SCDO Version 2
Released 15 April 2021
- property IRIs have been reused wherever possible (i.e. SCDO IRI were replaced by those from existing ontologies)
- Terms that were annotated with “Sufficient” by the “existence in other ontologies” annotation property had their IRIs replaced by the term in the external ontology that it was cross referenced to using the “database cross reference” annotation property.
- Remaining SCDO-specific IRIs have been updated to the standard OBO prefix, e.g. the IRI of “Clinical or Research Assessment Answer” was changed from “http://scdontology.h3abionet.org/ontology/SCDO_1000473” to “http://purl.obolibrary.org/obo/SCDO_1000473”
- Ontology annotations updated (we just had “place-holder” text there before).
- Removed annotations that were automatically ascribed to the “created_by” and “creation_date” annotation properties on the creation of new terms within WebProtege.
- Additional ELSI/consent-related terms added (especially types of consent during emergencies).
- Addition of the “Complication” sub-class, and a number of sub-classes below it, to the “Abnormal Phenotype” class.
- Additional terms/classes included during the process of mapping SickleinArica data elements to the SCDO.
- Additional upper level “Data Standards” class, containing sub-classes for mapping SickleInAfrica (SIA) SCD data elements to the SCDO:
- Clinical or Research Assessment Answer
- Clinical or Research Assessment Data Element
- Clinical or Research Assessment Question Type
- Clinical or Research Assessment Questionnaire
- Unit of Measurement
- Additional properties for mapping SCD data elements to the SCDO:
- is question type
- has answer option
- collects
- has answer standard unit
- has reference range standard unit
- has possible finding
- diagnosed using finding
- code requires phenotype
- is ICD-10-CM code type
- maximum number of selections allowed
- minimum number of selections allowed
- has LLN
- has ULN
- has LLN male
- has ULN male
- has LLN female
- has ULN female
- has LLN pediatric
- has ULN pediatric
- has sections
- has field label
- has redcap variable
- has answer options text
- has field note
- has field type
- In CRF section
- order in CRF section
- custom alignment
- has redcap validation
- has branching logic
- has redcap action tags
- has redcap max number validation
- has redcap min number validation
- has redcap field annotation
- has calculation equation
- has slider label
- show slider
- is identifier
- required field
- in matrix group
- requires additional code
- autocomplete
- “Country” term deprecated and replaced by more specific “National Origin” (existing term in Personal Attributes class) and “Country of Data Collection” (new term in Research class).
- Associations between ICD-10-CM codes below D57 to relevant SCDO classes using the code requires phenotype object property.
- Removed old erroneous ICD10 associations made with the has clinical code object property.
- Accompanying mappings files:
- SSSOM mappings file (scdo-sssom-xrefs.tsv) This file contains mappings of SCDO classes to classes in other OBO ontologies.
- SSSOM rename file (scdo-sssom-xrefs-rename.tsv) This file lists the SCDO IDs and corresponding OBO term IDs of SCDO terms that have had their URIs updated to that of their cross referenced term in an external OBO ontology.
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SCDO Version 1
Released 27 June 2019
- All class/term IRIs point to the SCDO website.
- Where classes/terms were incorporated from existing ontologies, the “definition source” and “database cross reference” annotation properties are used to refer to the source ontologies.
- Many novel (not in existing ontologies) sickle cell disease (SCD) terms are defined.
- Changes to some existing terms of note to the SCD community:
- The term ‘Beta Plus Thalassemia’ has been replaced with ‘Beta Minus Thalassemia’ (SCDO:0000110) based on the description of the concept ‘beta-zero’ (See Supplementary File Section 1 of the SCDO publication (https://doi.org/10.1093/database/baz118) for more details.
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Upcoming release:
SCDO Version 3
(currently being worked on)
- Added this dc:comment annotation:
When citing the main English version of the SCDO, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/scdo.owl. For other versions (e.g. translations or layperson versions), cite the relevant ontology file available at https://github.com/scdodev/scdo-ontology. When referencing a specific component of the SCDO, such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI).
- Removed dc:License (http://purl.org/dc/elements/1.1/license) annotation property and replaced with License (http://purl.org/dc/terms/license).
- Changed ontology license to http://creativecommons.org/licenses/by/4.0/
- Removed dc:LicenseDocument annotation property
- Removed Ontology Version IRI from curator’s version (scdo-edit.owl)
- Removed dc:abstract property (replaced with Description property - see here)
- Updated annotation property uris:
- dc:audience uri to: http://purl.org/dc/terms/audience (from http://purl.org/dc/elements/1.1/audience)
- dc:language uri to http://purl.org/dc/terms/language (from http://purl.org/dc/elements/1.1/language)
- dc:isReferencedBy uri to http://purl.org/dc/terms/isReferencedBy (from http://purl.org/dc/elements/1.1/isReferencedBy)
- dc:accrualMethod uri to http://purl.org/dc/terms/accrualMethod (from http://purl.org/dc/elements/1.1/accrualMethod)
- dc:accrualPeriodicity uri to http://purl.org/dc/terms/accrualPeriodicity (from http://purl.org/dc/elements/1.1/accrualPeriodicity)
- dc:accrualPolicy uri to (from http://purl.org/dc/elements/1.1/accrualPolicy)
- dc:available uri to http://purl.org/dc/terms/available (from http://purl.org/dc/elements/1.1/available)
- dc:conformsTo uri to http://purl.org/dc/terms/conformsTo (from http://purl.org/dc/elements/1.1/conformsTo)
- dc:coverage uri to http://purl.org/dc/terms/coverage (from http://purl.org/dc/elements/1.1/coverage)
- dc:issued uri to http://purl.org/dc/terms/issued (from http://purl.org/dc/elements/1.1/issued)
- Added new annotation property:
- Changed label of (and removed “skos:prefLabel” where relevant)
- dc:accessRights to Access Rights
- dc:issued to Date Issued
- dc:language to Language
- dc:audience to Audience
- dc:isReferencedBy to “Is Referenced By”
- dc:accrualMethod to “Accrual Method”
- dc:accrualPeriodicity to “Accrual Periodicity”
- dc:accrualPolicy to “Accrual Policy”
- dc:available to “Date Available”
- dc:conformsTo to “Conforms To”
- dc:coverage to Coverage
- rdfs:comment to Comment
- Added “en” language tag to relevant annotations:
- Title
- Abstract
- Access Rights
- Audience
- Comment
- Coverage
- Conforms To
- Accrual Method
- Accrual Periodicity
- Accrual Policy
- Date Available
- Updated Language to say “en” instead of “English”
New existence status applied to annotation property “existence in other ontologies”:
- Ontology definition taken from is not an OBO Foundry ontology
Fixed typos in SCDO-EDIT (curator’s) version:
- typo in label of SCDO:0001006 (from “Reticulocyte Count by Microsocopy” to “Reticulocyte Count by Microscopy”)
- typo in the definition for STATO:0000091/“Genome Wide Association Study” (changed “accross” to across”) → need to request STATO to make the update
- Typo in definition of “Minimum Age Value Specification”
- removed space in definition of “SCDO:0000080”/Aspartate Aminotransferase Level”
- Removed line break in definition of SCDO:0000530/”Hemoglobin E Disease”
- Changed exact synonym of Vaso-Occlusive Crisis (SCDO:0001229) from Vaso-Occlusive Crisis to Vasoocclusive Crisis
- Some urls in annotations of references were updated/fixed
- Updated definition of Data Use Requirements from “Requirements indicate additional conditions set for use of data” to “Requirements indicating additional conditions set for use of data.”
- Moved some exact synonyms from “Elevated Serum Alkaline Phosphatase” to “Decreased Serum Alkaline Phosphatase”:
- Reduced Circulating ALP
- Decreased Circulating Alkaline Phosphatase Level
- typo in label of SCDO:1000767/”Month 1 - 12” from “An answer to a question where the answer is a month between 1 - 12, selected form a list of months.” to “An answer to a question where the answer is a month between 1 - 12, selected from a list of months.”
- Prenatal Screening for Sickle Cell → Prenatal Screening for Sickle Cell Disease
- Moved some text from the definition of “Elevated Serum Alanine Aminotransferase” to a comment annotation.
- Fixed definitions for these terms (had a comment as the definition):
- Collaboration Required
- Thrombocytosis
- Time Limit on Use
- Geographical Restriction
- Publication Moratorium
- Acutely Severe Anemia
- Publication Moratorium → Had additional definition, which was changed to a comment (rdfs: comment)
- Deferred Consent → Consent that is taken later after enrollment into a study, especially in emergency situations.
- Moved definition of Basique (“Waiting for description for this.”) to curator note.
- Cerebral Collateral Flow
- Doppler Ultrasound Machine - 2 Megahertz
- Human Life Cycle Stage → Made more specific
- Data Anonymization
- Association -> instead used definition from the Semanticscience Integrated Ontology (SIO)
- Preventative Therapeutics -> Made more generic
- Genetic Testing -> Definition used from NCIT was actually defining Genetic Screening, so rather used definition from MESH
- Neonatal Screening for Sickle Cell -> from “Testing of neonates to identify those with major sickling diseases." to “Testing of neonates to detect those who have sickle cell disease or who are carriers of sickle cell disease.”
- Decreased Arterial Oxygen Saturation -> added “ where the arterial oxygen saturation was measured by a blood gas analyzer” at the end.
- Normal Arterial Oxygen Saturation -> added “with the oxygen saturation having been measured by a blood gas analyzer” at the end.
- Catheter -> changed from narrower definition of MESH term (MESH:D057785) to broader OBI term (OBI:0002830)
- D57.3 Sickle-cell trait -> from “The condition of being heterozygous for hemoglobin S.” to “ICD10CM code for the condition of being heterozygous for hemoglobin S.”
- Added “for children” to definition of “Coping Strategies Questionnaire revised for Sickle Cell Disease Children (CSQ-SCD Children)”.
- Added “ICD10CM code for the “ to the start of definition of “D57.0 Hb-SS disease with crisis”.
- Hereditary Methemoglobinemia -> changed to that of MONDO term as ORPHA term was obsoleted
- “Alkaline Phosphatase Level” -> removed additional definition “The proportion, quantity, or volume in whole blood, serum, or plasma of this enzyme, which hydrolyzes orthophosphoric monoesters.”
- “BCL11A Erythroid Enhancer”
- “Type of Body Temperature”
- “Increased Red Cell Osmotic Resistance”
- “D57.01 Hb-SS disease with acute chest syndrome”
- “D57.02 Hb-SS disease with splenic sequestration”
- “D57.1 Sickle-cell disease without crisis”
- “D57.20 Sickle-cell/Hb-C disease without crisis”
- “D57.21 Sickle-cell/Hb-C disease with crisis”
- “D57.211 Sickle-cell/Hb-C disease with acute chest syndrome”
- “D57.212 Sickle-cell/Hb-C disease with splenic sequestration”
- “D57.213 Sickle-cell/Hb-C disease with cerebral vascular involvement”
- “D57.214 Sickle-cell/Hb-C disease with dactylitis”
- “D57.218 Sickle-cell/Hb-C disease with crisis with other specified complication”
- “D57.219 Sickle-cell/Hb-C disease with crisis, unspecified”
Fixed some broken/ugly url links in annotations
- Definition source updated for:
- Ketamine
- Hemoglobin Variant Test
- Hemoglobin F Test
- Sickle Cell Chronic Lung Disease
- Alanine Aminotransferase Blood Test
- Sickle Cell Disease-S Beta Minus Thalassemia
- Medical Outcomes Study (MOS) Social Support Survey
- Globin Gene
- HMOX1
- Intestinal Fatty-Acid Binding Protein
- Hydration Therapy
- Sickle Cell Disease
- Hemoglobinopathy
- Sickle Cell Thalassemia
- Hemoglobin M Disease
- Cigarette Smoking Status
- Demographic Factor
- Diagnostic Biospecimen
- Gene Product
- Hemoglobin Trait
- Personal Attribute
- Phenotype
- Blood Smear
- Electrocardiographic Monitor
- Brain Electrical Activity
- Hepatic Iron Concentration
- Mid Upper Arm Circumference
- Cerebral Blood Flow Velocity
- Hemoglobin H Disease
- Acquired Methemoglobinemia
- Fungal Infection
- Voluntary
- Data
- Age
- Ethnic Group
- Gender
- National Origin
- Race
- Geographic Area
- Personal Medical History
- History of Transfusion
- Reproductive History
- Alcohol Use History
- Smoking History
- Sample
- Hyperbilirubinemia
- Person
Changed “definition source”:
- Of “Catheter” from MESH term MESH:D057785 URL to http://purl.obolibrary.org/obo/OBI_0002830
Changed the “database cross reference”:
- of “Abnormal Mean Corpuscular Hemoglobin Concentration” from HP:0025546 to MP:0005640, so that the IRI would be correct (for Mammalian Phenotype Ontology) in the compiled OWL file.
- “Asymptomatic Malaria” below “Asymptomatic”
- “Sickle Cell Anemia” as a parent class of “Sickle Cell Disease-SS” and “Sickle Cell Anemia Associated with Alpha Thalassemia”
- “Sickle Cell Anemia” also added below “Anemia” (in the Phenotype) class.
- Copied “Sickle Cell Anemia Associated with Alpha Thalassemia” below “Anemia”.
- “Acceptability” below “Quality of Health Care”
- “Hydroxyurea Therapy” below “Preventative Therapeutics”, “Supportive Therapeutics” and “Symptomatic Therapeutics”
- “Point-of-Care Test for Sickle Cell Disease” below “Hemoglobin Profile Assay”
- “Lateral Flow Immunoassays Point-of-Care Test for Sickle Cell Disease” below “Point-of-Care Test for Sickle Cell Disease”, with synonyms “LFIA POCT for SCD”
- “HemoTypeSC Rapid Test” below “Lateral Flow Immunoassays Point-of-Care Test for Sickle Cell Disease”
- “Diagnostic Biospecimen” below “Diagnostics”
- “Dried Blood Spot” below “Diagnostic Biospecimen”
- Gazelle Hemoglobin Testing under “Point-of-Care Test for Sickle Cell Disease” (as per SCDO WG discussions)
- “Malaria Case” below “Human Subject”.
- “Clinical Malaria” below “Comorbid Disease”.
- “Population Descriptor” below “Research”
- “Incidence Proportion” and “Incidence Rate” below “Population Descriptor”
- “Infectious Disease Incidence Proportion” below “Incidence Proportion”
- “Malaria Incidence Proportion” below “Infectious Disease Incidence Proportion”
- “Benign Ethnic Neutropenia” below “Neutropenia, with synonyms: Benign Neutropenia, Chronic Benign Neutropenia, Constitutional Neutropenia, Ethnic Neutropenia
- “Dried Blood Spot - Point-of Care Test (DBS-POCT) for Sickle Cell Disease (SCD)” below “Point-of-Care Test for Sickle Cell Disease”
- “Mutation Screening” below “Genetic Screening”
- “Sickle Cell Disease Screening” below “Mutation Screening”
- “Healthcare Facility Name” below “Information on Observation Details”
- “Abnormal Musculoskeletal Physiology” & “Abnormal Skeletal Morphology” below “Abnormality of the Skeletal System”
- “Limb Pain” below “Pain”, “Comorbid Disease” & “Abnormal musculoskeletal physiology”
- “Abnormal Carbohydrate Metabolism” below “Abnormality of Metabolism/Homeostasis”
- “G6PD Deficiency” below “Abnormal Carbohydrate Metabolism” and “Comorbid Disease”
- “Favism” below “G6PD Deficiency”
- “Sulfadoxine-Pyrimethamine” below “Malaria Chemoprophylaxis”
- “Monthly Sulfadoxine-Pyrimethamine” below “Sulfadoxine-Pyrimethamine”
- "Pyrimethamine" below "Malaria Chemoprophylaxis"
- "Metaprim" below "Pyrimethamine"
- "Chloroquine" below "Malaria Chemoprophylaxis"
- “Microscopy Assay” below “Imaging Assay”
- "Blood Sample" below "Diagnostic Biospecimen"
- “Serum Sample” below “Blood Sample”
- “Buffy Coat” below "Diagnostic Biospecimen"
- "Plasma Sample" below "Blood Sample"
- "Herbal Medicine" below "Complementary Therapy"
- “Herbal Medicine Agent" below "Drug"
- “Amodiaquine” below “Malaria Chemoprophylaxis”
- “Sulfadoxine-Pyrimethamine Plus Amodiaquine” below “Malaria Chemoprophylaxis”
- “Drug Resistance” below “Adverse Drug Event”
- “Sulphadoxine-Pyrimethamine Resistance” below “Drug Resistance”
- “Atovaquone-Proguanil” below “Malaria Chemoprophylaxis”
- “Atovaquone-Proguanil Resistance” below “Malaria Chemoprophylaxis”
- “Schoolgoing” below “Demographic Factor“
- “Primary School”, “Secondary School” and “Tertiary School” below “Clinical or Research Assessment Answer”
- “Schoolgoing Caregiver” and “Schoolgoing Participant” below “Schoolgoing”
- “Epidemiologic Factor” below “Research”
- “Environment and Public Health Terminology” as upper-level class
- “Public Health Term” below “Environment and Public Health Terminology”
- “Public Health” below “Public Health Terminology”
- “Environmental Term” below “Environment and Public Health Terminology”
- “Environment” below “Environment Terminology”
- “Disease Eradication” below “Public Health Term”
- “Communicable Disease Control” below “Public Health Term”
- “Malaria Control” below “Communicable Disease Control”
- “Malaria Chemotherapy” below “Curative Therapeutics”
- “Patient Recruitment” below “Study Design”
- “Recruitment Criteria” below “Study Design”
- “Person Descriptor” below “Research”
- “Person” below “Research” and below “Public Health Term”
- Below “Person Descriptor”:
- “Person by Activity Type”
- “Person by Age Group”
- “Person by Health Status”
- “Person by Legal Status”
- “Person by Living Situation”
- “Person by OccupationType”
- “Person by Other Characteristic”
- “Person by Relationship”
- “Mutation Carrier” below “Person by Health Status”
- “SCD Mutation Carrier” below “Mutation Carrier”
- “Site of Care Delivery” below “Environment”
- “Healthcare Facility” below “Site of Care Delivery”
- “Outpatient Care Facility”, “Hospital” and “Clinic” below “Healthcare Facility”
- “ICD-10-CM Coding Rules” below “Clinical Coding”
- New ICD10 codes:
- D57.04 Hb-SS disease with dactylitis
- D57.214 Sickle-cell/Hb-C disease with dactylitis
- D57.414 Sickle-cell thalassemia, unspecified, with dactylitis
- D57.434 Sickle-cell thalassemia beta zero with dactylitis
- D57.814 Other sickle-cell disorders with dactylitis
- K80 Cholelithiasis
- I63 Cerebral infarction
- Male Only Diagnosis Code
- Adult Code
- Newborn Code
- Pediatric Code
- Maternity Code
- Female Only Diagnosis Code
- Manifestation Code
- Present On Admission Exempt Code
- Questionable As Principal Diagnosis Code
- “Marital Status” below “Demographic Factor”
- “Finding of Marital or Partnership Status” below “Clinical or Research Assessment Answer”
- “Cohabiting” below “Finding of Marital or Partnership Status”
- “Vital Status” below “Personal Attribute”
- Added below “Vital Status”:
- “Alive”
- “Dead”
- “Lost To Follow-Up”
- “Pending”
- “Not Reported”
- “Symptom” below “Abnormal Phenotype”
- “Stroke Symptom” below “Symptom”
- “Symptoms Status” below “Personal Attribute”
- “Stroke Symptoms Status” below “Symptoms Status”
- “Number of SCD Pain Attacks in Past 12 Months” below “Frequency of Sickle Cell Pain Episodes”
- “Number Answer” below “Clinical or Research Assessment Answer”
- Below “Number Answer”:
- One
- Two
- Three
- Four or More
- None
- Four
- Five
- Six
- Seven
- Eight
- Nine
- "Last Pain Attack - When” below “Diagnostic Instrument Measurement”
- “Temporal Answer” below “Clinical or Research Assessment Answer”
- Below “Temporal Answer”:
- Never
- More Than 5 Years Ago
- 1-5 Years Ago
- 7-11 Months Ago
- 1-6 Months Ago
- 1-3 Weeks Ago
- Less Than 1 Week Ago
- Experiencing Currently/Today
- Less Than 1 Hour
- 1-12 Hours
- 13-23 Hours
- 1-3 Days
- 4-6 Days
- 1-2 Weeks
- More Than 2 Weeks
- “Worst Imaginable” below “Clinical or Research Assessment Answer”
- “Worst Pain Imaginable” below “Worst Imaginable”
- “Date of Death” and “Date of Sample Collection” below “Temporal Observable”
- “Calculated Age on Day of Consent (Years)” below “Age”
- “Blood Gas Analyzer” below “Diagnostic Device”
- “Decreased Peripheral Oxygen Saturation” below “Abnormal Blood Gas Level”
- “Normal Blood Oxygen Saturation” below “Normal Metabolism/Homeostasis Phenotype”
- “Normal Peripheral Oxygen Saturation” below “Normal Blood Oxygen Saturation”
- “Calculated Age on Day of Consent (Months)” below “Age”
- “Scheduled Follow-Up Visit” below “Follow-Up Visit”
- “Unscheduled Follow-Up Visit” below “Follow-Up Visit”
- “Tobacco Smoking History” below “Smoking History”
- “Tonsillectomy” below “Surgery”
- Added “Newborn Screening”, “NBS for Sickle Cell”, “Newborn Screening for Sickle Cell Disease”, “NBS for Sickle Cell Disease” and “NBS for SCD” as exact synonyms for “Neonatal Screening for Sickle Cell”
- Added “Sickle SCAN” to “Sickle SCAN Rapid Test”
- Added “Abnormal Thrombocyte Count” to “Abnormal Platelet Count”
- Added “Blood Granular Leukocyte Count” to “Blood Granulocyte Count”
- Added narrow synonym “Hermaphroditism” to “Intersex”
- Added “Normal Haemoglobin Concentration” to “Normal Hemoglobin Concentration”
- Added “Observation Details” to “Information on Observation Details”
- Added “Human Developmental Stage” to“Human Life Cycle Stage”
- Added “SCD-SS” to “Sickle Cell DIsease-SS”
- Added “Screening Tests” and “Genetic Screening Tests” to “Genetic Screening”
- Added “SLE” to “Systemic Lupus Erythematosus”
- Added “Medicine” to “Drug”
- Added “Physical Exam” to “Physical Examination”
- Added “Near-Patient Test for Sickle Cell Disease” and “Bedside Test for Sickle Cell Disease” for “Point-of-Care Test for Sickle Cell Disease”
- Added "Rapid Diagnostic Test for SCD" as a synonym of "Point-of-Care Test for Sickle Cell Disease".
- Added “Blood Serum Sample” to “Serum Sample”
- Added “Diagnostic Bio-Specimen”, “Diagnostic Biological Sample” and “Diagnostic Biological Specimen” to “Diagnostic Biospecimen”
- Added "HU" to "Hydroxyurea"
- Added “CQ” to “Chloroquine”
- Added “Flavoquine” to “Amodiaquine”
- Added “Severity of Illness” and “Patient Acuity” to “Disease Severity”
- Added “Symptomatic Sickle Cell Trait” to “Dominant Sickle Cell Disease”
- Added “Neonatal Screening for Sickle Cell Disease” to “Neonatal Screening for Sickle Cell”
- Added “Unknown” to “Do Not Know”
- Added to “Girdle Syndrome”:
- Added to “Sickle Cell Painful Event”:
- Sickle Cell Pain Attack
- Acute Sickle Cell Crisis
- Sickle Cell Painful Crisis
- Sickle Cell Pain Event
- Added “Oxygen Saturation Measured by Pulse Oximetry” to “Peripheral Oxygen Saturation”
- Added “Blood Gas Analysis” to “Arterial Blood Gas Test”
- Added “Routine Health Care Encounter” to “Routine Clinical Visit”
- Added “Follow-Up Health Care Encounter” to “Follow-Up Visit”
- Added “Data Point”, “Datum”, “Data Record” to “Data”
- Added “HbSS Disease” to “Sickle Cell Disease-SS”
- Added “HbSβThal Genotype” to “Hemoglobin Genotype S/Beta Thalassemia”
- Added “SCD-SC” to ”Sickle Cell Disease-SC”
- Added “SCD-SE” to “Sickle Cell Disease-SE”
- Added “Increased Haemoglobin Concentration” for “Increased Hemoglobin Concentration”
- Added “Decreased Haemoglobin Concentration” for “Decreased Hemoglobin Concentration”
Changed location of terms:
- Removed “Hydroxyurea” from below “Preventative Therapeutics”
- Removed “Sickle SCAN Rapid Test” from below “Hemoglobin Variant Test” and added it below ”Hemoglobin Profile Assay”
- Moved “Peripheral Blood Film” from below “Blood Smear” to below “Blood Test”
- Moved “Blood Smear” to below the new term “Diagnostic Biospecimen”
- Removed “SCD Management Details” from below “Therapeutics” because the definition for Therapeutics does not encompass its content
- Removed “Cordocentesis” from below “Hematology Screening Test” and added “Sickle Cell Disease Screening Test” as a child of “Hematology Screening Test” (based on the positioning of these terms in SNOMED CT)
- Moved “Solubility Test” below “Sickling Test” (as per SCDO WG discussions)
- Copied “Point-of-Care Test for Sickle Cell Disease” below “Sickle Cell Disease Screening Test”
- Moved “Sickling Test” below “Sickle Cell Disease Screening Test”
- Removed “Sickle SCAN Rapid Test” and “HemoTypeSC Rapid Test” from below “Type of SCD Test” (as already subclass of “Sickle Cell Disease Screening Test”
- Moved “Hemoglobin Electrophoresis” from below ”Hemoglobin Variant Test” to below “Hemoglobin Profile Assay”
- Moved “Epidemiologic Studies” to be a sub-class of “Epidemiologic Study Characteristics”, as per location in MESH
- Moved “Mutation carrier screening” below the new “Mutation Screening” term
- Removed “Sickle Cell Disease Screening Test” from below “Mutation Screening”
- Added “HemoTypeSC Rapid Test” below the new “Dried Blood Spot - Point-of Care Test (DBS-POCT) for Sickle Cell Disease (SCD)” term
- Moved “Hospital Name” below “Healthcare Facility Name”
- Moved “Osteomyelitis”, “Osteonecrosis”, “Bone Fragility”, “Joint Hypermobility” below “Abnormal Musculoskeletal Physiology”
- Moved “Arthritis”, “Hyperostosis”, “Frontal Bossing”, “Kyphosis”, “Spondylolisthesis”, “Osteopenia”, “Biconcave Vertebral Bodies”, “Osteoporosis”, “Scoliosis”, “Vertebral Collapse”, “Increased Bone Mineral Density” below “Abnormal Musculoskeletal Morphology”
- Moved “Septic Arthritis” below “Arthritis”
- Moved “Flexion Contracture” below “Abnormality of the Musculature”
- Moved “Dried Blood Spot” below “Blood Sample”
- Moved “Blood Smear” below “Blood Sample”
- Moved “Marital Status of Primary Caregiver”, “Occupation”, “Religion”, “Next of Kin Relationship to Participant” and “Gender Identity” below “Demographic Factor”
- Moved “Age of Onset” from below “Association” to below “Epidemiologic Factor”
- Moved “Disease Severity” from below “Association” to below “Diagnosis”
- Moved “Human Life Cycle Stage” from below “Association” to below “Demographic Factor”
- Moved “Treatment Efficacy” from below “Association” to below “Quality of Health Care”
- Moved “Association” from being an upper-level class to below “Research”
- Moved “Health Behaviour” from below “Environmental Disease Modifier” to below “Disease Modifier”
- Moved “Mutation Carrier Screening” and “Sickle Cell Disease Screening” from below “Mutation Screening” to below “Genetic Screening”
- Moved “Sickle Cell Disease Screening” from below “Genetic Screening” to below “
- Moved “Amniocentesis”, “Chorionic Villus Sampling” and “Cordocentesis” from below “Prenatal Screening for Sickle Cell Disease” to below “
- Moved “Current Marital Status” and “Marital Status of Primary Caregiver” below “Marital Status”
- Moved “Divorced”, “Never Been Married”, “Separated”, “Widowed” and “Married” to below “Finding of Marital or Partnership Status”
- Moved “Girdle Syndrome” from below “Abnormal Phenotype” to below “Pain”
- Moved “Year 1900 - Current” from below “Clinical or Research Assessment Answer” to below “Temporal Answer”
- Moved “Normal Arterial Oxygen Saturation” below “Normal Blood Oxygen Saturation”
- Moved any deprecated terms that were children of other deprecated terms to directly under “deprecated terms”.
- Moved “Malaria Case” from below “Human Subject” to below “Person by Health Status”
- Moved “Human Subject” from below “Research Characteristics” to below “Person by Activity Type”
- Moved “Age Range Category” from below “Research Characteristics” to below “Data Descriptor”
- Moved “Sample” from below “Personal Attribute” to below “Data Descriptor”
- Moved “Data” from below “Personal Attribute” to below “Research”
- Moved “Person” from below “Person Descriptor” to below “Research”
- Moved all deprecated terms that were children of other deprecated terms to directly under “deprecated terms” (as per ROBOT report recommendation)
- Moved “Splenectomy” from below “Symptomatic Therapeutics” to below “Surgery”
Added parent term to existing term:
- Added “Comorbid Disease” as a parent term of:
- Stroke
- Priapism
- Chest Pain
- Jaundice
- Sickle Cell Dactylitis (see curator note)
- Added “Abnormal Musculoskeletal Physiology” as a parent of “Bone Pain”
- Added “Comorbid Disease” as parent of “Abnormality of the Spleen”
- Added “Environmental Term” as parent of “Gene-Environment Interaction” below
- Added “Public Health Term” as parent of “Epidemiologic Factor”
- Added “Public Health Term” as parent of “Epidemiologic Study Characteristics”
- Added “Diagnostic Technique, Method, Test or Assay” as parent of “Sickle Cell Disease Screening Test”
- Added “Quality of Life Related SCD Symptoms and Complications” to “Girdle Syndrome”
- Added “Person by Other Characteristic” to “No-Show Patient”
- Added “Research” to “Data”
- Added “Public Health Term” to “Person Descriptor”
- Added “Surgery” as a parent of “Cholecystectomy”
- Removed suggestion of inclusion in ERO for “Manometer” and “Electrocardiogram”.
- Changed “Suggest update to description in NCIT (from "Alanine Aminotransferase Measurement")” to “Suggest update to label in NCIT (from "Alanine Aminotransferase Measurement")” for “Alanine Aminotransferase Blood Test”
- Changed note for “Sickle Cell Disease-SE to “Sufficient”
- Add note for “Chest Pain”:
- Not sure if chest pain can technically be classified as a "Comborbid Disease", as well as a "Constitutional Symptom"? Was placed below "Comorbid Disease" by request of SickleInAfrica members attending 8th conference in CT in Oct 2022.
- Add note for “Sickle Cell Dactylitis”:
- Added this below "Comorbid Disease" as SickleInAfrica members attending 8th conference in CT in Oct 2022 requested that "Dactylitis" be added below "Comorbid Disease", but we do not have "Dactylitis" as a term. Not sure whether to rather remove this as a comorbid disease and rather add "Dactylitis" and include it as a comorbid disease? If so, we might want to consider how to indicate that the combination of Dactylitis and SCD is the same as "Sickle Cell Dactylitis"?
- Mutation Screening
- Acute Sickle Cell Crisis -> replaced by “Sickle Cell Painful Event”, moved existing object property associations to this term
Removed Individuals/Instances:
- Removed “Individual 1” which was added in Oct 2022 as a test (http://purl.obolibrary.org/obo/SCDO_1000911)
- Updated “dc:comment” for “description adapted from source” annotation property to say that: “The use of this annotation property on SCDO terms was deprecated a few years ago. Instead, "existence in other ontologies" was adopted to indicate similar information.”
- Updated all labels of deprecated terms that started with “deprecated” to rather start with “obsolete” as per ROBOT report recommendation).
- Added “previous identifier” annotation property to be used to ascribe the SCDO term ID for terms that have their URLs replaced by external source term URLs
- Added “homepage” annotation property to display specific SCDO web page link for each term
Edits related to SCDO-DE mappings:
- Added sub-classes below “SickleInAfrica Core Data Element Instrument”:
- SickleInAfrica Core Data Element Instrument - IDs
- SickleInAfrica Core Data Element Instrument - Personal Details
- SickleInAfrica Core Data Element Instrument - Registry Consent
- SickleInAfrica Core Data Element Instrument - SCD Baseline
- SickleInAfrica Core Data Element Instrument - Visits
- SickleInAfrica Core Data Element Instrument - Labs
- Removed “has sections” annotations from “SickleInAfrica Core Data Element Instrument” term and added sections to the above new instrument names as necessary.
Auto-changes made by code for updating SCDO-DE mappings:
- Added sub-classes below “SickleInAfrica Core Data Element”:
- Additional properties for mapping SCD data elements to the SCDO:
- has coding rule
- possible additional code
Noted terms from external ontologies needing annotation updates:
- Definition of “Ketamine” needs updating in NCIT