", "Aragón", "Principado de Asturias", "Illes Balears", "Canarias", "Cantabria", "Castilla y León", "Castilla - La Mancha", "Cataluña", "Comunitat Valenciana", "Extremadura", "Galicia", "Comunidad de Madrid", "Región de Murcia", "Comunidad Foral de Navarra", "País Vasco", "La Rioja", "Ceuta", "Melilla" ], "examples": [ "Andalucía" ], "ontology": "GENEPIO:0001185", "type": "string", "description": "The state/province/territory of origin of the sample.", "classification": "Sample collection and processing", "label": "Autonomic Community", "fill_mode": "batch", "header": "N" }, "geo_loc_state_cod": { "examples": [ "01" ], "ontology": "", "type": "string", "description": "Official Code of the state/province/territory of origin of the sample.", "classification": "Sample collection and processing", "label": "Autonomic Community Code", "fill_mode": "batch", "header": "N" }, "geo_loc_region": { "enum": [ "Almería", "Cádiz", "Córdoba", "Granada", "Huelva", "Jaén", "Málaga", "Sevilla", "Huesca", "Teruel", "Zaragoza", "Asturias", "Illes Balears", "Las Palmas", "Santa Cruz de Tenerife", "Cantabria", "Ávila", "Burgos", "León", "Palencia", "Salamanca", "Segovia", "Soria", "Valladolid", "Zamora", "Albacete", "Ciudad Real", "Cuenca", "Guadalajara", "Toledo", "Barcelona", "Girona", "Lleida", "Tarragona", "Alicante/Alacant", "Castellón/Castelló", "Valencia/València", "Badajoz", "Cáceres", "A Coruña", "Lugo", "Ourense", "Pontevedra", "Madrid", "Murcia", "Navarra", "Araba/Álava", "Gipuzkoa", "Bizkaia", "La Rioja", "Ceuta", "Melilla" ], "examples": [ "Almería" ], "ontology": "NCIT:C87189", "type": "string", "description": "The county/region of origin of the sample.", "classification": "Sample collection and processing", "label": "Province", "fill_mode": "batch", "header": "N" }, "geo_loc_region_cod": { "examples": [ "04" ], "ontology": "", "type": "string", "description": "Official Code of the county/region of origin of the sample.", "classification": "Sample collection and processing", "label": "Province Code", "fill_mode": "batch", "header": "N" }, "geo_loc_city": { "examples": [ "Vancouver" ], "ontology": "GENEPIO:0001189", "type": "string", "description": "The city of origin of the sample.", "classification": "Sample collection and processing", "label": "City", "fill_mode": "batch", "header": "N" }, "geo_loc_city_cod": { "examples": [ "040139" ], "ontology": "", "type": "string", "description": "Official Code of the city of origin of the sample.", "classification": "Sample collection and processing", "label": "City Code", "fill_mode": "batch", "header": "N" }, "post_code": { "examples": [ "04120" ], "ontology": "NCIT:C25621", "type": "string", "description": "Post Code of the agency/institution that collected the sample.", "classification": "Sample collection and processing", "label": "Postal Code", "fill_mode": "batch", "header": "N" }, "dep_func": { "examples": [ "Servicios O Institutos De Salud De Las Comunidades Autónomas" ], "ontology": "", "type": "string", "description": "The type of entity to which the facility is affiliated", "classification": "Sample collection and processing", "label": "Functional Dependency", "fill_mode": "batch", "header": "N" }, "center_class_code": { "examples": [ "C11" ], "ontology": "", "type": "string", "description": "Official code of Institution’s functional classification or primary service purpose", "classification": "Sample collection and processing", "label": "Center Class Code", "fill_mode": "batch", "header": "N" }, "collecting_institution_function": { "examples": [ "Hospitales Generales" ], "ontology": "", "type": "string", "description": "Institution’s functional classification or primary service purpose", "classification": "Sample collection and processing", "label": "Center Class Function", "fill_mode": "batch", "header": "N" }, "lab_geo_loc_latitude": { "examples": [ "'36.8625108" ], "ontology": "EFO:0005020", "type": "string", "description": "The latitude coordinates of the geographical location of the agency/institution that collected the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory Latitude", "fill_mode": "batch", "header": "N" }, "lab_geo_loc_longitude": { "examples": [ "'-2.4467449" ], "ontology": "EFO:0005021", "type": "string", "description": "The longitude coordinates of the geographical location of the agency/institution that collected the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory Longitude", "fill_mode": "batch", "header": "N" }, "collecting_institution_phone": { "examples": [ "950016114" ], "ontology": "NCIT:C40978", "type": "string", "description": "Phone of the agency/institution that collected the sample.", "classification": "Sample collection and processing", "label": "Originating Laboratory Phone", "fill_mode": "batch", "header": "N" }, "geo_loc_latitude": { "examples": [ "38.98 N" ], "ontology": "OBI:0001620", "type": "string", "description": "The latitude coordinates of the geographical location of sample collection.", "classification": "Sample collection and processing", "label": "Geo Loc Latitude", "fill_mode": "batch", "header": "N" }, "geo_loc_longitude": { "examples": [ "77.11 W" ], "ontology": "OBI:0001621", "type": "string", "description": "The longitude coordinates of the geographical location of sample collection.", "classification": "Sample collection and processing", "label": "Geo Loc Longitude", "fill_mode": "batch", "header": "N" }, "study_type": { "enum": [ "Whole Genome Sequencing [SNOMED:51201000000109]", "Metagenomics [LOINC:103566-6]", "Transcriptome Analysis [GENEPIO:0001111", "Resequencing [NCIT:C41254", "Epigenetics [NCIT:C153190]", "Synthetic Genomics [NCIT:C84343]", "Forensic or Paleo-genomics [EDAM:3943]", "Gene Regulation Study [EDAM:0204]", "Cancer Genomics [NCIT:C18247]", "Population Genomics [EDAM:3796]", "RNASeq [OBI:0001177]", "Exome Sequencing [LOINC:LP248469-1]", "Pooled Clone Sequencing [OBI:2100402]", "Transcriptome Sequencing [NCIT:C124261]", "Other [NCIT:C17649]", "Not Provided [SNOMED:434941000124101]" ], "examples": [ "Whole Genome Sequencing [NCIT:C101294]" ], "ontology": "NCIT:C142175", "type": "string", "description": "The nature of the investigation or the investigational use for which the study is being done", "classification": "Public databases", "label": "Study type", "fill_mode": "batch", "header": "N" }, "anatomical_material": { "enum": [ "Air specimen [SNOMED:446302006]", "Amniotic Fluid [SNOMED:77012006]", "Aqueous Humor [SNOMED:425460003]", "Blood Clot [SNOMED:75753009]", "Body Fluid [SNOMED:32457005]", "Calculus [SNOMED:56381008]", "Cerebrospinal Fluid [SNOMED:258450006]", "Cerebrospinal Fluid [SNOMED:65216001]", "Cyst Fluid [SNOMED:734110008]", "Dialysate specimen [SNOMED:258454002]", "Erythrocyte [SNOMED:41898006]", "Fluid [SNOMED:255765007]", "Intravenous Fluid [SNOMED:118431008]", "Pericardial Fluid [SNOMED:34429004]", "Placenta [SNOMED:258538002]", "Platelet [SNOMED:16378004]", "Pleural Fluid [SNOMED:2778004]", "Synovial Fluid [SNOMED:6085005]", "Tissue [UBERON:0000479]", "Vitreous Humor [SNOMED:426101004]", "Blood [LOINC:4226865]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Blood [UBERON:0000178]" ], "ontology": "GENEPIO:0001211", "type": "string", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "classification": "Sample collection and processing", "label": "Anatomical Material", "fill_mode": "batch", "header": "N" }, "anatomical_part": { "enum": [ "Abdominal cavity [UBERON:0003684]", "Articulation [UBERON:0004905]", "Blood [LOINC:4226865]", "Blood [SNOMED:87612001]", "Bone [UBERON:0002481]", "Bone marrow [UBERON:0002371]", "Brain [UBERON:0000955]", "Breast [UBERON:0000310]", "Bronchus [UBERON:0002185]", "Calcareous tooth [UBERON:0001091]", "Cardiac valve [UBERON:0000946]", "Conjunctiva [UBERON:0001811]", "Cornea [UBERON:0000964]", "Duodenum [UBERON:0002114]", "Ear [UBERON:0001690]", "Endometrium [UBERON:0001295]", "Entire head and neck [SNOMED:361355005]", "Epidural space [UBERON:0003691]", "Esophagus [UBERON:0001043]", "Fascia [UBERON:0008982]", "Gallbladder [UBERON:0002110]", "Glans penis [UBERON:0001299]", "Intervertebral disc [UBERON:0001066]", "Intestine [UBERON:0000160]", "Liver [UBERON:0002107]", "Lung [UBERON:0002048]", "Lymph node [UBERON:0000029]", "Mayor vestibular gland [UBERON:0000460]", "Mediastinum [UBERON:0003728]", "Middle ear [UBERON:0001756]", "Mouth [UBERON:0000165]", "Muscle organ [UBERON:0001630]", "Nail [UBERON:0001705]", "Nasopharynx [UBERON:0003582]", "Oropharynx [UBERON:0001729]", "Pericardial sac [UBERON:0002406]", "Peritoneal cavity [UBERON:0001179]", "Pleura [UBERON:0000977]", "Pleural cavity [UBERON:0002402]", "Skin of body [UBERON:0002097]", "Skin ulcer [SNOMED:46742003]", "Soft tissue [SNOMED:87784001]", "Stomach [UBERON:0000945]", "Synovial joint [UBERON:0002217]", "Ureter [UBERON:0000056]", "Vagina [UBERON:0000996]", "Larynx [UBERON:0001737]", "Rectum [UBERON:0001052]", "Urethra [UBERON:0000057]", "Endocervix [UBERON:0000458]", "Prostate gland [UBERON:0002367]", "Uterus [UBERON:0000995]", "Kidney [UBERON:0002113]", "Nose [UBERON:0000004]", "Mammalian vulva [UBERON:0000997]", "Lower respiratory tract [SNOMED:447081004]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Nasopharynx [UBERON:0001728]" ], "ontology": "GENEPIO:0001214", "type": "string", "description": "A data field which describes the substance obtained from an anatomical part of an organism. ", "classification": "Sample collection and processing", "label": "Anatomical Part", "fill_mode": "batch", "header": "N" }, "collection_method": { "enum": [ "Amniocentesis [SNOMED:34536000]", "Suprapublic Aspiration [GENEPIO:0100028]", "Tracheal Aspiration [GENEPIO:0100029]", "Vacuum Aspiration [NCIT:C93274]", "Needle Biopsy [SNOMED:129249002]", "Filtration [SNOMED:702940009]", "Lavage [NCIT:C38068]", "Aspiration [SNOMED:14766002]", "Biopsy [SNOMED:86273004]", "Bronchoalveolar Lavage [SNOMED:258607008]", "Drainage procedure [SNOMED:122462000]", "Scraping [SNOMED:56757003]", "Swab [SNOMED:408098004]", "Wash [SNOMED:258610001]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Trachel Aspiration" ], "ontology": "LOINC:LP32732-7", "type": "string", "description": "A data field which describes the process used to collect the sample. ", "classification": "Sample collection and processing", "label": "Collection Method", "fill_mode": "batch", "header": "N" }, "body_product": { "enum": [ "Breast Milk [SNOMED:226789007]", "Feces [SNOMED:39477002]", "Mucus [SNOMED:49909006]", "Sweat [SNOMED:74616000]", "Tear [LOINC:LP7622-6]", "Bile [SNOMED:70150004]", "Blood [LOINC:4226865]", "Lochia [SNOMED:49636006]", "Meconium [UBERON:0007109]", "Plasma [SNOMED:50863008]", "Pus [SNOMED:11311000]", "Serum [SNOMED:67922002]", "Sputum [SNOMED:45710003]", "Urine [LOINC:LA30054-3]", "Tonsil [UBERON:0002372]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Feces" ], "ontology": "SNOMED:364684009", "type": "string", "description": "A data field which describes the substance excreted/secreted from an organism. ", "classification": "Sample collection and processing", "label": "Body Product", "fill_mode": "batch", "header": "N" }, "tax_id": { "examples": [ "2697049" ], "ontology": "NCIT:C164641", "type": "string", "description": "The NCBITaxon identifier for the organism being sequenced.", "classification": "Sample collection and processing", "label": "Tax ID", "fill_mode": "batch", "header": "N" }, "host_scientific_name": { "enum": [ "Bos taurus [SNOMED:34618005]", "Canis lupus familiaris [SNOMED:125079008]", "Chiroptera [SNOMED:388074005]", "Columbidae [SNOMED:107099008]", "Felis catus [SNOMED:448169003]", "Gallus gallus [SNOMED:47290002]", "Homo sapiens [SNOMED:337915000]", "Manis [SNOMED:43739001]", "Manis javanica [SNOMED:330131000009103]", "Neovison vison [SNOMED:447523007]", "Panthera leo [SNOMED:112507006]", "Panthera tigris [SNOMED:79047009]", "Rhinolophidae [SNOMED:392085002]", "Rhinolophus affinis [NCBITaxon:59477]", "Sus scrofa domesticus [SNOMED:331171000009105]", "Viverridae [SNOMED:388833006]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]" ], "examples": [ "Homo sapiens [NCBITaxon:9606]" ], "ontology": "GENEPIO:0001387", "type": "string", "description": "The taxonomic, or scientific name of the host.", "classification": "Host information", "label": "Host Scientific Name", "fill_mode": "batch", "header": "N" }, "host_disease": { "enum": [ "COVID-19 [SNOMED:840539006]", "Respiratory Syncytial Virus Infection [SNOMED:55735004]", "Influenza Infection [SNOMED:408687004]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "COVID-19 [MONDO:0100096]" ], "ontology": "SNOMED:64572001", "type": "string", "description": "The name of the disease experienced by the host.", "classification": "Host information", "label": "Host disease", "fill_mode": "batch", "header": "N" }, "purpose_of_sequencing": { "enum": [ "Baseline surveillance (random sampling) [GENEPIO:0100005]", "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", "Priority surveillance projects [GENEPIO:0100007]", "Screening for Variants of Concern (VOC) [GENEPIO:0100008]", "Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273]", "Sample has epidemiological link to Omicron Variant [GENEPIO:0100274]", "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]", "Re-infection surveillance [GENEPIO:0100010]", "Vaccine escape surveillance [GENEPIO:0100011]", "Travel-associated surveillance [GENEPIO:0100012]", "Domestic travel surveillance [GENEPIO:0100013]", "Interstate/ interprovincial travel surveillance [GENEPIO:0100275]", "Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]", "International travel surveillance [GENEPIO:0100014]", "Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015]", "Surveillance of international border crossing by air travel [GENEPIO:0100016]", "Surveillance of international border crossing by ground transport [GENEPIO:0100017]", "Surveillance from international worker testing [GENEPIO:0100018]", "Cluster/Outbreak investigation [GENEPIO:0100001]", "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]", "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]", "Research [LOINC:LP173021-9]", "Viral passage experiment [GENEPIO:0100023]", "Protocol testing [GENEPIO:0100024]", "Not Applicable [SNOMED:385432009]", "Not Collected [LOINC:LA4700-6]", "Not Provided [SNOMED:434941000124101]", "Missing [LOINC:LA14698-7]", "Restricted Access [GENEPIO:0001810]" ], "examples": [ "Baseline surveillance (random sampling) [GENEPIO:0100005]" ], "ontology": "GENEPIO:0001445", "type": "string", "description": "The reason that the sample was sequenced.", "classification": "Sequencing", "label": "Purpose of Sequencing", "fill_mode": "batch", "header": "N" }, "if_enrichment_panel_assay_version_other": { "examples": [ "2.1.3" ], "ontology": "0", "type": "string", "description": "A form or variant of software; one of a sequence of copies of a software program, each incorporating new modifications.", "classification": "Sequencing", "label": "If Enrichment panel/assay version Is Other, Specify", "fill_mode": "batch", "header": "N" }, "amplicon_pcr_primer_scheme": { "examples": [ "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" ], "ontology": "GENEPIO:0001456", "type": "string", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "classification": "Sequencing", "label": "Amplicon Pcr Primer Scheme", "fill_mode": "batch", "header": "N" }, "sequencing_instrument_platform": { "enum": [ "Oxford Nanopore [OBI:0002750]", "Illumina [OBI:0000759]", "Ion Torrent [GENEPIO:0002683]", "PacBio [GENEPIO:0001927]", "BGI [GENEPIO:0004324]", "MGI [GENEPIO:0004325]", "Other [NCIT:C17649]", "Not Provided [SNOMED:434941000124101]" ], "examples": [ "Illumina" ], "ontology": "GENEPIO:0000071", "type": "string", "description": "A sequencing plaform (brand) is a name of a company that produces sequencer equipment.", "classification": "Sequencing", "label": "Sequencing Instrument Platform", "fill_mode": "batch", "header": "N" }, "read_length": { "examples": [ "75" ], "ontology": "NCIT:C153362", "type": "integer", "minimum": 0, "maximum": 10000, "description": "Number of base pairs per read", "classification": "Sequencing", "label": "Read length", "fill_mode": "batch", "header": "N" }, "number_of_reads": { "examples": [ "75" ], "ontology": "NCIT:C153362", "type": "integer", "description": "The number of nucleotides successfully ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.", "classification": "Sequencing", "label": "Read count", "fill_mode": "batch", "header": "N" }, "sequence_file_R1_md5": { "examples": [ "b5242d60471e5a5a97b35531dbbe8c30" ], "ontology": "NCIT:C171276", "type": "string", "description": "Checksum md5 value to validate successful file transmission in R1", "classification": "Bioinformatics and QC metrics fields", "label": "Sequence fastq R1 md5", "fill_mode": "sample", "header": "N" }, "sequence_file_R2_md5": { "examples": [ "b5242d60471e5a5a97b35531dbbe8c30" ], "ontology": "NCIT:C171276", "type": "string", "description": "Checksum md5 value to validate successful file transmission in R2", "classification": "Bioinformatics and QC metrics fields", "label": "Sequence fastq R2 md5", "fill_mode": "sample", "header": "N" }, "sequence_file_path_R1": { "examples": [ "/User/Documents/RespLab/Data/" ], "ontology": "GENEPIO:0001478", "type": "string", "description": "The filepath of the r1 file.", "classification": "Files info", "label": "Filepath R1", "fill_mode": "batch", "header": "N" }, "sequence_file_path_R2": { "examples": [ "/User/Documents/RespLab/Data/" ], "ontology": "GENEPIO:0001479", "type": "string", "description": "The filepath of the r2 file.", "classification": "Files info", "label": "Filepath R2", "fill_mode": "batch", "header": "N" }, "fast5_filename": { "examples": [ "batch1a_sequences.fast5" ], "ontology": "GENEPIO:0001480", "type": "string", "description": "The user-specified filename of the FAST5 file.", "classification": "Files info", "label": "Filename fast5", "fill_mode": "batch", "header": "N" }, "fast5_filepath": { "examples": [ "/User/Documents/RespLab/Data/" ], "ontology": "GENEPIO:0001481", "type": "string", "description": "The filepath of the FAST5 file.", "classification": "Files info", "label": "Filepath fast5", "fill_mode": "batch", "header": "N" }, "bioinformatics_analysis_date": { "examples": [ "2022-07-15 00:00:00" ], "ontology": "OBI:0002471", "type": "string", "format": "date", "description": "The time of a sample analysis process YYYY-MM-DD", "classification": "Bioinformatics and QC metrics fields", "label": "processing_date", "fill_mode": "batch", "header": "N" }, "dehosting_method_software_name": { "examples": [ "KRAKEN2_KRAKEN2 " ], "ontology": "GENEPIO:0001459", "type": "string", "description": "The method used to remove host reads from the pathogen sequence.", "classification": "Bioinformatic Analysis fields", "label": "Dehosting Method", "fill_mode": "batch", "header": "N" }, "dehosting_method_software_version": { "examples": [ "2.4.1" ], "ontology": "LOINC:LA20883-7", "type": "string", "description": "The method version used to remove host reads from the pathogen sequence.", "classification": "Bioinformatic Analysis fields", "label": "Dehosting Method Version", "fill_mode": "batch", "header": "N" }, "reference_genome_accession": { "examples": [ "NC_045512.2" ], "ontology": "GENEPIO:0001485", "type": "string", "description": "A persistent, unique identifier of a genome database entry.", "classification": "Bioinformatics and QC metrics fields", "label": "Reference genome accession", "fill_mode": "batch", "header": "N" }, "bioinformatics_protocol_software_name": { "examples": [ "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" ], "ontology": "GENEPIO:0001489", "type": "string", "description": "The name of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", "label": "Bioinformatics protocol", "fill_mode": "batch", "header": "N" }, "if_bioinformatic_protocol_is_other_specify": { "examples": [ "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" ], "ontology": "0", "type": "string", "description": "The name of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", "label": "If bioinformatics protocol Is Other, Specify", "fill_mode": "batch", "header": "N" }, "bioinformatics_protocol_software_version": { "examples": [ "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" ], "ontology": "LOINC:LA20883-7", "type": "string", "description": "The version number of the bioinformatics protocol used.", "classification": "Bioinformatic Analysis fields", "label": "Bioinformatics protocol version", "fill_mode": "batch", "header": "N" }, "commercial_open_source_both": { "enum": [ "Commercial [SWO:1000002]", "Open Source [SWO:1000008]", "Both", "None", "Not Provided [SNOMED:434941000124101", "Not Applicable [GENEPIO:0001619]" ], "examples": [ "Commercial" ], "ontology": "0", "type": "string", "description": "If bioinformatics protocol used was open-source or commercial", "classification": "Bioinformatic Analysis fields", "label": "Commercial/Open-source/both", "fill_mode": "batch", "header": "N" }, "preprocessing_software_name": { "examples": [ "fastp" ], "ontology": "MS_1002386", "type": "string", "description": "Software used for preprocessing step.", "classification": "Bioinformatic Analysis fields", "label": "Preprocessing software", "fill_mode": "batch", "header": "N" }, "preprocessing_software_version": { "examples": [ "v5.3.1" ], "ontology": "LOINC:LA20883-7", "type": "string", "description": "Version of the preprocessing software used.", "classification": "Bioinformatic Analysis fields", "label": "Preprocessing software version", "fill_mode": "batch", "header": "N" }, "if_preprocessing_other": { "examples": [ "Seqtk" ], "ontology": "MS_1002386", "type": "string", "description": "Preprocessing software name other", "classification": "Bioinformatic Analysis fields", "label": "If preprocessing Is Other, Specify", "fill_mode": "batch", "header": "N" }, "preprocessing_params": { "examples": [ "--cut_mean_quality 30" ], "ontology": "NCIT:C44175", "type": "string", "description": "The parameters and settings used to perform preprocessing analysis.", "classification": "Bioinformatic Analysis fields", "label": "Preprocessing params", "fill_mode": "batch", "header": "N" }, "mapping_software_name": { "examples": [ "bowtie2" ], "ontology": "NCIT:C175896", "type": "string", "description": "Software used for mapping step.", "classification": "Bioinformatic Analysis fields", "label": "Mapping software", "fill_mode": "batch", "header": "N" }, "mapping_software_version": { "examples": [ "v7.0.1" ], "ontology": "LOINC:LA20883-7", "type": "string", "description": "Version of the mapper used.", "classification": "Bioinformatic Analysis fields", "label": "Mapping software version", "fill_mode": "batch", "header": "N" }, "if_mapping_other": { "examples": [ "Mosaik" ], "ontology": "0", "type": "string", "description": "Mapping software used other", "classification": "Bioinformatic Analysis fields", "label": "If mapping Is Other, Specify", "fill_mode": "batch", "header": "N" }, "mapping_params": { "examples": [ "--seed 1" ], "ontology": "NCIT:C44175", "type": "string", "description": "Parameters used for mapping step.", "classification": "Bioinformatic Analysis fields", "label": "Mapping params", "fill_mode": "batch", "header": "N" }, "assembly": { "examples": [ "Spades" ], "ontology": "GENEPIO:0000090", "type": "string", "description": "Software used for assembly of the pathogen genome.", "classification": "Bioinformatic Analysis fields", "label": "Assembly software", "fill_mode": "batch", "header": "N" }, "assembly_version": { "examples": [ "Spades" ], "ontology": "NCIT:C164455", "type": "string", "description": "Version of the software used for assembly of the pathogen genome.", "classification": "Bioinformatic Analysis fields", "label": "Assembly software version", "fill_mode": "batch", "header": "N" }, "if_assembly_other": { "examples": [ "v3.1" ], "ontology": "0", "type": "string", "description": "Assembly software version", "classification": "Bioinformatic Analysis fields", "label": "If assembly Is Other, Specify", "fill_mode": "batch", "header": "N" }, "assembly_params": { "examples": [ "-k 127,56,27" ], "ontology": "NCIT:C44175", "type": "string", "description": "The parameters and settings used to perform genome assembly.", "classification": "Bioinformatic Analysis fields", "label": "Assembly params", "fill_mode": "batch", "header": "N" }, "bioinfo_metadata_file": { "examples": [ "bioinfo_lab_metadata_COD-1111-BU_20250506140633_3C412C.json" ], "ontology": "CAO:000237", "type": "string", "description": "Bioinfo JSON with metadata information", "classification": "Bioinformatic Analysis fields", "label": "Bioinfo JSON", "fill_mode": "batch", "header": "N" }, "vcf_filename": { "examples": [ "Ivar" ], "ontology": "0", "type": "string", "description": "Name of the vcf file.", "classification": "Bioinformatic Variants", "label": "VCF filename", "fill_mode": "batch", "header": "N" }, "variant_calling_software_name": { "examples": [ "Ivar" ], "ontology": "EDAM:operation_3227", "type": "string", "description": "Software used for variant calling.", "classification": "Bioinformatic Variants", "label": "Variant calling software", "fill_mode": "batch", "header": "N" }, "variant_calling_software_version": { "examples": [ "v4.1" ], "ontology": "LOINC:LA20883-7", "type": "string", "description": "Variant calling software version", "classification": "Bioinformatic Variants", "label": "Variant calling software version", "fill_mode": "batch", "header": "N" }, "if_variant_calling_other": { "examples": [ "GATK HaplotypeCaller" ], "ontology": "0", "type": "string", "description": "Specify if you have used another variant calling software", "classification": "Bioinformatic Variants", "label": "If variant calling Is Other, Specify", "fill_mode": "batch", "header": "N" }, "variant_calling_params": { "examples": [ "-t 0.5 -Q 20" ], "ontology": "NCIT:C44175", "type": "string", "description": "Params used for variant calling", "classification": "Bioinformatic Variants", "label": "Variant calling params", "fill_mode": "batch", "header": "N" }, "consensus_sequence_name": { "examples": [ "2018086 NC_045512.2" ], "ontology": "GENEPIO:0001460", "type": "string", "description": "The name of the consensus sequence.", "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence name", "fill_mode": "batch", "header": "N" }, "consensus_sequence_filename": { "examples": [ "2018102.consensus.fa" ], "ontology": "GENEPIO:0001461", "type": "string", "description": "The name of the consensus sequence filename", "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence filename", "fill_mode": "batch", "header": "N" }, "consensus_sequence_md5": { "examples": [ "5gaskañlkdak3143242ñlkas" ], "ontology": "0", "type": "string", "description": "The md5 of the consensus sequence.", "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence name md5", "fill_mode": "batch", "header": "N" }, "consensus_sequence_filepath": { "examples": [ "/User/Documents/RespLab/Data/ncov123assembly.fasta" ], "ontology": "GENEPIO:0001462", "type": "string", "description": "The filepath of the consesnsus sequence file.", "classification": "Bioinformatic Analysis fields", "label": "Consensus sequence filepath", "fill_mode": "batch", "header": "N" }, "long_table_path": { "examples": [ "/User/Documents/RespLab/ncov123_longtable.tsv" ], "ontology": "0", "type": "string", "description": "The path where the long table including all variants and annotations is.", "classification": "Bioinformatic Analysis fields", "label": "Long table path", "fill_mode": "batch", "header": "N" }, "consensus_sequence_software_name": { "examples": [ "Ivar" ], "ontology": "GENEPIO:0001463", "type": "string", "description": "The name of software used to generate the consensus sequence.", "classification": "Bioinformatic Analysis fields", "label": "Consensus software", "fill_mode": "batch", "header": "N" }, "if_consensus_other": { "examples": [ "v1.3" ], "ontology": "0", "type": "string", "description": "Specify if you have used another consensus software", "classification": "Bioinformatic Analysis fields", "label": "If consensus Is Other, Specify", "fill_mode": "batch", "header": "N" }, "consensus_sequence_software_version": { "examples": [ "1.3" ], "ontology": "GENEPIO:0001469", "type": "string", "description": "The version of the software used to generate the consensus sequence.", "classification": "Bioinformatic Analysis fields", "label": "Consensus software version", "fill_mode": "batch", "header": "N" }, "consensus_params": { "examples": [ "AF > 0.75" ], "ontology": "NCIT:C44175", "type": "string", "description": "Parameters used for consensus generation", "classification": "Bioinformatic Analysis fields", "label": "Consensus params", "fill_mode": "batch", "header": "N" }, "consensus_genome_length": { "examples": [ "38677" ], "ontology": "GENEPIO:0001483", "type": "string", "description": "Size of the assembled genome described as the number of base pairs.", "classification": "Bioinformatics and QC metrics fields", "label": "Consensus genome length", "fill_mode": "batch", "header": "N" }, "depth_of_coverage_threshold": { "examples": [ "10x" ], "ontology": "GENEPIO:0001475", "type": "string", "description": "The threshold used as a cut-off for the depth of coverage.", "classification": "Bioinformatics and QC metrics fields", "label": "Depth of coverage threshold", "fill_mode": "batch", "header": "N" }, "number_of_reads_sequenced": { "examples": [ "387566" ], "ontology": "0", "type": "integer", "minimum": 0, "maximum": 50000000, "description": "The number of total reads generated by the sequencing process.", "classification": "Bioinformatics and QC metrics fields", "label": "Number of reads sequenced ", "fill_mode": "batch", "header": "N" }, "pass_reads": { "examples": [ "153812" ], "ontology": "GENEPIO:0000087", "type": "integer", "minimum": 0, "maximum": 50000000, "description": "Number of reads that pass quality control threshold", "classification": "Bioinformatics and QC metrics fields", "label": "Number of reads passing filters", "fill_mode": "batch", "header": "N" }, "per_reads_host": { "examples": [ "0.19" ], "ontology": "NCIT:C185251", "type": "number", "minimum": 0, "maximum": 100, "description": "Percentage of reads mapped to host", "classification": "Bioinformatics and QC metrics fields", "label": "%Reads host", "fill_mode": "batch", "header": "N" }, "per_reads_virus": { "examples": [ "99.69" ], "ontology": "NCIT:C185251", "type": "number", "minimum": 0, "maximum": 100, "description": "Percentage of reads mapped to virus", "classification": "Bioinformatics and QC metrics fields", "label": "%Reads virus", "fill_mode": "batch", "header": "N" }, "per_unmapped": { "examples": [ "0.13" ], "ontology": "0", "type": "number", "minimum": 0, "maximum": 100, "description": "Percentage of reads unmapped to virus or to host", "classification": "Bioinformatics and QC metrics fields", "label": "%Unmapped", "fill_mode": "batch", "header": "N" }, "depth_of_coverage_value": { "examples": [ "400" ], "ontology": "GENEPIO:0001474", "type": "integer", "minimum": 0, "maximum": 1000000, "description": "The average number of reads representing each nucleotide in the reconstructed sequence.", "classification": "Bioinformatics and QC metrics fields", "label": "Depth of coverage Mean value", "fill_mode": "batch", "header": "N" }, "per_genome_greater_10x": { "examples": [ "96" ], "ontology": "0", "type": "number", "minimum": 0, "maximum": 100, "description": "Percentage of genome with coverage greater than 10x", "classification": "Bioinformatics and QC metrics fields", "label": "% Genome > 10x", "fill_mode": "batch", "header": "N" }, "per_Ns": { "examples": [ "3" ], "ontology": "0", "type": "number", "minimum": 0, "maximum": 100, "description": "Percentage of Ns", "classification": "Bioinformatics and QC metrics fields", "label": "%Ns", "fill_mode": "batch", "header": "N" }, "number_of_Ns": { "examples": [ "2000" ], "ontology": "0", "type": "integer", "minimum": 0, "maximum": 100000, "description": "Number of Ns", "classification": "Bioinformatics and QC metrics fields", "label": "Number of Ns", "fill_mode": "batch", "header": "N" }, "ns_per_100_kbp": { "examples": [ "300" ], "ontology": "GENEPIO:0001484", "type": "number", "minimum": 0, "maximum": 100000, "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", "classification": "Bioinformatics and QC metrics fields", "label": "Ns per 100 kbp", "fill_mode": "batch", "header": "N" }, "number_of_variants_in_consensus": { "examples": [ "130" ], "ontology": "NCIT:C181350", "type": "integer", "minimum": 0, "maximum": 10000, "description": "The number of variants found in consensus sequence", "classification": "Bioinformatic Variants", "label": "Number of variants (AF > 75%)", "fill_mode": "batch", "header": "N" }, "number_of_variants_with_effect": { "examples": [ "93" ], "ontology": "NCIT:C181350", "type": "integer", "minimum": 0, "maximum": 10000, "description": "The number of missense variants", "classification": "Bioinformatic Variants", "label": "Number of variants with effect", "fill_mode": "batch", "header": "N" }, "number_of_sgene_frameshifts": { "examples": [ "0" ], "ontology": "GENEPIO:0001457", "type": "integer", "minimum": 0, "maximum": 1000, "description": "Number of frameshifts in Sgene", "classification": "Bioinformatics and QC metrics fields", "label": "Number of frameshifts in Sgene", "fill_mode": "batch", "header": "N" }, "number_of_unambiguous_bases": { "examples": [ "29000" ], "ontology": "GENEPIO:0001457", "type": "integer", "minimum": 0, "maximum": 30000, "description": "Number of unambiguous bases", "classification": "Bioinformatics and QC metrics fields", "label": "Number of unambiguous bases", "fill_mode": "batch", "header": "N" }, "per_ldmutations": { "examples": [ "98" ], "ontology": "GENEPIO:0001457", "type": "number", "minimum": 0, "maximum": 100, "description": "Percentage of Lineage Defining Mutations", "classification": "Bioinformatics and QC metrics fields", "label": "Percentage of Lineage Defining Mutations", "fill_mode": "batch", "header": "N" }, "per_sgene_ambiguous": { "examples": [ "0" ], "ontology": "GENEPIO:0001457", "type": "number", "minimum": 0, "maximum": 100, "description": "Percentage of sSgene ambiguous bases", "classification": "Bioinformatics and QC metrics fields", "label": "Percentage of sSgene ambiguous bases", "fill_mode": "batch", "header": "N" }, "per_sgene_coverage": { "examples": [ "99" ], "ontology": "GENEPIO:0001457", "type": "number", "minimum": 0, "maximum": 100, "description": "Percentage of Sgene coverage", "classification": "Bioinformatics and QC metrics fields", "label": "Percentage of Sgene coverage", "fill_mode": "batch", "header": "N" }, "qc_test": { "examples": [ "pass" ], "ontology": "GENEPIO:0001457", "type": "string", "description": "Quality control evaluation", "classification": "Bioinformatics and QC metrics fields", "label": "Quality control evaluation", "fill_mode": "batch", "header": "N" }, "qc_failed": { "examples": [ "(per_sgene_coverage < 98.0)" ], "ontology": "0", "type": "string", "description": "Quality control failed fields", "classification": "Bioinformatics and QC metrics fields", "label": "Quality control failed fields", "fill_mode": "batch", "header": "N" }, "schema_name": { "examples": [ "relecov_schema.json" ], "ontology": "0", "type": "string", "description": "Name of the JSON Schema", "classification": "Files info", "label": "Schema Name", "fill_mode": "batch", "header": "N" }, "schema_version": { "examples": [ "v3.0.0" ], "ontology": "0", "type": "string", "description": "Version of the JSON Schema", "classification": "Files info", "label": "Schema Version", "fill_mode": "batch", "header": "N" }, "variant_name": { "examples": [ "alpha" ], "ontology": "GENEPIO:0001498", "type": "string", "description": "The variant classification of the lineage i.e. alpha, beta, etc.", "classification": "Genomic Typing fields", "label": "Variant Name", "fill_mode": "batch", "header": "N" }, "variant_designation": { "enum": [ "Variant of Interest (VOI) [GENEPIO:0100083]", "Variant of Concern (VOC) [GENEPIO:0100082]", "Variant Under Monitoring (VUM) [GENEPIO:0100279]", "Not Provided [SNOMED:434941000124101]", "Not Applicable [GENEPIO:0001619]" ], "examples": [ "Variant of Concern (VOC) [GENEPIO:0100083]" ], "ontology": "GENEPIO:0001503", "type": "string", "description": "The variant classification of the lineage i.e. variant, variant of concern.", "classification": "Genomic Typing fields", "label": "Variant designation", "fill_mode": "batch", "header": "N" }, "gisaid_submitter_id": { "examples": [ "ID9876" ], "ontology": "NCIT:C54269", "type": "string", "description": "GISAID sequence ID.", "classification": "Public databases", "label": "GISAID submitter id", "fill_mode": "sample", "header": "N" }, "gisaid_covv_type": { "examples": [ "betacoronavirus" ], "ontology": "NCIT:C25284", "type": "string", "description": "default must remain 'betacoronavirus'", "classification": "Public databases", "label": "GISAID covv type", "fill_mode": "sample", "header": "N" }, "ena_analysis_accession": { "examples": [ "ERP123456" ], "ontology": "GENEPIO:0001145", "type": "string", "description": "A data field which describes the GenBank/ENA/DDBJ identifier assigned to the sequence in the International Nucleotide Sequence Database Collaboration (INSDC) archives. GenBank = National Genetic Sequence Data Base; ENA = European Nucleotide Archive; DDBJ = DNA DataBank of Japan Example Guidance: Store the accession returned from a GenBank/ENA/DDBJ submission (viral genome assembly).", "classification": "Public databases", "label": "Analysis Accession", "fill_mode": "batch", "header": "N" }, "ena_study_accession": { "examples": [ "e.g PRJEB39632" ], "ontology": "GENEPIO:0001136", "type": "string", "description": "An identifier data field which describes the International Nucleotide Sequence Database Collaboration (INSDC) accession number of the BioProject(s) to which the BioSample belongs.", "classification": "Public databases", "label": "Study accession", "fill_mode": "batch", "header": "N" }, "ena_experiment_accession": { "examples": [ "e.g ERX4331406" ], "ontology": "0", "type": "string", "description": "Experiment Accession", "classification": "Public databases", "label": "Experiment Accession", "fill_mode": "batch", "header": "N" }, "ena_run_accession": { "examples": [ "e.g ERX4331406" ], "ontology": "0", "type": "string", "description": "Run Identifier: A sequence of characters used to uniquely identify a particular run of a test on a particular batch of samples.", "classification": "Public databases", "label": "Run Accession", "fill_mode": "batch", "header": "N" }, "ena_submission_accession": { "examples": [ "e.g ERA2794974" ], "ontology": "0", "type": "string", "description": "Submission Accession", "classification": "Public databases", "label": "Submission Accession", "fill_mode": "batch", "header": "N" }, "ena_experiment_title": { "examples": [ "e.g Illumina MiSeq paired end sequencing" ], "ontology": "NCIT:C181729", "type": "string", "description": "Experiment Name: The name assigned to an experiment.", "classification": "Public databases", "label": "Experiment title", "fill_mode": "batch", "header": "N" }, "study_title": { "examples": [ "e.g SARS-CoV-2 genomes from late April in Stockholm" ], "ontology": "OPMI_0000380", "type": "string", "description": "Title of study", "classification": "Public databases", "label": "Study title", "fill_mode": "batch", "header": "N" }, "ena_study_alias": { "examples": [ "e.g Sweden" ], "ontology": "SIO_001066", "type": "string", "description": "A study is a process that realizes the steps of a study design.", "classification": "Public databases", "label": "Study alias", "fill_mode": "batch", "header": "N" }, "broker_name": { "examples": [ "P17157_1007" ], "ontology": "BU_ISCIII:045", "type": "string", "description": "Broker name", "classification": "Public databases", "label": "Broker Name", "fill_mode": "batch", "header": "N" }, "ena_first_created_date": { "examples": [ "e.g 2020-08-07" ], "ontology": "NCIT:C164483", "type": "string", "format": "date", "description": "The date on which the activity or entity is created.", "classification": "Public databases", "label": "First created date", "fill_mode": "batch", "header": "N" }, "host health state": { "examples": [ "Asymptomatic" ], "ontology": "GENEPIO:0001388", "type": "string", "description": "Status of the host", "classification": "Public databases", "label": "Host health state", "fill_mode": "batch", "header": "N" }, "ena_sample_description": { "examples": [ "Sample from Belgian Covid-19 patient. Sample was obtained at the Hospital AZ Rivierenland, in Antwerp, Belgium." ], "ontology": "sep:00196", "type": "string", "description": "Free text description of the sample.", "classification": "Public databases", "label": "Sample Description", "fill_mode": "batch", "header": "N" }, "file_format": { "enum": [ "BAM [EDAM:2572]", "CRAM [EDAM:3462]", "FASTQ [EDAM:1930]", "FASTA [EDAM:1929]", "Not Provided [SNOMED:434941000124101]" ], "examples": [ "BAM,CRAM,FASTQ" ], "ontology": "MS:1001459", "type": "string", "description": "The run data file model.", "classification": "Files info", "label": "File format", "fill_mode": "batch", "header": "N" }, "collector_name": { "examples": [ "John Smith, unknown" ], "ontology": "GENEPIO:0001797", "type": "string", "description": "Name of the person who collected the specimen", "classification": "Sample collection and processing", "label": "Sample collector name", "fill_mode": "batch", "header": "N" }, "experiment_alias": { "examples": [ "experiment_alias_7a" ], "ontology": "NCIT:C42790", "type": "string", "description": "A coordinated set of actions and observations designed to generate data, with the ultimate goal of discovery or hypothesis testing.", "classification": "Sample collection and processing", "label": "Experiment alias", "fill_mode": "batch", "header": "N" }, "run_alias": { "examples": [ "e.g ena-EXPERIMENT-KAROLINSKA INSITUTET-29-07-2020-14:50:07:151-1" ], "ontology": "NCIT:C117058", "type": "string", "description": "A sequence of characters used to uniquely identify a particular run of a test on a particular batch of samples.", "classification": "Sequencing", "label": "Run Alias", "fill_mode": "batch", "header": "N" }, "clade_assignment": { "examples": [ "B.1.1.7" ], "ontology": "NCIT:C179767", "type": "string", "description": "An indication of the taxonomic clade grouping of organisms.", "classification": "Genomic Typing fields", "label": "Clade Assignment", "fill_mode": "batch", "header": "N" }, "clade_assignment_software_name": { "examples": [ "Nextclade" ], "ontology": "GENEPIO:0001501", "type": "string", "description": "The name of the software used to determine the clade.", "classification": "Genomic Typing fields", "label": "Clade Assignment Software Name", "fill_mode": "batch", "header": "N" }, "if_clade_assignment_other": { "examples": [ "Custom Pipeline" ], "ontology": "0", "type": "string", "description": "Other software used to determine clade.", "classification": "Genomic Typing fields", "label": "Other Clade Assignment Software", "fill_mode": "batch", "header": "N" }, "clade_assignment_software_version": { "examples": [ "3.1.2" ], "ontology": "GENEPIO:0001502", "type": "string", "description": "The version of the software used to determine the clade.", "classification": "Genomic Typing fields", "label": "Clade Assignment Software Version", "fill_mode": "batch", "header": "N" }, "clade_assignment_software_database_version": { "examples": [ "1.2.1" ], "ontology": "MS:1001016", "type": "string", "description": "Version of the search database to determine the clade.", "classification": "Genomic Typing fields", "label": "Clade Assignment Software Database Version", "fill_mode": "batch", "header": "N" }, "clade_assignment_date": { "examples": [ "20241204" ], "ontology": "LOINC:40783184", "type": "string", "format": "date", "description": "Date when the clade analysis was performed via Nextclade", "classification": "Genomic Typing fields", "label": "Clade Assignment Date", "fill_mode": "batch", "header": "N" }, "lineage_assignment": { "examples": [ "KP.3.1.1" ], "ontology": "NCIT:C179767", "type": "string", "description": "An indication of the taxonomic lineage grouping of organisms.", "classification": "Genomic Typing fields", "label": "Lineage Assignment", "fill_mode": "batch", "header": "N" }, "lineage_assignment_software_name": { "examples": [ "Pangolin" ], "ontology": "GENEPIO:0001501", "type": "string", "description": "The name of the software used to determine the lineage.", "classification": "Genomic Typing fields", "label": "Lineage Assignment Software Name", "fill_mode": "batch", "header": "N" }, "if_lineage_assignment_other": { "examples": [ "Custom Pipeline" ], "ontology": "0", "type": "string", "description": "Other software used to determine lineage.", "classification": "Genomic Typing fields", "label": "Other Lineage Assignment Software", "fill_mode": "batch", "header": "N" }, "lineage_assignment_software_version": { "examples": [ "2.2.1" ], "ontology": "GENEPIO:0001502", "type": "string", "description": "The version of the software used to determine the lineage.", "classification": "Genomic Typing fields", "label": "Lineage Assignment Software Version", "fill_mode": "batch", "header": "N" }, "lineage_algorithm_software_version": { "examples": [ "PUSHER-v1.28" ], "ontology": "0", "type": "string", "description": "Version of the algorithm used by the lineage assignment software", "classification": "Genomic Typing fields", "label": "Lineage Algorithm Software Version", "fill_mode": "batch", "header": "N" }, "lineage_assignment_scorpio_version": { "examples": [ "1.1.3" ], "ontology": "NCIT:C111093", "type": "string", "description": "The version of the scorpio data used to determine the lineage.", "classification": "Genomic Typing fields", "label": "Lineage Assignment Scorpio Version", "fill_mode": "batch", "header": "N" }, "lineage_assignment_constellation_version": { "examples": [ "3.1.1" ], "ontology": "NCIT:C111093", "type": "string", "description": "The version of the constellations databases used to determine the lineage.", "classification": "Genomic Typing fields", "label": "Lineage Assignment Constellation Version", "fill_mode": "batch", "header": "N" }, "lineage_assignment_date": { "examples": [ "20241204" ], "ontology": "LOINC:40783184", "type": "string", "format": "date", "description": "Date when the lineage analysis was performed", "classification": "Genomic Typing fields", "label": "Lineage Assignment Date", "fill_mode": "batch", "header": "N" }, "lineage_assignment_file": { "examples": [ "lineage_analysis_results.csv" ], "ontology": "0", "type": "string", "description": "File containing results from lineage analysis", "classification": "Genomic Typing fields", "label": "Lineage Assignment File", "fill_mode": "batch", "header": "N" }, "lineage_assignment_database_version": { "examples": [ "2.26.0" ], "ontology": "0", "type": "string", "description": "Version of the lineage assignment database", "classification": "Genomic Typing fields", "label": "Pangolin Database Version", "fill_mode": "batch", "header": "N" }, "type_assignment": { "examples": [ "RSV-A" ], "ontology": "NCIT:C179767", "type": "string", "description": "An indication of the taxonomic grouping of organisms.", "classification": "Genomic Typing fields", "label": "Type Assignment", "fill_mode": "batch", "header": "N" }, "type_assignment_software_name": { "examples": [ "Nextclade" ], "ontology": "GENEPIO:0001501", "type": "string", "description": "The name of the software used to determine the type.", "classification": "Genomic Typing fields", "label": "Type Assignment Software Name", "fill_mode": "batch", "header": "N" }, "if_type_assignment_software_other": { "examples": [ "Manual curation" ], "ontology": "0", "type": "string", "description": "Other software iused to determine Type.", "classification": "Genomic Typing fields", "label": "Other Type Assignment Software", "fill_mode": "batch", "header": "N" }, "type_assignment_software_version": { "examples": [ "2.0.1" ], "ontology": "GENEPIO:0001502", "type": "string", "description": "The version of the software used to determine thetype.", "classification": "Genomic Typing fields", "label": "Type Assignment Software Version", "fill_mode": "batch", "header": "N" }, "type_assignment_software_database_version": { "examples": [ "1.5.2" ], "ontology": "MS:1001016", "type": "string", "description": "Version of the search database.", "classification": "Genomic Typing fields", "label": "Type Assignment Software Database Version", "fill_mode": "batch", "header": "N" }, "subtype_assignment": { "examples": [ "H1N1" ], "ontology": "NCIT:C179767", "type": "string", "description": "An indication of the taxonomic grouping of organisms.", "classification": "Genomic Typing fields", "label": "Subtype Assignment", "fill_mode": "batch", "header": "N" }, "subtype_assignment_software_name": { "examples": [ "Nextclade" ], "ontology": "GENEPIO:0001501", "type": "string", "description": "The name of the software used to determine the subtype.", "classification": "Genomic Typing fields", "label": "Subtype Assignment Software Name", "fill_mode": "batch", "header": "N" }, "if_subtype_assignment_software_other": { "examples": [ "Custom Pipeline" ], "ontology": "0", "type": "string", "description": "Other software used to determine Subtype.", "classification": "Genomic Typing fields", "label": "Other Subtype Assignment Software", "fill_mode": "batch", "header": "N" }, "subtype_assignment_software_version": { "examples": [ "3.2.2" ], "ontology": "GENEPIO:0001502", "type": "string", "description": "The version of the software used to determine the subtype.", "classification": "Genomic Typing fields", "label": " Subtype Assignment Software Version", "fill_mode": "batch", "header": "N" }, "subtype_assignment_software_database_version": { "examples": [ "3.1.3" ], "ontology": "MS:1001016", "type": "string", "description": "Version of the search database.", "classification": "Genomic Typing fields", "label": "Subtype Assignment Software Database Version", "fill_mode": "batch", "header": "N" } }, "required": [ "organism", "collecting_lab_sample_id", "isolate_sample_id", "sequencing_sample_id", "collecting_institution", "submitting_institution", "sample_collection_date", "host_common_name", "enrichment_panel", "enrichment_panel_version", "sequencing_instrument_model", "library_source", "library_strategy", "library_layout", "sequence_file_R1", "collecting_institution_code_1", "collecting_institution_code_2", "geo_loc_country", "geo_loc_state", "geo_loc_state_cod", "host_scientific_name", "sequencing_instrument_platform" ], "anyOf": [ { "required": [ "all_in_one_library_kit" ] }, { "required": [ "library_preparation_kit" ] } ] }