From cc50706780846dba3c2ab965b22af631ebfa7491 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Wed, 17 Mar 2021 16:22:43 -0700 Subject: [PATCH] vocabulary update --- template/canada_covid19/data.js | 61 +- template/canada_covid19/data.tsv | 2683 ++++++++++++++--------------- template/pha4ge/data.js | 508 +++--- template/pha4ge/data.tsv | 2773 ++++++++++++++---------------- template/pha4ge/export.js | 111 +- template/pha4ge/reference.html | 117 +- 6 files changed, 2993 insertions(+), 3260 deletions(-) diff --git a/template/canada_covid19/data.js b/template/canada_covid19/data.js index e34c57cf..84eb9ec6 100644 --- a/template/canada_covid19/data.js +++ b/template/canada_covid19/data.js @@ -239,6 +239,11 @@ var DATA = [ "field": "GISAID Accession (if known)" } ], + "NML_LIMS": [ + { + "field": "GISAID Accession ID" + } + ], "BIOSAMPLE": [ { "field": "GISAID_accession" @@ -3870,6 +3875,11 @@ var DATA = [ { "field": "Age Units" } + ], + "NML_LIMS": [ + { + "field": "PH_AGE_UNIT" + } ] }, "schema:ItemList": { @@ -5811,13 +5821,6 @@ var DATA = [ "description": "Whether there was prior SARS-CoV-2 treatment with an antiviral agent.", "guidance": "If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list.", "examples": "No prior antiviral treatment", - "exportField": { - "CNPHI": [ - { - "field": "prior_SARS-CoV-2_antiviral_treatment" - } - ] - }, "schema:ItemList": { "Prior antivrial treatment": {}, "No prior antivrial treatment": {}, @@ -5882,6 +5885,11 @@ var DATA = [ "field": "Reason for Sequencing" } ], + "NML_LIMS": [ + { + "field": "PH_REASON_FOR_SEQUENCING" + } + ], "BIOSAMPLE": [ { "field": "purpose_of_sequencing" @@ -5946,6 +5954,11 @@ var DATA = [ { "field": "Details on the Reason for Sequencing" } + ], + "NML_LIMS": [ + { + "field": "PH_REASON_FOR_SEQUENCING_DETAILS" + } ] } }, @@ -6054,6 +6067,11 @@ var DATA = [ { "field": "Sequencing Instrument" } + ], + "NML_LIMS": [ + { + "field": "ANALYSIS" + } ] }, "schema:ItemList": { @@ -6152,11 +6170,6 @@ var DATA = [ { "field": "Sequencing Protocol Name" } - ], - "NML_LIMS": [ - { - "field": "PH_TESTING_PROTOCOL" - } ] } }, @@ -6172,7 +6185,14 @@ var DATA = [ "requirement": "", "description": "The protocol used to generate the sequence.", "guidance": "Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. \"", - "examples": "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." + "examples": "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits.", + "exportField": { + "NML_LIMS": [ + { + "field": "PH_TESTING_PROTOCOL" + } + ] + } }, { "fieldName": "sequencing kit number", @@ -6295,6 +6315,11 @@ var DATA = [ { "field": "consensus sequence" } + ], + "NML_LIMS": [ + { + "field": "Consensus Sequence Method Name" + } ] } }, @@ -6316,6 +6341,11 @@ var DATA = [ { "field": "consensus sequence" } + ], + "NML_LIMS": [ + { + "field": "Consensus Sequence Method Version Name" + } ] } }, @@ -6953,6 +6983,11 @@ var DATA = [ { "field": "Authors" } + ], + "NML_LIMS": [ + { + "field": "PH_CANCOGEN_AUTHORS" + } ] } }, diff --git a/template/canada_covid19/data.tsv b/template/canada_covid19/data.tsv index 6ff8c739..e175b080 100644 --- a/template/canada_covid19/data.tsv +++ b/template/canada_covid19/data.tsv @@ -1,1419 +1,1264 @@ -Ontology ID parent class label datatype source data status requirement min value max value capitalize description guidance examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE ontology label definition definition source english synonym Parental Term Parental Term URL Issues / Status Other -ID SC % AL rdfs:label@en AL IAO:0000115@en A IAO:0000119 SPLIT=| AL oboInOwl:hasExactSynonym@en - Database Identifiers - Database Identifiers specimen collector sample ID xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_rona_99 Sample ID given by the sample provider Primary Specimen ID VD_LAB_NUMBER sample_name - Database Identifiers NML submitted specimen primary ID xs:token The primary ID of the specimen submitted thorough LaSER. Store the identifier for the specimen submitted through the NML LaSER system. SR20-12345 - Database Identifiers NML related specimen primary ID xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The primary ID of the related specimen previously submitted thorough LaSER Store the primary ID of the related specimen previously submitted thorough LaSER SR20-12345 Related Specimen ID|Related Specimen Relationship Type - Database Identifiers IRIDA sample name xs:token The identifier assigned to a sequenced isolate in IRIDA. Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 - Database Identifiers umbrella bioproject accession select UPPER The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. PRJNA623807 - Database Identifiers bioproject accession xs:token UPPER The INSDC accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 BioProject Accession PH_BIOPROJECT_ACCESSION bioproject_accession - Database Identifiers biosample accession xs:token UPPER The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION - Database Identifiers SRA accession xs:token UPPER The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 SRA Accession PH_SRA_ACCESSION - Database Identifiers GenBank accession xs:token UPPER The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 GenBank Accession - Database Identifiers GISAID accession xs:token UPPER The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) GISAID_accession - Sample collection and processing - Sample collection and processing sample collected by xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name collected_by CNPHI_EXPORT: Lev said it isn't useful because the client information is filled in when the client submits. It isn't filled in when Emma submits for others and then NML/CNPHI gets manually changed after submission. - Sample collection and processing sample collector contact email xs:token The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca - Sample collection and processing sample collector contact address xs:token The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address - Sample collection and processing sequence submitted by select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by - Sample collection and processing sequence submitter contact email xs:token The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca - Sample collection and processing sequence submitter contact address xs:token The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address - Sample collection and processing sample collection date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date - Sample collection and processing sample collection date precision select required Precision of date collected HC_TEXT2 - Sample collection and processing sample received date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 - Sample collection and processing geo_loc_name (country) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name - Sample collection and processing geo_loc_name (state/province/territory) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name - Sample collection and processing geo_loc_name (city) xs:token The city where the sample was collected. Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Medicine Hat Patient City - Sample collection and processing organism select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Taxonomic name of the organism. Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template. Severe acute respiratory syndrome coronavirus 2 Pathogen HC_CURRENT_ID organism - Sample collection and processing isolate xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Identifier of the specific isolate. Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/xxxxx/2020”. hCov-19/CANADA/prov_rona_99/2020 Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name - Sample collection and processing purpose of sampling select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling - Sample collection and processing purpose of sampling details xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. Details on the Reason for Sampling description - Sample collection and processing NML submitted specimen type select required The type of specimen submitted to the NML for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. swab Specimen Type PH_SPECIMEN_TYPE - Sample collection and processing NML related specimen relationship type select The relationship of the related specimen to the previous submission. Provide the specimen type of the original sample submitted from the pick list provided, so that additional specimen testing can be tracked in the system. Follow-up Related Specimen ID|Related Specimen Relationship Type - Sample collection and processing anatomical material select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Blood Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material - Sample collection and processing anatomical part select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Nasopharynx (NP) Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part - Sample collection and processing body product select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Feces Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product - Sample collection and processing environmental material select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Face mask Specimen source Environmental Material PH_ENVIRONMENTAL_MATERIAL isolation_source;environmental_material - Sample collection and processing environmental site select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Production Facility Specimen source Environmental Site PH_ENVIRONMENTAL_SITE isolation_source;environmental_site - Sample collection and processing collection device select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device - Sample collection and processing collection method select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Bronchoalveolar lavage (BAL) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method - Sample collection and processing collection protocol xs:token The name and version of a particular protocol used for sampling. Free text. BCRonaSamplingProtocol v. 1.2 - Sample collection and processing specimen processing multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Virus passage Passage details/history - Sample collection and processing lab host select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. Type of cell line used for propagation. Provide the name of the cell line using the picklist in the template. If not passaged, put "not applicable". Vero E6 cell line Passage details/history lab_host - Sample collection and processing passage number xs:nonNegativeInteger Not Applicable recommended Number of passages. Provide number of known passages. If not passaged, put "not applicable" 3 Passage details/history passage_history - Sample collection and processing passage method xs:token Not Applicable recommended Description of how organism was passaged. Free text. Provide a very short description (<10 words). If not passaged, put "not applicable". Passage details/history passage_method - Sample collection and processing biomaterial extracted select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The biomaterial extracted from samples for the purpose of sequencing. Provide the biomaterial extracted from the picklist in the template. RNA (total) - Host Information - Host Information host (common name) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put "not applicable. Human Animal Type PH_ANIMAL_TYPE - Host Information host (scientific name) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host - Host Information host health state select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Health status of the host at the time of sample collection. If known, select a descriptor from the pick list provided in the template. Symptomatic Patient status Host Health State PH_HOST_HEALTH host_health_state - Host Information host health status details select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized (ICU) Host Health State Details PH_HOST_HEALTH_DETAILS - Host Information host health outcome select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Disease outcome in the host. If known, select a descriptor from the pick list provided in the template. Recovered host_disease_outcome - Host Information host disease select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the disease experienced by the host. Select "COVID-19" from the pick list provided in the template. COVID-19 Host Disease PH_HOST_DISEASE host_disease - Host Information host age xs:decimal Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required 0 130 Age of host at the time of sampling. Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". 79 Patient age Patient Age PH_AGE host_age - Host Information host age unit select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The unit used to measure the host age, in either months or years. Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. Age Units - Host Information host age bin select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. 60 - 69 Host Age Category PH_AGE_GROUP - Host Information host gender select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The gender of the host at the time of sample collection. Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". male Gender Patient Sex VD_SEX host_sex - Host Information host residence geo_loc name (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The country of residence of the host. Select the country name from pick list provided in the template. United Kingdom - Host Information host residence geo_loc name (state/province/territory) select geo_loc_name (state/province/territory) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The state/province/territory of residence of the host. Select the province/territory name from pick list provided in the template. Quebec - Host Information host subject ID xs:token A unique identifier by which each host can be referred to e.g. #131 Provide the host identifier. Should be a unique, user-defined identifier. BCxy123 host_subject_id - Host Information symptom onset date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date on which the symptoms began or were first noted. ISO 8601 standard "YYYY-MM-DD". 2020-03-16 Symptoms Onset Date HC_ONSET_DATE - Host Information signs and symptoms multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician. Select all of the symptoms experienced by the host from the pick list. Chills (sudden cold sensation); Cough; Fever Symptoms HC_SYMPTOMS - Host Information pre-existing conditions and risk factors multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Asthma; Pregnancy; Smoking - Host Information complications multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Acute Respiratory Failure; Coma; Septicemia - Host vaccination information - Host vaccination information host vaccination status select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated - Host vaccination information vaccine name xs:token The name of the vaccine. Free text. Provide the name of the vaccine. Pfizer-BioNTech COVID-19 vaccine - Host vaccination information number of vaccine doses received xs:nonNegativeInteger The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 2 - Host vaccination information first dose vaccination date xs:date The date the host was first vaccinated. Provide the vaccination date in ISO 8601 standard format "YYYY-MM-DD". 2021-02-26 - Host vaccination information last dose vaccination date xs:date The date the host received their last dose of vaccine. Provide the date that the last dose of the vaccine was administered. Provide the last dose vaccination date in ISO 8601 standard format "YYYY-MM-DD". 2021-04-09 - Host exposure information - Host exposure information location of exposure geo_loc name (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The country where the host was likely exposed to the causative agent of the illness. Select the country name from pick list provided in the template. Canada - Host exposure information destination of most recent travel (city) xs:token The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information destination of most recent travel (state/province/territory) xs:token The name of the province that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information destination of most recent travel (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the country that was the destination of most recent travel. Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz United Kingdom Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information most recent travel departure date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date. 2020-03-16 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information most recent travel return date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date. 2020-04-26 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information travel history xs:token Travel history in last six months. Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Canada, Vancouver; USA, Seattle; Italy, Milan - Host exposure information exposure event select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Convention Additional location information Exposure Event PH_EXPOSURE - Host exposure information exposure contact level select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The exposure transmission contact type. Select direct or indirect exposure from the pick-list. Direct - Host exposure information host role multiple The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Patient - Host exposure information exposure setting multiple The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Healthcare Setting - Host exposure information exposure details xs:token Additional host exposure information. Free text description of the exposure. Host role - Other: Bus Driver - - - Host reinfection information - Host reinfection information prior SARS-CoV-2 infection select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether there was prior SARS-CoV-2 infection. Ik known, provide infromation about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. Yes - Host reinfection information prior SARS-CoV-2 infection isolate xs:token The identifier of the isolate found in the prior SARS-CoV-2 infection. Provide the isolate name of the most recent prior infection. Structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". SARS-CoV-2/human/USA/CA-CDPH-001/2020 - Host reinfection information prior SARS-CoV-2 infection date xs:date The date of diagnosis of the prior SARS-CoV-2 infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-23 - Host reinfection information prior SARS-CoV-2 antiviral treatment select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether there was prior SARS-CoV-2 treatment with an antiviral agent. If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. No prior antiviral treatment prior_SARS-CoV-2_antiviral_treatment - Host reinfection information prior SARS-CoV-2 antiviral treatment agent xs:token The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put "No treatment". If multiple antiviral agents were administered, list them all separated by commas. Remdesivir - Host reinfection information prior SARS-CoV-2 antiviral treatment date xs:date The date treatment was first administered during the prior SARS-CoV-2 infection. Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-28 - - - Sequencing - Sequencing purpose of sequencing select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) Reason for Sequencing purpose_of_sequencing - Sequencing purpose of sequencing details xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Screened for S gene target failure (S dropout) Details on the Reason for Sequencing - Sequencing sequencing date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 - Sequencing library ID xs:token recommended The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 - Sequencing amplicon size xs:token The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp - Sequencing library preparation kit xs:token The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT - Sequencing flow cell barcode xs:token The barcode of the flow cell used for sequencing. Provide the barcode of the flow cell used for sequencing the sample. FAB06069 - Sequencing sequencing instrument multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. MinIon Sequencing technology Sequencing Instrument - Sequencing sequencing protocol name xs:token recommended The name and version number of the sequencing protocol used. Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann Sequencing Protocol Name PH_TESTING_PROTOCOL - Sequencing sequencing protocol xs:token The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. - Sequencing sequencing kit number xs:token The manufacturer's kit number. Alphanumeric value. AB456XYZ789 - Sequencing amplicon pcr primer scheme xs:token The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv - - - Bioinformatics and QC metrics - Bioinformatics and QC metrics raw sequence data processing method xs:token recommended The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 - Bioinformatics and QC metrics dehosting method xs:token The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper - Bioinformatics and QC metrics consensus sequence name xs:token The name of the consensus sequence. Provide the name and version number of the consensus sequence. ncov123assembly3 - Bioinformatics and QC metrics consensus sequence filename xs:token The name of the consensus sequence file. Provide the name and version number of the consensus sequence FASTA file. ncov123assembly.fasta - Bioinformatics and QC metrics consensus sequence filepath xs:token The filepath of the consesnsus sequence file. Provide the filepath of the consensus sequence FASTA file. /User/Documents/RespLab/Data/ncov123assembly.fasta - Bioinformatics and QC metrics consensus sequence software name xs:token required The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. Ivar consensus sequence - Bioinformatics and QC metrics consensus sequence software version xs:decimal required The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 consensus sequence - Bioinformatics and QC metrics breadth of coverage value xs:token The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95% - Bioinformatics and QC metrics depth of coverage value xs:token The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Coverage - Bioinformatics and QC metrics depth of coverage threshold xs:token The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x - Bioinformatics and QC metrics r1 fastq filename xs:token recommended The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz - Bioinformatics and QC metrics r2 fastq filename xs:token recommended The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz - Bioinformatics and QC metrics r1 fastq filepath xs:token The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz - Bioinformatics and QC metrics r2 fastq filepath xs:token The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz - Bioinformatics and QC metrics fast5 filename xs:token The user-specified filename of the FAST5 file. Provide the FAST5 filename. rona123assembly.fast5 - Bioinformatics and QC metrics fast5 filepath xs:token The location of the FAST5 file within a user's file system. Provide the filepath for the FAST5 file. This information aids in data management. /User/Documents/RespLab/Data/rona123assembly.fast5 - Bioinformatics and QC metrics number of base pairs sequenced xs:nonNegativeInteger The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 - Bioinformatics and QC metrics consensus genome length xs:nonNegativeInteger Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). 38677 - Bioinformatics and QC metrics Ns per 100 kbp xs:decimal 0 The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence. Provide a numerical value (no need to include units). 330 - Bioinformatics and QC metrics reference genome accession xs:token A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 - Bioinformatics and QC metrics bioinformatics protocol xs:token The name and version number of the bioinformatics protocol used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can be provided in an SOP or protocol. Provide the name and version number of the protocol. https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members Bioinformatics Protocol - Lineage and Variant information - Lineage and Variant information lineage/clade name xs:token The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. B.1.1.7 - Lineage and Variant information lineage/clade analysis software name xs:token The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Pangolin - Lineage and Variant information lineage/clade analysis software version xs:token The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 2.1.10 - Lineage and Variant information variant designation select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The variant classification of the lineage/clade i.e. variant, variant of concern. If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. Variant of Concern - Lineage and Variant information variant evidence select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The evidence used to make the variant determination. Select whether the sample was screened using RT-qPCR or by sequencing from the pick list. RT-qPCR TaqPath assay: S gene target failure - Lineage and Variant information variant evidence details xs:token Details about the evidence used to make the variant determination. Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. - Pathogen diagnostic testing - Pathogen diagnostic testing gene name 1 select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI E (orf4) Gene Target 1 RESULT - CANCOGEN_SUBMITTED_RESLT_1 gene_name_1 - Pathogen diagnostic testing diagnostic pcr protocol 1 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. EGenePCRTest 2 - Pathogen diagnostic testing diagnostic pcr Ct value 1 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the diagnostic RT-PCR test. 21 Gene Target 1 CT Value RESULT - CANCOGEN_SUBMITTED_RESLT_1CT diagnostic_PCR_CT_value_1 - Pathogen diagnostic testing gene name 2 select gene name 1 Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI nsp12 (RdRp) Gene Target 2 RESULT - CANCOGEN_SUBMITTED_RESLT_2 gene_name_2 - Pathogen diagnostic testing diagnostic pcr protocol 2 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. RdRpGenePCRTest 3 - Pathogen diagnostic testing diagnostic pcr Ct value 2 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 36 Gene Target 2 CT Value RESULT - CANCOGEN_SUBMITTED_RESLT_2CT diagnostic_PCR_CT_value_2 - Pathogen diagnostic testing gene name 3 select gene name 1 Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI nsp12 (RdRp) Gene Target 3 - Pathogen diagnostic testing diagnostic pcr protocol 3 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. RdRpGenePCRTest 3 - Pathogen diagnostic testing diagnostic pcr Ct value 3 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 3 CT Value - Contributor acknowledgement - Contributor acknowledgement authors xs:token recommended Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors - Contributor acknowledgement DataHarmonizer provenance provenance DataHarmonizer provenance Additional Comments HC_COMMENTS - - - umbrella bioproject accession PRJNA623807 - - - - - - - - -GAZ_00002566 geo_loc_name (state/province/territory) Alberta CA-AB Province of Alberta Province (Canada) GAZ:00002561 -GAZ_00002562 geo_loc_name (state/province/territory) British Columbia CA-BC Province of British Columbia Province (Canada) GAZ:00002561 -GAZ_00002571 geo_loc_name (state/province/territory) Manitoba CA-MB Province of Manitoba Province (Canada) GAZ:00002561 -GAZ_00002570 geo_loc_name (state/province/territory) New Brunswick CA-NB Province of New Brunswick Province (Canada) GAZ:00002561 -GAZ_00002567 geo_loc_name (state/province/territory) Newfoundland and Labrador CA-NL Province of Newfoundland and Labrador Province (Canada) GAZ:00002561 CNPHI wants "Newfoundland and Labrador"; changed to http://purl.obolibrary.org/obo/GAZ_00002567 -GAZ_00002575 geo_loc_name (state/province/territory) Northwest Territories CA-NT Northwest Territories Territory (Canada) GAZ:00002573 -GAZ_00002565 geo_loc_name (state/province/territory) Nova Scotia CA-NS Province of Nova Scotia Province (Canada) GAZ:00002561 -GAZ:00002574 geo_loc_name (state/province/territory) Nunavut CA-NU Nunavut Territory (Canada) GAZ:00002573 -GAZ_00002563 geo_loc_name (state/province/territory) Ontario CA-ON Province of Ontario Province (Canada) GAZ:00002561 -GAZ_00002572 geo_loc_name (state/province/territory) Prince Edward Island CA-PE Province of Prince Edward Island Province (Canada) GAZ:00002561 -GAZ_00002569 geo_loc_name (state/province/territory) Quebec CA-QC Province of Quebec Province (Canada) GAZ:00002561 -GAZ_00002564 geo_loc_name (state/province/territory) Saskatchewan CA-SK Province of Saskatchewan Province (Canada) GAZ:00002561 -GAZ_00002576 geo_loc_name (state/province/territory) Yukon CA-YT Yukon Territory (Canada) GAZ:00002573 - -UO:0000035 host age unit month month -UO:0000036 host age unit year year - -UO:0000035 sample collection date precision year -UO:0000036 sample collection date precision month -UO:0000033 sample collection date precision day - -OBI:0000895 biomaterial extracted RNA (total) total RNA extract total RNA extract RNA extract OBI:0000880 -OBI:0000869 biomaterial extracted RNA (poly-A) polyA RNA extract polyA RNA extract, poly-A RNA extract RNA extract OBI:0000880 -OBI:0002627 biomaterial extracted RNA (ribo-depleted) ribosomal RNA-depleted RNA extract ribo-depleted RNA extract RNA extract OBI:0000880 - biomaterial extracted mRNA (messenger RNA) messenger RNA extract An extract which is the output of an extraction process in which messenger RNA molecules are isolated from a specimen. messenger RNA extract, mRNA extract, broader: cDNA extract, complementary DNA extract RNA extract OBI:0000880 "Make OBI term request in ""sequence"" tab - adjust fields to be suitable for OBI annotations. -Definition modelled on other `RNA extract` definitions but sitll needs review." -OBI:0002754 biomaterial extracted mRNA (cDNA) cDNA library processed material OBI:0000047 - - - signs and symptoms Abnormal lung auscultation Corrected spelling mistake "ausculation" -> "auscultation" -HP:0000223 signs and symptoms Abnormality of taste sensation SENSE_OF_TASTE Abnormality of taste sensation Abnormality of taste sensation "Abnormal nervous system physiology, -Abnormal tongue physiology" "HP:0012638, -HP:0030810" "Changed label to match the format of 'abnormality of the sense of smell'. - Rhiannon - -Removed ""label"" so it no longer shows up in the DH picklist as it was causing confusion and is more relevant to the ontology side than as a picklist value." - Abnormality of taste sensation Ageusia (complete loss of taste) AGEUSIA The loss of taste functions of the tongue https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165999/ complete loss of taste, complete lack of taste Abnormality of taste sensation HP_0000223 New term - Recommend making term request to HPO -HP:0031249 Abnormality of taste sensation Parageusia (distorted sense of taste) PARAGEUSIA Parageusia Dysgeusia, Metallic taste in mouth, Metallic taste, distorted sense of taste, distortion of the sense of taste Abnormality of taste sensation HP_0000223 Changed from 'Dysgeusia' to 'Parageusia' because that entry was in HP. - Rhiannon -HP_0000224 Abnormality of taste sensation Hypogeusia (reduced sense of taste) HYPOGEUSIA Decreased taste sensation The decrease in taste sensitivity. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165999/ Decreased taste, Lost taste, Decreased taste sensation, Hypogeusia, loss of taste, lack of taste, reduced sense of taste, new loss of taste Abnormality of taste sensation HP_0000223 "New term - -Recommend making syonym request to HPO" -HP:0004408 signs and symptoms Abnormality of the sense of smell SENSE_OF_SMELL Abnormality of the sense of smell Abnormal sense of smell, Abnormality of olfaction, Abnormality of the sense of smell, Smell defect "Abnormal nervous system physiology, -Abnormality of the nose" "HP:0012638, -HP:0000366" -HP_0000458 Abnormality of the sense of smell Anosmia (lost sense of smell) ANOSMIA Anosmia Lost smell, Loss of smell, new loss of smell Abnormality of the sense of smell HP_0004408 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0010528 -HP_0004409 Abnormality of the sense of smell Hyposmia (reduced sense of smell) HYPOSMIA Hyposmia Decreased smell sensation, Sense of smell impaired, reduced sense of smell Abnormality of the sense of smell HP_0004408 - signs and symptoms Acute Respiratory Distress Syndrome ARDS ARDS Appears under 'signs/symptoms' most frequently. -HP:0011446 signs and symptoms Altered mental status ALTERED_CONSCIOUS Abnormality of higher mental function altered consciousness, altered mental status, altered mental state Abnormal nervous system physiology HP:0012638 "Changed label to 'Altered mental status' since that was the most common usage in case report forms. - -May want to consider alternate parent term. " -HP:0011675 signs and symptoms Arrhythmia Arrhythmia Abnormal heart rate, Cardiac arrhythmia, Heart rhythm disorders, Irregular heartbeat, Cardiac arrhythmias, Cardiac rhythm disturbances, Arrhythmias, Irregular heart beat Abnormality of cardiovascular system electrophysiology HP:0030956 -HP:0100543 Altered mental status Cognitive impairment COGNITIVE Cognitive impairment Intellectual impairment, Mental impairment, Cognitive abnormality, Abnormality of cognition, Cognitive defects, Cognitive deficits, Cognitive impairment Abnormality of higher mental function HP:0011446 -HP_0001259 Altered mental status Coma COMA Coma Reduced consciousness/confusion HP_0004372 -HP_0001289 Altered mental status Confusion CONFUSION Confusion mental confusion, new confusion, new or worsening confusion, layperson: disorientation, mental disorientation, easily confused Reduced consciousness/confusion HP_0004372 Removed 'new confusion' term from the picklist and added it here as a synonym. - Rhiannon -HP_0031258 Confusion Delirium (sudden severe confusion) DELIRIUM Delirium Confusion HP_0001289 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0045057 - Altered mental status Inability to arouse (inability to stay awake) INABILITY_AWAKE Needs further review -HP_0000737 Altered mental status Irritability IRRITABILITY Irritability Irritable, Irritability "Impaired social interactions, -Abnormal emotion/affect behavior" "HP_0000735, -HP_0100851" -HP_0002371 Altered mental status Loss of speech LOSS_OF_SPEECH Loss of speech Neurological speech impairment HP_0002167 -HP_0025406 signs and symptoms Asthenia (generalized weakness) ASTHENIA Asthenia general weakness, generalized weakness, abnormal physical weakness, loss of energy, weakness Constitutional symptom HP_0025142 Changed label from "Asthenia (general weakness)" to "Asthenia (generalized weakness)" to improve CNPHI compatibility. -HP:0031352 signs and symptoms Chest tightness or pressure CHEST_TIGHT Chest tightness Tightness in chest, chest pressure Constitutional symptom HP:0025142 -HP:0025145 Chest tightness or pressure Rigors (fever shakes) RIGORS Rigors Rigours, fever shakes, severe shivering with chills, severe shaking with chills, repeated shaking with chills "Shivering, -Chills" "HP:0025144, -HP:0025143" consider adding/requesting parent term 'fever' -HP_0025143 signs and symptoms Chills (sudden cold sensation) Chills CHILLS Chills Constitutional symptom HP_0025142 - signs and symptoms Conjunctival injection Conjunctival hypermia -HP_0000509 signs and symptoms Conjunctivitis (pink eye) Conjunctivitis CONJUNCTIVITIS Conjunctivitis Pink eye "Inflammatory abnormality of the eye, -Abnormal conjunctiva morphology, -Red eye" "HP_0100533, -HP_0000502, -HP_0025337" Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0003799 - signs and symptoms Coryza -HP_0012735 signs and symptoms Cough COUGH Cough Coughing, Cough, new cough, worsening cough, new or worsening cough Functional respiratory abnormality HP_0002795 -HP:0031246 Cough Nonproductive cough (dry cough) NONPRODUCT_COUGH Nonproductive cough dry cough, dry coughing Cough HP:0012735 -HP:0031245 Cough Productive cough (wet cough) PRODUCTIVE_COUGH Productive cough wet cough, cough with sputum production Cough HP:0012735 -HP:0000961 signs and symptoms Cyanosis (blueish skin discolouration) CYANOSIS Cyanosis narrower: central cyanosis, peripheral cyanosis, related: hypoxima "Functional respiratory abnormality, -Dermatological manifestations of systemic disorders" "HP:0002795, -HP:0001005" "Caused by hypoxima, is related to covid toes/fingers. -Cyanosis is different from frostbite (chilblains) because it is rarely associated with pain." -HP:0001063 Cyanosis (blueish skin discolouration) Acrocyanosis ACROCYANOS Acrocyanosis Persistent blue color of hands, feet, or parts of face', related: peripheral cyanosis Cyanosis HP:0000961 Is characterized by 'peripheral cyanosis' but does not appear to be an exact synonym. - Acrocyanosis Circumoral cyanosis (bluish around mouth) CIRCUMORAL_CYANOSIS Circumoral cyanosis Cyanosis HP:0000961 "Considered a type of acrocyanosis by healthline.com (ref other). HP currently lists it as a sister class to 'acrocyanosis'. -However, it doesn't seem to be a clear consensus on whether it gets defined under 'central cyanosis' or 'peripheral cyanosis' (for e.g. see 'other')." "https://www.healthline.com/health/circumoral-cyanosis#:~:text=Circumoral%20cyanosis%20refers%20to%20blue,on%20their%20hands%20and%20feet. -https://pubmed.ncbi.nlm.nih.gov/2797223/" - Acrocyanosis Cyanotic face (bluish face) CYANOTIC_FACE cyanosis of the face "Acrocyanosis, -Central cyanosis" Didn't list it under 'central cyanosis' but it should be when ontologized. - Cyanosis (blueish skin discolouration) Central Cyanosis Bluish discoloration of the skin, mucous membranes, lips, tongue, and nail beds, associated with arterial desaturation. https://www.sciencedirect.com/topics/neuroscience/cyanosis - Central Cyanosis Cyanotic lips (bluish lips) CYANOTIC_LIPS Central cyanosis Has been stated to belong to 'central' and 'peripheral' cyanoses on different sources... Am only listing it under central at this time since some definitions of 'peripheral cyanosis' do not include lips. - Cyanosis (blueish skin discolouration) Peripheral Cyanosis Blues discoloration that occurs when there is increased oxygen uptake in peripheral tissues, often involving only the extremities; it is not associated with arterial desaturation. https://www.sciencedirect.com/topics/neuroscience/cyanosis cyanosis of the hands or feet, cyanosis of the extremities Characterizes 'acrocyanosis' but isn't considered an exact synonym. -HP_0002094 signs and symptoms Dyspnea (breathing difficulty) DYSPNEA Dyspnea Difficult to breathe, Trouble breathing, Breathing difficulty, Abnormal breathing, Dyspnoea, shotness of breath Functional respiratory abnormality HP_0002795 "Recommend making syonym request to HPO -Changed name from 'Shortness of breath (breathing difficulty)' to 'Dyspnea (breathing difficulty)' incase a data curator has 'Dyspnea' in their collection data and they do not know that it is synonymous with 'Shortness of breath' and 'breathing difficulty'. - Rhiannon" -HP_0002014 signs and symptoms Diarrhea (watery stool) Diarrhea, watery DIARRHEA Diarrhea Watery stool, Diarrhea, Diarrhoea Abdominal symptom HP_0011458 In GenEpiO - signs and symptoms Dry gangrene -HP_0002383 signs and symptoms Encephalitis (brain inflammation) Encephalitis ENCEPHALITIS Encephalitis Brain inflammation, inflammation of the brain Unusual CNS infection HP_0011450 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0019956 - signs and symptoms Encephalopathy unspecified encephalopathy -HP_0012378 signs and symptoms Fatigue (tiredness) Fatigue FATIGUE Fatigue Tiredness, Fatigue, Tired, new fatigue, worsening fatigue, new or worsening fatigue Constitutional symptom HP_0025142 In GenEpiO -HP_0001945 signs and symptoms Fever FEVER Fever Pyrexia, Hyperthermia, Fever, high body temperature, raised body temperature, elevated body temperature Abnormality of temperature regulation HP_0004370 In GenEpiO - Fever Fever (>=38°C) Fever -HP:0000206 signs and symptoms Glossitis (inflammation of the tongue) GLOSSITIS - signs and symptoms Ground Glass Opacities (GGO) indicates abnormalities in the lungs - has even been identified in 'true' asymptomatic patients (i.e. not presymptomatic). -HP_0002315 signs and symptoms Headache HEADACHE Headache Headache, Headaches Abnormality of nervous system physiology HP_0012638 In GenEpiO -HP_0002105 signs and symptoms Hemoptysis (coughing up blood) HEMOPTYSIS Hemoptysis Haemoptysis, Coughing up blood Abnormal sputum HP_0032016 -HP:0012417 signs and symptoms Hypocapnia Hypocapnia reduced carbon dioxide in the blood, hapocarbia, hypocapnea, narrower: deeply hypocapnic, normo/hypercapnic Abnormal blood carbon dioxide level HP:0500164 -HP_0002615 signs and symptoms Hypotension (low blood pressure) HYPOTENSION Hypotension Arterial hypotension, Low blood pressure Abnormal systemic blood pressure HP_0030972 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0005468 -HP_0012418 signs and symptoms Hypoxemia (low blood oxygen) HYPOXEMIA Hypoxemia Low blood oxygen level, oxygen deficiency in arterial blood, low level of oxygen in the blood, narrower: severe hypoxemia, silent hypoxemia, related: Hypoxia, Cyanosis Abnormal blood oxygen level HP_0500165 "Could also add ""Hypoxia"" and ""Silent Hypoxia"" (also associated with SARS-CoV-2). - -HP comment ""Note that hypoxemia is defined as a condition where arterial oxygen tension is below normal (80-100mmHg). Hypoxia is defined as the failure of oxygenation at the tissue level. Hypoxia is not measured directly by a standard laboratory value"" - -Leads to cyanosis - Rhiannon" - Hypoxemia (low blood oxygen) Silent hypoxemia An abnormally low level of blood oxygen incompatible with life without dyspnea. https://doi.org/10.1164/rccm.202006-2157CP laymans: happy hypoxia, related: hypocapnia An abnormally low level of blood oxygen incompatible with life without dyspnea. HP New Term Request -HP:0011029 signs and symptoms Internal hemorrhage (internal bleeding) INTERNAL_HEMORRHAGE Internal hemorrhage Internal haemorrhage Internal bleeding "Abnormality of blood circulation, -Abnormal bleeding" "HP:0011028, -HP:0001892" -NCIT:C121416 signs and symptoms Loss of Fine Movements LOSS_OF_FINE_MOVE Loss of Fine Movements Loss of fine movements, Loss of Fine Movements Clinical or Research Assessment Answer NCIT:C91106 "Could ask HP to add if we don't want to use NCIT. - -Should consider adding broader 'loss of movement'" -HP_0004396 signs and symptoms Low appetite LOW_APPETITE Poor appetite Decreased appetite, Poor appetite, loss of appetite, low appetite, anorexia Abdominal symptom HP_0011458 "In GenEpiO. -Could use 'Anorexia' which is also in HP (not refering to anorexia nervosa) - or request it with this term?" - signs and symptoms Malaise (general discomfort/unease) MALAISE Malaise A general feeling of discomfort, illness, or lack of well-being. https://medlineplus.gov/ency/article/003089.htm general discomfort/unease, general uneasiness, general discomfort, general unease, out-of-sorts feeling "New term - -Recommend making term request to HPO (note they already have it as ""related synonym"" to ""Fatigue""" - signs and symptoms Meningismus/nuchal rigidity -HP_0001324 signs and symptoms Muscle weakness MUSCLE_WEAK Muscle weakness Abnormal muscle physiology HP_0011804 Recommend changing this to 'muscle weakness' as 'weakness' could be mistakenly used when the intention is to refer to 'asthenia' which is weakness/exhaustion in the absence of true muscle weakness. - Rhiannon -HP_0001742 signs and symptoms Nasal obstruction (stuffy nose) NASAL_OBSTRUCT Nasal obstruction Obstruction of nose, Stuffy nose, Blockage of nose, Nasal obstruction, Nasal blockage, nasal congestion Abnormality of the nose HP_0000366 Recommend making syonym request to HPO -HP_0002018 signs and symptoms Nausea NAUSEA Nausea Nausea and vomiting HP_0002017 In GenEpiO - signs and symptoms Nose bleed - signs and symptoms Otitis - signs and symptoms Pain -HP:0002027 Pain Abdominal pain ABDOMINAL Abdominal pain Stomach pain, Abdominal pain, Pain in stomach, abdominal ache, belly ache, bellyache, narrower: stomach ache, stomachache, abdominal cramping? "Abdominal symptom, -Pain" "HP:0011458, -HP:0012531" -HP_0002829 Pain Arthralgia (painful joints) ARTHRALGIA Arthralgia painful joints, joint pain, joint inflammation, related: Arthritic pain, Joint pains, arthritis Pain HP_0012531 Don't use HP entry 'Arthralgia/arthritis' (HP:0005059) as it is refering to the disease diagnosis not the symptom. -HP_0100749 Pain Chest pain CHEST_PAIN Chest pain Chest pain, Thoracic pain Pain HP_0012531 Could add synonyms 'perisstent chest pain' but I'm not sure if this term is meant to be narrow enough to represent presistent vs acute. Could also consider 'chest pain' synonymous with 'chest pressure' instead of 'chest tightness'. - Rhiannon - Chest pain Pleuritic chest pain pleursy -HP_0003326 Pain Myalgia (muscle pain) MYALGIA Myalgia Muscle ache, Muscle pain, aches and pains, body aches Pain HP_0012531 In GenEpiO -HP_0025439 signs and symptoms Pharyngitis (sore throat) PHARYNGITIS Pharyngitis sore throat, pharyngalgia, pharyngodynia Abnormality of the pharynx HP_0000600 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0002258 - signs and symptoms Pharyngeal exudate - signs and symptoms Pleural effusion https://www.researchgate.net/publication/340720955_Pleural_effusion_as_an_initial_sign_of_coronavirus_disease_2019_COVID-19_pneumonia_a_case_report -HP:0002090 signs and symptoms Pneumonia Pneumonia Pneumonia "Respiratory tract infection, -Increased inflammatory response" "HP:0011947, -HP:0012649" Considered a sign/symptom on two case report forms. - signs and symptoms Prostration Appears on a provincial case report form. - signs and symptoms Pseudo-chilblains chilblains-like symptom, chilblains-like lesions, related: chilblains, chill burns, pernio, perniosis, broader: acro-ischemia, acrosyndromes, peripheral cyanosis? Inflammatory abnormality of the skin Revisit broader synonyms. Have address chilblains in HP but not pseudo-chilblains. #5822 - Pseudo-chilblains Pseudo-chilblains on fingers (covid fingers) PSEUDO-CHIBLAINS_F chilblains-like fingers, chilblains-like finger lesions, related: chilblains, chill burns, pernio, perniosis, finger cyanosis, broader: acro-ischemia, acrosyndromes, peripheral cyanosis? Revisit broader synonyms. - Pseudo-chilblains Pseudo-chilblains on toes (covid toes) PSEUDO-CHIBLAINS_T chilblains-like toes, chilblains-like toe lesions, related: chilblains, chill burns, pernio, perniosis, toe cyanosis broader: acro-ischemia, acrosyndromes, peripheral cyanosis? Revisit broader synonyms. -HP_0000988 signs and symptoms Rash RASH Skin rash exanthem, skin rash, rash "Abnormality of skin morphology, -Inflammatory abnormality of the skin" "HP_0011121, -HP_0011123" E.g. "COVID toes". -HP_0031417 signs and symptoms Rhinorrhea (runny nose) RHINORRHEA Rhinorrhea Runny Nose, Nasal Discharge Abnormal nasal mucus secretion HP_0031416 -HP_0001250 signs and symptoms Seizure SEIZURE Seizure Epileptic seizure, Seizures Abnormal nervous system physiology HP_0012638 -HP:0020219 Seizure Motor seizure MOTOR_SEIZURE Motor seizure Seizure HP:0001250 -HP:0025144 signs and symptoms Shivering (involuntary muscle twitching) SHIVERING Shivering Shivering, Shuddering Constitutional symptom HP:0025142 -HP_0001350 signs and symptoms Slurred speech SLURRED_SPEECH Slurred speech Abnormality of coordination HP_0011443 "In GenEpiO. - -Discuss whether this should go under 'altered consicousness' (is not currently organized as such in HP). - Rhiannon" - signs and symptoms Sneezing - signs and symptoms Sputum Production -HP:0001297 signs and symptoms Stroke STROKE Stroke Stroke Cerebrovascular accident Cerebral vascular events Abnormality of the cerebral vasculature HP:0100659 - signs and symptoms Swollen Lymph Nodes -HP_0002789 signs and symptoms Tachypnea (accelerated respiratory rate) TACHYPNEA Tachypnea Increased respiratory rate or depth of breathing, Polypnea, rapid breathing, accelerated respiratory rate Abnormal pattern of respiration HP_0002793 Changed to 'Tachypnea (accelerated respiratory rate)' as that form occurs 4/5 times on the case report forms. - signs and symptoms Vertigo (dizziness) Vertigo -HP_0002013 signs and symptoms Vomiting (throwing up) VOMITING Vomiting Throwing up, Vomiting, Emesis Nausea and vomiting HP_0002017 "In GenEpiO -Has subclasses: Episodic vomiting, Feculent vomiting, Projectile vomiting" - - host vaccination status Fully Vaccinated - host vaccination status Partially Vaccinated - host vaccination status Not Vaccinated - - prior SARS-CoV-2 antiviral treatment Prior antivrial treatment - prior SARS-CoV-2 antiviral treatment No prior antivrial treatment - prior SARS-CoV-2 antiviral treatment Unknown - - NML submitted specimen type Swab PH_SPECIMEN_TYPE:SWAB - NML submitted specimen type RNA PH_SPECIMEN_TYPE:RNA - NML submitted specimen type mRNA (cDNA) PH_SPECIMEN_TYPE:MRNA_CDNA - NML submitted specimen type Nucleic acid PH_SPECIMEN_TYPE:NUCLEIC_ACID - NML submitted specimen type Not Applicable PH_SPECIMEN_TYPE:NA - - - NML related specimen relationship type Acute - NML related specimen relationship type Convalescent - NML related specimen relationship type Familial - NML related specimen relationship type Follow-up - NML related specimen relationship type Previously Submitted - - - pre-existing conditions and risk factors Age 60+ - pre-existing conditions and risk factors Anemia - pre-existing conditions and risk factors Anorexia https://www.uptodate.com/contents/coronavirus-disease-2019-covid-19-arrhythmias-and-conduction-system-disease - pre-existing conditions and risk factors Birthing labor labor, labour - pre-existing conditions and risk factors Bone marrow failure - pre-existing conditions and risk factors Cancer malignancy Malignancy' is more common than 'cancer' on case collection forms. - Cancer Breast cancer - Cancer Colorectal cancer - Cancer Hematologic malignancy - Cancer Lung cancer - Cancer Metastatic disease - pre-existing conditions and risk factors Cancer treatment - Cancer treatment Cancer surgery - Cancer treatment Chemotherapy - Chemotherapy Adjuvant chemotherapy - pre-existing conditions and risk factors Cardiac disorder -HP:0011675 Cardiac disorder Arrhythmia Arrhythmia Abnormal heart rate, Cardiac arrhythmia, Heart rhythm disorders, Irregular heartbeat, Cardiac arrhythmias, Cardiac rhythm disturbances, Arrhythmias, Irregular heart beat Abnormality of cardiovascular system electrophysiology HP:0030956 - Cardiac disorder Cardiac disease cardiovascular disease, cardio-vascular disease, heart disease -HP:0001638 Cardiac disorder Cardiomyopathy Disease of the heart muscle Abnormal myocardium morphology HP:0001637 - Cardiac disorder Cardiac injury - Cardiac disorder Hypertension (high blood pressure) arterial hypertension -HP:0002615 Cardiac disorder Hypotension (low blood pressure) Hypotension Arterial hypotension, Low blood pressure Abnormal systemic blood pressure HP_0030972 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0005468 - pre-existing conditions and risk factors Cesarean section - pre-existing conditions and risk factors Chronic cough - pre-existing conditions and risk factors Chronic gastrointestinal disease chronic GI disease - pre-existing conditions and risk factors Chronic lung disease - pre-existing conditions and risk factors Corticosteroids - pre-existing conditions and risk factors Diabetes mellitus (diabetes) - Diabetes mellitus (diabetes) Type I diabetes mellitus (T1D) Insulin dependent diabetes mellitus (IDDM), juvenille diabetes - Diabetes mellitus (diabetes) Type II diabetes mellitus (T2D) adult-onset diabetes - pre-existing conditions and risk factors Eczema - pre-existing conditions and risk factors Electrolyte disturbance - Electrolyte disturbance Hypocalcemia - Electrolyte disturbance Hypokalemia - Electrolyte disturbance Hypomagnesemia -HP:0002383 pre-existing conditions and risk factors Encephalitis (brain inflammation) Encephalitis Brain inflammation, inflammation of the brain Unusual CNS infection HP_0011450 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0019956 - pre-existing conditions and risk factors Epilepsy - pre-existing conditions and risk factors Hemodialysis - pre-existing conditions and risk factors Hemoglobinopathy - pre-existing conditions and risk factors Human immunodeficiency virus (HIV) - Human immunodeficiency virus (HIV) Acquired immunodeficiency syndrome (AIDS) Stage 4 HIV - Human immunodeficiency virus (HIV) HIV and antiretroviral therapy (ART) narrower: HIV antiretroviral medication, HIV antiretroviral drug - pre-existing conditions and risk factors Immunocompromised narrower: immune deficiencies, immunosupressants - Immunocompromised Lupus systemic lupus erythematosus - pre-existing conditions and risk factors Inflammatory bowel disease (IBD) IBD, IBS, inflammatory bowel syndrome - Inflammatory bowel disease (IBD) Colitis - Colitis Ulcerative colitis - Inflammatory bowel disease (IBD) Crohn's disease - pre-existing conditions and risk factors Renal disorder kidney disorder - Renal disorder Renal disease kidney disease - Renal disorder Chronic renal disease chronic kidney disease - Renal disorder Renal failure kidney failure - pre-existing conditions and risk factors Liver disease hepatic disease - Liver disease Chronic liver disease - Chronic liver disease Fatty liver disease (FLD) Hepatic steatosis -HP:0003326 pre-existing conditions and risk factors Myalgia (muscle pain) Myalgia Muscle ache, Muscle pain, aches and pains, body aches Pain HP_0012531 In GenEpiO - pre-existing conditions and risk factors Myalgic encephalomyelitis (ME) chronic fatigue syndrome (CFS) - pre-existing conditions and risk factors Neurological disorder nervous system disorder - Neurological disorder Neuromuscular disorder - pre-existing conditions and risk factors Obesity - Obesity Severe obesity morbid obesity - pre-existing conditions and risk factors Respiratory disorder - Respiratory disorder Asthma - Respiratory disorder Chronic bronchitis - Respiratory disorder Chronic pulmonary disease chronic respiratory condition - Chronic pulmonary disease Chronic obstructive pulmonary disease - Respiratory disorder Emphysema - Respiratory disorder Lung disease - Lung disease Chronic lung disease - Lung disease Pulmonary fibrosis -HP:0002090 Respiratory disorder Pneumonia Pneumonia Pneumonia "Respiratory tract infection, -Increased inflammatory response" "HP:0011947, -HP:0012649" - Respiratory disorder Respiratory failure - Respiratory failure Adult respiratory distress syndrome - Respiratory failure Newborn respiratory distress syndrome - Respiratory disorder Tuberculosis - pre-existing conditions and risk factors Postpartum (≤6 weeks) All case forms specific ≤6 weeks - pre-existing conditions and risk factors Pregnancy pregnant person Gestation or trimester information usually requested - pre-existing conditions and risk factors Rheumatic disease - pre-existing conditions and risk factors Sickle cell disease - pre-existing conditions and risk factors Substance use Could instead go with 'substance user' - Substance use Alcohol abuse Could instead go with 'alcohol abuser' - Substance use Drug abuse Could instead go with 'drug abuser/user' - Drug abuse Injection drug abuse intravenous drug abuse Could instead go with 'injection drug abuser/user' - Substance use Smoking Could instead go with 'smoker' - Substance use Vaping Could instead go with 'vape user' -HP:0002789 pre-existing conditions and risk factors Tachypnea (accelerated respiratory rate) Tachypnea Increased respiratory rate or depth of breathing, Polypnea, rapid breathing, accelerated respiratory rate Abnormal pattern of respiration HP_0002793 - pre-existing conditions and risk factors Transplant transplant recipient? - Transplant Bone marrow transplant Alt: 'History of Bone Marrow Transplant' which is the label HP uses. - Transplant Cardiac transplant heart transplant - Transplant Hematopoietic stem cell transplant (HSCT) hematopoietic cell transplantation - Transplant Kidney transplant - Transplant Liver transplant - - variant designation Variant of Concern (VOC) - variant designation Variant of Interest (VOI) - - variant evidence RT-qPCR - variant evidence Sequencing - - complications Abnormal blood oxygen level O2 saturation <=95% Case report forms frequently record "O2 saturation <=95%". "The generally accepted standard is that a normal resting oxygen saturation of less than 95% is considered abnormal" (https://www.ncbi.nlm.nih.gov/books/NBK525974/) - complications Acute respiratory failure -HP:0011675 complications Arrhythmia (complication) Arrhythmia Abnormal heart rate, Cardiac arrhythmia, Heart rhythm disorders, Irregular heartbeat, Cardiac arrhythmias, Cardiac rhythm disturbances, Arrhythmias, Irregular heart beat Abnormality of cardiovascular system electrophysiology HP:0030956 - Arrhythmia (complication) Tachycardia May be considered synonymous with tachyarrhythmia (Ref other) - recommend looking into it further. https://en.wikipedia.org/wiki/Tachycardia - Tachycardia Polymorphic ventricular tachycardia (VT) - Tachycardia Tachyarrhythmia broader: narrower complex tachycardia (NCT), wide complex tachycardia https://www.sciencedirect.com/topics/medicine-and-dentistry/tachyarrhythmia#:~:text=Introduction,tachycardia%20(%E2%89%A5120%20ms). - complications Noncardiogenic pulmonary edema https://pubmed.ncbi.nlm.nih.gov/31194387/ - Noncardiogenic pulmonary edema Acute respiratory distress syndrome (ARDS) - Acute respiratory distress syndrome (ARDS) COVID-19 associated ARDS (CARDS) - Acute respiratory distress syndrome (ARDS) Neurogenic pulmonary edema (NPE) Do note equate to 'High Altitude Pulmonary Edema' (HAPE) as some are doing; they some of the symptoms may be similar, what's occuring in the lungs is significantly different. - complications Cardiac injury cardiac trauma https://www.gehealthcare.ca/en-CA/article/cardiac-complications-of-covid-19-signs-to-watch-for-on-the-ecg - complications Cardiac arrest - complications Cardiogenic shock - complications Blood clot - Blood clot Arterial clot - Blood clot Deep vein thrombosis (DVT) - Blood clot Pulmonary embolism (PE) -HP:0001638 complications Cardiomyopathy Disease of the heart muscle Abnormal myocardium morphology HP:0001637 - complications Central nervous system invasion Central nervous system invasion by SARS-CoV-2 - complications Stroke (complication) cerebrovascular event - Stroke (complication) Central Nervous System Vasculitis CNS vasculitis - Stroke (complication) Ischemic stroke - Ischemic stroke Acute ischemic stroke - complications Coma - complications Convulsions - complications COVID-19 associated coagulopathy (CAC) chronic, likely caused by DIC - complications Cystic fibrosis CF - complications Cytokine release syndrome cytokine storm, CRS, inflammatory storm - complications Disseminated intravascular coagulation (DIC) can often be the cause of blood clots in covid19 cases - complications Encephalopathy - complications Fulminant myocarditis - complications Guillain-Barré syndrome - complications Internal hemorrhage (complication; internal bleeding) - Internal hemorrhage (complication; internal bleeding) Intracerebral haemorrhage ICH - complications Kawasaki disease chronic - Kawasaki disease Typical Kawasaki disease - Kawasaki disease Incomplete Kawasaki disease - complications Kidney injury - Kidney injury Acute kidney injury AKI - complications Liver dysfunction - complications Liver injury liver damage - Liver injury Acute liver injury - complications Lung injury - Lung injury Acute lung injury - complications Meningitis - complications Migraine - complications Miscarriage - complications Multisystem inflammatory syndrome in children (MIS-C) pediatric multisystem inflammatory syndrome (PMIS), PIMS similar signs/symptoms to those of toxic shock syndrome or Kawasaki disease. - complications Muscle injury - complications Myalgic encephalomyelitis (ME) chronic fatigue syndrome (CFS) - complications Myocardial infarction (heart attack) MI - Myocardial infarction (heart attack) Acute myocardial infarction - Myocardial infarction (heart attack) Elevation myocardial infarction - Myocardial infarction (heart attack) ST-segment elevation myocardial infarction - complications Myocardial injury - complications Neonatal complications - complications Organ failure - Organ failure Heart failure not synonymous with 'cardciac arrest' - Organ failure Liver failure - complications Paralysis - complications Pneumothorax (collapsed lung) - Pneumothorax (collapsed lung) Spontaneous pneumothorax - Pneumothorax (collapsed lung) Spontaneous tension pneymothorax - complications Pneumonia (complication) - Pneumonia (complication) COVID-19 pneumonia COVID-19 infected pneumonia Redundant? - complications Pregancy complications pregnancy issues - complications Rhabdomyolysis - complications Secondary infection - Secondary infection Secondary staph infection - Secondary infection Secondary strep infection -HP:0001250 complications Seizure (complication) Seizure Epileptic seizure, Seizures Abnormal nervous system physiology HP_0012638 -HP:0020219 Seizure (complication) Motor seizure Motor seizure Seizure HP:0001250 - complications Sepsis - complications Septicemia - complications Shock - Shock Hyperinflammatory shock - Shock Refractory cardiogenic shock RCS - Shock Refractory cardiogenic plus vasoplegic shock - Shock Septic shock - complications Vasculitis inflammed blood vessels - complications Ventilation induced lung injury (VILI) - - - -UBERON_0000178 anatomical material Blood BLOOD blood organism substance UBERON_0000463 Use UBERON term. -UBERON_0006314 anatomical material Fluid FLUID bodily fluid organism substance, portion of body substance, body substance, body fluid or substance, portion of organism substance organism substance UBERON_0000463 Use UBERON term. -UBERON_0001836 Fluid Saliva SALIVA saliva spit, broader: oral fluid organism substance UBERON_0000463 "Use UBERON term. Add synonym. (ISSUE: People may be using this rather than more properly referencing oral fluid). - -Added ""oral fluid"" as a broader synonym since people are using them synonymously. - Rhiannon" -UBERON_0001359 Fluid Fluid (cerebrospinal (CSF)) FLUID_CSF cerebrospinal fluid organism substance UBERON_0000463 Use UBERON term. -UBERON_0002409 Fluid Fluid (pericardial) FLUID_PERICARDIAL pericardial fluid organism substance UBERON_0000463 Use UBERON term. -UBERON_0001087 Fluid Fluid (pleural) FLUID_PLEURAL pleural fluid organism substance UBERON_0000463 Use UBERON term. -UBERON_0036243 Fluid Fluid (vaginal) FLUID_VAGINAL vaginal fluid vaginal secretion, vaginal discharge bodily fluid UBERON_0006314 Use UBERON term. -UBERON_0000173 Fluid Fluid (amniotic) FLUID_AMNIOTIC amniotic fluid organism substance UBERON_0000463 Use UBERON term. -UBERON_0000479 anatomical material Tissue TISSUE tissue material anatomical entity UBERON_0000465 Use UBERON term. - - - -UBERON_0001245 anatomical part Anus ANUS anus anal opening, anal orifice, opening of terminal part of digestive tract - anatomical part Buccal mucosa BUCCAL_MUCOSA -UBERON_0002114 anatomical part Duodenum DUODENUM duodenum -UBERON_0000970 anatomical part Eye EYE eye - anatomical part Intestine INTESTINE -UBERON_0001052 anatomical part Rectum RECTUM rectum terminal portion of intestine -UBERON_0001003 anatomical part Skin SKIN skin epidermis -UBERON_0000945 anatomical part Stomach STOMACH stomach -UBERON_0001557 anatomical part Upper respiratory tract UPPER upper respiratory tract -UBERON_2001427 Upper respiratory tract Anterior Nares ANTERIOR_NARES anterior naris -UBERON_0001043 Upper respiratory tract Esophagus ESOPHAGUS esophagus oesophagus, gullet -UBERON_0002453 Upper respiratory tract Ethmoid sinus ETHMOID_SINUS ethmoid sinus ethmoidal sinus, ethmoidal bone sinus paranasal sinus - Upper respiratory tract Nasal Cavity NASAL_CAVITY -UBERON_0005921 Nasal Cavity Middle Nasal Turbinate MIDDLE_NASAL middle nasal concha middle nasal turbinate, middle turbinate, mid-nasal turbinate, nasal mid-turbinate, NMT Found UBERON entry "middle nasal concha" which is an exact synonym, but I think we should use "middle nasal turbinate" or "mid-nasal turbinate" since those are closer to the clincal usage forms (e.g. Mid-turbinate swab, Nasal mid-turbinate (NMT) swab, Deep Nasal Swab). https://www.fda.gov/media/136314/download -UBERON_0005922 Nasal Cavity Inferior Nasal Turbinate INFERIOR_NASAL inferior nasal concha inferior nasal turbinate -UBERON_0001728 Upper respiratory tract Nasopharynx (NP) NASOPHARYNX_NP nasopharynx -UBERON_0001729 Upper respiratory tract Oropharynx (OP) OROPHARYNX_OP oropharynx The area of the throat that gets swabbed. -UBERON_0001558 anatomical part Lower respiratory tract LOWER lower respiratory tract -UBERON_0002185 Lower respiratory tract Bronchus BRONCHUS bronchus bronchial trunk, bronchi, bronchial tissue, respiratory tube UBERON_0000117 -UBERON_0002048 Lower respiratory tract Lung LUNG lung -UBERON_0002186 Lung Bronchiole BRONCHIOLE bronchiole lobular bronchiole, bronchioli, bronchiolus, respiratory tube UBERON_0000117 -UBERON_0002169 Lung Alveolar sac ALVEOLAR_SAC alveolar sac respiratory tube UBERON_0000117 -UBERON_0009778 Lower respiratory tract Pleural sac PLEURAL_SAC pleural sac Perhaps not necessary. -UBERON_0002402 Pleural sac Pleural cavity PLEURAL_CAVITY pleural cavity Contains pleural fluid which gets collected for sampling. -UBERON_0003126 Lower respiratory tract Trachea TRACHEA trachea - - - - -UBERON_0001988 body product Feces FECES feces stool, faeces Could form relationship with "feces collection" from GenEpiO. -UBERON_0001088 body product Urine URINE urine -UBERON_0001089 body product Sweat SWEAT sweat -UBERON_0000912 body product Mucus MUCUS mucus mucosa -UBERON_0007311 Mucus Sputum SPUTUM sputum deep mucus, phlegm "Would this be better suited for ""body product sampled""? Moved from ""anatomical material sampled"" to body product sampled"", since the later contains ""mucus"" and sputums is a narrower synonym of ""mucus"". - -Could form relationship with ""sputum collection"" from GenEpiO." -UBERON_0001827 body product Tear TEAR secretion of lacrimal gland ocular secretion, tears, tear fluid, narrower: precorneal tear film (PCTF), basal tear, reflex tear, closed eye tear, eye-flush tear -UBERON_0006530 body product Fluid (seminal) FLUID_SEMINAL seminal fluid seminal plasma "secretion of exocrine gland, -male reproductive gland secretion" "UBERON_0000456, -UBERON_0006536" "Would this be better under ""body product""? -Rhiannon - -Use UBERON term." -UBERON_0001913 body product Breast Milk BREAST_MILK milk bodily fluid, mammary gland fluid/secretion UBERON_0006314, UBERON_0006539 Use UBERON term. - - prior SARS-CoV-2 infection Yes - prior SARS-CoV-2 infection No - prior SARS-CoV-2 infection Unknown - - - environmental material Air vent AIR_VENT air vent An opening that allows air to pass out of or into a confined space. https://www.lexico.com/definition/air_vent building part ENVO_01000420 new term -ENVO_00003896 environmental material Banknote BANKNOTE currency note no def. - environmental material Bed rail BED_RAIL bed rail A rail on the side of a bed designed to provide protection and security to individuals who cannot reliably support themselves, and can also be used as a precautionary measure for those who will be limited their bed for an extended period of time. https://www.1800wheelchair.ca/category/bed-rails/ bed railing, bedrail new term -ENVO_01000486 environmental material Building floor BUILDING_FLOOR building floor -ENVO_02000058 environmental material Cloth CLOTH cloth A textile comprised of a pliable material made usually by weaving, felting, or knitting natural or synthetic fibers and filaments. [ URL:http://www.merriam-webster.com/dictionary/cloth ] - environmental material Control panel CONTROL_PANEL control panel A dashboard full of buttons, levers and dials for configuring and controlling the equipment. https://www.yourdictionary.com/control-panel new term. -NCIT_C48950 environmental material Door DOOR Door not a good def. suggest: A hinged, sliding, or revolving barrier at the entrance to a building, room, or vehicle, or in the framework of a cupboard. https://www.lexico.com/en/definition/door add term to genepio. not a good definition - environmental material Door handle DOOR_HANDLE A mechanism used to open or close a door. https://en.wikipedia.org/wiki/Door_handle door knob - environmental material Face mask FACE_MASK Face mask A disposable mask worn by health professionals during procedures in surgery and nursing. https://en.wikipedia.org/wiki/Surgical_mask surgical mask, procedure mask, medical mask new term - environmental material Face shield FACE_SHIELD Face shield Personal protective equipment (PPE) that provides barrier protection to the facial area and related mucous membranes (eyes, nose, lips). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015006/ new term -FOODON:00002403 environmental material Food FOOD -FOODON:03490100 environmental material Food packaging FOOD_PACKAGING -ENVO:01000481 environmental material Glass GLASS term also in FoodOn (FOODON_03500040) - environmental material Handrail HANDRAIL handrail A rail fixed to posts or a wall for people to hold on to for support. https://www.lexico.com/en/definition/handrail new term. this term and bed rail could be put under ncit term "rail device" NCIT_C50130. would also need to be introduced into genepio - environmental material Hospital gown HOSPITAL_GOWN Hospital gown A long loose piece of clothing worn in a hospital by someone doing or having an operation, and is often used as clothing for bedridden patients. https://en.wikipedia.org/wiki/Patient_gown patient gown, johnny gown new term - environmental material Light switch LIGHT_SWITCH Light switch A switch most commonly used to operate electric lights, permanently connected equipment, or electrical outlets. https://en.wikipedia.org/wiki/Light_switch new term - environmental material Locker LOCKER Locker A small lockable closet or compartment, typically as one of a number placed together for public or general use, https://www.lexico.com/en/definition/locker - environmental material N95 mask N95_MASK N95 mask A particulate-filtering facepiece respirator that meets the U.S. National Institute for Occupational Safety and Health (NIOSH) N95 classification of air filtration, meaning that it filters at least 95% of airborne particles. https://en.wikipedia.org/wiki/N95_mask N95 respirator new term for OBI? - environmental material Nurse call button NURSE_CALL_BUTTON Nurse call button A button or cord found in hospitals and nursing homes, that allow patients in health care settings to alert a nurse or other health care staff member remotely of their need for help. Thay are usually found in places where patients are at their most vulnerable, such as beside their bed and in the bathroom. https://en.wikipedia.org/wiki/Nurse_call_button Call bell, hospital call bell new term - environmental material Paper PAPER Material manufactured in thin sheets from the pulp of wood or other fibrous substances, used for writing, drawing, or printing on, or as wrapping material. https://www.lexico.com/en/definition/paper paper product ENVO_00003895 new term for ENVO? -ENVO:01000060 environmental material Particulate matter PARTICULATE_MATTER -ENVO:01000404 environmental material Plastic PLASTIC term also in FoodOn (FOODON_03500036) - environmental material PPE gown PPE_GOWN PPE gown A type of gown worn by medical professionals in order to provide a barrier between patient and professional, and usually zips up at the back. https://en.wikipedia.org/wiki/PPE_gown personal protective equipment gown new term (NOT for OMIT). OBI? -ENVO_00002018 environmental material Sewage SEWAGE sewage -ENVO_01000990 environmental material Sink SINK sink fixture sink -ENVO_00001998 environmental material Soil SOIL soil - environmental material Stainless steel STAINLESS_STEEL new term for ENVO. Don't use OMIT_0014071 - it is a quality! - environmental material Tissue paper TISSUE_PAPER tissue paper Soft paper used for various purposes such as cleaning or as toilet tissue. https://www.dictionary.com/browse/tissue new term for ENVO - environmental material Toilet bowl TOILET_BOWL Toilet bowl The bowl of a toilet that can be flushed with water, used for defecation and urination. https://www.thefreedictionary.com/toilet+bowl new term -ENVO_00002006 environmental material Water WATER water CHEBI_15377 is not the best term - its referencing a chemical compound. BEST use ENVO: ENVO_00002006 which is environmental water - environmental material Wastewater WASTEWATER - environmental material Window WINDOW Window An opening in the wall or roof of a building or vehicle that is fitted with glass or other transparent material in a frame to admit light or air and allow people to see out. https://www.lexico.com/en/definition/window new term. existing usages of "window" are different. -ENVO:00002040 environmental material Wood WOOD wood The hard fibrous material that forms the main substance of the trunk or branches of a tree or shrub, used for fuel or timber. https://www.lexico.com/en/definition/wood add definition - - environmental site Acute care facility ACUTE_CARE_FACILITY Acute care facility A facility where a patient receives active but short-term treatment for a severe injury or episode of illness, an urgent medical condition, or during recovery from surgery. https://en.wikipedia.org/wiki/Acute_care building ENVO_00000073 new term. this should be parental term for hospital, urgent care facility, ambulatory care facility -ENVO:00003040 environmental site Animal house ANIMAL_HOUSE animal house this defintion is too vague. suggest: Any kind of shelter, refuge affording protection to animals. https://www.eionet.europa.eu/gemet/en/concept/428 add better def? -ENVO:01000422 environmental site Bathroom BATHROOM bathroom - environmental site Clinical assessment centre CLINICAL_ASSESSMENT_ building ENVO_00000073 - environmental site Conference venue CONFERENCE_VENUE The building where a conference is held. Emma building ENVO_00000073 new term -ENVO REQUEST environmental site Corridor CORRIDOR building corridor A long passage in a building from which doors lead into rooms. https://www.lexico.com/en/definition/corridor hallway, broader: hall, passage building part ENVO:01000420 "new term. -2020-07-14 - Moved from 'environmental material' to 'environmental site'/'environmental feature' -Moved 'hall' to broader synonym since it is not an exact synonym." -ENVO_01000927 environmental site Daycare DAYCARE day care building daycare add synonym -NCIT_C53513 environmental site Emergency room (ER) EMERGENCY_ROOM_ER Emergency Room ER, building ENVO_00000073 missing in genepio. should be housed in envo. - environmental site Family practice clinic FAMILY_PRACTICE_CLIN Family practice clinic A clinic where family physicians deliver a range of acute, chronic and preventive medical care services. https://en.wikipedia.org/wiki/Family_medicine family care clinic, general practice clinic, family medicine clinic, general medicine clinic building ENVO_00000073 new term. - environmental site Group home GROUP_HOME Group home A residential facility with the purpose of housing multiple residents with particular care needs. https://en.wikipedia.org/wiki/Group_home building ENVO_00000073 new term. - environmental site Homeless shelter HOMELESS_SHELTER Homeless shelter A type of homeless service agency which provide temporary residence for homeless individuals and families. https://en.wikipedia.org/wiki/Homeless_shelter building ENVO_00000073 new term -OBI_0000844 environmental site Hospital HOSPITAL hospital building ENVO_00000073 -NCIT_C53511 environmental site Intensive Care Unit (ICU) INTENSIVE_CARE_UNIT_ Intensive Care Unit building ENVO_00000073 missing in genepio. should be housed in envo. -GENEPIO_0001035 environmental site Long Term Care Facility LONG_TERM_CARE_FACIL long term care facility LTC, LTCF, Long-Term Care Facility building ENVO_00000073 add synonyms, need new parental term (see below for details) - environmental site Patient room PATIENT_ROOM Patient room / or examination room? or patient bed area? Room occupied by one or more individuals during a stay in a health facility. http://www.reference.md/files/D010/mD010362.html new term -ENVO_01001481 environmental site Prison PRISON public prision A facility in which inmates (or prisoners) are forcibly confined and denied a variety of freedoms under the authority of the state. https://en.wikipedia.org/wiki/Prison correctional facility, penitentiary, detention center, detention centre, correctional center, correctional centre, lock-up, remand center, remand centre; broad synonym jail, gaol building ENVO_00000073 new term. <- Why? envo has "public prision" ENVO_01001481. term is misspelled. <- put in an ISSUES request to ENVO to fix spelling. -ENVO_01000536 environmental site Production Facility PRODUCTION_FACILITY Factory Production Facility building ENVO_00000073 add synonym. food production facility (currently under "building" should go under "factory" as it's a type of factory) -NCIT_C17118 environmental site School SCHOOL School building ENVO_00000073 not in genepio - environmental site Sewage Plant SEWAGE_PLANT - environmental site Subway train SUBWAY_TRAIN Subway train A type of high-capacity public transport generally found in urban areas. https://en.wikipedia.org/wiki/Rapid_transit subway, rapid transit, metro, heavy rail train PCO_1001178 new term in ENVO - environmental site Wet market WET_MARKET Wet market A marketplace selling fresh meat, fish, produce, and other perishable goods as distinguished from "dry markets" that sell durable goods such as fabric and electronics. Not all wet markets sell live animals, but the term wet market is sometimes used to signify a live animal market in which vendors slaughter animals upon customer purchase. https://en.wikipedia.org/wiki/Wet_market market GENEPIO_0001022 new term - -NCIT:C52009 collection method Amniocentesis AMNIOCENTESIS Amniocentesis collecting specimen from organism OBI_0600005 A prenatal diagnostic sample of amniotic fluid that isn't commonly done for SARS-CoV-2 but has been done. -NCIT:C15631 collection method Aspiration ASPIRATION Aspiration aspirate, narrower: fine needle aspiration, nasopharyngeal aspiration, tracheal aspiration, endotracheal aspirate collecting specimen from organism OBI_0600005 - Aspiration Suprapubic Aspiration SUPRAPUBIC_ASPIRATIO - Aspiration Tracheal aspiration TRACHEAL_ASPIRATION TA - Aspiration Vacuum Aspiration VACUUM_ASPIRATION Suction Aspiration -OBI:0002650 collection method Biopsy BIOPSY Biopsy A specimen collection that obtains a sample of tissue from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. narrower: needle biopsy, fine needle aspiration collecting specimen from organism OBI_0600005 DONE. (new term being published to OBI (damion)) -OBI:0002651 Biopsy Needle Biopsy NEEDLE_BIOPSY Needle Biopsy A biopsy which uses an imaging procedure to guide a needle biopsy. - collection method Filtration FILTRATION - Filtration Air filtration AIR_FILTRATION -OBI:0600044 collection method Lavage LAVAGE lavage narrower: bronchoalveolar lavage (BAL), gastric lavage collecting specimen from organism OBI_0600005 Changed "Wash" to "Lavage". "editor note: This is not washing, in which case the material of interest is not the resulting fluid." -BTO:0000155 Lavage Bronchoalveolar lavage (BAL) BAL bronchoalveolar lavage (bal) OBI_0600044 lavage - Lavage Gastric Lavage GASTRIC_LAVAGE copy from OMIT_0006951 -NCIT:C15327 collection method Lumbar Puncture LUMBAR_PUNCTURE Lumbar Puncture spinal tap, LP collecting specimen from organism OBI_0600005 Existing synonyms are from current master GenEpiO branch and will not appear on Onto browsers. -MMO:0000344 collection method Necropsy NECROPSY necropsy autopsy (although usually only in reference to an animal). collecting specimen from organism OBI_0600005 "Should this term be included in this category? It's not so much a ""method"" as an examination that occured postmortem. - -Also, what if someone did a postmortem biopsy - can they put in both ""Necropsy"" and ""Biopsy"" or would they have to choose between the two? - -I think it's a useful term and should go somewhere, just perhaps not under ""collection method"". Should we (or do we already have) something along the lines of ""host condition"" at time of examination/sample collection?" -NCIT:c28221 collection method Phlebotomy PHLEBOTOMY phlebotomy narrower: venipuncture collecting specimen from organism OBI_0600005 -GENEPIO:0002116 collection method Rinsing RINSING rinsing for specimen collection collecting specimen from organism OBI_0600005 "editor note: This is not washing, in which case the material of interest is not the resulting fluid." - Rinsing Saline gargle (mouth rinse and gargle) - collection method Scraping SCRAPING narrower: conjunctival scraping, skin scraping -GENEPIO:0002117 collection method Swabbing SWABBING swabbing for specimen collection' narrower: nasopharyngeal (nasal) swab, oropharyngeal (throat) swab, depe nasal swab, throat swab, multitest swab, deep nasal or throat swab collecting specimen from organism OBI_0600005 As in "to swab" not "a swab". Alternative name suggestion: "Swabbing" - Swabbing Finger Prick FINGER_PRICK Is a "swab method" (ref. "other" column). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395662/ - collection method Wash WASH wash specimen narrower: nasal wash, nasopharyngeal wash, bronch wash Could use http://purl.obolibrary.org/obo/GENEPIO_0002116 and add as ExactSynonym. - collection method Washout Tear Collection WASHOUT Not sure if this is considered a narrower synonym of "wash". - - - collection device Air filter AIR_FILTER -NCIT:C113122 collection device Blood Collection Tube BLOOD_TUBE Blood Collection Tube narrower: vacutainer https://en.wikipedia.org/wiki/Vacutainer#Types_of_tubes -NCIT:C17611 collection device Bronchoscope BRONCHOSCOPE Bronchoscope Endoscope Device NCIT_C49940 Used in transbronchial biopsies (e.g. tiny forceps), bronchoalveolar lavage, and brush bopsies (e.g. fibrobronchoscope brush, endobronchoscope brush). Should add these subclasses as well. - collection device Collection Container CONTAINER narrower: collection tube, collection bottle, collectoin cup Should we have a universal "collection tube" as well as or rather than the narrower terms below? - collection device Collection Cup CUP - collection device Fibrobronchoscope Brush BRUSH - collection device Filter FILTER - collection device Fine Needle FINE_NEEDLE "As in ""fine needle aspiration"". - -Device used to generate sample, is it used to ""collect"" the sample?" - collection device Microcapillary tube MICROCAPILLARY_TUBE MCT -OBI:0001128 collection device Micropipette MICROPIPETTE -OBI:0000436 collection device Needle NEEDLE Device used to generate sample, is it used to "collect" the sample? -NCIT:C113675 collection device Serum Collection Tube SERUM_TUBE Serum Collection Tube Red Top Tube "Red Top Tube" is technically a narrower synonym, as there are more colours for different methods of isolating the serum (e.g. clot activator + serum seperation gel, clot activator no gel, thrombin) https://en.wikipedia.org/wiki/Vacutainer#Types_of_tubes - collection device Sputum Collection Tube SPUTUM_TUBE - collection device Suction Catheter SUCTION_CATHETER -NCIT:c17627 collection device Swab SWAB swab narrower: swab (flocked tapered), swab (spun polyester), swab (synthetic fiber), swab (wire shaft), swab (plastic shaft), swab (wooden shaft), swab (calcium alginate) Fun fact, calcium alginate swabs or swabs with wooden shafts may contain substances that inactivate some viruses. - collection device Urine Collection Tube URINE_TUBE Urine specimen tube Under consideration. - collection device Virus Transport Medium TRANSPORT_MEDIUM viral transport medium "Not sure if this belongs here or if it should be included at all. Included it just in case. - -Could also include other transport mediums, such as: Amies Transport Medium, Sterile Saline / Non-Bacteriostatic Saline" - - -NCBITaxon_9606 host (scientific name) Homo sapiens homo sapiens human Homo -NCBITaxon_9913 host (scientific name) Bos taurus Bos taurus cow, cattle, domestic cow -NCBITaxon_9615 host (scientific name) Canis lupus familiaris Canis lupus familiaris dog -NCBITaxon_9397 host (scientific name) Chiroptera Chiroptera bat -NCBITaxon_8930 host (scientific name) Columbidae Columbidae pigeon Aves NCBITaxon_8782 -NCBITaxon_9685 host (scientific name) Felis catus Felis catus cat, domestic cat Felidae NCBITaxon_9681 -NCBITaxon_9031 host (scientific name) Gallus gallus Gallus gallus chicken Aves NCBITaxon_8782 -NCBITaxon_9973 host (scientific name) Manis Manis pangolin, Smutsia -NCBITaxon_9974 host (scientific name) Manis javanica Manis javanica Sunda pangolin, Malayan pangolin, Javan pangolin Manis -NCBITaxon_452646 host (scientific name) Neovison vison Neovison -NCBITaxon_9689 host (scientific name) Panthera leo Panthera leo lion Felidae NCBITaxon_9681 -NCBITaxon_9694 host (scientific name) Panthera tigris Panthera tigris tiger Felidae NCBITaxon_9681 -NCBITaxon_58055 host (scientific name) Rhinolophidae Rhinolophidae horseshoe bat Chiroptera -NCBITaxon_59477 host (scientific name) Rhinolophus affinis Rhinolophus affinis intermediate horseshoe bat Rhinolophidae What level do we want these at? Include the parent and more specific level? Probably higher level would go on a form? -NCBITaxon_9825 host (scientific name) Sus scrofa domesticus Sus scrofa domesticus pig, domestic pig, swine -NCBITaxon_9673 host (scientific name) Viverridae Viverridae civet cats, civets Changed Onto ID from NCBITaxon_379583 (Feliformia) to NCBITaxon_9673 (Viverridae) - - -NCBITaxon_9605 host (common name) Human HUMAN homo homo sapien Do we want the scientific and host "human" to lead to different terms? Or both homo or homo sapiens -NCBITaxon_9397 host (common name) Bat BAT Chiroptera Chiroptera -NCBITaxon_9685 host (common name) Cat Felis catus Felis catus, domestic cat -NCBITaxon_9031 host (common name) Chicken Gallus gallus Gallus gallus -NCBITaxon_9673 host (common name) Civets CIVETS Viverridae Viverridae, civet cat Changed Onto ID from NCBITaxon_379583 (Feliformia) to NCBITaxon_9673 (Viverridae) -NCBITaxon_9913 host (common name) Cow bovine Bos taurus Bos taurus, cattle Labeled as "bovine" in CNPHI. -NCBITaxon_9615 host (common name) Dog Canis lupus familiaris Canis lupus familiaris -NCBITaxon_9689 host (common name) Lion LION Panthera leo Panthera leo - host (common name) Mink -NCBITaxon_9973 host (common name) Pangolin PANGOLIN Manis Manis -NCBITaxon_9823 host (common name) Pig porcine pig Sus scrofa domesticus, swine "Unlike other entries where the scienfic and common name entries are the same, ""pig"" has a separate entry that is well used apart from its scientific entry. - -Labeled as ""porcine"" in CNPHI." -NCBITaxon_8930 host (common name) Pigeon Columbidae Columbidae -NCBITaxon_9694 host (common name) Tiger Panthera tigris Panthera tigris - - - host health state Asymptomatic ASYMPTOMATIC - host health state Deceased DECEASED - host health state Healthy HEALTHY Is this refering to cases that were never ill to begin with? Otherwise how is this differentiated from recovered? - host health state Recovered RECOVERED - host health state Symptomatic SYMPTOMATIC - - - host health status details Hospitalized HOSPITALIZED - Hospitalized Hospitalized (Non-ICU) NON_ICU Could use NCIT_C3833 - Hospitalized Hospitalized (ICU) ICU - host health status details Mechanical Ventilation VENTILATION - host health status details Medically Isolated ISOLATED - Medically Isolated Medically Isolated (Negative Pressure) ISOLATED_NEGATIVE_PR - host health status details Self-quarantining SELF_QUARANTINING - - host health outcome Deceased - host health outcome Deteriorating - host health outcome Recovered - host health outcome Stable - - organism Severe acute respiratory syndrome coronavirus 2 2019-nCoV, Severe Acute Respiratory Syndrome Coronavirus 2 - organism RaTG13 - organism RmYN02 - - - purpose of sampling Cluster/Outbreak investigation - purpose of sampling Diagnostic testing -NCIT_c15429 purpose of sampling Research research activity - purpose of sampling Surveillance - - - purpose of sequencing Baseline surveillance (random sampling) - purpose of sequencing Targeted surveillance (non-random sampling) - Targeted surveillance (non-random sampling) Priority surveillance project - Priority surveillance project Screening for Variants of Concern (VoC) - Priority surveillance project Longitudinal surveillance (repeat sampling of individuals) - Priority surveillance project Re-infection surveillance - Priority surveillance project Vaccine escape surveillance - Priority surveillance project Travel-associated surveillance - Travel-associated surveillance Domestic travel surveillance - Travel-associated surveillance International travel surveillance - purpose of sequencing Cluster/Outbreak investigation - Cluster/Outbreak investigation Multi-jurisdictional outbreak investigation - Cluster/Outbreak investigation Intra-jurisdictional outbreak investigation - purpose of sequencing Research - Research Viral passage experiment - Research Protocol testing experiment - - - specimen processing Virus passage - specimen processing RNA re-extraction (post RT-PCR) - specimen processing Specimens pooled - lab host ???? lab host: Nonpermissive/Nonsusceptible to SARS-CoV-2: 3T3, A529, BHK21, DF-1, embryonated eggs, HEL, HeLa, HeLa-T, Hep-2, L20, L929, MDCK, MRC-5, PoK, RD, RD-A, RLL, RLK, RSL, RSK, - lab host 293/ACE2 cell line 293/hACE2 cell line, broader: human kidney cell line, embryonic kidney cell line, renal... "Possible parent term: - -293-derived cell" "Possible parent term: - -CLO_0037237" "Add new term. Still need definition. - -293/hACE2 to appears to be an exact synonym (with the h added from ""human"") but I am not 100% positive. - -Source: ATCC CRL-3216 - -RRID: CVCL_DR94" -BTO_0000195 lab host Caco2 cell line CACO-2 cell Caco-2 cell, CaCo 2 cell, Caco2 cell, broader: human gastrointestinal tract cell line, colorectal adenocarcinoma cell line, human colon epithelial cell line, human intestinal cell line colonic adenocarcinoma cell line BTO_0001913 "Use BTO term. Add synonyms. CLO also has an entry. - -Source: ATCC HTB-37 - -RRID: CVCL_0025" -BTO_0002750 lab host Calu3 cell line Calu-3 cell Calu-3, Calu-3 cell, Calu 3 cell, broader: human respiratory tract cell line, human lung adenocarcinoma cell line, human pulminary cell line lung adenocarcinoma cell line BTO_0001911 "Use BTO term. Add synonyms. -CLO also has an entry. - -Source: ATCC HTB-55 - -RRID: CVCL_0609" - lab host EFK3B cell line Efk3B cell, Efk-3B clone 3B cell, Eptesicus fucus kidney 3B cell, broader: big brown bat kidney cell line "Add new term. Still needs definition. - -Low susceptibility to SARS-CoV-2. - -Group: Bat cell line. -""Can be used to cultivate viruses from the Coronaviridae, Filoviridae, Herpesviridae, Paramyxoviridae and Rhabdoviridae."" (ref RRID) - -RRID: CVCL_GZ34" -BTO_0002181 lab host HEK293T cell line HEK-293T cell 293 T cell, HEK293T cell, 293T cell, 293-T cell, HEK-293T cell, HEK 293T cell, HEK 293 T cell, 293 T cell, human embryonic kidney 293T cell, 293tsA1609neo cell, broader: human embryonic kidney cell line derives from/develops from some HEK-293 cell "HEK-293 cell: - -BTO_0000007" "Use BTO term. Add synonyms. - -Moderate susceptibility to SARS-CoV-2. - -RRID: CVCL_0063" - lab host HRCE cell line human renal cortical epithelial cell line "New term. - -High susceptibility to SARS-CoV-2." -BTO_0001950 lab host Huh7 cell line Huh7 cell Huh-7 cell, Huh7 cell, HUH7.0 cell, JTC-39 cell, Japanese Tissue Culture-39 cell, broader: human liver cell line, liver hepatocullular carcinoma cell line, hepatocellular carcinoma cell line hepatoma cell line BTO_0000578 "Add BTO term. Add synonyms. CLO also has entry. - -Moderate susceptibility. - -Source: JCRB0403, JCRB cell bank of Okayama University - -RRID: CVCL_0336" -CLO_0007330 lab host LLCMk2 cell line LLC-MK subscript(2) cell LLC-Mk2 cell line, Lilly Laboratories Cell-Monkey Kidney 2 cell line, broader: non-human primate cell line, Macaca mulatta cell line, rhesus monkey kidney cell line immortal rhesus macaque kidney-derived cell line cell CLO_0000714 "Use CLO term. Add snyonyms, still needs definition. - -Source: ATCC CCL-7 - -RRID: CVCL_3009" -BTO_0000836 lab host MDBK cell line MDBK cell Mardin-Darby bovine kidney cell kidney cell line BTO_0000067 "Optional? Use BTO term. Add synonym(s). - -Has been tested for SARS-CoV-2 propagation but preprint does not yet show results." - lab host Mv1Lu cell line Mink lung epithelial cell, Mv 1 Lu cell "Was being used in combination with A549 but is recommended against due to it's low levels of replication. Not sure if it should be included anyway since some labs may have used it before this recommendation. - -Are all Mv1 Lu Cell lines Mv 1 Lu (NBL-7)? - -Source: ATCC CCL-64" -BTO_0002924 lab host NHBE cell line NHBE cell normal human bronchial epithelial cell bronchial epithelial cell line BTO_0002022 "Use BTO term. -Low susceptibility to SARS-CoV-2." -BTO_0001865 lab host PK-15 cell line PK-15 cell PK15 cell, PK(15) cell, PK 15 cell, PK (15) cell, Porcine Kidney-15 cell, Porcine Kidney 15 cell, broader: pig cell line, porcine kidney cell line, PK-2a cell line kidney cell line BTO_0000067 "Use BTO term. Add synonyms. CLO also has some entries. - -Source: ATCC CCL-33 - -RRID:CVCL_2160" -BTO_0002909 lab host RK-13 cell line RK 13 cell RK13 cell, RK 13 cell, Rabbit Kidney-13 cell, Rabbit Kidney 13 cell, broader: rabbit cell line, Oryctolagus cuniculus cell line renal epithelium cell line BTO_0002886 "Use BTO term. Add synonyms. CLO has entries also. - -Source: ATCC CCL-37 - -RRID: CVCL_3155" -BTO_0002035 lab host U251 cell line U-251MG cell U-251 cell, U251 cell, U-251MG cell, U251MG cell, U-251 MG cell, broader: human neuronal cell line, glioblastoma cell line glioma cell line BTO_0000711 "Modest results, look for more evidence of its use. It's lower replication rate may actually be an incentive to labs worried about exposure. - -Source: Sigma 09063001 (Sigma-Aldrich, St Louis, MO, USA)" -BTO_0001444 lab host Vero cell line Vero cell VeroCCL81 cell, Verda reno cell, African monkey kidney cell , broader: non-human primate cell line, vaccine production cell line, African green monkey cell line kidney cell line BTO_0000067 "Use BTO term. Add synonyms. CLO also has entries. - -No 100% certain as to whether ""African monkey kidney cell"" should be and exact or broader synonym. - -High susceptibility to SARS-CoV-2. - -RRID: CVCL_0059" https://en.wikipedia.org/wiki/Vero_cell -BTO:0004755 lab host Vero E6 cell line VERO C1008 cell VeroE6 cell, Vero-E6 cell, Vero E6 cell, Vero 76 clone E6 cell, Vero C1008 cell, Vero C 1008 cell, VeroC1008 cell, Vero 76 clone E-6 cell, broader: African green monkey kidney cell line, African green monkey cell line, African green monkey kidney epithelial cell line, non-human primate kidney cell line, vero derived cell line derives from/develops from some Vero cell "Vero cell: - -BTO_0001444" "Use BTO entry. Add synonyms. CLO also has entry. - -High susceptibility to SARS-CoV-2. Is a clone of Vero-76 cell line. - -Source: ATCC CCL-81, ATCC CRL-1586 - -RRID: CVCL_0574" - lab host VeroE6/TMPRSS2 cell line VeroE6/TMPRSS2 cell VeroE6 cells expressing the transmembrane serine protease TMPRSS2. https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?ID=8668 Vero E6/TMPRSS2 cell, Vero-E6/TMPRSS2 cell, broader: Vero C1008 cell, African green monkey cell line "Recommended parent term: - -VERO C1008 cell" "Recommended parent term: - -BTO:0004755" "Add new term. - -Recently engineered cell line highly susceptible to SARS-CoV-2. - -JCRB: JCRB1819 - -RRID: CVCL_YQ49" - - host disease COVID-19 - - host age bin 0 - 9 - host age bin 10 - 19 - host age bin 20 - 29 - host age bin 30 - 39 - host age bin 40 - 49 - host age bin 50 - 59 - host age bin 60 - 69 - host age bin 70 - 79 - host age bin 80 - 89 - host age bin 90 - 99 - host age bin 100+ - -OMRSE:00000009? host gender Female MALE Could use 'female gender role' from OMRSE -OMRSE:00000008? host gender Male FEMALE Could use 'male gender role' from OMRSE - host gender Non-binary gender NON_BINARY_GENDER Could request new term under OMRSE 'gender role' - host gender Transgender (Male to Female) TRANSGENDER Could request new term under OMRSE 'gender role' - host gender Transgender (Female to Male) TRANSGENDER - host gender Undeclared REFUSED - host gender Unknown UNKNOWN - - exposure event Mass Gathering - Mass Gathering Convention CONVENTION - Mass Gathering Convocation Added 2020/14/03 - Mass Gathering Agricultural Event - exposure event Religious Gathering RELIGIOUS - Religious Gathering Mass - exposure event Social Gathering SOCIAL - Social Gathering Baby Shower Added 2020/14/03 - Social Gathering Community Event Added 2020/14/03 - Social Gathering Family Gathering - Family Gathering Family Reunion - Social Gathering Funeral - Social Gathering Party - Social Gathering Potluck - Social Gathering Wedding - exposure event Other exposure event - - exposure contact level Contact with infected individual - Contact with infected individual Direct contact (direct human-to-human contact) - Contact with infected individual Indirect contact - Indirect contact Close contact (face-to-face, no direct contact) - Indirect contact Casual contact - - - host role Attendee - Attendee Student i.e. school attendee - host role Patient - Patient Inpatient - Patient Outpatient - host role Passenger Could include for pairing with modes of transport - host role Resident - host role Visitor - host role Volunteer - host role Work Only including narrower terms that appears on case report forms - Work Administrator - Work First Responder synonymous with emergency responder, frontline responder - First Responder Firefighter - First Responder Paramedic - First Responder Police Officer - Work Healthcare Worker - Work Nurse - Work Personal Care Aid - Work Pharmacist - Work Physician - Work Housekeeper - Work Kitchen Worker - Work Laboratory Worker - Work Rotational Worker - Work Seasonal Worker - Work Veterinarian - host role Social role Damion mentioned that we could include these roles (already in GenEpiO) - Social role Acquaintance of case - Social role Relative of case - Relative of case Child of case - Relative of case Parent of case - Relative of case Father of case Update (2020/08/28): Changed parent class to "parent" - Relative of case Mother of case Update (2020/08/28): Changed parent class to "parent" - Social role Spouse of case - host role Other Host Role - - exposure setting Human Exposure - Human Exposure Known COVID-19 Case - Human Exposure Patient Contact - Human Exposure Probable COVID-19 Case presumptive confirmed COVID-19 case Synonym "presumptive confirmed COVID-19 case" added because this is the language some Canadian provinces use (source: Interim national surveillance guidelines for human infection with Coronavirus disease (COVID-19)) - Human Exposure Person with Acute Respiratory Illness - Human Exposure Person with Fever and/or Cough - Human Exposure Person who Recently Travelled - exposure setting Occupational or Residency Exposure - Occupational or Residency Exposure Abbatoir - Occupational or Residency Exposure Animal Rescue - Occupational or Residency Exposure Childcare - Childcare Daycare repositioned under 'childcare' - 2020/08/19 - Occupational or Residency Exposure Funeral Home - Occupational or Residency Exposure Place of Worship - Place of Worship Church - Place of Worship Mosque - Place of Worship Temple - Occupational or Residency Exposure Nursery - Occupational or Residency Exposure Household - Occupational or Residency Exposure Community Service Centre - Occupational or Residency Exposure Correctional Facility prison - Occupational or Residency Exposure Dormitory - Occupational or Residency Exposure Farm - Occupational or Residency Exposure First Nations Reserve - Occupational or Residency Exposure Group Home can include terms like: personal care home, private senior's residence, retirement home, assisted/independent living, longoterm residential care centre - Occupational or Residency Exposure Healthcare Setting 5/8 forms specify direct patient contact, should we include that specification somewhere? - Healthcare Setting Ambulance ENVO request made - Healthcare Setting Acute Care Facility - Healthcare Setting Clinic - Healthcare Setting Community Health Centre - Healthcare Setting Hospital - Hospital Emergency Department - Hospital ICU - Hospital Ward - Healthcare Setting Laboratory - Healthcare Setting Long-Term Care Facility - Healthcare Setting Pharmacy - Healthcare Setting Physician's Office - Occupational or Residency Exposure Insecure Housing (Homeless) - Occupational or Residency Exposure Office - Occupational or Residency Exposure Outdoors - Outdoors Camp/camping - Outdoors Hiking - Outdoors Hunting - Occupational or Residency Exposure Petting zoo - Occupational or Residency Exposure Restaurant - Occupational or Residency Exposure Retail Store Retail Environment - Occupational or Residency Exposure School - Occupational or Residency Exposure Temporary Residence - Temporary Residence Homeless Shelter emergency shelter - Temporary Residence Hotel - Occupational or Residency Exposure Veterinary Care Clinic - exposure setting Travel Exposure - Travel Exposure Travelled Redundant? Essentially the same as 'Travel Exposure'? - Travelled Travelled on a Cruise Ship - Travelled Travelled on a Plane - Travelled Travelled on Ground Transport Renamed 'public transport' to 'ground transport' to distinguish from planes, which are also public transport. - Travelled Travelled outside Province/Territory - Travelled Travelled outside Canada - exposure setting Other Exposure Setting - - - -OBI_0000759 sequencing instrument Illumina illumina -OBI_0002128 Illumina Illumina Genome Analyzer illumina genome analyzer A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html Genome Analyzer DNA sequencer OBI_0400103 -OBI_0000703 Illumina Genome Analyzer Illumina Genome Analyzer II illumina genome analyzer ii DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000703&viewMode=All&siblings=true Genome Analyzer II DNA sequencer OBI_0400103 -OBI_0002000 Illumina Genome Analyzer Illumina Genome Analyzer IIx Genome Analyzer IIx The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0002000&viewMode=All&siblings=true Illumina GA IIx, Illumina Genome Analyzer IIx illumina genome analyzer ii OBI_0000703 - Illumina Illumina HiScanSQ illumina hiscan SQ DNA sequencer OBI_0400103 new term - Illumina Illumina HiSeq -OBI_0002129 Illumina Illumina HiSeq X Illumina HiSeq X The Illumina HiSeq X is an ultra-high-throughput sequencing machine developed by Illumina. https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0008567 Illumina HiSeq X high throughput sequencer http://www.ebi.ac.uk/efo/EFO_0002699 - Illumina HiSeq X Illumina HiSeq X Five Sets of 5 HiSeq X instruments make up the Illumina HiSeq X Five https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0008567 -OBI_0002129 Illumina HiSeq X Illumina HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. http://www.ontobee.org/ontology/OBI?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0002129 Illumina HiSeq X Ten, HiSeq X Ten DNA sequencer OBI_0400103 -OBI_0002022 Illumina Illumina HiSeq 1000 illumina hiseq 1000 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0002022&viewMode=All&siblings=true HiSeq 1000 DNA sequencer OBI_0400103 - Illumina Illumina HiSeq 1500 HiSeq 1500 -OBI_0002001 Illumina Illumina HiSeq 2000 illumina hiseq 2000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0002001&viewMode=All&siblings=true HiSeq 2000 DNA sequencer OBI_0400103 -OBI_0002002 Illumina Illumina HiSeq 2500 illumina hiseq 2500 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0002002&viewMode=All&siblings=true HiSeq 2500 DNA sequencer OBI_0400103 -OBI_0002048 Illumina Illumina HiSeq 3000 illumina hiseq 3000 A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0002048&viewMode=All&siblings=true HiSeq 3000 DNA sequencer OBI_0400103 -OBI_0002049 Illumina Illumina HiSeq 4000 illumina hiseq 4000 A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. http://www.illumina.com/systems/hiseq-3000-4000.html HiSeq 4000 DNA sequencer OBI_0400103 - Illumina Illumina iSeq -EFO:0008635 Illumina iSeq Illumina iSeq 100 illumina iseq 100 The Illumina iSeq 100 is a benchtop sequencing machine developed by Illumina. Its primary applications include small whole-genome sequencing, targeted sequencing of a set of genes or gene regions, gene expression analysis and 16S metagenomic sequencing. https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0008635&viewMode=All&siblings=true iSeq 100 high throughput sequencer http://www.ebi.ac.uk/efo/EFO_0002699 - Illumina Illumina NovaSeq -OBI_0002630 Illumina NovaSeq Illumina NovaSeq 6000 illumina novaseq 6000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run) http://www.illumina.com/systems/sequencing-platforms/novaseq.html NovaSeq 6000 DNA sequencer OBI_0400103 -http://www.ebi.ac.uk/efo/EFO_0008636 Illumina Illumina MiniSeq illumina miniseq The Illumina MiniSeq is a benchtop sequencing machine developed by Illumina and an output upto 8Gb. https://www.illumina.com/systems/sequencing-platforms/miniseq/specifications.html MiniSeq high throughput sequencer http://www.ebi.ac.uk/efo/EFO_0002699 -OBI_0002003 Illumina Illumina MiSeq MiSeq A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf illumina miseq DNA sequencer OBI_0400103 - Illumina Illumina NextSeq -OBI_0002021 Illumina Illumina NextSeq 500 nextseq 500 Illumina NextSeq 500 DNA sequencer OBI_0400103 - Illumina Illumina NextSeq 550 -OBI_0001856 sequencing instrument Pacific Biosciences pacific biosciences - Pacific Biosciences PacBio RS DNA sequencer OBI_0400103 -OBI_0002012 Pacific Biosciences PacBio RS II pacbio rs ii DNA sequencer OBI_0400103 -OBI_0002632 Pacific Biosciences PacBio Sequel pacbio sequel DNA sequencer OBI_0400103 -OBI_0002633 Pacific Biosciences PacBio Sequel II pacbio sequel ii DNA sequencer OBI_0400103 - sequencing instrument Ion Torrent -GENEPIO_0001935 Ion Torrent Ion Torrent PGM ion torrent pgm - Ion Torrent Ion Torrent Proton - Ion Torrent Ion Torrent S5 XL - Ion Torrent Ion Torrent S5 - sequencing instrument Oxford Nanopore - Oxford Nanopore GridION - Oxford Nanopore MinION - Oxford Nanopore PromethION - sequencing instrument BGI Genomics - BGI Genomics BGISEQ-500 - sequencing instrument MGI - MGI DNBSEQ-T7 - MGI DNBSEQ-G400 - MGI DNBSEQ-G400 FAST - MGI DNBSEQ-G50 - - -PR:P0DTC4 gene name 1 E gene (orf4) E gene E gene envelope small membrane protein (SARS-CoV-2) sM protein (SARS2), envelope protein (SARS2), PRO_0000449651, E protein (SARS2), E (SARS2), ORF4, GU280_gp04, E severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTC5 gene name 1 M gene (orf5) membrane protein (SARS-CoV-2) E1 glycoprotein (SARS2), membrane glycoprotein (SARS2), PRO_0000449652, matrix glycoprotein (SARS2), M (SARS2), M protein (SARS2), GU280_gp05, ORF5 severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTC9 gene name 1 N gene (orf9) nucleoprotein (SARS-CoV-2) protein N (SARS2), nucleocapsid protein (SARS2), NC (SARS2), PRO_0000449656, N (SARS2), GU280_gp10, ORF9, N, ORF9a, nucleocapsi phosphoprotein severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTC2 gene name 1 Spike gene (orf2) spike glycoprotein (SARS-CoV-2) peplomer protein (SARS2), surface glycoprotein (SARS2), S glycoprotein (SARS2), S (SARS2), E2 (SARS2), S, GU280_gp02, ORF2, ORF-2 narrower: spike protein S1, spike protein S2 severe acute respiratory syndrome coronavirus 2 protein PR:000050262 There are additional proteins in this category that have their signal peptide removed, but did not include entries for them as they seemed too narrow. -PR:000050281 gene name 1 orf1ab (rep) replicase polyprotein 1ab (SARS-CoV-2) pp1ab (SARS2), ORF1ab polyprotein (SARS2), PRO_0000449618, rep/iso:ORF1ab (SARS2), rep1a-1b, rep 1a-1b, rep1ab, rep Used in pick-list heirarchy instead of 'Rep'. -PR:P0DTC1-1 orf1ab (rep) orf1a (pp1a) replicase polyprotein 1a (SARS-CoV-2) pp1a (SARS2), PRO_0000449634, rep/iso:ORF1a (SARS2), ORF1a polyprotein (SARS2), rep1a, rep 1a rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050280 orf1a (pp1a) nsp11 non-structural protein 11 (SARS-CoV-2) nsp11 (SARS2), 'UniProtKB:P0DTC1, 4393-4405', PRO_0000449645, rep/Clv:nsp11 (SARS2) ORF1a proteolytic cleavage product (SARS-CoV-2) PR:000050282 -PR:000050270 orf1ab (rep) nsp1 host translation inhibitor nsp1 (SARS-CoV-2) nsp1 (SARS2), 'UniProtKB:P0DTD1, 1-180', PRO_0000449635, 'UniProtKB:P0DTC1, 1-180', leader protein (SARS2), PRO_0000449619, rep/Clv:nsp1 (SARS2), non-structural protein 1 (SARS2) rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050271 orf1ab (rep) nsp2 non-structural protein 2 (SARS-CoV-2) p65 homolog (SARS2), rep/Clv:nsp2 (SARS2), PRO_0000449620, 'UniProtKB:P0DTD1, 181-818', nsp2 (SARS2), PRO_0000449636, 'UniProtKB:P0DTC1, 181-818' rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050272 orf1ab (rep) nsp3 non-structural protein 3 (SARS-CoV-2) rep/Clv:nsp3 (SARS2), main proteinase (SARS2), nsp3 (SARS2), PLpro (SARS2), PRO_0000449621, papain-like proteinase (SARS2), PRO_0000449637, 'UniProtKB:P0DTC1, 819-2763', 'UniProtKB:P0DTD1, 819-2763', PL2-PRO, PL-PRO, SARS coronavirus main proteinase rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050273 orf1ab (rep) nsp4 non-structural protein 4 (SARS-CoV-2) nsp4 (SARS2), PRO_0000449622, 'UniProtKB:P0DTC1, 2764-3263', 'UniProtKB:P0DTD1, 2764-3263', PRO_0000449638, rep/Clv:nsp4 (SARS2) rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050274 orf1ab (rep) nsp5 3C-like proteinase (SARS-CoV-2) nsp5 (SARS2), 3CL-PRO (SARS2), 'UniProtKB:P0DTC1, 3264-3569', PRO_0000449623, rep/Clv:nsp5 (SARS2), 3CLp (SARS2), picornavirus 3C-like protease (SARS2), 'UniProtKB:P0DTD1, 3264-3569', PRO_0000449639, 3CLpro (SARS2) rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050275 orf1ab (rep) nsp6 non-structural protein 6 (SARS-CoV-2) PRO_0000449640, nsp6 (SARS2), 'UniProtKB:P0DTD1, 3570-3859', 'UniProtKB:P0DTC1, 3570-3859', PRO_0000449624, rep/Clv:nsp6 (SARS2) rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050276 orf1ab (rep) nsp7 non-structural protein 7 (SARS-CoV-2) UniProtKB:P0DTD1, 3860-3942', PRO_0000449641, 'UniProtKB:P0DTC1, 3860-3942', nsp7 (SARS2), PRO_0000449625, rep/Clv:nsp7 (SARS2) rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050277 orf1ab (rep) nsp8 non-structural protein 8 (SARS-CoV-2) rep/Clv:nsp8 (SARS2), PRO_0000449642. 'UniProtKB:P0DTC1, 3943-4140', PRO_0000449626, nsp8 (SARS2), 'UniProtKB:P0DTD1, 3943-4140' rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050278 orf1ab (rep) nsp9 non-structural protein 9 (SARS-CoV-2) UniProtKB:P0DTC1, 4141-4253', PRO_0000449643, nsp9 (SARS2), 'UniProtKB:P0DTD1, 4141-4253', rep/Clv:nsp9 (SARS2), PRO_0000449627 rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050279 orf1ab (rep) nsp10 non-structural protein 10 (SARS-CoV-2) GFL (SARS2), 'UniProtKB:P0DTC1, 4254-4392', PRO_0000449644, growth factor-like peptide (SARS2), rep/Clv:nsp10 (SARS2), 'UniProtKB:P0DTD1, 4254-4392', PRO_0000449628, nsp10 (SARS2) rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050284 orf1ab (rep) RdRp gene (nsp12) RNA-directed RNA polymerase (SARS-CoV-2) Pol (SARS2), RdRp (SARS2), 'UniProtKB:P0DTD1, 4393-5324', ORF1ab/Clv:nsp12 (SARS2), nsp12 (SARS2), PRO_0000449629, RNA dependent RNA Polymerase ORF1ab proteolytic cleavage product (SARS-CoV-2) PR:000050283 -PR:000050285 orf1ab (rep) hel gene (nsp13) helicase (SARS-CoV-2) PRO_0000449630, Hel (SARS2), ORF1ab/Clv:nsp13 (SARS2), 'UniProtKB:P0DTD1, 5325-5925', nsp13 (SARS2) ORF1a proteolytic cleavage product (SARS-CoV-2) PR:000050282 -PR:000050286 orf1ab (rep) exoN gene (nsp14) bifunctional exonuclease/methyltransferase (SARS-CoV-2) ExoN (SARS2), nsp14 (SARS2), PRO_0000449631, 'UniProtKB:P0DTD1, 5926-6452', ORF1ab/Clv:nsp14 (SARS2), guanine-N7 methyltransferase (SARS2), proofreading exoribonuclease, non-structural protein 14 ORF1a proteolytic cleavage product (SARS-CoV-2) PR:000050282 -PR:000050287 orf1ab (rep) nsp15 uridylate-specific endoribonuclease (SARS-CoV-2) nsp15 (SARS2), endoRNAse (SARS2), PRO_0000449632, ORF1ab/Clv:nsp15 (SARS2), 'UniProtKB:P0DTD1, 6453-6798', NendoU (SARS2) ORF1a proteolytic cleavage product (SARS-CoV-2) PR:000050282 -PR:000050288 orf1ab (rep) nsp16 2'-O-methyltransferase (SARS-CoV-2) UniProtKB:P0DTD1, 6799-7096', PRO_0000449633, ORF1ab/Clv:nsp16 (SARS2), 2'-O-ribose methyltransferase (SARS2), nsp16 (SARS2) ORF1ab proteolytic cleavage product (SARS-CoV-2) PR:000050283 -PR:P0DTC3 gene name 1 orf3a protein 3a (SARS-CoV-2) PRO_0000449650, protein X1 (SARS2), ORF3a (SARS2), accessory protein 3a (SARS2), protein U274 (SARS2), GU280_gp03, ORF3a, ORF-3a severe acute respiratory syndrome coronavirus 2 protein PR:000050262 - gene name 1 orf3b ORF-3b severe acute respiratory syndrome coronavirus 2 protein PR:000050262 Not yet listed on Uniprot nor PR/PRO. Saw it on GO gene list and found research papers referencing it (for example see 'other'). https://www.biorxiv.org/content/10.1101/2020.05.11.088179v1.full.pdf -PR:P0DTC6 gene name 1 orf6 (ns6) ORF6 protein (SARS-CoV-2) ns6 (SARS2), ORF6 (SARS2), PRO_0000449653, accessory protein 6 (SARS2), protein X3 (SARS2), GU280_gp06, ORF6, ORF-6 severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTC7 gene name 1 orf7a protein 7a (SARS-CoV-2) accessory protein 7a (SARS2), ORF7a (SARS2), protein U122 (SARS2), protein X4 (SARS2), ORF7a, GU280_gp07, ORF-7a severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTD8 gene name 1 orf7b (ns7b) protein 7b (SARS-CoV-2) accessory protein 7b (SARS2), non-structural protein 7b (SARS2), ORF7b (SARS2), ns7b (SARS2), PRO_0000449799, ORF7b, GU280_gp08, ORF-7b severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTC8 gene name 1 orf8 (ns8) ORF8 protein (SARS-CoV-2) ns8 (SARS2), ORF8 (SARS2), ORF8, GU280_gp09, ORF-8 severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTD2 gene name 1 orf9b protein 9b (SARS-CoV-2) accessory protein 9b (SARS2), PRO_0000449657, ORF-9b (SARS2), ORF9b (SARS2), ORF9b severe acute respiratory syndrome coronavirus 2 protein PR:000050262 - gene name 1 orf9c ORF-9c Not yet listed on Uniprot nor PR/PRO. Saw it on GO gene list and found research papers referencing it (for example see 'other'). https://www.biorxiv.org/content/10.1101/2020.03.22.002386v1.full.pdf -PR:A0A663DJA2 gene name 1 orf10 ORF10 protein (SARS-CoV-2) ORF10 (SARS2), ORF10, ORF-10 severe acute respiratory syndrome coronavirus 2 protein PR:000050262 - gene name 1 orf14 ORF-14 Uncharacterized at this time (2020/06/16); protein inferred from homology. https://www.uniprot.org/uniprot/P0DTD3 - gene name 1 SARS-COV-2 5' UTR - - - sequence submitted by National Microbiology Laboratory (NML) NML - sequence submitted by BCCDC Public Health Laboratory BCCDC - sequence submitted by Alberta Precision Labs (APL) - Alberta Precision Labs (APL) Alberta ProvLab North (APLN) APL-E - Alberta Precision Labs (APL) Alberta ProvLab South (APLS) APL-C - sequence submitted by Public Health Ontario (PHO) PHO - sequence submitted by Laboratoire de santé publique du Québec (LSPQ) LSPQ - sequence submitted by Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) RRPL - sequence submitted by Manitoba Cadham Provincial Laboratory CADHAM - sequence submitted by Nova Scotia Health Authority NS_QE_II - sequence submitted by New Brunswick - Vitalité Health Network GEORGES_L_DUMONT - sequence submitted by Newfoundland and Labrador - Eastern Health EASTERN_HEALTH - sequence submitted by Prince Edward Island - Health PEI PEI - sequence submitted by Ontario Institute for Cancer Research (OICR) OICR - sequence submitted by McMaster University MCMASTER - sequence submitted by McGill University MCGILL - sequence submitted by The Centre for Applied Genomics (TCAG) TCAG - sequence submitted by Sunnybrook Health Sciences Centre SUNNYBROOK - sequence submitted by Thunder Bay Regional Health Sciences Centre THUNDER_BAY - sequence submitted by Canadore College CANADORE - sequence submitted by Queen’s University / Kingston Health Sciences Centre QUEENS_UNIV - - - - -GAZ_00006882 geo_loc_name (country) Afghanistan afghanistan -GAZ_00002953 geo_loc_name (country) Albania albania -GAZ_00000563 geo_loc_name (country) Algeria algeria -GAZ_00003957 geo_loc_name (country) American Samoa american samoa -GAZ_00002948 geo_loc_name (country) Andorra andorra -GAZ_00001095 geo_loc_name (country) Angola angola -GAZ_00009159 geo_loc_name (country) Anguilla anguilla -GAZ_00000462 geo_loc_name (country) Antarctica antarctica -GAZ_00006883 geo_loc_name (country) Antigua and Barbuda antigua and barbuda -GAZ_00002928 geo_loc_name (country) Argentina ARGENTINA argentina -GAZ_00004094 geo_loc_name (country) Armenia armenia -GAZ_00004025 geo_loc_name (country) Aruba aruba -GAZ_00005901 geo_loc_name (country) Ashmore and Cartier Islands Territory of Ashmore and Cartier Islands Territory of Ashmore and Cartier Islands -GAZ_00000463 geo_loc_name (country) Australia AUSTRALIA australia -GAZ_00002942 geo_loc_name (country) Austria austria -GAZ_00004941 geo_loc_name (country) Azerbaijan azerbaijan -GAZ_00002733 geo_loc_name (country) Bahamas The Bahamas -GAZ_00005281 geo_loc_name (country) Bahrain bahrain -GAZ_00007117 geo_loc_name (country) Baker Island -GAZ_00003750 geo_loc_name (country) Bangladesh bangladesh -GAZ_00001251 geo_loc_name (country) Barbados barbados -GAZ_00005810 geo_loc_name (country) Bassas da India Ile Bassas da India -GAZ_00006886 geo_loc_name (country) Belarus belarus -GAZ_00002938 geo_loc_name (country) Belgium BELGIUM belgium -GAZ_00002934 geo_loc_name (country) Belize belize -GAZ_00000904 geo_loc_name (country) Benin benin -GAZ_00001264 geo_loc_name (country) Bermuda bermuda -GAZ_00003920 geo_loc_name (country) Bhutan bhutan -GAZ_00002511 geo_loc_name (country) Bolivia bolivia -GAZ_00025355 geo_loc_name (country) Borneo borneo -GAZ_00006887 geo_loc_name (country) Bosnia and Herzegovina bosnia and herzegovina -GAZ_00001097 geo_loc_name (country) Botswana botswana -GAZ_00001453 geo_loc_name (country) Bouvet Island bouvet island -GAZ_00002828 geo_loc_name (country) Brazil BRAZIL brazil -GAZ_00003961 geo_loc_name (country) British Virgin Islands british virgin islands -GAZ_00003901 geo_loc_name (country) Brunei -GAZ_00002950 geo_loc_name (country) Bulgaria bulgaria -GAZ_00000905 geo_loc_name (country) Burkina Faso burkina faso -GAZ_00001090 geo_loc_name (country) Burundi burundi -GAZ_00006888 geo_loc_name (country) Cambodia cambodia -GAZ_00001093 geo_loc_name (country) Cameroon cameroon -GAZ_00002560 geo_loc_name (country) Canada CA canada -GAZ_00001227 geo_loc_name (country) Cape Verde cape verde -GAZ_00003986 geo_loc_name (country) Cayman Islands cayman islands -GAZ_00001089 geo_loc_name (country) Central African Republic central african republic -GAZ_00000586 geo_loc_name (country) Chad chad -GAZ_00002825 geo_loc_name (country) Chile CHILE chile -GAZ_00002845 geo_loc_name (country) China CHINA china -GAZ_00005915 geo_loc_name (country) Christmas Island christmas island -GAZ_00005838 geo_loc_name (country) Clipperton Island -GAZ_00009721 geo_loc_name (country) Cocos Islands -GAZ_00002929 geo_loc_name (country) Colombia COLUMBIA colombia -GAZ_00005820 geo_loc_name (country) Comoros comoros -GAZ_00053798 geo_loc_name (country) Cook Islands cook islands -GAZ_00005917 geo_loc_name (country) Coral Sea Islands -GAZ_00002901 geo_loc_name (country) Costa Rica COSTA_RICA costa rica -GAZ_00000906 geo_loc_name (country) Cote d'Ivoire cote d'ivoire -GAZ_00002719 geo_loc_name (country) Croatia croatia -GAZ_00003762 geo_loc_name (country) Cuba cuba -GAZ_00004021 geo_loc_name (country) Curacao Currently using Onto ID for 'Curacao Island' rather than the 'Country of Curacao' (GAZ_00012582) - R -GAZ_00004006 geo_loc_name (country) Cyprus -GAZ_00002954 geo_loc_name (country) Czech Republic czech republic -GAZ_00001086 geo_loc_name (country) Democratic Republic of the Congo democratic republic of the congo -GAZ_00005852 geo_loc_name (country) Denmark DENMARK metropolitan denmark -GAZ_00000582 geo_loc_name (country) Djibouti djibouti -GAZ_00006890 geo_loc_name (country) Dominica dominica -GAZ_00003952 geo_loc_name (country) Dominican Republic dominican republic -GAZ_00002912 geo_loc_name (country) Ecuador ECUADOR ecuador -GAZ_00003934 geo_loc_name (country) Egypt egypt -GAZ_00002935 geo_loc_name (country) El Salvador el salvador -GAZ_00001091 geo_loc_name (country) Equatorial Guinea equatorial guinea -GAZ_00000581 geo_loc_name (country) Eritrea eritrea -GAZ_00002959 geo_loc_name (country) Estonia estonia -GAZ_00001099 geo_loc_name (country) Eswatini Swaziland -GAZ_00000567 geo_loc_name (country) Ethiopia ethiopia -GAZ_00005811 geo_loc_name (country) Europa Island Ile Europa Europa Island Should make synonym request to GAZ for "Europa Island" -GAZ_00001412 geo_loc_name (country) Falkland Islands (Islas Malvinas) Falkland Islands -GAZ_00059206 geo_loc_name (country) Faroe Islands faroe islands -GAZ_00006891 geo_loc_name (country) Fiji fiji -GAZ_00002937 geo_loc_name (country) Finland finland -GAZ_00003940 geo_loc_name (country) France FRANCE Metropolitan France -GAZ_00002516 geo_loc_name (country) French Guiana Guyane -GAZ_00002918 geo_loc_name (country) French Polynesia french polynesia -GAZ_00003753 geo_loc_name (country) French Southern and Antarctic Lands -GAZ_00001092 geo_loc_name (country) Gabon gabon -GAZ_00000907 geo_loc_name (country) Gambia gambia -GAZ_00009571 geo_loc_name (country) Gaza Strip gaza strip -GAZ_00004942 geo_loc_name (country) Georgia georgia -GAZ_00002646 geo_loc_name (country) Germany GERMANY germany -GAZ_00000908 geo_loc_name (country) Ghana ghana -GAZ_00003987 geo_loc_name (country) Gibraltar gibraltar -GAZ_00005808 geo_loc_name (country) Glorioso Islands -GAZ_00002945 geo_loc_name (country) Greece greece -GAZ_00001507 geo_loc_name (country) Greenland greenland -GAZ_02000573 geo_loc_name (country) Grenada -GAZ_00067142 geo_loc_name (country) Guadeloupe -GAZ_00003706 geo_loc_name (country) Guam Territory of Guam -GAZ_00002936 geo_loc_name (country) Guatemala guatemala -GAZ_00001550 geo_loc_name (country) Guernsey -GAZ_00000909 geo_loc_name (country) Guinea guinea -GAZ_00000910 geo_loc_name (country) Guinea-Bissau guinea-bissau -GAZ_00002522 geo_loc_name (country) Guyana GUYANA guyana -GAZ_00003953 geo_loc_name (country) Haiti haiti -GAZ_00009718 geo_loc_name (country) Heard Island and McDonald Islands -GAZ_00002894 geo_loc_name (country) Honduras honduras -GAZ_00003203 geo_loc_name (country) Hong Kong hong kong -GAZ_00007120 geo_loc_name (country) Howland Island -GAZ_00002952 geo_loc_name (country) Hungary hungary -GAZ_00000843 geo_loc_name (country) Iceland iceland -GAZ_00002839 geo_loc_name (country) India INDIA india -GAZ_00003727 geo_loc_name (country) Indonesia indonesia -GAZ_00004474 geo_loc_name (country) Iran iran -GAZ_00004483 geo_loc_name (country) Iraq iraq -GAZ_00002943 geo_loc_name (country) Ireland Republic of Ireland Currently only refering to Southern Ireland (Republic of Ireland), perhaps we should use GAZ_00004018 since it encompasses both and there is no seperate entry in the picklist for Northern island. - R -GAZ_00052477 geo_loc_name (country) Isle of Man isle of man -GAZ_00002476 geo_loc_name (country) Israel israel -GAZ_00002650 geo_loc_name (country) Italy italy -GAZ_00003781 geo_loc_name (country) Jamaica JAMAICA jamaica -GAZ_00005853 geo_loc_name (country) Jan Mayen -GAZ_00002747 geo_loc_name (country) Japan japan -GAZ_00007118 geo_loc_name (country) Jarvis Island -GAZ_00001551 geo_loc_name (country) Jersey -GAZ_00007114 geo_loc_name (country) Johnston Atoll -GAZ_00002473 geo_loc_name (country) Jordan jordan -GAZ_00005809 geo_loc_name (country) Juan de Nova Island -GAZ_00004999 geo_loc_name (country) Kazakhstan kazakhstan -GAZ_00001101 geo_loc_name (country) Kenya KENYA kenya -GAZ_00005682 geo_loc_name (country) Kerguelen Archipelago -GAZ_00007116 geo_loc_name (country) Kingman Reef -GAZ_00006894 geo_loc_name (country) Kiribati kiribati -GAZ_00011337 geo_loc_name (country) Kosovo kosovo -GAZ_00005285 geo_loc_name (country) Kuwait kuwait -GAZ_00006893 geo_loc_name (country) Kyrgyzstan kyrgyzstan -GAZ_00006889 geo_loc_name (country) Laos laos -GAZ_00002958 geo_loc_name (country) Latvia latvia -GAZ_00002478 geo_loc_name (country) Lebanon lebanon -GAZ_00001098 geo_loc_name (country) Lesotho lesotho -GAZ_00000911 geo_loc_name (country) Liberia liberia -GAZ_00000566 geo_loc_name (country) Libya libya -GAZ_00003858 geo_loc_name (country) Liechtenstein liechtenstein -GAZ_00007144 geo_loc_name (country) Line Islands -GAZ_00002960 geo_loc_name (country) Lithuania lithuania -GAZ_00002947 geo_loc_name (country) Luxembourg luxembourg -GAZ_00003202 geo_loc_name (country) Macau macau -GAZ_00001108 geo_loc_name (country) Madagascar -GAZ_00001105 geo_loc_name (country) Malawi malawi -GAZ_00003902 geo_loc_name (country) Malaysia malaysia -GAZ_00006924 geo_loc_name (country) Maldives Maldives Archipelago Maldives Archipelago -GAZ_00000584 geo_loc_name (country) Mali mali -GAZ_00005459 geo_loc_name (country) Malta -GAZ_00007161 geo_loc_name (country) Marshall Islands marshall islands -GAZ_00067143 geo_loc_name (country) Martinique Martinique Region -GAZ_00000583 geo_loc_name (country) Mauritania mauritania -GAZ_00003745 geo_loc_name (country) Mauritius -GAZ_00003943 geo_loc_name (country) Mayotte mayotte -GAZ_00002852 geo_loc_name (country) Mexico MEXICO mexico -GAZ_00005862 geo_loc_name (country) Micronesia micronesia -GAZ_00007112 geo_loc_name (country) Midway Islands Midway Atoll -GAZ_00003897 geo_loc_name (country) Moldova moldova -GAZ_00003857 geo_loc_name (country) Monaco monaco -GAZ_00008744 geo_loc_name (country) Mongolia mongolia -GAZ_00006898 geo_loc_name (country) Montenegro montenegro -GAZ_00003988 geo_loc_name (country) Montserrat montserrat -GAZ_00000565 geo_loc_name (country) Morocco morocco -GAZ_00001100 geo_loc_name (country) Mozambique mozambique -GAZ_00006899 geo_loc_name (country) Myanmar myanmar -GAZ_00001096 geo_loc_name (country) Namibia namibia -GAZ_00006900 geo_loc_name (country) Nauru nauru -GAZ_00007119 geo_loc_name (country) Navassa Island -GAZ_00004399 geo_loc_name (country) Nepal nepal -GAZ_00002946 geo_loc_name (country) Netherlands NETHERLANDS The Netherlands -GAZ_00005206 geo_loc_name (country) New Caledonia new caledonia -GAZ_00000469 geo_loc_name (country) New Zealand new zealand -GAZ_00002978 geo_loc_name (country) Nicaragua nicaragua -GAZ_00000585 geo_loc_name (country) Niger niger -GAZ_00000912 geo_loc_name (country) Nigeria NIGERIA nigeria -GAZ_00006902 geo_loc_name (country) Niue Niue Fekai Niue Fekai -GAZ_00005908 geo_loc_name (country) Norfolk Island Territory of NORFOLK ISLAND -GAZ_00002801 geo_loc_name (country) North Korea north korea DEMOCRATIC PEOPLE'S REPUBLIC OF KOREA -GAZ_00006895 geo_loc_name (country) North Macedonia Macedonia; Republic of Macedonia -GAZ_00002284 geo_loc_name (country) North Sea -GAZ_00003958 geo_loc_name (country) Northern Mariana Islands northern mariana islands -GAZ_00002699 geo_loc_name (country) Norway kingdom of norway Kingdom of Norway -GAZ_00005283 geo_loc_name (country) Oman oman -GAZ_00005246 geo_loc_name (country) Pakistan PAKISTAN pakistan -GAZ_00006905 geo_loc_name (country) Palau palau -GAZ_00002892 geo_loc_name (country) Panama panama -GAZ_00003922 geo_loc_name (country) Papua New Guinea papua new guinea -GAZ_00010832 geo_loc_name (country) Paracel Islands -GAZ_00002933 geo_loc_name (country) Paraguay paraguay Paraguay -GAZ_00002932 geo_loc_name (country) Peru peru Peru -GAZ_00004525 geo_loc_name (country) Philippines PHILIPPINE The Philippines -GAZ_00005867 geo_loc_name (country) Pitcairn Islands Pitcairn, Henderson, Ducie and Oeno Islands The Pitcairn Islands -GAZ_00002939 geo_loc_name (country) Poland poland -GAZ_00004126 geo_loc_name (country) Portugal Metropolitan Portugal Currently refering to 'Metropolitan Portgual' rather than the 'Portuguese Republic' (GAZ_00002944) aka 'Portugal' which seems incorrect to me. - R -GAZ_00006935 geo_loc_name (country) Puerto Rico Commonwealth of Puerto Rico -GAZ_00005286 geo_loc_name (country) Qatar qatar -GAZ_00001088 geo_loc_name (country) Republic of the Congo Republic of Congo -GAZ_00003945 geo_loc_name (country) Reunion Reunion Island -GAZ_00002951 geo_loc_name (country) Romania romania -GAZ_00023304 geo_loc_name (country) Ross Sea -GAZ_00002721 geo_loc_name (country) Russia russia -GAZ_00001087 geo_loc_name (country) Rwanda rwanda -GAZ_00000849 geo_loc_name (country) Saint Helena -GAZ_00006906 geo_loc_name (country) Saint Kitts and Nevis saint kitts-nevis Saint Kitts-Nevis -GAZ_00006909 geo_loc_name (country) Saint Lucia saint lucia -GAZ_00003942 geo_loc_name (country) Saint Pierre and Miquelon saint-pierre and miquelon -GAZ_00005841 geo_loc_name (country) Saint Martin -GAZ_02000565 geo_loc_name (country) Saint Vincent and the Grenadines saint vincent and the grenadines -GAZ_00006910 geo_loc_name (country) Samoa samoa -GAZ_00003102 geo_loc_name (country) San Marino san marino -GAZ_00006927 geo_loc_name (country) Sao Tome and Principe sao tome and principe -GAZ_00005279 geo_loc_name (country) Saudi Arabia saudi arabia -GAZ_00000913 geo_loc_name (country) Senegal senegal -GAZ_00002957 geo_loc_name (country) Serbia serbia -GAZ_00006922 geo_loc_name (country) Seychelles -GAZ_00000914 geo_loc_name (country) Sierra Leone sierra leone -GAZ_00003923 geo_loc_name (country) Singapore singapore -GAZ_00012579 geo_loc_name (country) Sint Maarten sint maarten -GAZ_00002956 geo_loc_name (country) Slovakia Slovak Republic -GAZ_00002955 geo_loc_name (country) Slovenia slovenia -GAZ_00005275 geo_loc_name (country) Solomon Islands solomon islands -GAZ_00001104 geo_loc_name (country) Somalia somalia -GAZ_00001094 geo_loc_name (country) South Africa south africa Republic of South Africa The actual onto label for this onto ID is 'Republic of South Africa' - are we overwritting onto labels for our ontology? - R -GAZ_00003990 geo_loc_name (country) South Georgia and the South Sandwich Islands -GAZ_00002802 geo_loc_name (country) South Korea south korea Republic of Korea -GAZ_00233439 geo_loc_name (country) South Sudan south sudan -GAZ_00003936 geo_loc_name (country) Spain Metropolitan Spain Shouldn't we be using 'Kingdom of Spain' (GAZ_00000591) rather than the narrower 'Metropolitan Spain'? - R -GAZ_00010831 geo_loc_name (country) Spratly Islands -GAZ_00003924 geo_loc_name (country) Sri Lanka sri lanka -GAZ_00002475 geo_loc_name (country) State of Palestine Palestinian Territories -GAZ_00000560 geo_loc_name (country) Sudan sudan -GAZ_00002525 geo_loc_name (country) Suriname -GAZ_00005396 geo_loc_name (country) Svalbard Svalbard Archipelago -GAZ_00001099 geo_loc_name (country) Swaziland Kingdom of Eswatini -GAZ_00002729 geo_loc_name (country) Sweden sweden -GAZ_00002941 geo_loc_name (country) Switzerland switzerland -GAZ_00002474 geo_loc_name (country) Syria syria -GAZ_00005341 geo_loc_name (country) Taiwan republic of china Republic of China -GAZ_00006912 geo_loc_name (country) Tajikistan tajikistan -GAZ_00001103 geo_loc_name (country) Tanzania tanzania -GAZ_00003744 geo_loc_name (country) Thailand thailand -GAZ_00006913 geo_loc_name (country) Timor-Leste timor-leste -GAZ_00000915 geo_loc_name (country) Togo togo -GAZ_00260188 geo_loc_name (country) Tokelau tokelau -GAZ_00006916 geo_loc_name (country) Tonga tonga -GAZ_00003767 geo_loc_name (country) Trinidad and Tobago trinidad and tobago -GAZ_00005812 geo_loc_name (country) Tromelin Island -GAZ_00000562 geo_loc_name (country) Tunisia tunisia -GAZ_00000558 geo_loc_name (country) Turkey turkey -GAZ_00005018 geo_loc_name (country) Turkmenistan turkmenistan -GAZ_00003955 geo_loc_name (country) Turks and Caicos Islands turks and caicos islands -GAZ_00009715 geo_loc_name (country) Tuvalu tuvalu -GAZ_00002459 geo_loc_name (country) United States of America US united states of america United States of America -GAZ_00001102 geo_loc_name (country) Uganda uganda -GAZ_00002724 geo_loc_name (country) Ukraine ukraine -GAZ_00005282 geo_loc_name (country) United Arab Emirates united arab emirates -GAZ_00002637 geo_loc_name (country) United Kingdom UNITEDKING united kingdom -GAZ_00002930 geo_loc_name (country) Uruguay URUGUAY uruguay -GAZ_00004979 geo_loc_name (country) Uzbekistan uzbekistan -GAZ_00006918 geo_loc_name (country) Vanuatu vanuatu -GAZ_00002931 geo_loc_name (country) Venezuela venezuela -GAZ_00003756 geo_loc_name (country) Viet Nam viet nam -GAZ_00003959 geo_loc_name (country) Virgin Islands United States Virgin Islands United States Virgin Islands -GAZ_00007111 geo_loc_name (country) Wake Island -GAZ_00007191 geo_loc_name (country) Wallis and Futuna Wallis and Futuna Islands Changed Onto ID from GAZ_00007192 to GAZ_00007191 since the former refers to the islands in general while the later refers to the territory. - R -GAZ_00009572 geo_loc_name (country) West Bank -GAZ_00000564 geo_loc_name (country) Western Sahara western sahara -GAZ_00005284 geo_loc_name (country) Yemen yemen -GAZ_00001107 geo_loc_name (country) Zambia zambia -GAZ_00001106 geo_loc_name (country) Zimbabwe zimbabwe - - \ No newline at end of file +Ontology ID parent class label datatype source data status requirement min value max value capitalize description guidance examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE +ID SC % + Database Identifiers + Database Identifiers specimen collector sample ID xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_rona_99 Sample ID given by the sample provider Primary Specimen ID VD_LAB_NUMBER sample_name + Database Identifiers NML submitted specimen primary ID xs:token The primary ID of the specimen submitted thorough LaSER. Store the identifier for the specimen submitted through the NML LaSER system. SR20-12345 + Database Identifiers NML related specimen primary ID xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The primary ID of the related specimen previously submitted thorough LaSER Store the primary ID of the related specimen previously submitted thorough LaSER SR20-12345 Related Specimen ID|Related Specimen Relationship Type + Database Identifiers IRIDA sample name xs:token The identifier assigned to a sequenced isolate in IRIDA. Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 + Database Identifiers umbrella bioproject accession select UPPER The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. PRJNA623807 + Database Identifiers bioproject accession xs:token UPPER The INSDC accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 BioProject Accession PH_BIOPROJECT_ACCESSION bioproject_accession + Database Identifiers biosample accession xs:token UPPER The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION + Database Identifiers SRA accession xs:token UPPER The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 SRA Accession PH_SRA_ACCESSION + Database Identifiers GenBank accession xs:token UPPER The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 GenBank Accession + Database Identifiers GISAID accession xs:token UPPER The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) GISAID Accession ID GISAID_accession + Sample collection and processing + Sample collection and processing sample collected by xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name collected_by + Sample collection and processing sample collector contact email xs:token The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca + Sample collection and processing sample collector contact address xs:token The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address + Sample collection and processing sequence submitted by select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by + Sample collection and processing sequence submitter contact email xs:token The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca + Sample collection and processing sequence submitter contact address xs:token The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address + Sample collection and processing sample collection date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date + Sample collection and processing sample collection date precision select required Precision of date collected HC_TEXT2 + Sample collection and processing sample received date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 + Sample collection and processing geo_loc_name (country) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name + Sample collection and processing geo_loc_name (state/province/territory) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name + Sample collection and processing geo_loc_name (city) xs:token The city where the sample was collected. Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Medicine Hat Patient City + Sample collection and processing organism select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Taxonomic name of the organism. Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template. Severe acute respiratory syndrome coronavirus 2 Pathogen HC_CURRENT_ID organism + Sample collection and processing isolate xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Identifier of the specific isolate. Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/xxxxx/2020”. hCov-19/CANADA/prov_rona_99/2020 Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name + Sample collection and processing purpose of sampling select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling + Sample collection and processing purpose of sampling details xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. Details on the Reason for Sampling description + Sample collection and processing NML submitted specimen type select required The type of specimen submitted to the NML for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. swab Specimen Type PH_SPECIMEN_TYPE + Sample collection and processing NML related specimen relationship type select The relationship of the related specimen to the previous submission. Provide the specimen type of the original sample submitted from the pick list provided, so that additional specimen testing can be tracked in the system. Follow-up Related Specimen ID|Related Specimen Relationship Type + Sample collection and processing anatomical material select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Blood Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material + Sample collection and processing anatomical part select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Nasopharynx (NP) Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part + Sample collection and processing body product select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Feces Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product + Sample collection and processing environmental material select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Face mask Specimen source Environmental Material PH_ENVIRONMENTAL_MATERIAL isolation_source;environmental_material + Sample collection and processing environmental site select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Production Facility Specimen source Environmental Site PH_ENVIRONMENTAL_SITE isolation_source;environmental_site + Sample collection and processing collection device select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device + Sample collection and processing collection method select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Bronchoalveolar lavage (BAL) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method + Sample collection and processing collection protocol xs:token The name and version of a particular protocol used for sampling. Free text. BCRonaSamplingProtocol v. 1.2 + Sample collection and processing specimen processing multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Virus passage Passage details/history + Sample collection and processing lab host select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. Type of cell line used for propagation. Provide the name of the cell line using the picklist in the template. If not passaged, put "not applicable". Vero E6 cell line Passage details/history lab_host + Sample collection and processing passage number xs:nonNegativeInteger Not Applicable recommended Number of passages. Provide number of known passages. If not passaged, put "not applicable" 3 Passage details/history passage_history + Sample collection and processing passage method xs:token Not Applicable recommended Description of how organism was passaged. Free text. Provide a very short description (<10 words). If not passaged, put "not applicable". Passage details/history passage_method + Sample collection and processing biomaterial extracted select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The biomaterial extracted from samples for the purpose of sequencing. Provide the biomaterial extracted from the picklist in the template. RNA (total) + Host Information + Host Information host (common name) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put "not applicable. Human Animal Type PH_ANIMAL_TYPE + Host Information host (scientific name) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host + Host Information host health state select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Health status of the host at the time of sample collection. If known, select a descriptor from the pick list provided in the template. Symptomatic Patient status Host Health State PH_HOST_HEALTH host_health_state + Host Information host health status details select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized (ICU) Host Health State Details PH_HOST_HEALTH_DETAILS + Host Information host health outcome select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Disease outcome in the host. If known, select a descriptor from the pick list provided in the template. Recovered host_disease_outcome + Host Information host disease select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the disease experienced by the host. Select "COVID-19" from the pick list provided in the template. COVID-19 Host Disease PH_HOST_DISEASE host_disease + Host Information host age xs:decimal Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required 0 130 Age of host at the time of sampling. Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". 79 Patient age Patient Age PH_AGE host_age + Host Information host age unit select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The unit used to measure the host age, in either months or years. Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. Age Units PH_AGE_UNIT + Host Information host age bin select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. 60 - 69 Host Age Category PH_AGE_GROUP + Host Information host gender select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The gender of the host at the time of sample collection. Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". male Gender Patient Sex VD_SEX host_sex + Host Information host residence geo_loc name (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The country of residence of the host. Select the country name from pick list provided in the template. United Kingdom + Host Information host residence geo_loc name (state/province/territory) select geo_loc_name (state/province/territory) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The state/province/territory of residence of the host. Select the province/territory name from pick list provided in the template. Quebec + Host Information host subject ID xs:token A unique identifier by which each host can be referred to e.g. #131 Provide the host identifier. Should be a unique, user-defined identifier. BCxy123 host_subject_id + Host Information symptom onset date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date on which the symptoms began or were first noted. ISO 8601 standard "YYYY-MM-DD". 2020-03-16 Symptoms Onset Date HC_ONSET_DATE + Host Information signs and symptoms multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician. Select all of the symptoms experienced by the host from the pick list. Chills (sudden cold sensation); Cough; Fever Symptoms HC_SYMPTOMS + Host Information pre-existing conditions and risk factors multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Asthma; Pregnancy; Smoking + Host Information complications multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Acute Respiratory Failure; Coma; Septicemia + Host vaccination information + Host vaccination information host vaccination status select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated + Host vaccination information vaccine name xs:token The name of the vaccine. Free text. Provide the name of the vaccine. Pfizer-BioNTech COVID-19 vaccine + Host vaccination information number of vaccine doses received xs:nonNegativeInteger The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 2 + Host vaccination information first dose vaccination date xs:date The date the host was first vaccinated. Provide the vaccination date in ISO 8601 standard format "YYYY-MM-DD". 2021-02-26 + Host vaccination information last dose vaccination date xs:date The date the host received their last dose of vaccine. Provide the date that the last dose of the vaccine was administered. Provide the last dose vaccination date in ISO 8601 standard format "YYYY-MM-DD". 2021-04-09 + Host exposure information + Host exposure information location of exposure geo_loc name (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The country where the host was likely exposed to the causative agent of the illness. Select the country name from pick list provided in the template. Canada + Host exposure information destination of most recent travel (city) xs:token The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information destination of most recent travel (state/province/territory) xs:token The name of the province that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information destination of most recent travel (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the country that was the destination of most recent travel. Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz United Kingdom Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information most recent travel departure date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date. 2020-03-16 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information most recent travel return date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date. 2020-04-26 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information travel history xs:token Travel history in last six months. Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Canada, Vancouver; USA, Seattle; Italy, Milan + Host exposure information exposure event select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Convention Additional location information Exposure Event PH_EXPOSURE + Host exposure information exposure contact level select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The exposure transmission contact type. Select direct or indirect exposure from the pick-list. Direct + Host exposure information host role multiple The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Patient + Host exposure information exposure setting multiple The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Healthcare Setting + Host exposure information exposure details xs:token Additional host exposure information. Free text description of the exposure. Host role - Other: Bus Driver + + + Host reinfection information + Host reinfection information prior SARS-CoV-2 infection select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether there was prior SARS-CoV-2 infection. Ik known, provide infromation about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. Yes + Host reinfection information prior SARS-CoV-2 infection isolate xs:token The identifier of the isolate found in the prior SARS-CoV-2 infection. Provide the isolate name of the most recent prior infection. Structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". SARS-CoV-2/human/USA/CA-CDPH-001/2020 + Host reinfection information prior SARS-CoV-2 infection date xs:date The date of diagnosis of the prior SARS-CoV-2 infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-23 + Host reinfection information prior SARS-CoV-2 antiviral treatment select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether there was prior SARS-CoV-2 treatment with an antiviral agent. If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. No prior antiviral treatment + Host reinfection information prior SARS-CoV-2 antiviral treatment agent xs:token The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put "No treatment". If multiple antiviral agents were administered, list them all separated by commas. Remdesivir + Host reinfection information prior SARS-CoV-2 antiviral treatment date xs:date The date treatment was first administered during the prior SARS-CoV-2 infection. Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-28 + + + Sequencing + Sequencing purpose of sequencing select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing + Sequencing purpose of sequencing details xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Screened for S gene target failure (S dropout) Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS + Sequencing sequencing date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 + Sequencing library ID xs:token recommended The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 + Sequencing amplicon size xs:token The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp + Sequencing library preparation kit xs:token The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT + Sequencing flow cell barcode xs:token The barcode of the flow cell used for sequencing. Provide the barcode of the flow cell used for sequencing the sample. FAB06069 + Sequencing sequencing instrument multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. MinIon Sequencing technology Sequencing Instrument ANALYSIS + Sequencing sequencing protocol name xs:token recommended The name and version number of the sequencing protocol used. Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann Sequencing Protocol Name + Sequencing sequencing protocol xs:token The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL + Sequencing sequencing kit number xs:token The manufacturer's kit number. Alphanumeric value. AB456XYZ789 + Sequencing amplicon pcr primer scheme xs:token The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv + + + Bioinformatics and QC metrics + Bioinformatics and QC metrics raw sequence data processing method xs:token recommended The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 + Bioinformatics and QC metrics dehosting method xs:token The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper + Bioinformatics and QC metrics consensus sequence name xs:token The name of the consensus sequence. Provide the name and version number of the consensus sequence. ncov123assembly3 + Bioinformatics and QC metrics consensus sequence filename xs:token The name of the consensus sequence file. Provide the name and version number of the consensus sequence FASTA file. ncov123assembly.fasta + Bioinformatics and QC metrics consensus sequence filepath xs:token The filepath of the consesnsus sequence file. Provide the filepath of the consensus sequence FASTA file. /User/Documents/RespLab/Data/ncov123assembly.fasta + Bioinformatics and QC metrics consensus sequence software name xs:token required The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. Ivar consensus sequence Consensus Sequence Method Name + Bioinformatics and QC metrics consensus sequence software version xs:decimal required The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 consensus sequence Consensus Sequence Method Version Name + Bioinformatics and QC metrics breadth of coverage value xs:token The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95% + Bioinformatics and QC metrics depth of coverage value xs:token The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Coverage + Bioinformatics and QC metrics depth of coverage threshold xs:token The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x + Bioinformatics and QC metrics r1 fastq filename xs:token recommended The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz + Bioinformatics and QC metrics r2 fastq filename xs:token recommended The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz + Bioinformatics and QC metrics r1 fastq filepath xs:token The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz + Bioinformatics and QC metrics r2 fastq filepath xs:token The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz + Bioinformatics and QC metrics fast5 filename xs:token The user-specified filename of the FAST5 file. Provide the FAST5 filename. rona123assembly.fast5 + Bioinformatics and QC metrics fast5 filepath xs:token The location of the FAST5 file within a user's file system. Provide the filepath for the FAST5 file. This information aids in data management. /User/Documents/RespLab/Data/rona123assembly.fast5 + Bioinformatics and QC metrics number of base pairs sequenced xs:nonNegativeInteger The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 + Bioinformatics and QC metrics consensus genome length xs:nonNegativeInteger Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). 38677 + Bioinformatics and QC metrics Ns per 100 kbp xs:decimal 0 The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence. Provide a numerical value (no need to include units). 330 + Bioinformatics and QC metrics reference genome accession xs:token A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 + Bioinformatics and QC metrics bioinformatics protocol xs:token The name and version number of the bioinformatics protocol used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can be provided in an SOP or protocol. Provide the name and version number of the protocol. https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members Bioinformatics Protocol + Lineage and Variant information + Lineage and Variant information lineage/clade name xs:token The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. B.1.1.7 + Lineage and Variant information lineage/clade analysis software name xs:token The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Pangolin + Lineage and Variant information lineage/clade analysis software version xs:token The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 2.1.10 + Lineage and Variant information variant designation select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The variant classification of the lineage/clade i.e. variant, variant of concern. If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. Variant of Concern + Lineage and Variant information variant evidence select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The evidence used to make the variant determination. Select whether the sample was screened using RT-qPCR or by sequencing from the pick list. RT-qPCR TaqPath assay: S gene target failure + Lineage and Variant information variant evidence details xs:token Details about the evidence used to make the variant determination. Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. + Pathogen diagnostic testing + Pathogen diagnostic testing gene name 1 select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI E (orf4) Gene Target 1 RESULT - CANCOGEN_SUBMITTED_RESLT_1 gene_name_1 + Pathogen diagnostic testing diagnostic pcr protocol 1 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. EGenePCRTest 2 + Pathogen diagnostic testing diagnostic pcr Ct value 1 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the diagnostic RT-PCR test. 21 Gene Target 1 CT Value RESULT - CANCOGEN_SUBMITTED_RESLT_1CT diagnostic_PCR_CT_value_1 + Pathogen diagnostic testing gene name 2 select gene name 1 Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI nsp12 (RdRp) Gene Target 2 RESULT - CANCOGEN_SUBMITTED_RESLT_2 gene_name_2 + Pathogen diagnostic testing diagnostic pcr protocol 2 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. RdRpGenePCRTest 3 + Pathogen diagnostic testing diagnostic pcr Ct value 2 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 36 Gene Target 2 CT Value RESULT - CANCOGEN_SUBMITTED_RESLT_2CT diagnostic_PCR_CT_value_2 + Pathogen diagnostic testing gene name 3 select gene name 1 Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI nsp12 (RdRp) Gene Target 3 + Pathogen diagnostic testing diagnostic pcr protocol 3 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. RdRpGenePCRTest 3 + Pathogen diagnostic testing diagnostic pcr Ct value 3 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 3 CT Value + Contributor acknowledgement + Contributor acknowledgement authors xs:token recommended Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_CANCOGEN_AUTHORS + Contributor acknowledgement DataHarmonizer provenance provenance DataHarmonizer provenance Additional Comments HC_COMMENTS + + + umbrella bioproject accession PRJNA623807 + + + + + + + + +GAZ_00002566 geo_loc_name (state/province/territory) Alberta CA-AB +GAZ_00002562 geo_loc_name (state/province/territory) British Columbia CA-BC +GAZ_00002571 geo_loc_name (state/province/territory) Manitoba CA-MB +GAZ_00002570 geo_loc_name (state/province/territory) New Brunswick CA-NB +GAZ_00002567 geo_loc_name (state/province/territory) Newfoundland and Labrador CA-NL +GAZ_00002575 geo_loc_name (state/province/territory) Northwest Territories CA-NT +GAZ_00002565 geo_loc_name (state/province/territory) Nova Scotia CA-NS +GAZ:00002574 geo_loc_name (state/province/territory) Nunavut CA-NU +GAZ_00002563 geo_loc_name (state/province/territory) Ontario CA-ON +GAZ_00002572 geo_loc_name (state/province/territory) Prince Edward Island CA-PE +GAZ_00002569 geo_loc_name (state/province/territory) Quebec CA-QC +GAZ_00002564 geo_loc_name (state/province/territory) Saskatchewan CA-SK +GAZ_00002576 geo_loc_name (state/province/territory) Yukon CA-YT + +UO:0000035 host age unit month +UO:0000036 host age unit year + +UO:0000035 sample collection date precision year +UO:0000036 sample collection date precision month +UO:0000033 sample collection date precision day + +OBI:0000895 biomaterial extracted RNA (total) +OBI:0000869 biomaterial extracted RNA (poly-A) +OBI:0002627 biomaterial extracted RNA (ribo-depleted) + biomaterial extracted mRNA (messenger RNA) +OBI:0002754 biomaterial extracted mRNA (cDNA) + + + signs and symptoms Abnormal lung auscultation +HP:0000223 signs and symptoms Abnormality of taste sensation SENSE_OF_TASTE + Abnormality of taste sensation Ageusia (complete loss of taste) AGEUSIA +HP:0031249 Abnormality of taste sensation Parageusia (distorted sense of taste) PARAGEUSIA +HP_0000224 Abnormality of taste sensation Hypogeusia (reduced sense of taste) HYPOGEUSIA +HP:0004408 signs and symptoms Abnormality of the sense of smell SENSE_OF_SMELL +HP_0000458 Abnormality of the sense of smell Anosmia (lost sense of smell) ANOSMIA +HP_0004409 Abnormality of the sense of smell Hyposmia (reduced sense of smell) HYPOSMIA + signs and symptoms Acute Respiratory Distress Syndrome ARDS +HP:0011446 signs and symptoms Altered mental status ALTERED_CONSCIOUS +HP:0011675 signs and symptoms Arrhythmia +HP:0100543 Altered mental status Cognitive impairment COGNITIVE +HP_0001259 Altered mental status Coma COMA +HP_0001289 Altered mental status Confusion CONFUSION +HP_0031258 Confusion Delirium (sudden severe confusion) DELIRIUM + Altered mental status Inability to arouse (inability to stay awake) INABILITY_AWAKE +HP_0000737 Altered mental status Irritability IRRITABILITY +HP_0002371 Altered mental status Loss of speech LOSS_OF_SPEECH +HP_0025406 signs and symptoms Asthenia (generalized weakness) ASTHENIA +HP:0031352 signs and symptoms Chest tightness or pressure CHEST_TIGHT +HP:0025145 Chest tightness or pressure Rigors (fever shakes) RIGORS +HP_0025143 signs and symptoms Chills (sudden cold sensation) Chills CHILLS + signs and symptoms Conjunctival injection +HP_0000509 signs and symptoms Conjunctivitis (pink eye) Conjunctivitis CONJUNCTIVITIS + signs and symptoms Coryza +HP_0012735 signs and symptoms Cough COUGH +HP:0031246 Cough Nonproductive cough (dry cough) NONPRODUCT_COUGH +HP:0031245 Cough Productive cough (wet cough) PRODUCTIVE_COUGH +HP:0000961 signs and symptoms Cyanosis (blueish skin discolouration) CYANOSIS +HP:0001063 Cyanosis (blueish skin discolouration) Acrocyanosis ACROCYANOS + Acrocyanosis Circumoral cyanosis (bluish around mouth) CIRCUMORAL_CYANOSIS + Acrocyanosis Cyanotic face (bluish face) CYANOTIC_FACE + Cyanosis (blueish skin discolouration) Central Cyanosis + Central Cyanosis Cyanotic lips (bluish lips) CYANOTIC_LIPS + Cyanosis (blueish skin discolouration) Peripheral Cyanosis +HP_0002094 signs and symptoms Dyspnea (breathing difficulty) DYSPNEA +HP_0002014 signs and symptoms Diarrhea (watery stool) Diarrhea, watery DIARRHEA + signs and symptoms Dry gangrene +HP_0002383 signs and symptoms Encephalitis (brain inflammation) Encephalitis ENCEPHALITIS + signs and symptoms Encephalopathy +HP_0012378 signs and symptoms Fatigue (tiredness) Fatigue FATIGUE +HP_0001945 signs and symptoms Fever FEVER + Fever Fever (>=38°C) Fever +HP:0000206 signs and symptoms Glossitis (inflammation of the tongue) GLOSSITIS + signs and symptoms Ground Glass Opacities (GGO) +HP_0002315 signs and symptoms Headache HEADACHE +HP_0002105 signs and symptoms Hemoptysis (coughing up blood) HEMOPTYSIS +HP:0012417 signs and symptoms Hypocapnia +HP_0002615 signs and symptoms Hypotension (low blood pressure) HYPOTENSION +HP_0012418 signs and symptoms Hypoxemia (low blood oxygen) HYPOXEMIA + Hypoxemia (low blood oxygen) Silent hypoxemia +HP:0011029 signs and symptoms Internal hemorrhage (internal bleeding) INTERNAL_HEMORRHAGE +NCIT:C121416 signs and symptoms Loss of Fine Movements LOSS_OF_FINE_MOVE +HP_0004396 signs and symptoms Low appetite LOW_APPETITE + signs and symptoms Malaise (general discomfort/unease) MALAISE + signs and symptoms Meningismus/nuchal rigidity +HP_0001324 signs and symptoms Muscle weakness MUSCLE_WEAK +HP_0001742 signs and symptoms Nasal obstruction (stuffy nose) NASAL_OBSTRUCT +HP_0002018 signs and symptoms Nausea NAUSEA + signs and symptoms Nose bleed + signs and symptoms Otitis + signs and symptoms Pain +HP:0002027 Pain Abdominal pain ABDOMINAL +HP_0002829 Pain Arthralgia (painful joints) ARTHRALGIA +HP_0100749 Pain Chest pain CHEST_PAIN + Chest pain Pleuritic chest pain +HP_0003326 Pain Myalgia (muscle pain) MYALGIA +HP_0025439 signs and symptoms Pharyngitis (sore throat) PHARYNGITIS + signs and symptoms Pharyngeal exudate + signs and symptoms Pleural effusion +HP:0002090 signs and symptoms Pneumonia + signs and symptoms Prostration + signs and symptoms Pseudo-chilblains + Pseudo-chilblains Pseudo-chilblains on fingers (covid fingers) PSEUDO-CHIBLAINS_F + Pseudo-chilblains Pseudo-chilblains on toes (covid toes) PSEUDO-CHIBLAINS_T +HP_0000988 signs and symptoms Rash RASH +HP_0031417 signs and symptoms Rhinorrhea (runny nose) RHINORRHEA +HP_0001250 signs and symptoms Seizure SEIZURE +HP:0020219 Seizure Motor seizure MOTOR_SEIZURE +HP:0025144 signs and symptoms Shivering (involuntary muscle twitching) SHIVERING +HP_0001350 signs and symptoms Slurred speech SLURRED_SPEECH + signs and symptoms Sneezing + signs and symptoms Sputum Production +HP:0001297 signs and symptoms Stroke STROKE + signs and symptoms Swollen Lymph Nodes +HP_0002789 signs and symptoms Tachypnea (accelerated respiratory rate) TACHYPNEA + signs and symptoms Vertigo (dizziness) +HP_0002013 signs and symptoms Vomiting (throwing up) VOMITING + + host vaccination status Fully Vaccinated + host vaccination status Partially Vaccinated + host vaccination status Not Vaccinated + + prior SARS-CoV-2 antiviral treatment Prior antivrial treatment + prior SARS-CoV-2 antiviral treatment No prior antivrial treatment + prior SARS-CoV-2 antiviral treatment Unknown + + NML submitted specimen type Swab PH_SPECIMEN_TYPE:SWAB + NML submitted specimen type RNA PH_SPECIMEN_TYPE:RNA + NML submitted specimen type mRNA (cDNA) PH_SPECIMEN_TYPE:MRNA_CDNA + NML submitted specimen type Nucleic acid PH_SPECIMEN_TYPE:NUCLEIC_ACID + NML submitted specimen type Not Applicable PH_SPECIMEN_TYPE:NA + + + NML related specimen relationship type Acute + NML related specimen relationship type Convalescent + NML related specimen relationship type Familial + NML related specimen relationship type Follow-up + NML related specimen relationship type Previously Submitted + + + pre-existing conditions and risk factors Age 60+ + pre-existing conditions and risk factors Anemia + pre-existing conditions and risk factors Anorexia + pre-existing conditions and risk factors Birthing labor + pre-existing conditions and risk factors Bone marrow failure + pre-existing conditions and risk factors Cancer + Cancer Breast cancer + Cancer Colorectal cancer + Cancer Hematologic malignancy + Cancer Lung cancer + Cancer Metastatic disease + pre-existing conditions and risk factors Cancer treatment + Cancer treatment Cancer surgery + Cancer treatment Chemotherapy + Chemotherapy Adjuvant chemotherapy + pre-existing conditions and risk factors Cardiac disorder +HP:0011675 Cardiac disorder Arrhythmia + Cardiac disorder Cardiac disease +HP:0001638 Cardiac disorder Cardiomyopathy + Cardiac disorder Cardiac injury + Cardiac disorder Hypertension (high blood pressure) +HP:0002615 Cardiac disorder Hypotension (low blood pressure) + pre-existing conditions and risk factors Cesarean section + pre-existing conditions and risk factors Chronic cough + pre-existing conditions and risk factors Chronic gastrointestinal disease + pre-existing conditions and risk factors Chronic lung disease + pre-existing conditions and risk factors Corticosteroids + pre-existing conditions and risk factors Diabetes mellitus (diabetes) + Diabetes mellitus (diabetes) Type I diabetes mellitus (T1D) + Diabetes mellitus (diabetes) Type II diabetes mellitus (T2D) + pre-existing conditions and risk factors Eczema + pre-existing conditions and risk factors Electrolyte disturbance + Electrolyte disturbance Hypocalcemia + Electrolyte disturbance Hypokalemia + Electrolyte disturbance Hypomagnesemia +HP:0002383 pre-existing conditions and risk factors Encephalitis (brain inflammation) + pre-existing conditions and risk factors Epilepsy + pre-existing conditions and risk factors Hemodialysis + pre-existing conditions and risk factors Hemoglobinopathy + pre-existing conditions and risk factors Human immunodeficiency virus (HIV) + Human immunodeficiency virus (HIV) Acquired immunodeficiency syndrome (AIDS) + Human immunodeficiency virus (HIV) HIV and antiretroviral therapy (ART) + pre-existing conditions and risk factors Immunocompromised + Immunocompromised Lupus + pre-existing conditions and risk factors Inflammatory bowel disease (IBD) + Inflammatory bowel disease (IBD) Colitis + Colitis Ulcerative colitis + Inflammatory bowel disease (IBD) Crohn's disease + pre-existing conditions and risk factors Renal disorder + Renal disorder Renal disease + Renal disorder Chronic renal disease + Renal disorder Renal failure + pre-existing conditions and risk factors Liver disease + Liver disease Chronic liver disease + Chronic liver disease Fatty liver disease (FLD) +HP:0003326 pre-existing conditions and risk factors Myalgia (muscle pain) + pre-existing conditions and risk factors Myalgic encephalomyelitis (ME) + pre-existing conditions and risk factors Neurological disorder + Neurological disorder Neuromuscular disorder + pre-existing conditions and risk factors Obesity + Obesity Severe obesity + pre-existing conditions and risk factors Respiratory disorder + Respiratory disorder Asthma + Respiratory disorder Chronic bronchitis + Respiratory disorder Chronic pulmonary disease + Chronic pulmonary disease Chronic obstructive pulmonary disease + Respiratory disorder Emphysema + Respiratory disorder Lung disease + Lung disease Chronic lung disease + Lung disease Pulmonary fibrosis +HP:0002090 Respiratory disorder Pneumonia + Respiratory disorder Respiratory failure + Respiratory failure Adult respiratory distress syndrome + Respiratory failure Newborn respiratory distress syndrome + Respiratory disorder Tuberculosis + pre-existing conditions and risk factors Postpartum (≤6 weeks) + pre-existing conditions and risk factors Pregnancy + pre-existing conditions and risk factors Rheumatic disease + pre-existing conditions and risk factors Sickle cell disease + pre-existing conditions and risk factors Substance use + Substance use Alcohol abuse + Substance use Drug abuse + Drug abuse Injection drug abuse + Substance use Smoking + Substance use Vaping +HP:0002789 pre-existing conditions and risk factors Tachypnea (accelerated respiratory rate) + pre-existing conditions and risk factors Transplant + Transplant Bone marrow transplant + Transplant Cardiac transplant + Transplant Hematopoietic stem cell transplant (HSCT) + Transplant Kidney transplant + Transplant Liver transplant + + variant designation Variant of Concern (VOC) + variant designation Variant of Interest (VOI) + + variant evidence RT-qPCR + variant evidence Sequencing + + complications Abnormal blood oxygen level + complications Acute respiratory failure +HP:0011675 complications Arrhythmia (complication) + Arrhythmia (complication) Tachycardia + Tachycardia Polymorphic ventricular tachycardia (VT) + Tachycardia Tachyarrhythmia + complications Noncardiogenic pulmonary edema + Noncardiogenic pulmonary edema Acute respiratory distress syndrome (ARDS) + Acute respiratory distress syndrome (ARDS) COVID-19 associated ARDS (CARDS) + Acute respiratory distress syndrome (ARDS) Neurogenic pulmonary edema (NPE) + complications Cardiac injury + complications Cardiac arrest + complications Cardiogenic shock + complications Blood clot + Blood clot Arterial clot + Blood clot Deep vein thrombosis (DVT) + Blood clot Pulmonary embolism (PE) +HP:0001638 complications Cardiomyopathy + complications Central nervous system invasion + complications Stroke (complication) + Stroke (complication) Central Nervous System Vasculitis + Stroke (complication) Ischemic stroke + Ischemic stroke Acute ischemic stroke + complications Coma + complications Convulsions + complications COVID-19 associated coagulopathy (CAC) + complications Cystic fibrosis + complications Cytokine release syndrome + complications Disseminated intravascular coagulation (DIC) + complications Encephalopathy + complications Fulminant myocarditis + complications Guillain-Barré syndrome + complications Internal hemorrhage (complication; internal bleeding) + Internal hemorrhage (complication; internal bleeding) Intracerebral haemorrhage + complications Kawasaki disease + Kawasaki disease Typical Kawasaki disease + Kawasaki disease Incomplete Kawasaki disease + complications Kidney injury + Kidney injury Acute kidney injury + complications Liver dysfunction + complications Liver injury + Liver injury Acute liver injury + complications Lung injury + Lung injury Acute lung injury + complications Meningitis + complications Migraine + complications Miscarriage + complications Multisystem inflammatory syndrome in children (MIS-C) + complications Muscle injury + complications Myalgic encephalomyelitis (ME) + complications Myocardial infarction (heart attack) + Myocardial infarction (heart attack) Acute myocardial infarction + Myocardial infarction (heart attack) Elevation myocardial infarction + Myocardial infarction (heart attack) ST-segment elevation myocardial infarction + complications Myocardial injury + complications Neonatal complications + complications Organ failure + Organ failure Heart failure + Organ failure Liver failure + complications Paralysis + complications Pneumothorax (collapsed lung) + Pneumothorax (collapsed lung) Spontaneous pneumothorax + Pneumothorax (collapsed lung) Spontaneous tension pneymothorax + complications Pneumonia (complication) + Pneumonia (complication) COVID-19 pneumonia + complications Pregancy complications + complications Rhabdomyolysis + complications Secondary infection + Secondary infection Secondary staph infection + Secondary infection Secondary strep infection +HP:0001250 complications Seizure (complication) +HP:0020219 Seizure (complication) Motor seizure + complications Sepsis + complications Septicemia + complications Shock + Shock Hyperinflammatory shock + Shock Refractory cardiogenic shock + Shock Refractory cardiogenic plus vasoplegic shock + Shock Septic shock + complications Vasculitis + complications Ventilation induced lung injury (VILI) + + + +UBERON_0000178 anatomical material Blood BLOOD +UBERON_0006314 anatomical material Fluid FLUID +UBERON_0001836 Fluid Saliva SALIVA +UBERON_0001359 Fluid Fluid (cerebrospinal (CSF)) FLUID_CSF +UBERON_0002409 Fluid Fluid (pericardial) FLUID_PERICARDIAL +UBERON_0001087 Fluid Fluid (pleural) FLUID_PLEURAL +UBERON_0036243 Fluid Fluid (vaginal) FLUID_VAGINAL +UBERON_0000173 Fluid Fluid (amniotic) FLUID_AMNIOTIC +UBERON_0000479 anatomical material Tissue TISSUE + + + +UBERON_0001245 anatomical part Anus ANUS + anatomical part Buccal mucosa BUCCAL_MUCOSA +UBERON_0002114 anatomical part Duodenum DUODENUM +UBERON_0000970 anatomical part Eye EYE + anatomical part Intestine INTESTINE +UBERON_0001052 anatomical part Rectum RECTUM +UBERON_0001003 anatomical part Skin SKIN +UBERON_0000945 anatomical part Stomach STOMACH +UBERON_0001557 anatomical part Upper respiratory tract UPPER +UBERON_2001427 Upper respiratory tract Anterior Nares ANTERIOR_NARES +UBERON_0001043 Upper respiratory tract Esophagus ESOPHAGUS +UBERON_0002453 Upper respiratory tract Ethmoid sinus ETHMOID_SINUS + Upper respiratory tract Nasal Cavity NASAL_CAVITY +UBERON_0005921 Nasal Cavity Middle Nasal Turbinate MIDDLE_NASAL +UBERON_0005922 Nasal Cavity Inferior Nasal Turbinate INFERIOR_NASAL +UBERON_0001728 Upper respiratory tract Nasopharynx (NP) NASOPHARYNX_NP +UBERON_0001729 Upper respiratory tract Oropharynx (OP) OROPHARYNX_OP +UBERON_0001558 anatomical part Lower respiratory tract LOWER +UBERON_0002185 Lower respiratory tract Bronchus BRONCHUS +UBERON_0002048 Lower respiratory tract Lung LUNG +UBERON_0002186 Lung Bronchiole BRONCHIOLE +UBERON_0002169 Lung Alveolar sac ALVEOLAR_SAC +UBERON_0009778 Lower respiratory tract Pleural sac PLEURAL_SAC +UBERON_0002402 Pleural sac Pleural cavity PLEURAL_CAVITY +UBERON_0003126 Lower respiratory tract Trachea TRACHEA + + + + +UBERON_0001988 body product Feces FECES +UBERON_0001088 body product Urine URINE +UBERON_0001089 body product Sweat SWEAT +UBERON_0000912 body product Mucus MUCUS +UBERON_0007311 Mucus Sputum SPUTUM +UBERON_0001827 body product Tear TEAR +UBERON_0006530 body product Fluid (seminal) FLUID_SEMINAL +UBERON_0001913 body product Breast Milk BREAST_MILK + + prior SARS-CoV-2 infection Yes + prior SARS-CoV-2 infection No + prior SARS-CoV-2 infection Unknown + + + environmental material Air vent AIR_VENT +ENVO_00003896 environmental material Banknote BANKNOTE + environmental material Bed rail BED_RAIL +ENVO_01000486 environmental material Building floor BUILDING_FLOOR +ENVO_02000058 environmental material Cloth CLOTH + environmental material Control panel CONTROL_PANEL +NCIT_C48950 environmental material Door DOOR + environmental material Door handle DOOR_HANDLE + environmental material Face mask FACE_MASK + environmental material Face shield FACE_SHIELD +FOODON:00002403 environmental material Food FOOD +FOODON:03490100 environmental material Food packaging FOOD_PACKAGING +ENVO:01000481 environmental material Glass GLASS + environmental material Handrail HANDRAIL + environmental material Hospital gown HOSPITAL_GOWN + environmental material Light switch LIGHT_SWITCH + environmental material Locker LOCKER + environmental material N95 mask N95_MASK + environmental material Nurse call button NURSE_CALL_BUTTON + environmental material Paper PAPER +ENVO:01000060 environmental material Particulate matter PARTICULATE_MATTER +ENVO:01000404 environmental material Plastic PLASTIC + environmental material PPE gown PPE_GOWN +ENVO_00002018 environmental material Sewage SEWAGE +ENVO_01000990 environmental material Sink SINK +ENVO_00001998 environmental material Soil SOIL + environmental material Stainless steel STAINLESS_STEEL + environmental material Tissue paper TISSUE_PAPER + environmental material Toilet bowl TOILET_BOWL +ENVO_00002006 environmental material Water WATER + environmental material Wastewater WASTEWATER + environmental material Window WINDOW +ENVO:00002040 environmental material Wood WOOD + + environmental site Acute care facility ACUTE_CARE_FACILITY +ENVO:00003040 environmental site Animal house ANIMAL_HOUSE +ENVO:01000422 environmental site Bathroom BATHROOM + environmental site Clinical assessment centre CLINICAL_ASSESSMENT_ + environmental site Conference venue CONFERENCE_VENUE +ENVO REQUEST environmental site Corridor CORRIDOR +ENVO_01000927 environmental site Daycare DAYCARE +NCIT_C53513 environmental site Emergency room (ER) EMERGENCY_ROOM_ER + environmental site Family practice clinic FAMILY_PRACTICE_CLIN + environmental site Group home GROUP_HOME + environmental site Homeless shelter HOMELESS_SHELTER +OBI_0000844 environmental site Hospital HOSPITAL +NCIT_C53511 environmental site Intensive Care Unit (ICU) INTENSIVE_CARE_UNIT_ +GENEPIO_0001035 environmental site Long Term Care Facility LONG_TERM_CARE_FACIL + environmental site Patient room PATIENT_ROOM +ENVO_01001481 environmental site Prison PRISON +ENVO_01000536 environmental site Production Facility PRODUCTION_FACILITY +NCIT_C17118 environmental site School SCHOOL + environmental site Sewage Plant SEWAGE_PLANT + environmental site Subway train SUBWAY_TRAIN + environmental site Wet market WET_MARKET + +NCIT:C52009 collection method Amniocentesis AMNIOCENTESIS +NCIT:C15631 collection method Aspiration ASPIRATION + Aspiration Suprapubic Aspiration SUPRAPUBIC_ASPIRATIO + Aspiration Tracheal aspiration TRACHEAL_ASPIRATION + Aspiration Vacuum Aspiration VACUUM_ASPIRATION +OBI:0002650 collection method Biopsy BIOPSY +OBI:0002651 Biopsy Needle Biopsy NEEDLE_BIOPSY + collection method Filtration FILTRATION + Filtration Air filtration AIR_FILTRATION +OBI:0600044 collection method Lavage LAVAGE +BTO:0000155 Lavage Bronchoalveolar lavage (BAL) BAL + Lavage Gastric Lavage GASTRIC_LAVAGE +NCIT:C15327 collection method Lumbar Puncture LUMBAR_PUNCTURE +MMO:0000344 collection method Necropsy NECROPSY +NCIT:c28221 collection method Phlebotomy PHLEBOTOMY +GENEPIO:0002116 collection method Rinsing RINSING + Rinsing Saline gargle (mouth rinse and gargle) + collection method Scraping SCRAPING +GENEPIO:0002117 collection method Swabbing SWABBING + Swabbing Finger Prick FINGER_PRICK + collection method Wash WASH + collection method Washout Tear Collection WASHOUT + + + collection device Air filter AIR_FILTER +NCIT:C113122 collection device Blood Collection Tube BLOOD_TUBE +NCIT:C17611 collection device Bronchoscope BRONCHOSCOPE + collection device Collection Container CONTAINER + collection device Collection Cup CUP + collection device Fibrobronchoscope Brush BRUSH + collection device Filter FILTER + collection device Fine Needle FINE_NEEDLE + collection device Microcapillary tube MICROCAPILLARY_TUBE +OBI:0001128 collection device Micropipette MICROPIPETTE +OBI:0000436 collection device Needle NEEDLE +NCIT:C113675 collection device Serum Collection Tube SERUM_TUBE + collection device Sputum Collection Tube SPUTUM_TUBE + collection device Suction Catheter SUCTION_CATHETER +NCIT:c17627 collection device Swab SWAB + collection device Urine Collection Tube URINE_TUBE + collection device Virus Transport Medium TRANSPORT_MEDIUM + + +NCBITaxon_9606 host (scientific name) Homo sapiens +NCBITaxon_9913 host (scientific name) Bos taurus +NCBITaxon_9615 host (scientific name) Canis lupus familiaris +NCBITaxon_9397 host (scientific name) Chiroptera +NCBITaxon_8930 host (scientific name) Columbidae +NCBITaxon_9685 host (scientific name) Felis catus +NCBITaxon_9031 host (scientific name) Gallus gallus +NCBITaxon_9973 host (scientific name) Manis +NCBITaxon_9974 host (scientific name) Manis javanica +NCBITaxon_452646 host (scientific name) Neovison vison +NCBITaxon_9689 host (scientific name) Panthera leo +NCBITaxon_9694 host (scientific name) Panthera tigris +NCBITaxon_58055 host (scientific name) Rhinolophidae +NCBITaxon_59477 host (scientific name) Rhinolophus affinis +NCBITaxon_9825 host (scientific name) Sus scrofa domesticus +NCBITaxon_9673 host (scientific name) Viverridae + + +NCBITaxon_9605 host (common name) Human HUMAN +NCBITaxon_9397 host (common name) Bat BAT +NCBITaxon_9685 host (common name) Cat +NCBITaxon_9031 host (common name) Chicken +NCBITaxon_9673 host (common name) Civets CIVETS +NCBITaxon_9913 host (common name) Cow bovine +NCBITaxon_9615 host (common name) Dog +NCBITaxon_9689 host (common name) Lion LION + host (common name) Mink +NCBITaxon_9973 host (common name) Pangolin PANGOLIN +NCBITaxon_9823 host (common name) Pig porcine +NCBITaxon_8930 host (common name) Pigeon +NCBITaxon_9694 host (common name) Tiger + + + host health state Asymptomatic ASYMPTOMATIC + host health state Deceased DECEASED + host health state Healthy HEALTHY + host health state Recovered RECOVERED + host health state Symptomatic SYMPTOMATIC + + + host health status details Hospitalized HOSPITALIZED + Hospitalized Hospitalized (Non-ICU) NON_ICU + Hospitalized Hospitalized (ICU) ICU + host health status details Mechanical Ventilation VENTILATION + host health status details Medically Isolated ISOLATED + Medically Isolated Medically Isolated (Negative Pressure) ISOLATED_NEGATIVE_PR + host health status details Self-quarantining SELF_QUARANTINING + + host health outcome Deceased + host health outcome Deteriorating + host health outcome Recovered + host health outcome Stable + + organism Severe acute respiratory syndrome coronavirus 2 + organism RaTG13 + organism RmYN02 + + + purpose of sampling Cluster/Outbreak investigation + purpose of sampling Diagnostic testing +NCIT_c15429 purpose of sampling Research + purpose of sampling Surveillance + + + purpose of sequencing Baseline surveillance (random sampling) + purpose of sequencing Targeted surveillance (non-random sampling) + Targeted surveillance (non-random sampling) Priority surveillance project + Priority surveillance project Screening for Variants of Concern (VoC) + Priority surveillance project Longitudinal surveillance (repeat sampling of individuals) + Priority surveillance project Re-infection surveillance + Priority surveillance project Vaccine escape surveillance + Priority surveillance project Travel-associated surveillance + Travel-associated surveillance Domestic travel surveillance + Travel-associated surveillance International travel surveillance + purpose of sequencing Cluster/Outbreak investigation + Cluster/Outbreak investigation Multi-jurisdictional outbreak investigation + Cluster/Outbreak investigation Intra-jurisdictional outbreak investigation + purpose of sequencing Research + Research Viral passage experiment + Research Protocol testing experiment + + + specimen processing Virus passage + specimen processing RNA re-extraction (post RT-PCR) + specimen processing Specimens pooled + + lab host 293/ACE2 cell line +BTO_0000195 lab host Caco2 cell line +BTO_0002750 lab host Calu3 cell line + lab host EFK3B cell line +BTO_0002181 lab host HEK293T cell line + lab host HRCE cell line +BTO_0001950 lab host Huh7 cell line +CLO_0007330 lab host LLCMk2 cell line +BTO_0000836 lab host MDBK cell line + lab host Mv1Lu cell line +BTO_0002924 lab host NHBE cell line +BTO_0001865 lab host PK-15 cell line +BTO_0002909 lab host RK-13 cell line +BTO_0002035 lab host U251 cell line +BTO_0001444 lab host Vero cell line +BTO:0004755 lab host Vero E6 cell line + lab host VeroE6/TMPRSS2 cell line + + host disease COVID-19 + + host age bin 0 - 9 + host age bin 10 - 19 + host age bin 20 - 29 + host age bin 30 - 39 + host age bin 40 - 49 + host age bin 50 - 59 + host age bin 60 - 69 + host age bin 70 - 79 + host age bin 80 - 89 + host age bin 90 - 99 + host age bin 100+ + +OMRSE:00000009? host gender Female MALE +OMRSE:00000008? host gender Male FEMALE + host gender Non-binary gender NON_BINARY_GENDER + host gender Transgender (Male to Female) TRANSGENDER + host gender Transgender (Female to Male) TRANSGENDER + host gender Undeclared REFUSED + host gender Unknown UNKNOWN + + exposure event Mass Gathering + Mass Gathering Convention CONVENTION + Mass Gathering Convocation + Mass Gathering Agricultural Event + exposure event Religious Gathering RELIGIOUS + Religious Gathering Mass + exposure event Social Gathering SOCIAL + Social Gathering Baby Shower + Social Gathering Community Event + Social Gathering Family Gathering + Family Gathering Family Reunion + Social Gathering Funeral + Social Gathering Party + Social Gathering Potluck + Social Gathering Wedding + exposure event Other exposure event + + exposure contact level Contact with infected individual + Contact with infected individual Direct contact (direct human-to-human contact) + Contact with infected individual Indirect contact + Indirect contact Close contact (face-to-face, no direct contact) + Indirect contact Casual contact + + + host role Attendee + Attendee Student + host role Patient + Patient Inpatient + Patient Outpatient + host role Passenger + host role Resident + host role Visitor + host role Volunteer + host role Work + Work Administrator + Work First Responder + First Responder Firefighter + First Responder Paramedic + First Responder Police Officer + Work Healthcare Worker + Work Nurse + Work Personal Care Aid + Work Pharmacist + Work Physician + Work Housekeeper + Work Kitchen Worker + Work Laboratory Worker + Work Rotational Worker + Work Seasonal Worker + Work Veterinarian + host role Social role + Social role Acquaintance of case + Social role Relative of case + Relative of case Child of case + Relative of case Parent of case + Relative of case Father of case + Relative of case Mother of case + Social role Spouse of case + host role Other Host Role + + exposure setting Human Exposure + Human Exposure Known COVID-19 Case + Human Exposure Patient Contact + Human Exposure Probable COVID-19 Case + Human Exposure Person with Acute Respiratory Illness + Human Exposure Person with Fever and/or Cough + Human Exposure Person who Recently Travelled + exposure setting Occupational or Residency Exposure + Occupational or Residency Exposure Abbatoir + Occupational or Residency Exposure Animal Rescue + Occupational or Residency Exposure Childcare + Childcare Daycare + Occupational or Residency Exposure Funeral Home + Occupational or Residency Exposure Place of Worship + Place of Worship Church + Place of Worship Mosque + Place of Worship Temple + Occupational or Residency Exposure Nursery + Occupational or Residency Exposure Household + Occupational or Residency Exposure Community Service Centre + Occupational or Residency Exposure Correctional Facility + Occupational or Residency Exposure Dormitory + Occupational or Residency Exposure Farm + Occupational or Residency Exposure First Nations Reserve + Occupational or Residency Exposure Group Home + Occupational or Residency Exposure Healthcare Setting + Healthcare Setting Ambulance + Healthcare Setting Acute Care Facility + Healthcare Setting Clinic + Healthcare Setting Community Health Centre + Healthcare Setting Hospital + Hospital Emergency Department + Hospital ICU + Hospital Ward + Healthcare Setting Laboratory + Healthcare Setting Long-Term Care Facility + Healthcare Setting Pharmacy + Healthcare Setting Physician's Office + Occupational or Residency Exposure Insecure Housing (Homeless) + Occupational or Residency Exposure Office + Occupational or Residency Exposure Outdoors + Outdoors Camp/camping + Outdoors Hiking + Outdoors Hunting + Occupational or Residency Exposure Petting zoo + Occupational or Residency Exposure Restaurant + Occupational or Residency Exposure Retail Store + Occupational or Residency Exposure School + Occupational or Residency Exposure Temporary Residence + Temporary Residence Homeless Shelter + Temporary Residence Hotel + Occupational or Residency Exposure Veterinary Care Clinic + exposure setting Travel Exposure + Travel Exposure Travelled + Travelled Travelled on a Cruise Ship + Travelled Travelled on a Plane + Travelled Travelled on Ground Transport + Travelled Travelled outside Province/Territory + Travelled Travelled outside Canada + exposure setting Other Exposure Setting + + + +OBI_0000759 sequencing instrument Illumina +OBI_0002128 Illumina Illumina Genome Analyzer +OBI_0000703 Illumina Genome Analyzer Illumina Genome Analyzer II +OBI_0002000 Illumina Genome Analyzer Illumina Genome Analyzer IIx + Illumina Illumina HiScanSQ + Illumina Illumina HiSeq +OBI_0002129 Illumina Illumina HiSeq X + Illumina HiSeq X Illumina HiSeq X Five +OBI_0002129 Illumina HiSeq X Illumina HiSeq X Ten +OBI_0002022 Illumina Illumina HiSeq 1000 + Illumina Illumina HiSeq 1500 +OBI_0002001 Illumina Illumina HiSeq 2000 +OBI_0002002 Illumina Illumina HiSeq 2500 +OBI_0002048 Illumina Illumina HiSeq 3000 +OBI_0002049 Illumina Illumina HiSeq 4000 + Illumina Illumina iSeq +EFO:0008635 Illumina iSeq Illumina iSeq 100 + Illumina Illumina NovaSeq +OBI_0002630 Illumina NovaSeq Illumina NovaSeq 6000 +http://www.ebi.ac.uk/efo/EFO_0008636 Illumina Illumina MiniSeq +OBI_0002003 Illumina Illumina MiSeq + Illumina Illumina NextSeq +OBI_0002021 Illumina Illumina NextSeq 500 + Illumina Illumina NextSeq 550 +OBI_0001856 sequencing instrument Pacific Biosciences + Pacific Biosciences PacBio RS +OBI_0002012 Pacific Biosciences PacBio RS II +OBI_0002632 Pacific Biosciences PacBio Sequel +OBI_0002633 Pacific Biosciences PacBio Sequel II + sequencing instrument Ion Torrent +GENEPIO_0001935 Ion Torrent Ion Torrent PGM + Ion Torrent Ion Torrent Proton + Ion Torrent Ion Torrent S5 XL + Ion Torrent Ion Torrent S5 + sequencing instrument Oxford Nanopore + Oxford Nanopore GridION + Oxford Nanopore MinION + Oxford Nanopore PromethION + sequencing instrument BGI Genomics + BGI Genomics BGISEQ-500 + sequencing instrument MGI + MGI DNBSEQ-T7 + MGI DNBSEQ-G400 + MGI DNBSEQ-G400 FAST + MGI DNBSEQ-G50 + + +PR:P0DTC4 gene name 1 E gene (orf4) E gene E gene +PR:P0DTC5 gene name 1 M gene (orf5) +PR:P0DTC9 gene name 1 N gene (orf9) +PR:P0DTC2 gene name 1 Spike gene (orf2) +PR:000050281 gene name 1 orf1ab (rep) +PR:P0DTC1-1 orf1ab (rep) orf1a (pp1a) +PR:000050280 orf1a (pp1a) nsp11 +PR:000050270 orf1ab (rep) nsp1 +PR:000050271 orf1ab (rep) nsp2 +PR:000050272 orf1ab (rep) nsp3 +PR:000050273 orf1ab (rep) nsp4 +PR:000050274 orf1ab (rep) nsp5 +PR:000050275 orf1ab (rep) nsp6 +PR:000050276 orf1ab (rep) nsp7 +PR:000050277 orf1ab (rep) nsp8 +PR:000050278 orf1ab (rep) nsp9 +PR:000050279 orf1ab (rep) nsp10 +PR:000050284 orf1ab (rep) RdRp gene (nsp12) +PR:000050285 orf1ab (rep) hel gene (nsp13) +PR:000050286 orf1ab (rep) exoN gene (nsp14) +PR:000050287 orf1ab (rep) nsp15 +PR:000050288 orf1ab (rep) nsp16 +PR:P0DTC3 gene name 1 orf3a + gene name 1 orf3b +PR:P0DTC6 gene name 1 orf6 (ns6) +PR:P0DTC7 gene name 1 orf7a +PR:P0DTD8 gene name 1 orf7b (ns7b) +PR:P0DTC8 gene name 1 orf8 (ns8) +PR:P0DTD2 gene name 1 orf9b + gene name 1 orf9c +PR:A0A663DJA2 gene name 1 orf10 + gene name 1 orf14 + gene name 1 SARS-COV-2 5' UTR + + + sequence submitted by National Microbiology Laboratory (NML) NML + sequence submitted by BCCDC Public Health Laboratory BCCDC + sequence submitted by Alberta Precision Labs (APL) + Alberta Precision Labs (APL) Alberta ProvLab North (APLN) APL-E + Alberta Precision Labs (APL) Alberta ProvLab South (APLS) APL-C + sequence submitted by Public Health Ontario (PHO) PHO + sequence submitted by Laboratoire de santé publique du Québec (LSPQ) LSPQ + sequence submitted by Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) RRPL + sequence submitted by Manitoba Cadham Provincial Laboratory CADHAM + sequence submitted by Nova Scotia Health Authority NS_QE_II + sequence submitted by New Brunswick - Vitalité Health Network GEORGES_L_DUMONT + sequence submitted by Newfoundland and Labrador - Eastern Health EASTERN_HEALTH + sequence submitted by Prince Edward Island - Health PEI PEI + sequence submitted by Ontario Institute for Cancer Research (OICR) OICR + sequence submitted by McMaster University MCMASTER + sequence submitted by McGill University MCGILL + sequence submitted by The Centre for Applied Genomics (TCAG) TCAG + sequence submitted by Sunnybrook Health Sciences Centre SUNNYBROOK + sequence submitted by Thunder Bay Regional Health Sciences Centre THUNDER_BAY + sequence submitted by Canadore College CANADORE + sequence submitted by Queen’s University / Kingston Health Sciences Centre QUEENS_UNIV + + + + +GAZ_00006882 geo_loc_name (country) Afghanistan +GAZ_00002953 geo_loc_name (country) Albania +GAZ_00000563 geo_loc_name (country) Algeria +GAZ_00003957 geo_loc_name (country) American Samoa +GAZ_00002948 geo_loc_name (country) Andorra +GAZ_00001095 geo_loc_name (country) Angola +GAZ_00009159 geo_loc_name (country) Anguilla +GAZ_00000462 geo_loc_name (country) Antarctica +GAZ_00006883 geo_loc_name (country) Antigua and Barbuda +GAZ_00002928 geo_loc_name (country) Argentina ARGENTINA +GAZ_00004094 geo_loc_name (country) Armenia +GAZ_00004025 geo_loc_name (country) Aruba +GAZ_00005901 geo_loc_name (country) Ashmore and Cartier Islands +GAZ_00000463 geo_loc_name (country) Australia AUSTRALIA +GAZ_00002942 geo_loc_name (country) Austria +GAZ_00004941 geo_loc_name (country) Azerbaijan +GAZ_00002733 geo_loc_name (country) Bahamas +GAZ_00005281 geo_loc_name (country) Bahrain +GAZ_00007117 geo_loc_name (country) Baker Island +GAZ_00003750 geo_loc_name (country) Bangladesh +GAZ_00001251 geo_loc_name (country) Barbados +GAZ_00005810 geo_loc_name (country) Bassas da India +GAZ_00006886 geo_loc_name (country) Belarus +GAZ_00002938 geo_loc_name (country) Belgium BELGIUM +GAZ_00002934 geo_loc_name (country) Belize +GAZ_00000904 geo_loc_name (country) Benin +GAZ_00001264 geo_loc_name (country) Bermuda +GAZ_00003920 geo_loc_name (country) Bhutan +GAZ_00002511 geo_loc_name (country) Bolivia +GAZ_00025355 geo_loc_name (country) Borneo +GAZ_00006887 geo_loc_name (country) Bosnia and Herzegovina +GAZ_00001097 geo_loc_name (country) Botswana +GAZ_00001453 geo_loc_name (country) Bouvet Island +GAZ_00002828 geo_loc_name (country) Brazil BRAZIL +GAZ_00003961 geo_loc_name (country) British Virgin Islands +GAZ_00003901 geo_loc_name (country) Brunei +GAZ_00002950 geo_loc_name (country) Bulgaria +GAZ_00000905 geo_loc_name (country) Burkina Faso +GAZ_00001090 geo_loc_name (country) Burundi +GAZ_00006888 geo_loc_name (country) Cambodia +GAZ_00001093 geo_loc_name (country) Cameroon +GAZ_00002560 geo_loc_name (country) Canada CA +GAZ_00001227 geo_loc_name (country) Cape Verde +GAZ_00003986 geo_loc_name (country) Cayman Islands +GAZ_00001089 geo_loc_name (country) Central African Republic +GAZ_00000586 geo_loc_name (country) Chad +GAZ_00002825 geo_loc_name (country) Chile CHILE +GAZ_00002845 geo_loc_name (country) China CHINA +GAZ_00005915 geo_loc_name (country) Christmas Island +GAZ_00005838 geo_loc_name (country) Clipperton Island +GAZ_00009721 geo_loc_name (country) Cocos Islands +GAZ_00002929 geo_loc_name (country) Colombia COLUMBIA +GAZ_00005820 geo_loc_name (country) Comoros +GAZ_00053798 geo_loc_name (country) Cook Islands +GAZ_00005917 geo_loc_name (country) Coral Sea Islands +GAZ_00002901 geo_loc_name (country) Costa Rica COSTA_RICA +GAZ_00000906 geo_loc_name (country) Cote d'Ivoire +GAZ_00002719 geo_loc_name (country) Croatia +GAZ_00003762 geo_loc_name (country) Cuba +GAZ_00004021 geo_loc_name (country) Curacao +GAZ_00004006 geo_loc_name (country) Cyprus +GAZ_00002954 geo_loc_name (country) Czech Republic +GAZ_00001086 geo_loc_name (country) Democratic Republic of the Congo +GAZ_00005852 geo_loc_name (country) Denmark DENMARK +GAZ_00000582 geo_loc_name (country) Djibouti +GAZ_00006890 geo_loc_name (country) Dominica +GAZ_00003952 geo_loc_name (country) Dominican Republic +GAZ_00002912 geo_loc_name (country) Ecuador ECUADOR +GAZ_00003934 geo_loc_name (country) Egypt +GAZ_00002935 geo_loc_name (country) El Salvador +GAZ_00001091 geo_loc_name (country) Equatorial Guinea +GAZ_00000581 geo_loc_name (country) Eritrea +GAZ_00002959 geo_loc_name (country) Estonia +GAZ_00001099 geo_loc_name (country) Eswatini +GAZ_00000567 geo_loc_name (country) Ethiopia +GAZ_00005811 geo_loc_name (country) Europa Island +GAZ_00001412 geo_loc_name (country) Falkland Islands (Islas Malvinas) +GAZ_00059206 geo_loc_name (country) Faroe Islands +GAZ_00006891 geo_loc_name (country) Fiji +GAZ_00002937 geo_loc_name (country) Finland +GAZ_00003940 geo_loc_name (country) France FRANCE +GAZ_00002516 geo_loc_name (country) French Guiana +GAZ_00002918 geo_loc_name (country) French Polynesia +GAZ_00003753 geo_loc_name (country) French Southern and Antarctic Lands +GAZ_00001092 geo_loc_name (country) Gabon +GAZ_00000907 geo_loc_name (country) Gambia +GAZ_00009571 geo_loc_name (country) Gaza Strip +GAZ_00004942 geo_loc_name (country) Georgia +GAZ_00002646 geo_loc_name (country) Germany GERMANY +GAZ_00000908 geo_loc_name (country) Ghana +GAZ_00003987 geo_loc_name (country) Gibraltar +GAZ_00005808 geo_loc_name (country) Glorioso Islands +GAZ_00002945 geo_loc_name (country) Greece +GAZ_00001507 geo_loc_name (country) Greenland +GAZ_02000573 geo_loc_name (country) Grenada +GAZ_00067142 geo_loc_name (country) Guadeloupe +GAZ_00003706 geo_loc_name (country) Guam +GAZ_00002936 geo_loc_name (country) Guatemala +GAZ_00001550 geo_loc_name (country) Guernsey +GAZ_00000909 geo_loc_name (country) Guinea +GAZ_00000910 geo_loc_name (country) Guinea-Bissau +GAZ_00002522 geo_loc_name (country) Guyana GUYANA +GAZ_00003953 geo_loc_name (country) Haiti +GAZ_00009718 geo_loc_name (country) Heard Island and McDonald Islands +GAZ_00002894 geo_loc_name (country) Honduras +GAZ_00003203 geo_loc_name (country) Hong Kong +GAZ_00007120 geo_loc_name (country) Howland Island +GAZ_00002952 geo_loc_name (country) Hungary +GAZ_00000843 geo_loc_name (country) Iceland +GAZ_00002839 geo_loc_name (country) India INDIA +GAZ_00003727 geo_loc_name (country) Indonesia +GAZ_00004474 geo_loc_name (country) Iran +GAZ_00004483 geo_loc_name (country) Iraq +GAZ_00002943 geo_loc_name (country) Ireland +GAZ_00052477 geo_loc_name (country) Isle of Man +GAZ_00002476 geo_loc_name (country) Israel +GAZ_00002650 geo_loc_name (country) Italy +GAZ_00003781 geo_loc_name (country) Jamaica JAMAICA +GAZ_00005853 geo_loc_name (country) Jan Mayen +GAZ_00002747 geo_loc_name (country) Japan +GAZ_00007118 geo_loc_name (country) Jarvis Island +GAZ_00001551 geo_loc_name (country) Jersey +GAZ_00007114 geo_loc_name (country) Johnston Atoll +GAZ_00002473 geo_loc_name (country) Jordan +GAZ_00005809 geo_loc_name (country) Juan de Nova Island +GAZ_00004999 geo_loc_name (country) Kazakhstan +GAZ_00001101 geo_loc_name (country) Kenya KENYA +GAZ_00005682 geo_loc_name (country) Kerguelen Archipelago +GAZ_00007116 geo_loc_name (country) Kingman Reef +GAZ_00006894 geo_loc_name (country) Kiribati +GAZ_00011337 geo_loc_name (country) Kosovo +GAZ_00005285 geo_loc_name (country) Kuwait +GAZ_00006893 geo_loc_name (country) Kyrgyzstan +GAZ_00006889 geo_loc_name (country) Laos +GAZ_00002958 geo_loc_name (country) Latvia +GAZ_00002478 geo_loc_name (country) Lebanon +GAZ_00001098 geo_loc_name (country) Lesotho +GAZ_00000911 geo_loc_name (country) Liberia +GAZ_00000566 geo_loc_name (country) Libya +GAZ_00003858 geo_loc_name (country) Liechtenstein +GAZ_00007144 geo_loc_name (country) Line Islands +GAZ_00002960 geo_loc_name (country) Lithuania +GAZ_00002947 geo_loc_name (country) Luxembourg +GAZ_00003202 geo_loc_name (country) Macau +GAZ_00001108 geo_loc_name (country) Madagascar +GAZ_00001105 geo_loc_name (country) Malawi +GAZ_00003902 geo_loc_name (country) Malaysia +GAZ_00006924 geo_loc_name (country) Maldives +GAZ_00000584 geo_loc_name (country) Mali +GAZ_00005459 geo_loc_name (country) Malta +GAZ_00007161 geo_loc_name (country) Marshall Islands +GAZ_00067143 geo_loc_name (country) Martinique +GAZ_00000583 geo_loc_name (country) Mauritania +GAZ_00003745 geo_loc_name (country) Mauritius +GAZ_00003943 geo_loc_name (country) Mayotte +GAZ_00002852 geo_loc_name (country) Mexico MEXICO +GAZ_00005862 geo_loc_name (country) Micronesia +GAZ_00007112 geo_loc_name (country) Midway Islands +GAZ_00003897 geo_loc_name (country) Moldova +GAZ_00003857 geo_loc_name (country) Monaco +GAZ_00008744 geo_loc_name (country) Mongolia +GAZ_00006898 geo_loc_name (country) Montenegro +GAZ_00003988 geo_loc_name (country) Montserrat +GAZ_00000565 geo_loc_name (country) Morocco +GAZ_00001100 geo_loc_name (country) Mozambique +GAZ_00006899 geo_loc_name (country) Myanmar +GAZ_00001096 geo_loc_name (country) Namibia +GAZ_00006900 geo_loc_name (country) Nauru +GAZ_00007119 geo_loc_name (country) Navassa Island +GAZ_00004399 geo_loc_name (country) Nepal +GAZ_00002946 geo_loc_name (country) Netherlands NETHERLANDS +GAZ_00005206 geo_loc_name (country) New Caledonia +GAZ_00000469 geo_loc_name (country) New Zealand +GAZ_00002978 geo_loc_name (country) Nicaragua +GAZ_00000585 geo_loc_name (country) Niger +GAZ_00000912 geo_loc_name (country) Nigeria NIGERIA +GAZ_00006902 geo_loc_name (country) Niue +GAZ_00005908 geo_loc_name (country) Norfolk Island +GAZ_00002801 geo_loc_name (country) North Korea +GAZ_00006895 geo_loc_name (country) North Macedonia +GAZ_00002284 geo_loc_name (country) North Sea +GAZ_00003958 geo_loc_name (country) Northern Mariana Islands +GAZ_00002699 geo_loc_name (country) Norway +GAZ_00005283 geo_loc_name (country) Oman +GAZ_00005246 geo_loc_name (country) Pakistan PAKISTAN +GAZ_00006905 geo_loc_name (country) Palau +GAZ_00002892 geo_loc_name (country) Panama +GAZ_00003922 geo_loc_name (country) Papua New Guinea +GAZ_00010832 geo_loc_name (country) Paracel Islands +GAZ_00002933 geo_loc_name (country) Paraguay +GAZ_00002932 geo_loc_name (country) Peru +GAZ_00004525 geo_loc_name (country) Philippines PHILIPPINE +GAZ_00005867 geo_loc_name (country) Pitcairn Islands +GAZ_00002939 geo_loc_name (country) Poland +GAZ_00004126 geo_loc_name (country) Portugal +GAZ_00006935 geo_loc_name (country) Puerto Rico +GAZ_00005286 geo_loc_name (country) Qatar +GAZ_00001088 geo_loc_name (country) Republic of the Congo +GAZ_00003945 geo_loc_name (country) Reunion +GAZ_00002951 geo_loc_name (country) Romania +GAZ_00023304 geo_loc_name (country) Ross Sea +GAZ_00002721 geo_loc_name (country) Russia +GAZ_00001087 geo_loc_name (country) Rwanda +GAZ_00000849 geo_loc_name (country) Saint Helena +GAZ_00006906 geo_loc_name (country) Saint Kitts and Nevis +GAZ_00006909 geo_loc_name (country) Saint Lucia +GAZ_00003942 geo_loc_name (country) Saint Pierre and Miquelon +GAZ_00005841 geo_loc_name (country) Saint Martin +GAZ_02000565 geo_loc_name (country) Saint Vincent and the Grenadines +GAZ_00006910 geo_loc_name (country) Samoa +GAZ_00003102 geo_loc_name (country) San Marino +GAZ_00006927 geo_loc_name (country) Sao Tome and Principe +GAZ_00005279 geo_loc_name (country) Saudi Arabia +GAZ_00000913 geo_loc_name (country) Senegal +GAZ_00002957 geo_loc_name (country) Serbia +GAZ_00006922 geo_loc_name (country) Seychelles +GAZ_00000914 geo_loc_name (country) Sierra Leone +GAZ_00003923 geo_loc_name (country) Singapore +GAZ_00012579 geo_loc_name (country) Sint Maarten +GAZ_00002956 geo_loc_name (country) Slovakia +GAZ_00002955 geo_loc_name (country) Slovenia +GAZ_00005275 geo_loc_name (country) Solomon Islands +GAZ_00001104 geo_loc_name (country) Somalia +GAZ_00001094 geo_loc_name (country) South Africa +GAZ_00003990 geo_loc_name (country) South Georgia and the South Sandwich Islands +GAZ_00002802 geo_loc_name (country) South Korea +GAZ_00233439 geo_loc_name (country) South Sudan +GAZ_00003936 geo_loc_name (country) Spain +GAZ_00010831 geo_loc_name (country) Spratly Islands +GAZ_00003924 geo_loc_name (country) Sri Lanka +GAZ_00002475 geo_loc_name (country) State of Palestine +GAZ_00000560 geo_loc_name (country) Sudan +GAZ_00002525 geo_loc_name (country) Suriname +GAZ_00005396 geo_loc_name (country) Svalbard +GAZ_00001099 geo_loc_name (country) Swaziland +GAZ_00002729 geo_loc_name (country) Sweden +GAZ_00002941 geo_loc_name (country) Switzerland +GAZ_00002474 geo_loc_name (country) Syria +GAZ_00005341 geo_loc_name (country) Taiwan +GAZ_00006912 geo_loc_name (country) Tajikistan +GAZ_00001103 geo_loc_name (country) Tanzania +GAZ_00003744 geo_loc_name (country) Thailand +GAZ_00006913 geo_loc_name (country) Timor-Leste +GAZ_00000915 geo_loc_name (country) Togo +GAZ_00260188 geo_loc_name (country) Tokelau +GAZ_00006916 geo_loc_name (country) Tonga +GAZ_00003767 geo_loc_name (country) Trinidad and Tobago +GAZ_00005812 geo_loc_name (country) Tromelin Island +GAZ_00000562 geo_loc_name (country) Tunisia +GAZ_00000558 geo_loc_name (country) Turkey +GAZ_00005018 geo_loc_name (country) Turkmenistan +GAZ_00003955 geo_loc_name (country) Turks and Caicos Islands +GAZ_00009715 geo_loc_name (country) Tuvalu +GAZ_00002459 geo_loc_name (country) United States of America US +GAZ_00001102 geo_loc_name (country) Uganda +GAZ_00002724 geo_loc_name (country) Ukraine +GAZ_00005282 geo_loc_name (country) United Arab Emirates +GAZ_00002637 geo_loc_name (country) United Kingdom UNITEDKING +GAZ_00002930 geo_loc_name (country) Uruguay URUGUAY +GAZ_00004979 geo_loc_name (country) Uzbekistan +GAZ_00006918 geo_loc_name (country) Vanuatu +GAZ_00002931 geo_loc_name (country) Venezuela +GAZ_00003756 geo_loc_name (country) Viet Nam +GAZ_00003959 geo_loc_name (country) Virgin Islands +GAZ_00007111 geo_loc_name (country) Wake Island +GAZ_00007191 geo_loc_name (country) Wallis and Futuna +GAZ_00009572 geo_loc_name (country) West Bank +GAZ_00000564 geo_loc_name (country) Western Sahara +GAZ_00005284 geo_loc_name (country) Yemen +GAZ_00001107 geo_loc_name (country) Zambia +GAZ_00001106 geo_loc_name (country) Zimbabwe \ No newline at end of file diff --git a/template/pha4ge/data.js b/template/pha4ge/data.js index 07084631..d3f78e21 100644 --- a/template/pha4ge/data.js +++ b/template/pha4ge/data.js @@ -27,22 +27,22 @@ var DATA = [ "field": "Sample ID given by the sample provider" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "sample_name" } ], - "SRA": [ + "NCBI_SRA": [ { "field": "sample_name" } ], - "Genbank": [ + "NCBI_Genbank": [ { "field": "sample_name" } ], - "Genbank_source_modifiers": [ + "NCBI_Genbank_source_modifiers": [ { "field": "sequence_ID" } @@ -62,9 +62,7 @@ var DATA = [ "description": "The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort.", "guidance": "Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject.", "examples": "PRJNA623807", - "schema:ItemList": { - "PRJNA623807": {} - } + "schema:ItemList": {} }, { "fieldName": "bioproject accession", @@ -80,17 +78,17 @@ var DATA = [ "guidance": "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. ", "examples": "PRJNA12345", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "bioproject_accession" } ], - "SRA": [ + "NCBI_SRA": [ { "field": "bioproject_accession" } ], - "Genbank_source_modifiers": [ + "NCBI_Genbank_source_modifiers": [ { "field": "BioProject" } @@ -111,17 +109,17 @@ var DATA = [ "guidance": "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN.", "examples": "SAMN14180202", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "biosample_accession" } ], - "Genbank": [ + "NCBI_Genbank": [ { "field": "biosample_accession" } ], - "Genbank_source_modifiers": [ + "NCBI_Genbank_source_modifiers": [ { "field": "BioSample" } @@ -170,12 +168,12 @@ var DATA = [ "guidance": "Store the accession returned from the GISAID submission.", "examples": "EPI_ISL_123456", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "GISAID_accession" } ], - "Genbank_source_modifiers": [ + "NCBI_Genbank_source_modifiers": [ { "field": "GISAID-accesion" } @@ -196,12 +194,12 @@ var DATA = [ "guidance": "GISAID virus names should be in the format \"hCoV-19/Country/Identifier/year\".", "examples": "hCoV-19/Canada/prov_rona_99/2020", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "GISAID_virus_name" } ], - "Genbank_source_modifiers": [ + "NCBI_Genbank_source_modifiers": [ { "field": "GISAID-virus-name" } @@ -252,7 +250,7 @@ var DATA = [ "field": "Originating lab" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "collected_by" } @@ -319,7 +317,7 @@ var DATA = [ "field": "Submitting lab" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "sequenced_by" } @@ -340,7 +338,7 @@ var DATA = [ "guidance": "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca", "examples": "RespLab@lab.ca", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "sequence_submitter_contact_email" } @@ -393,12 +391,12 @@ var DATA = [ "field": "Collection date" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "collection_date" } ], - "Genbank_source_modifiers": [ + "NCBI_Genbank_source_modifiers": [ { "field": "collection-date" } @@ -450,12 +448,12 @@ var DATA = [ "field": "Location" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "geo_loc_name" } ], - "Genbank_source_modifiers": [ + "NCBI_Genbank_source_modifiers": [ { "field": "country" } @@ -755,7 +753,7 @@ var DATA = [ "guidance": "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz", "examples": "Western Cape", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "geo_loc_name" } @@ -804,7 +802,7 @@ var DATA = [ "guidance": "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\".", "examples": "38.98 N", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "lat_lon" } @@ -825,7 +823,7 @@ var DATA = [ "guidance": "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\".", "examples": "77.11 W", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "lat_lon" } @@ -852,16 +850,15 @@ var DATA = [ "guidance": "Use \"Severe acute respiratory syndrome coronavirus 2\". This value is provided in the template.", "examples": "Severe acute respiratory syndrome coronavirus 2", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "organism" } ] }, "schema:ItemList": { - "Severe acute respiratory syndrome coronavirus 2": {}, - "RaTG13": {}, - "RmYN02": {} + "Coronaviridae": {}, + "Severe acute respiratory syndrome coronavirus 2": {} } }, { @@ -889,12 +886,12 @@ var DATA = [ "field": "Virus name" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "isolate" } ], - "Genbank_source_modifiers": [ + "NCBI_Genbank_source_modifiers": [ { "field": "isolate" } @@ -935,7 +932,7 @@ var DATA = [ "guidance": "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field. ", "examples": "Diagnostic testing", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "purpose_of_sampling" } @@ -1026,7 +1023,7 @@ var DATA = [ "field": "Specimen source" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "isolation_source|anatomical_material" } @@ -1072,7 +1069,7 @@ var DATA = [ "field": "Specimen source" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "isolation_source|anatomical_part" } @@ -1146,7 +1143,7 @@ var DATA = [ "field": "Specimen source" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "isolation_source|body_product" } @@ -1191,7 +1188,7 @@ var DATA = [ "field": "Specimen source" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "isolation_source|environmental_material" } @@ -1258,7 +1255,7 @@ var DATA = [ "field": "Specimen source" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "isolation_source|environmental_site" } @@ -1313,7 +1310,7 @@ var DATA = [ "field": "Specimen source" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "isolation_source|collection_device" } @@ -1364,7 +1361,7 @@ var DATA = [ "field": "Specimen source" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "isolation_source|collection_method" } @@ -1511,13 +1508,7 @@ var DATA = [ "ontology_id": "", "datatype": "xs:nonNegativeInteger", "source": "", - "dataStatus": [ - "Not Applicable", - "Missing", - "Not Collected", - "Not Provided", - "Restricted Access" - ], + "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", "requirement": "", @@ -1530,7 +1521,7 @@ var DATA = [ "field": "Passage details/history" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "passage_number" } @@ -1562,7 +1553,7 @@ var DATA = [ "field": "Passage details/history" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "passage_method" } @@ -1675,7 +1666,7 @@ var DATA = [ "field": "Host" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "host" } @@ -1725,7 +1716,7 @@ var DATA = [ "field": "Patient status" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "host_health_state" } @@ -1794,7 +1785,7 @@ var DATA = [ "guidance": "Select \"COVID-19\" from the pick list provided in the template.", "examples": "COVID-19", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "host_disease" } @@ -1824,7 +1815,7 @@ var DATA = [ "guidance": "If known, select a descriptor from the pick list provided in the template.", "examples": "Recovered", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "host_disease_outcome" } @@ -1862,7 +1853,7 @@ var DATA = [ "field": "Patient age" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "host_age" } @@ -1951,7 +1942,7 @@ var DATA = [ "field": "Gender" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "host_sex" } @@ -2016,7 +2007,7 @@ var DATA = [ "guidance": "Provide the host identifier. Should be a unique, user-defined identifier.", "examples": "BCxy123", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "host_subject_id" } @@ -2214,7 +2205,7 @@ var DATA = [ "xs:minInclusive": "", "xs:maxInclusive": "", "requirement": "", - "description": "Patient pre-existing conditions and risk factors.\nPre-existing condition: A medical condition that existed prior to the current infection.\nRisk Factor: A variable associated with an increased risk of disease or infection.", + "description": "Patient pre-existing conditions and risk factors. Pre-existing condition: A medical condition that existed prior to the current infection. Risk Factor: A variable associated with an increased risk of disease or infection.", "guidance": "Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team.", "examples": "Asthma", "schema:ItemList": { @@ -2563,7 +2554,7 @@ var DATA = [ "guidance": "Select the vaccination status of the host from the pick list.", "examples": "Fully Vaccinated", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "prior_SARS-CoV-2_vaccination" } @@ -2572,7 +2563,7 @@ var DATA = [ "schema:ItemList": { "Fully Vaccinated": { "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "prior_SARS-CoV-2_vaccination", "value": "Yes" @@ -2582,7 +2573,7 @@ var DATA = [ }, "Partially Vaccinated": { "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "prior_SARS-CoV-2_vaccination", "value": "Yes" @@ -2592,7 +2583,7 @@ var DATA = [ }, "Not Vaccinated": { "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "prior_SARS-CoV-2_vaccination", "value": "No" @@ -2616,7 +2607,7 @@ var DATA = [ "guidance": "Free text. Provide the name of the vaccine.", "examples": "BNT162b2, Pfizer-BioNTech", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "vaccine_received" } @@ -2651,7 +2642,7 @@ var DATA = [ "guidance": "Provide the vaccination date in ISO 8601 standard format \"YYYY-MM-DD\".", "examples": "2021-02-26", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "date_of_prior_SARS-CoV-2_vaccination_(1st_dose)" } @@ -2697,7 +2688,7 @@ var DATA = [ "guidance": "Select the country name from pick list provided in the template.", "examples": "Canada", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "location_of_exposure_geo_loc_name_(country)" } @@ -2794,7 +2785,7 @@ var DATA = [ "guidance": "Provide the travel return date.", "examples": "2020-04-26", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "recent_travel_history_return_date" } @@ -2815,7 +2806,7 @@ var DATA = [ "guidance": "Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first.", "examples": "Canada, Vancouver; USA, Seattle; Italy, Milan", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "receent_travel_history_location" } @@ -2847,7 +2838,7 @@ var DATA = [ "field": "Additional location information" } ], - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "exposure_event" } @@ -3131,7 +3122,7 @@ var DATA = [ "guidance": "If known, provide infromation about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list.", "examples": "Yes", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "prior_SARS-CoV-2_infection" } @@ -3153,7 +3144,7 @@ var DATA = [ "guidance": "Provide the isolate name of the most recent prior infection. Structure the \"isolate\" name to be ICTV/INSDC compliant in the following format: \"SARS-CoV-2/host/country/sampleID/date\".", "examples": "SARS-CoV-2/human/USA/CA-CDPH-001/2020", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "virus_isolate_of_prior_infection" } @@ -3174,7 +3165,7 @@ var DATA = [ "guidance": "Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format \"YYYY-MM-DD\".", "examples": "2021-01-23", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "date_of_prior_SARS-CoV-2_infection" } @@ -3201,7 +3192,7 @@ var DATA = [ "guidance": "If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list.", "examples": "No prior antiviral treatment", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "prior_SARS-CoV-2_antiviral_treatment" } @@ -3210,7 +3201,7 @@ var DATA = [ "schema:ItemList": { "Prior antivrial treatment": { "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "prior_SARS-CoV-2_antiviral_treatment", "value": "Yes" @@ -3220,7 +3211,7 @@ var DATA = [ }, "No prior antivrial treatment": { "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "prior_SARS-CoV-2_antiviral_treatment", "value": "No" @@ -3245,7 +3236,7 @@ var DATA = [ "guidance": "Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put \"No treatment\". If multiple antiviral agents were administered, list them all separated by commas.", "examples": "Remdesivir", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "antiviral_treatment_agent" } @@ -3266,7 +3257,7 @@ var DATA = [ "guidance": "Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format \"YYYY-MM-DD\".", "examples": "2021-01-28", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "date_of_prior_SARS-CoV-2_antiviral_treatment" } @@ -3317,7 +3308,7 @@ var DATA = [ "guidance": "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field. ", "examples": "Baseline surveillance (random sampling)", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "purpose_of_sequencing" } @@ -3330,7 +3321,8 @@ var DATA = [ "Priority surveillance project": { "schema:ItemList": { "Screening for Variants of Concern (VoC)": {}, - "Longitudinal surveillance (repeat sampling)": {}, + "Longitudinal surveillance (repeat sampling of individuals)": {}, + "Re-infection surveillance": {}, "Vaccine escape surveillance": {}, "Travel-associated surveillance": { "schema:ItemList": { @@ -3410,7 +3402,7 @@ var DATA = [ "guidance": "The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID.", "examples": "XYZ_123345", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "library_ID" } @@ -3431,7 +3423,7 @@ var DATA = [ "guidance": "Provide the amplicon size, including the units.", "examples": "300bp", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "amplicon_size" } @@ -3491,7 +3483,7 @@ var DATA = [ "field": "Sequencing technology" } ], - "Genbank": [ + "NCBI_Genbank": [ { "field": "sequencing_technology" } @@ -3500,7 +3492,7 @@ var DATA = [ "schema:ItemList": { "Illumina": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA" @@ -3510,7 +3502,7 @@ var DATA = [ "schema:ItemList": { "Illumina Genome Analyzer": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA|instrument_model:Illumina Genome Analyzer" @@ -3520,7 +3512,7 @@ var DATA = [ "schema:ItemList": { "Illumina Genome Analyzer II": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA|instrument_model:Illumina Genome Analyzer II" @@ -3530,7 +3522,7 @@ var DATA = [ }, "Illumina Genome Analyzer IIx": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA|instrument_model:Illumina Genome Analyzer IIx" @@ -3542,7 +3534,7 @@ var DATA = [ }, "Illumina HiScanSQ": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA|instrument_model:Illumina HiScanSQ" @@ -3552,7 +3544,7 @@ var DATA = [ }, "Illumina HiSeq": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA" @@ -3562,7 +3554,7 @@ var DATA = [ }, "Illumina HiSeq X": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA" @@ -3572,7 +3564,7 @@ var DATA = [ "schema:ItemList": { "Illumina HiSeq X Five": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA|instrument_model: Illumina HiSeq X Five" @@ -3582,7 +3574,7 @@ var DATA = [ }, "Illumina HiSeq X Ten": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA|instrument_model:Illumina HiSeq X Ten" @@ -3594,7 +3586,7 @@ var DATA = [ }, "Illumina HiSeq 1000": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA|instrument_model:Illumina HiSeq 1000" @@ -3604,7 +3596,7 @@ var DATA = [ }, "Illumina HiSeq 1500": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA" @@ -3614,7 +3606,7 @@ var DATA = [ }, "Illumina HiSeq 2000": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA|instrument_model:Illumina HiSeq 2000" @@ -3624,7 +3616,7 @@ var DATA = [ }, "Illumina HiSeq 2500": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA|instrument_model:Illumina HiSeq 2500" @@ -3634,7 +3626,7 @@ var DATA = [ }, "Illumina HiSeq 3000": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA" @@ -3644,7 +3636,7 @@ var DATA = [ }, "Illumina HiSeq 4000": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA" @@ -3654,7 +3646,7 @@ var DATA = [ }, "Illumina iSeq": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA" @@ -3664,7 +3656,7 @@ var DATA = [ "schema:ItemList": { "Illumina iSeq 100": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA" @@ -3676,7 +3668,7 @@ var DATA = [ }, "Illumina NovaSeq": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA" @@ -3686,7 +3678,7 @@ var DATA = [ "schema:ItemList": { "Illumina NovaSeq 6000": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA" @@ -3698,7 +3690,7 @@ var DATA = [ }, "Illumina MiniSeq": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA" @@ -3708,7 +3700,7 @@ var DATA = [ }, "Illumina MiSeq": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA|instrument_model:Illumina MiSeq" @@ -3718,7 +3710,7 @@ var DATA = [ }, "Illumina NextSeq": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA" @@ -3728,7 +3720,7 @@ var DATA = [ }, "Illumina NextSeq 500": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA|instrument_model:Illumina NextSeq 500" @@ -3738,7 +3730,7 @@ var DATA = [ }, "Illumina NextSeq 550": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ILLUMINA" @@ -3750,7 +3742,7 @@ var DATA = [ }, "Pacific Biosciences": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "PACBIO_SMRT" @@ -3760,7 +3752,7 @@ var DATA = [ "schema:ItemList": { "PacBio RS": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "PACBIO_SMRT|instrument_model:PacBio RS" @@ -3770,7 +3762,7 @@ var DATA = [ }, "PacBio RS II": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "PACBIO_SMRT|instrument_model:PacBio RS II" @@ -3780,7 +3772,7 @@ var DATA = [ }, "PacBio Sequel": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "PACBIO_SMRT" @@ -3790,7 +3782,7 @@ var DATA = [ }, "PacBio Sequel II": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "PACBIO_SMRT" @@ -3802,7 +3794,7 @@ var DATA = [ }, "Ion Torrent": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ION_TORRENT" @@ -3812,7 +3804,7 @@ var DATA = [ "schema:ItemList": { "Ion Torrent PGM": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ION_TORRENT|instrument_model:Ion Torrent PGM" @@ -3822,7 +3814,7 @@ var DATA = [ }, "Ion Torrent Proton": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ION_TORRENT|instrument_model:Ion Torrent Proton" @@ -3832,7 +3824,7 @@ var DATA = [ }, "Ion Torrent S5 XL": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ION_TORRENT" @@ -3842,7 +3834,7 @@ var DATA = [ }, "Ion Torrent S5": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "ION_TORRENT" @@ -3854,7 +3846,7 @@ var DATA = [ }, "Oxford Nanopore": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "OXFORD_NANOPORE" @@ -3864,7 +3856,7 @@ var DATA = [ "schema:ItemList": { "GridION": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "OXFORD_NANOPORE|instrument_model:GridION" @@ -3874,7 +3866,7 @@ var DATA = [ }, "MinION": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "OXFORD_NANOPORE|instrument_model:MinION" @@ -3884,7 +3876,7 @@ var DATA = [ }, "PromethION": { "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "platform", "value": "OXFORD_NANOPORE" @@ -3923,7 +3915,7 @@ var DATA = [ "guidance": "Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION", "examples": "https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "sequencing_protocol_name" } @@ -3944,7 +3936,7 @@ var DATA = [ "guidance": "Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. \"", "examples": "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits.", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "design_description" } @@ -3979,7 +3971,7 @@ var DATA = [ "guidance": "Provide the name and version of the primer scheme used to generate the amplicons for sequencing.", "examples": "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "amplicon _PCR_primer_scheme" } @@ -4005,7 +3997,7 @@ var DATA = [ "guidance": "Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3", "examples": "Porechop 0.2.3", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "raw_sequence_data_processing_method" } @@ -4026,7 +4018,7 @@ var DATA = [ "guidance": "Provide the name and version number of the software used to remove host reads.", "examples": "Nanostripper", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "dehosting_method" } @@ -4047,7 +4039,7 @@ var DATA = [ "guidance": "Provide the name and version number of the consensus sequence.", "examples": "ncov123assembly3", "exportField": { - "Genbank": [ + "NCBI_Genbank": [ { "field": "assembly_name" } @@ -4068,7 +4060,7 @@ var DATA = [ "guidance": "Provide the name and version number of the consensus sequence FASTA file.", "examples": "ncov123assembly.fasta", "exportField": { - "Genbank": [ + "NCBI_Genbank": [ { "field": "filename" } @@ -4103,7 +4095,7 @@ var DATA = [ "guidance": "Provide the name of the software used to generate the consensus sequence.", "examples": "Ivar", "exportField": { - "Genbank": [ + "NCBI_Genbank": [ { "field": "assembly_method" } @@ -4124,7 +4116,7 @@ var DATA = [ "guidance": "Provide the version of the software used to generate the consensus sequence.", "examples": "1.3", "exportField": { - "Genbank": [ + "NCBI_Genbank": [ { "field": "assembly_method_version" } @@ -4164,7 +4156,7 @@ var DATA = [ "field": "Coverage" } ], - "Genbank": [ + "NCBI_Genbank": [ { "field": "genome_coverage" } @@ -4325,7 +4317,7 @@ var DATA = [ "guidance": "Provide the accession number of the reference genome.", "examples": "NC_045512.2", "exportField": { - "Genbank": [ + "NCBI_Genbank": [ { "field": "reference_genome" } @@ -4418,7 +4410,7 @@ var DATA = [ } }, { - "fieldName": "variant evidence", + "fieldName": "variant evidence details", "capitalize": "", "ontology_id": "", "datatype": "xs:token", @@ -4427,7 +4419,7 @@ var DATA = [ "xs:minInclusive": "", "xs:maxInclusive": "", "requirement": "", - "description": "The evidence used to make the variant determination.", + "description": "Details about the evidence used to make the variant determination.", "guidance": "Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here.", "examples": "RT-qPCR TaqPath assay: S gene target failure" } @@ -4456,7 +4448,7 @@ var DATA = [ "guidance": "Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI", "examples": "E (orf4)", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "diagnostic_gene_name_1" } @@ -4518,7 +4510,7 @@ var DATA = [ "guidance": "The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control.", "examples": "EGenePCRTest 2", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "diagnostic_pcr_protocol_value_1" } @@ -4539,7 +4531,7 @@ var DATA = [ "guidance": "Provide the CT value of the sample from the diagnostic RT-PCR test.", "examples": "21", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "diagnostic_pcr_Ct_value_1" } @@ -4566,7 +4558,7 @@ var DATA = [ "guidance": "Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI", "examples": "nsp12 (RdRp)", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "diagnostic_gene_name_2" } @@ -4588,7 +4580,7 @@ var DATA = [ "guidance": "The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control.", "examples": "RdRpGenePCRTest 3", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "diagnostic_pcr_protocol_value_2" } @@ -4609,7 +4601,7 @@ var DATA = [ "guidance": "Provide the CT value of the sample from the second diagnostic RT-PCR test.", "examples": "36", "exportField": { - "BIOSAMPLE": [ + "NCBI_BIOSAMPLE": [ { "field": "diagnostic_pcr_Ct_value_2" } @@ -4670,48 +4662,6 @@ var DATA = [ { "fieldName": "NCBI SRA information", "children": [ - { - "fieldName": "bioproject_accession", - "capitalize": "", - "ontology_id": "", - "datatype": "xs:token", - "source": "", - "dataStatus": null, - "xs:minInclusive": "", - "xs:maxInclusive": "", - "requirement": "prepopulate", - "description": "This will be populated by the PHA4GE field \"bioproject accession\".", - "guidance": "Populate the \"bioproject accession\" field.", - "examples": "" - }, - { - "fieldName": "sample_name", - "capitalize": "", - "ontology_id": "", - "datatype": "xs:token", - "source": "", - "dataStatus": null, - "xs:minInclusive": "", - "xs:maxInclusive": "", - "requirement": "prepopulate", - "description": "This will be populated by the PHA4GE field \"biosample accession\".", - "guidance": "Populate the \"biosample accession\" field.", - "examples": "" - }, - { - "fieldName": "library_ID", - "capitalize": "", - "ontology_id": "", - "datatype": "xs:token", - "source": "", - "dataStatus": null, - "xs:minInclusive": "", - "xs:maxInclusive": "", - "requirement": "prepopulate", - "description": "This will be populated by the PHA4GE field \"library ID\".", - "guidance": "Populate the \"library ID\" field.", - "examples": "" - }, { "fieldName": "title", "capitalize": "", @@ -4726,7 +4676,7 @@ var DATA = [ "guidance": "Format: {methodology} of {organism}: {sample info}", "examples": "Genomic sequencing of SARS-CoV-2: Nasopharynx (NP), Swab", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "title" } @@ -4747,7 +4697,7 @@ var DATA = [ "guidance": "Provide the library strategy by selecting a value from the pick list. For amplicon sequencing select \"AMPLICON\". ", "examples": "", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "library_strategy" } @@ -4793,7 +4743,7 @@ var DATA = [ "guidance": "Provide the library source by selecting a value from the pick list. For amplicon sequencing select \"Viral RNA\". ", "examples": "", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "library_source" } @@ -4823,7 +4773,7 @@ var DATA = [ "guidance": "Provide the library selection by selecting a value from the pick list. For amplicon sequencing select \"PCR\". ", "examples": "", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "library_selection" } @@ -4873,7 +4823,7 @@ var DATA = [ "guidance": "Provide the library layout by selecting a value from the pick list. For Illumina instruments, select \"PAIRED\". For Oxford Nanopore instruments, select \"SINGLE\".", "examples": "", "exportField": { - "SRA": [ + "NCBI_SRA": [ { "field": "library_layout" } @@ -4884,36 +4834,6 @@ var DATA = [ "paired": {} } }, - { - "fieldName": "platform", - "capitalize": "", - "ontology_id": "", - "datatype": "select", - "source": "", - "dataStatus": null, - "xs:minInclusive": "", - "xs:maxInclusive": "", - "requirement": "prepopulate", - "description": "This will be populated by the PHA4GE field \"sequencing instrument\".", - "guidance": "Only a limited set of sequencing platforms are available in the NCBI pick list. If a value appears to be missing, contact PHA4GE and report the issue.", - "examples": "", - "schema:ItemList": {} - }, - { - "fieldName": "instrument_model", - "capitalize": "", - "ontology_id": "", - "datatype": "select", - "source": "", - "dataStatus": null, - "xs:minInclusive": "", - "xs:maxInclusive": "", - "requirement": "prepopulate", - "description": "This will be populated by the PHA4GE field \"sequencing instrument\".", - "guidance": "Only a limited set of sequencing instruments are available in the NCBI pick list. If a value appears to be missing, contact PHA4GE and report the issue.", - "examples": "", - "schema:ItemList": {} - }, { "fieldName": "filetype", "capitalize": "", @@ -4927,6 +4847,13 @@ var DATA = [ "description": "See NCBI SRA template for details.", "guidance": "Provide the filetype by selecting a value from the pick list. ", "examples": "", + "exportField": { + "NCBI_SRA": [ + { + "field": "filetype" + } + ] + }, "schema:ItemList": { "bam": {}, "sra": {}, @@ -4953,124 +4880,150 @@ var DATA = [ "xs:maxInclusive": "", "requirement": "", "description": "See NCBI SRA template for details.", - "guidance": "Provide the filename recorded in the Bioinformatics and QC metrics section.", - "examples": "" + "guidance": "Provide the appropriate filename recorded in the Bioinformatics and QC metrics section. If sequence data is \"paired\", provide the second filename under \"Filename 2\".", + "examples": "", + "exportField": { + "NCBI_SRA": [ + { + "field": "filename" + } + ] + } }, { - "fieldName": "amplicon _PCR_primer_scheme", + "fieldName": "filename 2", "capitalize": "", "ontology_id": "", - "datatype": "xs:token", + "datatype": "", "source": "", "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", - "requirement": "prepopulate", - "description": "This will be populated by the PHA4GE field \"amplicon PCR primer scheme\".", - "guidance": "Populate the \"amplicon PCR primer scheme\" field.", - "examples": "" - }, + "requirement": "", + "description": "See NCBI SRA template for details.", + "guidance": "Provide the appropriate filename recorded in the Bioinformatics and QC metrics section.", + "examples": "", + "exportField": { + "NCBI_SRA": [ + { + "field": "filename 2" + } + ] + } + } + ] + }, + { + "fieldName": "Contributor acknowledgement", + "children": [ { - "fieldName": "amplicon_size", + "fieldName": "authors", "capitalize": "", "ontology_id": "", - "datatype": "xs:nonNegativeInteger", + "datatype": "xs:token", "source": "", "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", - "requirement": "prepopulate", - "description": "This will be populated by the PHA4GE field \"amplicon size\".", - "guidance": "Populate the \"amplicon size\" field.", - "examples": "" + "requirement": "recommended", + "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", + "guidance": "Include the first and last names of all individuals that should be attributed, separated by a comma.", + "examples": "Tejinder Singh, Fei Hu, Joe Blogs", + "exportField": { + "GISAID": [ + { + "field": "Authors" + } + ] + } }, { - "fieldName": "sequencing_protocol_name", + "fieldName": "DataHarmonizer provenance", "capitalize": "", "ontology_id": "", - "datatype": "xs:token", + "datatype": "provenance", "source": "", "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", - "requirement": "prepopulate", - "description": "This will be populated by the PHA4GE field \"sequencing protocol name\".", - "guidance": "Populate the \"sequencing protocol name\" field.", - "examples": "" - }, + "requirement": "", + "description": "", + "guidance": "", + "examples": "", + "exportField": { + "GISAID": [ + { + "field": "DataHarmonizer provenance" + } + ] + } + } + ] + }, + { + "fieldName": "data status", + "children": [ { - "fieldName": "raw_sequence_data_processing_method", + "fieldName": "Not Applicable", "capitalize": "", "ontology_id": "", - "datatype": "xs:token", + "datatype": "", "source": "", "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", - "requirement": "prepopulate", - "description": "This will be populated by the PHA4GE field \"raw sequence data processing method\".", - "guidance": "Populate the \"raw sequence data processing method\" field.", + "requirement": "", + "description": "", + "guidance": "", "examples": "" }, { - "fieldName": "dehosting_method", + "fieldName": "Missing", "capitalize": "", "ontology_id": "", - "datatype": "xs:token", + "datatype": "", "source": "", "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", - "requirement": "prepopulate", - "description": "This will be populated by the PHA4GE field \"dehosting method\".", - "guidance": "Populate the \"dehosting method\" field.", + "requirement": "", + "description": "", + "guidance": "", "examples": "" }, { - "fieldName": "sequence_submitter_contact_email", + "fieldName": "Not Collected", "capitalize": "", "ontology_id": "", - "datatype": "xs:token", + "datatype": "", "source": "", "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", - "requirement": "prepopulate", - "description": "This will be populated by the PHA4GE field \"sequence submitter contact email\".", - "guidance": "Populate the \"sequence submitter contact email\" field.", + "requirement": "", + "description": "", + "guidance": "", "examples": "" - } - ] - }, - { - "fieldName": "Contributor acknowledgement", - "children": [ + }, { - "fieldName": "authors", + "fieldName": "Not Provided", "capitalize": "", "ontology_id": "", - "datatype": "xs:token", + "datatype": "", "source": "", "dataStatus": null, "xs:minInclusive": "", "xs:maxInclusive": "", - "requirement": "recommended", - "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", - "guidance": "Include the first and last names of all individuals that should be attributed, separated by a comma.", - "examples": "Tejinder Singh, Fei Hu, Joe Blogs", - "exportField": { - "GISAID": [ - { - "field": "Authors" - } - ] - } + "requirement": "", + "description": "", + "guidance": "", + "examples": "" }, { - "fieldName": "DataHarmonizer provenance", + "fieldName": "Restricted Access", "capitalize": "", "ontology_id": "", - "datatype": "provenance", + "datatype": "", "source": "", "dataStatus": null, "xs:minInclusive": "", @@ -5078,14 +5031,7 @@ var DATA = [ "requirement": "", "description": "", "guidance": "", - "examples": "", - "exportField": { - "GISAID": [ - { - "field": "DataHarmonizer provenance" - } - ] - } + "examples": "" } ] } diff --git a/template/pha4ge/data.tsv b/template/pha4ge/data.tsv index 21637701..fe296544 100644 --- a/template/pha4ge/data.tsv +++ b/template/pha4ge/data.tsv @@ -1,1465 +1,1310 @@ -Ontology ID parent class label datatype source data status requirement min value max value capitalize description guidance examples EXPORT_GISAID EXPORT_BIOSAMPLE EXPORT_SRA EXPORT_Genbank EXPORT_Genbank_source_modifiers ontology label definition definition source english synonym Parental Term Parental Term URL Issues / Status Other -ID SC % AL rdfs:label@en AL IAO:0000115@en A IAO:0000119 SPLIT=| AL oboInOwl:hasExactSynonym@en - Database Identifiers - Database Identifiers specimen collector sample ID xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_rona_99 Sample ID given by the sample provider sample_name sample_name sample_name sequence_ID - Database Identifiers umbrella bioproject accession select UPPER The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. PRJNA623807 - Database Identifiers bioproject accession xs:token UPPER The INSDC accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA12345 bioproject_accession bioproject_accession BioProject - Database Identifiers biosample accession xs:token recommended UPPER The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. SAMN14180202 biosample_accession biosample_accession BioSample - Database Identifiers SRA accession xs:token UPPER The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 - Database Identifiers GenBank/ENA/DDBJ accession xs:token UPPER The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 - Database Identifiers GISAID accession xs:token UPPER The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_123456 GISAID_accession GISAID-accesion - Database Identifiers GISAID virus name xs:token UPPER The user-defined GISAID virus name assigned to the sequence. GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". hCoV-19/Canada/prov_rona_99/2020 GISAID_virus_name GISAID-virus-name - Database Identifiers host specimen voucher xs:token UPPER Identifier for the physical specimen. Include a URI (Uniform Resource Identifier) in the form of a URL providing a direct link to the physical host specimen. If the specimen was destroyed in the process of analysis, electronic images (e-vouchers) are an adequate substitute for a physical host voucher specimen. If a URI is not available, a museum-provided globally unique identifier (GUID) can be used. If no persistent unique identifier is available, follow the INSDC guidance for populating the voucher_specimen attribute using standard triplets for institution codes (i.e., /specimen_voucher="[:[:]]"): http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542, INSDC triplet example: UAM:Mamm:52179 - Sample collection and processing - Sample collection and processing sample collected by xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). Public Health Agency of Canada Originating lab collected_by CNPHI_EXPORT: Lev said it isn't useful because the client information is filled in when the client submits. It isn't filled in when Emma submits for others and then NML/CNPHI gets manually changed after submission. - Sample collection and processing sample collector contact email xs:token The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca johnnyblogs@lab.ca - Sample collection and processing sample collector contact address xs:token The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address - Sample collection and processing sequence submitted by xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Centers for Disease Control and Prevention Submitting lab sequenced_by - Sample collection and processing sequence submitter contact email xs:token The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequence_submitter_contact_email - Sample collection and processing sequence submitter contact address xs:token The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address - Sample collection and processing sample collection date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-19 Collection date collection_date collection-date - Sample collection and processing sample received date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 - Sample collection and processing geo_loc_name (country) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The country where the sample was collected. Provide the country name from the controlled vocabulary provided. South Africa Location geo_loc_name country - Sample collection and processing geo_loc_name (state/province/territory) xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The state/province/territory where the sample was collected. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Western Cape geo_loc_name - Sample collection and processing geo_loc name (county/region) xs:token The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire - Sample collection and processing geo_loc_name (city) xs:token The city where the sample was collected. Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver - Sample collection and processing geo_loc latitude xs:token The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon - Sample collection and processing geo_loc longitude xs:token The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon - Sample collection and processing organism select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Taxonomic name of the organism. Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template. Severe acute respiratory syndrome coronavirus 2 organism - Sample collection and processing isolate xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Identifier of the specific isolate. This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the "isolate" name is propagated throughtout different databases. As such, structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". SARS-CoV-2/human/USA/CA-CDPH-001/2020 Virus name isolate isolate - Sample collection and processing culture collection xs:token The name of the source collection and unique culture identifier. Format: ":[:]". For more information, see http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier. /culture_collection="ATCC:26370" - Sample collection and processing purpose of sampling select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing purpose_of_sampling - Sample collection and processing purpose of sampling details xs:token The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. Screening of bat specimens in museum collections. - Sample collection and processing sample plan name xs:token The name of the sample plan implemented for sample collection. Provide the name and version of the sample plan outlining the sample strategy. CanCOGeN Sampling Strategy 1.0 - Sample collection and processing sample collected in quarantine select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether the sample was collected from an individual in quarantine. Whether a sample was collected under quarantine conditions (e.g. self-quarantining, medically isolated, staying at a quarantine hotel) can inform public health measure assessments. Use the picklist provided in the template. Yes - Sample collection and processing anatomical material select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Blood Specimen source isolation_source|anatomical_material - Sample collection and processing anatomical part select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Nasopharynx Specimen source isolation_source|anatomical_part - Sample collection and processing body product select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Feces Specimen source isolation_source|body_product - Sample collection and processing environmental material select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Face mask Specimen source isolation_source|environmental_material - Sample collection and processing environmental site select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Hospital room Specimen source isolation_source|environmental_site - Sample collection and processing collection device select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source isolation_source|collection_device - Sample collection and processing collection method select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Bronchoalveolar lavage (BAL) Specimen source isolation_source|collection_method - Sample collection and processing collection protocol xs:token The name and version of a particular protocol used for sampling. Free text. SC2SamplingProtocol 1.2 - Sample collection and processing specimen processing multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Virus passage Passage details/history - Sample collection and processing lab host select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. Type of cell line used for propagation. Provide the name of the cell line using the picklist in the template. If not passaged, put "not applicable". Vero E6 cell line Passage details/history - Sample collection and processing passage number xs:nonNegativeInteger Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Number of passages. Provide number of known passages. If not passaged, put "not applicable" 3 Passage details/history passage_number - Sample collection and processing passage method xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Description of how organism was passaged. Free text. Provide a very short description (<10 words). If not passaged, put "not applicable". AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain. Passage details/history passage_method - Sample collection and processing biomaterial extracted select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The biomaterial extracted from samples for the purpose of sequencing. Provide the biomaterial extracted from the picklist in the template. RNA (total) - Sample collection and processing data abstraction details xs:token A description of how any data elements were altered to preserve patient privacy. If applicable, provide a description of how each data element was abstracted. Jitter added to publicly shared collection dates to prevent re-identifiability. - Host Information - Host Information host (common name) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put "not applicable. Human - Host Information host (scientific name) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host - Host Information host health state select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Health status of the host at the time of sample collection. If known, select a descriptor from the pick list provided in the template. Asymptomatic Patient status host_health_state - Host Information host health status details select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized (ICU) - Host Information host disease select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the disease experienced by the host. Select "COVID-19" from the pick list provided in the template. COVID-19 host_disease - Host Information host health outcome select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Disease outcome in the host. If known, select a descriptor from the pick list provided in the template. Recovered host_disease_outcome - Host Information host age xs:decimal Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended 0 130 Age of host at the time of sampling. Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". 79 Patient age host_age - Host Information host age unit select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended The unit used to measure the host age, in either months or years. Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. years - Host Information host age bin select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. - Host Information host gender select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended The gender of the host at the time of sample collection. Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". male Gender host_sex - Host Information host residence geo_loc name (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The country of residence of the host. Select the country name from pick list provided in the template. Canada - Host Information host ethnicity xs:token The self-identified ethnicity(ies) of the host. If known, provide the self-identified ethnicity or ethnicities of the host as a free text description. This is highly sensitive information which must be treated respectfully and carefully when sharing. The information may have implications for equitable access and benefit sharing. Consult your privacy officer, data steward and/or cultural services representative. Indigenous, European - Host Information host subject ID xs:token A unique identifier by which each host can be referred to e.g. #131 Provide the host identifier. Should be a unique, user-defined identifier. BCxy123 host_subject_id - Host Information symptom onset date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date on which the symptoms began or were first noted. ISO 8601 standard "YYYY-MM-DD". 16-03-2020 - Host Information signs and symptoms multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician. Select all of the symptoms experienced by the host from the pick list. Cough, Fever, Chills - Host Information pre-existing conditions and risk factors multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access "Patient pre-existing conditions and risk factors. -Pre-existing condition: A medical condition that existed prior to the current infection. -Risk Factor: A variable associated with an increased risk of disease or infection." Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Asthma - Host Information complications multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Acute Respiratory Failure - Host vaccination information - Host vaccination information host vaccination status select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated prior_SARS-CoV-2_vaccination - Host vaccination information vaccine name xs:token The name of the vaccine. Free text. Provide the name of the vaccine. BNT162b2, Pfizer-BioNTech vaccine_received - Host vaccination information number of vaccine doses received xs:nonNegativeInteger The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 2 - Host vaccination information first dose vaccination date xs:date The date the host was first vaccinated. Provide the vaccination date in ISO 8601 standard format "YYYY-MM-DD". 2021-02-26 date_of_prior_SARS-CoV-2_vaccination_(1st_dose) - Host vaccination information last dose vaccination date xs:date The date the host received their last dose of vaccine. Provide the date that the last dose of the vaccine was administered. Provide the last dose vaccination date in ISO 8601 standard format "YYYY-MM-DD". 2021-04-09 - Host exposure information - Host exposure information location of exposure geo_loc name (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The country where the host was likely exposed to the causative agent of the illness. Select the country name from pick list provided in the template. Canada location_of_exposure_geo_loc_name_(country) - Host exposure information destination of most recent travel (city) xs:token The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City - Host exposure information destination of most recent travel (state/province/territory) xs:token The name of the province that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California - Host exposure information destination of most recent travel (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the country that was the destination of most recent travel. Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz United Kingdom - Host exposure information most recent travel departure date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date. 2020-03-16 - Host exposure information most recent travel return date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date. 2020-04-26 recent_travel_history_return_date - Host exposure information travel history xs:token Travel history in last six months. Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Canada, Vancouver; USA, Seattle; Italy, Milan receent_travel_history_location - Host exposure information exposure event select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Convention Additional location information exposure_event - Host exposure information exposure contact level select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The exposure transmission contact type. Select direct or indirect exposure from the pick-list. Direct - Host exposure information host role multiple The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Patient - Host exposure information exposure setting multiple The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Healthcare Setting - Host exposure information exposure details xs:token Additional host exposure information. Free text description of the exposure. Host role - Other: Bus Driver - - - Host reinfection information - Host reinfection information prior SARS-CoV-2 infection select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether there was prior SARS-CoV-2 infection. If known, provide infromation about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. Yes prior_SARS-CoV-2_infection - Host reinfection information prior SARS-CoV-2 infection isolate xs:token The identifier of the isolate found in the prior SARS-CoV-2 infection. Provide the isolate name of the most recent prior infection. Structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". SARS-CoV-2/human/USA/CA-CDPH-001/2020 virus_isolate_of_prior_infection - Host reinfection information prior SARS-CoV-2 infection date xs:date The date of diagnosis of the prior SARS-CoV-2 infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-23 date_of_prior_SARS-CoV-2_infection - Host reinfection information prior SARS-CoV-2 antiviral treatment select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether there was prior SARS-CoV-2 treatment with an antiviral agent. If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. No prior antiviral treatment prior_SARS-CoV-2_antiviral_treatment - Host reinfection information prior SARS-CoV-2 antiviral treatment agent xs:token The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put "No treatment". If multiple antiviral agents were administered, list them all separated by commas. Remdesivir antiviral_treatment_agent - Host reinfection information prior SARS-CoV-2 antiviral treatment date xs:date The date treatment was first administered during the prior SARS-CoV-2 infection. Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-28 date_of_prior_SARS-CoV-2_antiviral_treatment - - - Sequencing - Sequencing purpose of sequencing select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) purpose_of_sequencing +Ontology ID parent class label datatype source data status requirement min value max value capitalize description guidance examples EXPORT_GISAID EXPORT_NCBI_BIOSAMPLE EXPORT_NCBI_SRA EXPORT_NCBI_Genbank EXPORT_NCBI_Genbank_source_modifiers +ID SC % + Database Identifiers + Database Identifiers specimen collector sample ID xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_rona_99 Sample ID given by the sample provider sample_name sample_name sample_name sequence_ID + Database Identifiers umbrella bioproject accession select UPPER The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. PRJNA623807 + Database Identifiers bioproject accession xs:token UPPER The INSDC accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA12345 bioproject_accession bioproject_accession BioProject + Database Identifiers biosample accession xs:token recommended UPPER The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. SAMN14180202 biosample_accession biosample_accession BioSample + Database Identifiers SRA accession xs:token UPPER The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 + Database Identifiers GenBank/ENA/DDBJ accession xs:token UPPER The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 + Database Identifiers GISAID accession xs:token UPPER The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_123456 GISAID_accession GISAID-accesion + Database Identifiers GISAID virus name xs:token UPPER The user-defined GISAID virus name assigned to the sequence. GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". hCoV-19/Canada/prov_rona_99/2020 GISAID_virus_name GISAID-virus-name + Database Identifiers host specimen voucher xs:token UPPER Identifier for the physical specimen. Include a URI (Uniform Resource Identifier) in the form of a URL providing a direct link to the physical host specimen. If the specimen was destroyed in the process of analysis, electronic images (e-vouchers) are an adequate substitute for a physical host voucher specimen. If a URI is not available, a museum-provided globally unique identifier (GUID) can be used. If no persistent unique identifier is available, follow the INSDC guidance for populating the voucher_specimen attribute using standard triplets for institution codes (i.e., /specimen_voucher="[:[:]]"): http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542, INSDC triplet example: UAM:Mamm:52179 + Sample collection and processing + Sample collection and processing sample collected by xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). Public Health Agency of Canada Originating lab collected_by + Sample collection and processing sample collector contact email xs:token The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca johnnyblogs@lab.ca + Sample collection and processing sample collector contact address xs:token The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address + Sample collection and processing sequence submitted by xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Centers for Disease Control and Prevention Submitting lab sequenced_by + Sample collection and processing sequence submitter contact email xs:token The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequence_submitter_contact_email + Sample collection and processing sequence submitter contact address xs:token The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address + Sample collection and processing sample collection date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-19 Collection date collection_date collection-date + Sample collection and processing sample received date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 + Sample collection and processing geo_loc_name (country) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The country where the sample was collected. Provide the country name from the controlled vocabulary provided. South Africa Location geo_loc_name country + Sample collection and processing geo_loc_name (state/province/territory) xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The state/province/territory where the sample was collected. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Western Cape geo_loc_name + Sample collection and processing geo_loc name (county/region) xs:token The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire + Sample collection and processing geo_loc_name (city) xs:token The city where the sample was collected. Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver + Sample collection and processing geo_loc latitude xs:token The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon + Sample collection and processing geo_loc longitude xs:token The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon + Sample collection and processing organism select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Taxonomic name of the organism. Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template. Severe acute respiratory syndrome coronavirus 2 organism + Sample collection and processing isolate xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required Identifier of the specific isolate. This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the "isolate" name is propagated throughtout different databases. As such, structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". SARS-CoV-2/human/USA/CA-CDPH-001/2020 Virus name isolate isolate + Sample collection and processing culture collection xs:token The name of the source collection and unique culture identifier. Format: ":[:]". For more information, see http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier. /culture_collection="ATCC:26370" + Sample collection and processing purpose of sampling select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing purpose_of_sampling + Sample collection and processing purpose of sampling details xs:token The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. Screening of bat specimens in museum collections. + Sample collection and processing sample plan name xs:token The name of the sample plan implemented for sample collection. Provide the name and version of the sample plan outlining the sample strategy. CanCOGeN Sampling Strategy 1.0 + Sample collection and processing sample collected in quarantine select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether the sample was collected from an individual in quarantine. Whether a sample was collected under quarantine conditions (e.g. self-quarantining, medically isolated, staying at a quarantine hotel) can inform public health measure assessments. Use the picklist provided in the template. Yes + Sample collection and processing anatomical material select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Blood Specimen source isolation_source|anatomical_material + Sample collection and processing anatomical part select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Nasopharynx Specimen source isolation_source|anatomical_part + Sample collection and processing body product select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Feces Specimen source isolation_source|body_product + Sample collection and processing environmental material select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Face mask Specimen source isolation_source|environmental_material + Sample collection and processing environmental site select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Hospital room Specimen source isolation_source|environmental_site + Sample collection and processing collection device select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source isolation_source|collection_device + Sample collection and processing collection method select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma.griffiths@bccdc.ca. If not applicable, do not leave blank. Choose a null value. Bronchoalveolar lavage (BAL) Specimen source isolation_source|collection_method + Sample collection and processing collection protocol xs:token The name and version of a particular protocol used for sampling. Free text. SC2SamplingProtocol 1.2 + Sample collection and processing specimen processing multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Virus passage Passage details/history + Sample collection and processing lab host select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. Type of cell line used for propagation. Provide the name of the cell line using the picklist in the template. If not passaged, put "not applicable". Vero E6 cell line Passage details/history + Sample collection and processing passage number xs:nonNegativeInteger Number of passages. Provide number of known passages. If not passaged, put "not applicable" 3 Passage details/history passage_number + Sample collection and processing passage method xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Description of how organism was passaged. Free text. Provide a very short description (<10 words). If not passaged, put "not applicable". AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain. Passage details/history passage_method + Sample collection and processing biomaterial extracted select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The biomaterial extracted from samples for the purpose of sequencing. Provide the biomaterial extracted from the picklist in the template. RNA (total) + Sample collection and processing data abstraction details xs:token A description of how any data elements were altered to preserve patient privacy. If applicable, provide a description of how each data element was abstracted. Jitter added to publicly shared collection dates to prevent re-identifiability. + Host Information + Host Information host (common name) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put "not applicable. Human + Host Information host (scientific name) select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host + Host Information host health state select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Health status of the host at the time of sample collection. If known, select a descriptor from the pick list provided in the template. Asymptomatic Patient status host_health_state + Host Information host health status details select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized (ICU) + Host Information host disease select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The name of the disease experienced by the host. Select "COVID-19" from the pick list provided in the template. COVID-19 host_disease + Host Information host health outcome select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Disease outcome in the host. If known, select a descriptor from the pick list provided in the template. Recovered host_disease_outcome + Host Information host age xs:decimal Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended 0 130 Age of host at the time of sampling. Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". 79 Patient age host_age + Host Information host age unit select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended The unit used to measure the host age, in either months or years. Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. years + Host Information host age bin select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. + Host Information host gender select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access recommended The gender of the host at the time of sample collection. Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". male Gender host_sex + Host Information host residence geo_loc name (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The country of residence of the host. Select the country name from pick list provided in the template. Canada + Host Information host ethnicity xs:token The self-identified ethnicity(ies) of the host. If known, provide the self-identified ethnicity or ethnicities of the host as a free text description. This is highly sensitive information which must be treated respectfully and carefully when sharing. The information may have implications for equitable access and benefit sharing. Consult your privacy officer, data steward and/or cultural services representative. Indigenous, European + Host Information host subject ID xs:token A unique identifier by which each host can be referred to e.g. #131 Provide the host identifier. Should be a unique, user-defined identifier. BCxy123 host_subject_id + Host Information symptom onset date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date on which the symptoms began or were first noted. ISO 8601 standard "YYYY-MM-DD". 16-03-2020 + Host Information signs and symptoms multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician. Select all of the symptoms experienced by the host from the pick list. Cough, Fever, Chills + Host Information pre-existing conditions and risk factors multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Patient pre-existing conditions and risk factors. Pre-existing condition: A medical condition that existed prior to the current infection. Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Asthma + Host Information complications multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Acute Respiratory Failure + Host vaccination information + Host vaccination information host vaccination status select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated prior_SARS-CoV-2_vaccination + Host vaccination information vaccine name xs:token The name of the vaccine. Free text. Provide the name of the vaccine. BNT162b2, Pfizer-BioNTech vaccine_received + Host vaccination information number of vaccine doses received xs:nonNegativeInteger The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 2 + Host vaccination information first dose vaccination date xs:date The date the host was first vaccinated. Provide the vaccination date in ISO 8601 standard format "YYYY-MM-DD". 2021-02-26 date_of_prior_SARS-CoV-2_vaccination_(1st_dose) + Host vaccination information last dose vaccination date xs:date The date the host received their last dose of vaccine. Provide the date that the last dose of the vaccine was administered. Provide the last dose vaccination date in ISO 8601 standard format "YYYY-MM-DD". 2021-04-09 + Host exposure information + Host exposure information location of exposure geo_loc name (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The country where the host was likely exposed to the causative agent of the illness. Select the country name from pick list provided in the template. Canada location_of_exposure_geo_loc_name_(country) + Host exposure information destination of most recent travel (city) xs:token The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City + Host exposure information destination of most recent travel (state/province/territory) xs:token The name of the province that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California + Host exposure information destination of most recent travel (country) select geo_loc_name (country) Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the country that was the destination of most recent travel. Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz United Kingdom + Host exposure information most recent travel departure date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date. 2020-03-16 + Host exposure information most recent travel return date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date. 2020-04-26 recent_travel_history_return_date + Host exposure information travel history xs:token Travel history in last six months. Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Canada, Vancouver; USA, Seattle; Italy, Milan receent_travel_history_location + Host exposure information exposure event select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Convention Additional location information exposure_event + Host exposure information exposure contact level select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The exposure transmission contact type. Select direct or indirect exposure from the pick-list. Direct + Host exposure information host role multiple The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Patient + Host exposure information exposure setting multiple The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Healthcare Setting + Host exposure information exposure details xs:token Additional host exposure information. Free text description of the exposure. Host role - Other: Bus Driver + + + Host reinfection information + Host reinfection information prior SARS-CoV-2 infection select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether there was prior SARS-CoV-2 infection. If known, provide infromation about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. Yes prior_SARS-CoV-2_infection + Host reinfection information prior SARS-CoV-2 infection isolate xs:token The identifier of the isolate found in the prior SARS-CoV-2 infection. Provide the isolate name of the most recent prior infection. Structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". SARS-CoV-2/human/USA/CA-CDPH-001/2020 virus_isolate_of_prior_infection + Host reinfection information prior SARS-CoV-2 infection date xs:date The date of diagnosis of the prior SARS-CoV-2 infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-23 date_of_prior_SARS-CoV-2_infection + Host reinfection information prior SARS-CoV-2 antiviral treatment select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Whether there was prior SARS-CoV-2 treatment with an antiviral agent. If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. No prior antiviral treatment prior_SARS-CoV-2_antiviral_treatment + Host reinfection information prior SARS-CoV-2 antiviral treatment agent xs:token The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put "No treatment". If multiple antiviral agents were administered, list them all separated by commas. Remdesivir antiviral_treatment_agent + Host reinfection information prior SARS-CoV-2 antiviral treatment date xs:date The date treatment was first administered during the prior SARS-CoV-2 infection. Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-28 date_of_prior_SARS-CoV-2_antiviral_treatment + + + Sequencing + Sequencing purpose of sequencing select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) purpose_of_sequencing Sequencing purpose of sequencing details xs:token Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The description of why the sample was sequenced providing specific details. "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. -" Screened for S gene target failure (S dropout) - Sequencing sequencing date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 - Sequencing library ID xs:token recommended The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID - Sequencing amplicon size xs:token The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp amplicon_size - Sequencing library preparation kit xs:token The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT - Sequencing flow cell barcode xs:token The barcode of the flow cell used for sequencing. Provide the barcode of the flow cell used for sequencing the sample. FAB06069 - Sequencing sequencing instrument multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. MinIon Sequencing technology sequencing_technology - Sequencing sequencing protocol name xs:token recommended The name and version number of the sequencing protocol used. Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann sequencing_protocol_name - Sequencing sequencing protocol xs:token The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. design_description - Sequencing sequencing kit number xs:token The manufacturer's kit number. Alphanumeric value. AB456XYZ789 - Sequencing amplicon pcr primer scheme xs:token The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv amplicon _PCR_primer_scheme - - - Bioinformatics and QC metrics - Bioinformatics and QC metrics raw sequence data processing method xs:token recommended The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 raw_sequence_data_processing_method - Bioinformatics and QC metrics dehosting method xs:token recommended The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper dehosting_method - Bioinformatics and QC metrics consensus sequence name xs:token The name of the consensus sequence. Provide the name and version number of the consensus sequence. ncov123assembly3 assembly_name - Bioinformatics and QC metrics consensus sequence filename xs:token The name of the consensus sequence file. Provide the name and version number of the consensus sequence FASTA file. ncov123assembly.fasta filename - Bioinformatics and QC metrics consensus sequence filepath xs:token The filepath of the consesnsus sequence file. Provide the filepath of the consensus sequence FASTA file. /User/Documents/RespLab/Data/ncov123assembly.fasta - Bioinformatics and QC metrics consensus sequence software name xs:token required The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. Ivar assembly_method - Bioinformatics and QC metrics consensus sequence software version xs:decimal required The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 assembly_method_version - Bioinformatics and QC metrics breadth of coverage value xs:token The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95% - Bioinformatics and QC metrics depth of coverage value xs:token The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Coverage genome_coverage - Bioinformatics and QC metrics depth of coverage threshold xs:token The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x - Bioinformatics and QC metrics r1 fastq filename xs:token The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz - Bioinformatics and QC metrics r2 fastq filename xs:token The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz - Bioinformatics and QC metrics r1 fastq filepath xs:token The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz - Bioinformatics and QC metrics r2 fastq filepath xs:token The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz - Bioinformatics and QC metrics fast5 filename xs:token The user-specified filename of the FAST5 file. Provide the FAST5 filename. rona123assembly.fast5 - Bioinformatics and QC metrics fast5 filepath xs:token The location of the FAST5 file within a user's file system. Provide the filepath for the FAST5 file. This information aids in data management. /User/Documents/RespLab/Data/rona123assembly.fast5 - Bioinformatics and QC metrics number of base pairs sequenced xs:nonNegativeInteger The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 - Bioinformatics and QC metrics consensus genome length xs:nonNegativeInteger Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). 38677 - Bioinformatics and QC metrics Ns per 100 kbp xs:decimal 0 The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence. Provide a numerical value (no need to include units). 330 - Bioinformatics and QC metrics reference genome accession xs:token A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 reference_genome - Bioinformatics and QC metrics bioinformatics protocol xs:token The name and version number of the bioinformatics protocol used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can be provided in an SOP or protocol. Provide the name and version number of the protocol. https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members - Lineage and Variant information - Lineage and Variant information lineage/clade name xs:token The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. B.1.1.7 - Lineage and Variant information lineage/clade analysis software name xs:token The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Pangolin - Lineage and Variant information lineage/clade analysis software version xs:token The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 2.1.10 - Lineage and Variant information variant designation select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The variant classification of the lineage/clade i.e. variant, variant of concern. If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. Variant of Concern - Lineage and Variant information variant evidence xs:token The evidence used to make the variant determination. Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. RT-qPCR TaqPath assay: S gene target failure - Pathogen diagnostic testing - Pathogen diagnostic testing gene name 1 select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI E (orf4) diagnostic_gene_name_1 - Pathogen diagnostic testing diagnostic pcr protocol 1 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. EGenePCRTest 2 diagnostic_pcr_protocol_value_1 - Pathogen diagnostic testing diagnostic pcr Ct value 1 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the diagnostic RT-PCR test. 21 diagnostic_pcr_Ct_value_1 - Pathogen diagnostic testing gene name 2 select gene name 1 Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI nsp12 (RdRp) diagnostic_gene_name_2 - Pathogen diagnostic testing diagnostic pcr protocol 2 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. RdRpGenePCRTest 3 diagnostic_pcr_protocol_value_2 - Pathogen diagnostic testing diagnostic pcr Ct value 2 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 36 diagnostic_pcr_Ct_value_2 - Pathogen diagnostic testing gene name 3 select gene name 1 Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI nsp12 (RdRp) - Pathogen diagnostic testing diagnostic pcr protocol 3 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. RdRpGenePCRTest 3 - Pathogen diagnostic testing diagnostic pcr Ct value 3 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 - - NCBI SRA information - NCBI SRA information bioproject_accession xs:token prepopulate This will be populated by the PHA4GE field "bioproject accession". Populate the "bioproject accession" field. - NCBI SRA information sample_name xs:token prepopulate This will be populated by the PHA4GE field "biosample accession". Populate the "biosample accession" field. - NCBI SRA information library_ID xs:token prepopulate This will be populated by the PHA4GE field "library ID". Populate the "library ID" field. - NCBI SRA information title xs:token Short description that will identify the dataset on public pages. Format: {methodology} of {organism}: {sample info} Genomic sequencing of SARS-CoV-2: Nasopharynx (NP), Swab title - NCBI SRA information library_strategy select See NCBI SRA template for details. Provide the library strategy by selecting a value from the pick list. For amplicon sequencing select "AMPLICON". library_strategy - NCBI SRA information library_source select See NCBI SRA template for details. Provide the library source by selecting a value from the pick list. For amplicon sequencing select "Viral RNA". library_source - NCBI SRA information library_selection select See NCBI SRA template for details. Provide the library selection by selecting a value from the pick list. For amplicon sequencing select "PCR". library_selection - NCBI SRA information library_layout select See NCBI SRA template for details. Provide the library layout by selecting a value from the pick list. For Illumina instruments, select "PAIRED". For Oxford Nanopore instruments, select "SINGLE". library_layout - NCBI SRA information platform select prepopulate This will be populated by the PHA4GE field "sequencing instrument". Only a limited set of sequencing platforms are available in the NCBI pick list. If a value appears to be missing, contact PHA4GE and report the issue. - NCBI SRA information instrument_model select prepopulate This will be populated by the PHA4GE field "sequencing instrument". Only a limited set of sequencing instruments are available in the NCBI pick list. If a value appears to be missing, contact PHA4GE and report the issue. - NCBI SRA information filetype select See NCBI SRA template for details. Provide the filetype by selecting a value from the pick list. - NCBI SRA information filename xs:token See NCBI SRA template for details. Provide the filename recorded in the Bioinformatics and QC metrics section. - NCBI SRA information amplicon _PCR_primer_scheme xs:token prepopulate This will be populated by the PHA4GE field "amplicon PCR primer scheme". Populate the "amplicon PCR primer scheme" field. - NCBI SRA information amplicon_size xs:nonNegativeInteger prepopulate This will be populated by the PHA4GE field "amplicon size". Populate the "amplicon size" field. - NCBI SRA information sequencing_protocol_name xs:token prepopulate This will be populated by the PHA4GE field "sequencing protocol name". Populate the "sequencing protocol name" field. - NCBI SRA information raw_sequence_data_processing_method xs:token prepopulate This will be populated by the PHA4GE field "raw sequence data processing method". Populate the "raw sequence data processing method" field. - NCBI SRA information dehosting_method xs:token prepopulate This will be populated by the PHA4GE field "dehosting method". Populate the "dehosting method" field. - NCBI SRA information sequence_submitter_contact_email xs:token prepopulate This will be populated by the PHA4GE field "sequence submitter contact email". Populate the "sequence submitter contact email" field. - - Contributor acknowledgement - Contributor acknowledgement authors xs:token recommended Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors - Contributor acknowledgement DataHarmonizer provenance provenance DataHarmonizer provenance - - - umbrella bioproject accession PRJNA623807 - - -UO:0000035 host age unit month month -UO:0000036 host age unit year year - -UO:0000035 sample collection date precision year -UO:0000036 sample collection date precision month -UO:0000033 sample collection date precision day - -OBI:0000895 biomaterial extracted RNA (total) total RNA extract total RNA extract RNA extract OBI:0000880 -OBI:0000869 biomaterial extracted RNA (poly-A) polyA RNA extract polyA RNA extract, poly-A RNA extract RNA extract OBI:0000880 -OBI:0002627 biomaterial extracted RNA (ribo-depleted) ribosomal RNA-depleted RNA extract ribo-depleted RNA extract RNA extract OBI:0000880 - biomaterial extracted mRNA (messenger RNA) messenger RNA extract An extract which is the output of an extraction process in which messenger RNA molecules are isolated from a specimen. messenger RNA extract, mRNA extract, broader: cDNA extract, complementary DNA extract RNA extract OBI:0000880 "Make OBI term request in ""sequence"" tab - adjust fields to be suitable for OBI annotations. -Definition modelled on other `RNA extract` definitions but sitll needs review." -OBI:0002754 biomaterial extracted mRNA (cDNA) cDNA library processed material OBI:0000047 - - - signs and symptoms Abnormal lung auscultation Corrected spelling mistake "ausculation" -> "auscultation" -HP:0000223 signs and symptoms Abnormality of taste sensation Abnormality of taste sensation Abnormality of taste sensation "Abnormal nervous system physiology, -Abnormal tongue physiology" "HP:0012638, -HP:0030810" "Changed label to match the format of 'abnormality of the sense of smell'. - Rhiannon - -Removed ""label"" so it no longer shows up in the DH picklist as it was causing confusion and is more relevant to the ontology side than as a picklist value." - Abnormality of taste sensation Ageusia (complete loss of taste) The loss of taste functions of the tongue https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165999/ complete loss of taste, complete lack of taste Abnormality of taste sensation HP_0000223 New term - Recommend making term request to HPO -HP:0031249 Abnormality of taste sensation Parageusia (distorted sense of taste) Parageusia Dysgeusia, Metallic taste in mouth, Metallic taste, distorted sense of taste, distortion of the sense of taste Abnormality of taste sensation HP_0000223 Changed from 'Dysgeusia' to 'Parageusia' because that entry was in HP. - Rhiannon -HP_0000224 Abnormality of taste sensation Hypogeusia (reduced sense of taste) Decreased taste sensation The decrease in taste sensitivity. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165999/ Decreased taste, Lost taste, Decreased taste sensation, Hypogeusia, loss of taste, lack of taste, reduced sense of taste, new loss of taste Abnormality of taste sensation HP_0000223 "New term - -Recommend making syonym request to HPO" -HP:0004408 signs and symptoms Abnormality of the sense of smell Abnormality of the sense of smell Abnormal sense of smell, Abnormality of olfaction, Abnormality of the sense of smell, Smell defect "Abnormal nervous system physiology, -Abnormality of the nose" "HP:0012638, -HP:0000366" -HP_0000458 Abnormality of the sense of smell Anosmia (lost sense of smell) Anosmia Lost smell, Loss of smell, new loss of smell Abnormality of the sense of smell HP_0004408 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0010528 -HP_0004409 Abnormality of the sense of smell Hyposmia (reduced sense of smell) Hyposmia Decreased smell sensation, Sense of smell impaired, reduced sense of smell Abnormality of the sense of smell HP_0004408 - signs and symptoms Acute Respiratory Distress Syndrome ARDS Appears under 'signs/symptoms' most frequently. -HP:0011446 signs and symptoms Altered mental status Abnormality of higher mental function altered consciousness, altered mental status, altered mental state Abnormal nervous system physiology HP:0012638 "Changed label to 'Altered mental status' since that was the most common usage in case report forms. - -May want to consider alternate parent term. " -HP:0011675 signs and symptoms Arrhythmia Arrhythmia Abnormal heart rate, Cardiac arrhythmia, Heart rhythm disorders, Irregular heartbeat, Cardiac arrhythmias, Cardiac rhythm disturbances, Arrhythmias, Irregular heart beat Abnormality of cardiovascular system electrophysiology HP:0030956 -HP:0100543 Altered mental status Cognitive impairment Cognitive impairment Intellectual impairment, Mental impairment, Cognitive abnormality, Abnormality of cognition, Cognitive defects, Cognitive deficits, Cognitive impairment Abnormality of higher mental function HP:0011446 -HP_0001259 Altered mental status Coma Coma Reduced consciousness/confusion HP_0004372 -HP_0001289 Altered mental status Confusion Confusion mental confusion, new confusion, new or worsening confusion, layperson: disorientation, mental disorientation, easily confused Reduced consciousness/confusion HP_0004372 Removed 'new confusion' term from the picklist and added it here as a synonym. - Rhiannon -HP_0031258 Confusion Delirium (sudden severe confusion) Delirium Confusion HP_0001289 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0045057 - Altered mental status Inability to arouse (inability to stay awake) Needs further review -HP_0000737 Altered mental status Irritability Irritability Irritable, Irritability "Impaired social interactions, -Abnormal emotion/affect behavior" "HP_0000735, -HP_0100851" -HP_0002371 Altered mental status Loss of speech Loss of speech Neurological speech impairment HP_0002167 -HP_0025406 signs and symptoms Asthenia (generalized weakness) Asthenia general weakness, generalized weakness, abnormal physical weakness, loss of energy, weakness Constitutional symptom HP_0025142 Changed label from "Asthenia (general weakness)" to "Asthenia (generalized weakness)" to improve CNPHI compatibility. -HP:0031352 signs and symptoms Chest tightness or pressure Chest tightness Tightness in chest, chest pressure Constitutional symptom HP:0025142 -HP:0025145 Chest tightness or pressure Rigors (fever shakes) Rigors Rigours, fever shakes, severe shivering with chills, severe shaking with chills, repeated shaking with chills "Shivering, -Chills" "HP:0025144, -HP:0025143" consider adding/requesting parent term 'fever' -HP_0025143 signs and symptoms Chills (sudden cold sensation) Chills Constitutional symptom HP_0025142 - signs and symptoms Conjunctival injection Conjunctival hypermia -HP_0000509 signs and symptoms Conjunctivitis (pink eye) Conjunctivitis Pink eye "Inflammatory abnormality of the eye, -Abnormal conjunctiva morphology, -Red eye" "HP_0100533, -HP_0000502, -HP_0025337" Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0003799 - signs and symptoms Coryza -HP_0012735 signs and symptoms Cough Cough Coughing, Cough, new cough, worsening cough, new or worsening cough Functional respiratory abnormality HP_0002795 -HP:0031246 Cough Nonproductive cough (dry cough) Nonproductive cough dry cough, dry coughing Cough HP:0012735 -HP:0031245 Cough Productive cough (wet cough) Productive cough wet cough, cough with sputum production Cough HP:0012735 -HP:0000961 signs and symptoms Cyanosis (blueish skin discolouration) Cyanosis narrower: central cyanosis, peripheral cyanosis, related: hypoxima "Functional respiratory abnormality, -Dermatological manifestations of systemic disorders" "HP:0002795, -HP:0001005" "Caused by hypoxima, is related to covid toes/fingers. -Cyanosis is different from frostbite (chilblains) because it is rarely associated with pain." -HP:0001063 Cyanosis (blueish skin discolouration) Acrocyanosis Acrocyanosis Persistent blue color of hands, feet, or parts of face', related: peripheral cyanosis Cyanosis HP:0000961 Is characterized by 'peripheral cyanosis' but does not appear to be an exact synonym. - Acrocyanosis Circumoral cyanosis (bluish around mouth) Circumoral cyanosis Cyanosis HP:0000961 "Considered a type of acrocyanosis by healthline.com (ref other). HP currently lists it as a sister class to 'acrocyanosis'. -However, it doesn't seem to be a clear consensus on whether it gets defined under 'central cyanosis' or 'peripheral cyanosis' (for e.g. see 'other')." "https://www.healthline.com/health/circumoral-cyanosis#:~:text=Circumoral%20cyanosis%20refers%20to%20blue,on%20their%20hands%20and%20feet. -https://pubmed.ncbi.nlm.nih.gov/2797223/" - Acrocyanosis Cyanotic face (bluish face) cyanosis of the face "Acrocyanosis, -Central cyanosis" Didn't list it under 'central cyanosis' but it should be when ontologized. - Cyanosis (blueish skin discolouration) Central Cyanosis Bluish discoloration of the skin, mucous membranes, lips, tongue, and nail beds, associated with arterial desaturation. https://www.sciencedirect.com/topics/neuroscience/cyanosis - Central Cyanosis Cyanotic lips (bluish lips) Central cyanosis Has been stated to belong to 'central' and 'peripheral' cyanoses on different sources... Am only listing it under central at this time since some definitions of 'peripheral cyanosis' do not include lips. - Cyanosis (blueish skin discolouration) Peripheral Cyanosis Blues discoloration that occurs when there is increased oxygen uptake in peripheral tissues, often involving only the extremities; it is not associated with arterial desaturation. https://www.sciencedirect.com/topics/neuroscience/cyanosis cyanosis of the hands or feet, cyanosis of the extremities Characterizes 'acrocyanosis' but isn't considered an exact synonym. -HP_0002094 signs and symptoms Dyspnea (breathing difficulty) Dyspnea Difficult to breathe, Trouble breathing, Breathing difficulty, Abnormal breathing, Dyspnoea, shotness of breath Functional respiratory abnormality HP_0002795 "Recommend making syonym request to HPO -Changed name from 'Shortness of breath (breathing difficulty)' to 'Dyspnea (breathing difficulty)' incase a data curator has 'Dyspnea' in their collection data and they do not know that it is synonymous with 'Shortness of breath' and 'breathing difficulty'. - Rhiannon" -HP_0002014 signs and symptoms Diarrhea (watery stool) Diarrhea Watery stool, Diarrhea, Diarrhoea Abdominal symptom HP_0011458 In GenEpiO - signs and symptoms Dry gangrene -HP_0002383 signs and symptoms Encephalitis (brain inflammation) Encephalitis Brain inflammation, inflammation of the brain Unusual CNS infection HP_0011450 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0019956 - signs and symptoms Encephalopathy unspecified encephalopathy -HP_0012378 signs and symptoms Fatigue (tiredness) Fatigue Tiredness, Fatigue, Tired, new fatigue, worsening fatigue, new or worsening fatigue Constitutional symptom HP_0025142 In GenEpiO -HP_0001945 signs and symptoms Fever Fever Pyrexia, Hyperthermia, Fever, high body temperature, raised body temperature, elevated body temperature Abnormality of temperature regulation HP_0004370 In GenEpiO - Fever Fever (>=38°C) -HP:0000206 signs and symptoms Glossitis (inflammation of the tongue) - signs and symptoms Ground Glass Opacities (GGO) indicates abnormalities in the lungs - has even been identified in 'true' asymptomatic patients (i.e. not presymptomatic). -HP_0002315 signs and symptoms Headache Headache Headache, Headaches Abnormality of nervous system physiology HP_0012638 In GenEpiO -HP_0002105 signs and symptoms Hemoptysis (coughing up blood) Hemoptysis Haemoptysis, Coughing up blood Abnormal sputum HP_0032016 -HP:0012417 signs and symptoms Hypocapnia Hypocapnia reduced carbon dioxide in the blood, hapocarbia, hypocapnea, narrower: deeply hypocapnic, normo/hypercapnic Abnormal blood carbon dioxide level HP:0500164 -HP_0002615 signs and symptoms Hypotension (low blood pressure) Hypotension Arterial hypotension, Low blood pressure Abnormal systemic blood pressure HP_0030972 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0005468 -HP_0012418 signs and symptoms Hypoxemia (low blood oxygen) Hypoxemia Low blood oxygen level, oxygen deficiency in arterial blood, low level of oxygen in the blood, narrower: severe hypoxemia, silent hypoxemia, related: Hypoxia, Cyanosis Abnormal blood oxygen level HP_0500165 "Could also add ""Hypoxia"" and ""Silent Hypoxia"" (also associated with SARS-CoV-2). - -HP comment ""Note that hypoxemia is defined as a condition where arterial oxygen tension is below normal (80-100mmHg). Hypoxia is defined as the failure of oxygenation at the tissue level. Hypoxia is not measured directly by a standard laboratory value"" - -Leads to cyanosis - Rhiannon" - Hypoxemia (low blood oxygen) Silent hypoxemia An abnormally low level of blood oxygen incompatible with life without dyspnea. https://doi.org/10.1164/rccm.202006-2157CP laymans: happy hypoxia, related: hypocapnia An abnormally low level of blood oxygen incompatible with life without dyspnea. HP New Term Request -HP:0011029 signs and symptoms Internal hemorrhage (internal bleeding) Internal hemorrhage Internal haemorrhage Internal bleeding "Abnormality of blood circulation, -Abnormal bleeding" "HP:0011028, -HP:0001892" -NCIT:C121416 signs and symptoms Loss of Fine Movements Loss of Fine Movements Loss of fine movements, Loss of Fine Movements Clinical or Research Assessment Answer NCIT:C91106 "Could ask HP to add if we don't want to use NCIT. - -Should consider adding broader 'loss of movement'" -HP_0004396 signs and symptoms Low appetite Poor appetite Decreased appetite, Poor appetite, loss of appetite, low appetite, anorexia Abdominal symptom HP_0011458 "In GenEpiO. -Could use 'Anorexia' which is also in HP (not refering to anorexia nervosa) - or request it with this term?" - signs and symptoms Malaise (general discomfort/unease) Malaise A general feeling of discomfort, illness, or lack of well-being. https://medlineplus.gov/ency/article/003089.htm general discomfort/unease, general uneasiness, general discomfort, general unease, out-of-sorts feeling "New term - -Recommend making term request to HPO (note they already have it as ""related synonym"" to ""Fatigue""" - signs and symptoms Meningismus/nuchal rigidity -HP_0001324 signs and symptoms Muscle weakness Muscle weakness Abnormal muscle physiology HP_0011804 Recommend changing this to 'muscle weakness' as 'weakness' could be mistakenly used when the intention is to refer to 'asthenia' which is weakness/exhaustion in the absence of true muscle weakness. - Rhiannon -HP_0001742 signs and symptoms Nasal obstruction (stuffy nose) Nasal obstruction Obstruction of nose, Stuffy nose, Blockage of nose, Nasal obstruction, Nasal blockage, nasal congestion Abnormality of the nose HP_0000366 Recommend making syonym request to HPO -HP_0002018 signs and symptoms Nausea Nausea Nausea and vomiting HP_0002017 In GenEpiO - signs and symptoms nose bleed - signs and symptoms otitis - signs and symptoms Pain -HP:0002027 Pain Abdominal pain Abdominal pain Stomach pain, Abdominal pain, Pain in stomach, abdominal ache, belly ache, bellyache, narrower: stomach ache, stomachache, abdominal cramping? "Abdominal symptom, -Pain" "HP:0011458, -HP:0012531" -HP_0002829 Pain Arthralgia (painful joints) Arthralgia painful joints, joint pain, joint inflammation, related: Arthritic pain, Joint pains, arthritis Pain HP_0012531 Don't use HP entry 'Arthralgia/arthritis' (HP:0005059) as it is refering to the disease diagnosis not the symptom. -HP_0100749 Pain Chest pain Chest pain Chest pain, Thoracic pain Pain HP_0012531 Could add synonyms 'perisstent chest pain' but I'm not sure if this term is meant to be narrow enough to represent presistent vs acute. Could also consider 'chest pain' synonymous with 'chest pressure' instead of 'chest tightness'. - Rhiannon - Chest pain Pleuritic chest pain pleursy -HP_0003326 Pain Myalgia (muscle pain) Myalgia Muscle ache, Muscle pain, aches and pains, body aches Pain HP_0012531 In GenEpiO -HP_0025439 signs and symptoms Pharyngitis (sore throat) Pharyngitis sore throat, pharyngalgia, pharyngodynia Abnormality of the pharynx HP_0000600 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0002258 - signs and symptoms Pharyngeal exudate - signs and symptoms Pleural effusion https://www.researchgate.net/publication/340720955_Pleural_effusion_as_an_initial_sign_of_coronavirus_disease_2019_COVID-19_pneumonia_a_case_report -HP:0002090 signs and symptoms Pneumonia Pneumonia Pneumonia "Respiratory tract infection, -Increased inflammatory response" "HP:0011947, -HP:0012649" Considered a sign/symptom on two case report forms. - signs and symptoms Prostration Appears on a provincial case report form. - signs and symptoms Pseudo-chilblains chilblains-like symptom, chilblains-like lesions, related: chilblains, chill burns, pernio, perniosis, broader: acro-ischemia, acrosyndromes, peripheral cyanosis? Inflammatory abnormality of the skin Revisit broader synonyms. Have address chilblains in HP but not pseudo-chilblains. #5822 - Pseudo-chilblains Pseudo-chilblains on fingers (covid fingers) chilblains-like fingers, chilblains-like finger lesions, related: chilblains, chill burns, pernio, perniosis, finger cyanosis, broader: acro-ischemia, acrosyndromes, peripheral cyanosis? Revisit broader synonyms. - Pseudo-chilblains Pseudo-chilblains on toes (covid toes) chilblains-like toes, chilblains-like toe lesions, related: chilblains, chill burns, pernio, perniosis, toe cyanosis broader: acro-ischemia, acrosyndromes, peripheral cyanosis? Revisit broader synonyms. -HP_0000988 signs and symptoms Rash Skin rash exanthem, skin rash, rash "Abnormality of skin morphology, -Inflammatory abnormality of the skin" "HP_0011121, -HP_0011123" E.g. "COVID toes". -HP_0031417 signs and symptoms Rhinorrhea (runny nose) Rhinorrhea Runny Nose, Nasal Discharge Abnormal nasal mucus secretion HP_0031416 -HP_0001250 signs and symptoms Seizure Seizure Epileptic seizure, Seizures Abnormal nervous system physiology HP_0012638 -HP:0020219 Seizure Motor seizure Motor seizure Seizure HP:0001250 -HP:0025144 signs and symptoms Shivering (involuntary muscle twitching) Shivering Shivering, Shuddering Constitutional symptom HP:0025142 -HP_0001350 signs and symptoms Slurred speech Slurred speech Abnormality of coordination HP_0011443 "In GenEpiO. - -Discuss whether this should go under 'altered consicousness' (is not currently organized as such in HP). - Rhiannon" - signs and symptoms Sneezing - signs and symptoms Sputum Production -HP:0001297 signs and symptoms Stroke Stroke Stroke Cerebrovascular accident Cerebral vascular events Abnormality of the cerebral vasculature HP:0100659 - signs and symptoms Swollen Lymph Nodes -HP_0002789 signs and symptoms Tachypnea (accelerated respiratory rate) Tachypnea Increased respiratory rate or depth of breathing, Polypnea, rapid breathing, accelerated respiratory rate Abnormal pattern of respiration HP_0002793 Changed to 'Tachypnea (accelerated respiratory rate)' as that form occurs 4/5 times on the case report forms. - signs and symptoms Vertigo (dizziness) Vertigo -HP_0002013 signs and symptoms Vomiting (throwing up) Vomiting Throwing up, Vomiting, Emesis Nausea and vomiting HP_0002017 "In GenEpiO -Has subclasses: Episodic vomiting, Feculent vomiting, Projectile vomiting" - - host vaccination status Fully Vaccinated prior_SARS-CoV-2_vaccination:Yes - host vaccination status Partially Vaccinated prior_SARS-CoV-2_vaccination:Yes - host vaccination status Not Vaccinated prior_SARS-CoV-2_vaccination:No - - prior SARS-CoV-2 antiviral treatment Prior antivrial treatment prior_SARS-CoV-2_antiviral_treatment:Yes - prior SARS-CoV-2 antiviral treatment No prior antivrial treatment prior_SARS-CoV-2_antiviral_treatment:No - prior SARS-CoV-2 antiviral treatment Unknown - - - - pre-existing conditions and risk factors Age 60+ - pre-existing conditions and risk factors Anemia - pre-existing conditions and risk factors Anorexia https://www.uptodate.com/contents/coronavirus-disease-2019-covid-19-arrhythmias-and-conduction-system-disease - pre-existing conditions and risk factors Birthing labor labor, labour - pre-existing conditions and risk factors Bone marrow failure - pre-existing conditions and risk factors Cancer malignancy Malignancy' is more common than 'cancer' on case collection forms. - Cancer Breast cancer - Cancer Colorectal cancer - Cancer Hematologic malignancy - Cancer Lung cancer - Cancer Metastatic disease - pre-existing conditions and risk factors Cancer treatment - Cancer treatment Cancer surgery - Cancer treatment Chemotherapy - Chemotherapy Adjuvant chemotherapy - pre-existing conditions and risk factors Cardiac disorder -HP:0011675 Cardiac disorder Arrhythmia Arrhythmia Abnormal heart rate, Cardiac arrhythmia, Heart rhythm disorders, Irregular heartbeat, Cardiac arrhythmias, Cardiac rhythm disturbances, Arrhythmias, Irregular heart beat Abnormality of cardiovascular system electrophysiology HP:0030956 - Cardiac disorder Cardiac disease cardiovascular disease, cardio-vascular disease, heart disease -HP:0001638 Cardiac disorder Cardiomyopathy Disease of the heart muscle Abnormal myocardium morphology HP:0001637 - Cardiac disorder Cardiac injury - Cardiac disorder Hypertension (high blood pressure) arterial hypertension -HP:0002615 Cardiac disorder Hypotension (low blood pressure) Hypotension Arterial hypotension, Low blood pressure Abnormal systemic blood pressure HP_0030972 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0005468 - pre-existing conditions and risk factors Cesarean section - pre-existing conditions and risk factors Chronic cough - pre-existing conditions and risk factors Chronic gastrointestinal disease chronic GI disease - pre-existing conditions and risk factors Chronic lung disease - pre-existing conditions and risk factors Corticosteroids - pre-existing conditions and risk factors Diabetes mellitus (diabetes) - Diabetes mellitus (diabetes) Type I diabetes mellitus (T1D) Insulin dependent diabetes mellitus (IDDM), juvenille diabetes - Diabetes mellitus (diabetes) Type II diabetes mellitus (T2D) adult-onset diabetes - pre-existing conditions and risk factors Eczema - pre-existing conditions and risk factors Electrolyte disturbance - Electrolyte disturbance Hypocalcemia - Electrolyte disturbance Hypokalemia - Electrolyte disturbance Hypomagnesemia -HP:0002383 pre-existing conditions and risk factors Encephalitis (brain inflammation) Encephalitis Brain inflammation, inflammation of the brain Unusual CNS infection HP_0011450 Also in MONDO (ref. "Other") http://purl.obolibrary.org/obo/MONDO_0019956 - pre-existing conditions and risk factors Epilepsy - pre-existing conditions and risk factors Hemodialysis - pre-existing conditions and risk factors Hemoglobinopathy - pre-existing conditions and risk factors Human immunodeficiency virus (HIV) - Human immunodeficiency virus (HIV) Acquired immunodeficiency syndrome (AIDS) Stage 4 HIV - Human immunodeficiency virus (HIV) HIV and antiretroviral therapy (ART) narrower: HIV antiretroviral medication, HIV antiretroviral drug - pre-existing conditions and risk factors Immunocompromised narrower: immune deficiencies, immunosupressants - Immunocompromised Lupus systemic lupus erythematosus - pre-existing conditions and risk factors Inflammatory bowel disease (IBD) IBD, IBS, inflammatory bowel syndrome - Inflammatory bowel disease (IBD) Colitis - Colitis Ulcerative colitis - Inflammatory bowel disease (IBD) Crohn's disease - pre-existing conditions and risk factors Renal disorder kidney disorder - Renal disorder Renal disease kidney disease - Renal disorder Chronic renal disease chronic kidney disease - Renal disorder Renal failure kidney failure - pre-existing conditions and risk factors Liver disease hepatic disease - Liver disease Chronic liver disease - Chronic liver disease Fatty liver disease (FLD) Hepatic steatosis -HP:0003326 pre-existing conditions and risk factors Myalgia (muscle pain) Myalgia Muscle ache, Muscle pain, aches and pains, body aches Pain HP_0012531 In GenEpiO - pre-existing conditions and risk factors Myalgic encephalomyelitis (ME) chronic fatigue syndrome (CFS) - pre-existing conditions and risk factors Neurological disorder nervous system disorder - Neurological disorder Neuromuscular disorder - pre-existing conditions and risk factors Obesity - Obesity Severe obesity morbid obesity - pre-existing conditions and risk factors Respiratory disorder - Respiratory disorder Asthma - Respiratory disorder Chronic bronchitis - Respiratory disorder Chronic pulmonary disease chronic respiratory condition - Chronic pulmonary disease Chronic obstructive pulmonary disease - Respiratory disorder Emphysema - Respiratory disorder Lung disease - Lung disease Chronic lung disease - Lung disease Pulmonary fibrosis -HP:0002090 Respiratory disorder Pneumonia Pneumonia Pneumonia "Respiratory tract infection, -Increased inflammatory response" "HP:0011947, -HP:0012649" - Respiratory disorder Respiratory failure - Respiratory failure Adult respiratory distress syndrome - Respiratory failure Newborn respiratory distress syndrome - Respiratory disorder Tuberculosis - pre-existing conditions and risk factors Postpartum (≤6 weeks) All case forms specific ≤6 weeks - pre-existing conditions and risk factors Pregnancy pregnant person Gestation or trimester information usually requested - pre-existing conditions and risk factors Rheumatic disease - pre-existing conditions and risk factors Sickle cell disease - pre-existing conditions and risk factors Substance use Could instead go with 'substance user' - Substance use Alcohol abuse Could instead go with 'alcohol abuser' - Substance use Drug abuse Could instead go with 'drug abuser/user' - Drug abuse Injection drug abuse intravenous drug abuse Could instead go with 'injection drug abuser/user' - Substance use Smoking Could instead go with 'smoker' - Substance use Vaping Could instead go with 'vape user' -HP:0002789 pre-existing conditions and risk factors Tachypnea (accelerated respiratory rate) Tachypnea Increased respiratory rate or depth of breathing, Polypnea, rapid breathing, accelerated respiratory rate Abnormal pattern of respiration HP_0002793 - pre-existing conditions and risk factors Transplant transplant recipient? - Transplant Bone marrow transplant Alt: 'History of Bone Marrow Transplant' which is the label HP uses. - Transplant Cardiac transplant heart transplant - Transplant Hematopoietic stem cell transplant (HSCT) hematopoietic cell transplantation - Transplant Kidney transplant - Transplant Liver transplant - - variant designation Variant of Concern (VOC) - variant designation Variant of Interest (VOI) - - complications Abnormal blood oxygen level O2 saturation <=95% Case report forms frequently record "O2 saturation <=95%". "The generally accepted standard is that a normal resting oxygen saturation of less than 95% is considered abnormal" (https://www.ncbi.nlm.nih.gov/books/NBK525974/) - complications Acute respiratory failure -HP:0011675 complications Arrhythmia (complication) Arrhythmia Abnormal heart rate, Cardiac arrhythmia, Heart rhythm disorders, Irregular heartbeat, Cardiac arrhythmias, Cardiac rhythm disturbances, Arrhythmias, Irregular heart beat Abnormality of cardiovascular system electrophysiology HP:0030956 - Arrhythmia (complication) Tachycardia May be considered synonymous with tachyarrhythmia (Ref other) - recommend looking into it further. https://en.wikipedia.org/wiki/Tachycardia - Tachycardia Polymorphic ventricular tachycardia (VT) - Tachycardia Tachyarrhythmia broader: narrower complex tachycardia (NCT), wide complex tachycardia https://www.sciencedirect.com/topics/medicine-and-dentistry/tachyarrhythmia#:~:text=Introduction,tachycardia%20(%E2%89%A5120%20ms). - complications Noncardiogenic pulmonary edema https://pubmed.ncbi.nlm.nih.gov/31194387/ - Noncardiogenic pulmonary edema Acute respiratory distress syndrome (ARDS) - Acute respiratory distress syndrome (ARDS) COVID-19 associated ARDS (CARDS) - Acute respiratory distress syndrome (ARDS) Neurogenic pulmonary edema (NPE) Do note equate to 'High Altitude Pulmonary Edema' (HAPE) as some are doing; they some of the symptoms may be similar, what's occuring in the lungs is significantly different. - complications Cardiac injury cardiac trauma https://www.gehealthcare.ca/en-CA/article/cardiac-complications-of-covid-19-signs-to-watch-for-on-the-ecg - complications Cardiac arrest - complications Cardiogenic shock - complications Blood clot - Blood clot Arterial clot - Blood clot Deep vein thrombosis (DVT) - Blood clot Pulmonary embolism (PE) -HP:0001638 complications Cardiomyopathy Disease of the heart muscle Abnormal myocardium morphology HP:0001637 - complications Central nervous system invasion Central nervous system invasion by SARS-CoV-2 - complications Stroke (complication) cerebrovascular event - Stroke (complication) Central Nervous System Vasculitis CNS vasculitis - Stroke (complication) Ischemic stroke - Ischemic stroke Acute ischemic stroke - complications Coma - complications Convulsions - complications COVID-19 associated coagulopathy (CAC) chronic, likely caused by DIC - complications Cystic fibrosis CF - complications Cytokine release syndrome cytokine storm, CRS, inflammatory storm - complications Disseminated intravascular coagulation (DIC) can often be the cause of blood clots in covid19 cases - complications Encephalopathy - complications Fulminant myocarditis - complications Guillain-Barré syndrome - complications Internal hemorrhage (complication; internal bleeding) - Internal hemorrhage (complication; internal bleeding) Intracerebral haemorrhage ICH - complications Kawasaki disease chronic - Kawasaki disease Typical Kawasaki disease - Kawasaki disease Incomplete Kawasaki disease - complications Kidney injury - Kidney injury Acute kidney injury AKI - complications Liver dysfunction - complications Liver injury liver damage - Liver injury Acute liver injury - complications Lung injury - Lung injury Acute lung injury - complications Meningitis - complications Migraine - complications Miscarriage - complications Multisystem inflammatory syndrome in children (MIS-C) pediatric multisystem inflammatory syndrome (PMIS), PIMS similar signs/symptoms to those of toxic shock syndrome or Kawasaki disease. - complications Muscle injury - complications Myalgic encephalomyelitis (ME) chronic fatigue syndrome (CFS) - complications Myocardial infarction (heart attack) MI - Myocardial infarction (heart attack) Acute myocardial infarction - Myocardial infarction (heart attack) Elevation myocardial infarction - Myocardial infarction (heart attack) ST-segment elevation myocardial infarction - complications Myocardial injury - complications Neonatal complications - complications Organ failure - Organ failure Heart failure not synonymous with 'cardciac arrest' - Organ failure Liver failure - complications Paralysis - complications Pneumothorax (collapsed lung) - Pneumothorax (collapsed lung) Spontaneous pneumothorax - Pneumothorax (collapsed lung) Spontaneous tension pneymothorax - complications Pneumonia (complication) - Pneumonia (complication) COVID-19 pneumonia COVID-19 infected pneumonia Redundant? - complications Pregancy complications pregnancy issues - complications Rhabdomyolysis - complications Secondary infection - Secondary infection Secondary staph infection - Secondary infection Secondary strep infection -HP:0001250 complications Seizure (complication) Seizure Epileptic seizure, Seizures Abnormal nervous system physiology HP_0012638 -HP:0020219 Seizure (complication) Motor seizure Motor seizure Seizure HP:0001250 - complications Sepsis - complications Septicemia - complications Shock - Shock Hyperinflammatory shock - Shock Refractory cardiogenic shock RCS - Shock Refractory cardiogenic plus vasoplegic shock - Shock Septic shock - complications Vasculitis inflammed blood vessels - complications Ventilation induced lung injury (VILI) - - sample collected in quarantine Yes - sample collected in quarantine No - sample collected in quarantine Unknown - - -UBERON_0000178 anatomical material Blood blood organism substance UBERON_0000463 Use UBERON term. -UBERON_0006314 anatomical material Fluid bodily fluid organism substance, portion of body substance, body substance, body fluid or substance, portion of organism substance organism substance UBERON_0000463 Use UBERON term. -UBERON_0001836 Fluid Saliva saliva spit, broader: oral fluid organism substance UBERON_0000463 "Use UBERON term. Add synonym. (ISSUE: People may be using this rather than more properly referencing oral fluid). - -Added ""oral fluid"" as a broader synonym since people are using them synonymously. - Rhiannon" -UBERON_0001359 Fluid Fluid (cerebrospinal (CSF)) cerebrospinal fluid organism substance UBERON_0000463 Use UBERON term. -UBERON_0002409 Fluid Fluid (pericardial) pericardial fluid organism substance UBERON_0000463 Use UBERON term. -UBERON_0001087 Fluid Fluid (pleural) pleural fluid organism substance UBERON_0000463 Use UBERON term. -UBERON_0036243 Fluid Fluid (vaginal) vaginal fluid vaginal secretion, vaginal discharge bodily fluid UBERON_0006314 Use UBERON term. -UBERON_0000173 Fluid Fluid (amniotic) amniotic fluid organism substance UBERON_0000463 Use UBERON term. -UBERON_0000479 anatomical material Tissue tissue material anatomical entity UBERON_0000465 Use UBERON term. - - - -UBERON_0001245 anatomical part Anus anus anal opening, anal orifice, opening of terminal part of digestive tract - anatomical part Buccal mucosa -UBERON_0002114 anatomical part Duodenum duodenum -UBERON_0000970 anatomical part Eye eye - anatomical part Intestine -UBERON_0001052 anatomical part Rectum rectum terminal portion of intestine -UBERON_0001003 anatomical part Skin skin epidermis -UBERON_0000945 anatomical part Stomach stomach -UBERON_0001557 anatomical part Upper respiratory tract upper respiratory tract -UBERON_2001427 Upper respiratory tract Anterior Nares anterior naris -UBERON_0001043 Upper respiratory tract Esophagus esophagus oesophagus, gullet -UBERON_0002453 Upper respiratory tract Ethmoid sinus ethmoid sinus ethmoidal sinus, ethmoidal bone sinus paranasal sinus - Upper respiratory tract Nasal Cavity -UBERON_0005921 Nasal Cavity Middle Nasal Turbinate middle nasal concha middle nasal turbinate, middle turbinate, mid-nasal turbinate, nasal mid-turbinate, NMT Found UBERON entry "middle nasal concha" which is an exact synonym, but I think we should use "middle nasal turbinate" or "mid-nasal turbinate" since those are closer to the clincal usage forms (e.g. Mid-turbinate swab, Nasal mid-turbinate (NMT) swab, Deep Nasal Swab). https://www.fda.gov/media/136314/download -UBERON_0005922 Nasal Cavity Inferior Nasal Turbinate inferior nasal concha inferior nasal turbinate -UBERON_0001728 Upper respiratory tract Nasopharynx (NP) nasopharynx -UBERON_0001729 Upper respiratory tract Oropharynx (OP) oropharynx The area of the throat that gets swabbed. -UBERON_0001558 anatomical part Lower respiratory tract lower respiratory tract -UBERON_0002185 Lower respiratory tract Bronchus bronchus bronchial trunk, bronchi, bronchial tissue, respiratory tube UBERON_0000117 -UBERON_0002048 Lower respiratory tract Lung lung -UBERON_0002186 Lung Bronchiole bronchiole lobular bronchiole, bronchioli, bronchiolus, respiratory tube UBERON_0000117 -UBERON_0002169 Lung Alveolar sac alveolar sac respiratory tube UBERON_0000117 -UBERON_0009778 Lower respiratory tract Pleural sac pleural sac Perhaps not necessary. -UBERON_0002402 Pleural sac Pleural cavity pleural cavity Contains pleural fluid which gets collected for sampling. -UBERON_0003126 Lower respiratory tract Trachea trachea - - - - -UBERON_0001988 body product Feces feces stool, faeces Could form relationship with "feces collection" from GenEpiO. -UBERON_0001088 body product Urine urine -UBERON_0001089 body product Sweat sweat -UBERON_0000912 body product Mucus mucus mucosa -UBERON_0007311 Mucus Sputum sputum deep mucus, phlegm "Would this be better suited for ""body product sampled""? Moved from ""anatomical material sampled"" to body product sampled"", since the later contains ""mucus"" and sputums is a narrower synonym of ""mucus"". - -Could form relationship with ""sputum collection"" from GenEpiO." -UBERON_0001827 body product Tear secretion of lacrimal gland ocular secretion, tears, tear fluid, narrower: precorneal tear film (PCTF), basal tear, reflex tear, closed eye tear, eye-flush tear -UBERON_0006530 body product Fluid (seminal) seminal fluid seminal plasma "secretion of exocrine gland, -male reproductive gland secretion" "UBERON_0000456, -UBERON_0006536" "Would this be better under ""body product""? -Rhiannon - -Use UBERON term." -UBERON_0001913 body product Breast Milk milk bodily fluid, mammary gland fluid/secretion UBERON_0006314, UBERON_0006539 Use UBERON term. - - - - - environmental material Air vent air vent An opening that allows air to pass out of or into a confined space. https://www.lexico.com/definition/air_vent building part ENVO_01000420 new term -ENVO_00003896 environmental material Banknote currency note no def. - environmental material Bed rail bed rail A rail on the side of a bed designed to provide protection and security to individuals who cannot reliably support themselves, and can also be used as a precautionary measure for those who will be limited their bed for an extended period of time. https://www.1800wheelchair.ca/category/bed-rails/ bed railing, bedrail new term -ENVO_01000486 environmental material Building floor building floor -ENVO_02000058 environmental material Cloth cloth A textile comprised of a pliable material made usually by weaving, felting, or knitting natural or synthetic fibers and filaments. [ URL:http://www.merriam-webster.com/dictionary/cloth ] - environmental material Control panel control panel A dashboard full of buttons, levers and dials for configuring and controlling the equipment. https://www.yourdictionary.com/control-panel new term. -NCIT_C48950 environmental material Door Door not a good def. suggest: A hinged, sliding, or revolving barrier at the entrance to a building, room, or vehicle, or in the framework of a cupboard. https://www.lexico.com/en/definition/door add term to genepio. not a good definition - environmental material Door handle A mechanism used to open or close a door. https://en.wikipedia.org/wiki/Door_handle door knob - environmental material Face mask Face mask A disposable mask worn by health professionals during procedures in surgery and nursing. https://en.wikipedia.org/wiki/Surgical_mask surgical mask, procedure mask, medical mask new term - environmental material Face shield Face shield Personal protective equipment (PPE) that provides barrier protection to the facial area and related mucous membranes (eyes, nose, lips). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015006/ new term -FOODON:00002403 environmental material Food -FOODON:03490100 environmental material Food packaging -ENVO:01000481 environmental material Glass term also in FoodOn (FOODON_03500040) - environmental material Handrail handrail A rail fixed to posts or a wall for people to hold on to for support. https://www.lexico.com/en/definition/handrail new term. this term and bed rail could be put under ncit term "rail device" NCIT_C50130. would also need to be introduced into genepio - environmental material Hospital gown Hospital gown A long loose piece of clothing worn in a hospital by someone doing or having an operation, and is often used as clothing for bedridden patients. https://en.wikipedia.org/wiki/Patient_gown patient gown, johnny gown new term - environmental material Light switch Light switch A switch most commonly used to operate electric lights, permanently connected equipment, or electrical outlets. https://en.wikipedia.org/wiki/Light_switch new term - environmental material Locker Locker A small lockable closet or compartment, typically as one of a number placed together for public or general use, https://www.lexico.com/en/definition/locker - environmental material N95 mask N95 mask A particulate-filtering facepiece respirator that meets the U.S. National Institute for Occupational Safety and Health (NIOSH) N95 classification of air filtration, meaning that it filters at least 95% of airborne particles. https://en.wikipedia.org/wiki/N95_mask N95 respirator new term for OBI? - environmental material Nurse call button Nurse call button A button or cord found in hospitals and nursing homes, that allow patients in health care settings to alert a nurse or other health care staff member remotely of their need for help. Thay are usually found in places where patients are at their most vulnerable, such as beside their bed and in the bathroom. https://en.wikipedia.org/wiki/Nurse_call_button Call bell, hospital call bell new term - environmental material Paper Material manufactured in thin sheets from the pulp of wood or other fibrous substances, used for writing, drawing, or printing on, or as wrapping material. https://www.lexico.com/en/definition/paper paper product ENVO_00003895 new term for ENVO? -ENVO:01000060 environmental material Particulate matter -ENVO:01000404 environmental material Plastic term also in FoodOn (FOODON_03500036) - environmental material PPE gown PPE gown A type of gown worn by medical professionals in order to provide a barrier between patient and professional, and usually zips up at the back. https://en.wikipedia.org/wiki/PPE_gown personal protective equipment gown new term (NOT for OMIT). OBI? -ENVO_00002018 environmental material Sewage sewage -ENVO_01000990 environmental material Sink sink fixture sink -ENVO_00001998 environmental material Soil soil - environmental material Stainless steel new term for ENVO. Don't use OMIT_0014071 - it is a quality! - environmental material Tissue paper tissue paper Soft paper used for various purposes such as cleaning or as toilet tissue. https://www.dictionary.com/browse/tissue new term for ENVO - environmental material Toilet bowl Toilet bowl The bowl of a toilet that can be flushed with water, used for defecation and urination. https://www.thefreedictionary.com/toilet+bowl new term -ENVO_00002006 environmental material Water water CHEBI_15377 is not the best term - its referencing a chemical compound. BEST use ENVO: ENVO_00002006 which is environmental water - environmental material Wastewater - environmental material Window Window An opening in the wall or roof of a building or vehicle that is fitted with glass or other transparent material in a frame to admit light or air and allow people to see out. https://www.lexico.com/en/definition/window new term. existing usages of "window" are different. -ENVO:00002040 environmental material Wood wood The hard fibrous material that forms the main substance of the trunk or branches of a tree or shrub, used for fuel or timber. https://www.lexico.com/en/definition/wood add definition - - environmental site Acute care facility Acute care facility A facility where a patient receives active but short-term treatment for a severe injury or episode of illness, an urgent medical condition, or during recovery from surgery. https://en.wikipedia.org/wiki/Acute_care building ENVO_00000073 new term. this should be parental term for hospital, urgent care facility, ambulatory care facility -ENVO:00003040 environmental site Animal house animal house this defintion is too vague. suggest: Any kind of shelter, refuge affording protection to animals. https://www.eionet.europa.eu/gemet/en/concept/428 add better def? -ENVO:01000422 environmental site Bathroom bathroom - environmental site Clinical assessment centre building ENVO_00000073 - environmental site Conference venue The building where a conference is held. Emma building ENVO_00000073 new term -ENVO REQUEST environmental site Corridor building corridor A long passage in a building from which doors lead into rooms. https://www.lexico.com/en/definition/corridor hallway, broader: hall, passage building part ENVO:01000420 "new term. -2020-07-14 - Moved from 'environmental material' to 'environmental site'/'environmental feature' -Moved 'hall' to broader synonym since it is not an exact synonym." -ENVO_01000927 environmental site Daycare day care building daycare add synonym -NCIT_C53513 environmental site Emergency room (ER) Emergency Room ER, building ENVO_00000073 missing in genepio. should be housed in envo. - environmental site Family practice clinic Family practice clinic A clinic where family physicians deliver a range of acute, chronic and preventive medical care services. https://en.wikipedia.org/wiki/Family_medicine family care clinic, general practice clinic, family medicine clinic, general medicine clinic building ENVO_00000073 new term. - environmental site Group home Group home A residential facility with the purpose of housing multiple residents with particular care needs. https://en.wikipedia.org/wiki/Group_home building ENVO_00000073 new term. - environmental site Homeless shelter Homeless shelter A type of homeless service agency which provide temporary residence for homeless individuals and families. https://en.wikipedia.org/wiki/Homeless_shelter building ENVO_00000073 new term -OBI_0000844 environmental site Hospital hospital building ENVO_00000073 -NCIT_C53511 environmental site Intensive Care Unit (ICU) Intensive Care Unit building ENVO_00000073 missing in genepio. should be housed in envo. -GENEPIO_0001035 environmental site Long Term Care Facility long term care facility LTC, LTCF, Long-Term Care Facility building ENVO_00000073 add synonyms, need new parental term (see below for details) - environmental site Patient room Patient room / or examination room? or patient bed area? Room occupied by one or more individuals during a stay in a health facility. http://www.reference.md/files/D010/mD010362.html new term -ENVO_01001481 environmental site Prison public prision A facility in which inmates (or prisoners) are forcibly confined and denied a variety of freedoms under the authority of the state. https://en.wikipedia.org/wiki/Prison correctional facility, penitentiary, detention center, detention centre, correctional center, correctional centre, lock-up, remand center, remand centre; broad synonym jail, gaol building ENVO_00000073 new term. <- Why? envo has "public prision" ENVO_01001481. term is misspelled. <- put in an ISSUES request to ENVO to fix spelling. -ENVO_01000536 environmental site Production Facility Factory Production Facility building ENVO_00000073 add synonym. food production facility (currently under "building" should go under "factory" as it's a type of factory) -NCIT_C17118 environmental site School School building ENVO_00000073 not in genepio - environmental site Sewage Plant - environmental site Subway train Subway train A type of high-capacity public transport generally found in urban areas. https://en.wikipedia.org/wiki/Rapid_transit subway, rapid transit, metro, heavy rail train PCO_1001178 new term in ENVO - environmental site Wet market Wet market A marketplace selling fresh meat, fish, produce, and other perishable goods as distinguished from "dry markets" that sell durable goods such as fabric and electronics. Not all wet markets sell live animals, but the term wet market is sometimes used to signify a live animal market in which vendors slaughter animals upon customer purchase. https://en.wikipedia.org/wiki/Wet_market market GENEPIO_0001022 new term - -NCIT:C52009 collection method Amniocentesis Amniocentesis collecting specimen from organism OBI_0600005 A prenatal diagnostic sample of amniotic fluid that isn't commonly done for SARS-CoV-2 but has been done. -NCIT:C15631 collection method Aspiration Aspiration aspirate, narrower: fine needle aspiration, nasopharyngeal aspiration, tracheal aspiration, endotracheal aspirate collecting specimen from organism OBI_0600005 - Aspiration Suprapubic Aspiration - Aspiration Tracheal aspiration TA - Aspiration Vacuum Aspiration Suction Aspiration -OBI:0002650 collection method Biopsy Biopsy A specimen collection that obtains a sample of tissue from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. narrower: needle biopsy, fine needle aspiration collecting specimen from organism OBI_0600005 DONE. (new term being published to OBI (damion)) -OBI:0002651 Biopsy Needle Biopsy Needle Biopsy A biopsy which uses an imaging procedure to guide a needle biopsy. - collection method Filtration - Filtration Air filtration -OBI:0600044 collection method Lavage lavage narrower: bronchoalveolar lavage (BAL), gastric lavage collecting specimen from organism OBI_0600005 Changed "Wash" to "Lavage". "editor note: This is not washing, in which case the material of interest is not the resulting fluid." -BTO:0000155 Lavage Bronchoalveolar lavage (BAL) bronchoalveolar lavage (bal) OBI_0600044 lavage - Lavage Gastric Lavage copy from OMIT_0006951 -NCIT:C15327 collection method Lumbar Puncture Lumbar Puncture spinal tap, LP collecting specimen from organism OBI_0600005 Existing synonyms are from current master GenEpiO branch and will not appear on Onto browsers. -MMO:0000344 collection method Necropsy necropsy autopsy (although usually only in reference to an animal). collecting specimen from organism OBI_0600005 "Should this term be included in this category? It's not so much a ""method"" as an examination that occured postmortem. - -Also, what if someone did a postmortem biopsy - can they put in both ""Necropsy"" and ""Biopsy"" or would they have to choose between the two? - -I think it's a useful term and should go somewhere, just perhaps not under ""collection method"". Should we (or do we already have) something along the lines of ""host condition"" at time of examination/sample collection?" -NCIT:c28221 collection method Phlebotomy phlebotomy narrower: venipuncture collecting specimen from organism OBI_0600005 -GENEPIO:0002116 collection method Rinsing rinsing for specimen collection collecting specimen from organism OBI_0600005 "editor note: This is not washing, in which case the material of interest is not the resulting fluid." - Rinsing Saline gargle (mouth rinse and gargle) - collection method Scraping narrower: conjunctival scraping, skin scraping -GENEPIO:0002117 collection method Swabbing swabbing for specimen collection' narrower: nasopharyngeal (nasal) swab, oropharyngeal (throat) swab, depe nasal swab, throat swab, multitest swab, deep nasal or throat swab collecting specimen from organism OBI_0600005 As in "to swab" not "a swab". Alternative name suggestion: "Swabbing" - Swabbing Finger Prick Is a "swab method" (ref. "other" column). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395662/ - collection method Wash wash specimen narrower: nasal wash, nasopharyngeal wash, bronch wash Could use http://purl.obolibrary.org/obo/GENEPIO_0002116 and add as ExactSynonym. - collection method Washout Tear Collection Not sure if this is considered a narrower synonym of "wash". - - collection device Air filter -NCIT:C113122 collection device Blood Collection Tube Blood Collection Tube narrower: vacutainer https://en.wikipedia.org/wiki/Vacutainer#Types_of_tubes -NCIT:C17611 collection device Bronchoscope Bronchoscope Endoscope Device NCIT_C49940 Used in transbronchial biopsies (e.g. tiny forceps), bronchoalveolar lavage, and brush bopsies (e.g. fibrobronchoscope brush, endobronchoscope brush). Should add these subclasses as well. - collection device Collection Container narrower: collection tube, collection bottle, collectoin cup Should we have a universal "collection tube" as well as or rather than the narrower terms below? - collection device Collection Cup - collection device Fibrobronchoscope Brush - collection device Filter - collection device Fine Needle "As in ""fine needle aspiration"". - -Device used to generate sample, is it used to ""collect"" the sample?" - collection device Microcapillary tube MCT -OBI:0001128 collection device Micropipette -OBI:0000436 collection device Needle Device used to generate sample, is it used to "collect" the sample? -NCIT:C113675 collection device Serum Collection Tube Serum Collection Tube Red Top Tube "Red Top Tube" is technically a narrower synonym, as there are more colours for different methods of isolating the serum (e.g. clot activator + serum seperation gel, clot activator no gel, thrombin) https://en.wikipedia.org/wiki/Vacutainer#Types_of_tubes - collection device Sputum Collection Tube - collection device Suction Catheter -NCIT:c17627 collection device Swab swab narrower: swab (flocked tapered), swab (spun polyester), swab (synthetic fiber), swab (wire shaft), swab (plastic shaft), swab (wooden shaft), swab (calcium alginate) Fun fact, calcium alginate swabs or swabs with wooden shafts may contain substances that inactivate some viruses. - collection device Urine Collection Tube Urine specimen tube Under consideration. - collection device Virus Transport Medium viral transport medium "Not sure if this belongs here or if it should be included at all. Included it just in case. - -Could also include other transport mediums, such as: Amies Transport Medium, Sterile Saline / Non-Bacteriostatic Saline" - - -NCBITaxon_9606 host (scientific name) Homo sapiens homo sapiens human Homo -NCBITaxon_9913 host (scientific name) Bos taurus Bos taurus cow, cattle, domestic cow -NCBITaxon_9615 host (scientific name) Canis lupus familiaris Canis lupus familiaris dog -NCBITaxon_9397 host (scientific name) Chiroptera Chiroptera bat -NCBITaxon_8930 host (scientific name) Columbidae Columbidae pigeon Aves NCBITaxon_8782 -NCBITaxon_9685 host (scientific name) Felis catus Felis catus cat, domestic cat Felidae NCBITaxon_9681 -NCBITaxon_9031 host (scientific name) Gallus gallus Gallus gallus chicken Aves NCBITaxon_8782 -NCBITaxon_9973 host (scientific name) Manis Manis pangolin, Smutsia -NCBITaxon_9974 host (scientific name) Manis javanica Manis javanica Sunda pangolin, Malayan pangolin, Javan pangolin Manis -NCBITaxon_452646 host (scientific name) Neovison vison Neovison -NCBITaxon_9689 host (scientific name) Panthera leo Panthera leo lion Felidae NCBITaxon_9681 -NCBITaxon_9694 host (scientific name) Panthera tigris Panthera tigris tiger Felidae NCBITaxon_9681 -NCBITaxon_58055 host (scientific name) Rhinolophidae Rhinolophidae horseshoe bat Chiroptera -NCBITaxon_59477 host (scientific name) Rhinolophus affinis Rhinolophus affinis intermediate horseshoe bat Rhinolophidae What level do we want these at? Include the parent and more specific level? Probably higher level would go on a form? -NCBITaxon_9825 host (scientific name) Sus scrofa domesticus Sus scrofa domesticus pig, domestic pig, swine -NCBITaxon_9673 host (scientific name) Viverridae Viverridae civet cats, civets Changed Onto ID from NCBITaxon_379583 (Feliformia) to NCBITaxon_9673 (Viverridae) - - -NCBITaxon_9605 host (common name) Human homo homo sapien Do we want the scientific and host "human" to lead to different terms? Or both homo or homo sapiens -NCBITaxon_9397 host (common name) Bat Chiroptera Chiroptera -NCBITaxon_9685 host (common name) Cat Felis catus Felis catus, domestic cat -NCBITaxon_9031 host (common name) Chicken Gallus gallus Gallus gallus -NCBITaxon_9673 host (common name) Civets Viverridae Viverridae, civet cat Changed Onto ID from NCBITaxon_379583 (Feliformia) to NCBITaxon_9673 (Viverridae) -NCBITaxon_9913 host (common name) Cow Bos taurus Bos taurus, cattle Labeled as "bovine" in CNPHI. -NCBITaxon_9615 host (common name) Dog Canis lupus familiaris Canis lupus familiaris -NCBITaxon_9689 host (common name) Lion Panthera leo Panthera leo - host (common name) Mink -NCBITaxon_9973 host (common name) Pangolin Manis Manis -NCBITaxon_9823 host (common name) Pig pig Sus scrofa domesticus, swine "Unlike other entries where the scienfic and common name entries are the same, ""pig"" has a separate entry that is well used apart from its scientific entry. - -Labeled as ""porcine"" in CNPHI." -NCBITaxon_8930 host (common name) Pigeon Columbidae Columbidae -NCBITaxon_9694 host (common name) Tiger Panthera tigris Panthera tigris - - - host health state Asymptomatic - host health state Deceased - host health state Healthy Is this refering to cases that were never ill to begin with? Otherwise how is this differentiated from recovered? - host health state Recovered - host health state Symptomatic - - - host health status details Hospitalized - Hospitalized Hospitalized (Non-ICU) Could use NCIT_C3833 - Hospitalized Hospitalized (ICU) - host health status details Mechanical Ventilation - host health status details Medically Isolated - Medically Isolated Medically Isolated (Negative Pressure) - host health status details Self-quarantining - - host health outcome Deceased - host health outcome Deteriorating - host health outcome Recovered - host health outcome Stable - - organism Severe acute respiratory syndrome coronavirus 2 2019-nCoV, Severe Acute Respiratory Syndrome Coronavirus 2 - organism RaTG13 - organism RmYN02 - - - purpose of sampling Cluster/Outbreak investigation - purpose of sampling Diagnostic testing -NCIT_c15429 purpose of sampling Research research activity - purpose of sampling Surveillance - - - purpose of sequencing Baseline surveillance (random sampling) - purpose of sequencing Targeted surveillance (non-random sampling) - Targeted surveillance (non-random sampling) Priority surveillance project - Priority surveillance project Screening for Variants of Concern (VoC) - Priority surveillance project Longitudinal surveillance (repeat sampling) - Priority surveillance project Vaccine escape surveillance - Priority surveillance project Travel-associated surveillance - Travel-associated surveillance Domestic travel surveillance - Travel-associated surveillance International travel surveillance - purpose of sequencing Cluster/Outbreak investigation - Cluster/Outbreak investigation Multi-jurisdictional outbreak investigation - Cluster/Outbreak investigation Intra-jurisdictional outbreak investigation - purpose of sequencing Research - Research Viral passage experiment - Research Protocol testing experiment - - - specimen processing Virus passage - specimen processing RNA re-extraction (post RT-PCR) - specimen processing Specimens pooled - lab host ???? lab host: Nonpermissive/Nonsusceptible to SARS-CoV-2: 3T3, A529, BHK21, DF-1, embryonated eggs, HEL, HeLa, HeLa-T, Hep-2, L20, L929, MDCK, MRC-5, PoK, RD, RD-A, RLL, RLK, RSL, RSK, - lab host 293/ACE2 cell line 293/hACE2 cell line, broader: human kidney cell line, embryonic kidney cell line, renal... "Possible parent term: - -293-derived cell" "Possible parent term: - -CLO_0037237" "Add new term. Still need definition. - -293/hACE2 to appears to be an exact synonym (with the h added from ""human"") but I am not 100% positive. - -Source: ATCC CRL-3216 - -RRID: CVCL_DR94" -BTO_0000195 lab host Caco2 cell line CACO-2 cell Caco-2 cell, CaCo 2 cell, Caco2 cell, broader: human gastrointestinal tract cell line, colorectal adenocarcinoma cell line, human colon epithelial cell line, human intestinal cell line colonic adenocarcinoma cell line BTO_0001913 "Use BTO term. Add synonyms. CLO also has an entry. - -Source: ATCC HTB-37 - -RRID: CVCL_0025" -BTO_0002750 lab host Calu3 cell line Calu-3 cell Calu-3, Calu-3 cell, Calu 3 cell, broader: human respiratory tract cell line, human lung adenocarcinoma cell line, human pulminary cell line lung adenocarcinoma cell line BTO_0001911 "Use BTO term. Add synonyms. -CLO also has an entry. - -Source: ATCC HTB-55 - -RRID: CVCL_0609" - lab host EFK3B cell line Efk3B cell, Efk-3B clone 3B cell, Eptesicus fucus kidney 3B cell, broader: big brown bat kidney cell line "Add new term. Still needs definition. - -Low susceptibility to SARS-CoV-2. - -Group: Bat cell line. -""Can be used to cultivate viruses from the Coronaviridae, Filoviridae, Herpesviridae, Paramyxoviridae and Rhabdoviridae."" (ref RRID) - -RRID: CVCL_GZ34" -BTO_0002181 lab host HEK293T cell line HEK-293T cell 293 T cell, HEK293T cell, 293T cell, 293-T cell, HEK-293T cell, HEK 293T cell, HEK 293 T cell, 293 T cell, human embryonic kidney 293T cell, 293tsA1609neo cell, broader: human embryonic kidney cell line derives from/develops from some HEK-293 cell "HEK-293 cell: - -BTO_0000007" "Use BTO term. Add synonyms. - -Moderate susceptibility to SARS-CoV-2. - -RRID: CVCL_0063" - lab host HRCE cell line human renal cortical epithelial cell line "New term. - -High susceptibility to SARS-CoV-2." -BTO_0001950 lab host Huh7 cell line Huh7 cell Huh-7 cell, Huh7 cell, HUH7.0 cell, JTC-39 cell, Japanese Tissue Culture-39 cell, broader: human liver cell line, liver hepatocullular carcinoma cell line, hepatocellular carcinoma cell line hepatoma cell line BTO_0000578 "Add BTO term. Add synonyms. CLO also has entry. - -Moderate susceptibility. - -Source: JCRB0403, JCRB cell bank of Okayama University - -RRID: CVCL_0336" -CLO_0007330 lab host LLCMk2 cell line LLC-MK subscript(2) cell LLC-Mk2 cell line, Lilly Laboratories Cell-Monkey Kidney 2 cell line, broader: non-human primate cell line, Macaca mulatta cell line, rhesus monkey kidney cell line immortal rhesus macaque kidney-derived cell line cell CLO_0000714 "Use CLO term. Add snyonyms, still needs definition. - -Source: ATCC CCL-7 - -RRID: CVCL_3009" -BTO_0000836 lab host MDBK cell line MDBK cell Mardin-Darby bovine kidney cell kidney cell line BTO_0000067 "Optional? Use BTO term. Add synonym(s). - -Has been tested for SARS-CoV-2 propagation but preprint does not yet show results." - lab host Mv1Lu cell line Mink lung epithelial cell, Mv 1 Lu cell "Was being used in combination with A549 but is recommended against due to it's low levels of replication. Not sure if it should be included anyway since some labs may have used it before this recommendation. - -Are all Mv1 Lu Cell lines Mv 1 Lu (NBL-7)? - -Source: ATCC CCL-64" -BTO_0002924 lab host NHBE cell line NHBE cell normal human bronchial epithelial cell bronchial epithelial cell line BTO_0002022 "Use BTO term. -Low susceptibility to SARS-CoV-2." -BTO_0001865 lab host PK-15 cell line PK-15 cell PK15 cell, PK(15) cell, PK 15 cell, PK (15) cell, Porcine Kidney-15 cell, Porcine Kidney 15 cell, broader: pig cell line, porcine kidney cell line, PK-2a cell line kidney cell line BTO_0000067 "Use BTO term. Add synonyms. CLO also has some entries. - -Source: ATCC CCL-33 - -RRID:CVCL_2160" -BTO_0002909 lab host RK-13 cell line RK 13 cell RK13 cell, RK 13 cell, Rabbit Kidney-13 cell, Rabbit Kidney 13 cell, broader: rabbit cell line, Oryctolagus cuniculus cell line renal epithelium cell line BTO_0002886 "Use BTO term. Add synonyms. CLO has entries also. - -Source: ATCC CCL-37 - -RRID: CVCL_3155" -BTO_0002035 lab host U251 cell line U-251MG cell U-251 cell, U251 cell, U-251MG cell, U251MG cell, U-251 MG cell, broader: human neuronal cell line, glioblastoma cell line glioma cell line BTO_0000711 "Modest results, look for more evidence of its use. It's lower replication rate may actually be an incentive to labs worried about exposure. - -Source: Sigma 09063001 (Sigma-Aldrich, St Louis, MO, USA)" -BTO_0001444 lab host Vero cell line Vero cell VeroCCL81 cell, Verda reno cell, African monkey kidney cell , broader: non-human primate cell line, vaccine production cell line, African green monkey cell line kidney cell line BTO_0000067 "Use BTO term. Add synonyms. CLO also has entries. - -No 100% certain as to whether ""African monkey kidney cell"" should be and exact or broader synonym. - -High susceptibility to SARS-CoV-2. - -RRID: CVCL_0059" https://en.wikipedia.org/wiki/Vero_cell -BTO:0004755 lab host Vero E6 cell line VERO C1008 cell VeroE6 cell, Vero-E6 cell, Vero E6 cell, Vero 76 clone E6 cell, Vero C1008 cell, Vero C 1008 cell, VeroC1008 cell, Vero 76 clone E-6 cell, broader: African green monkey kidney cell line, African green monkey cell line, African green monkey kidney epithelial cell line, non-human primate kidney cell line, vero derived cell line derives from/develops from some Vero cell "Vero cell: - -BTO_0001444" "Use BTO entry. Add synonyms. CLO also has entry. - -High susceptibility to SARS-CoV-2. Is a clone of Vero-76 cell line. - -Source: ATCC CCL-81, ATCC CRL-1586 - -RRID: CVCL_0574" - lab host VeroE6/TMPRSS2 cell line VeroE6/TMPRSS2 cell VeroE6 cells expressing the transmembrane serine protease TMPRSS2. https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?ID=8668 Vero E6/TMPRSS2 cell, Vero-E6/TMPRSS2 cell, broader: Vero C1008 cell, African green monkey cell line "Recommended parent term: - -VERO C1008 cell" "Recommended parent term: - -BTO:0004755" "Add new term. - -Recently engineered cell line highly susceptible to SARS-CoV-2. - -JCRB: JCRB1819 - -RRID: CVCL_YQ49" - - host disease COVID-19 - - host age bin 0 - 9 - host age bin 10 - 19 - host age bin 20 - 29 - host age bin 30 - 39 - host age bin 40 - 49 - host age bin 50 - 59 - host age bin 60 - 69 - host age bin 70 - 79 - host age bin 80 - 89 - host age bin 90 - 99 - host age bin 100+ - -OMRSE:00000009? host gender Female Could use 'female gender role' from OMRSE -OMRSE:00000008? host gender Male Could use 'male gender role' from OMRSE - host gender Non-binary gender Could request new term under OMRSE 'gender role' - host gender Transgender (Male to Female) Could request new term under OMRSE 'gender role' - host gender Transgender (Female to Male) - host gender Undeclared - host gender Unknown - - exposure event Mass Gathering - Mass Gathering Convention - Mass Gathering Convocation Added 2020/14/03 - Mass Gathering Agricultural Event - exposure event Religious Gathering - Religious Gathering Mass - exposure event Social Gathering - Social Gathering Baby Shower Added 2020/14/03 - Social Gathering Community Event Added 2020/14/03 - Social Gathering Family Gathering - Family Gathering Family Reunion - Social Gathering Funeral - Social Gathering Party - Social Gathering Potluck - Social Gathering Wedding - exposure event Other exposure event - - exposure contact level Contact with infected individual - Contact with infected individual Direct contact (direct human-to-human contact) - Contact with infected individual Indirect contact - Indirect contact Close contact (face-to-face, no direct contact) - Indirect contact Casual contact - - - host role Attendee - Attendee Student i.e. school attendee - host role Patient - Patient Inpatient - Patient Outpatient - host role Passenger Could include for pairing with modes of transport - host role Resident - host role Visitor - host role Volunteer - host role Work Only including narrower terms that appears on case report forms - Work Administrator - Work First Responder synonymous with emergency responder, frontline responder - First Responder Firefighter - First Responder Paramedic - First Responder Police Officer - Work Healthcare Worker - Work Nurse - Work Personal Care Aid - Work Pharmacist - Work Physician - Work Housekeeper - Work Kitchen Worker - Work Laboratory Worker - Work Rotational Worker - Work Seasonal Worker - Work Veterinarian - host role Social role Damion mentioned that we could include these roles (already in GenEpiO) - Social role Acquaintance of case - Social role Relative of case - Relative of case Child of case - Relative of case Parent of case - Relative of case Father of case Update (2020/08/28): Changed parent class to "parent" - Relative of case Mother of case Update (2020/08/28): Changed parent class to "parent" - Social role Spouse of case - host role Other Host Role - - exposure setting Human Exposure - Human Exposure Known COVID-19 Case - Human Exposure Patient Contact - Human Exposure Probable COVID-19 Case - Human Exposure Person with Acute Respiratory Illness - Human Exposure Person with Fever and/or Cough - Human Exposure Person who Recently Travelled - exposure setting Occupational or Residency Exposure - Occupational or Residency Exposure Abbatoir - Occupational or Residency Exposure Animal Rescue - Occupational or Residency Exposure Childcare - Childcare Daycare repositioned under 'childcare' - 2020/08/19 - Occupational or Residency Exposure Funeral Home - Occupational or Residency Exposure Place of Worship - Place of Worship Church - Place of Worship Mosque - Place of Worship Temple - Occupational or Residency Exposure Nursery - Occupational or Residency Exposure Household - Occupational or Residency Exposure Community Service Centre - Occupational or Residency Exposure Correctional Facility prison - Occupational or Residency Exposure Dormitory - Occupational or Residency Exposure Farm - Occupational or Residency Exposure First Nations Reserve - Occupational or Residency Exposure Group Home can include terms like: personal care home, private senior's residence, retirement home, assisted/independent living, longoterm residential care centre - Occupational or Residency Exposure Healthcare Setting 5/8 forms specify direct patient contact, should we include that specification somewhere? - Healthcare Setting Ambulance ENVO request made - Healthcare Setting Acute Care Facility - Healthcare Setting Clinic - Healthcare Setting Community Health Centre - Healthcare Setting Hospital - Hospital Emergency Department - Hospital ICU - Hospital Ward - Healthcare Setting Laboratory - Healthcare Setting Long-Term Care Facility - Healthcare Setting Pharmacy - Healthcare Setting Physician's Office - Occupational or Residency Exposure Insecure Housing (Homeless) - Occupational or Residency Exposure Office - Occupational or Residency Exposure Outdoors - Outdoors Camp/camping - Outdoors Hiking - Outdoors Hunting - Occupational or Residency Exposure Petting zoo - Occupational or Residency Exposure Restaurant - Occupational or Residency Exposure Retail Store Retail Environment - Occupational or Residency Exposure School - Occupational or Residency Exposure Temporary Residence - Temporary Residence Homeless Shelter emergency shelter - Temporary Residence Hotel - Occupational or Residency Exposure Veterinary Care Clinic - exposure setting Travel Exposure - Travel Exposure Travelled Redundant? Essentially the same as 'Travel Exposure'? - Travelled Travelled on a Cruise Ship - Travelled Travelled on a Plane - Travelled Travelled on Ground Transport Renamed 'public transport' to 'ground transport' to distinguish from planes, which are also public transport. - Travelled Travelled outside Province/Territory - Travelled Travelled outside Canada - exposure setting Other Exposure Setting - - Host reinfection information prior SARS-CoV-2 infection select - prior SARS-CoV-2 infection Yes - prior SARS-CoV-2 infection No - prior SARS-CoV-2 infection Unknown - - -OBI_0000759 sequencing instrument Illumina platform:ILLUMINA illumina -OBI_0002128 Illumina Illumina Genome Analyzer platform:ILLUMINA|instrument_model:Illumina Genome Analyzer illumina genome analyzer A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html Genome Analyzer DNA sequencer OBI_0400103 -OBI_0000703 Illumina Genome Analyzer Illumina Genome Analyzer II platform:ILLUMINA|instrument_model:Illumina Genome Analyzer II illumina genome analyzer ii DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000703&viewMode=All&siblings=true Genome Analyzer II DNA sequencer OBI_0400103 -OBI_0002000 Illumina Genome Analyzer Illumina Genome Analyzer IIx platform:ILLUMINA|instrument_model:Illumina Genome Analyzer IIx Genome Analyzer IIx The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0002000&viewMode=All&siblings=true Illumina GA IIx, Illumina Genome Analyzer IIx illumina genome analyzer ii OBI_0000703 - Illumina Illumina HiScanSQ platform:ILLUMINA|instrument_model:Illumina HiScanSQ illumina hiscan SQ DNA sequencer OBI_0400103 new term - Illumina Illumina HiSeq platform:ILLUMINA -OBI_0002129 Illumina Illumina HiSeq X platform:ILLUMINA Illumina HiSeq X The Illumina HiSeq X is an ultra-high-throughput sequencing machine developed by Illumina. https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0008567 Illumina HiSeq X high throughput sequencer http://www.ebi.ac.uk/efo/EFO_0002699 - Illumina HiSeq X Illumina HiSeq X Five platform:ILLUMINA|instrument_model: Illumina HiSeq X Five Sets of 5 HiSeq X instruments make up the Illumina HiSeq X Five https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0008567 -OBI_0002129 Illumina HiSeq X Illumina HiSeq X Ten platform:ILLUMINA|instrument_model:Illumina HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. http://www.ontobee.org/ontology/OBI?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0002129 Illumina HiSeq X Ten, HiSeq X Ten DNA sequencer OBI_0400103 -OBI_0002022 Illumina Illumina HiSeq 1000 platform:ILLUMINA|instrument_model:Illumina HiSeq 1000 illumina hiseq 1000 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0002022&viewMode=All&siblings=true HiSeq 1000 DNA sequencer OBI_0400103 - Illumina Illumina HiSeq 1500 platform:ILLUMINA HiSeq 1500 -OBI_0002001 Illumina Illumina HiSeq 2000 platform:ILLUMINA|instrument_model:Illumina HiSeq 2000 illumina hiseq 2000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0002001&viewMode=All&siblings=true HiSeq 2000 DNA sequencer OBI_0400103 -OBI_0002002 Illumina Illumina HiSeq 2500 platform:ILLUMINA|instrument_model:Illumina HiSeq 2500 illumina hiseq 2500 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0002002&viewMode=All&siblings=true HiSeq 2500 DNA sequencer OBI_0400103 -OBI_0002048 Illumina Illumina HiSeq 3000 platform:ILLUMINA illumina hiseq 3000 A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0002048&viewMode=All&siblings=true HiSeq 3000 DNA sequencer OBI_0400103 -OBI_0002049 Illumina Illumina HiSeq 4000 platform:ILLUMINA illumina hiseq 4000 A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. http://www.illumina.com/systems/hiseq-3000-4000.html HiSeq 4000 DNA sequencer OBI_0400103 - Illumina Illumina iSeq platform:ILLUMINA -EFO:0008635 Illumina iSeq Illumina iSeq 100 platform:ILLUMINA illumina iseq 100 The Illumina iSeq 100 is a benchtop sequencing machine developed by Illumina. Its primary applications include small whole-genome sequencing, targeted sequencing of a set of genes or gene regions, gene expression analysis and 16S metagenomic sequencing. https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0008635&viewMode=All&siblings=true iSeq 100 high throughput sequencer http://www.ebi.ac.uk/efo/EFO_0002699 - Illumina Illumina NovaSeq platform:ILLUMINA -OBI_0002630 Illumina NovaSeq Illumina NovaSeq 6000 platform:ILLUMINA illumina novaseq 6000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run) http://www.illumina.com/systems/sequencing-platforms/novaseq.html NovaSeq 6000 DNA sequencer OBI_0400103 -http://www.ebi.ac.uk/efo/EFO_0008636 Illumina Illumina MiniSeq platform:ILLUMINA illumina miniseq The Illumina MiniSeq is a benchtop sequencing machine developed by Illumina and an output upto 8Gb. https://www.illumina.com/systems/sequencing-platforms/miniseq/specifications.html MiniSeq high throughput sequencer http://www.ebi.ac.uk/efo/EFO_0002699 -OBI_0002003 Illumina Illumina MiSeq platform:ILLUMINA|instrument_model:Illumina MiSeq MiSeq A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf illumina miseq DNA sequencer OBI_0400103 - Illumina Illumina NextSeq platform:ILLUMINA -OBI_0002021 Illumina Illumina NextSeq 500 platform:ILLUMINA|instrument_model:Illumina NextSeq 500 nextseq 500 Illumina NextSeq 500 DNA sequencer OBI_0400103 - Illumina Illumina NextSeq 550 platform:ILLUMINA -OBI_0001856 sequencing instrument Pacific Biosciences platform:PACBIO_SMRT pacific biosciences - Pacific Biosciences PacBio RS platform:PACBIO_SMRT|instrument_model:PacBio RS DNA sequencer OBI_0400103 -OBI_0002012 Pacific Biosciences PacBio RS II platform:PACBIO_SMRT|instrument_model:PacBio RS II pacbio rs ii DNA sequencer OBI_0400103 -OBI_0002632 Pacific Biosciences PacBio Sequel platform:PACBIO_SMRT pacbio sequel DNA sequencer OBI_0400103 -OBI_0002633 Pacific Biosciences PacBio Sequel II platform:PACBIO_SMRT pacbio sequel ii DNA sequencer OBI_0400103 - sequencing instrument Ion Torrent platform:ION_TORRENT -GENEPIO_0001935 Ion Torrent Ion Torrent PGM platform:ION_TORRENT|instrument_model:Ion Torrent PGM ion torrent pgm - Ion Torrent Ion Torrent Proton platform:ION_TORRENT|instrument_model:Ion Torrent Proton - Ion Torrent Ion Torrent S5 XL platform:ION_TORRENT - Ion Torrent Ion Torrent S5 platform:ION_TORRENT - sequencing instrument Oxford Nanopore platform:OXFORD_NANOPORE - Oxford Nanopore GridION platform:OXFORD_NANOPORE|instrument_model:GridION - Oxford Nanopore MinION platform:OXFORD_NANOPORE|instrument_model:MinION - Oxford Nanopore PromethION platform:OXFORD_NANOPORE - sequencing instrument BGI Genomics - BGI Genomics BGISEQ-500 - sequencing instrument MGI - MGI DNBSEQ-T7 - MGI DNBSEQ-G400 - MGI DNBSEQ-G400 FAST - MGI DNBSEQ-G50 - - -PR:P0DTC4 gene name 1 E gene (orf4) envelope small membrane protein (SARS-CoV-2) sM protein (SARS2), envelope protein (SARS2), PRO_0000449651, E protein (SARS2), E (SARS2), ORF4, GU280_gp04, E severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTC5 gene name 1 M gene (orf5) membrane protein (SARS-CoV-2) E1 glycoprotein (SARS2), membrane glycoprotein (SARS2), PRO_0000449652, matrix glycoprotein (SARS2), M (SARS2), M protein (SARS2), GU280_gp05, ORF5 severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTC9 gene name 1 N gene (orf9) nucleoprotein (SARS-CoV-2) protein N (SARS2), nucleocapsid protein (SARS2), NC (SARS2), PRO_0000449656, N (SARS2), GU280_gp10, ORF9, N, ORF9a, nucleocapsi phosphoprotein severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTC2 gene name 1 Spike gene (orf2) spike glycoprotein (SARS-CoV-2) peplomer protein (SARS2), surface glycoprotein (SARS2), S glycoprotein (SARS2), S (SARS2), E2 (SARS2), S, GU280_gp02, ORF2, ORF-2 narrower: spike protein S1, spike protein S2 severe acute respiratory syndrome coronavirus 2 protein PR:000050262 There are additional proteins in this category that have their signal peptide removed, but did not include entries for them as they seemed too narrow. -PR:000050281 gene name 1 orf1ab (rep) replicase polyprotein 1ab (SARS-CoV-2) pp1ab (SARS2), ORF1ab polyprotein (SARS2), PRO_0000449618, rep/iso:ORF1ab (SARS2), rep1a-1b, rep 1a-1b, rep1ab, rep Used in pick-list heirarchy instead of 'Rep'. -PR:P0DTC1-1 orf1ab (rep) orf1a (pp1a) replicase polyprotein 1a (SARS-CoV-2) pp1a (SARS2), PRO_0000449634, rep/iso:ORF1a (SARS2), ORF1a polyprotein (SARS2), rep1a, rep 1a rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050280 orf1a (pp1a) nsp11 non-structural protein 11 (SARS-CoV-2) nsp11 (SARS2), 'UniProtKB:P0DTC1, 4393-4405', PRO_0000449645, rep/Clv:nsp11 (SARS2) ORF1a proteolytic cleavage product (SARS-CoV-2) PR:000050282 -PR:000050270 orf1ab (rep) nsp1 host translation inhibitor nsp1 (SARS-CoV-2) nsp1 (SARS2), 'UniProtKB:P0DTD1, 1-180', PRO_0000449635, 'UniProtKB:P0DTC1, 1-180', leader protein (SARS2), PRO_0000449619, rep/Clv:nsp1 (SARS2), non-structural protein 1 (SARS2) rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050271 orf1ab (rep) nsp2 non-structural protein 2 (SARS-CoV-2) p65 homolog (SARS2), rep/Clv:nsp2 (SARS2), PRO_0000449620, 'UniProtKB:P0DTD1, 181-818', nsp2 (SARS2), PRO_0000449636, 'UniProtKB:P0DTC1, 181-818' rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050272 orf1ab (rep) nsp3 non-structural protein 3 (SARS-CoV-2) rep/Clv:nsp3 (SARS2), main proteinase (SARS2), nsp3 (SARS2), PLpro (SARS2), PRO_0000449621, papain-like proteinase (SARS2), PRO_0000449637, 'UniProtKB:P0DTC1, 819-2763', 'UniProtKB:P0DTD1, 819-2763', PL2-PRO, PL-PRO, SARS coronavirus main proteinase rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050273 orf1ab (rep) nsp4 non-structural protein 4 (SARS-CoV-2) nsp4 (SARS2), PRO_0000449622, 'UniProtKB:P0DTC1, 2764-3263', 'UniProtKB:P0DTD1, 2764-3263', PRO_0000449638, rep/Clv:nsp4 (SARS2) rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050274 orf1ab (rep) nsp5 3C-like proteinase (SARS-CoV-2) nsp5 (SARS2), 3CL-PRO (SARS2), 'UniProtKB:P0DTC1, 3264-3569', PRO_0000449623, rep/Clv:nsp5 (SARS2), 3CLp (SARS2), picornavirus 3C-like protease (SARS2), 'UniProtKB:P0DTD1, 3264-3569', PRO_0000449639, 3CLpro (SARS2) rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050275 orf1ab (rep) nsp6 non-structural protein 6 (SARS-CoV-2) PRO_0000449640, nsp6 (SARS2), 'UniProtKB:P0DTD1, 3570-3859', 'UniProtKB:P0DTC1, 3570-3859', PRO_0000449624, rep/Clv:nsp6 (SARS2) rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050276 orf1ab (rep) nsp7 non-structural protein 7 (SARS-CoV-2) UniProtKB:P0DTD1, 3860-3942', PRO_0000449641, 'UniProtKB:P0DTC1, 3860-3942', nsp7 (SARS2), PRO_0000449625, rep/Clv:nsp7 (SARS2) rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050277 orf1ab (rep) nsp8 non-structural protein 8 (SARS-CoV-2) rep/Clv:nsp8 (SARS2), PRO_0000449642. 'UniProtKB:P0DTC1, 3943-4140', PRO_0000449626, nsp8 (SARS2), 'UniProtKB:P0DTD1, 3943-4140' rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050278 orf1ab (rep) nsp9 non-structural protein 9 (SARS-CoV-2) UniProtKB:P0DTC1, 4141-4253', PRO_0000449643, nsp9 (SARS2), 'UniProtKB:P0DTD1, 4141-4253', rep/Clv:nsp9 (SARS2), PRO_0000449627 rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050279 orf1ab (rep) nsp10 non-structural protein 10 (SARS-CoV-2) GFL (SARS2), 'UniProtKB:P0DTC1, 4254-4392', PRO_0000449644, growth factor-like peptide (SARS2), rep/Clv:nsp10 (SARS2), 'UniProtKB:P0DTD1, 4254-4392', PRO_0000449628, nsp10 (SARS2) rep gene proteolytic cleavage product (SARS-CoV-2) PR:000050281 -PR:000050284 orf1ab (rep) RdRp gene (nsp12) RNA-directed RNA polymerase (SARS-CoV-2) Pol (SARS2), RdRp (SARS2), 'UniProtKB:P0DTD1, 4393-5324', ORF1ab/Clv:nsp12 (SARS2), nsp12 (SARS2), PRO_0000449629, RNA dependent RNA Polymerase ORF1ab proteolytic cleavage product (SARS-CoV-2) PR:000050283 -PR:000050285 orf1ab (rep) hel gene (nsp13) helicase (SARS-CoV-2) PRO_0000449630, Hel (SARS2), ORF1ab/Clv:nsp13 (SARS2), 'UniProtKB:P0DTD1, 5325-5925', nsp13 (SARS2) ORF1a proteolytic cleavage product (SARS-CoV-2) PR:000050282 -PR:000050286 orf1ab (rep) exoN gene (nsp14) bifunctional exonuclease/methyltransferase (SARS-CoV-2) ExoN (SARS2), nsp14 (SARS2), PRO_0000449631, 'UniProtKB:P0DTD1, 5926-6452', ORF1ab/Clv:nsp14 (SARS2), guanine-N7 methyltransferase (SARS2), proofreading exoribonuclease, non-structural protein 14 ORF1a proteolytic cleavage product (SARS-CoV-2) PR:000050282 -PR:000050287 orf1ab (rep) nsp15 uridylate-specific endoribonuclease (SARS-CoV-2) nsp15 (SARS2), endoRNAse (SARS2), PRO_0000449632, ORF1ab/Clv:nsp15 (SARS2), 'UniProtKB:P0DTD1, 6453-6798', NendoU (SARS2) ORF1a proteolytic cleavage product (SARS-CoV-2) PR:000050282 -PR:000050288 orf1ab (rep) nsp16 2'-O-methyltransferase (SARS-CoV-2) UniProtKB:P0DTD1, 6799-7096', PRO_0000449633, ORF1ab/Clv:nsp16 (SARS2), 2'-O-ribose methyltransferase (SARS2), nsp16 (SARS2) ORF1ab proteolytic cleavage product (SARS-CoV-2) PR:000050283 -PR:P0DTC3 gene name 1 orf3a protein 3a (SARS-CoV-2) PRO_0000449650, protein X1 (SARS2), ORF3a (SARS2), accessory protein 3a (SARS2), protein U274 (SARS2), GU280_gp03, ORF3a, ORF-3a severe acute respiratory syndrome coronavirus 2 protein PR:000050262 - gene name 1 orf3b ORF-3b severe acute respiratory syndrome coronavirus 2 protein PR:000050262 Not yet listed on Uniprot nor PR/PRO. Saw it on GO gene list and found research papers referencing it (for example see 'other'). https://www.biorxiv.org/content/10.1101/2020.05.11.088179v1.full.pdf -PR:P0DTC6 gene name 1 orf6 (ns6) ORF6 protein (SARS-CoV-2) ns6 (SARS2), ORF6 (SARS2), PRO_0000449653, accessory protein 6 (SARS2), protein X3 (SARS2), GU280_gp06, ORF6, ORF-6 severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTC7 gene name 1 orf7a protein 7a (SARS-CoV-2) accessory protein 7a (SARS2), ORF7a (SARS2), protein U122 (SARS2), protein X4 (SARS2), ORF7a, GU280_gp07, ORF-7a severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTD8 gene name 1 orf7b (ns7b) protein 7b (SARS-CoV-2) accessory protein 7b (SARS2), non-structural protein 7b (SARS2), ORF7b (SARS2), ns7b (SARS2), PRO_0000449799, ORF7b, GU280_gp08, ORF-7b severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTC8 gene name 1 orf8 (ns8) ORF8 protein (SARS-CoV-2) ns8 (SARS2), ORF8 (SARS2), ORF8, GU280_gp09, ORF-8 severe acute respiratory syndrome coronavirus 2 protein PR:000050262 -PR:P0DTD2 gene name 1 orf9b protein 9b (SARS-CoV-2) accessory protein 9b (SARS2), PRO_0000449657, ORF-9b (SARS2), ORF9b (SARS2), ORF9b severe acute respiratory syndrome coronavirus 2 protein PR:000050262 - gene name 1 orf9c ORF-9c Not yet listed on Uniprot nor PR/PRO. Saw it on GO gene list and found research papers referencing it (for example see 'other'). https://www.biorxiv.org/content/10.1101/2020.03.22.002386v1.full.pdf -PR:A0A663DJA2 gene name 1 orf10 ORF10 protein (SARS-CoV-2) ORF10 (SARS2), ORF10, ORF-10 severe acute respiratory syndrome coronavirus 2 protein PR:000050262 - gene name 1 orf14 ORF-14 Uncharacterized at this time (2020/06/16); protein inferred from homology. https://www.uniprot.org/uniprot/P0DTD3 - gene name 1 SARS-COV-2 5' UTR - - - - - -GAZ_00006882 geo_loc_name (country) Afghanistan afghanistan -GAZ_00002953 geo_loc_name (country) Albania albania -GAZ_00000563 geo_loc_name (country) Algeria algeria -GAZ_00003957 geo_loc_name (country) American Samoa american samoa -GAZ_00002948 geo_loc_name (country) Andorra andorra -GAZ_00001095 geo_loc_name (country) Angola angola -GAZ_00009159 geo_loc_name (country) Anguilla anguilla -GAZ_00000462 geo_loc_name (country) Antarctica antarctica -GAZ_00006883 geo_loc_name (country) Antigua and Barbuda antigua and barbuda -GAZ_00002928 geo_loc_name (country) Argentina argentina -GAZ_00004094 geo_loc_name (country) Armenia armenia -GAZ_00004025 geo_loc_name (country) Aruba aruba -GAZ_00005901 geo_loc_name (country) Ashmore and Cartier Islands Territory of Ashmore and Cartier Islands Territory of Ashmore and Cartier Islands -GAZ_00000463 geo_loc_name (country) Australia australia -GAZ_00002942 geo_loc_name (country) Austria austria -GAZ_00004941 geo_loc_name (country) Azerbaijan azerbaijan -GAZ_00002733 geo_loc_name (country) Bahamas The Bahamas -GAZ_00005281 geo_loc_name (country) Bahrain bahrain -GAZ_00007117 geo_loc_name (country) Baker Island -GAZ_00003750 geo_loc_name (country) Bangladesh bangladesh -GAZ_00001251 geo_loc_name (country) Barbados barbados -GAZ_00005810 geo_loc_name (country) Bassas da India Ile Bassas da India -GAZ_00006886 geo_loc_name (country) Belarus belarus -GAZ_00002938 geo_loc_name (country) Belgium belgium -GAZ_00002934 geo_loc_name (country) Belize belize -GAZ_00000904 geo_loc_name (country) Benin benin -GAZ_00001264 geo_loc_name (country) Bermuda bermuda -GAZ_00003920 geo_loc_name (country) Bhutan bhutan -GAZ_00002511 geo_loc_name (country) Bolivia bolivia -GAZ_00025355 geo_loc_name (country) Borneo borneo -GAZ_00006887 geo_loc_name (country) Bosnia and Herzegovina bosnia and herzegovina -GAZ_00001097 geo_loc_name (country) Botswana botswana -GAZ_00001453 geo_loc_name (country) Bouvet Island bouvet island -GAZ_00002828 geo_loc_name (country) Brazil brazil -GAZ_00003961 geo_loc_name (country) British Virgin Islands british virgin islands -GAZ_00003901 geo_loc_name (country) Brunei -GAZ_00002950 geo_loc_name (country) Bulgaria bulgaria -GAZ_00000905 geo_loc_name (country) Burkina Faso burkina faso -GAZ_00001090 geo_loc_name (country) Burundi burundi -GAZ_00006888 geo_loc_name (country) Cambodia cambodia -GAZ_00001093 geo_loc_name (country) Cameroon cameroon -GAZ_00002560 geo_loc_name (country) Canada canada -GAZ_00001227 geo_loc_name (country) Cape Verde cape verde -GAZ_00003986 geo_loc_name (country) Cayman Islands cayman islands -GAZ_00001089 geo_loc_name (country) Central African Republic central african republic -GAZ_00000586 geo_loc_name (country) Chad chad -GAZ_00002825 geo_loc_name (country) Chile chile -GAZ_00002845 geo_loc_name (country) China china -GAZ_00005915 geo_loc_name (country) Christmas Island christmas island -GAZ_00005838 geo_loc_name (country) Clipperton Island -GAZ_00009721 geo_loc_name (country) Cocos Islands -GAZ_00002929 geo_loc_name (country) Colombia colombia -GAZ_00005820 geo_loc_name (country) Comoros comoros -GAZ_00053798 geo_loc_name (country) Cook Islands cook islands -GAZ_00005917 geo_loc_name (country) Coral Sea Islands -GAZ_00002901 geo_loc_name (country) Costa Rica costa rica -GAZ_00000906 geo_loc_name (country) Cote d'Ivoire cote d'ivoire -GAZ_00002719 geo_loc_name (country) Croatia croatia -GAZ_00003762 geo_loc_name (country) Cuba cuba -GAZ_00004021 geo_loc_name (country) Curacao Currently using Onto ID for 'Curacao Island' rather than the 'Country of Curacao' (GAZ_00012582) - R -GAZ_00004006 geo_loc_name (country) Cyprus -GAZ_00002954 geo_loc_name (country) Czech Republic czech republic -GAZ_00001086 geo_loc_name (country) Democratic Republic of the Congo democratic republic of the congo -GAZ_00005852 geo_loc_name (country) Denmark metropolitan denmark -GAZ_00000582 geo_loc_name (country) Djibouti djibouti -GAZ_00006890 geo_loc_name (country) Dominica dominica -GAZ_00003952 geo_loc_name (country) Dominican Republic dominican republic -GAZ_00002912 geo_loc_name (country) Ecuador ecuador -GAZ_00003934 geo_loc_name (country) Egypt egypt -GAZ_00002935 geo_loc_name (country) El Salvador el salvador -GAZ_00001091 geo_loc_name (country) Equatorial Guinea equatorial guinea -GAZ_00000581 geo_loc_name (country) Eritrea eritrea -GAZ_00002959 geo_loc_name (country) Estonia estonia -GAZ_00001099 geo_loc_name (country) Eswatini Swaziland -GAZ_00000567 geo_loc_name (country) Ethiopia ethiopia -GAZ_00005811 geo_loc_name (country) Europa Island Ile Europa Europa Island Should make synonym request to GAZ for "Europa Island" -GAZ_00001412 geo_loc_name (country) Falkland Islands (Islas Malvinas) Falkland Islands -GAZ_00059206 geo_loc_name (country) Faroe Islands faroe islands -GAZ_00006891 geo_loc_name (country) Fiji fiji -GAZ_00002937 geo_loc_name (country) Finland finland -GAZ_00003940 geo_loc_name (country) France Metropolitan France -GAZ_00002516 geo_loc_name (country) French Guiana Guyane -GAZ_00002918 geo_loc_name (country) French Polynesia french polynesia -GAZ_00003753 geo_loc_name (country) French Southern and Antarctic Lands -GAZ_00001092 geo_loc_name (country) Gabon gabon -GAZ_00000907 geo_loc_name (country) Gambia gambia -GAZ_00009571 geo_loc_name (country) Gaza Strip gaza strip -GAZ_00004942 geo_loc_name (country) Georgia georgia -GAZ_00002646 geo_loc_name (country) Germany germany -GAZ_00000908 geo_loc_name (country) Ghana ghana -GAZ_00003987 geo_loc_name (country) Gibraltar gibraltar -GAZ_00005808 geo_loc_name (country) Glorioso Islands -GAZ_00002945 geo_loc_name (country) Greece greece -GAZ_00001507 geo_loc_name (country) Greenland greenland -GAZ_02000573 geo_loc_name (country) Grenada -GAZ_00067142 geo_loc_name (country) Guadeloupe -GAZ_00003706 geo_loc_name (country) Guam Territory of Guam -GAZ_00002936 geo_loc_name (country) Guatemala guatemala -GAZ_00001550 geo_loc_name (country) Guernsey -GAZ_00000909 geo_loc_name (country) Guinea guinea -GAZ_00000910 geo_loc_name (country) Guinea-Bissau guinea-bissau -GAZ_00002522 geo_loc_name (country) Guyana guyana -GAZ_00003953 geo_loc_name (country) Haiti haiti -GAZ_00009718 geo_loc_name (country) Heard Island and McDonald Islands -GAZ_00002894 geo_loc_name (country) Honduras honduras -GAZ_00003203 geo_loc_name (country) Hong Kong hong kong -GAZ_00007120 geo_loc_name (country) Howland Island -GAZ_00002952 geo_loc_name (country) Hungary hungary -GAZ_00000843 geo_loc_name (country) Iceland iceland -GAZ_00002839 geo_loc_name (country) India india -GAZ_00003727 geo_loc_name (country) Indonesia indonesia -GAZ_00004474 geo_loc_name (country) Iran iran -GAZ_00004483 geo_loc_name (country) Iraq iraq -GAZ_00002943 geo_loc_name (country) Ireland Republic of Ireland Currently only refering to Southern Ireland (Republic of Ireland), perhaps we should use GAZ_00004018 since it encompasses both and there is no seperate entry in the picklist for Northern island. - R -GAZ_00052477 geo_loc_name (country) Isle of Man isle of man -GAZ_00002476 geo_loc_name (country) Israel israel -GAZ_00002650 geo_loc_name (country) Italy italy -GAZ_00003781 geo_loc_name (country) Jamaica jamaica -GAZ_00005853 geo_loc_name (country) Jan Mayen -GAZ_00002747 geo_loc_name (country) Japan japan -GAZ_00007118 geo_loc_name (country) Jarvis Island -GAZ_00001551 geo_loc_name (country) Jersey -GAZ_00007114 geo_loc_name (country) Johnston Atoll -GAZ_00002473 geo_loc_name (country) Jordan jordan -GAZ_00005809 geo_loc_name (country) Juan de Nova Island -GAZ_00004999 geo_loc_name (country) Kazakhstan kazakhstan -GAZ_00001101 geo_loc_name (country) Kenya kenya -GAZ_00005682 geo_loc_name (country) Kerguelen Archipelago -GAZ_00007116 geo_loc_name (country) Kingman Reef -GAZ_00006894 geo_loc_name (country) Kiribati kiribati -GAZ_00011337 geo_loc_name (country) Kosovo kosovo -GAZ_00005285 geo_loc_name (country) Kuwait kuwait -GAZ_00006893 geo_loc_name (country) Kyrgyzstan kyrgyzstan -GAZ_00006889 geo_loc_name (country) Laos laos -GAZ_00002958 geo_loc_name (country) Latvia latvia -GAZ_00002478 geo_loc_name (country) Lebanon lebanon -GAZ_00001098 geo_loc_name (country) Lesotho lesotho -GAZ_00000911 geo_loc_name (country) Liberia liberia -GAZ_00000566 geo_loc_name (country) Libya libya -GAZ_00003858 geo_loc_name (country) Liechtenstein liechtenstein -GAZ_00007144 geo_loc_name (country) Line Islands -GAZ_00002960 geo_loc_name (country) Lithuania lithuania -GAZ_00002947 geo_loc_name (country) Luxembourg luxembourg -GAZ_00003202 geo_loc_name (country) Macau macau -GAZ_00001108 geo_loc_name (country) Madagascar -GAZ_00001105 geo_loc_name (country) Malawi malawi -GAZ_00003902 geo_loc_name (country) Malaysia malaysia -GAZ_00006924 geo_loc_name (country) Maldives Maldives Archipelago Maldives Archipelago -GAZ_00000584 geo_loc_name (country) Mali mali -GAZ_00005459 geo_loc_name (country) Malta -GAZ_00007161 geo_loc_name (country) Marshall Islands marshall islands -GAZ_00067143 geo_loc_name (country) Martinique Martinique Region -GAZ_00000583 geo_loc_name (country) Mauritania mauritania -GAZ_00003745 geo_loc_name (country) Mauritius -GAZ_00003943 geo_loc_name (country) Mayotte mayotte -GAZ_00002852 geo_loc_name (country) Mexico mexico -GAZ_00005862 geo_loc_name (country) Micronesia micronesia -GAZ_00007112 geo_loc_name (country) Midway Islands Midway Atoll -GAZ_00003897 geo_loc_name (country) Moldova moldova -GAZ_00003857 geo_loc_name (country) Monaco monaco -GAZ_00008744 geo_loc_name (country) Mongolia mongolia -GAZ_00006898 geo_loc_name (country) Montenegro montenegro -GAZ_00003988 geo_loc_name (country) Montserrat montserrat -GAZ_00000565 geo_loc_name (country) Morocco morocco -GAZ_00001100 geo_loc_name (country) Mozambique mozambique -GAZ_00006899 geo_loc_name (country) Myanmar myanmar -GAZ_00001096 geo_loc_name (country) Namibia namibia -GAZ_00006900 geo_loc_name (country) Nauru nauru -GAZ_00007119 geo_loc_name (country) Navassa Island -GAZ_00004399 geo_loc_name (country) Nepal nepal -GAZ_00002946 geo_loc_name (country) Netherlands The Netherlands -GAZ_00005206 geo_loc_name (country) New Caledonia new caledonia -GAZ_00000469 geo_loc_name (country) New Zealand new zealand -GAZ_00002978 geo_loc_name (country) Nicaragua nicaragua -GAZ_00000585 geo_loc_name (country) Niger niger -GAZ_00000912 geo_loc_name (country) Nigeria nigeria -GAZ_00006902 geo_loc_name (country) Niue Niue Fekai Niue Fekai -GAZ_00005908 geo_loc_name (country) Norfolk Island Territory of NORFOLK ISLAND -GAZ_00002801 geo_loc_name (country) North Korea north korea DEMOCRATIC PEOPLE'S REPUBLIC OF KOREA -GAZ_00006895 geo_loc_name (country) North Macedonia Macedonia; Republic of Macedonia -GAZ_00002284 geo_loc_name (country) North Sea -GAZ_00003958 geo_loc_name (country) Northern Mariana Islands northern mariana islands -GAZ_00002699 geo_loc_name (country) Norway kingdom of norway Kingdom of Norway -GAZ_00005283 geo_loc_name (country) Oman oman -GAZ_00005246 geo_loc_name (country) Pakistan pakistan -GAZ_00006905 geo_loc_name (country) Palau palau -GAZ_00002892 geo_loc_name (country) Panama panama -GAZ_00003922 geo_loc_name (country) Papua New Guinea papua new guinea -GAZ_00010832 geo_loc_name (country) Paracel Islands -GAZ_00002933 geo_loc_name (country) Paraguay paraguay Paraguay -GAZ_00002932 geo_loc_name (country) Peru peru Peru -GAZ_00004525 geo_loc_name (country) Philippines The Philippines -GAZ_00005867 geo_loc_name (country) Pitcairn Islands Pitcairn, Henderson, Ducie and Oeno Islands The Pitcairn Islands -GAZ_00002939 geo_loc_name (country) Poland poland -GAZ_00004126 geo_loc_name (country) Portugal Metropolitan Portugal Currently refering to 'Metropolitan Portgual' rather than the 'Portuguese Republic' (GAZ_00002944) aka 'Portugal' which seems incorrect to me. - R -GAZ_00006935 geo_loc_name (country) Puerto Rico Commonwealth of Puerto Rico -GAZ_00005286 geo_loc_name (country) Qatar qatar -GAZ_00001088 geo_loc_name (country) Republic of the Congo Republic of Congo -GAZ_00003945 geo_loc_name (country) Reunion Reunion Island -GAZ_00002951 geo_loc_name (country) Romania romania -GAZ_00023304 geo_loc_name (country) Ross Sea -GAZ_00002721 geo_loc_name (country) Russia russia -GAZ_00001087 geo_loc_name (country) Rwanda rwanda -GAZ_00000849 geo_loc_name (country) Saint Helena -GAZ_00006906 geo_loc_name (country) Saint Kitts and Nevis saint kitts-nevis Saint Kitts-Nevis -GAZ_00006909 geo_loc_name (country) Saint Lucia saint lucia -GAZ_00003942 geo_loc_name (country) Saint Pierre and Miquelon saint-pierre and miquelon -GAZ_00005841 geo_loc_name (country) Saint Martin -GAZ_02000565 geo_loc_name (country) Saint Vincent and the Grenadines saint vincent and the grenadines -GAZ_00006910 geo_loc_name (country) Samoa samoa -GAZ_00003102 geo_loc_name (country) San Marino san marino -GAZ_00006927 geo_loc_name (country) Sao Tome and Principe sao tome and principe -GAZ_00005279 geo_loc_name (country) Saudi Arabia saudi arabia -GAZ_00000913 geo_loc_name (country) Senegal senegal -GAZ_00002957 geo_loc_name (country) Serbia serbia -GAZ_00006922 geo_loc_name (country) Seychelles -GAZ_00000914 geo_loc_name (country) Sierra Leone sierra leone -GAZ_00003923 geo_loc_name (country) Singapore singapore -GAZ_00012579 geo_loc_name (country) Sint Maarten sint maarten -GAZ_00002956 geo_loc_name (country) Slovakia Slovak Republic -GAZ_00002955 geo_loc_name (country) Slovenia slovenia -GAZ_00005275 geo_loc_name (country) Solomon Islands solomon islands -GAZ_00001104 geo_loc_name (country) Somalia somalia -GAZ_00001094 geo_loc_name (country) South Africa south africa Republic of South Africa The actual onto label for this onto ID is 'Republic of South Africa' - are we overwritting onto labels for our ontology? - R -GAZ_00003990 geo_loc_name (country) South Georgia and the South Sandwich Islands -GAZ_00002802 geo_loc_name (country) South Korea south korea Republic of Korea -GAZ_00233439 geo_loc_name (country) South Sudan south sudan -GAZ_00003936 geo_loc_name (country) Spain Metropolitan Spain Shouldn't we be using 'Kingdom of Spain' (GAZ_00000591) rather than the narrower 'Metropolitan Spain'? - R -GAZ_00010831 geo_loc_name (country) Spratly Islands -GAZ_00003924 geo_loc_name (country) Sri Lanka sri lanka -GAZ_00002475 geo_loc_name (country) State of Palestine Palestinian Territories -GAZ_00000560 geo_loc_name (country) Sudan sudan -GAZ_00002525 geo_loc_name (country) Suriname -GAZ_00005396 geo_loc_name (country) Svalbard Svalbard Archipelago -GAZ_00001099 geo_loc_name (country) Swaziland Kingdom of Eswatini -GAZ_00002729 geo_loc_name (country) Sweden sweden -GAZ_00002941 geo_loc_name (country) Switzerland switzerland -GAZ_00002474 geo_loc_name (country) Syria syria -GAZ_00005341 geo_loc_name (country) Taiwan republic of china Republic of China -GAZ_00006912 geo_loc_name (country) Tajikistan tajikistan -GAZ_00001103 geo_loc_name (country) Tanzania tanzania -GAZ_00003744 geo_loc_name (country) Thailand thailand -GAZ_00006913 geo_loc_name (country) Timor-Leste timor-leste -GAZ_00000915 geo_loc_name (country) Togo togo -GAZ_00260188 geo_loc_name (country) Tokelau tokelau -GAZ_00006916 geo_loc_name (country) Tonga tonga -GAZ_00003767 geo_loc_name (country) Trinidad and Tobago trinidad and tobago -GAZ_00005812 geo_loc_name (country) Tromelin Island -GAZ_00000562 geo_loc_name (country) Tunisia tunisia -GAZ_00000558 geo_loc_name (country) Turkey turkey -GAZ_00005018 geo_loc_name (country) Turkmenistan turkmenistan -GAZ_00003955 geo_loc_name (country) Turks and Caicos Islands turks and caicos islands -GAZ_00009715 geo_loc_name (country) Tuvalu tuvalu -GAZ_00002459 geo_loc_name (country) United States of America united states of america United States of America -GAZ_00001102 geo_loc_name (country) Uganda uganda -GAZ_00002724 geo_loc_name (country) Ukraine ukraine -GAZ_00005282 geo_loc_name (country) United Arab Emirates united arab emirates -GAZ_00002637 geo_loc_name (country) United Kingdom united kingdom -GAZ_00002930 geo_loc_name (country) Uruguay uruguay -GAZ_00004979 geo_loc_name (country) Uzbekistan uzbekistan -GAZ_00006918 geo_loc_name (country) Vanuatu vanuatu -GAZ_00002931 geo_loc_name (country) Venezuela venezuela -GAZ_00003756 geo_loc_name (country) Viet Nam viet nam -GAZ_00003959 geo_loc_name (country) Virgin Islands United States Virgin Islands United States Virgin Islands -GAZ_00007111 geo_loc_name (country) Wake Island -GAZ_00007191 geo_loc_name (country) Wallis and Futuna Wallis and Futuna Islands Changed Onto ID from GAZ_00007192 to GAZ_00007191 since the former refers to the islands in general while the later refers to the territory. - R -GAZ_00009572 geo_loc_name (country) West Bank -GAZ_00000564 geo_loc_name (country) Western Sahara western sahara -GAZ_00005284 geo_loc_name (country) Yemen yemen -GAZ_00001107 geo_loc_name (country) Zambia zambia -GAZ_00001106 geo_loc_name (country) Zimbabwe zimbabwe - - library_strategy WGA - library_strategy WGS - library_strategy WXS - library_strategy RNA-Seq - library_strategy miRNA-Seq - library_strategy WCS - library_strategy CLONE - library_strategy POOLCLONE - library_strategy AMPLICON - library_strategy CLONEEND - library_strategy FINISHING - library_strategy ChIP-Seq - library_strategy MNase-Seq - library_strategy DNase-Hypersensitivity - library_strategy Bisulfite-Seq - library_strategy Tn-Seq - library_strategy EST - library_strategy FL-cDNA - library_strategy CTS - library_strategy MRE-Seq - library_strategy MeDIP-Seq - library_strategy MBD-Seq - library_strategy OTHER - - library_source GENOMIC - library_source TRANSCRIPTOMIC - library_source METAGENOMIC - library_source METATRANSCRIPTOMIC - library_source SYNTHETIC - library_source VIRAL RNA - library_source OTHER - - library_selection RANDOM - library_selection PCR - library_selection RANDOM PCR - library_selection RT-PCR - library_selection HMPR - library_selection MF - library_selection CF-S - library_selection CF-M - library_selection CF-H - library_selection CF-T - library_selection MDA - library_selection MSLL - library_selection cDNA - library_selection ChIP - library_selection MNase - library_selection DNAse - library_selection Hybrid Selection - library_selection Reduced Representation - library_selection Restriction Digest - library_selection 5-methylcytidine antibody - library_selection MBD2 protein methyl-CpG binding domain - library_selection CAGE - library_selection RACE - library_selection size fractionation - library_selection Padlock probes capture method - library_selection other - library_selection unspecified - - library_layout single - library_layout paired - - filetype bam - filetype sra - filetype kar - filetype srf - filetype sff - filetype fastq - filetype tab - filetype 454_native - filetype Helicos_native - filetype SOLiD_native - filetype PacBio_HDF5 - filetype CompleteGenomics_native \ No newline at end of file +" Screened for S gene target failure (S dropout) + Sequencing sequencing date xs:date Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 + Sequencing library ID xs:token recommended The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID + Sequencing amplicon size xs:token The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp amplicon_size + Sequencing library preparation kit xs:token The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT + Sequencing flow cell barcode xs:token The barcode of the flow cell used for sequencing. Provide the barcode of the flow cell used for sequencing the sample. FAB06069 + Sequencing sequencing instrument multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access required The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. MinIon Sequencing technology sequencing_technology + Sequencing sequencing protocol name xs:token recommended The name and version number of the sequencing protocol used. Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann sequencing_protocol_name + Sequencing sequencing protocol xs:token The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. design_description + Sequencing sequencing kit number xs:token The manufacturer's kit number. Alphanumeric value. AB456XYZ789 + Sequencing amplicon pcr primer scheme xs:token The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv amplicon _PCR_primer_scheme + + + Bioinformatics and QC metrics + Bioinformatics and QC metrics raw sequence data processing method xs:token recommended The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 raw_sequence_data_processing_method + Bioinformatics and QC metrics dehosting method xs:token recommended The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper dehosting_method + Bioinformatics and QC metrics consensus sequence name xs:token The name of the consensus sequence. Provide the name and version number of the consensus sequence. ncov123assembly3 assembly_name + Bioinformatics and QC metrics consensus sequence filename xs:token The name of the consensus sequence file. Provide the name and version number of the consensus sequence FASTA file. ncov123assembly.fasta filename + Bioinformatics and QC metrics consensus sequence filepath xs:token The filepath of the consesnsus sequence file. Provide the filepath of the consensus sequence FASTA file. /User/Documents/RespLab/Data/ncov123assembly.fasta + Bioinformatics and QC metrics consensus sequence software name xs:token required The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. Ivar assembly_method + Bioinformatics and QC metrics consensus sequence software version xs:decimal required The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 assembly_method_version + Bioinformatics and QC metrics breadth of coverage value xs:token The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95% + Bioinformatics and QC metrics depth of coverage value xs:token The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Coverage genome_coverage + Bioinformatics and QC metrics depth of coverage threshold xs:token The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x + Bioinformatics and QC metrics r1 fastq filename xs:token The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz + Bioinformatics and QC metrics r2 fastq filename xs:token The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz + Bioinformatics and QC metrics r1 fastq filepath xs:token The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz + Bioinformatics and QC metrics r2 fastq filepath xs:token The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz + Bioinformatics and QC metrics fast5 filename xs:token The user-specified filename of the FAST5 file. Provide the FAST5 filename. rona123assembly.fast5 + Bioinformatics and QC metrics fast5 filepath xs:token The location of the FAST5 file within a user's file system. Provide the filepath for the FAST5 file. This information aids in data management. /User/Documents/RespLab/Data/rona123assembly.fast5 + Bioinformatics and QC metrics number of base pairs sequenced xs:nonNegativeInteger The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 + Bioinformatics and QC metrics consensus genome length xs:nonNegativeInteger Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). 38677 + Bioinformatics and QC metrics Ns per 100 kbp xs:decimal 0 The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence. Provide a numerical value (no need to include units). 330 + Bioinformatics and QC metrics reference genome accession xs:token A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 reference_genome + Bioinformatics and QC metrics bioinformatics protocol xs:token The name and version number of the bioinformatics protocol used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can be provided in an SOP or protocol. Provide the name and version number of the protocol. https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members + Lineage and Variant information + Lineage and Variant information lineage/clade name xs:token The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. B.1.1.7 + Lineage and Variant information lineage/clade analysis software name xs:token The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Pangolin + Lineage and Variant information lineage/clade analysis software version xs:token The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 2.1.10 + Lineage and Variant information variant designation select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The variant classification of the lineage/clade i.e. variant, variant of concern. If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. Variant of Concern + Lineage and Variant information variant evidence details xs:token Details about the evidence used to make the variant determination. Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. RT-qPCR TaqPath assay: S gene target failure + Pathogen diagnostic testing + Pathogen diagnostic testing gene name 1 select Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI E (orf4) diagnostic_gene_name_1 + Pathogen diagnostic testing diagnostic pcr protocol 1 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. EGenePCRTest 2 diagnostic_pcr_protocol_value_1 + Pathogen diagnostic testing diagnostic pcr Ct value 1 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the diagnostic RT-PCR test. 21 diagnostic_pcr_Ct_value_1 + Pathogen diagnostic testing gene name 2 select gene name 1 Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI nsp12 (RdRp) diagnostic_gene_name_2 + Pathogen diagnostic testing diagnostic pcr protocol 2 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. RdRpGenePCRTest 3 diagnostic_pcr_protocol_value_2 + Pathogen diagnostic testing diagnostic pcr Ct value 2 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 36 diagnostic_pcr_Ct_value_2 + Pathogen diagnostic testing gene name 3 select gene name 1 Not Applicable; Missing; Not Collected; Not Provided; Restricted Access The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI nsp12 (RdRp) + Pathogen diagnostic testing diagnostic pcr protocol 3 xs:token The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. RdRpGenePCRTest 3 + Pathogen diagnostic testing diagnostic pcr Ct value 3 xs:token The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 + + NCBI SRA information + NCBI SRA information title xs:token Short description that will identify the dataset on public pages. Format: {methodology} of {organism}: {sample info} Genomic sequencing of SARS-CoV-2: Nasopharynx (NP), Swab title + NCBI SRA information library_strategy select See NCBI SRA template for details. Provide the library strategy by selecting a value from the pick list. For amplicon sequencing select "AMPLICON". library_strategy + NCBI SRA information library_source select See NCBI SRA template for details. Provide the library source by selecting a value from the pick list. For amplicon sequencing select "Viral RNA". library_source + NCBI SRA information library_selection select See NCBI SRA template for details. Provide the library selection by selecting a value from the pick list. For amplicon sequencing select "PCR". library_selection + NCBI SRA information library_layout select See NCBI SRA template for details. Provide the library layout by selecting a value from the pick list. For Illumina instruments, select "PAIRED". For Oxford Nanopore instruments, select "SINGLE". library_layout + NCBI SRA information filetype select See NCBI SRA template for details. Provide the filetype by selecting a value from the pick list. filetype + NCBI SRA information filename xs:token See NCBI SRA template for details. Provide the appropriate filename recorded in the Bioinformatics and QC metrics section. If sequence data is "paired", provide the second filename under "Filename 2". filename + NCBI SRA information filename 2 See NCBI SRA template for details. Provide the appropriate filename recorded in the Bioinformatics and QC metrics section. filename 2 + + Contributor acknowledgement + Contributor acknowledgement authors xs:token recommended Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors + Contributor acknowledgement DataHarmonizer provenance provenance DataHarmonizer provenance + + + data status select + data status Not Applicable + data status Missing + data status Not Collected + data status Not Provided + data status Restricted Access + + + +UO:0000035 host age unit month +UO:0000036 host age unit year + +UO:0000035 sample collection date precision year +UO:0000036 sample collection date precision month +UO:0000033 sample collection date precision day + +OBI:0000895 biomaterial extracted RNA (total) +OBI:0000869 biomaterial extracted RNA (poly-A) +OBI:0002627 biomaterial extracted RNA (ribo-depleted) + biomaterial extracted mRNA (messenger RNA) +OBI:0002754 biomaterial extracted mRNA (cDNA) + + + signs and symptoms Abnormal lung auscultation +HP:0000223 signs and symptoms Abnormality of taste sensation + Abnormality of taste sensation Ageusia (complete loss of taste) +HP:0031249 Abnormality of taste sensation Parageusia (distorted sense of taste) +HP_0000224 Abnormality of taste sensation Hypogeusia (reduced sense of taste) +HP:0004408 signs and symptoms Abnormality of the sense of smell +HP_0000458 Abnormality of the sense of smell Anosmia (lost sense of smell) +HP_0004409 Abnormality of the sense of smell Hyposmia (reduced sense of smell) + signs and symptoms Acute Respiratory Distress Syndrome +HP:0011446 signs and symptoms Altered mental status +HP:0011675 signs and symptoms Arrhythmia +HP:0100543 Altered mental status Cognitive impairment +HP_0001259 Altered mental status Coma +HP_0001289 Altered mental status Confusion +HP_0031258 Confusion Delirium (sudden severe confusion) + Altered mental status Inability to arouse (inability to stay awake) +HP_0000737 Altered mental status Irritability +HP_0002371 Altered mental status Loss of speech +HP_0025406 signs and symptoms Asthenia (generalized weakness) +HP:0031352 signs and symptoms Chest tightness or pressure +HP:0025145 Chest tightness or pressure Rigors (fever shakes) +HP_0025143 signs and symptoms Chills (sudden cold sensation) + signs and symptoms Conjunctival injection +HP_0000509 signs and symptoms Conjunctivitis (pink eye) + signs and symptoms Coryza +HP_0012735 signs and symptoms Cough +HP:0031246 Cough Nonproductive cough (dry cough) +HP:0031245 Cough Productive cough (wet cough) +HP:0000961 signs and symptoms Cyanosis (blueish skin discolouration) +HP:0001063 Cyanosis (blueish skin discolouration) Acrocyanosis + Acrocyanosis Circumoral cyanosis (bluish around mouth) + Acrocyanosis Cyanotic face (bluish face) + Cyanosis (blueish skin discolouration) Central Cyanosis + Central Cyanosis Cyanotic lips (bluish lips) + Cyanosis (blueish skin discolouration) Peripheral Cyanosis +HP_0002094 signs and symptoms Dyspnea (breathing difficulty) +HP_0002014 signs and symptoms Diarrhea (watery stool) + signs and symptoms Dry gangrene +HP_0002383 signs and symptoms Encephalitis (brain inflammation) + signs and symptoms Encephalopathy +HP_0012378 signs and symptoms Fatigue (tiredness) +HP_0001945 signs and symptoms Fever + Fever Fever (>=38°C) +HP:0000206 signs and symptoms Glossitis (inflammation of the tongue) + signs and symptoms Ground Glass Opacities (GGO) +HP_0002315 signs and symptoms Headache +HP_0002105 signs and symptoms Hemoptysis (coughing up blood) +HP:0012417 signs and symptoms Hypocapnia +HP_0002615 signs and symptoms Hypotension (low blood pressure) +HP_0012418 signs and symptoms Hypoxemia (low blood oxygen) + Hypoxemia (low blood oxygen) Silent hypoxemia +HP:0011029 signs and symptoms Internal hemorrhage (internal bleeding) +NCIT:C121416 signs and symptoms Loss of Fine Movements +HP_0004396 signs and symptoms Low appetite + signs and symptoms Malaise (general discomfort/unease) + signs and symptoms Meningismus/nuchal rigidity +HP_0001324 signs and symptoms Muscle weakness +HP_0001742 signs and symptoms Nasal obstruction (stuffy nose) +HP_0002018 signs and symptoms Nausea + signs and symptoms nose bleed + signs and symptoms otitis + signs and symptoms Pain +HP:0002027 Pain Abdominal pain +HP_0002829 Pain Arthralgia (painful joints) +HP_0100749 Pain Chest pain + Chest pain Pleuritic chest pain +HP_0003326 Pain Myalgia (muscle pain) +HP_0025439 signs and symptoms Pharyngitis (sore throat) + signs and symptoms Pharyngeal exudate + signs and symptoms Pleural effusion +HP:0002090 signs and symptoms Pneumonia + signs and symptoms Prostration + signs and symptoms Pseudo-chilblains + Pseudo-chilblains Pseudo-chilblains on fingers (covid fingers) + Pseudo-chilblains Pseudo-chilblains on toes (covid toes) +HP_0000988 signs and symptoms Rash +HP_0031417 signs and symptoms Rhinorrhea (runny nose) +HP_0001250 signs and symptoms Seizure +HP:0020219 Seizure Motor seizure +HP:0025144 signs and symptoms Shivering (involuntary muscle twitching) +HP_0001350 signs and symptoms Slurred speech + signs and symptoms Sneezing + signs and symptoms Sputum Production +HP:0001297 signs and symptoms Stroke + signs and symptoms Swollen Lymph Nodes +HP_0002789 signs and symptoms Tachypnea (accelerated respiratory rate) + signs and symptoms Vertigo (dizziness) +HP_0002013 signs and symptoms Vomiting (throwing up) + + host vaccination status Fully Vaccinated prior_SARS-CoV-2_vaccination:Yes + host vaccination status Partially Vaccinated prior_SARS-CoV-2_vaccination:Yes + host vaccination status Not Vaccinated prior_SARS-CoV-2_vaccination:No + + prior SARS-CoV-2 antiviral treatment Prior antivrial treatment prior_SARS-CoV-2_antiviral_treatment:Yes + prior SARS-CoV-2 antiviral treatment No prior antivrial treatment prior_SARS-CoV-2_antiviral_treatment:No + prior SARS-CoV-2 antiviral treatment Unknown + + + + pre-existing conditions and risk factors Age 60+ + pre-existing conditions and risk factors Anemia + pre-existing conditions and risk factors Anorexia + pre-existing conditions and risk factors Birthing labor + pre-existing conditions and risk factors Bone marrow failure + pre-existing conditions and risk factors Cancer + Cancer Breast cancer + Cancer Colorectal cancer + Cancer Hematologic malignancy + Cancer Lung cancer + Cancer Metastatic disease + pre-existing conditions and risk factors Cancer treatment + Cancer treatment Cancer surgery + Cancer treatment Chemotherapy + Chemotherapy Adjuvant chemotherapy + pre-existing conditions and risk factors Cardiac disorder +HP:0011675 Cardiac disorder Arrhythmia + Cardiac disorder Cardiac disease +HP:0001638 Cardiac disorder Cardiomyopathy + Cardiac disorder Cardiac injury + Cardiac disorder Hypertension (high blood pressure) +HP:0002615 Cardiac disorder Hypotension (low blood pressure) + pre-existing conditions and risk factors Cesarean section + pre-existing conditions and risk factors Chronic cough + pre-existing conditions and risk factors Chronic gastrointestinal disease + pre-existing conditions and risk factors Chronic lung disease + pre-existing conditions and risk factors Corticosteroids + pre-existing conditions and risk factors Diabetes mellitus (diabetes) + Diabetes mellitus (diabetes) Type I diabetes mellitus (T1D) + Diabetes mellitus (diabetes) Type II diabetes mellitus (T2D) + pre-existing conditions and risk factors Eczema + pre-existing conditions and risk factors Electrolyte disturbance + Electrolyte disturbance Hypocalcemia + Electrolyte disturbance Hypokalemia + Electrolyte disturbance Hypomagnesemia +HP:0002383 pre-existing conditions and risk factors Encephalitis (brain inflammation) + pre-existing conditions and risk factors Epilepsy + pre-existing conditions and risk factors Hemodialysis + pre-existing conditions and risk factors Hemoglobinopathy + pre-existing conditions and risk factors Human immunodeficiency virus (HIV) + Human immunodeficiency virus (HIV) Acquired immunodeficiency syndrome (AIDS) + Human immunodeficiency virus (HIV) HIV and antiretroviral therapy (ART) + pre-existing conditions and risk factors Immunocompromised + Immunocompromised Lupus + pre-existing conditions and risk factors Inflammatory bowel disease (IBD) + Inflammatory bowel disease (IBD) Colitis + Colitis Ulcerative colitis + Inflammatory bowel disease (IBD) Crohn's disease + pre-existing conditions and risk factors Renal disorder + Renal disorder Renal disease + Renal disorder Chronic renal disease + Renal disorder Renal failure + pre-existing conditions and risk factors Liver disease + Liver disease Chronic liver disease + Chronic liver disease Fatty liver disease (FLD) +HP:0003326 pre-existing conditions and risk factors Myalgia (muscle pain) + pre-existing conditions and risk factors Myalgic encephalomyelitis (ME) + pre-existing conditions and risk factors Neurological disorder + Neurological disorder Neuromuscular disorder + pre-existing conditions and risk factors Obesity + Obesity Severe obesity + pre-existing conditions and risk factors Respiratory disorder + Respiratory disorder Asthma + Respiratory disorder Chronic bronchitis + Respiratory disorder Chronic pulmonary disease + Chronic pulmonary disease Chronic obstructive pulmonary disease + Respiratory disorder Emphysema + Respiratory disorder Lung disease + Lung disease Chronic lung disease + Lung disease Pulmonary fibrosis +HP:0002090 Respiratory disorder Pneumonia + Respiratory disorder Respiratory failure + Respiratory failure Adult respiratory distress syndrome + Respiratory failure Newborn respiratory distress syndrome + Respiratory disorder Tuberculosis + pre-existing conditions and risk factors Postpartum (≤6 weeks) + pre-existing conditions and risk factors Pregnancy + pre-existing conditions and risk factors Rheumatic disease + pre-existing conditions and risk factors Sickle cell disease + pre-existing conditions and risk factors Substance use + Substance use Alcohol abuse + Substance use Drug abuse + Drug abuse Injection drug abuse + Substance use Smoking + Substance use Vaping +HP:0002789 pre-existing conditions and risk factors Tachypnea (accelerated respiratory rate) + pre-existing conditions and risk factors Transplant + Transplant Bone marrow transplant + Transplant Cardiac transplant + Transplant Hematopoietic stem cell transplant (HSCT) + Transplant Kidney transplant + Transplant Liver transplant + + variant designation Variant of Concern (VOC) + variant designation Variant of Interest (VOI) + + complications Abnormal blood oxygen level + complications Acute respiratory failure +HP:0011675 complications Arrhythmia (complication) + Arrhythmia (complication) Tachycardia + Tachycardia Polymorphic ventricular tachycardia (VT) + Tachycardia Tachyarrhythmia + complications Noncardiogenic pulmonary edema + Noncardiogenic pulmonary edema Acute respiratory distress syndrome (ARDS) + Acute respiratory distress syndrome (ARDS) COVID-19 associated ARDS (CARDS) + Acute respiratory distress syndrome (ARDS) Neurogenic pulmonary edema (NPE) + complications Cardiac injury + complications Cardiac arrest + complications Cardiogenic shock + complications Blood clot + Blood clot Arterial clot + Blood clot Deep vein thrombosis (DVT) + Blood clot Pulmonary embolism (PE) +HP:0001638 complications Cardiomyopathy + complications Central nervous system invasion + complications Stroke (complication) + Stroke (complication) Central Nervous System Vasculitis + Stroke (complication) Ischemic stroke + Ischemic stroke Acute ischemic stroke + complications Coma + complications Convulsions + complications COVID-19 associated coagulopathy (CAC) + complications Cystic fibrosis + complications Cytokine release syndrome + complications Disseminated intravascular coagulation (DIC) + complications Encephalopathy + complications Fulminant myocarditis + complications Guillain-Barré syndrome + complications Internal hemorrhage (complication; internal bleeding) + Internal hemorrhage (complication; internal bleeding) Intracerebral haemorrhage + complications Kawasaki disease + Kawasaki disease Typical Kawasaki disease + Kawasaki disease Incomplete Kawasaki disease + complications Kidney injury + Kidney injury Acute kidney injury + complications Liver dysfunction + complications Liver injury + Liver injury Acute liver injury + complications Lung injury + Lung injury Acute lung injury + complications Meningitis + complications Migraine + complications Miscarriage + complications Multisystem inflammatory syndrome in children (MIS-C) + complications Muscle injury + complications Myalgic encephalomyelitis (ME) + complications Myocardial infarction (heart attack) + Myocardial infarction (heart attack) Acute myocardial infarction + Myocardial infarction (heart attack) Elevation myocardial infarction + Myocardial infarction (heart attack) ST-segment elevation myocardial infarction + complications Myocardial injury + complications Neonatal complications + complications Organ failure + Organ failure Heart failure + Organ failure Liver failure + complications Paralysis + complications Pneumothorax (collapsed lung) + Pneumothorax (collapsed lung) Spontaneous pneumothorax + Pneumothorax (collapsed lung) Spontaneous tension pneymothorax + complications Pneumonia (complication) + Pneumonia (complication) COVID-19 pneumonia + complications Pregancy complications + complications Rhabdomyolysis + complications Secondary infection + Secondary infection Secondary staph infection + Secondary infection Secondary strep infection +HP:0001250 complications Seizure (complication) +HP:0020219 Seizure (complication) Motor seizure + complications Sepsis + complications Septicemia + complications Shock + Shock Hyperinflammatory shock + Shock Refractory cardiogenic shock + Shock Refractory cardiogenic plus vasoplegic shock + Shock Septic shock + complications Vasculitis + complications Ventilation induced lung injury (VILI) + + sample collected in quarantine Yes + sample collected in quarantine No + sample collected in quarantine Unknown + + +UBERON_0000178 anatomical material Blood +UBERON_0006314 anatomical material Fluid +UBERON_0001836 Fluid Saliva +UBERON_0001359 Fluid Fluid (cerebrospinal (CSF)) +UBERON_0002409 Fluid Fluid (pericardial) +UBERON_0001087 Fluid Fluid (pleural) +UBERON_0036243 Fluid Fluid (vaginal) +UBERON_0000173 Fluid Fluid (amniotic) +UBERON_0000479 anatomical material Tissue + + + +UBERON_0001245 anatomical part Anus + anatomical part Buccal mucosa +UBERON_0002114 anatomical part Duodenum +UBERON_0000970 anatomical part Eye + anatomical part Intestine +UBERON_0001052 anatomical part Rectum +UBERON_0001003 anatomical part Skin +UBERON_0000945 anatomical part Stomach +UBERON_0001557 anatomical part Upper respiratory tract +UBERON_2001427 Upper respiratory tract Anterior Nares +UBERON_0001043 Upper respiratory tract Esophagus +UBERON_0002453 Upper respiratory tract Ethmoid sinus + Upper respiratory tract Nasal Cavity +UBERON_0005921 Nasal Cavity Middle Nasal Turbinate +UBERON_0005922 Nasal Cavity Inferior Nasal Turbinate +UBERON_0001728 Upper respiratory tract Nasopharynx (NP) +UBERON_0001729 Upper respiratory tract Oropharynx (OP) +UBERON_0001558 anatomical part Lower respiratory tract +UBERON_0002185 Lower respiratory tract Bronchus +UBERON_0002048 Lower respiratory tract Lung +UBERON_0002186 Lung Bronchiole +UBERON_0002169 Lung Alveolar sac +UBERON_0009778 Lower respiratory tract Pleural sac +UBERON_0002402 Pleural sac Pleural cavity +UBERON_0003126 Lower respiratory tract Trachea + + + + +UBERON_0001988 body product Feces +UBERON_0001088 body product Urine +UBERON_0001089 body product Sweat +UBERON_0000912 body product Mucus +UBERON_0007311 Mucus Sputum +UBERON_0001827 body product Tear +UBERON_0006530 body product Fluid (seminal) +UBERON_0001913 body product Breast Milk + + + + + environmental material Air vent +ENVO_00003896 environmental material Banknote + environmental material Bed rail +ENVO_01000486 environmental material Building floor +ENVO_02000058 environmental material Cloth + environmental material Control panel +NCIT_C48950 environmental material Door + environmental material Door handle + environmental material Face mask + environmental material Face shield +FOODON:00002403 environmental material Food +FOODON:03490100 environmental material Food packaging +ENVO:01000481 environmental material Glass + environmental material Handrail + environmental material Hospital gown + environmental material Light switch + environmental material Locker + environmental material N95 mask + environmental material Nurse call button + environmental material Paper +ENVO:01000060 environmental material Particulate matter +ENVO:01000404 environmental material Plastic + environmental material PPE gown +ENVO_00002018 environmental material Sewage +ENVO_01000990 environmental material Sink +ENVO_00001998 environmental material Soil + environmental material Stainless steel + environmental material Tissue paper + environmental material Toilet bowl +ENVO_00002006 environmental material Water + environmental material Wastewater + environmental material Window +ENVO:00002040 environmental material Wood + + environmental site Acute care facility +ENVO:00003040 environmental site Animal house +ENVO:01000422 environmental site Bathroom + environmental site Clinical assessment centre + environmental site Conference venue +ENVO REQUEST environmental site Corridor +ENVO_01000927 environmental site Daycare +NCIT_C53513 environmental site Emergency room (ER) + environmental site Family practice clinic + environmental site Group home + environmental site Homeless shelter +OBI_0000844 environmental site Hospital +NCIT_C53511 environmental site Intensive Care Unit (ICU) +GENEPIO_0001035 environmental site Long Term Care Facility + environmental site Patient room +ENVO_01001481 environmental site Prison +ENVO_01000536 environmental site Production Facility +NCIT_C17118 environmental site School + environmental site Sewage Plant + environmental site Subway train + environmental site Wet market + +NCIT:C52009 collection method Amniocentesis +NCIT:C15631 collection method Aspiration + Aspiration Suprapubic Aspiration + Aspiration Tracheal aspiration + Aspiration Vacuum Aspiration +OBI:0002650 collection method Biopsy +OBI:0002651 Biopsy Needle Biopsy + collection method Filtration + Filtration Air filtration +OBI:0600044 collection method Lavage +BTO:0000155 Lavage Bronchoalveolar lavage (BAL) + Lavage Gastric Lavage +NCIT:C15327 collection method Lumbar Puncture +MMO:0000344 collection method Necropsy +NCIT:c28221 collection method Phlebotomy +GENEPIO:0002116 collection method Rinsing + Rinsing Saline gargle (mouth rinse and gargle) + collection method Scraping +GENEPIO:0002117 collection method Swabbing + Swabbing Finger Prick + collection method Wash + collection method Washout Tear Collection + + collection device Air filter +NCIT:C113122 collection device Blood Collection Tube +NCIT:C17611 collection device Bronchoscope + collection device Collection Container + collection device Collection Cup + collection device Fibrobronchoscope Brush + collection device Filter + collection device Fine Needle + collection device Microcapillary tube +OBI:0001128 collection device Micropipette +OBI:0000436 collection device Needle +NCIT:C113675 collection device Serum Collection Tube + collection device Sputum Collection Tube + collection device Suction Catheter +NCIT:c17627 collection device Swab + collection device Urine Collection Tube + collection device Virus Transport Medium + + +NCBITaxon_9606 host (scientific name) Homo sapiens +NCBITaxon_9913 host (scientific name) Bos taurus +NCBITaxon_9615 host (scientific name) Canis lupus familiaris +NCBITaxon_9397 host (scientific name) Chiroptera +NCBITaxon_8930 host (scientific name) Columbidae +NCBITaxon_9685 host (scientific name) Felis catus +NCBITaxon_9031 host (scientific name) Gallus gallus +NCBITaxon_9973 host (scientific name) Manis +NCBITaxon_9974 host (scientific name) Manis javanica +NCBITaxon_452646 host (scientific name) Neovison vison +NCBITaxon_9689 host (scientific name) Panthera leo +NCBITaxon_9694 host (scientific name) Panthera tigris +NCBITaxon_58055 host (scientific name) Rhinolophidae +NCBITaxon_59477 host (scientific name) Rhinolophus affinis +NCBITaxon_9825 host (scientific name) Sus scrofa domesticus +NCBITaxon_9673 host (scientific name) Viverridae + + +NCBITaxon_9605 host (common name) Human +NCBITaxon_9397 host (common name) Bat +NCBITaxon_9685 host (common name) Cat +NCBITaxon_9031 host (common name) Chicken +NCBITaxon_9673 host (common name) Civets +NCBITaxon_9913 host (common name) Cow +NCBITaxon_9615 host (common name) Dog +NCBITaxon_9689 host (common name) Lion + host (common name) Mink +NCBITaxon_9973 host (common name) Pangolin +NCBITaxon_9823 host (common name) Pig +NCBITaxon_8930 host (common name) Pigeon +NCBITaxon_9694 host (common name) Tiger + + + host health state Asymptomatic + host health state Deceased + host health state Healthy + host health state Recovered + host health state Symptomatic + + + host health status details Hospitalized + Hospitalized Hospitalized (Non-ICU) + Hospitalized Hospitalized (ICU) + host health status details Mechanical Ventilation + host health status details Medically Isolated + Medically Isolated Medically Isolated (Negative Pressure) + host health status details Self-quarantining + + host health outcome Deceased + host health outcome Deteriorating + host health outcome Recovered + host health outcome Stable + + organism Coronaviridae + organism Severe acute respiratory syndrome coronavirus 2 + + + + + + + purpose of sampling Cluster/Outbreak investigation + purpose of sampling Diagnostic testing +NCIT_c15429 purpose of sampling Research + purpose of sampling Surveillance + + + purpose of sequencing Baseline surveillance (random sampling) + purpose of sequencing Targeted surveillance (non-random sampling) + Targeted surveillance (non-random sampling) Priority surveillance project + Priority surveillance project Screening for Variants of Concern (VoC) + Priority surveillance project Longitudinal surveillance (repeat sampling of individuals) + Priority surveillance project Re-infection surveillance + Priority surveillance project Vaccine escape surveillance + Priority surveillance project Travel-associated surveillance + Travel-associated surveillance Domestic travel surveillance + Travel-associated surveillance International travel surveillance + purpose of sequencing Cluster/Outbreak investigation + Cluster/Outbreak investigation Multi-jurisdictional outbreak investigation + Cluster/Outbreak investigation Intra-jurisdictional outbreak investigation + purpose of sequencing Research + Research Viral passage experiment + Research Protocol testing experiment + + + specimen processing Virus passage + specimen processing RNA re-extraction (post RT-PCR) + specimen processing Specimens pooled + + lab host 293/ACE2 cell line +BTO_0000195 lab host Caco2 cell line +BTO_0002750 lab host Calu3 cell line + lab host EFK3B cell line +BTO_0002181 lab host HEK293T cell line + lab host HRCE cell line +BTO_0001950 lab host Huh7 cell line +CLO_0007330 lab host LLCMk2 cell line +BTO_0000836 lab host MDBK cell line + lab host Mv1Lu cell line +BTO_0002924 lab host NHBE cell line +BTO_0001865 lab host PK-15 cell line +BTO_0002909 lab host RK-13 cell line +BTO_0002035 lab host U251 cell line +BTO_0001444 lab host Vero cell line +BTO:0004755 lab host Vero E6 cell line + lab host VeroE6/TMPRSS2 cell line + + host disease COVID-19 + + host age bin 0 - 9 + host age bin 10 - 19 + host age bin 20 - 29 + host age bin 30 - 39 + host age bin 40 - 49 + host age bin 50 - 59 + host age bin 60 - 69 + host age bin 70 - 79 + host age bin 80 - 89 + host age bin 90 - 99 + host age bin 100+ + +OMRSE:00000009? host gender Female +OMRSE:00000008? host gender Male + host gender Non-binary gender + host gender Transgender (Male to Female) + host gender Transgender (Female to Male) + host gender Undeclared + host gender Unknown + + exposure event Mass Gathering + Mass Gathering Convention + Mass Gathering Convocation + Mass Gathering Agricultural Event + exposure event Religious Gathering + Religious Gathering Mass + exposure event Social Gathering + Social Gathering Baby Shower + Social Gathering Community Event + Social Gathering Family Gathering + Family Gathering Family Reunion + Social Gathering Funeral + Social Gathering Party + Social Gathering Potluck + Social Gathering Wedding + exposure event Other exposure event + + exposure contact level Contact with infected individual + Contact with infected individual Direct contact (direct human-to-human contact) + Contact with infected individual Indirect contact + Indirect contact Close contact (face-to-face, no direct contact) + Indirect contact Casual contact + + + host role Attendee + Attendee Student + host role Patient + Patient Inpatient + Patient Outpatient + host role Passenger + host role Resident + host role Visitor + host role Volunteer + host role Work + Work Administrator + Work First Responder + First Responder Firefighter + First Responder Paramedic + First Responder Police Officer + Work Healthcare Worker + Work Nurse + Work Personal Care Aid + Work Pharmacist + Work Physician + Work Housekeeper + Work Kitchen Worker + Work Laboratory Worker + Work Rotational Worker + Work Seasonal Worker + Work Veterinarian + host role Social role + Social role Acquaintance of case + Social role Relative of case + Relative of case Child of case + Relative of case Parent of case + Relative of case Father of case + Relative of case Mother of case + Social role Spouse of case + host role Other Host Role + + exposure setting Human Exposure + Human Exposure Known COVID-19 Case + Human Exposure Patient Contact + Human Exposure Probable COVID-19 Case + Human Exposure Person with Acute Respiratory Illness + Human Exposure Person with Fever and/or Cough + Human Exposure Person who Recently Travelled + exposure setting Occupational or Residency Exposure + Occupational or Residency Exposure Abbatoir + Occupational or Residency Exposure Animal Rescue + Occupational or Residency Exposure Childcare + Childcare Daycare + Occupational or Residency Exposure Funeral Home + Occupational or Residency Exposure Place of Worship + Place of Worship Church + Place of Worship Mosque + Place of Worship Temple + Occupational or Residency Exposure Nursery + Occupational or Residency Exposure Household + Occupational or Residency Exposure Community Service Centre + Occupational or Residency Exposure Correctional Facility + Occupational or Residency Exposure Dormitory + Occupational or Residency Exposure Farm + Occupational or Residency Exposure First Nations Reserve + Occupational or Residency Exposure Group Home + Occupational or Residency Exposure Healthcare Setting + Healthcare Setting Ambulance + Healthcare Setting Acute Care Facility + Healthcare Setting Clinic + Healthcare Setting Community Health Centre + Healthcare Setting Hospital + Hospital Emergency Department + Hospital ICU + Hospital Ward + Healthcare Setting Laboratory + Healthcare Setting Long-Term Care Facility + Healthcare Setting Pharmacy + Healthcare Setting Physician's Office + Occupational or Residency Exposure Insecure Housing (Homeless) + Occupational or Residency Exposure Office + Occupational or Residency Exposure Outdoors + Outdoors Camp/camping + Outdoors Hiking + Outdoors Hunting + Occupational or Residency Exposure Petting zoo + Occupational or Residency Exposure Restaurant + Occupational or Residency Exposure Retail Store + Occupational or Residency Exposure School + Occupational or Residency Exposure Temporary Residence + Temporary Residence Homeless Shelter + Temporary Residence Hotel + Occupational or Residency Exposure Veterinary Care Clinic + exposure setting Travel Exposure + Travel Exposure Travelled + Travelled Travelled on a Cruise Ship + Travelled Travelled on a Plane + Travelled Travelled on Ground Transport + Travelled Travelled outside Province/Territory + Travelled Travelled outside Canada + exposure setting Other Exposure Setting + + Host reinfection information prior SARS-CoV-2 infection select + prior SARS-CoV-2 infection Yes + prior SARS-CoV-2 infection No + prior SARS-CoV-2 infection Unknown + + +OBI_0000759 sequencing instrument Illumina platform:ILLUMINA +OBI_0002128 Illumina Illumina Genome Analyzer platform:ILLUMINA|instrument_model:Illumina Genome Analyzer +OBI_0000703 Illumina Genome Analyzer Illumina Genome Analyzer II platform:ILLUMINA|instrument_model:Illumina Genome Analyzer II +OBI_0002000 Illumina Genome Analyzer Illumina Genome Analyzer IIx platform:ILLUMINA|instrument_model:Illumina Genome Analyzer IIx + Illumina Illumina HiScanSQ platform:ILLUMINA|instrument_model:Illumina HiScanSQ + Illumina Illumina HiSeq platform:ILLUMINA +OBI_0002129 Illumina Illumina HiSeq X platform:ILLUMINA + Illumina HiSeq X Illumina HiSeq X Five platform:ILLUMINA|instrument_model: Illumina HiSeq X Five +OBI_0002129 Illumina HiSeq X Illumina HiSeq X Ten platform:ILLUMINA|instrument_model:Illumina HiSeq X Ten +OBI_0002022 Illumina Illumina HiSeq 1000 platform:ILLUMINA|instrument_model:Illumina HiSeq 1000 + Illumina Illumina HiSeq 1500 platform:ILLUMINA +OBI_0002001 Illumina Illumina HiSeq 2000 platform:ILLUMINA|instrument_model:Illumina HiSeq 2000 +OBI_0002002 Illumina Illumina HiSeq 2500 platform:ILLUMINA|instrument_model:Illumina HiSeq 2500 +OBI_0002048 Illumina Illumina HiSeq 3000 platform:ILLUMINA +OBI_0002049 Illumina Illumina HiSeq 4000 platform:ILLUMINA + Illumina Illumina iSeq platform:ILLUMINA +EFO:0008635 Illumina iSeq Illumina iSeq 100 platform:ILLUMINA + Illumina Illumina NovaSeq platform:ILLUMINA +OBI_0002630 Illumina NovaSeq Illumina NovaSeq 6000 platform:ILLUMINA +http://www.ebi.ac.uk/efo/EFO_0008636 Illumina Illumina MiniSeq platform:ILLUMINA +OBI_0002003 Illumina Illumina MiSeq platform:ILLUMINA|instrument_model:Illumina MiSeq + Illumina Illumina NextSeq platform:ILLUMINA +OBI_0002021 Illumina Illumina NextSeq 500 platform:ILLUMINA|instrument_model:Illumina NextSeq 500 + Illumina Illumina NextSeq 550 platform:ILLUMINA +OBI_0001856 sequencing instrument Pacific Biosciences platform:PACBIO_SMRT + Pacific Biosciences PacBio RS platform:PACBIO_SMRT|instrument_model:PacBio RS +OBI_0002012 Pacific Biosciences PacBio RS II platform:PACBIO_SMRT|instrument_model:PacBio RS II +OBI_0002632 Pacific Biosciences PacBio Sequel platform:PACBIO_SMRT +OBI_0002633 Pacific Biosciences PacBio Sequel II platform:PACBIO_SMRT + sequencing instrument Ion Torrent platform:ION_TORRENT +GENEPIO_0001935 Ion Torrent Ion Torrent PGM platform:ION_TORRENT|instrument_model:Ion Torrent PGM + Ion Torrent Ion Torrent Proton platform:ION_TORRENT|instrument_model:Ion Torrent Proton + Ion Torrent Ion Torrent S5 XL platform:ION_TORRENT + Ion Torrent Ion Torrent S5 platform:ION_TORRENT + sequencing instrument Oxford Nanopore platform:OXFORD_NANOPORE + Oxford Nanopore GridION platform:OXFORD_NANOPORE|instrument_model:GridION + Oxford Nanopore MinION platform:OXFORD_NANOPORE|instrument_model:MinION + Oxford Nanopore PromethION platform:OXFORD_NANOPORE + sequencing instrument BGI Genomics + BGI Genomics BGISEQ-500 + sequencing instrument MGI + MGI DNBSEQ-T7 + MGI DNBSEQ-G400 + MGI DNBSEQ-G400 FAST + MGI DNBSEQ-G50 + + +PR:P0DTC4 gene name 1 E gene (orf4) +PR:P0DTC5 gene name 1 M gene (orf5) +PR:P0DTC9 gene name 1 N gene (orf9) +PR:P0DTC2 gene name 1 Spike gene (orf2) +PR:000050281 gene name 1 orf1ab (rep) +PR:P0DTC1-1 orf1ab (rep) orf1a (pp1a) +PR:000050280 orf1a (pp1a) nsp11 +PR:000050270 orf1ab (rep) nsp1 +PR:000050271 orf1ab (rep) nsp2 +PR:000050272 orf1ab (rep) nsp3 +PR:000050273 orf1ab (rep) nsp4 +PR:000050274 orf1ab (rep) nsp5 +PR:000050275 orf1ab (rep) nsp6 +PR:000050276 orf1ab (rep) nsp7 +PR:000050277 orf1ab (rep) nsp8 +PR:000050278 orf1ab (rep) nsp9 +PR:000050279 orf1ab (rep) nsp10 +PR:000050284 orf1ab (rep) RdRp gene (nsp12) +PR:000050285 orf1ab (rep) hel gene (nsp13) +PR:000050286 orf1ab (rep) exoN gene (nsp14) +PR:000050287 orf1ab (rep) nsp15 +PR:000050288 orf1ab (rep) nsp16 +PR:P0DTC3 gene name 1 orf3a + gene name 1 orf3b +PR:P0DTC6 gene name 1 orf6 (ns6) +PR:P0DTC7 gene name 1 orf7a +PR:P0DTD8 gene name 1 orf7b (ns7b) +PR:P0DTC8 gene name 1 orf8 (ns8) +PR:P0DTD2 gene name 1 orf9b + gene name 1 orf9c +PR:A0A663DJA2 gene name 1 orf10 + gene name 1 orf14 + gene name 1 SARS-COV-2 5' UTR + + + + + +GAZ_00006882 geo_loc_name (country) Afghanistan +GAZ_00002953 geo_loc_name (country) Albania +GAZ_00000563 geo_loc_name (country) Algeria +GAZ_00003957 geo_loc_name (country) American Samoa +GAZ_00002948 geo_loc_name (country) Andorra +GAZ_00001095 geo_loc_name (country) Angola +GAZ_00009159 geo_loc_name (country) Anguilla +GAZ_00000462 geo_loc_name (country) Antarctica +GAZ_00006883 geo_loc_name (country) Antigua and Barbuda +GAZ_00002928 geo_loc_name (country) Argentina +GAZ_00004094 geo_loc_name (country) Armenia +GAZ_00004025 geo_loc_name (country) Aruba +GAZ_00005901 geo_loc_name (country) Ashmore and Cartier Islands +GAZ_00000463 geo_loc_name (country) Australia +GAZ_00002942 geo_loc_name (country) Austria +GAZ_00004941 geo_loc_name (country) Azerbaijan +GAZ_00002733 geo_loc_name (country) Bahamas +GAZ_00005281 geo_loc_name (country) Bahrain +GAZ_00007117 geo_loc_name (country) Baker Island +GAZ_00003750 geo_loc_name (country) Bangladesh +GAZ_00001251 geo_loc_name (country) Barbados +GAZ_00005810 geo_loc_name (country) Bassas da India +GAZ_00006886 geo_loc_name (country) Belarus +GAZ_00002938 geo_loc_name (country) Belgium +GAZ_00002934 geo_loc_name (country) Belize +GAZ_00000904 geo_loc_name (country) Benin +GAZ_00001264 geo_loc_name (country) Bermuda +GAZ_00003920 geo_loc_name (country) Bhutan +GAZ_00002511 geo_loc_name (country) Bolivia +GAZ_00025355 geo_loc_name (country) Borneo +GAZ_00006887 geo_loc_name (country) Bosnia and Herzegovina +GAZ_00001097 geo_loc_name (country) Botswana +GAZ_00001453 geo_loc_name (country) Bouvet Island +GAZ_00002828 geo_loc_name (country) Brazil +GAZ_00003961 geo_loc_name (country) British Virgin Islands +GAZ_00003901 geo_loc_name (country) Brunei +GAZ_00002950 geo_loc_name (country) Bulgaria +GAZ_00000905 geo_loc_name (country) Burkina Faso +GAZ_00001090 geo_loc_name (country) Burundi +GAZ_00006888 geo_loc_name (country) Cambodia +GAZ_00001093 geo_loc_name (country) Cameroon +GAZ_00002560 geo_loc_name (country) Canada +GAZ_00001227 geo_loc_name (country) Cape Verde +GAZ_00003986 geo_loc_name (country) Cayman Islands +GAZ_00001089 geo_loc_name (country) Central African Republic +GAZ_00000586 geo_loc_name (country) Chad +GAZ_00002825 geo_loc_name (country) Chile +GAZ_00002845 geo_loc_name (country) China +GAZ_00005915 geo_loc_name (country) Christmas Island +GAZ_00005838 geo_loc_name (country) Clipperton Island +GAZ_00009721 geo_loc_name (country) Cocos Islands +GAZ_00002929 geo_loc_name (country) Colombia +GAZ_00005820 geo_loc_name (country) Comoros +GAZ_00053798 geo_loc_name (country) Cook Islands +GAZ_00005917 geo_loc_name (country) Coral Sea Islands +GAZ_00002901 geo_loc_name (country) Costa Rica +GAZ_00000906 geo_loc_name (country) Cote d'Ivoire +GAZ_00002719 geo_loc_name (country) Croatia +GAZ_00003762 geo_loc_name (country) Cuba +GAZ_00004021 geo_loc_name (country) Curacao +GAZ_00004006 geo_loc_name (country) Cyprus +GAZ_00002954 geo_loc_name (country) Czech Republic +GAZ_00001086 geo_loc_name (country) Democratic Republic of the Congo +GAZ_00005852 geo_loc_name (country) Denmark +GAZ_00000582 geo_loc_name (country) Djibouti +GAZ_00006890 geo_loc_name (country) Dominica +GAZ_00003952 geo_loc_name (country) Dominican Republic +GAZ_00002912 geo_loc_name (country) Ecuador +GAZ_00003934 geo_loc_name (country) Egypt +GAZ_00002935 geo_loc_name (country) El Salvador +GAZ_00001091 geo_loc_name (country) Equatorial Guinea +GAZ_00000581 geo_loc_name (country) Eritrea +GAZ_00002959 geo_loc_name (country) Estonia +GAZ_00001099 geo_loc_name (country) Eswatini +GAZ_00000567 geo_loc_name (country) Ethiopia +GAZ_00005811 geo_loc_name (country) Europa Island +GAZ_00001412 geo_loc_name (country) Falkland Islands (Islas Malvinas) +GAZ_00059206 geo_loc_name (country) Faroe Islands +GAZ_00006891 geo_loc_name (country) Fiji +GAZ_00002937 geo_loc_name (country) Finland +GAZ_00003940 geo_loc_name (country) France +GAZ_00002516 geo_loc_name (country) French Guiana +GAZ_00002918 geo_loc_name (country) French Polynesia +GAZ_00003753 geo_loc_name (country) French Southern and Antarctic Lands +GAZ_00001092 geo_loc_name (country) Gabon +GAZ_00000907 geo_loc_name (country) Gambia +GAZ_00009571 geo_loc_name (country) Gaza Strip +GAZ_00004942 geo_loc_name (country) Georgia +GAZ_00002646 geo_loc_name (country) Germany +GAZ_00000908 geo_loc_name (country) Ghana +GAZ_00003987 geo_loc_name (country) Gibraltar +GAZ_00005808 geo_loc_name (country) Glorioso Islands +GAZ_00002945 geo_loc_name (country) Greece +GAZ_00001507 geo_loc_name (country) Greenland +GAZ_02000573 geo_loc_name (country) Grenada +GAZ_00067142 geo_loc_name (country) Guadeloupe +GAZ_00003706 geo_loc_name (country) Guam +GAZ_00002936 geo_loc_name (country) Guatemala +GAZ_00001550 geo_loc_name (country) Guernsey +GAZ_00000909 geo_loc_name (country) Guinea +GAZ_00000910 geo_loc_name (country) Guinea-Bissau +GAZ_00002522 geo_loc_name (country) Guyana +GAZ_00003953 geo_loc_name (country) Haiti +GAZ_00009718 geo_loc_name (country) Heard Island and McDonald Islands +GAZ_00002894 geo_loc_name (country) Honduras +GAZ_00003203 geo_loc_name (country) Hong Kong +GAZ_00007120 geo_loc_name (country) Howland Island +GAZ_00002952 geo_loc_name (country) Hungary +GAZ_00000843 geo_loc_name (country) Iceland +GAZ_00002839 geo_loc_name (country) India +GAZ_00003727 geo_loc_name (country) Indonesia +GAZ_00004474 geo_loc_name (country) Iran +GAZ_00004483 geo_loc_name (country) Iraq +GAZ_00002943 geo_loc_name (country) Ireland +GAZ_00052477 geo_loc_name (country) Isle of Man +GAZ_00002476 geo_loc_name (country) Israel +GAZ_00002650 geo_loc_name (country) Italy +GAZ_00003781 geo_loc_name (country) Jamaica +GAZ_00005853 geo_loc_name (country) Jan Mayen +GAZ_00002747 geo_loc_name (country) Japan +GAZ_00007118 geo_loc_name (country) Jarvis Island +GAZ_00001551 geo_loc_name (country) Jersey +GAZ_00007114 geo_loc_name (country) Johnston Atoll +GAZ_00002473 geo_loc_name (country) Jordan +GAZ_00005809 geo_loc_name (country) Juan de Nova Island +GAZ_00004999 geo_loc_name (country) Kazakhstan +GAZ_00001101 geo_loc_name (country) Kenya +GAZ_00005682 geo_loc_name (country) Kerguelen Archipelago +GAZ_00007116 geo_loc_name (country) Kingman Reef +GAZ_00006894 geo_loc_name (country) Kiribati +GAZ_00011337 geo_loc_name (country) Kosovo +GAZ_00005285 geo_loc_name (country) Kuwait +GAZ_00006893 geo_loc_name (country) Kyrgyzstan +GAZ_00006889 geo_loc_name (country) Laos +GAZ_00002958 geo_loc_name (country) Latvia +GAZ_00002478 geo_loc_name (country) Lebanon +GAZ_00001098 geo_loc_name (country) Lesotho +GAZ_00000911 geo_loc_name (country) Liberia +GAZ_00000566 geo_loc_name (country) Libya +GAZ_00003858 geo_loc_name (country) Liechtenstein +GAZ_00007144 geo_loc_name (country) Line Islands +GAZ_00002960 geo_loc_name (country) Lithuania +GAZ_00002947 geo_loc_name (country) Luxembourg +GAZ_00003202 geo_loc_name (country) Macau +GAZ_00001108 geo_loc_name (country) Madagascar +GAZ_00001105 geo_loc_name (country) Malawi +GAZ_00003902 geo_loc_name (country) Malaysia +GAZ_00006924 geo_loc_name (country) Maldives +GAZ_00000584 geo_loc_name (country) Mali +GAZ_00005459 geo_loc_name (country) Malta +GAZ_00007161 geo_loc_name (country) Marshall Islands +GAZ_00067143 geo_loc_name (country) Martinique +GAZ_00000583 geo_loc_name (country) Mauritania +GAZ_00003745 geo_loc_name (country) Mauritius +GAZ_00003943 geo_loc_name (country) Mayotte +GAZ_00002852 geo_loc_name (country) Mexico +GAZ_00005862 geo_loc_name (country) Micronesia +GAZ_00007112 geo_loc_name (country) Midway Islands +GAZ_00003897 geo_loc_name (country) Moldova +GAZ_00003857 geo_loc_name (country) Monaco +GAZ_00008744 geo_loc_name (country) Mongolia +GAZ_00006898 geo_loc_name (country) Montenegro +GAZ_00003988 geo_loc_name (country) Montserrat +GAZ_00000565 geo_loc_name (country) Morocco +GAZ_00001100 geo_loc_name (country) Mozambique +GAZ_00006899 geo_loc_name (country) Myanmar +GAZ_00001096 geo_loc_name (country) Namibia +GAZ_00006900 geo_loc_name (country) Nauru +GAZ_00007119 geo_loc_name (country) Navassa Island +GAZ_00004399 geo_loc_name (country) Nepal +GAZ_00002946 geo_loc_name (country) Netherlands +GAZ_00005206 geo_loc_name (country) New Caledonia +GAZ_00000469 geo_loc_name (country) New Zealand +GAZ_00002978 geo_loc_name (country) Nicaragua +GAZ_00000585 geo_loc_name (country) Niger +GAZ_00000912 geo_loc_name (country) Nigeria +GAZ_00006902 geo_loc_name (country) Niue +GAZ_00005908 geo_loc_name (country) Norfolk Island +GAZ_00002801 geo_loc_name (country) North Korea +GAZ_00006895 geo_loc_name (country) North Macedonia +GAZ_00002284 geo_loc_name (country) North Sea +GAZ_00003958 geo_loc_name (country) Northern Mariana Islands +GAZ_00002699 geo_loc_name (country) Norway +GAZ_00005283 geo_loc_name (country) Oman +GAZ_00005246 geo_loc_name (country) Pakistan +GAZ_00006905 geo_loc_name (country) Palau +GAZ_00002892 geo_loc_name (country) Panama +GAZ_00003922 geo_loc_name (country) Papua New Guinea +GAZ_00010832 geo_loc_name (country) Paracel Islands +GAZ_00002933 geo_loc_name (country) Paraguay +GAZ_00002932 geo_loc_name (country) Peru +GAZ_00004525 geo_loc_name (country) Philippines +GAZ_00005867 geo_loc_name (country) Pitcairn Islands +GAZ_00002939 geo_loc_name (country) Poland +GAZ_00004126 geo_loc_name (country) Portugal +GAZ_00006935 geo_loc_name (country) Puerto Rico +GAZ_00005286 geo_loc_name (country) Qatar +GAZ_00001088 geo_loc_name (country) Republic of the Congo +GAZ_00003945 geo_loc_name (country) Reunion +GAZ_00002951 geo_loc_name (country) Romania +GAZ_00023304 geo_loc_name (country) Ross Sea +GAZ_00002721 geo_loc_name (country) Russia +GAZ_00001087 geo_loc_name (country) Rwanda +GAZ_00000849 geo_loc_name (country) Saint Helena +GAZ_00006906 geo_loc_name (country) Saint Kitts and Nevis +GAZ_00006909 geo_loc_name (country) Saint Lucia +GAZ_00003942 geo_loc_name (country) Saint Pierre and Miquelon +GAZ_00005841 geo_loc_name (country) Saint Martin +GAZ_02000565 geo_loc_name (country) Saint Vincent and the Grenadines +GAZ_00006910 geo_loc_name (country) Samoa +GAZ_00003102 geo_loc_name (country) San Marino +GAZ_00006927 geo_loc_name (country) Sao Tome and Principe +GAZ_00005279 geo_loc_name (country) Saudi Arabia +GAZ_00000913 geo_loc_name (country) Senegal +GAZ_00002957 geo_loc_name (country) Serbia +GAZ_00006922 geo_loc_name (country) Seychelles +GAZ_00000914 geo_loc_name (country) Sierra Leone +GAZ_00003923 geo_loc_name (country) Singapore +GAZ_00012579 geo_loc_name (country) Sint Maarten +GAZ_00002956 geo_loc_name (country) Slovakia +GAZ_00002955 geo_loc_name (country) Slovenia +GAZ_00005275 geo_loc_name (country) Solomon Islands +GAZ_00001104 geo_loc_name (country) Somalia +GAZ_00001094 geo_loc_name (country) South Africa +GAZ_00003990 geo_loc_name (country) South Georgia and the South Sandwich Islands +GAZ_00002802 geo_loc_name (country) South Korea +GAZ_00233439 geo_loc_name (country) South Sudan +GAZ_00003936 geo_loc_name (country) Spain +GAZ_00010831 geo_loc_name (country) Spratly Islands +GAZ_00003924 geo_loc_name (country) Sri Lanka +GAZ_00002475 geo_loc_name (country) State of Palestine +GAZ_00000560 geo_loc_name (country) Sudan +GAZ_00002525 geo_loc_name (country) Suriname +GAZ_00005396 geo_loc_name (country) Svalbard +GAZ_00001099 geo_loc_name (country) Swaziland +GAZ_00002729 geo_loc_name (country) Sweden +GAZ_00002941 geo_loc_name (country) Switzerland +GAZ_00002474 geo_loc_name (country) Syria +GAZ_00005341 geo_loc_name (country) Taiwan +GAZ_00006912 geo_loc_name (country) Tajikistan +GAZ_00001103 geo_loc_name (country) Tanzania +GAZ_00003744 geo_loc_name (country) Thailand +GAZ_00006913 geo_loc_name (country) Timor-Leste +GAZ_00000915 geo_loc_name (country) Togo +GAZ_00260188 geo_loc_name (country) Tokelau +GAZ_00006916 geo_loc_name (country) Tonga +GAZ_00003767 geo_loc_name (country) Trinidad and Tobago +GAZ_00005812 geo_loc_name (country) Tromelin Island +GAZ_00000562 geo_loc_name (country) Tunisia +GAZ_00000558 geo_loc_name (country) Turkey +GAZ_00005018 geo_loc_name (country) Turkmenistan +GAZ_00003955 geo_loc_name (country) Turks and Caicos Islands +GAZ_00009715 geo_loc_name (country) Tuvalu +GAZ_00002459 geo_loc_name (country) United States of America +GAZ_00001102 geo_loc_name (country) Uganda +GAZ_00002724 geo_loc_name (country) Ukraine +GAZ_00005282 geo_loc_name (country) United Arab Emirates +GAZ_00002637 geo_loc_name (country) United Kingdom +GAZ_00002930 geo_loc_name (country) Uruguay +GAZ_00004979 geo_loc_name (country) Uzbekistan +GAZ_00006918 geo_loc_name (country) Vanuatu +GAZ_00002931 geo_loc_name (country) Venezuela +GAZ_00003756 geo_loc_name (country) Viet Nam +GAZ_00003959 geo_loc_name (country) Virgin Islands +GAZ_00007111 geo_loc_name (country) Wake Island +GAZ_00007191 geo_loc_name (country) Wallis and Futuna +GAZ_00009572 geo_loc_name (country) West Bank +GAZ_00000564 geo_loc_name (country) Western Sahara +GAZ_00005284 geo_loc_name (country) Yemen +GAZ_00001107 geo_loc_name (country) Zambia +GAZ_00001106 geo_loc_name (country) Zimbabwe + + library_strategy WGA + library_strategy WGS + library_strategy WXS + library_strategy RNA-Seq + library_strategy miRNA-Seq + library_strategy WCS + library_strategy CLONE + library_strategy POOLCLONE + library_strategy AMPLICON + library_strategy CLONEEND + library_strategy FINISHING + library_strategy ChIP-Seq + library_strategy MNase-Seq + library_strategy DNase-Hypersensitivity + library_strategy Bisulfite-Seq + library_strategy Tn-Seq + library_strategy EST + library_strategy FL-cDNA + library_strategy CTS + library_strategy MRE-Seq + library_strategy MeDIP-Seq + library_strategy MBD-Seq + library_strategy OTHER + + library_source GENOMIC + library_source TRANSCRIPTOMIC + library_source METAGENOMIC + library_source METATRANSCRIPTOMIC + library_source SYNTHETIC + library_source VIRAL RNA + library_source OTHER + + library_selection RANDOM + library_selection PCR + library_selection RANDOM PCR + library_selection RT-PCR + library_selection HMPR + library_selection MF + library_selection CF-S + library_selection CF-M + library_selection CF-H + library_selection CF-T + library_selection MDA + library_selection MSLL + library_selection cDNA + library_selection ChIP + library_selection MNase + library_selection DNAse + library_selection Hybrid Selection + library_selection Reduced Representation + library_selection Restriction Digest + library_selection 5-methylcytidine antibody + library_selection MBD2 protein methyl-CpG binding domain + library_selection CAGE + library_selection RACE + library_selection size fractionation + library_selection Padlock probes capture method + library_selection other + library_selection unspecified + + library_layout single + library_layout paired + + filetype bam + filetype sra + filetype kar + filetype srf + filetype sff + filetype fastq + filetype tab + filetype 454_native + filetype Helicos_native + filetype SOLiD_native + filetype PacBio_HDF5 + filetype CompleteGenomics_native \ No newline at end of file diff --git a/template/pha4ge/export.js b/template/pha4ge/export.js index bf8bcefc..75f0bed4 100644 --- a/template/pha4ge/export.js +++ b/template/pha4ge/export.js @@ -5,7 +5,7 @@ * @param {Object} data See `data.js`. * @param {Object} xlsx SheetJS variable. */ -var exportBioSample = (baseName, hot, data, xlsx, fileType) => { +var exportNCBI_BioSample = (baseName, hot, data, xlsx, fileType) => { // Create an export table with template's headers (2nd row) and remaining rows of data const ExportHeaders = new Map([ ['sample_name', []], @@ -57,7 +57,7 @@ var exportBioSample = (baseName, hot, data, xlsx, fileType) => { const sourceFields = getFields(data); const sourceFieldNameMap = getFieldNameMap(sourceFields); // Fills in the above mapping (or just set manually above) - getHeaderMap(ExportHeaders, sourceFields, 'BIOSAMPLE'); + getHeaderMap(ExportHeaders, sourceFields, 'NCBI_BIOSAMPLE'); // Copy headers to 1st row of new export table const outputMatrix = [[...ExportHeaders.keys()]]; @@ -87,8 +87,113 @@ var exportBioSample = (baseName, hot, data, xlsx, fileType) => { runBehindLoadingScreen(exportFile, [outputMatrix, baseName, fileType, xlsx]); }; +var exportNCBI_SRA = (baseName, hot, data, xlsx, fileType) => { + + const ExportHeaders = new Map([]); + const sourceFields = getFields(data); + const sourceFieldNameMap = getFieldNameMap(sourceFields); + // Fills in the above mapping (or just set manually above) + getHeaderMap(ExportHeaders, sourceFields, 'NCBI_SRA'); + + // Copy headers to 1st row of new export table + const outputMatrix = [[...ExportHeaders.keys()]]; + + for (const inputRow of getTrimmedData(hot)) { + const outputRow = []; + for (const [headerName, sources] of ExportHeaders) { + + // Otherwise apply source (many to one) to target field transform: + const value = getMappedField(inputRow, sources, sourceFields,sourceFieldNameMap, '|') + outputRow.push(value); + } + outputMatrix.push(outputRow); + } + + runBehindLoadingScreen(exportFile, [outputMatrix, baseName, fileType, xlsx]); +}; + +var exportNCBI_Genbank = (baseName, hot, data, xlsx, fileType) => { + + const ExportHeaders = new Map([]); + const sourceFields = getFields(data); + const sourceFieldNameMap = getFieldNameMap(sourceFields); + // Fills in the above mapping (or just set manually above) + getHeaderMap(ExportHeaders, sourceFields, 'NCBI_Genbank'); + + // Copy headers to 1st row of new export table + const outputMatrix = [[...ExportHeaders.keys()]]; + + for (const inputRow of getTrimmedData(hot)) { + const outputRow = []; + for (const [headerName, sources] of ExportHeaders) { + + // Otherwise apply source (many to one) to target field transform: + const value = getMappedField(inputRow, sources, sourceFields,sourceFieldNameMap, '|') + outputRow.push(value); + } + outputMatrix.push(outputRow); + } + + runBehindLoadingScreen(exportFile, [outputMatrix, baseName, fileType, xlsx]); +}; + +var exportNCBI_Genbank_source_modifiers = (baseName, hot, data, xlsx, fileType) => { + + const ExportHeaders = new Map([]); + const sourceFields = getFields(data); + const sourceFieldNameMap = getFieldNameMap(sourceFields); + // Fills in the above mapping (or just set manually above) + getHeaderMap(ExportHeaders, sourceFields, 'NCBI_Genbank_source_modifiers'); + + // Copy headers to 1st row of new export table + const outputMatrix = [[...ExportHeaders.keys()]]; + + for (const inputRow of getTrimmedData(hot)) { + const outputRow = []; + for (const [headerName, sources] of ExportHeaders) { + + // Otherwise apply source (many to one) to target field transform: + const value = getMappedField(inputRow, sources, sourceFields,sourceFieldNameMap, '|') + outputRow.push(value); + } + outputMatrix.push(outputRow); + } + + runBehindLoadingScreen(exportFile, [outputMatrix, baseName, fileType, xlsx]); +}; + + +var exportGISAID = (baseName, hot, data, xlsx, fileType) => { + + const ExportHeaders = new Map([]); + const sourceFields = getFields(data); + const sourceFieldNameMap = getFieldNameMap(sourceFields); + // Fills in the above mapping (or just set manually above) + getHeaderMap(ExportHeaders, sourceFields, 'GISAID'); + + // Copy headers to 1st row of new export table + const outputMatrix = [[...ExportHeaders.keys()]]; + + for (const inputRow of getTrimmedData(hot)) { + const outputRow = []; + for (const [headerName, sources] of ExportHeaders) { + + // Otherwise apply source (many to one) to target field transform: + const value = getMappedField(inputRow, sources, sourceFields,sourceFieldNameMap, '|') + outputRow.push(value); + } + outputMatrix.push(outputRow); + } + + runBehindLoadingScreen(exportFile, [outputMatrix, baseName, fileType, xlsx]); +}; // A list of the export functions keyed by the Export menu name they should appear as: var EXPORT_FORMATS = { - "BioSample": {'method': exportBioSample,'fileType': 'xls', 'status': 'published'}, + "NCBI_BioSample": {'method': exportNCBI_BioSample,'fileType': 'xls', 'status': 'published'}, + "NCBI_SRA": {'method': exportNCBI_SRA,'fileType': 'xls', 'status': 'published'}, + "NCBI_Genbank": {'method': exportNCBI_Genbank,'fileType': 'xls', 'status': 'published'}, + "NCBI_Genbank_source_modifiers": {'method': exportNCBI_Genbank_source_modifiers,'fileType': 'xls', 'status': 'published'}, + "GISAID": {'method': exportGISAID,'fileType': 'xls', 'status': 'published'} + }; diff --git a/template/pha4ge/reference.html b/template/pha4ge/reference.html index be09ab0e..5c1cdf5d 100644 --- a/template/pha4ge/reference.html +++ b/template/pha4ge/reference.html @@ -402,7 +402,7 @@

    Guidelines for Biosample metadata collection and submission

    Number of passages. Provide number of known passages. If not passaged, put "not applicable" 3 - ['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access'] + None @@ -574,9 +574,7 @@

    Guidelines for Biosample metadata collection and submission

    pre-existing conditions and risk factors - Patient pre-existing conditions and risk factors. -Pre-existing condition: A medical condition that existed prior to the current infection. -Risk Factor: A variable associated with an increased risk of disease or infection. + Patient pre-existing conditions and risk factors. Pre-existing condition: A medical condition that existed prior to the current infection. Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Asthma ['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access'] @@ -1158,8 +1156,8 @@

    Guidelines for Biosample metadata collection and submission

    - variant evidence - The evidence used to make the variant determination. + variant evidence details + Details about the evidence used to make the variant determination. Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. RT-qPCR TaqPath assay: S gene target failure None @@ -1255,33 +1253,6 @@

    Guidelines for Biosample metadata collection and submission

    NCBI SRA information

    - - bioproject_accession - This will be populated by the PHA4GE field "bioproject accession". - Populate the "bioproject accession" field. - - None - - - - - sample_name - This will be populated by the PHA4GE field "biosample accession". - Populate the "biosample accession" field. - - None - - - - - library_ID - This will be populated by the PHA4GE field "library ID". - Populate the "library ID" field. - - None - - - title Short description that will identify the dataset on public pages. @@ -1327,24 +1298,6 @@

    Guidelines for Biosample metadata collection and submission

    - - platform - This will be populated by the PHA4GE field "sequencing instrument". - Only a limited set of sequencing platforms are available in the NCBI pick list. If a value appears to be missing, contact PHA4GE and report the issue. - - None - - - - - instrument_model - This will be populated by the PHA4GE field "sequencing instrument". - Only a limited set of sequencing instruments are available in the NCBI pick list. If a value appears to be missing, contact PHA4GE and report the issue. - - None - - - filetype See NCBI SRA template for details. @@ -1357,81 +1310,85 @@

    Guidelines for Biosample metadata collection and submission

    filename See NCBI SRA template for details. - Provide the filename recorded in the Bioinformatics and QC metrics section. + Provide the appropriate filename recorded in the Bioinformatics and QC metrics section. If sequence data is "paired", provide the second filename under "Filename 2". None - amplicon _PCR_primer_scheme - This will be populated by the PHA4GE field "amplicon PCR primer scheme". - Populate the "amplicon PCR primer scheme" field. + filename 2 + See NCBI SRA template for details. + Provide the appropriate filename recorded in the Bioinformatics and QC metrics section. None + +

    Contributor acknowledgement

    + + - amplicon_size - This will be populated by the PHA4GE field "amplicon size". - Populate the "amplicon size" field. - + authors + Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. + Include the first and last names of all individuals that should be attributed, separated by a comma. + Tejinder Singh, Fei Hu, Joe Blogs None - sequencing_protocol_name - This will be populated by the PHA4GE field "sequencing protocol name". - Populate the "sequencing protocol name" field. + DataHarmonizer provenance + + None + +

    data status

    + + - raw_sequence_data_processing_method - This will be populated by the PHA4GE field "raw sequence data processing method". - Populate the "raw sequence data processing method" field. + Not Applicable + + None - dehosting_method - This will be populated by the PHA4GE field "dehosting method". - Populate the "dehosting method" field. + Missing + + None - sequence_submitter_contact_email - This will be populated by the PHA4GE field "sequence submitter contact email". - Populate the "sequence submitter contact email" field. + Not Collected + + None - -

    Contributor acknowledgement

    - - - authors - Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. - Include the first and last names of all individuals that should be attributed, separated by a comma. - Tejinder Singh, Fei Hu, Joe Blogs + Not Provided + + + None - DataHarmonizer provenance + Restricted Access