From 679e2f63ab11bd48d452b9b61df96a3044f7716e Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Sat, 5 Sep 2020 09:17:02 -0700 Subject: [PATCH] Aug 27 language updates (#100) * Aug 27 language updates signs and symptoms comorbidities * added host age bin --- data.js | 571 ++++++++++++++++++++++++++++++++++++++++++++++--- data.tsv | 459 +++++++++++++++++++++++++++++++++------ reference.html | 65 ++++++ 3 files changed, 996 insertions(+), 99 deletions(-) diff --git a/data.js b/data.js index 7c9ab0e4..0f683f0b 100644 --- a/data.js +++ b/data.js @@ -860,7 +860,6 @@ const DATA = [ "Building floor": {}, "Cloth": {}, "Control panel": {}, - "Corridor": {}, "Door": {}, "Door handle": {}, "Face mask": {}, @@ -875,7 +874,6 @@ const DATA = [ "N95 mask": {}, "Nurse call button": {}, "Paper": {}, - "Particulate matter": {}, "Plastic": {}, "PPE gown": {}, "Sewage": {}, @@ -915,12 +913,17 @@ const DATA = [ "Bathroom": {}, "Clinical assessment centre": {}, "Conference venue": {}, + "Corridor": {}, "Daycare": {}, "Emergency room (ER)": {}, "Family practice clinic": {}, "Group home": {}, "Homeless shelter": {}, - "Hospital": {}, + "Hospital": { + "Emergency Department": {}, + "ICU": {}, + "Ward": {} + }, "Intensive Care Unit (ICU)": {}, "Long Term Care Facility": {}, "Patient room": {}, @@ -1373,6 +1376,38 @@ const DATA = [ "examples": "79", "GISAID": "Patient age" }, + { + "fieldName": "host age bin", + "capitalize": "", + "ontology_id": "", + "datatype": "select", + "source": "", + "dataStatus": [ + "Not Applicable", + "Missing", + "Not Collected", + "Not Provided", + "Restricted Access" + ], + "xs:minInclusive": "", + "xs:maxInclusive": "", + "requirement": "required", + "description": "Age of host at the time of sampling, expressed as an age group.", + "guidance": "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value.", + "examples": "60 - 69", + "GISAID": "", + "vocabulary": { + "0 - 9": {}, + "10 - 19": {}, + "20 - 29": {}, + "30 - 39": {}, + "40 - 49": {}, + "50 - 59": {}, + "60 - 69": {}, + "70 - 79": {}, + "80+": {} + } + }, { "fieldName": "host gender", "capitalize": "", @@ -1480,8 +1515,8 @@ const DATA = [ "examples": "Cough; Fever; Chills", "GISAID": "", "vocabulary": { - "Abdominal pain": {}, - "Abnormality of the sense of taste": { + "Abnormal lung ausculation": {}, + "Abnormality of taste sensation": { "Ageusia (complete loss of taste)": {}, "Parageusia (distorted sense of taste)": {}, "Hypogeusia (reduced sense of taste)": {} @@ -1490,66 +1525,358 @@ const DATA = [ "Anosmia (lost sense of smell)": {}, "Hyposmia (reduced sense of smell)": {} }, - "Altered consciousness": { + "Acute Respiratory Distress Syndrome": {}, + "Altered mental status": { "Cognitive impairment": {}, "Coma": {}, "Confusion": { "Delirium (sudden severe confusion)": {} }, "Inability to arouse (inability to stay awake)": {}, + "Irritability": {}, "Loss of speech": {} }, - "Arthralgia (painful joints)": {}, - "Asthenia (generalized weakness)": {}, - "Chest pain": {}, + "Arrhythmia": {}, + "Asthenia (general weakness)": {}, "Chest tightness or pressure": { "Rigors (fever shakes)": {} }, "Chills (sudden cold sensation)": {}, + "Conjunctival injection": {}, "Conjunctivitis (pink eye)": {}, + "Coryza": {}, "Cough": { "Nonproductive cough (dry cough)": {}, "Productive cough (wet cough)": {} }, - "Cyanosis (blueish skin discolouration)": { + "Cyanosis": { "Acrocyanosis": { "Circumoral cyanosis (bluish around mouth)": {}, - "Cyanotic face (bluish face)": {}, - "Cyanotic lips (bluish lips)": {}, - "Pseudo-chilblains on fingers (covid fingers)": {}, - "Pseudo-chilblains on toes (covid toes)": {} - } + "Cyanotic face (bluish face)": {} + }, + "Central Cyanosis": { + "Cyanotic lips (bluish lips)": {} + }, + "Peripheral Cyanosis": {} }, + "Dyspnea (breathing difficulty)": {}, "Diarrhea (watery stool)": {}, + "Dry gangrene": {}, "Encephalitis (brain inflammation)": {}, + "Encephalopathy": {}, "Fatigue (tiredness)": {}, - "Fever": {}, + "Fever": { + "Fever (\u226538\u00b0C)": {} + }, "Glossitis (inflammation of the tongue)": {}, + "Ground Glass Opacities (GGO)": {}, "Headache": {}, "Hemoptysis (coughing up blood)": {}, + "Hypocapnia": {}, "Hypotension (low blood pressure)": {}, "Hypoxemia (low blood oxygen)": {}, + "Silent hypoxemia": {}, "Internal hemorrhage (internal bleeding)": {}, - "Irritability": {}, "Loss of Fine Movements": {}, "Low appetite": {}, "Malaise (general discomfort/unease)": {}, - "Myalgia (muscle pain)": {}, + "Meningismus/nuchal rigidity": {}, + "Muscle weakness": {}, "Nasal obstruction (stuffy nose)": {}, "Nausea": {}, + "nose bleed": {}, + "otitis": {}, + "Pain": { + "Abdominal pain": {}, + "Arthralgia (painful joints)": {}, + "Chest pain": { + "Pleuritic chest pain": {} + }, + "Myalgia (muscle pain)": {} + }, "Pharyngitis (sore throat)": {}, + "Pharyngeal exudate": {}, + "Pleural effusion": {}, + "Pneumonia": {}, + "Prostration": {}, + "Pseudo-chilblains": { + "Pseudo-chilblains on fingers (covid fingers)": {}, + "Pseudo-chilblains on toes (covid toes)": {} + }, "Rash": {}, "Rhinorrhea (runny nose)": {}, "Seizure": { "Motor seizure": {} }, "Shivering (involuntary muscle twitching)": {}, - "Dyspnea (breathing difficulty)": {}, "Slurred speech": {}, + "Sneezing": {}, + "Sputum Production": {}, "Stroke": {}, - "Tachypnea (rapid breathing)": {}, - "Vomiting (throwing up)": {}, - "Muscle weakness": {} + "Swollen Lymph Nodes": {}, + "Tachypnea (accelerated respiratory rate)": {}, + "Vertigo (dizziness)": {}, + "Vomiting (throwing up)": {} + } + }, + { + "fieldName": "pre-existing conditions and risk factors", + "capitalize": "", + "ontology_id": "", + "datatype": "multiple", + "source": "", + "dataStatus": [ + "Not Applicable", + "Missing", + "Not Collected", + "Not Provided", + "Restricted Access" + ], + "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.", + "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; Pregnancy; Smoker", + "GISAID": "", + "vocabulary": { + "Age 60+": {}, + "Anemia": {}, + "Anorexia": {}, + "Birthing labor": {}, + "Bone marrow failure": {}, + "Cancer": { + "Breast cancer": {}, + "Colorectal cancer": {}, + "Hematologic malignancy": {}, + "Lung cancer": {}, + "Metastatic disease": {} + }, + "Cancer treatment": { + "Cancer surgery": {}, + "Chemotherapy": { + "Adjuvant chemotherapy": {} + } + }, + "Cardiac disorder": { + "Arrhythmia": {}, + "Cardiac disease": {}, + "Cardiomyopathy": {}, + "Cardiac injury": {}, + "Hypertension (high blood pressure)": {}, + "Hypotension (low blood pressure)": {} + }, + "Cesarean section": {}, + "Chronic cough": {}, + "Chronic gastrointestinal disease": {}, + "Chronic lung disease": {}, + "Corticosteroids": {}, + "Diabetes mellitus (diabetes)": { + "Type I diabetes mellitus (T1D)": {}, + "Type II diabetes mellitus (T2D)": {} + }, + "Eczema": {}, + "Electrolyte disturbance": { + "Hypocalcemia": {}, + "Hypokalemia": {}, + "Hypomagnesemia": {} + }, + "Encephalitis (brain inflammation)": {}, + "Epilepsy": {}, + "Hemodialysis": {}, + "Hemoglobinopathy": {}, + "Human immunodeficiency virus (HIV)": { + "Acquired immunodeficiency syndrome (AIDS)": {}, + "HIV and antiretroviral therapy (ART)": {} + }, + "Immunocompromised": { + "Lupus": {} + }, + "Inflammatory bowel disease (IBD)": { + "Colitis": { + "Ulcerative colitis": {} + }, + "Crohn's disease": {} + }, + "Renal disorder": { + "Renal disease": {}, + "Chronic renal disease": {}, + "Renal failure": {} + }, + "Liver disease": { + "Chronic liver disease": { + "Fatty liver disease (FLD)": {} + } + }, + "Myalgia (muscle pain)": {}, + "Myalgic encephalomyelitis (ME)": {}, + "Neurological disorder": { + "Neuromuscular disorder": {} + }, + "Obesity": { + "Severe obesity": {} + }, + "Respiratory disorder": { + "Asthma": {}, + "Chronic bronchitis": {}, + "Chronic pulmonary disease": { + "Chronic obstructive pulmonary disease": {} + }, + "Emphysema": {}, + "Lung disease": { + "Chronic lung disease": {}, + "Pulmonary fibrosis": {} + }, + "Pneumonia": {}, + "Respiratory failure": { + "Adult respiratory distress syndrome": {}, + "Newborn respiratory distress syndrome": {} + }, + "Tuberculosis": {} + }, + "Postpartum (\u22646 weeks)": {}, + "Pregnancy": {}, + "Rheumatic disease": {}, + "Sickle cell disease": {}, + "Substance use": { + "Alcohol abuse": {}, + "Drug abuse": { + "Injection drug abuse": {} + }, + "Smoking": {}, + "Vaping": {} + }, + "Tachypnea (accelerated respiratory rate)": {}, + "Transplant": { + "Bone marrow transplant": {}, + "Cardiac transplant": {}, + "Hematopoietic stem cell transplant (HSCT)": {}, + "Kidney transplant": {}, + "Liver transplant": {} + } + } + }, + { + "fieldName": "complications", + "capitalize": "", + "ontology_id": "", + "datatype": "multiple", + "source": "", + "dataStatus": [ + "Not Applicable", + "Missing", + "Not Collected", + "Not Provided", + "Restricted Access" + ], + "xs:minInclusive": "", + "xs:maxInclusive": "", + "requirement": "", + "description": "Patient medical complications that are believed to have occurred as result of host disease.", + "guidance": "Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team.", + "examples": "Acute Respiratory Failure; Coma; Septicemia", + "GISAID": "", + "vocabulary": { + "Abnormal blood oxygen level": {}, + "Acute respiratory failure": {}, + "Arrhythmia (complication)": { + "Tachycardia": { + "Polymorphic ventricular tachycardia (VT)": {}, + "Tachyarrhythmia": {} + } + }, + "Noncardiogenic pulmonary edema": { + "Acute respiratory distress syndrome (ARDS)": { + "COVID-19 associated ARDS (CARDS)": {}, + "Neurogenic pulmonary edema (NPE)": {} + } + }, + "Cardiac injury": {}, + "Cardiac arrest": {}, + "Cardiogenic shock": {}, + "Blood clot": { + "Arterial clot": {}, + "Deep vein thrombosis (DVT)": {}, + "Pulmonary embolism (PE)": {} + }, + "Cardiomyopathy": {}, + "Central nervous system invasion": {}, + "Stroke (complication)": { + "Central Nervous System Vasculitis": {}, + "Ischemic stroke": { + "Acute ischemic stroke": {} + } + }, + "Coma": {}, + "Convulsions": {}, + "COVID-19 associated coagulopathy (CAC)": {}, + "Cystic fibrosis": {}, + "Cytokine release syndrome": {}, + "Disseminated intravascular coagulation (DIC)": {}, + "Encephalopathy": {}, + "Fulminant myocarditis": {}, + "Guillain-Barr\u00e9 syndrome": {}, + "Internal hemorrhage (complication; internal bleeding)": { + "Intracerebral haemorrhage": {} + }, + "Kawasaki disease": { + "Typical Kawasaki disease": {}, + "Incomplete Kawasaki disease": {} + }, + "Kidney injury": { + "Acute kidney injury": {} + }, + "Liver dysfunction": {}, + "Liver injury": { + "Acute liver injury": {} + }, + "Lung injury": { + "Acute lung injury": {} + }, + "Meningitis": {}, + "Migraine": {}, + "Miscarriage": {}, + "Multisystem inflammatory syndrome in children (MIS-C)": {}, + "Muscle injury": {}, + "Myalgic encephalomyelitis (ME)": {}, + "Myocardial infarction (heart attack)": { + "Acute myocardial infarction": {}, + "Elevation myocardial infarction": {}, + "ST-segment elevation myocardial infarction": {} + }, + "Myocardial injury": {}, + "Neonatal complications": {}, + "Organ failure": { + "Heart failure": {}, + "Liver failure": {} + }, + "Paralysis": {}, + "Pneumothorax (collapsed lung)": { + "Spontaneous pneumothorax": {}, + "Spontaneous tension pneymothorax": {} + }, + "Pneumonia (complication)": { + "COVID-19 pneumonia": {} + }, + "Pregancy complications": {}, + "Rhabdomyolysis": {}, + "Secondary infection": { + "Secondary staph infection": {}, + "Secondary strep infection": {} + }, + "Seizure (complication)": { + "Motor seizure": {} + }, + "Sepsis": {}, + "Septicemia": {}, + "Shock": { + "Hyperinflammatory shock": {}, + "Refractory cardiogenic shock": {}, + "Refractory cardiogenic plus vasoplegic shock": {}, + "Septic shock": {} + }, + "Vasculitis": {}, + "Ventilation induced lung injury (VILI)": {} } } ] @@ -1615,17 +1942,197 @@ const DATA = [ "examples": "Mass gathering (convention)", "GISAID": "Additional location information", "vocabulary": { - "Mass gathering (convention)": {}, - "Mass gathering (religious)": {}, - "Mass gathering (social e.g. funeral, wedding etc.)": {}, - "Mass gathering (office)": {}, - "Occupational exposure (hospital worker)": {}, - "Occupational exposure (hospital visit)": {}, - "Occupational exposure (frontline response)": {}, - "Occupational exposure (healthcare work with the public)": {}, - "Occupational exposure (retail)": {}, - "Occupational exposure (restaurant)": {} + "Mass Gathering": { + "Convention": {}, + "Convocation": {}, + "Agricultural Event": {} + }, + "Religious Gathering": { + "Mass": {} + }, + "Social Gathering": { + "Baby Shower": {}, + "Community Event": {}, + "Family Gathering": { + "Family Reunion": {} + }, + "Funeral": {}, + "Party": {}, + "Potluck": {}, + "Wedding": {} + }, + "Other": {} } + }, + { + "fieldName": "direct/indirect exposure", + "capitalize": "", + "ontology_id": "", + "datatype": "select", + "source": "", + "dataStatus": null, + "xs:minInclusive": "", + "xs:maxInclusive": "", + "requirement": "", + "description": "The exposure transmission contact type.", + "guidance": "Select direct or indirect exposure from the pick-list.", + "examples": "Direct", + "GISAID": "", + "vocabulary": { + "Direct": {}, + "Indirect": {}, + "Unknown": {} + } + }, + { + "fieldName": "host role", + "capitalize": "", + "ontology_id": "", + "datatype": "multiple", + "source": "", + "dataStatus": null, + "xs:minInclusive": "", + "xs:maxInclusive": "", + "requirement": "", + "description": "The role of the host in relation to the exposure setting.", + "guidance": "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.", + "examples": "Patient", + "GISAID": "", + "vocabulary": { + "Attendee": { + "Student": {} + }, + "Patient": { + "Inpatient": {}, + "Outpatient": {} + }, + "Passenger": {}, + "Resident": {}, + "Visitor": {}, + "Volunteer": {}, + "Work": { + "Administrator": {}, + "First Responder": { + "Firefighter": {}, + "Paramedic": {}, + "Police Officer": {} + }, + "Housekeeper": {}, + "Kitchen Worker": {}, + "Laboratory Worker": {}, + "Nurse": {}, + "Personal Care Aid": {}, + "Pharmacist": {}, + "Physician": {}, + "Vet": {} + }, + "Social role": { + "Acquaintance": {}, + "Child": {}, + "Parent": { + "Father": {}, + "Mother": {} + }, + "Spouse": {} + }, + "Other": {} + } + }, + { + "fieldName": "exposure setting", + "capitalize": "", + "ontology_id": "", + "datatype": "multiple", + "source": "", + "dataStatus": null, + "xs:minInclusive": "", + "xs:maxInclusive": "", + "requirement": "", + "description": "The setting leading to exposure.", + "guidance": "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team.", + "examples": "Healthcare Setting", + "GISAID": "", + "vocabulary": { + "Human Exposure": { + "Known COVID-19 Case": {}, + "Patient Contact": {}, + "Probable COVID-19 Case": {}, + "Person with Acute Respiratory Illness": {}, + "Person with Fever and/or Cough": {}, + "Person who Recently Travelled": {} + }, + "Occupational or Residency Exposure": { + "Abbatoir": {}, + "Animal Rescue": {}, + "Childcare": { + "Daycare": {} + }, + "Place of Worship": { + "Church": {}, + "Mosque": {}, + "Temple": {} + }, + "Nursery": {}, + "Household": {}, + "Community Service Centre": {}, + "Correctional Facility": {}, + "Dormitory": {}, + "Farm": {}, + "First Nations Reserve": {}, + "Group Home": {}, + "Healthcare Setting": { + "Ambulance": {}, + "Acute Care Facility": {}, + "Clinic": {}, + "Community Health Centre": {}, + "Hospital": {}, + "Laboratory": {}, + "Long-Term Care Facility": {}, + "Pharmacy": {}, + "Physician's Office": {} + }, + "Insecure Housing (Homeless)": {}, + "Office": {}, + "Outdoors": { + "Camp/camping": {}, + "Hiking": {}, + "Hunting": {} + }, + "Petting zoo": {}, + "Restaurant": {}, + "Retail Store": {}, + "School": {}, + "Temporary Residence": { + "Homeless Shelter": {}, + "Hotel": {} + }, + "Vet": {} + }, + "Travel Exposure": { + "Travelled": {}, + "Travelled on a Cruise Ship": {}, + "Travelled on a Plane": {}, + "Travelled on Ground Transport": {}, + "Travelled outside Province/Territory": {}, + "Travelled outside Canada": {} + }, + "Other": {} + } + }, + { + "fieldName": "exposure details", + "capitalize": "", + "ontology_id": "", + "datatype": "xs:token", + "source": "", + "dataStatus": null, + "xs:minInclusive": "", + "xs:maxInclusive": "", + "requirement": "", + "description": "Additional host exposure information.", + "guidance": "Free text description of the exposure.", + "examples": "Host role - Other: Bus Driver", + "GISAID": "" } ] }, diff --git a/data.tsv b/data.tsv index 5be53fb7..c316f9dd 100644 --- a/data.tsv +++ b/data.tsv @@ -46,15 +46,24 @@ ID SC % 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 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 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, put "missing". 79 Patient age + 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 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, put "missing". male Gender Host Information host origin 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 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 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 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. 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; Pregnancy; Smoker + Host Information complications multiple Not Applicable; Missing; Not Collected; Not Provided; Restricted Access Patient medical complications that are believed to have occurred as 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 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 travel history xs:token Travel outside the country 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. Mass gathering (convention) Additional location information + Host exposure information direct/indirect exposure select 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 Sequencing 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 library insert size xs:token The insert size of the library being sequenced (i.e. the length of the DNA inserted between the adaptors). Provide the insert size in base pairs. 300 @@ -130,70 +139,276 @@ GAZ_00002576 geo_loc_name (province/territory) Yukon Territory -HP:0002027 signs and symptoms Abdominal pain -HP:0000223 signs and symptoms Abnormality of the sense of taste - Abnormality of the sense of taste Ageusia (complete loss of taste) -HP:0031249 Abnormality of the sense of taste Parageusia (distorted sense of taste) -HP_0000224 Abnormality of the sense of taste Hypogeusia (reduced sense of taste) + signs and symptoms Abnormal lung ausculation +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) -HP:0011446 signs and symptoms Altered consciousness -HP:0100543 Altered consciousness Cognitive impairment -HP_0001259 Altered consciousness Coma -HP_0001289 Altered consciousness Confusion + 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 consciousness Inability to arouse (inability to stay awake) -HP_0002371 Altered consciousness Loss of speech -HP_0002829 signs and symptoms Arthralgia (painful joints) -HP_0025406 signs and symptoms Asthenia (generalized weakness) -HP_0100749 signs and symptoms Chest pain + 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 (general 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) -HP_0012735 signs and symptoms Cough + 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 +HP:0000961 signs and symptoms Cyanosis +HP:0001063 Cyanosis Acrocyanosis Acrocyanosis Circumoral cyanosis (bluish around mouth) Acrocyanosis Cyanotic face (bluish face) - Acrocyanosis Cyanotic lips (bluish lips) - Acrocyanosis Pseudo-chilblains on fingers (covid fingers) - Acrocyanosis Pseudo-chilblains on toes (covid toes) + Cyanosis Central Cyanosis + Central Cyanosis Cyanotic lips (bluish lips) + Cyanosis 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) + signs and symptoms Silent hypoxemia HP:0011029 signs and symptoms Internal hemorrhage (internal bleeding) -HP_0000737 signs and symptoms Irritability NCIT:C121416 signs and symptoms Loss of Fine Movements HP_0004396 signs and symptoms Low appetite signs and symptoms Malaise (general discomfort/unease) -HP_0003326 signs and symptoms Myalgia (muscle pain) + 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_0002094 signs and symptoms Dyspnea (breathing difficulty) HP_0001350 signs and symptoms Slurred speech + signs and symptoms Sneezing + signs and symptoms Sputum Production HP:0001297 signs and symptoms Stroke -HP_0002789 signs and symptoms Tachypnea (rapid breathing) + 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) -HP_0001324 signs and symptoms Muscle weakness + 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 + + + + 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 UBERON_0006314 anatomical material Fluid @@ -254,14 +469,13 @@ ENVO_00003896 environmental material Banknote ENVO_01000486 environmental material Building floor ENVO_02000058 environmental material Cloth environmental material Control panel - environmental material Corridor NCIT_C48950 environmental material Door environmental material Door handle environmental material Face mask environmental material Face shield - environmental material Food - environmental material Food packaging -ENVO_01000481 environmental material Glass +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 @@ -269,8 +483,8 @@ ENVO_01000481 environmental material Glass environmental material N95 mask environmental material Nurse call button environmental material Paper - environmental material Particulate matter -ENVO_01000404 environmental material Plastic +ENVO:01000060 Particulate matter +ENVO:01000404 environmental material Plastic environmental material PPE gown ENVO_00002018 environmental material Sewage ENVO_01000990 environmental material Sink @@ -280,17 +494,14 @@ ENVO_00001998 environmental material Soil environmental material Toilet bowl ENVO_00002006 environmental material Water environmental material Window -ENVO_00002040 environmental material Wood - - - - +ENVO:00002040 environmental material Wood environmental site Acute care facility -ENVO_00003040 environmental site Animal house -ENVO_01000422 environmental site Bathroom +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 @@ -307,8 +518,8 @@ NCIT_C17118 environmental site School environmental site Subway train environmental site Wet market -NCIT_C52009 collection method Amniocentesis -NCIT_C15631 collection method Aspiration +NCIT:C52009 collection method Amniocentesis +NCIT:C15631 collection method Aspiration Aspiration Suprapubic Aspiration Aspiration Tracheal aspiration Aspiration Vacuum Aspiration @@ -316,35 +527,34 @@ 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) +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 +NCIT:C15327 collection method Lumbar Puncture +MMO:0000344 collection method Necropsy +NCIT:c28221 collection method Phlebotomy +GENEPIO:0002116 collection method Rinsing collection method Scraping -GENEPIO_0002117 collection method Swabbing +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 +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 - collection device Micropipette - collection device Needle -NCIT_C113675 collection device Serum Collection 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 +NCIT:c17627 collection device Swab collection device Urine Collection Tube collection device Virus Transport Medium @@ -400,7 +610,6 @@ NCBITaxon_9694 host (common name) Tiger host health outcome Recovered host health outcome Stable - organism Severe acute respiratory syndrome coronavirus 2 organism RaTG13 organism RmYN02 @@ -436,23 +645,139 @@ BTO:0004755 lab host Vero E6 cell line host disease COVID-19 - host gender Female - host gender Male + 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+ + +OMRSE:00000009? host gender Female +OMRSE:00000008? host gender Male host gender Non-binary gender host gender Transgender host gender Undeclared - exposure event Mass gathering (convention) - exposure event Mass gathering (religious) - exposure event Mass gathering (social e.g. funeral, wedding etc.) - exposure event Mass gathering (office) - exposure event Occupational exposure (hospital worker) - exposure event Occupational exposure (hospital visit) - exposure event Occupational exposure (frontline response) - exposure event Occupational exposure (healthcare work with the public) - exposure event Occupational exposure (retail) - exposure event Occupational exposure (restaurant) + 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 + + + direct/indirect exposure Direct + direct/indirect exposure Indirect + direct/indirect exposure Unknown + + + 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 Housekeeper + Work Kitchen Worker + Work Laboratory Worker + Work Nurse + Work Personal Care Aid + Work Pharmacist + Work Physician + Work Vet + host role Social role + Social role Acquaintance + Social role Child + Social role Parent + Parent Father + Parent Mother + Social role Spouse + host role Other + + + 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 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 Vet + exposure setting Travel Exposure + Travel Exposure Travelled + Travel Exposure Travelled on a Cruise Ship + Travel Exposure Travelled on a Plane + Travel Exposure Travelled on Ground Transport + Travel Exposure Travelled outside Province/Territory + Travel Exposure Travelled outside Canada + exposure setting Other + OBI_0000759 sequencing instrument ILLUMINA diff --git a/reference.html b/reference.html index 4ba4d12e..6d36dde1 100644 --- a/reference.html +++ b/reference.html @@ -429,6 +429,15 @@

CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission + + host age bin + 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 + ['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access'] + + + host gender The gender of the host at the time of sample collection. @@ -474,6 +483,26 @@

CanCOGeN Guidelines for Covid19 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. + 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; Smoker + ['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access'] + + + + + complications + Patient medical complications that are believed to have occurred as 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 + ['Not Applicable', 'Missing', 'Not Collected', 'Not Provided', 'Restricted Access'] + + +

Host exposure information

@@ -505,6 +534,42 @@

CanCOGeN Guidelines for Covid19 Biosample metadata collection and submission + + direct/indirect exposure + The exposure transmission contact type. + Select direct or indirect exposure from the pick-list. + Direct + None + + + + + host role + 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 + None + + + + + exposure setting + 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 + None + + + + + exposure details + Additional host exposure information. + Free text description of the exposure. + Host role - Other: Bus Driver + None + + +

Sequencing