scdo.owl
type: Ontology
dc:LicenseDocument: LicenseDocument
dc:abstract: abstract for SCDO
dc:accessRights: description of SCDO's access rights
dc:accrualMethod: accrualMethod
dc:accrualPeriodicity: accrualPeriodicity
dc:accrualPolicy: accrualPolicy
dc:audience: description of SCDO's audience
dc:available: available
dc:conformsTo: the standard(s) to which the SCDO conforms
dc:coverage: coverage of SCDO
dc:isReferencedBy: isReferencedBy
dc:issued: issued
language: language
dc:license: license

dc:LicenseDocument
type: AnnotationProperty
description: A legal document giving official permission to do something with a Resource.
definition source: LicenseDocument
description adapted from source: no
property has curation status: ontology annotation property
preferred label: License Document

dc:abstract
type: AnnotationProperty
description: A summary of the resource.
definition source: abstract
description adapted from source: no
property has curation status: ontology annotation property
preferred label: Abstract

dc:accessRights
type: AnnotationProperty
description: Information about who can access the resource or an indication of its security status.
definition source: accessRights
description adapted from source: no
property has curation status: ontology annotation property
preferred label: Access Rights

dc:accrualMethod
type: AnnotationProperty
description: The method by which items are added to a collection.
definition source: accrualMethod
description adapted from source: no
property has curation status: ontology annotation property
preferred label: Accrual Method

dc:accrualPeriodicity
type: AnnotationProperty
description: The frequency with which items are added to a collection.
definition source: accrualPeriodicity
description adapted from source: no
property has curation status: ontology annotation property
preferred label: Accrual Periodicity

dc:accrualPolicy
type: AnnotationProperty
description: The policy governing the addition of items to a collection.
definition source: accrualPolicy
description adapted from source: no
property has curation status: ontology annotation property
preferred label: Accrual Policy

dc:audience
type: AnnotationProperty
description: A class of entity for whom the resource is intended or useful.
definition source: audience
description adapted from source: no
property has curation status: ontology annotation property
preferred label: Audience

dc:available
type: AnnotationProperty
description: Date (often a range) that the resource became or will become available.
definition source: available
description adapted from source: no
property has curation status: ontology annotation property
preferred label: Date Available

dc:conformsTo
type: AnnotationProperty
description: An established standard to which the described resource conforms.
definition source: conformsTo
description adapted from source: no
property has curation status: ontology annotation property
preferred label: Conforms To

dc:coverage
description: The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant.
definition source: coverage
description adapted from source: no
property has curation status: ontology annotation property
preferred label: Coverage

dc:creator
type: AnnotationProperty
description: An entity primarily responsible for making the resource. (This property is used in the SCDO when a term was created by the SCDO Working Group.)
definition source: creator
description adapted from source: no
property has curation status: ready for release
preferred label: Creator

dc:description
type: AnnotationProperty
description: A formal account of the class/term.
definition source: description
description adapted from source: yes
property has curation status: pending vetting by the SCDO developers

dc:isReferencedBy
type: AnnotationProperty
description: A related resource that references, cites, or otherwise points to the described resource.
definition source: isReferencedBy
description adapted from source: no
property has curation status: ontology annotation property
preferred label: Is Referenced By

dc:issued
type: AnnotationProperty
description: Date of formal issuance (e.g., publication) of the resource.
definition source: issued
description adapted from source: no
property has curation status: ontology annotation property
preferred label: Date Issued

dc:language
description: A language of the resource.
definition source: language
description adapted from source: no
property has curation status: ontology annotation property
comment: Recommended best practice is to use a controlled vocabulary such as RFC 4646 [RFC4646].
preferred label: Language

dc:license
type: AnnotationProperty
description: A legal document giving official permission to do something with the resource.
definition source: license
description adapted from source: no
property has curation status: ontology annotation property
preferred label: License

dc:source
type: AnnotationProperty
description: A related resource from which the described class/term's annotations are derived.
definition source: source
description adapted from source: yes
property has curation status: pending vetting by the SCDO developers

abbreviation
type: AnnotationProperty
description: A shortened form of a word or phrase, in this case a class/term. It consists of a group of letters taken from the word or phrase.
dc:source: http://www.ontobee.org/ontology/UBERON
database cross reference: http://www.ontobee.org/ontology/UBERON
definition source: Abbreviation
description adapted from source: yes
property has curation status: metadata complete - requires restrictions and relationships

curator note
type: AnnotationProperty
description: An administrative note of use for a curator but of no use for a user.
database cross reference: IAO:0000232
definition source: IAO_0000232
description adapted from source: no
property has curation status: organizational term

database cross reference
type: AnnotationProperty
description: A database cross-reference. An annotation which directs one to information contained within a database.
database cross reference: SBO:0000554
definition source: SBO:0000554
property has curation status: metadata complete - requires restrictions and relationships
hasExactSynonym: DbXref
hasExactSynonym: Xref
hasExactSynonym: database cross-reference
hasExactSynonym: database_cross_reference
hasExactSynonym: db xref
hasExactSynonym: hasDbXref

definition source
type: AnnotationProperty
description: A source from where the formal description was derived. This can be in the form of a link to a relevant webpage, the IRI of a term in an existing ontology, a reference to specific literature, etc.
database cross reference: IAO:0000119
definition source: IAO_0000119
description adapted from source: yes
property has curation status: metadata complete - requires restrictions and relationships
preferred label: description source

description adapted from source
type: AnnotationProperty
creator: SCDO
description: An assertion of whether or not the term/class description is an adaptation of the description in the description source.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion.
property has curation status: metadata complete - requires restrictions and relationships
comment: 'yes' indicates that only the description has been adaptation from the source. 'no' indicates that neither the label nor the description have been adapted from the source. 'only label adapted' indicates that only the label has been adapted from the source but the description is the same as that provided by the source. 'label and description adapted' indicates that both the label and the description have been adapted from the source.
comment: This property is required unless dc:creator is "SCDO".
range: no
range: yes

has age of onset
type: AnnotationProperty
creator: SCDO
description: A relation between a disease and the age, developmental stage, or period of life at which the disease or the initial symptoms or manifestations of the disease usually appear in individuals.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion. This property might be better suited as a data property? If as a data property, perhaps there should be a standardised way of inputting age of onset?
property has curation status: metadata complete - requires restrictions and relationships

has cross-cultural adaptation
type: AnnotationProperty
creator: SCDO
description: A relation between a measure (e.g. a survey) and how the measure has been adapted cross-culturally.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes.
property has curation status: metadata complete - requires restrictions and relationships

has disease stage
type: AnnotationProperty
creator: SCDO
description: A relationship between a condition/disease and a description of how the condition/disease is staged/graded.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion.
property has curation status: metadata complete - requires restrictions and relationships
comment: Staging provided is disease/phenotype specific.

has protocol
type: AnnotationProperty
creator: SCDO
description: A relation between a measurement and a plan specification for obtaining the measurement that has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion. To be applied to "Measurement", "Test, Method or Assay", "Therapeutics"
property has curation status: metadata complete - requires restrictions and relationships

has recommended procedure
type: AnnotationProperty
creator: SCDO
description: A relation between a measure or measurement and the recommended procedure used by the measure or used to obtain the measurement.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion.
property has curation status: metadata complete - requires restrictions and relationships

has respondents
type: AnnotationProperty
creator: SCDO
description: A relation between a measure (e.g. a survey) and the measure's respondents (people who respond). Respondents can be types or groups of people or people with a specific relationship to the main person of interest in the measure.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes.
description adapted from source: no
property has curation status: metadata complete - requires restrictions and relationships
comment: If the main person of interest responds, "Self" is indicated. If a person other than the main person of interest can respond, "Proxy" is indicated. If the proxy responder has a specific relationship (Family Members; Health Care Provider or Care-giver) to the main person of interest, that relationship should be indicated in brackets after "Proxy", e.g. Proxy (Health Care Provider or Care-giver). If more than one type of proxy responder is relevant, these should be listed and separated by ";", e.g. Proxy (Family Members; Health Care Provider or Care-giver)

has target population
type: AnnotationProperty
creator: SCDO
description: A relation between a measure (e.g. a survey) and the population that the measure was designed to target.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes.
property has curation status: metadata complete - requires restrictions and relationships
comment: Possible values used in the SCDO: Healthy Population; Clinic Patients (Children and/or Adults with SCD); Family Members; and/or Health Care Provider

has translations
type: AnnotationProperty
creator: SCDO
description: An account of known translations of a measure into other languages (other than English).
curator note: Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes.
property has curation status: metadata complete - requires restrictions and relationships

has_application_toward
type: AnnotationProperty
description: A relation between a planned process and an objective it can be used to achieve.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion.
definition source: http://www.ontobee.org/ontology/ERO
property has curation status: metadata complete - requires restrictions and relationships

imported from
type: AnnotationProperty
description: For external terms/classes, the ontology from which the term was imported.
database cross reference: IAO:0000412
definition source: IAO_0000412
description adapted from source: no
property has curation status: metadata complete - requires restrictions and relationships

is caused by
type: AnnotationProperty
curator note: Eventually to be replaced by "is caused by" object property
property has curation status: metadata incomplete

is characterised by
type: AnnotationProperty
creator: SCDO
description: A relationship between a condition (a phenotype or disease) and a description of distinctive characteristics or essential features.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion.
property has curation status: metadata complete - requires restrictions and relationships

property has curation status
type: AnnotationProperty
description: Description inherent in name (not provided by source)
dc:source: IAO_0000114
description adapted from source: Only label adapted
property has curation status: organizational term
comment: Used for properties, not classes. For classes, use "has curation status" object property.

selection criteria met
type: AnnotationProperty
creator: SCDO
description: A relation between a selected entity and the predefined criteria that were met by the entity and that made it eligible for selection.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes.
property has curation status: metadata complete - requires restrictions and relationships

validated for age ranges
type: AnnotationProperty
creator: SCDO
description: A relation between a measure and the age ranges for which the measure has been validated.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes.
property has curation status: metadata complete - requires restrictions and relationships

freely available
type: AnnotationProperty
creator: SCDO
description: A relation between a measure (e.g. a survey) and an indication of whether the measure is freely available.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes.
property has curation status: metadata complete - requires restrictions and relationships
comment: 'yes' indicates that the measure is freely available. 'no' indicates that the measure is not freely available.

abbre
type: AnnotationProperty

hasBroadSynonym
type: AnnotationProperty
description: An alias in which the alias is broader than the primary class name. Example: cell division is a broad synonym of cytokinesis.
description adapted from source: no
property has curation status: pending vetting by the SCDO developers

hasExactSynonym
type: AnnotationProperty
description: An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle.
description adapted from source: no
property has curation status: pending vetting by the SCDO developers

hasNarrowSynonym
type: AnnotationProperty
description: An alias in which the alias is narrower than the primary class name. Example: pyrimidine-dimer repair by photolyase is a narrow synonym of photoreactive repair.
description adapted from source: no
property has curation status: pending vetting by the SCDO developers

hasRelatedSynonym
type: AnnotationProperty
description: An alias in which the alias is related to the primary class name, but not necessarily broader or narrower. Example: cytochrome bc1 complex is a related synonym of ubiquinol-cytochrome-c reductase activity; virulence is a related synonym of pathogenesis.
description adapted from source: no
property has curation status: pending vetting by the SCDO developers

rdfs:comment
description: Additional information describing the class/term.
description adapted from source: yes
property has curation status: pending vetting by the SCDO developers

rdfs:label
description: A human-readable name for the class/term.
description adapted from source: yes
property has curation status: pending vetting by the SCDO developers

rdfs:seeAlso
description: Further information about the class/term.
description adapted from source: yes
property has curation status: pending vetting by the SCDO developers

skos:prefLabel
type: AnnotationProperty
description: A preferred label.
description adapted from source: yes
property has curation status: pending vetting by the SCDO developers

age of onset modified by
type: ObjectProperty
sub property of: topObjectProperty
domain: Phenotype
range: Disease Modifier
description: A relationship between a phenotype and a disease modifier, where the disease modifier modifies the age of onset of the phenotype. Age of onset is defined as "The age group in which disease manifestations appear." (HPO)
definition source: HP_0003674
description adapted from source: Label and description adapted
property has curation status: pending vetting by the SCDO developers

has clinical code
type: ObjectProperty
domain: Hemoglobinopathy
range: Clinical Coding
creator: SCDO
description: A relationship between a Sickle Cell Disease Variant and a relevant ICD-10-CM Diagnosis Code.
property has curation status: pending vetting by the SCDO developers

has curation status
type: ObjectProperty
domain: Thing
range: curation status specification
description: Description inherent in name (not provided by source).
dc:source: IAO_0000114
curator note: Every class must have this property.
database cross reference: IAO:0000114
property has curation status: organizational term
comment: Used only for classes, not properties. For properties, use "property has curation status" annotation property.

has measurement
type: ObjectProperty
sub property of: topObjectProperty
domain: Diagnostic Device
domain: Phenotype
domain: Diagnostic Tool
range: Measurement
creator: SCDO
description: A relation that holds between an entity (device, instrument) or a process (test, assy or method) and a measurement.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion. Could be replaced by RO property "has output" (RO:0002234): "P has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p."
property has curation status: pending vetting by the SCDO developers

has medical device
type: ObjectProperty
sub property of: topObjectProperty
domain: Measurement
domain: Therapeutics
domain: Diagnostic Tool
range: Diagnostic Device
range: Therapeutic Device
creator: SCDO
description: A relation between a process (test, method, assay, therapy, etc.) and a specific medical device used in the process.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion.
property has curation status: pending vetting by the SCDO developers

has phenotype
type: ObjectProperty
domain: Phenotype
range: Phenotype
description: A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
curator note: If required later, specify as inverse of "phenotype of" in Protege.
definition source: RO_0002200
description adapted from source: no
property has curation status: metadata complete - requires restrictions and relationships

has diagnostic tool
type: ObjectProperty
sub property of: topObjectProperty
domain: Diagnostic Device
domain: Measurement
range: Diagnostic Tool
creator: SCDO
description: A relationship between a measurement and the test, method or assay used to produce the measurement, or between a device and the test, method or assay in which the device is used.
property has curation status: pending vetting by the SCDO developers

caused by
type: ObjectProperty
sub property of: topObjectProperty
domain: Phenotype
range: Disease Modifier
range: Phenotype
range: Therapeutics
creator: SCDO
description: A relationship between a condition (a phenotype or disease) and an entity (a genotype, genetic variation or environment, which could be an existing condition) where the entity has a causal role for the condition.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion.
property has curation status: metadata complete - requires restrictions and relationships

diagnosed by
type: ObjectProperty
domain: Phenotype
range: Measurement
range: Diagnostic Tool
creator: SCDO
description: A relation between a phenotype and one or more diagnostic tools.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion.
property has curation status: metadata complete - requires restrictions and relationships

treated with
type: ObjectProperty
domain: Phenotype
range: Therapeutics
creator: SCDO
description: A relation between a phenotype and a type of treatment or a specific treatment.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion. If required later, specify as inverse of "treats" in Protege.
property has curation status: pending vetting by the SCDO developers

mortality modified by
type: ObjectProperty
sub property of: topObjectProperty
domain: Phenotype
range: Disease Modifier
creator: SCDO
description: A relationship between a phenotype and a disease modifier, where the disease modifier modifies the mortality (due to the phenotype) of the SCD sufferer.
property has curation status: pending vetting by the SCDO developers

phenotype of
type: ObjectProperty
domain: Phenotype
range: Phenotype
description: Inverse of "has phenotype" object property.
curator note: If required later, specify as inverse of "has phenotype" in Protege.
definition source: RO_0002201
description adapted from source: no
property has curation status: metadata complete - requires restrictions and relationships

results_in
type: ObjectProperty
domain: Phenotype
range: Phenotype
range: Quality of Life and Care
range: Therapeutics
description: Description inherent in name (not provided by source)
dc:source: IDO_0000660
curator note: This property is to be split up into two other properties: "has consequences" and "has symptoms". [Could request that the Infectious Disease Ontology (IDO) defines this term explicitly.]
database cross reference: IDO:0000660
property has curation status: metadata complete - requires restrictions and relationships

temporal pattern modified by
type: ObjectProperty
sub property of: topObjectProperty
domain: Phenotype
range: Disease Modifier
description: A relationship between a phenotype and a disease modifier, where the disease modifier modifies the temporal pattern of the phenotype. Temporal pattern is defined as "The speed at which disease manifestations appear and develop." (HPO)
definition source: HP_0011008
description adapted from source: Label and description adapted
property has curation status: metadata complete - requires restrictions and relationships

essential measure
type: ObjectProperty
domain: Measurement
domain: Personal Attribute
domain: Quality of Life and Care
domain: Diagnostic Tool
range: Measurement
range: Personal Attribute
range: Diagnostic Tool
creator: SCDO
description: A measure that is critical to the collection of the measure at hand or is necessary for the interpretation of results for the measure at hand. Without such information, the data collected would be incomplete or misleading.
property has curation status: pending vetting by the SCDO developers
comment: Essential measures have been attributed according to information in PhenX.

modified by
type: ObjectProperty
sub property of: topObjectProperty
domain: Phenotype
range: Disease Modifier
creator: SCDO
description: A relationship between a phenotype and a disease modifier, where the phenotype is modified by the disease modifier.
curator note: If required later, specify as inverse of "modifies" in Protege.
property has curation status: pending vetting by the SCDO developers

modifies
type: ObjectProperty
sub property of: topObjectProperty
domain: Disease Modifier
range: Phenotype
creator: SCDO
description: A relationship between a disease modifier and a phenotype, where the disease modifier modifies the phenotype.
curator note: If required later, specify as inverse of "modified by" in Protege.
property has curation status: pending vetting by the SCDO developers

treats
type: ObjectProperty
domain: Therapeutics
range: Phenotype
creator: SCDO
description: A relation between a type of treatment or a specific treatment and a phenotype, where the type of treatment or specific treatment treats the phenotype.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion. If required later, specify as inverse of "treated with" in Protege.
property has curation status: pending vetting by the SCDO developers

has causal mutation
type: ObjectProperty

has molecular phenotype
type: ObjectProperty

topObjectProperty
curator note: Add properties that link diagnostic tools or measurements back to phenotypes..."diagnoses" when linked to a diagnosis? "detects" when linked to a phenotype that is a deviation from normal (e.g. an increased level of something).

Abdominal Ultrasound
type: Class
subclass of: Ultrasonography Test
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A type of imaging test used to look at organs in the abdomen, including the liver, gallbladder, spleen, pancreas, and kidneys. The blood vessels that lead to some of these organs, such as the inferior vena cava and aorta, can also be examined with ultrasound.
definition source: 003777.htm
description adapted from source: yes
hasExactSynonym: Abdominal Sonogram
hasNarrowSynonym: Right Upper Quadrant Sonogram

Ability to Carry Out Activities of Daily Living
type: Class
subclass of: Physical Health
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The performance of the basic activities of self care, such as dressing, ambulation, or eating.
abbreviation: ADL
database cross reference: MESH:D000203
definition source: D000203
description adapted from source: Only label adapted
hasExactSynonym: ADL
hasExactSynonym: Daily Living Activities
hasExactSynonym: Daily Living Activity
hasExactSynonym: Self Care (Rehabilitation)
hasExactSynonym: Self-Care

Abnormal Hemoglobin Structure Present in SCD
type: Class
subclass of: Abnormality of Erythrocytes
subclass of: SCD Molecular Phenotype
subclass of: Restriction
  on property: has curation status
  has value: accepted by SCDO WG (WS2)
creator: SCDO
description: Abnormality in the structure and function of the oxygen-carrying protein of erythrocytes.
abbreviation: Abnormal Hb Structure
curator note: Consider inclusion of other sub-classes of this term in the Human Phenotype Ontology. - Elevated hemoglobin A1c - Imbalanced Hemoglobin Synthesis (and the 2 terms below this) Methemoglobina Others from MESH?: Hemoglobin E, J, M, Methemoglobin?
database cross reference: HP:0011902

Abnormality of Erythrocytes
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: accepted by SCDO WG (WS2)
description: Abnormality in structure and function of the Red Blood Cell.
curator note: Are there other relevant erythrocyte abnormalities that can be included as children here? If not, this class can be removed and just keep "Abnormal Hemoglobin".
database cross reference: HP:0001877
definition source: HP_0001877
description adapted from source: yes
hasExactSynonym: Abnormality of Erythroid Lineage Cell
hasExactSynonym: Abnormality of Red Blood Cells
hasExactSynonym: Abnormality of red blood cell

Acetaminophen
type: Class
subclass of: Non Opioid
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: Acetaminophen, also known as paracetamol, is commonly used for its analgesic and antipyretic effects. Its therapeutic effects are similar to salicylates, but it lacks anti-inflammatory, antiplatelet, and gastric ulcerative effects.

Acne
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: results_in
  some values from: Infection
subclass of: Restriction
  on property: results_in
  some values from: Skin Inflammation
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A skin condition in which there is an increase in sebum secretion by the pilosebaceous apparatus associated with open comedones (blackheads), closed comedones (whiteheads), and pustular nodules (papules, pustules, and cysts).
dc:source: HP_0001061
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0001061
description adapted from source: no
has disease stage: Grade 1, 2, 3, 4.
is caused by: Clogging of the skin pores by dead skin cells, sebum and sometimes bacteria.
is characterised by: Blemishes characterized by pustules (pimples), blackheads, whiteheads, papules, nodules, cysts.

Acquired Methemoglobinemia
type: Class
subclass of: Methemoglobinemia
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Methemoglobinemia that is caused by exposure to certain drugs (xylocaine and benzene) and nitrate-rich foods.
dc:source: http://www.orpha.net/consor/cgi-bin/Disease_Search.php
database cross reference: C98805
definition source: C98805
description adapted from source: no

Activated Partial Thromboplastin Time
type: Class
subclass of: Blood Coagulation Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The time needed for plasma to form a fibrin clot after the addition of calcium and a phospholipid reagent. It is used to evaluate the intrinsic clotting system.
dc:source: CMO_0000210
database cross reference: CMO:0000210
description adapted from source: no
hasExactSynonym: APTT; Quick

Acute Chest Syndrome
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Chest X-Ray
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: treated with
  some values from: Blood Transfusion
subclass of: Restriction
  on property: treated with
  some values from: Hematopoietic Stem Cell Transplantation
subclass of: Restriction
  on property: treated with
  some values from: Hydration
subclass of: Restriction
  on property: treated with
  some values from: Hydroxyurea
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: treated with
  some values from: Gene Therapy
subclass of: Restriction
  on property: results_in
  some values from: Hospitalization
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Acute onset of respiratory symptoms and/or signs and an X-ray consistent with alveolar consolidation but not atelectasis, involving at least one complete lung segment.
dc:source: Castro et al 1994 Blood; Knight et al 1999 Ped Pulm; Vichinsky et al 2000 NEJM; Ballas et al 2010 Am J Hem; Miller et al 2012 Am J Respir Crit Care Med.
abbreviation: ACS
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
curator note: further work
definition source: Castro et al 1994 Blood
description adapted from source: yes
is caused by: Several possible etiologies including infections by various classes of microorganisms, pulmonary fat emobolism, infarction and pulmonary embolism.
is characterised by: Acute onset of respiratory symptoms and signs including fever, cough, dsypnea, chest pain, tachypnea, respiratory distress, crackes and wheezes.
comment: Treatments: Curative therapies such as BMT and/or gene therapy; Disease modifying therapies such as hydroxyurea and chronic transfusion; Acutely- antibiotics, oxygen, adequate hydration, bronchodilators when there is airway hyperresponsiveness, transfusion- simple or exchange as appropriate, physical therapy and, when necessary, assisted ventilation.

Acute Complications of Sickle Cell Disease
type: Class
subclass of: Phenotype of Sickle Cell Disease
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A condition that co-exists or follows from sickle cell disease and that has a severe and rapid onset of symptoms with short duration.
definition source: http://bioportal.bioontology.org/ontologies/NCIT
definition source: Q000150
description adapted from source: yes
hasExactSynonym: Acute Complications of SCD

Acute Kidney Injury
type: Class
subclass of: Kidney Failure
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Glomerular Filtration Rate
subclass of: Restriction
  on property: diagnosed by
  some values from: Serum Creatinine Level
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Measurement
subclass of: Restriction
  on property: treated with
  some values from: Renal Dialysis
subclass of: Restriction
  on property: treated with
  some values from: Supportive Therapeutics
subclass of: Restriction
  on property: results_in
  some values from: Azotaemia
subclass of: Restriction
  on property: results_in
  some values from: Hyperkalemia
subclass of: Restriction
  on property: results_in
  some values from: Edema
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia). Acute renal failure is usually classified into prerenal (response to severe volume depletion), intrinsic (response to acute cytotoxic, ischemic, or inflammatory insults) and postrenal (response to obstruction of the passage of urine) etiologies.
dc:source: acute-kidney-injury
abbreviation: AKI
curator note: Further work
curator note: Provide source for additional info.
curator note: There is conflicting positioning of this term in different ontologies. Need an expert to decide descriptions and positioning of this and related terms.
database cross reference: HP:0001919
definition source: HP_0001919
description adapted from source: yes
has age of onset: Can occur at any age.
has disease stage: "Yes: Stage determined by both serum creatinine and urine output: Stage 1: creatinine elevated 1.5-1.9 times baseline OR >0.3mg/dl (26.5 mmol/l) increase OR urine output <0.5ml/kg/h for 6-12 hours Stage 2: creatinine elevated 2.0-2.9 times baseline OR urine output <0.5ml/kg/h for >=12 hours Stage 3: creatinine elevated >=3.0 times baseline OR elevation to >=4.0 mg/dl (353.6 mmol/l) increase OR urine output <0.5ml/kg/h for 6-12 hours OR Initiation of renal replacement therapy OR in patients <18 years, decrease in eGFR to <35 ml/min per 1.73 m2 OR urine output <0.3 ml/kg/h for >=24 hours OR Anuria for X12 hours".
is caused by: Variety of causes - may be related to profound volume depletion, acute tubular injury, hypoperfusion, sickle cell crisis, interstitial nephritis, rapidly progressive glomerulonephritis, intrinsic renal disease, obstructive renal disease.
is characterised by: AKI is defined as the following (Not Graded): Increase in SCr by >=0.3 mg/dl (>=26.5 lmol/l) within 48 hours; or increase in SCr to >=1.5 times baseline, which is known or presumed to have occurred within the prior 7 days; or urine volume <0.5 ml/kg/h for 6 hours.
hasExactSynonym: Acute Kidney Failure
hasExactSynonym: Acute Renal Failure

Acute Non-Specific Wheezing Episode
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: diagnosed by
  some values from: Pulmonary Function Test
subclass of: Restriction
  on property: results_in
  some values from: Acute Chest Syndrome
subclass of: Restriction
  on property: results_in
  some values from: SCD Related Pain
subclass of: Restriction
  on property: results_in
  some values from: Stroke
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An acute onset of wheezing in a person with SCD who has no co-morbid asthma.
dc:source: Cohen et al 2011 Am J Hematol., Glassberg et al 2014 Curr Opin Pediatr., Knight-Madden et al 2014 Ped Resp Rev
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
description adapted from source: yes
is caused by: Etiology may be unclear. May be related to inflammation of SCD and/or viral lower respiratory tract infection.
is characterised by: Normal Chest X-ray
comment: PFTs may be done to asses for airway hyper-responsiveness.

Acute Sickle Cell Pain Management
type: Class
subclass of: Sickle Cell Pain Management
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Sickle cell pain management that aims to heal the acute process.
definition source: Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014.
description adapted from source: yes
hasExactSynonym: Acute Sickle Cell Pain Treatment

Acute Tubular Necrosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Serum Creatinine Level
subclass of: Restriction
  on property: treated with
  some values from: Renal Dialysis
subclass of: Restriction
  on property: treated with
  some values from: Supportive Therapeutics
subclass of: Restriction
  on property: results_in
  some values from: Acute Kidney Injury
subclass of: Restriction
  on property: results_in
  some values from: Kidney Failure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Acute injury of renal tubular cells that usually results from prolonged renal ischemia, nephrotoxins, or sepsis.
dc:source: HP_0008682
abbreviation: ATN
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0008682
description adapted from source: yes
has age of onset: Can occur at any age.
is caused by: Renal ischemia (which can occur due to prolonged prerenal states), nephrotoxins, or sepsis. In sickle cell disease, may occur due to renal ischemia related to sickle crisis.
is characterised by: Loss of kidney function, reduced urine output, elevated serum creatinine.
hasExactSynonym: Renal Tubular Necrosis

Acute Upper Respiratory Tract Infection
type: Class
subclass of: Infection
subclass of: Restriction
  on property: diagnosed by
  some values from: Chest X-Ray
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: treated with
  some values from: Symptomatic Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An acute respiratory illness with no lower respiratory tract signs or infiiltrate on chest radiograph.
dc:source: OAE_0000358
abbreviation: URTI
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: OAE:0000358
description adapted from source: yes
is caused by: Various microorganisms, usually viral.
is characterised by: Acute onset of respiratory symptoms and signs including cough, coryza +/- fever.
hasExactSynonym: URTI

Adherence
type: Class
subclass of: Mental Health
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The extent to which a person's behaviour - taking medications, following a diet and/or executing life style changes, corresponds to agreed recommendations by a health care provider.
dc:source: D010349
database cross reference: MESH:D010349
definition source: www.who.int/chp/knowledge/publications/adherence_full_report.pdf
description adapted from source: no
hasExactSynonym: Adherence to Long Term Therapy
hasExactSynonym: Patient Adherence
hasExactSynonym: Patient Compliance
hasExactSynonym: Patient Cooperation

Adjuvant
type: Class
subclass of: Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Any pharmacological or immunological agent that modifies the effect of other agents such as drugs or vaccines while having few if any direct effects when given by itself.
database cross reference: CHEBI:60809
definition source: CHEBI_60809
description adapted from source: no
hasExactSynonym: Adjuvant Medicine

Adult Migraine Questionnaire
type: Class
subclass of: Migraine Questionnaire
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The Self-Administered Questionnaire for Migraine is a 20-item questionnaire that assesses the frequency of severe headaches, the level of pain, whether the person is taking medications, and associated complications such as nausea.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX130501
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has protocol: PhenX protocol: Migraine #130501

Adult Sickle Cell Quality-of-Life Measurement Information System (ASCQ-Me)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: ASCQ-Me (Adult Sickle Cell Quality of Life Measurement Information System) is a patient-reported outcome measurement system that assesses the physical, social, and emotional impact of sickle cell disease (SCD). ASCQ-Me includes questions that enable adults with SCD to describe their functioning and well-being. ASCQ-Me measures are available as 5 item short forms or can be administered as computer adaptive tests. Measures include: Pain Impact; Stiffness Impact (5-item short form); Sleep Impact; Social Functioning Impact; Emotional Impact; Pain Episodes – Frequency and Severity.
dc:source: http://www.phenxtoolkit.org/index.php
dc:source: Keller SD, Yang M, Treadwell MJ, Werner EM, Hassell KL (2014).Patient reports of health outcome for adults living with sickle cell disease: development and testing of the ASCQ-Me item banks. Health and Quality of Life Outcomes,12,125.
abbreviation: ASCQ-Me
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: Cross-cultural adaptation underway in Brazil. ASCQ-Me's development using modern measurement theory facilitates cross cultural adaptation.
has respondents: Self
has target population: Clinic Patients (Adults with SCD)
has translations: Spanish; Portuguese
selection criteria met: Rigor in development, using modern measurement theory and aligned with PROMIS measurement development.
validated for age ranges: 18 years and older
freely available: no
hasExactSynonym: ASCQ-Me
hasExactSynonym: Adult Sickle Cell Quality-of-Life Measurement Information System

Adverse Drug Event
type: Class
subclass of: Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An adverse event that occurs after a drug administration.
abbreviation: ADE
curator note: Should this be a sub-class of "Environmental Disease Modifier"?
database cross reference: OAE:0000005
definition source: OAE_0000005
description adapted from source: no
hasExactSynonym: ADE
hasExactSynonym: ADR
hasExactSynonym: Adverse Drug Reaction
hasExactSynonym: Drug Adverse Event

Agarose Gel Electrophoresis
type: Class
subclass of: Electrophoresis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Electrophoresis in which agar or agarose gel is used as the diffusion medium.
database cross reference: D004587
definition source: D004587
description adapted from source: no
hasBroadSynonym: Gel Electrophoresis
hasExactSynonym: Agar Gel Electrophoresis

Age
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: How long something has existed; elapsed time since birth.
curator note: Still must add many sub-classes of "Age" in NCIT.
database cross reference: NCIT:C25150
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Aged
hasExactSynonym: Chronological Age
hasExactSynonym: Postnatal Age

Agenesis of Corpus Callosum
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Ultrasonography Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: treated with
  some values from: Genetic Counseling
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: treated with
  some values from: Supportive Therapeutics
subclass of: Restriction
  on property: treated with
  some values from: Symptomatic Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A rare congenital disorder characterized by a partial or complete absence (agenesis) of an area of the brain that connects the two cerebral hemispheres.
dc:source: agenesis-of-corpus-callosum
abbreviation: ACC
curator note: Include links to relevant Therapeutics.
definition source: agenesis-of-corpus-callosum
description adapted from source: yes
is caused by: The cause of agenesis of corpus callosum is usually not known, but it can be inherited as either an autosomal recessive trait or an X-linked dominant trait. It can also be caused by an infection or injury during the twelfth to the twenty-second week of pregnancy (intrauterine) leading to developmental disturbance of the fetal brain. Intrauterine exposure to alcohol (Fetal alcohol syndrome) can also result in ACC. In some cases mental retardation may result, but intelligence may be only mildly impaired and subtle psychosocial symptoms may be present.
is characterised by: Agenesis of corpus callosum (ACC) may initially become evident through the onset of epileptic seizures during the first weeks of life or within the first two years. However, not all individuals with ACC have seizures.
hasExactSynonym: ACC
comment: Agenesis of Corpus Callosum produces symptoms during the first two years of life in approximately ninety percent of those affected. It has been thought to be a very rare condition but the increased use of neuro-imaging techniques, such as MRI, is resulting in an increased rate of diagnosis. This condition may also be identified during pregnancy through an ultrasound. Currently, the highest estimate of incidence is 7 in 1000 individuals.

Alanine Transaminase Blood Test
type: Class
subclass of: Blood Test
subclass of: Liver Function Assay
subclass of: Restriction
  on property: has measurement
  some values from: Alanine Transaminase Level
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A test to measures the level of the alanine transaminase (ALT) enzyme in the blood.
definition source: 003473.htm
description adapted from source: yes
has_application_toward: This test is used to determine if a person has liver damage, as ALT is an enzyme found in a high level in the liver and injury to the liver results in release of ALT into the blood.
hasExactSynonym: ALT Blood Test
hasExactSynonym: Serum ALT Blood Test

Alanine Transaminase Level
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Alanine Transaminase Blood Test
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A quantitative measurement of the amount of alanine aminotransferase present in a sample of serum.
dc:source: VT_0001573
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: Only label adapted
hasExactSynonym: ALT Level
hasExactSynonym: Alanine Aminotransferase Level
hasExactSynonym: Alanine Transaminase Level
hasExactSynonym: Blood Alanine Transaminase Amount
hasExactSynonym: Circulating Alanine Transaminase Level
hasExactSynonym: Glutamic-Pyruvic Transaminase Level
hasExactSynonym: Serum ALT Measurement
hasExactSynonym: Serum Alanine Aminotransferase Measurement
hasExactSynonym: Serum Alanine Transaminase Measurement
hasExactSynonym: Serum SGPT Measurement
comment: Serum concentration is increased in viral hepatitis and myocardial infarction.

Albinism
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Cancer
subclass of: Restriction
  on property: results_in
  some values from: Blindness
subclass of: Restriction
  on property: results_in
  some values from: Visual Impairment
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Albinism is a defect of melanin production that results in little or no color (pigment) in the skin, hair, and eyes.
dc:source: HP_0001022
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0001022
description adapted from source: yes
has disease stage: Oculocutaneous, Ocular albinism, Hermansky-Pudlak syndrome.
is caused by: Genetic disorder.
is characterised by: Absence of color in the hair, skin, or iris of the eye, lighter than normal skin and hair, patchy, missing skin color.
hasExactSynonym: Achromasia

Albuminuria
type: Class
subclass of: Proteinuria
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin Concentration
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin Excretion Rate
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin-Creatinine Ratio
subclass of: Restriction
  on property: treated with
  some values from: Angiotensin-Converting Enzyme Inhibitors
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Chronic Kidney Disease
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Increased concentration of albumin in the urine; more than 30mg in 24hours or urine albumin creatinine ratio (ACR) >30 mg/g or >3 mg/mmol.
dc:source: introduction
curator note: Include as sub-class?: macroalbuminuia (possibly now referred to as "high level albuminuria"...see PhenX protocol for " Urinary Microalbumin Assay")
definition source: introduction
definition source: HP:0012592
description adapted from source: yes
has age of onset: When assessed by albuminuria, often presents within second decade of life in sickle cell disease and prevalence increases with age.
has disease stage: YES: Categories - A1 (Normal to midly increased, fomerly normalbuminuria - UACR<30mg/g or 3mg/mmol), A2 (moderately increased or microalbuminuria - UACR 30-300 mg/g or 3-30mg/mmol); A3 - (Severely increased or previously macroalbuminuria - >300mg/g or >30mg/mmol).
is caused by: Nonspecific finding of many forms of kidney disease, including diabetes, glomerular disease, sickle cell disease.
is characterised by: Albumin excretion > 30mg in 24hr (Urine ACR >30 mg/gm creatinine or >3 mg/mmol).

Alcohol - Lifetime Use
type: Class
subclass of: Alcohol Use History
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Record of whether or not the respondent has ever consumed any alcoholic beverage during his or her entire life.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Alcohol - Lifetime Use #030101
comment: The PhenX protocol can be used to assess the participant’s lifetime exposure to alcohol. The question is often used as a prelude to more detailed questions about alcohol use to screen out individuals who have ever consumed alcohol.

Alcohol Intake
type: Class
subclass of: Lifestyle
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A drinking behavior associated with the intake of alcohol.
database cross reference: NBO:0000131
definition source: NBO_0000131
description adapted from source: Only label adapted
hasExactSynonym: Alcohol Consumption

Alcohol Use History
type: Class
subclass of: Personal Medical History
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A description of an individual's current and past experience with alcoholic beverage consumption.
curator note: Add other terms in the PhenX "Alcohol Use" collection?
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no

Alpha Thalassemia
type: Class
subclass of: Constitutional Genetic Disorder
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A disorder characterized by reduced synthesis of the alpha chains of hemoglobin. The severity of this condition can vary from mild anemia to death, depending on the number of genes deleted.
database cross reference: MeSH:D017085
definition source: D017085
description adapted from source: no
hasExactSynonym: A-Thalassemia
hasExactSynonym: Alpha-Thalassemia

Alpha Thalassemia Silent Carrier
type: Class
subclass of: Hemoglobin Trait Other than C,D,E,S,O-Arab
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A condition in which a person has reduced protein production from one of the four alpha-globin alleles.
database cross reference: NCIT:C95536
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Alpha-Thalassemia Silent Carrier

Alpha Thalassemia Trait
type: Class
subclass of: Hemoglobin Trait Other than C,D,E,S,O-Arab
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A condition in which a person has reduced protein production from two of the four alpha-globin alleles.
database cross reference: NCIT:C95535
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Alpha-Thalassemia Trait

Alpha-Adrenergic Agents
type: Class
subclass of: Antihypertensive Agents
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Drugs that selectively bind to and activate alpha adrenergic receptors.
database cross reference: MESH:D000316
definition source: D000316
description adapted from source: no
hasBroadSynonym: Adrenergic
hasBroadSynonym: Alpha-Adrenergic
hasExactSynonym: Adrenergic Alpha Agonists
hasExactSynonym: Alpha Adrenergic Receptor Agonist
hasRelatedSynonym: Alpha-Adrenergic Receptor

Alpha-Globins
type: Class
subclass of: Globin Loci
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Members of the alpha-globin family. In humans, they are encoded in a gene cluster on chromosome 16. They include zeta-globin and alpha-globin. There are also pseudogenes of zeta (theta-zeta) and alpha (theta-alpha) in the cluster. Adult hemoglobin is comprised of 2 alpha-globin chains and 2 beta-globin chains.
database cross reference: MESH:D055542
definition source: D055542
description adapted from source: no

Amniotic Fluid Testing
type: Class
subclass of: Prenatal Screening for Sickle Cell
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: test
comment: Amniotic fluid may be tested at 14 to 16 weeks to provide a definitive answer

Analgesia
type: Class
subclass of: Symptomatic Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Methods of pain relief that may be used with or in place of analgesics.
database cross reference: MeSH:D000698
definition source: D000698
description adapted from source: no
hasExactSynonym: Analgesias
comment: Includes cognitive behavior therapy, acupuncture for pain, hypnosis, transcutaneous electrical nerve stimulation (TENS) and massage.

Analgesics
type: Class
subclass of: Symptomatic Therapeutics
subclass of: Restriction
  on property: treats
  some values from: Cerebral Hemorrhage
subclass of: Restriction
  on property: treats
  some values from: Hyperostosis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Compounds capable of relieving pain without the loss of consciousness.
database cross reference: MESH:D000700
definition source: D000700
description adapted from source: yes
hasExactSynonym: Analgesic Agent
hasExactSynonym: Analgesic Drugs
hasExactSynonym: Anodynes
hasExactSynonym: Pain Killers
hasExactSynonym: Painkiller
hasExactSynonym: Painkillers
hasRelatedSynonym: Antinociceptive Agents

Anesthetic Complication AE
type: Class
subclass of: Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An adverse drug event that results in unexpected and unwanted events due to anesthetic drug treatment.
database cross reference: OAE:0002348
definition source: OAE_0002348
description adapted from source: no

Angioid Streaks
type: Class
subclass of: Ophthalmologic Complication
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Grayish, brown, or dark red streaks caused by cracks in Bruch’s membrane that are histologically characterized by calcium deposition. Angioid streaks are most characteristic of sickle cell anemia and can occur to a lesser extent in other sickle cell syndromes, but not in sickle cell trait.
dc:source: Sickle Cell Retinopathy
dc:source: Nagpal KC, Asdourian G, Goldbaum M, et al. Angioid streaks and sickle haemoglobinopathies. Br J Ophthalmol 1976;60:31-34.
definition source: Ballas et al 2010 Am J Hematol
description adapted from source: no
comment: Angioid streaks are a phenomenon seen in many retinal diseases including non-proliferative sickle retinopathy (NPSR) and proliferative sickle retinopathy (PSR).
comment: Diagnostic Criteria: Eye exam using direct and indirect ophthalmoscopy as well as slit lamp biomicroscopy. The fundus will have red-orange to brown bands in affected areas, and they may emanate from the optic disk.

Angiotensin-Converting Enzyme Inhibitors
type: Class
subclass of: Antihypertensive Agents
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A class of drugs whose main indications are the treatment of hypertension and heart failure. They exert their hemodynamic effect mainly by inhibiting the renin-angiotensin system. They also modulate sympathetic nervous system activity and increase prostaglandin synthesis. They cause mainly vasodilation and mild natriuresis without affecting heart rate and contractility.
database cross reference: MESH:D000806
definition source: D000806
description adapted from source: no
hasExactSynonym: ACE
hasExactSynonym: ACE Inhibitors
hasExactSynonym: Angiotensin Converting Enzyme
hasExactSynonym: Angiotensin Converting Enzyme Inhibitors

Annual Family Income
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Household Roster-Relationships
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The respondent's total family income from the last calendar year.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Include under QoL? The PhenX protocol is U.S. specific. Is there one relevant to the African setting?
database cross reference: PX11100
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has_application_toward: Family income is often associated with the health of those who live in a residence. For example, a family with a total income below the poverty level often does not have access to the same quality of health care; enough money for the basic necessities (food, rent, gas); or live in a safe or desirable neighborhood.
comment: "Household" is defined as the entire group of persons who live in the sample unit. It may consist of several persons living together or one person living alone. It includes the household reference person and any relatives living in the unit as well as roomers, employees, or other persons not related to the reference person. "Family" is defined as an individual or a group of two or more related persons who are living together in the same household; for example, the reference person, his or her spouse, foster son, daughter, son-in-law, and their children, and the wife’s uncle. Also, unmarried couples (same-sex and opposite-sex couples) are considered as belonging to the same family. Additional groups of persons living in the household who are related to each other but not the reference person are considered to be separate families. There can be more than one family living in the same household. Each family is considered a separate case and should be interviewed separately. "Reference Person (Family)" is the person or one of the persons in the family, equal to or greater than the age of others who live at the residence, who is generally the first person mentioned in the family roster. Generally, this person is age 18 years or older and the same person that owns or rents the housing unit. A reference person is designated to provide information about family members who live in the household. However, if the reference person is not available, the information can be obtained for another family member age 18 years or older.

Anti-Inflammatory Agent
type: Class
subclass of: Non Opioid
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Substance that reduces or suppresses inflammation.
database cross reference: MESH:D000893
definition source: D000893
description adapted from source: no
hasExactSynonym: Anti Inflammatories
hasExactSynonym: Anti Inflammatory Agents
hasExactSynonym: Anti-Inflammatories
hasExactSynonym: Anti-Inflammatory Agents
hasExactSynonym: Anti-Inflammatory Drug
hasExactSynonym: Antiinflammatories
hasExactSynonym: Antiinflammatory Agents

Antibiotic
type: Class
subclass of: Symptomatic Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Substances naturally produced by microorganisms or their derivatives that selectively target microorganisms not humans. Antibiotics kill or inhibit the growth of microorganisms by targeting components of the microbial cell absent from human cells, including bacterial cell walls, cell membrane, and 30S or 50S ribosomal subunits. These substances are used in the treatment of bacterial and other microbial infections.
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Antibiotic Agents
hasExactSynonym: Antibiotic Drugs
hasExactSynonym: Antibiotics
hasExactSynonym: Antimicrobial
hasExactSynonym: Antimicrobial Agent

Antihistamine
type: Class
subclass of: Symptomatic Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Drugs that bind to but do not activate histamine receptors, thereby blocking the actions of histamine or histamine agonists. Classical antihistaminics block the histamine H1 receptors only.
database cross reference: MESH:D006633
definition source: D006633
description adapted from source: Only label adapted
hasExactSynonym: Histamine Antagonist

Antihypertensive Agents
type: Class
subclass of: Supportive Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Used in the treatment of acute or chronic vascular hypertension regardless of pharmacological mechanism. Among the antihypertensive agents are diuretics; (especially Diuretics, Thiazide); Adrenergic Beta-Antagonists; Adrenergic Alpha-Antagonistics; Angiotensin-Converting Enzyme Inhibitors; Calcium Channel Blockers; Ganglionic Blockers; and Vasodilator Agents.
database cross reference: MESH:D000959
definition source: D000959
description adapted from source: no
hasExactSynonym: Agents, Antihypertensive
hasExactSynonym: Anti-Hypertensives
hasExactSynonym: Antihypertensives

Anxiety
type: Class
subclass of: Behavioral Abnormality
subclass of: Mental Health
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A neurological and physiological symptom characterized by a painful or apprehensive uneasiness of mind usually over an impending or anticipated ill. Physical symptoms include increased blood pressure (rapid heartbeat), trembling or dizziness.
dc:source: anxiety
database cross reference: SYMP:0000412
definition source: SYMP_0000412
definition source: anxiety
description adapted from source: yes
hasExactSynonym: Anxiety symptoms
hasExactSynonym: Panic
hasExactSynonym: Worry
comment: Anxiety and anxious symptoms are more prevalent among children and adults with SCD compared with the general population
comment: People with anxiety disorders usually have recurring intrusive thoughts or concerns.

Apolipoprotein L1
type: Class
subclass of: Non-Globin Loci
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: This gene encodes a secreted high density lipoprotein which binds to apolipoprotein A-I.
abbreviation: APOL1
definition source: http://www.ncbi.nlm.nih.gov/gene/8542
description adapted from source: yes
hasExactSynonym: APOL1
comment: Official Full Name: apolipoprotein L1; Gene ID: 8542; Chromosome: 22; Position: 36253071..36267531 (GRCh38.p2); Variants
preferred label: APOL1

Aquatic Rehabilitation
type: Class
subclass of: Rehabilitation
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Exercises performed in or underwater for conditioning or rehabilitation (e.g., in injured athletes or patients with joint diseases).
dc:source: Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014
definition source: aquatic+therapy
description adapted from source: no
hasExactSynonym: Aqua Therapy
hasExactSynonym: Hydrotherapy

Arterial Blood Gas Test
type: Class
subclass of: Blood Test
subclass of: Restriction
  on property: has measurement
  some values from: Oxygen Saturation of Arterial Blood
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A blood test that measures the pH of the blood, the partial pressure of arterial carbon dioxide and oxygen, the bicarbonate level.
dc:source: Arterial blood gas
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX90200
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Arterial Blood Gas (ABG) #090201
has_application_toward: An ABG test measures the blood gas tension values of arterial oxygen tension (PaO2), arterial carbon dioxide tension (PaCO2), and acidity (pH). In addition, arterial oxygen saturation (SaO2) can be determined. Such information is vital when caring for patients with critical illness or respiratory disease.
hasExactSynonym: ABG Test
comment: An ABG test involves puncturing an artery with a thin needle and syringe and drawing a small volume of blood. The most common puncture site is the radial artery at the wrist, but sometimes the femoral artery in the groin or other sites are used. The blood can also be drawn from an arterial catheter.

Arteriovenous Malformation
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Abnormal formation of blood vessels that shunt arterial blood directly into veins without passing through the CAPILLARIES. They usually are crooked, dilated, and with thick vessel walls. A common type is the congenital arteriovenous fistula. The lack of blood flow and oxygen in the capillaries can lead to tissue damage in the affected areas.
database cross reference: MESH:D001165
definition source: D001165
description adapted from source: Only label adapted
hasExactSynonym: Arteriovenous Malformations

Artesunate
type: Class
subclass of: Malaria Prophylaxis
subclass of: Supportive Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Artesunate is part of the artemisinin group of drugs that treat malaria. It is a semi-synthetic derivative of artemisinin that is water-soluble and may therefore be given by injection. It is on the World Health Organization’s List of Essential Medicines.
database cross reference: DB09274
definition source: DB09274
description adapted from source: no

Arthralgia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: treated with
  some values from: Anti-Inflammatory Agent
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Depression
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: has curation status
  has value: accepted by SCDO WG (WS2)
description: Joint pain.
curator note: Provide source for additional info.
database cross reference: HP:0002829
definition source: HP_0002829
description adapted from source: no
is caused by: Inflammatory diseases, autoimmune diseases, infection, trauma.
is characterised by: Pain in one or more joints.
hasExactSynonym: Arthralgias
hasExactSynonym: Joint pain

Arthritis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: results_in
  some values from: Chronic Pain in a Specific Tissue or Organ
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: has curation status
  has value: accepted by SCDO WG (WS2)
description: Inflammation of a joint.
curator note: Provide source for additional info.
database cross reference: HP:0001369
definition source: HP_0001369
description adapted from source: no
is caused by: Infection (bacteria), ischemia, joint injury (trauma, surgery), degeneration.
is characterised by: Joint pain, joint swelling, stiffness, lack of function.

ASCQ-Me - Quality of Life in SCD
type: Class
subclass of: Adult Sickle Cell Quality-of-Life Measurement Information System (ASCQ-Me)
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: This protocol includes 30 self-administered questions from the short form of the Adult Sickle Cell Quality of Life Measurement Information System (ASCQ-Me). Domains covered include emotional impact (5 items), social functioning impact (5 items), sleep impact (5 items), stiffness impact (5 items), pain episode (5 items), and pain frequency (5 items).
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has respondents: Self
has target population: Clinic Patients (Adults with SCD)
validated for age ranges: 18 and older
comment: Life stage: Adult

Aspartate Aminotransferase Blood Test
type: Class
subclass of: Blood Test
subclass of: Heart Function Test
subclass of: Liver Function Assay
subclass of: Restriction
  on property: has measurement
  some values from: Aspartate Aminotransferase Level
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A bioassay to measure levels of aspartate aminotransferase (AST), which is released into the blood following tissue damage.
dc:source: VT_0000203
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX811200
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Aspartate Aminotransferase Level #811201
has_application_toward: Aids in diagnosis of viral hepatitis.
has_application_toward: Elevated levels of red blood cell aspartate aminotransferase (AST) are reflective of hemolysis associated with sickle cell disease. Additionally, elevated levels of AST are associated with myocardial infarction, liver disease, hemolysis and anemia, pancreatitis, muscle damage or inflammation, trauma and mononucleosis.
hasExactSynonym: AST Blood Test
hasExactSynonym: Serum AST Blood Test
comment: The PhenX protocol provides instructions for drawing, processing and storing blood according to the National Health and Nutrition Examination Survey (NHANES) methods. Because there are many comparable assays for measuring red blood cell aspartate aminotransferase (AST), the protocol also provides basic guidelines to aid comparability among different studies.

Aspartate Aminotransferase Level
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Aspartate Aminotransferase Blood Test
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A quantitative measurement of the amount of aspartate aminotransferase present in a sample of serum.
database cross reference: NCIT:C61018
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: Only label adapted
hasExactSynonym: AST Level
hasExactSynonym: Aspartate Aminotransferase Measurement
hasExactSynonym: Aspartate Transaminase Level
hasExactSynonym: Blood Aspartate Transaminase Amount
hasExactSynonym: Red Blood Cell Aspartate Aminotransferase Level
hasExactSynonym: Serum Aspartate Aminotransferase Measurement
hasExactSynonym: Serum Aspartate Transaminase Measurement
hasExactSynonym: Serum SGOT Measurement

ASQE-Me - Quality of Care in SCD
type: Class
subclass of: Adult Sickle Cell Quality-of-Life Measurement Information System (ASCQ-Me)
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A set of 27 questions administered to adults with sickle cell disease (SCD) to determine the quality of care that they have received from health care providers.
dc:source: http://www.phenxtoolkit.org/index.php
dc:source: Keller, S. D., Yang, M., Treadwell, M. J., Werner, E. M., & Hassell, K. L. (2014). Patient reports of health outcome for adults living with sickle cell disease: Development and testing of the ASCQ-Me item banks. Health and Quality of Life Outcomes, 12(1), 125. doi:10.1186/s12955-014-0125-0
dc:source: http//www.phenxtoolkit.org/index.php?pageLink=browse.protocols&id=820100
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Quality of Care - Adults #820101
has respondents: Self
has target population: Clinic Patients (Adults with SCD)
has_application_toward: These questions are used to assess the patient-reported health care needs and quality of service from health care providers for individuals with chronic conditions such as sickle cell disease (SCD).
validated for age ranges: 18 and older
hasExactSynonym: ASCQ-Me Quality of Care Module

Diagnostic Technique, Method, Test or Assay
type: Class
subclass of: Diagnostic Tool
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: A planned process with the objective of producing diagnostic information about the material entity that is the evaluant, by physically examining it or its proxies.
curator note: Use structuring of sub-classes within MESH's "Diagnostic Techniques and Procedures" and NCIT's "Diagnostic Procedure" to inform structuring of terms in this class.
database cross reference: OBI:0000070
definition source: OBI_0000070
description adapted from source: yes
hasNarrowSynonym: Diagnostic Assay
hasNarrowSynonym: Diagnostic Method
hasNarrowSynonym: Diagnostic Procedure
hasNarrowSynonym: Diagnostic Technique
hasNarrowSynonym: Diagnostic Test

Assessment of Short-Axis Cardiac Function by MRI
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: This measure is a magnetic resonance imaging (MRI) method of capturing an individual’s heart performance, and is considered the gold standard for capturing ventricular volumes and mass. It is used to detect cardiac abnormalities, such as cardiomyopathies, myocardial fibrosis, and infarction.
dc:source: Short Axis Function 20May2015.doc
definition source: Short Axis Function 20May2015.doc
description adapted from source: no
has recommended procedure: The American College of Radiology - North American Society for Cardiovascular Imaging - Society for Pediatric Radiology (ACR-NASCI-SPR) “Practice Parameter for the Performance and Interpretation of Cardiac Magnetic Resonance Imaging (MRI)” Amended 2014 (Resolution 39) outlines principles for performing high-quality cardiac MRI in adult and pediatric participants. Topics covered include indications, qualifications and responsibilities of personnel, safety guidelines and possible contraindications, specifications of the examination, documentation, equipment specifications, quality control and improvement, safety, infection control, and patient education.

Asthma
type: Class
subclass of: Phenotype
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A form of bronchial disorder with three distinct components: airway hyper-responsiveness, airway inflammation, and intermittent airway obstruction. It is characterized by spasmodic contraction of airway smooth muscle, wheezing and dyspnea.
curator note: Further work
curator note: Include a copy of this term below "Comorbid Disease" and/or below "Respiratory System".
database cross reference: MESH:D001249
definition source: D001249
description adapted from source: yes

Ataxia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Genetic Testing
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: diagnosed by
  some values from: Patient Symptom Report
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: treated with
  some values from: Occupational Therapy
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: treated with
  some values from: Supportive Therapeutics
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Ataxia is a term for a group of disorders that affect co-ordination, balance and speech.
dc:source: Introduction.aspx
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Perhaps add "Cerebellar Ataxia" subclass?
curator note: Further work
description adapted from source: yes
has age of onset: The outlook for ataxia can vary considerably and largely depends on the type of ataxia you have. Some types may remain relatively stable or even improve with time, but most will get progressively worse over many years. Life expectancy is generally shorter than normal for people with hereditary ataxia, although some people can live well into their 50s, 60s or beyond. In more severe cases, the condition can be fatal in childhood or early adulthood. For acquired ataxia, the outlook depends on the underlying cause. Some cases may improve or stay the same, while other cases may get gradually worse over time and reduce life expectancy.
has disease stage: There are many different types of ataxia, which can be divided into three broad categories: 1.Acquired ataxia - where symptoms develop as the result of trauma, a stroke, multiple sclerosis (MS), a brain tumour, nutritional deficiencies, or other problems that damage the brain or nervous system. 2.Hereditary ataxia - where symptoms develop slowly over many years and are caused by faulty genes that a person inherits from their parents; the most common type is Friedreich's ataxia. 3.Idiopathic late-onset cerebellar ataxia (ILOCA) - where the brain is progressively damaged over time for reasons that are unclear.
is caused by: Ataxia usually results from damage to a part of the brain called the cerebellum, but it can also be caused by damage to other parts of the nervous system. This damage can be part of an underlying condition such as MS, or can be caused by a head injury, lack of oxygen to the brain, or long-term, excessive alcohol consumption. Hereditary ataxia is caused by a faulty gene passed on by family members, who may or may not be affected.
is characterised by: Any part of the body can be affected, but people with ataxia often have difficulties with: balance and walking; speaking; swallowing; tasks that require a high degree of control, such as writing and eating; vision. The exact symptoms and their severity vary depending on the type of ataxia a person has.

Atopic Dermatitis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: results_in
  some values from: Infection
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A chronic inflammatory genetically determined disease of the skin manifested by lichenification, excoriation, and crusting, mainly on the flexural surfaces of the elbow and knee.
dc:source: HP_0001047
dc:source: Medscape: Atopic dermatitis: Author: Brian S Kim, MD; Chief Editor: William D James, MD.
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0001047
description adapted from source: no
has disease stage: Pruritus, Eczematous changes that vary with age, Chronic and relapsing course, Early age of onset, Atopy (IgE reactivity), Xerosis, Personal history of asthma or hay fever or a history of atopic diseases in a first-degree relative in patients younger than 4 years, Onset younger than age 2 years (not used if child is aged < 4 y.
is caused by: Genetics, Enviromental: infections, hygiene, climate, allergens, probiotics.
is characterised by: Incessant pruritus, xerosis, lichenification, eczematous lesions, atopy, chronic relapsing course.

Atrophic Brain
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Acquired diminution of the size of the brain associated with wasting as from death and reabsorbtion of cells, diminished cellular proliferation, decreased cellular volume, pressure, ischemia, malnutrition, reduced function or malfunction, or hormonal changes.
database cross reference: MP:0012506
definition source: MP_0012506
description adapted from source: no
hasExactSynonym: Brain Atrophy

Attention Deficit Hyperactivity Disorder
type: Class
subclass of: Behavioral Abnormality
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Attention deficit hyperactivity disorder (ADHD) manifests at age 2-3 years or by first grade at the latest. The main symptoms are distractibility, impulsivity, hyperactivity, and often trouble organizing tasks and projects, difficulty going to sleep, and social problems from being aggressive, loud, or impatient.
dc:source: index.shtml
abbreviation: ADHD
curator note: Provide source for additional info.
database cross reference: HP:0007018
definition source: HP_0007018
description adapted from source: no
has disease stage: Has three subtypes: Predominantly hyperactive-impulsive: Most symptoms (six or more) are in the hyperactivity-impulsivity categories. Fewer than six symptoms of inattention are present, although inattention may still be present to some degree. Predominantly inattentive: The majority of symptoms (six or more) are in the inattention category and fewer than six symptoms of hyperactivity-impulsivity are present, although hyperactivity-impulsivity may still be present to some degree. Children with this subtype are less likely to act out or have difficulties getting along with other children. They may sit quietly, but they are not paying attention to what they are doing. Therefore, the child may be overlooked, and parents and teachers may not notice that he or she has ADHD. Combined hyperactive-impulsive and inattentive: Six or more symptoms of inattention and six or more symptoms of hyperactivity-impulsivity are present. Most children have the combined type of ADHD.
is characterised by: Symptoms of inattention may: Be easily distracted, miss details, forget things, and frequently switch from one activity to another.Have difficulty focusing on one thing.Become bored with a task after only a few minutes, unless they are doing something enjoyable.Have difficulty focusing attention on organizing and completing a task or learning something new.Have trouble completing or turning in homework assignments, often losing things (e.g., pencils, toys, assignments) needed to complete tasks or activities.Not seem to listen when spoken to.Daydream, become easily confused, and move slowly.Have difficulty processing information as quickly and accurately as others.Struggle to follow instructions. Children who have symptoms of hyperactivity may: Fidget and squirm in their seats.Talk nonstop.Dash around, touching or playing with anything and everything in sight.Have trouble sitting still during dinner, school, and story time.Be constantly in motion.Have difficulty doing quiet tasks or activities. Children who have symptoms of impulsivity may: Be very impatient.Blurt out inappropriate comments, show their emotions without restraint, and act without regard for consequences.Have difficulty waiting for things they want or waiting their turns in games.Often interrupt conversations or others' activities.
hasExactSynonym: ADHD

Azoospermia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Absence of any measurable level of sperm in a male's semen.
dc:source: HP_0000027
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000027
description adapted from source: yes
is caused by: Hypopituitarism, hyperprolactinemia, testosterone, chemotherapy, abnormalities of the testes, physical obstruction of the posttesticular genital tracts.
hasExactSynonym: Absent sperm in semen

Azotaemia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Renal Dialysis
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An increased concentration of nitrogen compounds in the blood including blood urea, creatinine.
dc:source: HP_0002157
curator note: Perhaps move to below "Endocrine and Metabolic"? Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0002157
description adapted from source: yes
is caused by: Any cause of kidney injury or kidney failure.
is characterised by: Elevation of blood urea nitrogen (BUN) and creatinine.
hasExactSynonym: Azotaemia

B-cell CLL/lymphoma 11A
type: Class
subclass of: Non-Globin Loci
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein.
abbreviation: BCL11A
curator note: Link to "Hereditary Persistence of fetal hemoglobin".
definition source: http://www.ncbi.nlm.nih.gov/gene/53335
description adapted from source: yes
comment: Official Full Name: B-cell CLL/lymphoma 11A; Gene ID: 53335; Chromosome: 2; Position: 60451167..60553498 (GRCh38.p2); Variants
preferred label: BCL11A

Back Pain
type: Class
subclass of: Pain
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: treated with
  some values from: Anti-Inflammatory Agent
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the back.
dc:source: HP_0003418
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0003418
description adapted from source: no
is caused by: muscle strain, trauma, surgery, fracture, osteoporosis, fibromialgia, spinal disc herniation.
is characterised by: Pain in the lower back.
hasExactSynonym: Lower back pain.

Bacteria
type: Class
subclass of: Infectious Agent
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal.
database cross reference: MESH:D001419
definition source: D001419
description adapted from source: yes

Bacterial Endocarditis
type: Class
subclass of: Bacterial Infection
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: treated with
  some values from: Antifungal
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Infective endocarditis (IE) is defined as an infection of the endocardial surface of the heart, which may include one or more heart valves, the mural endocardium, or a septal effect.
dc:source: HP_0006689
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0006689
description adapted from source: yes
is caused by: Bacterial infection.
is characterised by: Multi-systemic manifestations with or without heart vegetations.
hasExactSynonym: Infective endocarditis

Bacterial Infection
type: Class
subclass of: Infection
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: An acute infectious disorder caused by gram positive or gram negative bacteria. Representative examples include pneumococcal, streptococcal, salmonella and meningeal infections.
curator note: Remove if subclasses not added below this. Perhaps use as Disease Modifier?
database cross reference: C2890
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no

Beck Anxiety Inventory (BAI)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The BAI is the most widely used instument for measuring anxiety. It consists of 21 items to assess how bothersome a symptom of anxiety has been for the subject over the past month. Scoring the BAI is based on a 0-3 point scale with higher scores indicating severity.
dc:source: Beck, A. T., Epstein, N., Brown, G., & Steer, R. A. (1988). An inventory for measuring clinical anxiety: psychometric properties. Journal of Consulting and Clinical Psychology, 56, 893-897.
abbreviation: BAI
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self
has target population: Clinic Patients
has translations: Spanish
validated for age ranges: 17 years and older
freely available: yes
hasExactSynonym: BAI
hasExactSynonym: Beck Anxiety Inventory

Beck Depression Inventory-II (BDI-II)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The BDI-II is the most widely used instrument for measuring depression. It consists of 21 items to assess the intensity of depression in clinical and normal patients. Each item is a list of four statements arranged in increasing severity about a particular symptom of depression, and rated on a scale of 0 to 3.
dc:source: Beck A.T., Ward C. H., Mendelson M., Mock J., & Erbaugh J. (1961) An inventory for measuring depression. Archives of General Psychiatry, 4, 561-571.
abbreviation: BDI-II
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self
has target population: Clinic Patients
has translations: Spanish
validated for age ranges: 13 years and older
freely available: yes
hasExactSynonym: BDI-II
hasExactSynonym: Beck Depression Inventory-II

Behavior Rating Inventory of Executive Function
type: Class
subclass of: Executive Function Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The Behavior Rating Inventory of Executive Function (BRIEF) is a detailed questionnaire designed to assess executive function behaviors of children and adolescents in the school and home environments. The BRIEF is completed by parents and teachers and is a proprietary instrument available online from PAR at www4.parinc.com.
dc:source: http://www.phenxtoolkit.org/index.php
abbreviation: BRIEF
database cross reference: PX131102
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Executive Function - Child #131102
has respondents: Proxy (Parent; Teacher)
has translations: Spanish
validated for age ranges: 5 to 18 years old
freely available: No. The BRIEF is a proprietary instrument and is available online from PAR at www4.parinc.com. A fee is associated with the BRIEF and is dependent upon various factors, such as if the BRIEF is purchased as a kit (i.e., questionnaires, manuals, and scoring forms) or in individual components.
hasExactSynonym: BRIEF

Behavioral Abnormality
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An abnormality of mental functioning including various affective, behavioural, cognitive and perceptual abnormalities.
curator note: This term was changed from "Mental Health" to the HPO term "Behavioral Abnormality". The sub-class "Developmental Delay" was moved below the new "Neurodevelopmental Abnormality" class.
database cross reference: HP:0000708
definition source: HP_0000708
description adapted from source: no
hasExactSynonym: Behavioral Changes
hasExactSynonym: Behavioral Disorders
hasExactSynonym: Behavioral Disturbances
hasExactSynonym: Behavioral Problems
hasExactSynonym: Behavioral Symptoms
hasExactSynonym: Behavioral/Psychiatric Abnormalities
hasExactSynonym: Behavioural/Psychiatric Abnormality
hasExactSynonym: Psychiatric Disorders
hasExactSynonym: Psychiatric Disturbances

Behavioural
type: Class
subclass of: Mental Health
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The actions or reactions of a person in response to a situation or stimuli.
hasExactSynonym: Behaviour

Beliefs About Causes of Illness
type: Class
subclass of: Health Beliefs
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The relating of causes to the effects they produce. Causes are termed necessary when they must always precede an effect and sufficient when they initiate or produce an effect. Any of several factors may be associated with the potential disease causation or outcome, including predisposing factors, enabling factors, precipitating factors, reinforcing factors, and risk factors.
curator note: Description needs to be modified, as it is actually the description for the term "Causality".
database cross reference: MESH:D015984
definition source: D015984
hasExactSynonym: Beliefs about Causality
comment: Cultural beliefs, such as re-incarnation and witchcraft, may influence notions on causality of sickle cell disease.

Beliefs About Remedies and Treatment
type: Class
subclass of: Health Beliefs
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A collective cultural expression for all behavior patterns acquired and socially transmitted through symbols regarding healing.
database cross reference: MESH:D003469
definition source: http://www.ncbi.nlm.nih.gov/mesh/68003469
description adapted from source: yes
hasExactSynonym: Background, Cultural
hasExactSynonym: Backgrounds, Cultural
hasExactSynonym: Belief
hasExactSynonym: Beliefs
hasExactSynonym: Cultural Background
hasExactSynonym: Cultural Backgrounds
hasExactSynonym: Cultures
hasExactSynonym: Custom
hasExactSynonym: Customs

Beta Plus Thalassemia
type: Class
subclass of: Beta Thalassemia
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A beta-thalassemia caused by the reduced (beta+) synthesis of the beta globin chains of the hemoglobin (Hb) tetramer.
definition source: A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed
description adapted from source: yes
hasExactSynonym: Beta + Thalassemia
hasExactSynonym: Beta Plus-Thalassemia
hasExactSynonym: Beta+ Thalassemia
hasExactSynonym: Beta-Plus-Thalassemia

Beta Thalassemia
type: Class
subclass of: Constitutional Genetic Disorder
subclass of: Hemoglobinopathy Occuring in Heterozygous State in Sickle Cell Disease Variants
subclass of: Restriction
  on property: has phenotype
  some values from: Increased Hemoglobin A2
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A thalassemia characterized by the reduced (beta plus) or absent (beta zero) synthesis of the beta globin chains of hemoglobin, resulting in variable outcomes ranging from severe anemia to clinically asymptomatic individuals.
database cross reference: DOID:12241
definition source: Beta thalassemia
definition source: DOID_12241
definition source: A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed
description adapted from source: yes
has age of onset: Infancy
hasBroadSynonym: Erythroblastic Anemia
hasExactSynonym: Beta Thalassemias
hasExactSynonym: Beta Type Thalassemia
hasExactSynonym: Beta-Thalassemia
hasExactSynonym: Beta-Thalassemias
hasExactSynonym: Hemoglobin F Disease
hasExactSynonym: Mediterranean Anemia
hasNarrowSynonym: Cooley's Anemia
hasNarrowSynonym: Thalassemia Intermedia
hasNarrowSynonym: Thalassemia Major
hasNarrowSynonym: Thalassemia Minor

Beta Thalassemia Intermedia
type: Class
subclass of: Clinical Phenotype of Beta Thalassemia
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A homozygous (B+/B+) or compound heterozygous (B0/B+) form of beta-thalassemia characterized by mild to moderate anemia which does not or only occasionally requires transfusion.
dc:source: Beta thalassemia
dc:source: http://www.orpha.net/consor4.01/www/cgi-bin/Disease_Search.php
database cross reference: ORPHA:231222
definition source: http://www.orpha.net/consor4.01/www/cgi-bin/Disease_Search.php
description adapted from source: yes
hasExactSynonym: B+/B+
hasExactSynonym: B0/B+
hasExactSynonym: Beta-Thalassemia Intermedia
hasExactSynonym: Thalassemia Intermedia
comment: BT intermedia is caused by minor and/or silent mutations in the HBB gene (11p15.5) encoding the beta-chains of hemoglobin (Hb), in the homozygous or compound heterozygous state.

Beta Thalassemia Major
type: Class
subclass of: Clinical Phenotype of Beta Thalassemia
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A homozygous form of beta-thalassemia characterized by mild to moderate anemia which does not or only occasionally requires transfusion.
database cross reference: ORPHA:231214
definition source: Beta thalassemia
definition source: http://www.orpha.net/consor4.01/www/cgi-bin/Disease_Search.php
description adapted from source: yes
hasExactSynonym: B0/B0
hasExactSynonym: Beta-Thalassemia Major
hasExactSynonym: Cooley Anemia
hasExactSynonym: Cooley's Anemia
hasExactSynonym: Mediterranean anemia
hasExactSynonym: Thalassemia Major

Beta Thalassemia Trait
type: Class
subclass of: Clinical Phenotype of Beta Thalassemia
subclass of: Hemoglobin Trait Other than C,D,E,S,O-Arab
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The inheritance of only one mutated beta-globin allele (beta+ or beta0).
dc:source: typesofbetathalassemia.php
curator note: This term is a sub-class of "Hemoglobin Trait" and of "Clinical Phenotype of Beta-Thalassemia".
definition source: Beta thalassemia
description adapted from source: yes
hasExactSynonym: B+/B
hasExactSynonym: B0/B
hasExactSynonym: Beta-Thalassemia Trait
hasExactSynonym: Heterozygosity for Beta-Thalassemia
hasExactSynonym: Heterozygous Beta-Thalassemia
hasExactSynonym: Thalassemia Minor
comment: Usually asymptomatic other than a possible mild anemia.

Beta Zero Thalassemia
type: Class
subclass of: Beta Thalassemia
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A beta-thalassemia caused by the absent (beta0) synthesis of the beta globin chains of the hemoglobin (Hb) tetramer.
dc:source: Hb-F-only
definition source: A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed
description adapted from source: yes
hasExactSynonym: Beta 0 Thalassemia
hasExactSynonym: Beta Zero-Thalassemia
hasExactSynonym: Beta-Zero-Thalassemia
hasExactSynonym: Beta0 Thalassemia
hasExactSynonym: Hb Beta Zero-Thalassemia
hasExactSynonym: Hb F only

Beta-Globins
type: Class
subclass of: Globin Loci
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Members of the beta-globin family. In humans, they are encoded in a gene cluster on chromosome 11. They include epsilon-globin, gamma-globin, delta-globin and beta-globin. There is also a pseudogene of beta (theta-beta) in the gene cluster. Adult hemoglobin is comprised of two alpha globin chains and two beta-globin chains.
database cross reference: MESH:D055544
definition source: D055544
description adapted from source: no

Beta-Globin Haplotype
type: Class
subclass of: Beta-Globins
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Defined arrays of polymorphic gene sites that are inherited together across the genetic vicinity of the beta-globin gene or gene cluster on chromosome 11.
definition source: Nagel, et. al. NEngl J Med. 1985 Apr 4;312(14):880-4
description adapted from source: yes
hasExactSynonym: Beta-S haplotypes
hasExactSynonym: Beta-haplotypes;
hasExactSynonym: HbS haplotypes
hasExactSynonym: β-globin haplotype
hasExactSynonym: βS haplotype
comment: Haplotype designated as: Cameroon Type; Senegal Type; Cantral African Rebuplic Type (CAR or Bantu); Benin Type; Saudi, Arab, or Middle Eastern type; Indian Type; Atypical; must specifiy the method (RFLP, SNPs, etc) and number of markers used for designation.

Biconcave Vertebral Bodies
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Exaggerated concavity of the anterior or posterior surface of the vertebral body, i.e., the upper and lower vertebral endplates are hollowed inward.
dc:source: HP_0004586
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0004586
description adapted from source: no
is caused by: Develop following chronic microvascular infarctions by sickled red blood cells that occlude the single arterial supply to the central area of the vertebral bodies,resulting in defective bone development in defective bone development develop following.
is characterised by: Biconcavity and the bone softening of the vertebral bodies radiologically and lower back pain.
hasExactSynonym: Biconcave Vertebrae
hasExactSynonym: Fish Mouth Deformity
hasExactSynonym: Fish Vertebrae
hasExactSynonym: Step Vertebrae

Bilirubin Blood Test
type: Class
subclass of: Blood Test
subclass of: Liver Function Assay
subclass of: Restriction
  on property: has measurement
  some values from: Blood Bilirubin Level
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A bioassay to measure levels of bilirubin, a yellow substance found in bile produced when the liver breaks down old red blood cells.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX810900
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has protocol: PhenX protocol: Bilirubin Leve #810901
has recommended procedure: The PhenX protocol provides instructions for drawing, processing, and storing blood according to the National Health and Nutrition Examination Survey (NHANES) methods. Because there are many comparable assays for measuring bilirubin, the protocol also provides basic guidelines to aid comparability among different studies.
has_application_toward: Abnormal bilirubin levels are associated with liver disease, gallstones, pancreatic cancer, anemia, and hemolytic diseases, including sickle cell disease.
comment: Bilirubin levels can be combined with other indirect markers of hemolysis (Haptoglobin Level, Reticulocyte Count, Aspartate Aminotransferase Level, and Lactate Dehydrogenase Level) by principle component analysis (PCA) to derive a hemolytic component for sickle cell disease patients.

Biochemical Assay
type: Class
subclass of: Chemical Assay
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: An analytical in vitro procedure used to detect, quantify and/or study the binding or activity of a biological molecule, such as an enzyme.
definition source: biochemical-assays
description adapted from source: yes

Biological Disease Modifier
type: Class
subclass of: Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
creator: SCDO
description: A biological factor that modifies one or more aspects of sickle cell disease (SCD) (such as temporal pattern, age of onset and mortality) for specific phenotype(s) in the Phenotype class.

Birthplace
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The country in which the respondent was born.
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
hasExactSynonym: Place of Birth

Birthplace of Biological Father
type: Class
subclass of: Birthplace of Parents
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
creator: SCDO
description: The country in which the respondent's biological father was born.

Birthplace of Biological Mother
type: Class
subclass of: Birthplace of Parents
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
creator: SCDO
description: The country in which the respondent's biological mother was born.

Birthplace of Grandparents
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The country or countires in which the respondent's biological grandparents were born.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has_application_toward: The main reason to capture the birthplaces of grandparents (maternal and paternal) is to indicate additional information about the ancestral background of the respondent.

Birthplace of Maternal Grandfather
type: Class
subclass of: Birthplace of Grandparents
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
creator: SCDO
description: The country in which the respondent's biological maternal (on the mother's side of the family) grandfather was born.

Birthplace of Maternal Grandmother
type: Class
subclass of: Birthplace of Grandparents
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
creator: SCDO
description: The country in which the respondent's biological maternal (on the mother's side of the family) grandmother was born.

Birthplace of Parents
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The country or countires in which the respondent's biological parents were born.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has_application_toward: The main reason birthplace of parents (mother and father) is captured is to indicate additional information about the ancestral background of the respondent e.g., whether the respondent is second generation or not.

Birthplace of Paternal Grandfather
type: Class
subclass of: Birthplace of Grandparents
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
creator: SCDO
description: The country in which the respondent's biological paternal (on the father's side of the family) grandfather was born.

Birthplace of Paternal Grandmother
type: Class
subclass of: Birthplace of Grandparents
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
creator: SCDO
description: The country in which the respondent's biological paternal (on the father's side of the family) grandmother was born.

Black Sunburst Lesion
type: Class
subclass of: Ophthalmologic Complication
subclass of: Restriction
  on property: diagnosed by
  some values from: Ophthalmoscopy
subclass of: Restriction
  on property: diagnosed by
  some values from: Slit-Lamp Examination
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Black lesions in the retina that form at the border of perfused and nonperfused retina that are caused by the migration of hyperplastic retinal pigment epithelial cells into sensory retina. The sensory retina surrounding the lesion is atrophic.
definition source: Ballas et al 2010 Am J Hematol
description adapted from source: no
comment: Diagnostic Criteria: The black sunburst lesion appears as a flat, round or oval black patch about 0.5 to 2 disc diameters in size that can be visualized with direct or indirect ophthalmoscope or by slit lamp biomicroscopy. The borders of the lesion can be stellate or spiculated in appearance.

Blood Test
type: Class
subclass of: Physiological Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Test used in the analysis of the hemic system.
definition source: D006403
description adapted from source: Only label adapted
hasExactSynonym: Blood Assay
hasExactSynonym: Blood Tests
hasExactSynonym: Hematologic Test
hasExactSynonym: Hematologic Tests
hasExactSynonym: Hematological Test

Blood Bilirubin Level
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Bilirubin Blood Test
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The amount of bilirubin found in a specific volume of blood.
database cross reference: CMO:0000123
definition source: CMO_0000123
description adapted from source: no
hasExactSynonym: Bilirubin Level

Blood Cell Measurement
type: Class
subclass of: Blood Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A value resulting from the quantification of a morphological or physiological parameter of blood cells, i.e. cells native to the circulation, including those of erythroid, lymphoid, myeloid and monocytic lineages. A cell is a membrane-enclosed protoplasmic mass constituting the smallest structural unit of an organism that is capable of independent functioning.
curator note: Perhaps include missing sub-classes of "Blood Cell Measurement" from the Clinical Measurement Ontology?
database cross reference: CMO:0000036
definition source: CMO_0000036
description adapted from source: no

Blood Chemistry Measurement
type: Class
subclass of: Blood Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A quantification of a parameter of the chemical composition of blood.
database cross reference: CMO:0000023
definition source: CMO_0000023
description adapted from source: no

Blood Coagulation Measurement
type: Class
subclass of: Blood Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Measurement to assess the sequential process through which multiple factors of the blood interact to form an insoluble fibrin clot.
dc:source: Purpose2
database cross reference: CMO:0000204
definition source: CMO_0000204
description adapted from source: no
has_application_toward: Clotting disorders can cause a dangerous amount of bleeding or clotting. If your doctor suspects you have a clotting disorder, they may recommend one or more coagulation tests. These tests measure various proteins and how they function. Conditions that can cause coagulation problems include: liver disease; thrombophilia, which is excessive clotting; hemophilia, which is an inability to clot normally; Coagulation tests are also useful in monitoring people who take medications that affect clotting ability. Coagulation tests are sometimes recommended before surgery.
comment: Factor V Assay; This test measures Factor V, a substance involved in clotting. An abnormally low level may be indicative of liver disease, primary fibrinolysis (a breakdown of clots), or disseminated intravascular coagulation (DIC). Fibrinogen Level; Fibrinogen is a protein made by your liver. This test measures how much fibrinogen is in your blood. Abnormal results may be a sign of excessive bleeding or hemorrhage, fibrinolysis, or placental abruption, which is a separation of the placenta from the uterine wall. Other names for this test include factor I and hypo-fibrinogenemia test. Prothrombin Time (PT or PT-INR); Prothrombin is another protein produced in your liver. The prothrombin time (PT) test measures how well and how long it takes your blood to clot. It normally takes about 25 to 30 seconds. It may take longer if you take blood thinners. Other reasons for abnormal results include hemophilia, liver disease, and malabsorption. It’s also useful in monitoring those who take medications that affect clotting, such as warfarin. Results are given in the number of seconds it takes to clot. Sometimes the PT test uses a calculation called the international normalized ratio (INR) to compare results of different laboratories. The PT test is usually ordered with another clotting test called an activated partial thromboplastin time (aPTT). Another version called the model for end stage liver disease (MELD) is used to assess people who need a liver transplant. Platelet Count; Platelets are cells in the blood that help your blood clot. You may have an abnormally low number if you’re on chemotherapy, take certain medications, or have had a massive blood transfusion. Other causes of a low platelet count are celiac disease, vitamin K deficiency, and leukemia. An abnormally high number of platelets may be caused by anemia, primary thrombocythemia, or chronic myelogenous leukemia. Thrombin Time; Thrombin time measures how well fibrinogen is working. Abnormal results may be due …

Blood Component Transfusion
type: Class
subclass of: Blood Transfusion
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The transfer of blood components such as erythrocytes, leukocytes, platelets, and plasma from a donor to a recipient or back to the donor. This process differs from the procedures undertaken in plasmapheresis and types of cytapheresis; (plateletpheresis and leukapheresis) where, following the removal of plasma or the specific cell components, the remainder is transfused back to the donor.
database cross reference: MESH:D016913
definition source: D016913
description adapted from source: no

Blood Culture
type: Class
subclass of: Blood Test
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A laboratory test to check for bacteria or other microorganisms in a blood sample. Most cultures check for bacteria.
dc:source: 003744.htm
abbreviation: BC
definition source: 003744.htm
description adapted from source: yes
hasExactSynonym: BC
hasExactSynonym: Culture Blood
hasExactSynonym: Haemoculture
hasExactSynonym: Hemoculture
comment: An abnormal (positive) result means that germs were identified in the blood. The medical term for this is bacteremia. This can be the result of sepsis. Sepsis is a medical emergency and requires the patient be admitted to a hospital for treatment. Sometimes, an abnormal result can be due to contamination. This means bacteria may be found, but it came from the patient's skin or from the lab equipment, instead of the blood. This is called a false-positive result. It means the patient does not have a true infection.

Blood Differential White Blood Cell Count
type: Class
subclass of: White Blood Cell Count
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The number of each type of leukocyte present in a specific volume of blood, usually 1 cubic millimeter.
curator note: Perhaps add sub-classes from "Clinical Measurement Ontology"?
database cross reference: CMO:0000366
definition source: CMO_0000366
description adapted from source: no
hasExactSynonym: Blood Differential Leukocyte Count
hasExactSynonym: Blood Differential WBC Count
hasExactSynonym: WBC Differential Count
preferred label: White Blood Cell Differential Count

Blood Flow Assay
type: Class
subclass of: Blood Test
subclass of: Restriction
  on property: has curation status
  has value: uncurated
preferred label: Blood Flow Test

Blood Flow Measurement
type: Class
subclass of: Blood Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Techniques used to measure velocity and amount of blood flow and circulation in the living system.
dc:source: http://purl.bioontology.org/ontology/CSP/0573-0635
database cross reference: CSP:0573-0635
description adapted from source: no
hasExactSynonym: blood flow impedance

Blood Measurement
type: Class
subclass of: Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A measurement of the blood, it's contents, cells or other factors contained within the blood.
database cross reference: CMO:0000035
definition source: CMO_0000035
description adapted from source: no

Blood Pressure Measurement
type: Class
subclass of: Blood Measurement
subclass of: Restriction
  on property: has medical device
  some values from: Sphygmomanometer
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Measurement of the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood.
dc:source: 007490.htm
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: CMO:0000003
database cross reference: PX040300
definition source: CMO_0000003
description adapted from source: no
has protocol: PhenX protocol: Blood Pressure (Adult/Primary) #040301
has_application_toward: Blood pressure is used to assess the risk of heart attack, stroke, heart failure, and kidney failure.
hasNarrowSynonym: Blood pressure reading
hasNarrowSynonym: Diastolic blood pressure
hasNarrowSynonym: Measuring blood pressure
hasNarrowSynonym: Systolic blood pressure
comment: Normal blood pressure is when the top number (systolic blood pressure) is below 120 most of the time, and the bottom number (diastolic blood pressure) is below 80 most of the time (written as 120/80 mm Hg). If your blood pressure numbers are 120/80 or higher but below 140/90, it is called pre-hypertension.

Blood Transfusion
type: Class
subclass of: Preventative Therapeutics
subclass of: Symptomatic Therapeutics
subclass of: Restriction
  on property: results_in
  some values from: Hemochromatosis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The introduction of whole blood or blood component directly into the blood stream. (Dorland, 27th ed)
dc:source: http://www.hindawi.com/journals/ah/2010/272940/
dc:source: Radha Raghupathy, Deepa Manwani, and Jane A. Little, “Iron Overload in Sickle Cell Disease,” Advances in Hematology, vol. 2010, Article ID 272940, 9 pages, 2010. doi:10.1155/2010/272940
database cross reference: MESH:D001803
definition source: D001803
description adapted from source: no
comment: The major and unavoidable complication of transfusions in sickle cell disease is iron overload.
comment: Transfusion is well-defined as prophylaxis (stroke) and as therapy (acute chest syndrome and stroke) for major complications of sickle cell disease and has been instituted, based on less conclusive data, for a range of additional complications, such as priapism, vaso-occlusive crises, leg ulcers, pulmonary hypertension, and during complicated pregnancies.

Body Height
type: Class
subclass of: Whole Body Morphological Measurement
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: The distance from the sole to the crown of the head with body standing on a flat surface and fully extended.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: EFO:0004339
database cross reference: PX020703
definition source: EFO_0004339
description adapted from source: no
has protocol: PhenX protocol: Height - Standing Height #020703
has recommended procedure: Ask the participant to remove hair ornaments, jewelry, buns, or braids from the top of the head that interfere with the measurement. Shoes should be removed. Ask the participant to stand erect against the backboard with the body weight evenly distributed and both feet flat on the stadiometer platform (Exhibit 1). The participant’s feet should be positioned with the heels together and toes pointed slightly outward at approximately a 60 degree angle. Check to be sure that the back of the head, shoulder blades, buttocks, and heels make contact with the backboard of the stadiometer. NOTE: Depending on the overall body conformation of the individual, all four contact points - head, shoulders, buttocks, and heels - may or may not touch the stadiometer backboard (Exhibit 2). For example, elderly survey participants may have kyphosis, a forward curvature of the spine that appears as a hump at the upper back. In particular, dowager’s hump is a form of kyphosis that creates a hump at the back of the neck. Additionally, some overweight survey participants cannot stand straight while touching all four contact points to the backboard. In such instances it is important to obtain the best measurement possible according to the protocol. Stature measurements are made with the head aligned in the Frankfort horizontal plane (Exhibit 2). The head is in the Frankfort plane when the horizontal line from the ear canal to the lower border of the orbit of the eye is parallel to the floor and perpendicular to the vertical backboard (see Exhibit 2). Many people will assume this position naturally, but for some survey participants the examiner may need to gently tilt the head up or down to achieve the proper alignment. Instruct the survey participant to look straight ahead. If you cannot position the participant such that his or her trunk remains vertical above the waist, that the arms and shoulders are relaxed, and that the head is positioned in the Frankfort plane, be sure to note this in th…
hasExactSynonym: Height

Body Morphological Measurement
type: Class
subclass of: Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Measurement of the structure or forms of the entire body or parts of the body of an organism.
curator note: Include the term "Body Composition" from PhenX? Any other relevant terms missing as sub-classes here?
database cross reference: CMO:0000021
definition source: CMO_0000021
description adapted from source: no
hasExactSynonym: Anthropometric Measurement
hasExactSynonym: Anthropometrics
hasExactSynonym: Morphometry

Body Temperature
type: Class
subclass of: Measurement
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: A measurement of the heat in an individual’s body, which is reported in either degrees Fahrenheit or Celsius.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX810100
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Body Temperature - Oral Thermometers #810102
has protocol: PhenX protocol: Body Temperature - Tympanic Thermometers #810101
has_application_toward: Body temperature is associated with the presence or absence of various illnesses and infections and having an abnormal temperature can be an indication for additional medical testing.

Body Weight
type: Class
subclass of: Whole Body Morphological Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The mass or quantity of heaviness of an individual. It is expressed by units of pounds or kilograms.
dc:source: D001835
dc:source: bodyweight.html
curator note: Add these terms from PhenX?: - Weight Loss/Gain - Birth Weight
database cross reference: D001835
description adapted from source: no
has_application_toward: A sudden, unexpected change in weight can be a sign of a medical problem. Causes for sudden weight loss can include: Thyroid problems; Cancer; Infectious diseases; Digestive diseases; Certain medicines. Sudden weight gain can be due to medicines, thyroid problems, heart failure, and kidney disease.
hasExactSynonym: Weight

Bone Fragility
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: SCD Related Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An abnormally increased tendency to fractures of bones caused by an abnormal reduction in bone strength that is generally associated with an increased risk of fracture.
curator note: Provide source for additional info.
database cross reference: HP:0002659
definition source: HP_0002659
description adapted from source: no
is caused by: Osteoporosis, cancer, inherited bone disorders, bone cyst.
hasExactSynonym: Abnormal Susceptibility to Fractures
hasExactSynonym: Increased Bone Fragility

Bone Pain
type: Class
subclass of: Pain
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: treated with
  some values from: Anti-Inflammatory Agent
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Depression
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to bone.
curator note: Provide source for additional info. Perhaps include below "Pain" under "Nervous System"?
database cross reference: HP:0002653
definition source: HP_0002653
description adapted from source: no
is caused by: A number of diseases may cause bone pain including osteoarthritis, Paget's disease, sickle cell anemia, and bone cancer. Acute leukemia;Acute rheumatic fever, a very dangerous disease that can cause permanent cardiac damage. Bursitis;Fibromyalgia like disease has been studied as a cause of joint pain in the child.Hypermobility syndrome can present with knee or ankle pain;Injury such as a fracture. Juvenile rheumatoid arthritis;Lupus;Lyme disease, which is transmitted by ticks and is characterized by debilatating polyarthritis, neurologic symptoms, and erythema migrans.;Osteomyelitis;Osteosarcoma.Septic arthritis, a severe infection of the joint that can lead to permanent joint damage.Synovitis;Viral diseases, including the measles, influenza, mononucleosis, chickenpox, and mumps.
is characterised by: Stimulation of specialized pain-sensitive nerve fibers (nociceptors) that innervate bone tissue leads to the sensation of bone pain. Bone pain originates from both the periosteum and the bone marrow which relay nociceptive signals to the brain creating the sensation of pain. Bone tissue is innervated by both myelinated (A beta and A delta fiber) and unmyelinated (C fiber) sensory neurons. In combination, they can provide an initial burst of pain, initiated by the faster myelinated fibers, followed by a slower and longer lasting dull pain initiated by unmyelinated fibers

Bone Sclerosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
subclass of: Restriction
  on property: has curation status
  has value: example likely to be removed
description: An increase in bone density, such that the bone is more radiopaque than normal on a plain film.
curator note: Replace with "Osteosclerosis" ?
definition source: bone+sclerosis
description adapted from source: no

Brachial Artery Ultrasound Imaging
type: Class
subclass of: Ultrasonography Test
subclass of: Vascular Endothelial Function Test
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A noninvasive method to assess the endothelial dysfunction in the brachial artery.
abbreviation: BAUI
definition source: Endothelial dysfunction
description adapted from source: yes
has recommended procedure: Flow-mediated dilation (FMD) of the brachial artery is a high-frequency ultrasound method to obtain imaging of the brachial artery to assess endothelial function.
has_application_toward: Endothelial function has been associated as a factor in the pathology of various medical conditions, such as congestive heart failure, atherosclerosis, and hypertension.
hasExactSynonym: BAUI

Bradykinesia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Bradykinesia literally means slow movement, and is used clinically to denote a slowness in the execution of movement (in contrast to hypokinesia, which is used to refer to slowness in the initiation of movement).
dc:source: winter14pg6.html
database cross reference: HP:0002067
definition source: HP_0002067
description adapted from source: no
hasExactSynonym: Slow Movements
comment: Bradykinesia is a major symptom of Parkinson's disease.

Brain Abscess
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Culture
subclass of: Restriction
  on property: diagnosed by
  some values from: Chest X-Ray
subclass of: Restriction
  on property: diagnosed by
  some values from: Complete Blood Count
subclass of: Restriction
  on property: diagnosed by
  some values from: Electroencephalogram
subclass of: Restriction
  on property: diagnosed by
  some values from: Electroencephalograph
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: diagnosed by
  some values from: Radiography
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: treated with
  some values from: Antifungal
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A brain abscess is a collection of pus, immune cells, and other material in the brain, usually from a bacterial or fungal infection.
dc:source: 000783.htm
database cross reference: HP:0030049
definition source: HP_0030049
description adapted from source: no
is caused by: Brain abscesses commonly occur when bacteria or fungi infect part of the brain. As a result, swelling and irritation (inflammation) develop. Infected brain cells, white blood cells, live and dead bacteria, or fungi collect in an area of the brain. Tissue forms around this area and creates a mass, or abscess. They can arise from the following: lung infection, A weakened immune system (such as in AIDS patients), Chronic disease, such as cancer, Drugs that suppress the immune system (corticosteroids or chemotherapy), Congenital heart disease.
is characterised by: Symptoms may develop slowly, over a period of 2 weeks, or they may develop suddenly. They may include: Changes in mental status, such as confusion, slow response or thinking, unable to focus, or sleepiness, Decreased ability to feel sensation, Fever and chills, Headache, seizures, or stiff neck, Language problems, Loss of muscle function, typically on one side, Vision changes, Vomiting, Weakness
comment: A brain abscess is a medical emergency. Pressure inside the skull may become high enough to be life threatening. You will need to stay in the hospital until the condition is stable. Some people may need life support. Medicine, not surgery, is recommended if you have: A small abscess (less than 2 cm); An abscess deep in the brain; An abscess and meningitis; Several abscesses (rare); Shunts in the brain for hydrocephalus (in some cases the shunt may need to be removed temporarily or replaced); An infection called toxoplasmosis in a person with HIV; You may be prescribed several different types of antibiotics to make sure treatment works. Antifungal medicines may also be prescribed if the infection is likely caused by a fungus. Surgery is needed if: Increased pressure in the brain continues or gets worse; The brain abscess does not get smaller after medicine; The brain abscess contains gas (produced by some types of bacteria); The brain abscess might break open (rupture); Surgery consists of opening the skull, exposing the brain, and draining the abscess. Laboratory tests are often done to examine the fluid. This helps identify the cause of the infection, so that the right antibiotics or antifungal medicine can be prescribed. Needle aspiration guided by CT or MRI scan may be needed for a deep abscess. During this procedure, medicines may be injected directly into the mass. Certain diuretics and steroids may also be used to reduce the swelling of the brain.

Brain Electrical Activity
type: Class
subclass of: Measurement
subclass of: Restriction
  on property: has medical device
  some values from: Electroencephalograph
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: Voltages between parts of the brain that are detectable with an electroencephalograph.
database cross reference: 0487-1238
definition source: http://purl.bioontology.org/ontology/CSP/0487-1238
description adapted from source: no
hasExactSynonym: Brain Oscillography
hasExactSynonym: Brain electrophysiological activity
hasExactSynonym: EEG activity

Breakthrough Pain
type: Class
subclass of: Chronic Sickle Cell Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Originally used to describe patients with cancer pain who were maintained on a stable dose of analgesics, breakthrough pain was defined as a flair-up of sudden pain unresponsive to usual therapy. Such a flare-up is usually sudden and incidental, and can last from a few seconds to a few hours. There are currently no data that clearly describe or can be used to define breakthrough pain in SCD.
definition source: Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
description adapted from source: yes

Brief Illness Perception Questionnaire (B-IPQ)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The Brief IPQ has 9 items, 8 new items from the IPQ plus a causal question. All of the items except the causal question are rated using a 0-to-10-response scale. Five of the items assess Cognitive Illness Representations: Consequences (Item 1), Timeline (Item 2), Personal Control (Item 3), Treatment Control (Item 4), and Identity (Item 5). Two of the items assess Emotional Representations: Concern (Item 6) and Emotions (Item 8). One item assesses Illness Comprehensibility (Item 7). Assessment of the Causal Representation is by an open-ended response item adapted, which asks patients to list the three most important causal factors in their illness (Item 9). Responses to the causal item can be grouped into categories such as stress, lifestyle, hereditary, etc, determined by the particular illness studied, and categorical analysis can then be performed.
dc:source: Broadbent E, Petrie KJ, Main J, Weinman, J. (2006). The brief illness perception questionnaire. Journal of Psychosomatic Research, 60, 631-637.
abbreviation: B-IPQ
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self
has target population: Clinic Patients
has translations: Many
selection criteria met: Good psychometric properties, widely used, has been translated into several languages.
validated for age ranges: Adults
freely available: yes
hasExactSynonym: B-IPQ
hasExactSynonym: Brief Illness Perception Questionnaire

Brief RCOPE
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Brief RCOPE is a 14-item instrument. Responses on the Brief RCOPE indicate the frequency with which participants have used R/S coping behaviors on a Likert scale of 1 ("not at all") to 4 ("a great deal.") The scale has been used to examine positive and negative religious coping, including in teens with SCD.
dc:source: Pargament K, Koenig H, Perez L. The many methods of religious coping: development and initial validation of the RCOPE. J Clin Psychol. 2000;56:519-543.
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has respondents: Self; Proxy (Parent report)
has target population: Children with SCD and their parents.
selection criteria met: Demonstrated validity in SCD studies.
validated for age ranges: Children and adults

Bronchodilator Responsiveness
type: Class
subclass of: Respiratory System Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Bronchodilator Responsiveness Test
subclass of: Restriction
  on property: essential measure
  some values from: Spirometry
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A change in pulmonary function in response to inhaled bronchodilator medications.
abbreviation: BDR
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
hasExactSynonym: BDR

Bronchodilator Responsiveness Test
type: Class
subclass of: Pulmonary Function Test
subclass of: Restriction
  on property: has measurement
  some values from: Bronchodilator Responsiveness
subclass of: Restriction
  on property: essential measure
  some values from: Spirometry
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A test to assess an individual's change in pulmonary function in response to inhaled bronchodilator medications.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Bronchodilator Responsiveness (BDR) #090301
has recommended procedure: A series of spirometry maneuvers is performed to obtain acceptable and reproducible results. An inhaled bronchodilator medication is administered, and a second series of spirometry maneuvers is performed.
has_application_toward: To assess bronchial hyper-responsiveness, which is often seen in asthma and chronic obstructive pulmonary disease.
hasExactSynonym: BDR Test

Built Environment
type: Class
subclass of: Physical Environment
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Physical surroundings or conditions of a building, or collection of buildings and the influence of these factors on the individual.
database cross reference: MESH:D006272
definition source: D006272
description adapted from source: yes
hasNarrowSynonym: Health Facility Environment

Caesarian Section
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Endometritis
subclass of: Restriction
  on property: results_in
  some values from: Infection
subclass of: Restriction
  on property: results_in
  some values from: Postpartum Hemorrhage
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Delivery of a fetus through surgical incisions made through the abdominal wall (laparotomy) and the uterine wall (hysterotomy).
database cross reference: HP:0011410
definition source: HP_0011410
description adapted from source: no

Cancer
type: Class
subclass of: Comorbid Disease
subclass of: Restriction
  on property: caused by
  some values from: Infection
subclass of: Restriction
  on property: caused by
  some values from: Lifestyle
subclass of: Restriction
  on property: treated with
  some values from: X-Ray Therapy
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A disease characterized by abnormal and uncontrolled cell division.
database cross reference: OBI:1110053
definition source: OBI_1110053
description adapted from source: no
hasExactSynonym: Malignancy
hasExactSynonym: Malignant Neoplasia
hasExactSynonym: Malignant Neoplasm
hasExactSynonym: Malignant Tumor
hasExactSynonym: Malignant Tumour
hasRelatedSynonym: Oncology

Capillary Electrophoresis
type: Class
subclass of: Electrophoresis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A highly-sensitive (in the picomolar range, which is 10,000-fold more sensitive than conventional electrophoresis) and efficient technique that allows separation of proteins; nucleic acids; and carbohydrates. (Segen, Dictionary of Modern Medicine, 1992)
database cross reference: D019075
definition source: D019075
description adapted from source: no
hasExactSynonym: Capillary Electrophoreses
hasExactSynonym: Capillary Zone Electrophoreses
hasExactSynonym: Capillary Zone Electrophoresis

Cardioscope
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Electrocardiography
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An instrument which, by means of a cathode-ray oscillograph, projects an electrocardiographic record on a luminous screen.
definition source: cardioscope
description adapted from source: no

Cardiovascular Measurement
type: Class
subclass of: Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels.
database cross reference: CMO:0000001
definition source: CMO_0000001
description adapted from source: no

Cardiovascular System
type: Class
subclass of: from phenotype
description: Anatomical system that has as its parts the heart and blood vessels.
database cross reference: UBERON:0004535
definition source: UBERON_0004535
description adapted from source: no
hasExactSynonym: CV system

Case Reports
type: Class
subclass of: Publication Type
description: Clinical presentations that may be followed by evaluative studies that eventually lead to a diagnosis.
database cross reference: MESH:D002363
definition source: D002363
description adapted from source: no
hasExactSynonym: Case Histories
hasExactSynonym: Case Studies
hasExactSynonym: Case Study

Case-Control Studies
type: Class
subclass of: Epidemiologic Studies
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.
definition source: D016022

Catheter
type: Class
subclass of: Diagnostic Device
subclass of: Therapeutic Device
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Right Heart Catheterization
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A flexible, tubular device that is used to carry fluids into or from a blood vessel, hollow organ, or body cavity.
curator note: Add info (rdfs:comment) about how catheters are used in different therapeutics. Link relevant Therapeutics term(s) to this term via "has medical device".
database cross reference: MESH:D057785
definition source: D057785
description adapted from source: Only label adapted
hasExactSynonym: Cannula
hasExactSynonym: Cannulas
hasExactSynonym: Catheters

Causal Adverse Drug Event
type: Class
subclass of: Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A drug adverse event that is caused by a drug administration. Here a causal effect is established between the drug administration and the adverse event.
database cross reference: OAE:0000095
definition source: OAE_0000095
description adapted from source: no

Causal Adverse Drug Event Due to Drug-Drug Interaction
type: Class
subclass of: Causal Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A causal adverse drug event that is induced by a drug-drug interaction.
database cross reference: OAE:0000179
definition source: OAE_0000179
description adapted from source: no

Causal Adverse Drug Event Due to Food-Drug Interaction
type: Class
subclass of: Causal Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A causal adverse drug event that is induced by a food-drug interaction.
database cross reference: OAE:0000180
definition source: OAE_0000180
description adapted from source: no

Causal Adverse Drug Event Due to Genetic Predisposition
type: Class
subclass of: Causal Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A causal adverse drug event that is induced by genetic predisposition.
database cross reference: OAE:0000181
definition source: OAE_0000181
description adapted from source: no

Causal Adverse Drug Event Due to SNP
type: Class
subclass of: Causal Adverse Drug Event Due to Genetic Predisposition
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A causal adverse drug event due to genetic predisposition that is specifically induced by SNP.
database cross reference: OAE:0000182
definition source: OAE_0000182
description adapted from source: no

Cell Free Hemoglobin Blood Test
type: Class
subclass of: Blood Test
subclass of: Restriction
  on property: has measurement
  some values from: Cell Free Hemoglobin Level
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A bioassay to measure cell free hemoglobin concentration.
definition source: Cell Free Hemoglobin 09July2015.doc
description adapted from source: Only label adapted
has recommended procedure: The PhenX protocol provides instructions for drawing, processing and storing blood according to the National Health and Nutrition Examination Survey (NHANES) methods. As there are many comparable assays for measuring cell free hemoglobin levels, the protocol also provides basic guidelines to aid comparability among different studies.
has_application_toward: Cell free hemoglobin levels can be used to diagnose or monitor the severity of hemolytic anemia that is often associated with sickle cell disease, thalassemia and other disorders.
hasExactSynonym: Cell Free Hemoglobin Assay

Cell Free Hemoglobin Level
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Cell Free Hemoglobin Blood Test
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The determination of the amount of free hemoglobin present in a sample.
dc:source: http://journals.plos.org/plosone/article
dc:source: Cell Free Hemoglobin 09July2015.doc
dc:source: PMC3578950
dc:source: PMC3662353
curator note: If wanting to include "Plasma Hemoglobin Level" i the future, see CMO:0000588 for a description. synonyms: Plasma Free Hemoglobin (PFHb) Level, Plasma Hemoglobin Level.
database cross reference: NCIT:C127617
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: Only label adapted
has_application_toward: Cell free hemoglobin levels can be used to diagnose or monitor the severity of hemolytic anemia that is often associated with sickle cell disease, thalassemia and other disorders.
hasExactSynonym: Cell Free Haemoglobin Level
hasExactSynonym: Cell Free Hemoglobin Concentration
hasExactSynonym: Extracellular Hb
hasExactSynonym: Extracellular Hemoglobin
hasExactSynonym: Free Haemoglobin Measurement
hasExactSynonym: Free Hemoglobin Measurement
hasExactSynonym: HGBFR
comment: Reference range for healthy individuals: up to 5 mg/dL hemoglobin.

Central Sleep Apnea
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A sleep apnea that is characterized by a malfunction of the basic neurological controls for breathing rate and the failure to give the signal to inhale, causing the individual to miss one or more cycles of breathing.
dc:source: con-20030485
database cross reference: DOID:9220
definition source: DOID 9220
description adapted from source: no
is caused by: Central sleep apnea may occur as a result of other conditions, such as heart failure and stroke. Sleeping at a high altitude also may cause central sleep apnea

Cerebellar Hemorrhage
type: Class
subclass of: Intracranial Hemorrhage
subclass of: Restriction
  on property: results_in
  some values from: Stroke
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Cerebellar haemorrhage is a form of intracranial haemorrhage.
dc:source: cerebellar-haemorrhage
curator note: Provide more detailed description. Provide source for additional info. Need to include this term mentioned here to the SCDO: obstructive hydrocephalus
description adapted from source: no
is caused by: Is most frequently seen in the setting of poorly controlled hypertension, although this can of course also be secondary to an underlying lesion (e.g. tumour or vascular malformation) or due to supratentorial surgery (see remote cerebellar haemorrhage).
is characterised by: Clinical presentation depends on the size and speed of enlargement of the haemorrhage. Unlike pontine haemorrhages which are usually obvious to both the clinician and the patient, cerebellar haemorrhages, if small enough, can present relatively subtly. Cerebellar signs (e.g. ataxia, nystagmus). Larger bleeds can impair consciousness and obstruct the fourth ventricle resulting in obstructive hydrocephalus.
comment: As with other haemorrhagic strokes, CT is usually the first, and often the only imaging investigation obtained. As with other acute haemorrhages, cerebellar haemorrhages appear as regions of hypderdensity within the cerebellar hemispheres. Extension into the fourth ventricle or subarachnoid space is relatively common.

Cerebral Aneurysm
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A ballooning or dilatation arising from a weakened area in the wall of a blood vessel in the brain.
dc:source: HP_0004944
dc:source: cerebral aneurysm 85,p08772
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
database cross reference: HP:0004944
description adapted from source: yes
is caused by: Risk factors include: High blood pressure (hypertension), Hardening of the arteries (atherosclerosis), Bloodstream infections, Cigarette smoking
is characterised by: Symptoms of an unruptured brain aneurysm may include: Headaches, Dizziness, Eye pain, Vision deficits (problems with seeing), Double or blurry vision, Seizures. A rupturing brain aneurysm may have any of the symptoms listed above, as well as: Sudden, severe headache, Nausea, Vomiting, Loss of consciousness, Facial pain, Numbness, Weakness, Paralysis.
hasExactSynonym: Brain Aneurysms
hasExactSynonym: Cerebral Artery Aneurysm
hasExactSynonym: Intracranial Aneurysms
comment: About 46 percent of patients do not survive the first hemorrhage, and if the aneurysm is not repaired in time and a second hemorrhage occurs, about 80 percent of patients die.
comment: Brain aneurysms are treated using one or more of the following methods, depending on the location and size of the aneurysm and whether or not it has ruptured, as well as the individual patient’s needs: Microsurgical clipping , Endovascular coiling , Flow diversion with stents , Artery occlusion and bypass, Observation.

Cerebral Atrophy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Atrophy (wasting, decrease in size of cells or tissue) affecting the cerebrum. Atrophy may be progressive over time.
dc:source: cerebral atrophy.htm
database cross reference: HP:0002059
definition source: HP_0002059
description adapted from source: no
is caused by: Diseases that cause cerebral atrophy include: stroke and traumatic brain injury, Alzheimer's disease, Pick's disease, and fronto-temporal dementia, cerebral palsy, in which lesions (damaged areas) may impair motor coordination, Huntington's disease, and other hereditary diseases that are associated with genetic mutations, leukodystrophies, such as Krabbe disease, which destroy the myelin sheath that protects axons, mitochondrial encephalomyopathies, such as Kearns-Sayre syndrome, which interfere with the basic functions of neurons, multiple sclerosis, which causes inflammation, myelin damage, and lesions in cerebral tissue, infectious diseases, such as encephalitis, neurosyphilis, and AIDS, in which an infectious agent or the inflammatory reaction to it destroys neurons and their axons.
is characterised by: Symptoms of cerebral atrophy: Many diseases that cause cerebral atrophy are associated with dementia, seizures, and a group of language disorders called the aphasias. Dementia is characterized by a progressive impairment of memory and intellectual function that is severe enough to interfere with social and work skills. Memory, orientation, abstraction, ability to learn, visual-spatial perception, and higher executive functions such as planning, organizing, and sequencing may also be impaired.Seizures can take different forms, appearing as disorientation, repetitive movements, loss of consciousness, or convulsions. Aphasias are a group of disorders characterized by disturbances in speaking and understanding language. Receptive aphasia causes impaired comprehension. Expressive aphasia is reflected in odd choices of words, the use of partial phrases, disjointed clauses, and incomplete sentences.
hasExactSynonym: Cortical Atrophy
hasExactSynonym: Degeneration of Cerebrum
hasExactSynonym: Supratentorial Atrophy

Cerebral Blood Flow Assay
type: Class
subclass of: Blood Flow Assay
subclass of: Restriction
  on property: has curation status
  has value: uncurated
hasExactSynonym: Stroke Risk Test
preferred label: Cerebral Flow Test

Cerebral Blood Flow Velocity
type: Class
subclass of: Cerebrovascular Hemodynamics
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Transcranial Doppler Ultrasonography
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A value equal to the total volume flow divided by the cross-sectional area of the vascular bed.
dc:source: D001783
database cross reference: MESH:D001783
description adapted from source: no
hasExactSynonym: Velocity, Blood Flow

Cerebral Collateral Flow
type: Class
subclass of: Cerebrovascular Hemodynamics
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Transcranial Doppler Ultrasonography
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Cerebral Edema
type: Class
subclass of: Edema
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Abnormal accumulation of fluid in the brain.
curator note: Provide source for additional info.
database cross reference: HP:0002181
definition source: HP_0002181
description adapted from source: no
is caused by: The accumulation of excess fluid in a fluid compartment.
is characterised by: Edema can be caused by a variety of factors, including conditions that affect osmotic pressure, such as hypotonic fluid overload, which allows the movement of water into the intracellular space, or hypoproteinemia, which decreases the concentration of plasma proteins and permits the passage of fluid out of the blood vessels into the tissue spaces. Other factors include poor lymphatic drainage; conditions that cause increased capillary pressure, such as excessive retention of salt and water and heart failure; and conditions that increase capillary permeability, such as inflammation
hasBroadSynonym: Brain Swelling
hasBroadSynonym: Swelling of the Brain
hasExactSynonym: Brain Edema
hasExactSynonym: Brain Oedema
hasExactSynonym: Cerebral Oedema

Cerebral Function Assay
type: Class
subclass of: Physiological Assay
subclass of: Restriction
  on property: has curation status
  has value: uncurated
preferred label: Cerebral Function Test

Cerebral Hemorrhage
type: Class
subclass of: Intracranial Hemorrhage
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: diagnosed by
  some values from: Fluorescein Angiography
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: treated with
  some values from: Occupational Therapy
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Confusion
subclass of: Restriction
  on property: results_in
  some values from: Depression
subclass of: Restriction
  on property: results_in
  some values from: Seizure
subclass of: Restriction
  on property: results_in
  some values from: Fatigue
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Hemorrhage into the parenchyma of the brain.
curator note: Perhaps rather use MESH term. Get synonyms from MESH term. Provide source for additional info.
database cross reference: HP:0001342
definition source: HP_0001342
description adapted from source: no
is caused by: High blood pressure is the most common cause of intracerebral hemorrhage. In younger people, another common cause is abnormally formed blood vessels in the brain. Other causes include:head injury or trauma, ruptured cerebral aneurysm (weak spot in a blood vessel that bursts), arteriovenous malformation (a grouping of malformed blood vessels in the brain that disrupts normal blood flow), use of blood thinners, bleeding tumors, cocaine use (can cause severe hypertension and lead to hemorrhage), bleeding disorders (e.g., hemophilia, sickle cell anemia).
is characterised by: Sudden weakness, tingling, or paralysis in the face, arm, or leg, especially if it occurs on only one side of the body, sudden onset of severe headache, trouble swallowing, trouble with vision in one or both eyes, loss of balance and coordination, dizziness, trouble with language skills (reading, writing, speaking, understanding), nausea, vomiting, apathy, sleepiness, lethargy, loss of consciousness, confusion, delirium.

Cerebral Vasculitis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Cerebrospinal Fluid Pleocytosis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Inflammation of the blood vessels within the brain.
curator note: Provide source for additional info.
database cross reference: HP:0005318
definition source: HP_0005318
description adapted from source: no
has age of onset: Cranial arteritis is the most frequent form of vasculitis affecting persons over 50 years of age. In Europe prevalences of 15-30/100,000 and an incidence of 18/100,000 have been reported.
is characterised by: Major symptoms of cerebral angiitis are stroke, headache and encephalopathy. Other symptoms include seizures, cranial nerve palsies or myelopathies. Inflammatory signs and symptoms in particular may lead to the early suspect of vasculitis. The differential diagnosis includes a wide range of conditions, such as degenerative vasopathies, embolic diseases, or coagulation disorders.

Cerebral Venous Sinus Thrombosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: diagnosed by
  some values from: Ultrasound Machine
subclass of: Restriction
  on property: diagnosed by
  some values from: Fluorescein Angiography
subclass of: Restriction
  on property: results_in
  some values from: Cerebral Hemorrhage
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Formation of a blood clot (thrombus) inside a cerebral vein, causing the obstruction of blood flow.
dc:source: cerebral venous sinus thrombosis 134,69
database cross reference: HP:0005305
definition source: HP_0005305
description adapted from source: no
has age of onset: It affects about 5 people in 1 million each year. The risk for this kind of stroke in newborns is greatest during the first month. Overall, about 3 out of 300,000 children and teens up to age 18 will have a stroke.
is characterised by: Physical symptoms include: Headache, blurred vision, fainting or loss of consciousness, loss of control over movement in part of the body, seizures, coma.
hasExactSynonym: Blood Clot in Cerebral Vein
hasExactSynonym: Cerebral Thrombosis
hasExactSynonym: Cerebral Vein Thrombosis
hasExactSynonym: Cerebral Venous Thrombosis

Cerebrospinal Fluid Pleocytosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An increased white blood cell count in the cerebrospinal fluid.
dc:source: pleocytosis
database cross reference: HP:0012229
definition source: HP_0012229
description adapted from source: no
is caused by: May be caused by infectious and noninfectious processes. Polymorphonuclear pleocytosis indicates acute suppurative meningitis. Mononuclear cells are seen in viral infections (meningoencephalitis, aseptic meningitis), syphilis, neuroborreliosis, tuberculous meningitis, multiple sclerosis, brain abscess and brain tumors.
hasExactSynonym: CSF Pleocytosis

Cerebrovascular Hemodynamics
type: Class
subclass of: Blood Flow Measurement
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Cervical Cord Compression
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: diagnosed by
  some values from: Radiography
subclass of: Restriction
  on property: diagnosed by
  some values from: X-Ray Image
subclass of: Restriction
  on property: treated with
  some values from: Ibuprofen
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Compression of the spinal cord in the cervical region, generally manifested by paresthesias and numbness, weakness, difficulty walking, abnormalities of coordination, and neck pain or stiffness.
dc:source: http://orthoinfo.aaos.org/topic.cfm
database cross reference: HP:0002341
definition source: HP_0002341
description adapted from source: no
is caused by: Arises from degenerative changes that occur in the spine as we age. These degenerative changes in the disks are often called arthritis or spondylosis. Rheumatoid arthritis. Rheumatoid arthritis is an autoimmune disease. This means that the immune system attacks its own tissues. In rheumatoid arthritis, immune cells attack the synovium, the thin membrane that lines the joints. As the synovium swells, it may lead to pain and stiffness and, in severe cases, destruction of the facet joints in the cervical spine. When this occurs, the upper vertebra may slide forward on top of the lower vertebra, reducing the amount of space available for the spinal cord.Injury. An injury to the neck - such as from a car accident, sports, or a fall - may also lead to myelopathy.For example, a "rear end" car collision may result in hyperextension, a backward motion of the neck beyond its normal limits, or hyperflexion, a forward motion of the neck beyond its normal limits. Because these types of injuries often affect the muscles and ligaments that support the vertebrae, they may lead to spinal cord compression.
is characterised by: Changes in reflexes - including the presence of hyper-reflexia, a condition in which reflexes are exaggerated or overactive. Numbness and weakness in the arms, hands, and fingers.Trouble walking, loss of balance, or weakness in the legs. Atrophy - a condition in which muscles deteriorate and shrink in size.
hasExactSynonym: Cervical Cord Compression Myelopathy
hasExactSynonym: Cervical Spondylotic Myelopathy
hasExactSynonym: Spinal Cord Compression

Chemical Assay
type: Class
subclass of: Diagnostic Technique, Method, Test or Assay
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: The analysis of a sample material, called an analyte, using a set of chemical procedures.
dc:source: chemical-assay-80cfe6f498d34be5
definition source: chemical-assay-80cfe6f498d34be5
description adapted from source: yes
has_application_toward: The objective is to determine the identity of the analyte's unknown components, isolate them and quantify them.

Chest X-Ray
type: Class
subclass of: Radiography
subclass of: Restriction
  on property: has medical device
  some values from: X-Ray Machine
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A medical imaging assessment of the chest wall, airways, lungs, pulmonary vessels, heart, mediastinum, and pleura.
dc:source: 02 Chest Radiography.pdf
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX810200
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Chest X-ray #810201
has_application_toward: This measure is used to show the size, shape, and structures of the chest. Information from this measure is used to determine the presence and etiology of disorders that involve the chest, evaluate the signs and symptoms potentially related to the respiratory, cardiovascular and upper gastrointestinal systems and the musculoskeletal system of the thorax, and to follow the course of disease.
hasExactSynonym: Chest Radiograph

Child Health Questionnaire (CHQ)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The Child Health Questionnaire (CHQ) is a family of general quality of life surveys that measures 14 unique physical and psychosocial concepts. The parent form is available in 2 lengths - the CHQ-PF50 and the CHQ-PF28. The child self-reported version of the CHQ consists of 87 items (CHQ-CF87).
dc:source: Landgraf, J. M., Abetz, L., and Ware, J. E. (1996). Child health questionnaire (CHQ): A user's manual (1st Ed.). Boston, M.A.: The Health Institute, New England Medical Center.
dc:source: Panepinto JA, O'Mahar KM, DeBaun MR, Rennie KM, Scott JP. Validity of the child health questionnaire for use in children with sickle cell disease. J Pediatr Hematol Oncol. 2004 Sep;26(9):574-8.
dc:source: Wrotniak BH, Schall JI, Brault ME, Balmer DF, Stallings VA. Health-related quality of life in children with sickle cell disease using the child health questionnaire. J Pediatr Health Care. 2014 Jan-Feb;28(1):14-22. doi: 10.1016/j.pedhc.2012.09.004. Epub 2012 Nov 8.
abbreviation: CHQ
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self, Proxy
has target population: Healthy Children; Children with Medical Conditions
has translations: French, isiXhosa, isiZulu, Portuguese, Punjabi, Sesotho, Temil, Telugu, Gujarati
selection criteria met: Demonstrated validity with SCD populations; at least two publications using the measure in SCD.
validated for age ranges: 5 to 18 years (child report 10 - 18 years; parent report 5 - 18 years)
freely available: yes
hasExactSynonym: CHQ
hasExactSynonym: Child Health Questionnaire

Child-Reported Parental Education Attainment
type: Class
subclass of: Personal Attribute
subclass of: Socioeconomic Status
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A parent's highest level of education obtained, as reporsted by the child.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX210200
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Child-Reported Parental Education Attainment #210201
has_application_toward: Parental education is correlated with income and job attainment and can be used as a proxy for assessing socioeconomic status in the family of origin. Many studies show that socioeconomic status at different points in life is associated with diverse aspects of health and cognition.

Children's Depression Inventory 2 (CDI 2)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The CDI-2 is a 27-item self-report scale that helps to assess cognitive, affective and behavioral signs of depression in children and adolescents. Each item is scored on a scale from 0 to 2.
dc:source: Kovacs, M. (1985). The Children's Depression, Inventory (CDI). Psychopharmacology Bulletin, 21, 995-998.
abbreviation: CDI 2
abbreviation: CDI-2
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self
has target population: Clinic Patients
validated for age ranges: 7 to 17 years
freely available: yes
hasExactSynonym: CDI 2
hasExactSynonym: CDI-2
hasExactSynonym: Children's Depression Inventory 2
hasExactSynonym: Children's Depression Inventory-2

Children's Health Locus of Control Scale (CHLC)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: This seeks to measure how much children and adolescents believe their own health-related behaviors will influence their health. It is a 20 item scale that contains 3 additional practice items and is a yes or no format. It contains 3 factors: belief in internality, belief in powerful others and belief in chance. There is a shorter 9-item version of the scale which is comparable to the full version and adapted for use in Egyptian children.
dc:source: Abdel Gawwad E, Ahmed MH, Kamal MM. Developing and testing of an Egyptian version of Children's Health Locus of Control scale. J Egypt Public Health Assoc. 1999; 74(1-2):139-73.
dc:source: Deaux EB. Health Locus of Control in Chukotka children. Alaska Med. 1992 Jul-Sep; 34(3):135-9.
dc:source: Parcel G.S. and Meyer M.P. (1978) Development of an instrument to measure children's health locus of control. Health Education Monographs, 6, 149-159.
abbreviation: CHLC
curator note: Check and show which source was used for the description.
description adapted from source: yes
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self
has target population: Healthy Children; Children with Medical Conditions
has translations: English, Russian, a 9- item shorter Egyptian version
selection criteria met: Has adequate reliability, construct validity and internal consistency.
validated for age ranges: Children and Adolescents
freely available: no
hasExactSynonym: CHLC
hasExactSynonym: Children's Health Locus of Control Scale

Cholecystectomy
type: Class
subclass of: Supportive Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Surgical removal of the gallbladder.
database cross reference: MESH:D002763
definition source: D002763
hasExactSynonym: Cholecystectomies

Chorionic Villus Sampling
type: Class
subclass of: Prenatal Screening for Sickle Cell
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: cvs
abbreviation: CVS
is characterised by: Either a needle is inserted through the woman's abdomen or a tube inserted through the woman's vagina and cervix is used to obtain a tissue sample from the placenta.
hasExactSynonym: CVS
comment: Performed between the tenth and twelfth week of pregnancy.

Chronic Complications of Sickle Cell Disease
type: Class
subclass of: Phenotype of Sickle Cell Disease
subclass of: Restriction
  on property: has phenotype
  some values from: Chronic Kidney Disease
subclass of: Restriction
  on property: has phenotype
  some values from: Chronic Sickle Cell Pain
subclass of: Restriction
  on property: has phenotype
  some values from: Leg Ulcer
subclass of: Restriction
  on property: has phenotype
  some values from: Ophthalmologic Complication
subclass of: Restriction
  on property: has phenotype
  some values from: Osteonecrosis
subclass of: Restriction
  on property: has phenotype
  some values from: Pulmonary Hypertension
subclass of: Restriction
  on property: has phenotype
  some values from: Stuttering Priapism
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A condition that co-exists or follows from sickle cell disease and that has a slow, creeping onset, slow progress and long continuance of disease manifestations.
dc:source: Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014.
curator note: Used info in "Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014" to link to relevant phenotypes.
definition source: Q000150
definition source: HP_0011010
description adapted from source: yes
comment: Chronic complications of SCD can affect almost any organ, and certain acute complications, such as stroke and priapism, often evolve into chronic phases that require special approaches to management.

Chronic Kidney Disease
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has measurement
  some values from: Glomerular Filtration Rate
subclass of: Restriction
  on property: has measurement
  some values from: Urine Albumin-Creatinine Ratio
subclass of: Restriction
  on property: diagnosed by
  some values from: Creatinine Blood Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Cystatin C Measurement
subclass of: Restriction
  on property: diagnosed by
  some values from: Glomerular Filtration Rate
subclass of: Restriction
  on property: diagnosed by
  some values from: Serum Creatinine Level
subclass of: Restriction
  on property: diagnosed by
  some values from: Urinary Albumin Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Urinary Creatinine Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin Concentration
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin Excretion Rate
subclass of: Restriction
  on property: treated with
  some values from: Antihypertensive Agents
subclass of: Restriction
  on property: treated with
  some values from: Renal Dialysis
subclass of: Restriction
  on property: treated with
  some values from: Renal Transplant
subclass of: Restriction
  on property: results_in
  some values from: Kidney Failure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Chronic kidney disease (CKD) is defined as either having a glomerular filtration rate (GFR) of <60 mL/min/1.73 mL for >3 months with or without kidney damage or having evidence of kidney damage for 3 months, with or without decreased GFR. Evidence of kidney damage includes pathologic abnormalities or markers of kidney damage (i.e., proteinuria) independent of cause. Kidney disease severity is classified into five stages according to the level of GFR and presence of albuminuria.
dc:source: classification-of-chronic-kidney-disease-2
dc:source: NHLBI SCD New guidelines 2014.
abbreviation: CKD
curator note: Move some info from the description to a comment.
definition source: NHLBI SCD New guidelines 2014.
description adapted from source: yes
has age of onset: When assessed by albuminuria, often presents in second decade of life in sickle cell disease and prevalence increases with age.
has disease stage: CKD is classified using a combination of GFR and ACR categories
is caused by: Sickle cell disease, hypertension, diabetes, polycystic kidney disease, glomerulonephritis, various other causes.
is characterised by: Reduced glomerular filtration, elevated creatinine, anemia, bone disease, uremia.
hasExactSynonym: Chronic Renal Failure

Chronic Kidney Injury
type: Class
subclass of: Kidney Failure
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Test
subclass of: Restriction
  on property: treated with
  some values from: Renal Dialysis
subclass of: Restriction
  on property: treated with
  some values from: Renal Transplant
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Is a long-term condition where the kidneys don't work as well as they should.
dc:source: symptoms
abbreviation: CKD
curator note: There is conflicting positioning of this term in different ontologies. Need an expert to decide descriptions and positioning of this and related terms.
description adapted from source: no
is caused by: High blood pressure, diabetes , high cholesterol, kidney infections, kidney inflammation, polycystic kidney disease, blockages in the flow of urine and regular use of certain medicines.
hasExactSynonym: CKD

Chronic Neuropathic Pain
type: Class
subclass of: Chronic Sickle Cell Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: This pain is usually described as burning, numb, tingling, lancinating, shooting, or paroxysmal in nature and is associated with a sensation of pins and needles. Its severity is also enhanced by exposure to either cold or heat.
definition source: Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
description adapted from source: yes
comment: This pain can be secondary to either peripheral or central nerve injury or nerve dysfunction. SCD-related neuropathic pain has two etiologies. The first is tissue damage secondary to occlusion of blood vessels that supply the nerves as can be found in mental nerve neuropathy and spinal cord infarction.290-292 The second seems to be chronic pain. Persistent chronic pain, the resulting inflammation, and/or pain management seem to lead to neuropathic pain.

Chronic Pain in a Specific Tissue or Organ
type: Class
subclass of: Chronic Sickle Cell Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: This pain occurs in a specific tissue or organ and is usually described as constant and deep, nagging, and achy in nature.
dc:source: Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
definition source: Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
description adapted from source: yes
comment: Such as avascular necrosis (AVN) of the hips, or leg ulcers.
comment: This pain can occur in the chest, back, abdomen, extremities, neck, or head and is difficult to treat.

Chronic Pain often of Unclear Etiology
type: Class
subclass of: Chronic Sickle Cell Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Intractable chronic pain without obvious pathology where the only complaint is the patient's self-report of pain that does not go away.
dc:source: Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
definition source: blood-2012-04-383430
description adapted from source: no
comment: This type of chronic sickle cell pain may be an extension of recurrent acute painful episodes. Therefore, early and aggressive intervention in treating acute sickle cell pain may reduce the development of chronic pain.

Chronic Restrictive Lung Disease
type: Class
subclass of: Phenotype
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Restrictive lung disease is a category of extrapulmonary, pleural, or parenchymal respiratory diseases that restrict lung expansion, resulting in a decreased lung volume, an increased work of breathing, and inadequate ventilation and/or oxygenation. Pulmonary function test demonstrates a decrease in the forced vital capacity.
dc:source: HP_0002091
curator note: Wikipedia was used as the description source. Perhaps rather use NCIT's "Restrictive Lung Disease", and then use wikipedia as source for additional info. Did not find "Chronic Restrictive Lung Disease" in ontologies, but did find "Chronic Obstructive Lung Disease"...perhaps there was confusion between these terms when giving the name?
database cross reference: HP:0002091
hasExactSynonym: Restrictive Lung Disease
hasExactSynonym: Restrictive Ventilatory Defect
comment: The list is not exhaustive.

Chronic Sickle Cell Pain
type: Class
subclass of: SCD Related Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Pain that does not resolve and lasts for more than three months.
definition source: http://www.google.co.za/url
definition source: Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
description adapted from source: no
hasExactSynonym: SCD-Associated Chronic Pain

Chronic Sickle Cell Pain Management
type: Class
subclass of: Sickle Cell Pain Management
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Sickle cell pain management that aims to restore function and improve the quality of life.
dc:source: Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014.
definition source: Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014.
description adapted from source: yes
hasExactSynonym: Chronic Sickle Cell Pain Treatment
comment: The goals of providing adequate pain relief to improve functionality and quality of life must be balanced by the need to minimize the risk of abuse, misuse, or diversion of opioids—medications which are a mainstay in managing chronic pain in people with SCD. Believing the patient’s report of pain is critical to optimizing therapeutic outcomes and achieving adequate pain relief and maintaining or improving functionality and the person’s quality of life.

Cigarette Smoking Status
type: Class
subclass of: Smoking History
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The respondent's cigarette smoking status in his or her entire life.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Cigarette Smoking Status - Adolescent #030603
has protocol: PhenX protocol: Cigarette Smoking Status - Adult #030604
comment: Can be used to assess the participant’s lifetime exposure to cigarette use, it determines smoking status, i.e., if they are a Current Every-Day Smoker or a Current Some-Day Smoker, a Former Smoker, or a Non Smoker or a Never Smoker.

Climate
type: Class
subclass of: Physical Environment
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Meteorological conditions, including temperature, precipitation, and wind, that characteristically prevail in a particular region; includes regions of the earth having particular meteorological conditions.
database cross reference: 1035-6799
definition source: http://bioportal.bioontology.org/ontologies/CRISP
description adapted from source: no
hasNarrowSynonym: Antarctic Climate
hasNarrowSynonym: Arctic Climate
hasNarrowSynonym: Cold Climate
hasNarrowSynonym: Desert Climate
hasNarrowSynonym: Hot Climate
hasNarrowSynonym: Tropical Climate
hasRelatedSynonym: Climatic Variables
hasRelatedSynonym: Seasons

Clinical Coding
type: Class
subclass of: Medical Records
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Process of substituting a symbol or code for a term such as a diagnosis or procedure. (from Slee's Health Care Terms, 3d ed.)
curator note: Add specific Sickle Cell Disease related codes as instances/individuals below *Clinical Coding*? (see ICD-10 codes here: www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-)
database cross reference: MESH:D059019
definition source: D059019
description adapted from source: no

Clinical Competence
type: Class
subclass of: Quality of Health Care
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The capability to perform acceptably those duties directly related to patient care; Health care services are respectful of and responsive to the health beliefs, practices and cultural and linguistic needs of diverse patients.
dc:source: MeSH: Culturally Competent Care; MeSH: Clinical Competence
curator note: The description is a combination of the descriptions given for "Clinical Competence" and "Culturally Competent Care" in MESH. Perhaps the two different terms should be described separately?
database cross reference: MESH:D002983
definition source: D002983
definition source: D065246
description adapted from source: yes
hasExactSynonym: Clinical Competencies
hasExactSynonym: Clinical Competency
hasExactSynonym: Clinical Skill
hasExactSynonym: Competencies, Clinical
hasExactSynonym: Competency, Clinical
hasExactSynonym: Skill, Clinical
hasExactSynonym: Skills, Clinical
comment: Culturally Competent Care: The provider and the patient each bring their individual learned patterns of language and culture to the health care experience which must be transcended to achieve equal access and quality health care. *** The term was merged.

Clinical Conference
type: Class
subclass of: Publication Type
description: Work that consists of a conference of physicians on their observations of a patient at the bedside, regarding the physical state, laboratory and other diagnostic findings, clinical manifestations, results of current therapy, etc. A clinical conference usually ends with a confirmation or correction of clinical findings by a pathological diagnosis performed by a pathologist. "Clinical conference" is often referred to as a "clinico-pathological conference."
database cross reference: MESH:D016429
definition source: D016429
description adapted from source: no
hasExactSynonym: Clinico-Pathologic Conference
hasExactSynonym: Clinico-Pathological Conference

Clinical Diagnostic Questionnaire
type: Class
subclass of: Questionnaire
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Clinical Neuropathy Assessment
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A physician administered examination to assess peripheral neuropathy.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX130200
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Clinical Neuropathy Assessment #130201
has_application_toward: A clinical neuropathy assessment measures the severity of symptoms and disability associated with peripheral neuropathy caused by a number of disorders including tumors, infections, autoimmune diseases and inherited disorders such as Charcot-Marie-Tooth disease.

Clinical Phenotype of Beta Thalassemia
type: Class
subclass of: Beta Thalassemia
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Clinical Study
type: Class
subclass of: Publication Type
description: A work that reports on the results of a research study to evaluate interventions or exposures on biomedical or health-related outcomes. The two main types of clinical studies are interventional studies (clinical trials) and observational studies. While most clinical studies concern humans, this publication type may be used for clinical veterinary articles meeting the requisites for humans.
database cross reference: MESH:D000068397
definition source: http://purl.bioontology.org/ontology/MESH/D000068397
description adapted from source: no

Clinical Studies as Topic
type: Class
subclass of: Study Design
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Works about research studies that evaluate interventions or exposures on biomedical or health-related outcomes. The two main types of clinical studies are interventional studies (clinical trials) and observational studies.
curator note: Term to be adapted as necessary to match EDDA Study Designs Taxonomy
database cross reference: MESH:D000068456
definition source: http://purl.bioontology.org/ontology/MESH/D000068456
description adapted from source: no

Clinical Trial
type: Class
subclass of: Clinical Study
description: A work that reports on the results of a clinical study in which participants are assigned to receive one or more interventions so that researchers can evaluate the interventions on biomedical or health-related outcomes. The assignments are determined by the study protocol. Participants may receive diagnostic, therapeutic, or other types of interventions. While most clinical trials concern humans, this publication type may be used for clinical veterinary articles meeting the requisites for humans.
database cross reference: MESH:D016430
definition source: D016430
description adapted from source: no
hasExactSynonym: Intervention Study

Clinical Trial, Phase I
type: Class
subclass of: Clinical Trial
description: Work that is the report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques based on a small number of healthy persons and conducted over the period of about a year in either the United States or a foreign country.
database cross reference: MESH:D017426
definition source: D017426
description adapted from source: no
hasExactSynonym: Clinical Trial, Phase 1

Clinical Trial, Phase II
type: Class
subclass of: Clinical Trial
description: Work that is a report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques based on several hundred volunteers, including a limited number of patients, and conducted over a period of about two years in either the United States or a foreign country.
database cross reference: MESH:D017427
definition source: D017427
description adapted from source: no
hasExactSynonym: Clinical Trial, Phase 2

Clinical Trial, Phase IV
type: Class
subclass of: Clinical Trial
description: Work that is a report of a planned post-marketing study of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques that have been approved for general sale after clinical trials, phases I, II, and III. These studies, conducted in the United States or a foreign country, often garner additional data about the safety and efficacy of a product.
database cross reference: MESH:D017429
definition source: D017429
description adapted from source: no
hasExactSynonym: Clinical Trial, Phase 4

Clinical Trial, Phase III
type: Class
subclass of: Clinical Trial
description: Work that is a report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques after phase II trials. A large enough group of patients is studied and closely monitored by physicians for adverse response to long-term exposure, over a period of about three years in either the United States or a foreign country.
database cross reference: MESH:D017428
definition source: D017428
description adapted from source: no
hasExactSynonym: Clinical Trial, Phase 3

Clinical Trials as Topic
type: Class
subclass of: Clinical Studies as Topic
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Works about pre-planned studies of the safety, efficacy, or optimum dosage schedule (if appropriate) of one or more diagnostic, therapeutic, or prophylactic drugs, devices, or techniques selected according to predetermined criteria of eligibility and observed for predefined evidence of favorable and unfavorable effects. This concept includes clinical trials conducted both in the U.S. and in other countries.
definition source: D002986

Cognitive Therapy
type: Class
subclass of: Behavior Therapy
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A direct form of psychotherapy based on the interpretation of situations (cognitive structure of experiences) that determine how an individual feels and behaves. It is based on the premise that cognition, the process of acquiring knowledge and forming beliefs, is a primary determinant of mood and behavior. The therapy uses behavioral and verbal techniques to identify and correct negative thinking that is at the root of the aberrant behavior.
abbreviation: CBT
database cross reference: MESH:D015928
definition source: D015928
description adapted from source: no
hasBroadSynonym: Therapies
hasExactSynonym: CBT
hasExactSynonym: Cognition Therapies
hasExactSynonym: Cognition Therapy
hasExactSynonym: Cognitive Behavioral Therapies
hasExactSynonym: Cognitive Behavioral Therapy
hasExactSynonym: Cognitive Behaviour Therapy
hasExactSynonym: Cognitive Psychotherapies
hasExactSynonym: Cognitive Psychotherapy
hasExactSynonym: Cognitive Therapies

Cohort Studies
type: Class
subclass of: Epidemiologic Studies
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Studies in which subsets of a defined population are identified. These groups may or may not be exposed to factors hypothesized to influence the probability of the occurrence of a particular disease or other outcome. Cohorts are defined populations which, as a whole, are followed in an attempt to determine distinguishing subgroup characteristics.
definition source: D015331

Colorimetric Test
type: Class
subclass of: Biochemical Assay
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: A test which produces colour change in the sample.
database cross reference: CHMO:0002580
definition source: CHMO_0002580
description adapted from source: no

Coma
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Culture
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A profound state of unconsciousness associated with depressed cerebral activity from which the individual cannot be aroused.
dc:source: http://purl.bioontology.org/ontology/MEDLINEPLUS/C0009421
curator note: The specific type of Blood Test (s) used to diagnose a coma should be specified. Named Individual removed (is diagnosed by): As in any neurologic condition, history and examination form the cornerstone of diagnosis when the patient is in a coma; however, history must be obtained from family, friends, or EMS. The Glasgow Coma Scale is a system of examining a comatose patient. It is helpful for evaluating the depth of the coma, tracking the patient's progress, and predicting (somewhat) the ultimate outcome of the coma. The Glasgow Coma Scale assigns a different number of points for exam results in three different categories: opening the eyes, verbal response (using words or voice to respond), and motor response (moving a part of the body). Fifteen is the largest possible number of total points, indicating the highest level of functioning. The highest level of functioning would be demonstrated by an individual who spontaneously opens his/her eyes, gives appropriate answers to questions about his/her situation, and can carry out a command (such as "move your leg" or "nod your head"). Three is the least possible number of total points and would be given to a patient for whom not even a painful stimulus is sufficient to provoke a response. In the middle are those patients who may be able to respond, but who require an intense or painful stimulus, and whose response may demonstrate some degree of brain malfunctioning (such as a person whose only response to pain in a limb is to bend that limb in toward the body). When performed as part of the admission examination, a Glasgow score of three to five points often suggests that the patient has likely suffered fatal brain damage, while eight or more points indicates that the patient's chances for recovery are good. Expansion of the pupils and respiratory pattern are also important. Metabolic causes of coma are diagnosed from blood work and urinalysis to evaluate blood chemistry, drug screen, and blood cell abnormalities that ma…
database cross reference: MEDLINEPLUS:C0009421
database cross reference: MESH:D003128
definition source: D003128
description adapted from source: yes
is caused by: Result of something that interferes with the functioning of the cerebral cortex and/or the functioning of the structures which make up the RAS. In fact, a huge and varied number of conditions can result in coma. A good way of categorizing these conditions is to consider the anatomic and the metabolic causes of coma. Anatomic causes of coma are those conditions that disrupt the normal physical architecture of the brain structures responsible for consciousness, either at the level of the cerebal cortex or the brainstem, while metabolic causes of coma consist of those conditions that change the chemical environment of the brain, thereby adversely affecting function.
is characterised by: There are many metabolic causes of coma, including:A decrease in the delivery to the brain of substances necessary for appropriate brain functioning, such as oxygen, glucose (sugar), and sodium.The presence of certain substances that disrupt the functioning of neurons. Drugs or alcohol in toxic quantities can result in neuronal dysfunction, as can substances normally found in the body, but that, due to some diseased state, accumulate at toxic levels. Accumulated substances that might cause coma include ammonia due to liver disease, ketones due to uncontrolled diabetes, or carbon dioxide due to a severe asthma attack.
hasExactSynonym: Comas
hasRelatedSynonym: Comatose

Community
type: Class
subclass of: Social Environment
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A community is a social group of organisms sharing an environment, normally with shared interests.
dc:source: http://bioportal.bioontology.org/ontologies/SWEET
description adapted from source: no
description adapted from source: yes

Comorbid Disease
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: The presence of co-existing or additional diseases with reference to an initial diagnosis or with reference to the index condition that is the subject of study. Comorbidity may affect the ability of affected individuals to function and also their survival; it may be used as a prognostic indicator for length of hospital stay, cost factors, and outcome or survival.
curator note: As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Joseph Telfair Include here: Asthma Osteonecrosis of the Femoral Head Restrictive Lung Disease (currently Chronic Restrictive Lung Disease in SCDO) Retinopathy Cardiac Dysfunction Renal Dysfunction/Renal Failure ...and others
database cross reference: MeSH:D015897
description adapted from source: Label and description adapted
hasExactSynonym: Additional Disease
hasExactSynonym: Co-Existing Disease
hasExactSynonym: Co-Morbid Disease
hasRelatedSynonym: Co-Morbidity
hasRelatedSynonym: Comorbidity
comment: Comorbidity may affect the ability of affected individuals to function and also their survival; it may be used as a prognostic indicator for length of hospital stay, cost factors, and outcome or survival. (source : MSH)

Comparative Study
type: Class
subclass of: Publication Type
description: Comparison of outcomes, results, responses, etc for different techniques, therapeutic approaches or other inputs.
database cross reference: MESH:D003160
definition source: D003160
description adapted from source: no

Complete Blood Count
type: Class
subclass of: Blood Cell Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Venipuncture
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: History of Transfusion
subclass of: Restriction
  on property: essential measure
  some values from: Medication Inventory
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The calculation of the cellular elements of the blood, usually including cell counts for white and red blood cells and platelets.
dc:source: 003642.htm
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: CMO:0000364
definition source: CMO_0000364
description adapted from source: no
has protocol: PhenX protocol: Complete Blood Count (CBC) #220501
has_application_toward: A complete blood count (CBC) is a commonly performed lab test. It can be used to detect or monitor many different health conditions.
hasExactSynonym: Blood Cell Count
hasExactSynonym: Blood Cell Number
hasExactSynonym: CBC
hasExactSynonym: FBC
hasExactSynonym: Full Blood Count
comment: RBC count: Male: 4.7 to 6.1 million cells/mcL Female: 4.2 to 5.4 million cells/mcL WBC count:4,500 to 10,000 cells/mcL Hematocrit:Male: 40.7 to 50.3% Female: 36.1 to 44.3% Hemoglobin:Male: 13.8 to 17.2 gm/dL Female: 12.1 to 15.1 gm/dL Red blood cell indices:MCV: 80 to 95 femtoliter MCH: 27 to 31 pg/cell MCHC: 32 to 36 gm/dL Platelet count:150,000 to 450,000/dL

Complementary Therapy
type: Class
subclass of: Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Therapeutic practices which are not currently considered an integral part of conventional allopathic medical practice. They may lack biomedical explanations but as they become better researched some (physical therapy modalities; diet; acupuncture) become widely accepted whereas others (humors, radium therapy) quietly fade away, yet are important historical footnotes. Therapies are termed as Complementary when used in addition to conventional treatments and as Alternative when used instead of conventional treatment. Year introduced: 2002(1986)
database cross reference: MESH:D000529
definition source: D000529
description adapted from source: Only label adapted
hasExactSynonym: Complementary Medicine
hasRelatedSynonym: Alternative Therapy

Compound Heterozygous Hemoglobinopathy
type: Class
subclass of: from phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Compound heterozygosity in medical genetics is the condition of having two heterogeneous recessive alleles at a particular locus that can cause genetic disease in a heterozygous state.
dc:source: Compound heterozygosity

Confusion
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Dementia
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Confusion is the inability to think as clearly or quickly as you normally do. You may feel disoriented and have difficulty paying attention, remembering, and making decisions
dc:source: http://pennstatehershey.adam.com/content.aspx
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info. Perhaps move below "Behavioral Abnormality"?
description adapted from source: no
is caused by: Alcohol or drug intoxication, brain tumor, head trauma or head injury (concussion), fever, fluid and electrolyte imbalance, illness in an elderly person, such as loss of brain function (dementia), illness in a person with existing neurological disease, such as a stroke, infections, lack of sleep (sleep deprivation), low blood sugar, ;ow levels of oxygen (for example, from chronic lung disorders), medications, nutritional deficiencies, especially niacin, thiamine, or vitamin B12, seizures, sudden drop in body temperature (hypothermia).
comment: Confusion may come on quickly or slowly over time, depending on the cause. Many times, confusion lasts for a short time and goes away. Other times, it is permanent and not curable. It may be associated with delirium or dementia.

Conjugate Pneumococcal Vaccine
type: Class
subclass of: Streptococcus Pneumoniae Vaccine
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An active immunizing vaccine used to prevent infection by the bacterium Streptococcus pneumoniae. It consists of a solution of saccharides of the capsular antigens of Streptococcus serotypes individually conjugated to proteins.
dc:source: index.html
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasBroadSynonym: Conjugate Vaccine
hasBroadSynonym: Pneumococcal Vaccine
hasExactSynonym: Pneumococcal Conjugate Vaccine
comment: Pneumococcal conjugate vaccine is recommended for all babies and children younger than 2 years old, all adults 65 years or older, and people 2 through 64 years old with certain medical conditions.

Conjunctival Comma Sign
type: Class
subclass of: Ophthalmologic Complication
subclass of: Restriction
  on property: diagnosed by
  some values from: Slit-Lamp Examination
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Dark red, comma- or corkscrew-shaped vascular fragment that appears to be isolated from neighboring blood vessels in the conjunctiva. Normally benign, this lesion can serve as the first diagnostic sign of sickle cell retinopathy. The conjunctival comma sign results from transient vaso-occlusive processes in the microvasculature of bulbar conjunctiva. It is not seen in sickle trait, but is common in SCD.
definition source: Ballas et al 2010 Am J Hematol
description adapted from source: no
comment: Diagnostic Criteria: These fragments can be visualized with any instrument that provides moderate magnification, such as a slit lamp or even a direct ophthalmoscope at +10 diopters.

Consensus Development Conference
type: Class
subclass of: Publication Type
description: A work that consists of summary statements representing the majority and current agreement of physicians, scientists, and other professionals meeting to reach a consensus on a selected subject.
database cross reference: MESH:D016446
definition source: D016446
description adapted from source: no

Consensus Development Conference, NIH
type: Class
subclass of: Consensus Development Conference
description: Work consisting of summary statements, from a conference sponsored by NIH, representing the majority of current opinion of physicians, scientists, and other professionals on a selected subject.
database cross reference: MESH:D016447
definition source: D016447
description adapted from source: no
hasExactSynonym: NIH Consensus Development Conference

Constitutional Genetic Disorder
type: Class
subclass of: Genetic Disorder
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: A genetic disorder inherited during conception that is part of all cells in the organism.
curator note: Perhaps remove this class but keep sub-classes? Or include the class "Acquired Genetic Disorder" as a sibling of this class if terms are included that can be sub-classes of it?
database cross reference: OGMS:0000051
definition source: OGMS_0000051
description adapted from source: no

Consumer Assessment of Healthcare Providers and Systems (CAHPS) Health Plan Survey 4.0 Child Medicaid Questionnaire
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A measure of patient and family experiences of health care for children treated for sickle cell disease (SCD).
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Quality of Care - Children #820102
has respondents: Proxy (Primary caregiver)
validated for age ranges: Children and adolescents, ages 17 and younger
comment: This measure includes general questions about access to care and quality of care and additional questions about the services provided to children with chronic conditions. Items CC1-CC38 of the questionnaire are version 4.0 of the Children with Chronic Conditions Item Set.

Continuous Ambulatory ECG
type: Class
subclass of: Heart Function Test
subclass of: Restriction
  on property: has medical device
  some values from: Electrocardiographic Monitor
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A continuous electrocardiographic (ECG) recording that utilizes one or more leads that both records and stores data directly to a device worn by the subject, such that the subject need not be restricted to a medical facility, and may be able to participate in their customary activities of daily living.
database cross reference: C123446
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no

Controlled Before-After Studies
type: Class
subclass of: Epidemiologic Studies
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A study in which observations are made before and after an intervention, both in a group that receives the intervention and in a control group that does not.
definition source: D065187

Controlled Clinical Trial
type: Class
subclass of: Clinical Trial
description: A work that reports on a clinical trial involving one or more test treatments, at least one control treatment, specified outcome measures for evaluating the studied intervention, and a bias-free method for assigning patients to the test treatment. The treatment may be drugs, devices, or procedures studied for diagnostic, therapeutic, or prophylactic effectiveness. Control measures include placebos, active medicine, no-treatment, dosage forms and regimens, historical comparisons, etc. When randomization using mathematical techniques, such as the use of a random numbers table, is employed to assign patients to test or control treatments, the trial is characterized as a randomized controlled trial.
database cross reference: MESH:D018848
definition source: D018848
description adapted from source: no

Controlled Clinical Trials as Topic
type: Class
subclass of: Clinical Trials as Topic
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Works about clinical trials involving one or more test treatments, at least one control treatment, specified outcome measures for evaluating the studied intervention, and a bias-free method for assigning patients to the test treatment. The treatment may be drugs, devices, or procedures studied for diagnostic, therapeutic, or prophylactic effectiveness. Control measures include placebos, active medicines, no-treatment, dosage forms and regimens, historical comparisons, etc. When randomization using mathematical techniques, such as the use of a random numbers table, is employed to assign patients to test or control treatments, the trials are characterized as RANDOMIZED CONTROLLED TRIALS AS TOPIC.
definition source: D018849

Coping Skill
type: Class
subclass of: Mental Health
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A state of harmony between internal needs and external demands and the processes used in achieving this condition.
database cross reference: MESH:D000223
definition source: D000223
description adapted from source: Only label adapted
hasExactSynonym: Adaptive Behavior
hasExactSynonym: Adaptive Behaviors
hasExactSynonym: Coping Behavior
hasExactSynonym: Coping Behaviors
hasExactSynonym: Coping Skills
hasExactSynonym: Psychologic Adaptation
hasExactSynonym: Psychological Adaptation

Coping Strategies Questionnaire revised for Sickle Cell Disease (CSQ-SCD)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The CSQ-SCD consists of 78 items, which make up seven scales related to coping with pain in general: Diverting attention, Reinterpreting pain sensations, Calming self-statements, Ignoring pain sensations, Praying and hoping, Catastrophising, and Increasing activity level; together with six scales developed as specifically relevant to sickle cell disease: Fear self-statements, Anger self-statements, Isolation, Taking fluids, Resting, and Heat/cold/massage. Patients rated their use of each response from 0 = never to 6 = always, and scores were averaged to produce a mean for each scale. Two additional aspects were assessed by single items: perceived ability to control pain was rated from 0 = no control to 6 = complete control, and perceived ability to decrease pain was rated from 0 = can’t decrease it at all to 6 = can decrease it completely.
dc:source: Gil K.M., Abrams M.R., Phillips G. and Keefe F.J. (1989). Sickle cell disease pain: Relation of coping strategies to adjustment. Journal of Consulting and Clinical Psychology, 57, 725-731.
abbreviation: CSQ-SCD
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self
has target population: Adults with SCD
selection criteria met: Demonstrated validity with SCD populations USA and UK; several publications.
validated for age ranges: Adults
hasExactSynonym: CSQ-SCD
hasExactSynonym: Coping Strategies Questionnaire revised for Sickle Cell Disease

Coping Strategies Questionnaire revised for Sickle Cell Disease Children (CSQ-SCD Children)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The CSQ-SCD consists of 78 items, which make up seven scales related to coping with pain in general: Diverting attention, Reinterpreting pain sensations, Calming self-statements, Ignoring pain sensations, Praying and hoping, Catastrophising, and Increasing activity level; together with six scales developed as specifically relevant to sickle cell disease: Fear self-statements, Anger self-statements, Isolation, Taking fluids, Resting, and Heat/cold/massage. Patients rated their use of each response from 0 = never to 6 = always, and scores were averaged to produce a mean for each scale. Two additional aspects were assessed by single items: perceived ability to control pain was rated from 0 = no control to 6 = complete control, and perceived ability to decrease pain was rated from 0 = can’t decrease it at all to 6 = can decrease it completely.
dc:source: Gil K.M., Williams D.A., Thompson, R.J. and Kinney, T.R. (1991). Sickle cell disease in children and adolescents: The relation of child and parent pain coping strategies to adjustment. Journal of Pediatric Psychology, 16, 643-663.
abbreviation: CSQ-SCD Children
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self
has target population: Children with SCD
selection criteria met: Demonstrated validity with SCD populations USA and UK; several publications.
validated for age ranges: Children
hasExactSynonym: CSQ-SCD Children

Corticosteroid-Induced Adverse Event
type: Class
subclass of: Causal Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: S1526054213001218
dc:source: https://www.ncbi.nlm.nih.gov/pubmed/18717146
dc:source: https://www.ncbi.nlm.nih.gov/pubmed/19331266

Corticostroid-Induced Vaso-Occlusive Adverse Event
type: Class
subclass of: Corticosteroid-Induced Adverse Event
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: https://www.ncbi.nlm.nih.gov/pubmed/18717146

Cost of Illness
type: Class
subclass of: Healthcare Access
subclass of: Mental Health
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The personal cost of acute or chronic disease. The cost to the patient may be an economic, social, or psychological cost or personal loss to self, family, or immediate community. The cost of illness may be reflected in absenteeism, productivity, response to treatment, peace of mind, or quality of life. It differs from health care costs, meaning the societal cost of providing services related to the delivery of health care, rather than personal impact on individuals.
database cross reference: MESH:D017281
definition source: D017281
description adapted from source: no
hasExactSynonym: Burden of Illness
hasExactSynonym: Cost of Disease
hasExactSynonym: Cost of Sickness
hasExactSynonym: Costs of Disease
hasExactSynonym: Disease Cost
hasExactSynonym: Disease Costs
hasExactSynonym: Economic Burden of Disease
hasExactSynonym: Sickness Cost
hasRelatedSynonym: Affordability
hasRelatedSynonym: Health Insurance

Cost-Effectiveness of Healthcare
type: Class
subclass of: Health Utility
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Cost-effectiveness analysis compares the costs and health effects of an intervention to assess the extent to which it can be regarded as providing value for money. This informs decision-makers who have to determine where to allocate limited healthcare resources.
definition source: Cost-effect.pdf
description adapted from source: no
hasBroadSynonym: Health Economics

Creatinine Blood Test
type: Class
subclass of: Blood Test
subclass of: Kidney Function Test
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: History of Kidney Failure
subclass of: Restriction
  on property: essential measure
  some values from: History of Type I and Type 2 Diabetes
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Serum Creatinine Level
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A bioassay to measure the serum concentration of creatinine, a metabolite of muscle creatine that is filtered out of blood by the kidneys.
dc:source: 003475.htm
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX141400
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has protocol: PhenX protocol: Serum Creatinine Assay #141401
has_application_toward: Serum creatinine concentration is the most standardized way to calculate glomerular filtration rate (GFR) as a measure of kidney function. Creatinine is removed from the body entirely by the kidneys. If kidney function is not normal, the creatinine level in the blood will increase. This is because less creatinine is released through the urine.
hasExactSynonym: Blood Creatinine Assay
hasExactSynonym: Blood Creatinine Test
hasExactSynonym: Serum Creatinine
hasExactSynonym: Serum Creatinine Assay
comment: A normal result is 0.7 to 1.3 mg/dL for men and 0.6 to 1.1 mg/dL for women. Women usually have a lower creatinine level than men. This is because women usually have less muscle mass than men. Creatinine level varies based on a person's size and muscle mass.
comment: Creatinine can also be measured with a urine test.

Crisis Intervention
type: Class
subclass of: Psychotherapy
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Brief therapeutic approach which is ameliorative rather than curative of acute psychiatric emergencies. Used in contexts such as emergency rooms of psychiatric or general hospitals, or in the home or place of crisis occurrence, this treatment approach focuses on interpersonal and intrapsychic factors and environmental modification. (APA Thesaurus of Psychological Index Terms, 7th ed)
database cross reference: MESH:D003419
definition source: D003419
description adapted from source: no
hasExactSynonym: Crisis Interventions
hasExactSynonym: Interventions, Crisis
hasNarrowSynonym: Critical Incident Stress Debriefing

Cross-Sectional Studies
type: Class
subclass of: Epidemiologic Studies
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Studies in which the presence or absence of disease or other health-related variables are determined in each member of the study population or in a representative sample at one particular time. This contrasts with longitudinal studies which are followed over a period of time.
database cross reference: MESH:D003430
definition source: D003430

Culture
type: Class
subclass of: Quality of Life
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A collective expression for all behaviour patterns acquired and socially transmitted through symbols. Culture includes customs, traditions, and language.
database cross reference: MESH:D003469
definition source: D003469
description adapted from source: no
hasExactSynonym: Cultural Beliefs
hasExactSynonym: Cultural Values
comment: Religion may also be part of some cultures.

curation status specification
type: Class
subclass of: Restriction
  on property: has curation status
  has value: organizational term
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO developers
description: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
database cross reference: IAO:0000078
definition source: IAO_0000078
description adapted from source: no

Curative Therapeutics
type: Class
subclass of: Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: Therapeutics relating to or used in the cure of diseases.
definition source: curative
description adapted from source: yes

Current Age
type: Class
subclass of: Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The respondent's current age using his or her date of birth.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX010100
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Current Age #010101
has_application_toward: Current age is a critical component of a respondent's demographic background. Date of birth (DOB)/current age is essential to medical research because it captures the age at the time of the clinical visit or diagnosis. Age is related to nearly all diseases and conditions and is the strongest potential confounder of other effects on these processes. Current age is often used to stratify respondents for more valid comparison (e.g., obesity of males aged 40-45 in Mississippi).

Current Educational Attainment
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: essential measure
  some values from: Annual Family Income
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The respondent's highest educational attainment at the current time.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Include under QoL (Education)? Include below the Disease Modifier, Socioeconomic Status? ("Child-Reported Parental Education Attainment" is there)
database cross reference: PX11000
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Current Educational Attainment #011001
has_application_toward: Education is correlated to occupation and income and is one of the key components of combined measures of "socioeconomic status."

Current Employment Status
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The respondent's current employment status.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Include under QoL?
database cross reference: PX11300
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Current Employment Status #011301
has_application_toward: The purpose of this question is to ascertain whether the respondent is presently in the labor force. Employed persons differ considerably from those who are not employed in terms of their health, health insurance, and demographic characteristics (e.g., age). Moreover, nonemployed persons are also heterogeneous, representing those who are retired, in school, homemakers, not seeking work, and others. These nonemployed individuals also vary in health, health insurance, and demographic characteristics.

Current Marital Status
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The respondent's current marital status.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX10900
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Current Marital Status #010902
has_application_toward: Marital status has been linked to health and mortality.

Cutaneous Hyperpigmentation
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A darkening of the skin related to an increase in melanin production and deposition.
database cross reference: HP:0000953
definition source: HP_0000953
description adapted from source: no
hasExactSynonym: Increased Skin Pigmentation
hasExactSynonym: Skin Hyperpigmentation

Cyanosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Hypoxemia
subclass of: Restriction
  on property: results_in
  some values from: Ischemia
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A bluish or purplish discoloration of the skin and mucous membranes due to an increase in the amount of deoxygenated hemoglobin in the blood or a structural defect in the hemoglobin molecule.
dc:source: HP_0000961
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000961
description adapted from source: no
has disease stage: Central and peripheral cyanosis.
is caused by: Cardiac, pulmonary, central nervous system, blood disorders, high altitude, hypothermia.
is characterised by: Bluish discolouration around the mouth, lips, tongue, fingers and toes.
hasExactSynonym: Cyanotic

Cystatin C Measurement
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A quantification of serum cystatin C (formerly gamma trace, post-gamma-globulin or neuroendocrine basic polypeptide), an extracellular cystatin subtype that is abundantly expressed in bodily fluids.
dc:source: test
dc:source: D055316
database cross reference: EFO:0004617
definition source: D055316
definition source: EFO_0004617
description adapted from source: yes
has_application_toward: Cystatin C may be used as an alternative to creatinine and creatinine clearance to screen for and monitor kidney dysfunction in those with known or suspected kidney disease. It may be especially useful in those cases where creatinine measurement is not appropriate, for instance, in those who have liver cirrhosis, are very obese, are malnourished, or have reduced muscle mass. Measuring cystatin C may also be useful in the early detection of kidney disease when other test results may still be normal and an affected person may have few, if any, symptoms. Researchers are exploring other uses of cystatin C, such as using it alone or in combination with blood creatinine for estimating the glomerular filtration rate (GFR). A recent study found that an equation for eGFR that includes both creatinine and cystatin C was more accurate than one that uses either of these alone and could be used to confirm chronic kidney disease (CKD) in people with an eGFR near 60, the threshold for CKD. In addition to kidney dysfunction, it has been associated with an increased risk of cardiovascular disease and heart failure in older adults.
hasExactSynonym: Cystatin 3
hasExactSynonym: Gamma Trace
hasExactSynonym: Gamma-Trace
hasExactSynonym: Neuroendocrine Basic Polypeptide
hasExactSynonym: Post gamma Globulin
hasExactSynonym: Post-Gamma-Globulin
comment: Cystatin C is encoded by the CST3 gene, may play a role in the inhibition of interstitial cysteine proteases, and is mainly used as a biomarker of kidney function and kidney disease.

D57 Sickle-cell disorders
type: Class
subclass of: ICD-10-CM Diagnosis Codes
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57
definition source: D57-
hasExactSynonym: D57

D57.0 Hb-SS disease with crisis
type: Class
subclass of: D57 Sickle-cell disorders
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Broad term used to describe several different acute conditions occurring with sickle cell disease, including aplastic crisis, hemolytic crisis, and vasoocclusive crisis.
abbreviation: D57.0
definition source: D57.0
description adapted from source: no
hasExactSynonym: D57.0

D57.01 Hb-SS disease with acute chest syndrome
type: Class
subclass of: D57.0 Hb-SS disease with crisis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.01
definition source: D57.01
hasExactSynonym: D57.01

D57.02 Hb-SS disease with splenic sequestration
type: Class
subclass of: D57.0 Hb-SS disease with crisis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.02
definition source: D57.02
hasExactSynonym: D57.02

D57.1 Sickle-cell disease without crisis
type: Class
subclass of: D57 Sickle-cell disorders
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.1
definition source: D57.1
hasExactSynonym: D57.1

D57.2 Sickle-cell/Hb-C disease
type: Class
subclass of: D57 Sickle-cell disorders
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: One of the sickle cell disorders characterized by the presence of both hemoglobin s and hemoglobin c. It is similar to, but less severe than sickle cell anemia.
abbreviation: D57.2
definition source: D57.2
description adapted from source: no
hasExactSynonym: D57.2

D57.20 Sickle-cell/Hb-C disease without crisis
type: Class
subclass of: D57.2 Sickle-cell/Hb-C disease
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.20
definition source: D57.20
hasExactSynonym: D57.20

D57.21 Sickle-cell/Hb-C disease with crisis
type: Class
subclass of: D57.2 Sickle-cell/Hb-C disease
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.21
definition source: D57.21
hasExactSynonym: D57.21

D57.211 Sickle-cell/Hb-C disease with acute chest syndrome
type: Class
subclass of: D57.21 Sickle-cell/Hb-C disease with crisis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.211
definition source: D57.211
hasExactSynonym: D57.211

D57.212 Sickle-cell/Hb-C disease with splenic sequestration
type: Class
subclass of: D57.21 Sickle-cell/Hb-C disease with crisis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.212
definition source: D57.212
hasExactSynonym: D57.212

D57.219 Sickle-cell/Hb-C disease with crisis, unspecified
type: Class
subclass of: D57.21 Sickle-cell/Hb-C disease with crisis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.219
definition source: D57.219
hasExactSynonym: D57.219

D57.3 Sickle-cell trait
type: Class
subclass of: D57 Sickle-cell disorders
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The condition of being heterozygous for hemoglobin s.
abbreviation: D57.3
definition source: D57.3
description adapted from source: no
hasExactSynonym: D57.3

D57.4 Sickle-cell thalassemia
type: Class
subclass of: D57 Sickle-cell disorders
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.4
definition source: D57.4
hasExactSynonym: D57.4

D57.40 Sickle-cell thalassemia without crisis
type: Class
subclass of: D57.4 Sickle-cell thalassemia
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Hemolytic anemia, in which patients are heterozygous for both the sickle cell gene and a thalassemia gene.
abbreviation: D57.40
definition source: D57.40
description adapted from source: no
hasExactSynonym: D57.40

D57.41 Sickle-cell thalassemia with crisis
type: Class
subclass of: D57.4 Sickle-cell thalassemia
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.41
definition source: D57.41
hasExactSynonym: D57.41

D57.411 Sickle-cell thalassemia with acute chest syndrome
type: Class
subclass of: D57.41 Sickle-cell thalassemia with crisis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.411
definition source: D57.411
hasExactSynonym: D57.411

D57.412 Sickle-cell thalassemia with splenic sequestration
type: Class
subclass of: D57.41 Sickle-cell thalassemia with crisis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.412
definition source: D57.412
hasExactSynonym: D57.412

D57.419 Sickle-cell thalassemia with crisis, unspecified
type: Class
subclass of: D57.41 Sickle-cell thalassemia with crisis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.419
definition source: D57.419
hasExactSynonym: D57.419

D57.8 Other sickle-cell disorders
type: Class
subclass of: D57 Sickle-cell disorders
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.8
definition source: D57.8
hasExactSynonym: D57.8

D57.80 Other sickle-cell disorders without crisis
type: Class
subclass of: D57.8 Other sickle-cell disorders
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.80
definition source: D57.80
hasExactSynonym: D57.80

D57.81 Other sickle-cell disorders with crisis
type: Class
subclass of: D57.8 Other sickle-cell disorders
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.81
definition source: D57.81
hasExactSynonym: D57.81

D57.811 Other sickle-cell disorders with acute chest syndrome
type: Class
subclass of: D57.81 Other sickle-cell disorders with crisis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.811
definition source: D57.811
hasExactSynonym: D57.811

D57.812 Other sickle-cell disorders with splenic sequestration
type: Class
subclass of: D57.81 Other sickle-cell disorders with crisis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.812
definition source: D57.812
hasExactSynonym: D57.812

D57.819 Other sickle-cell disorders with crisis, unspecified
type: Class
subclass of: D57.81 Other sickle-cell disorders with crisis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.819
definition source: D57.819
hasExactSynonym: D57.819

Delayed Puberty
type: Class
subclass of: Phenotype
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Depression
subclass of: Restriction
  on property: results_in
  some values from: Infertility
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Immaturity of the sexual organs at a given age.
dc:source: diagnosis-and-treatment-of-delayed-puberty
curator note: This term replaced "Delayed Sexual Maturation" in QoL.
database cross reference: MP:0001938
definition source: MP_0001938
description adapted from source: no
is caused by: Congenital abnormalities: Cryptorchidism, Klinefelter's syndrome, Other chromosomal abnormalities, Mutation in the FSH and LH receptor gene, Disorders of androgen biosynthesis, Myotonic dystrophy, Congenital anorchia, Varicocele, infections,radiation, Alkylating and antineoplastic agents, Suramin, Ketoconazole, Glucocorticoids, Environmental toxins, trauma, Testicular torsion, Bilateral orchiectomy, Chronic systemic diseases: cirrhosis, chronic renal failure, HIV infection, severe anemias, idiopathic.
hasExactSynonym: Delayed Development of Secondary Sex Characteristics
hasExactSynonym: Delayed Onset of Sexual Maturity
hasExactSynonym: Delayed Pubertal Development
hasExactSynonym: Delayed Sexual Maturation
hasExactSynonym: Delayed Sexual Maturity
hasExactSynonym: Pubertal Delay
comment: Absence or incomplete development of secondary sexual characteristics bounded by an age at which 95 percent of children of that sex and culture have initiated sexual maturation.
comment: Individuals with SCD generally do catch up in development.

Delta Beta Thalassaemia
type: Class
subclass of: Hemoglobinopathy Occuring in Heterozygous State in Sickle Cell Disease Variants
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, 106-KB DEL
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: Delta-beta-thalassemia is a form of beta-thalassemia characterized by decreased or absent synthesis of the delta- and beta-globin chains with a compensatory increase in expression of fetal gamma-chain synthesis.
dc:source: http://purl.bioontology.org/ontology/SNOMEDCT/16360009
definition source: http://www.orpha.net/consor/cgi-bin/OC_Exp.php
description adapted from source: no
hasExactSynonym: F thalassaemia
comment: Synonym need to be checked
comment: The condition is found in many ethnic groups but is most common in Greece and Italy.

Delta Thalassaemia
type: Class
subclass of: Hemoglobinopathy Occuring in Heterozygous State in Sickle Cell Disease Variants
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A hereditary disorder characterized by reduced or absent delta-globin thus effecting the level of hemoglobin A2, a minor component of adult hemoglobin monitored in the diagnosis of beta-thalassemia.
database cross reference: MESH:D055538
definition source: D055538
description adapted from source: no
hasExactSynonym: Delta Thalassaemias
hasExactSynonym: Delta-Thalassaemia
hasExactSynonym: Delta-Thalassaemias

Dementia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A loss of global cognitive ability of sufficient amount to interfere with normal social or occupational function. Dementia represents a loss of previously present cognitive abilities, generally in adults, and can affect memory, thinking, language, judgment, and behavior.
dc:source: HP_0000726
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000726
description adapted from source: no
is caused by: Dementia is caused by damage to brain cells. This damage interferes with the ability of brain cells to communicate with each other.
hasExactSynonym: Dementia Progressive
hasExactSynonym: Progressive Dementia

Dengue Fever
type: Class
subclass of: Viral Infection
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An acute febrile disease transmitted by the bite of AEDES mosquitoes infected with DENGUE VIRUS. It is self-limiting and characterized by fever, myalgia, headache, and rash. SEVERE DENGUE is a more virulent form of dengue.
database cross reference: MeSH:D003715
definition source: D003715
description adapted from source: no
hasExactSynonym: Break Bone Fever
hasExactSynonym: Break-Bone fever
hasExactSynonym: Breakbone Fever
hasExactSynonym: Dengue

Dental System
type: Class
subclass of: from phenotype
description: The system pertaining to teeth, oral cavity, and associated structures.
definition source: dentistry
description adapted from source: yes

deprecated terms
type: Class
subclass of: Thing
subclass of: Restriction
  on property: has curation status
  has value: organizational term
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: Terms that are no longer being used in the ontology.

Depression
type: Class
subclass of: Behavioral Abnormality
subclass of: Mental Health
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: treated with
  some values from: Psychotherapy
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A common mental disorder, characterized by sadness, hopelessness, loss of interest or pleasure, feelings of guilt or low self-worth, disturbed sleep or appetite, feelings of tiredness, and poor concentration. Depression can be long-lasting or recurrent, substantially impairing an individual's ability to function at work or school or cope with daily life.
dc:source: depression
definition source: en
description adapted from source: yes
is characterised by: Depression is closely associated with a lack of confidence and self-esteem and with an inability to express strong feelings. Repressed anger is thought to be a powerful contributor to depression. The person feels inadequate to cope with the situations that arise in everyday life and so feels insecure. Severely depressed patients usually express three basic feelings associated with their mental state. These are a lack of desire for socializing or physical activity, feelings of worthlessness and loss of self esteem, and thoughts of self-injury or destruction.
hasExactSynonym: Depressive Symptoms
hasExactSynonym: Low Mood
hasRelatedSynonym: Helplessness
hasRelatedSynonym: Hopelessness
comment: At its most severe, depression can lead to suicide. When mild, people can be treated without medicines but when depression is moderate or severe they may need medication and professional talking treatments. Depression is a disorder that can be reliably diagnosed and treated by non-specialists as part of primary health care. Specialist care is needed for a small proportion of individuals with complicated depression or those who do not respond to first-line treatments.
comment: There is a higher prevalence of depressive symptoms in children and adults with SCD compared with the general population (Mastandrea et al 2015 Sao Paulo Med J 2015;133:421-7. Wallen et al BMC Psychiatry 2014;14:207. Treadwell et al Clin J Pain 2014;30:902-14)

Dexterity
type: Class
subclass of: Physical Health
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Skill in performing tasks, especially with the hands.
definition source: dexterity
description adapted from source: yes

Diabetes Insipidus
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A state of excessive water excretion and hypotonic (dilute) polyuria. Diabetes insipidus may be due to failure of vasopressin (AVP) release (central or neurogenic diabetes insipidus) or to a failure of the kidney to respond to AVP (nephrogenic diabetes insipidus).
dc:source: Diabetes insipidus
database cross reference: HP:0000873
definition source: HP_0000873
description adapted from source: no
is caused by: Primary polydipsia. Central: most often is idiopatic, but may be due to trauma, pituitary surgery, or hypoxic or ischemic encephalopathy or rare familial cases. Nephrogenic: chronic lithium use and hypercalcemia in adults, or inherited defects in children.

Diabetes Mellitus
type: Class
subclass of: Comorbid Disease
subclass of: Restriction
  on property: treated with
  some values from: Healthy Diet
subclass of: Restriction
  on property: treated with
  some values from: Lifestyle Therapy
subclass of: Restriction
  on property: results_in
  some values from: Chronic Kidney Disease
subclass of: Restriction
  on property: results_in
  some values from: Stroke
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A group of abnormalities characterized by hyperglycemia and glucose intolerance.
dc:source: PMC2613584
database cross reference: HP:0000819
definition source: HP_0000819
description adapted from source: no
is caused by: Genetic predisposition, obesity, metabolic syndrome, inadequate diet, iron deposit in the pancreas.
is characterised by: Polyuria, polydipsia, polyphagia, unintentional weight loss, fatigue, weakness, lethargy, hyperglycemia,recurrent infections, skin and vulvar itching.

Diabetic Ketoacidosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Hydration
subclass of: Restriction
  on property: results_in
  some values from: Cerebral Edema
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A type of diabetic metabolic abnormality with an accumulation of ketone bodies.
abbreviation: DKA
curator note: Should this term not be below Diabetes Mellitus (DM)? And also included below DM below "Comorbid Disease"? Probably not caused by DM, as it is classified as a type of DM?
database cross reference: HP:0001953
definition source: HP_0001953
description adapted from source: no
is caused by: Diabetes Mellitus
is characterised by: Ketoacidosis and hyperglycemia.
hasExactSynonym: Diabetic Ketosis

Diagnostic Device
type: Class
subclass of: Diagnostics
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: A medical device used to diagnose medical conditions.
database cross reference: ERO:0001448
definition source: ERO_0001448
description adapted from source: no

Diagnostics
type: Class
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
creator: SCDO
description: Diagnostic tools (including the instruments, laboratory assays and methods of patient examination) used for differential diagnosis, the measurements obtained using these tools, and the diagnostic devices used in obtaining the measurements.

Diclofenac
type: Class
subclass of: Anti-Inflammatory Agent
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A non-steroidal anti-inflammatory agent (NSAID) with antipyretic and analgesic actions. It is primarily available as the sodium salt.
database cross reference: DB00586
definition source: DB00586
description adapted from source: no
hasExactSynonym: 2-((2,6-dichlorophenyl)amino)benzeneacetic acid
hasExactSynonym: Diclofenac Acid
hasExactSynonym: [2-(2,6-dichloroanilino)phenyl]acetic acid

Diet, Food, and Nutrition
type: Class
subclass of: Lifestyle
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Concepts involved with nutritional physiology, including categories of substances eaten for sustenance, nutritional phenomena and processes, eating patterns and habits, and measurable nutritional parameters.
curator note: Should this term rather be replaced by more specific terms such as Dietary Intake? Or have such terms as sub-classes?
database cross reference: MESH:D000066888
definition source: http://purl.bioontology.org/ontology/MESH/D000066888
description adapted from source: no
hasRelatedSynonym: Consommation
hasRelatedSynonym: Dietary Intake

Diffusion Capacity by Biochemical Methods
type: Class
subclass of: Diffusion Capacity Test
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Diffusion Capacity of Lung
type: Class
subclass of: Respiratory System Measurement
subclass of: Restriction
  on property: essential measure
  some values from: Body Height
subclass of: Restriction
  on property: essential measure
  some values from: Body Weight
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The amount of a gas taken up, by the pulmonary capillary blood from the alveolar gas, per minute per unit of average pressure of the gradient of the gas across the blood-air barrier.
abbreviation: DL
database cross reference: D011653
definition source: D011653
description adapted from source: Only label adapted
hasExactSynonym: Alveolar membrane diffusion capacity
hasExactSynonym: DL
hasExactSynonym: Diffusing Capacity
hasExactSynonym: Membrane diffusion capacity
hasExactSynonym: Pulmonary Diffusing Capacity

Diffusion Capacity Test
type: Class
subclass of: Pulmonary Function Test
subclass of: Restriction
  on property: has measurement
  some values from: Diffusion Capacity of Lung
subclass of: Restriction
  on property: essential measure
  some values from: Body Height
subclass of: Restriction
  on property: essential measure
  some values from: Body Weight
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Clinical assessment to determine the capacity of an individual’s lung to exchange gases (e.g., oxygen and carbon dioxide) across the alveolar-capillary interface.
dc:source: 03 Lung Function Diffusion Capacity.pdf
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Need to add more synonyms. Need to add equipment used for this test under "Devices" and link to them below.
database cross reference: PX810300
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has protocol: Single-breath carbon monoxide diffusing capacity (DLCO) PhenX protocol: Lung Function - Diffusion Capacity #810301
has_application_toward: Diffusion capacity is used to assess the structural and functional properties of the lung and can detect and quantify symptoms associated with conditions that impact the lung, such as sickle cell disease, cystic fibrosis, and obstructive airways disease.
hasExactSynonym: Lung Function - Diffusion Capacity

Disability-Adjusted Life Year (DALY)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Calculation: DALY = YLL + YLD - The YLL basically correspond to the number of deaths multiplied by the standard life expectancy at the age at which death occurs. The basic formula for YLL (without yet including other social preferences discussed below), is the following for a given cause, age and sex: YLL = N x L where: N = number of deaths L = standard life expectancy at age of death in years. Because YLL measure the incident stream of lost years of life due to deaths, an incidence perspective has also been taken for the calculation of YLD in the original Global Burden of Disease Study for year 1990 and in subsequent WHO updates for years 2000 to 2004. To estimate YLD for a particular cause in a particular time period, the number of incident cases in that period is multiplied by the average duration of the disease and a weight factor that reflects the severity of the disease on a scale from 0 (perfect health) to 1 (dead). The basic formula for YLD is the following (again, without applying social preferences): YLD = I x DW x L where: I = number of incident cases; DW = disability weight; L = average duration of the case until remission or death (years). Prevalence YLD - The recent GBD 2010 study published by IHME in December 2012 used an updated life expectancy standard for the calculation of YLL and based the YLD calculation on prevalence rather than incidence: YLD = P x DW where: P = number of prevalent cases; DW = disability weight.
abbreviation: DALY
curator note: Review description. Perhaps move some info to a comment? Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self; Proxy
has target population: All
selection criteria met: WHO Global Burden of Disease assessment, also used in SCD studies
validated for age ranges: Children and adults
freely available: no
hasExactSynonym: DALY

Disability-Adjusted Life Year (DALY) - removed - see Quality of Life and Care Measure
type: Class
subclass of: Health Utility
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete

Disaster
type: Class
subclass of: Physical Environment
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: Sudden calamitous events producing great material damage, loss, and distress. They are the result of natural phenomena such as earthquakes, floods, etc. Calamities producing great damage, loss of life, and distress. They include results of natural phenomena and man-made phenomena. Normal conditions of existence are disrupted and the level of impact exceeds the capacity of the hazard-affected community.
database cross reference: MESH:D004190
definition source: D004190
description adapted from source: no
hasExactSynonym: Disasters
hasExactSynonym: Natural Disaster
hasExactSynonym: Natural Disasters

Disease Modifier
type: Class
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
creator: SCDO
description: A biological or environmental factor that modifies one or more aspects of sickle cell disease (SCD) (such as temporal pattern, age of onset and mortality) for specific phenotype(s) in the Phenotype class.
curator note: These article contains a recent description of disease modifiers for SCD: http://www.nejm.org/doi/10.1056/NEJMra1510865 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4562292/ Paper mentioning haplotypes and severity: https://www.nature.com/scitable/topicpage/sickle-cell-anemia-a-look-at-global-8756219 Initially, the HP term "Clinical Modifier" (HP:0012823) was used to define this class, but its usage was found to be more "ontology-based" than what the SCDO intended.
hasExactSynonym: Phenotypic Modifier
comment: Temporal pattern is defined as "The speed at which disease manifestations appear and develop." (HPO)

Diuresis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Acute Kidney Injury
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Increased volume of urine produced and excreted.
curator note: Provide source for additional info.
database cross reference: MP:0001762
definition source: MP_0001762
description adapted from source: Only label adapted
is caused by: May be caused by an increaesed osmotic load (mannitol, glucose) in the urine or induced by medicaitons that prevent sodium resorption from the urine (diuretics).
is characterised by: Increase in urine volume.
hasExactSynonym: Increased Urine Output
hasExactSynonym: Increased Urine Volume
hasExactSynonym: Polyuria

Doppler Ultrasound Machine - 2 Megahertz
type: Class
subclass of: Ultrasound Machine
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Drug Clearance Decreased AE
type: Class
subclass of: Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An adverse event that has an outcome of a decreased amount of the drug excreted by the body.
database cross reference: OAE:0000887
definition source: OAE_0000887
description adapted from source: no

Drug Dependence AE
type: Class
subclass of: Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An adverse drug event that results in the development of a dependence on the drug.
database cross reference: OAE:0000888
definition source: OAE_0000888
description adapted from source: no

Drug Intake
type: Class
subclass of: Lifestyle
subclass of: Restriction
  on property: has curation status
  has value: uncurated
curator note: This seemed an obvious addition to the modifier class?

Drug Intolerance AE
type: Class
subclass of: Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A drug AE that has an outcome of lower threshold to the normal pharmacologic action of a drug.
database cross reference: OAE:0000891
definition source: OAE_0000891
description adapted from source: no

Drug Withdrawal Syndrome AE
type: Class
subclass of: Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An adverse event that results in symptoms that occur after the discontinuation of the use of a certain drug.
database cross reference: OAE:0000893
definition source: OAE_0000893
description adapted from source: no

Drug-Induced Neuropathy AE
type: Class
subclass of: Causal Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A neuropathy AE that is induced by a drug administration.
database cross reference: OAE:0000165
definition source: OAE_0000165
description adapted from source: no

Dysarthria
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Motor Aphasia
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Dysarthric speech is a general description referring to a neurological speech disorder characterized by poor articulation. Depending on the involved neurological structures, dysarthria may be further classified as spastic, flaccid, ataxic, hyperkinetic and hypokinetic, or mixed.
dc:source: HP_0001260
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info. Use description to add sub-classes of types of Dysarthria? Use text in comments to add relevant terms regarding disease progression? And link to these terms with results_in.
database cross reference: HP:0001260
description adapted from source: no
is caused by: In a person with dysarthria, a nerve, brain, or muscle disorder makes it difficult to use or control the muscles of the mouth, tongue, larynx, or vocal cords. The muscles may be weak or completely paralyzed. Or, it may be hard for the muscles to work together. Dysarthria may be the result of brain damage due to: brain injury, brain tumor, dementia, disease that causes the brain to lose its function (degenerative brain disease); multiple sclerosis ; parkinson disease; stroke. Dysarthria may result from damage to the nerves that supply the muscles that help you talk, or to the muscles themselves from: Face or neck trauma,Surgery for head and neck cancer, such as partial or total removal of the tongue or voice box;Dysarthria may be caused by diseases that affect nerves and muscles (neuromuscular diseases): Cerebral palsy;. Muscular dystrophy; Myasthenia gravis; Other causes may include: Alcohol intoxication; Poorly fitting dentures; Side effects of medications that act on the central nervous system, such as narcotics, phenytoin, or carbamazepine .
is characterised by: Depending on its cause, dysarthria may develop slowly or occur suddenly. People with dysarthria have trouble making certain sounds or words.Their speech is poorly pronounced (such as slurring), and the rhythm or speed of their speech changes. Other symptoms include: sounding as though they are mumbling; speaking softly or in a whisper; speaking in a nasal or stuffy, hoarse, strained, or breathy voice. A person with dysarthria may also drool and have problems chewing or swallowing. It may be difficult to move the lips, tongue, or jaw.
hasExactSynonym: Dysarthric Speech
comment: Depending on the cause of dysarthria, symptoms may improve, stay the same, or get worse slowly or quickly. Patients with amyotrophic lateral sclerosis (ALS or Lou Gehrig disease) eventually lose the ability to speak. Few people with Parkinson disease or multiple sclerosis lose the ability to speak. Dysarthria caused by medication or poorly fitting dentures can be reversed. Dysarthria caused by a stroke or brain injury will not get worse, and may improve. Dysarthria after surgery to the tongue or voice box should not get worse, and may improve with therapy.

Dyslipidemia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Healthy Diet
subclass of: Restriction
  on property: treated with
  some values from: Healthy Lifestyle
subclass of: Restriction
  on property: treated with
  some values from: Exercise
subclass of: Restriction
  on property: results_in
  some values from: Stroke
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Anomalous concentrations of fat-soluble substances (molecules composed of carbon and hydrogen and are characteristically insoluble in water) in the blood.
curator note: Provide source for additional info.
database cross reference: MP:0003949
definition source: MP_0003949
description adapted from source: no
is caused by: Primary (familial, Type I- V), acquired (secundary): diabetes mellitus, some drugs (thiazide diuretics, beta-blockers, estrogens), hypothyroidism, renal failure, nephrotic syndrome, alcohol consumption, endocrine disorders, metabolic disorders, diet, lifestyle, elevation of insulin levels, obesity, metabolic syndrome.
hasExactSynonym: Abnormal Circulating Lipid Level

Ear, Nose and Throat
type: Class
subclass of: from phenotype
description: The combined specialties of diseases of the ear, pharynx, and larynx, including the upper respiratory tract and diseases of the head and neck, tracheobronchial tree, and esophagus.
abbreviation: ENT
definition source: ear+nose+and+throat
description adapted from source: no
hasExactSynonym: Otolaryngology

Ecchymosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A small hemorrhagic spot, larger than a petechia, in the skin or mucous membrane forming a nonelevated, rounded or irregular, blue or purplish patch.
dc:source: HP_0000978
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000978
description adapted from source: yes
is caused by: Various underlying conditions that predispose to rupture of blood vessels and seeping of blood into the tissue e.g trauma, primary or secondary thrombocytopenia, infections.
is characterised by: Red, purple or black skin discolouration of an inch or more with or without pain, inflammation or spread to surrounding areas.
hasExactSynonym: Bruise Easily
hasExactSynonym: Easy Bruisability

ECG Abnormalities
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Abnormal electrical activity in the heart as indicated by an electrocardiogram (ECG).
dc:source: Overview1
database cross reference: OAE:0000909
definition source: OAE_0000909
description adapted from source: yes
is characterised by: There are many different aspects that fall under ECG abnormalities. Often people experience chest pain/discomfort difficulty breathing, heart palpitations, etc.
hasExactSynonym: EKG abnormalities
hasExactSynonym: Electrocardiogram Abnormalities
hasRelatedSynonym: Electrocardiogram Result Abnormal AE

Echocardiogram
type: Class
subclass of: Ultrasonography Test
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A physiological assay that uses standard ultrasound techniques to take two-dimensional pictures of the cardiovascular system and can produce accurate assessment of the velocity of blood and cardiac tissue at any arbitrary point using pulsed or continuous wave Doppler ultrasound.
dc:source: 003869.htm
database cross reference: ERO:0000385
definition source: ERO_0000385
description adapted from source: no
has_application_toward: This test is done to evaluate the valves and chambers of the heart from the outside of your body. The echocardiogram can help detect: Abnormal heart valves; Abnormal heart rhythms; Congenital heart disease; Damage to the heart muscle from a heart attack; Heart murmurs; Inflammation (pericarditis) or fluid in the sac around the heart (pericardial effusion); Infection on or around the heart valves (infectious endocarditis); Pulmonary hypertension; Ability of the heart to pump (for people with heart failure); Source of a blood clot after a stroke or a Transient ischemic attack.
hasExactSynonym: Cardiac ECHO
hasExactSynonym: Cardiac US Scan
hasExactSynonym: Diagnostic Ultrasound of Heart
hasExactSynonym: Echocardiographic procedure
hasExactSynonym: Echocardiography
hasExactSynonym: US Scan of Heart
hasExactSynonym: Ultrasonic cardiography
hasExactSynonym: Ultrasonography of Heart
hasExactSynonym: Ultrasound of Heart
comment: A normal echocardiogram reveals normal heart valves and chambers and normal heart wall movement.

Echocardiography Machine
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Heart Valve Function Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Ultrasonic recording of the size, motion, and composition of the heart and surrounding tissues. The standard approach is transthoracic.
dc:source: D004452
database cross reference: MESH:D004452
definition source: D004452
description adapted from source: no
hasExactSynonym: Cross Sectional Echocardiography

Eclampsia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Antihypertensive Agents
subclass of: Restriction
  on property: treated with
  some values from: Urine Measurement
subclass of: Restriction
  on property: results_in
  some values from: Coma
subclass of: Restriction
  on property: results_in
  some values from: Kidney Failure
subclass of: Restriction
  on property: results_in
  some values from: Preterm Delivery
subclass of: Restriction
  on property: results_in
  some values from: Seizure
subclass of: Restriction
  on property: results_in
  some values from: Stroke
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An acute and life-threatening complication of pregnancy, which is characterized by the appearance of tonic-clonic seizures, usually in a patient who had developed pre-eclampsia. Eclampsia includes seizures and coma that happen during pregnancy but are not due to preexisting or organic brain disorders.
dc:source: HP_0100601
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0100601
description adapted from source: no
is caused by: Abnormal development of placental vessels, low flow blood of the placental vessels.
is characterised by: High blood pressure, proteinuria, edema, seizures, it can causes headache, visual abnormalities, abdominal pain, nausea, vomiting.

Ectopic Pregnancy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Infection
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A fertilized egg attaches and begins development in a location other than in the inner lining of the uterus, most commonly in the Fallopian tube.
curator note: Provide source for additional info.
database cross reference: MP:0009668
definition source: MP_0009668
description adapted from source: no
is caused by: Infection, surgery, congenital anomalies, tumors, anatomic distortion of the tube that can be accompanied by functional impairment due to damaged ciliary activity, sterilization, previous genital infections, in-utero diethylstilbestrol (DES) exposure, intrauterine contraceptive devices.
is characterised by: Vaginal bleeding, abdominal pain in first trimester of pregnancy. Tubal rupture may cause life-threatening haemorrhage.

Education
type: Class
subclass of: Quality of Life
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Acquisition of knowledge as a result of instruction in a formal course of study.
database cross reference: MESH:D004493
definition source: D004493
description adapted from source: no
hasExactSynonym: Schooling
comment: Education may also take place outside the formal course of study. Sickle cell disease may impact negatively on education and consequently on the quality of life. (SCDO WG)

Electrocardiogram
type: Class
subclass of: Electrocardiograph
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The visual output that an electrocardiograph produces.
dc:source: http://bioportal.bioontology.org/ontologies/ERO
dc:source: http://bioportal.bioontology.org/ontologies/NCIT
definition source: electrocardiogram
has_application_toward: The graph can show that there are abnormal conditions, such as blocked arteries, changes in electrolytes (particles with electrical charges), and changes in the way electrical currents pass through the heart tissue.
hasBroadSynonym: Electrocardiography
hasExactSynonym: ECG
hasExactSynonym: EKG
hasRelatedSynonym: Arrhythmia
comment: It is a noninvasive recording produced by an electrocardiographic device.

Electrocardiographic Monitor
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Device which makes prolonged electrocardiographic recordings on a portable tape recorder (Holter-type system) or solid-state device ("real-time" system), while the patient undergoes normal daily activities; useful in the diagnosis and management of intermittent cardiac arrhythmias and transient myocardial ischemia.
dc:source: http://bioportal.bioontology.org/ontologies/CRISP/
definition source: http://bioportal.bioontology.org/ontologies/CRISP/
description adapted from source: no
has_application_toward: The diagnosis and management of intermittent cardiac arrhythmias and transient myocardial ischemia.
hasExactSynonym: Ambulatory Electrocardiographic Monitor
hasExactSynonym: Electrocardiocorder

Electrocardiography
type: Class
subclass of: Heart Function Test
subclass of: Restriction
  on property: has medical device
  some values from: Cardioscope
subclass of: Restriction
  on property: has medical device
  some values from: Electrocardiograph
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Recording of the moment-to-moment electromotive forces of the heart as projected onto various sites on the body's surface, delineated as a scalar function of time. The recording is monitored by a tracing on slow moving chart paper or by observing it on a cardioscope, which is a cathode ray tube display.
dc:source: ERO_0000383
database cross reference: ERO:0000383
definition source: http://bioportal.bioontology.org/ontologies/MESH/
description adapted from source: Only label adapted
hasExactSynonym: ECG
hasExactSynonym: EKG
comment: It is a noninvasive recording produced by an electrocardiographic device.
preferred label: Electrocardiography Assay

Electroencephalogram
type: Class
subclass of: Electroencephalograph
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A graphic record of the electrical activity of the brain as recorded by an electroencephalograph.
definition source: electroencephalogram
description adapted from source: no

Electroencephalograph
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An instrument that measures electrical potentials on the scalp and generates a record of the electrical activity of the brain.
definition source: electroencephalograph
description adapted from source: no
hasExactSynonym: Encephalograph

Electroencephalography
type: Class
subclass of: Cerebral Function Assay
subclass of: Restriction
  on property: has measurement
  some values from: Brain Electrical Activity
subclass of: Restriction
  on property: has medical device
  some values from: Electroencephalograph
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Recording of electric currents developed in the brain by means of electrodes applied to the scalp, to the surface of the brain, or placed within the substance of the brain.
database cross reference: D004569
definition source: D004569
description adapted from source: no
preferred label: Electroencephalography Assay

Electron Microscope
type: Class
subclass of: Microscope
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Electronic Health Records
type: Class
subclass of: Health Records
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Media that facilitate transportability of pertinent information concerning patient's illness across varied providers and geographic locations. Some versions include direct linkages to online consumer health information that is relevant to the health conditions and treatments related to a specific patient.
database cross reference: D057286
definition source: D057286
hasExactSynonym: Electronic Health Record
hasExactSynonym: Electronic Medical Record
hasExactSynonym: Electronic Medical Records

Electrophoresis
type: Class
subclass of: Chemical Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: An electrochemical process in which macromolecules or colloidal particles with a net electric charge migrate in a solution under the influence of an electric current.
dc:source: test
curator note: Perhaps change label to "Hemoglobin Electrophoresis"? Exactsynonym "Hb ELP". See dc:source provided.
database cross reference: D004586
definition source: D004586
description adapted from source: no

Elevated Hepatic Iron Concentration
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Hepatic Iron Concentration
subclass of: Restriction
  on property: diagnosed by
  some values from: Liver Biopsy
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: An increased level of iron in liver tissues.
dc:source: HP_0012465
database cross reference: HP:0012465
definition source: HP_0012465
description adapted from source: no
comment: This abnormality can be measured by liver biopsy or by hepatic magnetic resonance imaging.

EMG Abnormality
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A test that shows an abnormal result of the test of the muscles and the nerves that control the muscles.
dc:source: 003929.htm
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
description adapted from source: yes
is caused by: Disorders or conditions that cause abnormal results include the following:Alcoholic neuropathy; Amyotrophic lateral sclerosis (ALS); Axillary nerve dysfunction; Becker muscular dystrophy; Brachial plexopathy; Carpal tunnel syndrome; Cubital tunnel syndrome; Cervical spondylosis; Common peroneal nerve dysfunction; Denervation (reduced nerve stimulation of a muscle); Dermatomyositis; Distal median nerve dysfunction; Duchenne muscular dystrophy; Facioscapulohumeral muscular dystrophy (Landouzy-Dejerine); Familial periodic paralysis; Femoral nerve dysfunction; Friedreich ataxia; Guillain-Barre syndrome; Lambert-Eaton syndrome; Mononeuritis multiplex; Mononeuropathy; Myopathy (muscle degeneration caused by a number of disorders, including muscular dystrophy); Myasthenia gravis; Peripheral neuropathy; Polymyositis; Radial nerve dysfunction; Sciatic nerve dysfunction; Sensorimotor polyneuropathy; Shy-Drager syndrome; Thyrotoxic periodic paralysis.
hasExactSynonym: Abnormal Electromyography (EMG).

Encephalopathy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Electroencephalography
subclass of: Restriction
  on property: diagnosed by
  some values from: Imaging Assay
subclass of: Restriction
  on property: treated with
  some values from: Diet, Food, and Nutrition
subclass of: Restriction
  on property: treated with
  some values from: Renal Dialysis
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A term that means brain disease, damage, or malfunction. In general, it is manifested by an altered mental state.
dc:source: HP_0001298
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info. Specify which Blood Tests and Which Imaging Tests are used to diagnose.
database cross reference: HP:0001298
description adapted from source: yes
is caused by: Encephalopathy may be caused by infectious agent (bacteria, virus, or prion), metabolic or mitochondrial dysfunction, brain tumor or increased pressure in the skull, prolonged exposure to toxic elements (including solvents, drugs, radiation, paints, industrial chemicals, and certain metals), chronic progressive trauma, poor nutrition, or lack of oxygen or blood flow to the brain.
is characterised by: Depending on the type and severity of encephalopathy, common neurological symptoms are progressive loss of memory and cognitive ability, subtle personality changes, inability to concentrate, lethargy, and progressive loss of consciousness. Other neurological symptoms may include myoclonus (involuntary twitching of a muscle or group of muscles), nystagmus (rapid, involuntary eye movement), tremor, muscle atrophy and weakness, dementia, seizures, and loss of ability to swallow or speak.

End Stage Kidney Disease
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Glomerular Filtration Rate
subclass of: Restriction
  on property: diagnosed by
  some values from: Hyperkalemia
subclass of: Restriction
  on property: diagnosed by
  some values from: Serum Creatinine Level
subclass of: Restriction
  on property: treated with
  some values from: Renal Dialysis
subclass of: Restriction
  on property: treated with
  some values from: Renal Transplant
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A degree of kidney failure severe enough to require dialysis or kidney transplantation for survival characterized by a severe reduction in glomerular filtration rate (less than 15 ml/min/1.73 m2) and other manifestations including increased serum creatinine, greater than 3 months.
dc:source: HP_0003774
abbreviation: ESKD
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0003774
description adapted from source: yes
has age of onset: Variable.
is caused by: Final outcome of any form of kidney disease ; may be caused by diabetes, hypertension, glomerular disease, polycystic kidney disease, sickle cell disease, chronic toxic injury.
is characterised by: Elevated serum creatinine, uremia, acidosis, hyperkalemia, hyperphosphatemia, secondary hyperpararthyroidism, anemia, hypertension, fluid retention.
hasExactSynonym: ESKD
hasExactSynonym: End Stage Renal Disease
hasExactSynonym: End Stage Renal Disease (ESRD)

Endocrine and Metabolic
type: Class
subclass of: from phenotype
description: The system pertaining to the stomach, intestines, and associated organs including liver, gallbladder, and pancreas.
definition source: gastroenterology
description adapted from source: yes
hasExactSynonym: Gastroenterology

Endometriosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The growth of endometrial tissue outside the uterus.
curator note: Provide source for additional info.
database cross reference: HP:0030127
definition source: HP_0030127
description adapted from source: no
is caused by: The cause has not been definitively established
is characterised by: Pelvic pain, severe dysmenorrhea, dyspareunia and infertility, or it may be asymptomatic, and incidentally discovered at laparoscopy or exploratory surgery.

Endometritis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Infertility
subclass of: Restriction
  on property: results_in
  some values from: Sepsis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Local accumulation of fluid, plasma proteins, and leukocytes in the endometrium.
curator note: Provide source for additional info.
database cross reference: MP:0009360
definition source: MP_0009360
description adapted from source: Only label adapted
is caused by: Bacteria, mycoplasma, Neisseria gonorrhoeae, Chlamydia trachomatis, and herpes simplex virus and cytomegalovirus in HIV infected women, rarely clostridium sp, and streptococcal or staphylococcal toxic shock syndrome.
is characterised by: Fever, tachycardia that parallels the rise in temperature, midline lower abdominal pain, and uterine tenderness.
hasExactSynonym: Endometrial Inflammation
hasExactSynonym: Endometrium Inflammation

Enuresis
type: Class
subclass of: Phenotype
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Lack of the ability to control the urinary bladder leading to involuntary urination at an age where control of the bladder should already be possible.
database cross reference: HP:0000805
definition source: HP_0000805
description adapted from source: no
comment: Enuresis may affect children's social relationships (spending time with peers overnight) and cause embarrassment.

Environmental Disease Modifier
type: Class
subclass of: Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
creator: SCDO
description: An environmental factor that modifies one or more aspects of sickle cell disease (SCD) (such as temporal pattern, age of onset and mortality) for specific phenotype(s) in the Phenotype class.
curator note: Perhaps include MESH term "Life Change Events" as a main sub-class, with "Disaster" (under Physical Environment") copied below it?

Enzymatic Assay
type: Class
subclass of: Biochemical Assay
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: A method used to measure the relative activity of a specific enzyme or its concentration in solution. Typically an enzyme substrate is added to a buffer solution containing enzyme and the rate of conversion of substrate to product is measured under controlled conditions.
database cross reference: D057075
definition source: D057075
description adapted from source: yes
comment: Many classical enzymatic assay methods involve the use of synthetic colorimetric substrates and measuring the reaction rates using a spectrophotometer. Sensitive detection methods use enzymes to indirectly measure substances that would normally be difficult to quantitate.

Epidemiologic Studies
type: Class
subclass of: Study Design
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Studies designed to examine associations, commonly, hypothesized causal relations. They are usually concerned with identifying or measuring the effects of risk factors or exposures. The common types of analytic study are case-control studies; cohort studies; and cross-sectional studies.
curator note: Term to be adapted as necessary to match EDDA Study Designs Taxonomy
definition source: D016021

Epidemiologic Study Characteristics as Topic
type: Class
subclass of: Research Activity
description: Types and formulations of studies used in epidemiological and clinical research.
curator note: Term to be adapted as necessary to match EDDA Study Designs Taxonomy
database cross reference: MESH:D016020
definition source: D016020
description adapted from source: no
hasExactSynonym: Epidemiologic Study Characteristics
preferred label: Epidemiologic Study Characteristic

Epigenetic Disorder
type: Class
subclass of: Genetic Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence.
database cross reference: OGMS:0000046
definition source: OGMS_0000046
description adapted from source: no
hasExactSynonym: Epigenomic Disorder

Epilepsy Screener
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A questionnaire to assess epilepsy, a condition characterized by recurrent seizures and which is a component of over 40 neurological disorders (Aminoff, et al., 2005).
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX130400
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Epilepsy Screener #130401
has respondents: Self
has_application_toward: This measure is used to screen people for the presence of epilepsy. Epilepsy can be caused by genetics or environmental factors such as pesticides (Meisler and Kearney, 2005). People with epilepsy are more likely to also suffer from migraines, depression, anxiety, attention-deficit/hyperactivity disorder and autism (Pliplys et al, 2007, Levinsohn, 2007).
validated for age ranges: Adult, aged 18 or older

General Health Questionnaire (GHQ)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The GHQ is a screening device for identifying minor psychiatric disorders in the general population and within community or non-psychiatric clinical settings such as primary care or general medical outpatients. Suitable for all ages from adolescent upwards (not children), it assesses the respondent’s current state and asks if that differs from his or her usual state. It is therefore sensitive to short-term psychiatric disorders but not to long-standing attributes of the respondent. The self-administered questionnaire focuses on two major areas: inability to carry out normal functions; appearance of new and distressing phenomena. It is available in the following versions: GHQ-60 – the fully detailed 60-item questionnaire; GHQ-30 – a short form without items relating to physical illness; GHQ-28 – a 28 item scaled version – assesses somatic symptoms, anxiety and insomnia, social dysfunction and severe depression; GHQ-12 – quick, reliable and sensitive short form, ideal for research studies.
abbreviation: GHQ
definition source: Goldberg, David; Hillier, Valerie (1979). "A scaled version of the General Health Questionnaire". Psychological Medicine. Cambridge University Press. 9 (01): 139–145.
description adapted from source: yes

Generalised Anxiety Disorder Questionnaire (GAD-7)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The GAD-7 is a self-administered patient questionnaire used as a screening tool and severity measure for generalised anxiety disorder. The GAD-7 score is calculated by assigning scores of 0, 1, 2, and 3, to the response categories of 'not at all', 'several days', 'more than half the days', and 'nearly every day', respectively, and adding together the scores for the seven questions. Scores of 5, 10, and 15 are taken as the cut-off points for mild, moderate and severe anxiety, respectively. When used as a screening tool, further evaluation is recommended when the score is 10 or greater.
dc:source: Spitzer RL, Kroenke K, Williams JB, et al; A brief measure for assessing generalized anxiety disorder: the GAD-7. Archives of Internal Medicine. 2006;166(10):1092-7.
abbreviation: GAD-7
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has respondents: Patient Reported Outcome
has target population: Clinic Patients
has translations: Numerous
selection criteria met: Widely used around the world, also used in SCD
validated for age ranges: Adults 18 years and older
freely available: no
hasExactSynonym: GAD-7
hasExactSynonym: Generalised Anxiety Disorder Questionnaire

Genetic Counseling
type: Class
subclass of: Genetic Service
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An educational process that provides information and advice to individuals or families about a genetic condition that may affect them. The purpose is to help individuals make informed decisions about marriage, reproduction, and other health management issues based on information about the genetic disease, the available diagnostic tests, and management programs. Psychosocial support is usually offered.
database cross reference: MESH:D005817
definition source: D005817
hasExactSynonym: Prenatal Genetic Counseling

Genetic Disease Modifier
type: Class
subclass of: Biological Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
creator: SCDO
description: A biological disease modifier that is of a genetic nature.

Genetic Disorder
type: Class
subclass of: Genetic Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome.
database cross reference: OGMS:0000047
definition source: OGMS_0000047
description adapted from source: no

Genetic Screening
type: Class
subclass of: Genetic Testing
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Testing to determine if there is a predisposition or indication of a possible genetic or a chromosomal abnormality.
database cross reference: NCIT:C92803
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no

Genetic Service
type: Class
subclass of: Preventative Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Organized services to provide diagnosis, treatment, and prevention of genetic disorders.
database cross reference: MESH:D033142
definition source: D033142
description adapted from source: no
hasExactSynonym: Genetic Services

Genetic Technique
type: Class
subclass of: Diagnostic Technique, Method, Test or Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.
curator note: This and its sub-classes need work!
database cross reference: MESH:D005821
definition source: D005821
description adapted from source: no
hasExactSynonym: Genetic Technic
hasExactSynonym: Genetic Technics
hasExactSynonym: Genetic Techniques

Genetic Testing
type: Class
subclass of: Genetic Technique
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The process of isolating and testing the DNA of an embryo or a person to detect the presence of genetic alterations or defects that may predispose to the future development of a disease or disorder.
curator note: What about the overlap of this term with "Genetic Testing" in Therapeutics? Note: "Genetic Test" is a SNOMED CT term.
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: Only label adapted
hasExactSynonym: Genetic Analysis
hasExactSynonym: Genetic Examination
hasExactSynonym: Genetic Test

Genome Wide Association Study
type: Class
subclass of: Genetic Technique
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Genome wide association study is a kind of study whose objective is to detect association between genetic markers (SNP or otherwise) accross the genome and a trait which may be a disease or another phenotype (e.g. trait of agronomic relevance in animal or plant studies). Genome wide association study compare the allele frequencies in 2 populations, one free of the trait used as control, the other one showing the trait use as 'case'. GWAS studies implement case-control design.
database cross reference: STATO:0000091
definition source: STATO_0000091
description adapted from source: no
hasExactSynonym: GWAS

Geographic Location
type: Class
subclass of: Physical Environment
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A reference to a place on the Earth, by its name or by its geographical location.
database cross reference: GAZ:00000448
definition source: GAZ_00000448
description adapted from source: no
hasBroadSynonym: Geography
hasExactSynonym: Geographic Region
hasRelatedSynonym: Geographical Variables

Gingival Bleeding
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Hemorrhage affecting the gingiva.
database cross reference: HP:0000225
definition source: HP_0000225
description adapted from source: no
hasExactSynonym: Bleeding Gums
hasExactSynonym: Gingival Hemorrhage

Glaucoma (Secondary to Presence of Blood in the Anterior Chamber of the Eye)
type: Class
subclass of: Ophthalmologic Complication
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: diagnosed by
  some values from: Retinal Examination
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Blindness
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Elevated ocular pressure caused by clogging of the trabecular meshwork and by impaired aqueous humor outflow from blood in the anterior chamber (due to ocular trauma or surgery).
dc:source: Ballas et al 2010 Am J Hematol
dc:source: Mowatt et al 2010 Eur J Ophthalmol
database cross reference: EFO:0000516
definition source: Ballas et al 2010 Am J Hematol
description adapted from source: no
is caused by: Often follows trauma, which may be minimal, or surgery.
is characterised by: Raised intraocular pressure.
hasExactSynonym: Glaucomas
comment: Diagnostic Criteria: Measurement of intraocular pressure. Glaucoma is present if intraocular pressure exceeds 24 mmHg for any consecutive 24-hour period, when measured every six hours.
preferred label: Glaucoma

Global Mental Status Screener
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A test to assess the respondent's overall mental capability.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX130700
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Global Mental Status Screener - Adult #130701
has protocol: PhenX protocol: Global Mental Status Screener - Child #130702
has_application_toward: This measure quickly screens a variety of cognitive domains to determine a respondent's general mental status. It can be used to detect impaired mental status caused by a variety of conditions including head injury, stroke, infections, brain tumors, developmental defects and neurodegenerative disorders such as Alzheimer's disease.

Globin Loci
type: Class
subclass of: Modifier Gene
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A superfamily of proteins containing the globin fold which is composed of 6-8 alpha helices arranged in a characteristic heme enclosing structure.
database cross reference: MESH:D005914
definition source: OGMS_0000046
description adapted from source: no

Glomerular Filtration Rate
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Measurement of the flow rate of filtered fluid through the kidney, calculated either by comparative measurements of substances in the blood and urine, or estimated from a blood test.
database cross reference: EF:0005208
definition source: EFO_0005208
description adapted from source: no
has protocol: Cockcroft-Gault Calculator (or Equation), MDRD GFR Calculator, CKD-EPI Creatinine Calculator (or Equation)
hasExactSynonym: GFR

Glomerulonephritis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Hematuria
subclass of: Restriction
  on property: diagnosed by
  some values from: Proteinuria
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: End Stage Kidney Disease
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Inflammatory lesion of the glomerulus that may result in proteinuria and/or hematuria and progressive renal injury.
dc:source: HP_0000099
abbreviation: GN
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
description adapted from source: yes
has age of onset: May occur at any age.
has disease stage: no
is caused by: Variety of causes - in sickle cell disease, most common lesion is focal segmental glomerulosclerosis (FSGS) but also reported Membranoproliferative glomerulonephritis and other forms of glomerulonephritis.
is characterised by: Patients with hematuria may have dark-colored urine. Glomerulonephritis may lead to the proteinuria and "foamy" appearance of the urine. If the latter is substantial, patients may develop clinically evident edema.
hasExactSynonym: Glomerular Nephritis

Glomerulopathy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Nonspecific term referring to any disease, inflammatory or noninflammatory, affecting the glomeruli of the nephron.
database cross reference: HP:0100820
definition source: HP_0100820
description adapted from source: yes
hasExactSynonym: Glomerulopathies

Glomerulosclerosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Scarring and fibrosis within the glomerulus.
dc:source: HP_0000096
dc:source: NHLBI 2014 Guidelines
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000096
description adapted from source: yes
is caused by: Any form of injury to the kidney can lead to glomerulosclerosis.
is characterised by: Histologically noted by scarring and fibrosis in the glomerulus.
hasExactSynonym: Glomerular Sclerosis

Glucose-6-Phosphate Dehydrogenase
type: Class
subclass of: Non-Globin Loci
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: This gene encodes glucose-6-phosphate dehydrogenase.
abbreviation: G6PD
definition source: http://www.ncbi.nlm.nih.gov/gene/2539
description adapted from source: yes
hasExactSynonym: G-6-PD
comment: Official Full Name: glucose-6-phosphate dehydrogenase; Gene ID: 2539; Chromosome: X; Position: 154531390..154547586 (GRCh38.p2); Variants
preferred label: G6PD

Granulomatosis
type: Class
subclass of: Infection
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Any disease characterized by the formation of numerous granulomas.
curator note: Source needed for additional information.
database cross reference: HP:0002955
definition source: HP_0002955
description adapted from source: yes
has disease stage: Allergic (Churg-strauss syndrome), eosinophilic (langerhan cell histiocytosis), langerhans (langerhan cell histiocytosis), lymphomatoid, siderotica, wegeners.
is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation.
is characterised by: Predominant multisystemic involvement.

Growth Delay
type: Class
subclass of: Phenotype
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: treated with
  some values from: Cognitive Therapy
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A deficiency or slowing down of growth pre- and postnatally greater than two standard deviations from the age- and sex-related normal.
dc:source: 003021.htm
curator note: This term replaced "Delayed Growth" in QoL.
database cross reference: HP:0001510
definition source: HP_0001510
description adapted from source: yes
is caused by: Genetic background, intrauterine disease, malnutrition, chronic illness, drugs, hormone disorders, neurologic disorders, emotional deprivation.
is characterised by: Short stature or weight, low development.
hasExactSynonym: Delayed Growth
hasExactSynonym: Growth Deficiency
hasExactSynonym: Growth Failure
hasExactSynonym: Growth Retardation
hasExactSynonym: Poor Growth
hasExactSynonym: Retarded Growth
hasRelatedSynonym: Very Poor Growth
comment: Poor or abnormally slow height or weight gain in a child younger than age 5.

Haptoglobin Blood Test
type: Class
subclass of: Blood Test
subclass of: Restriction
  on property: has measurement
  some values from: Haptoglobin Level
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A bioassay to measure haptoglobin, which is produced by the liver and transports hemoglobin to the liver for recycling.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX10800
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has protocol: PhenX protocol: Haptoglobin Level #810801
has recommended procedure: The PhenX protocol provides instructions for drawing, processing, and storing blood according to the National Health and Nutrition Examination Survey (NHANES) methods. Because there are many comparable assays for measuring haptoglobin, the protocol also provides basic guidelines to aid comparability among different studies.
has_application_toward: Low levels of haptoglobin are an indirect marker of hemolysis and anemia.

Haptoglobin Level
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Haptoglobin Blood Test
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A quantifictaion of blood haptoglobin.
dc:source: http://bioportal.bioontology.org/ontologies/EFO
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: efo:EFO_0004640
definition source: http://bioportal.bioontology.org/ontologies/EFO
description adapted from source: Label and description adapted
has_application_toward: Used as in the diagnosis of tranfusion reaction and haemolytic anaemia. Low levels of haptoglobin are an indirect marker of hemolysis and anemia.
hasExactSynonym: Haptoglobin Levels
hasExactSynonym: Haptoglobin Measurement

Health Behaviour
type: Class
subclass of: Environmental Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The actions taken by an individual to maintain, attain, and protect their good health. Health behavior reflects a person's health beliefs.
curator note: Include: gaining better control of your diabetes lowering cholesterol lowering blood pressure maintaining a healthy body weight eating a balanced diet Perhaps this description should be changed to include behaviour that isn't necessarily positive? Such as that given by the Psychology Ontology? Then include these from MESH: - Treatment Refusal - Vaccination Refusal Initially, this description was used for the MeSH term (D015438): "Behaviors expressed by individuals to protect, maintain or promote their health status. For example, proper diet, and appropriate exercise are activities perceived to influence health status. Life style is closely associated with health behavior and factors influencing life style are socioeconomic, educational, and cultural." But this description seems to have changed and no longer refers to the same thing. Now it is: "Combination of HEALTH KNOWLEDGE, ATTITUDES, PRACTICE which underlie actions taken by individuals regarding their health."
database cross reference: NCIT:C16663
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no

Health Beliefs
type: Class
subclass of: Culture
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: People's beliefs about health problems, perceived benefits of action and barriers to action, and self-efficacy explain engagement (or lack of engagement) in health-promoting behaviour.
dc:source: From the Health-Belief Model

Health Financing
type: Class
subclass of: Health System
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Health financing is concerned with how financial resources are generated, allocated and used in health systems. Health financing policy focuses on how to move closer to universal coverage with issues related to: (i) how and from where to raise sufficient funds for health; (ii) how to overcome financial barriers that exclude many poor from accessing health services; or (iii) how to provide an equitable and efficient mix of health services.
definition source: en
description adapted from source: no
hasExactSynonym: Health Care Costs
hasExactSynonym: Health Care Resources
hasExactSynonym: Healthcare Costs
hasExactSynonym: Healthcare Resources

Health Insurance Coverage
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Whether the respondent is covered by health insurance or some other form of health care coverage at the time of the interview.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Include below QoL? The protocol seems to be somewhat U.S. specific. Is it fine to use or is there one more relevant to the African setting?
database cross reference: PX11500
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has_application_toward: Individuals who do not have health insurance do not visit health care providers on a regular basis or for preventive testing (e.g., prostate examination) and may be more vulnerable to illness or disease. Usually, individuals who do not have health insurance are those who cannot afford to pay the insurance premiums and are not eligible for government programs (e.g., immigrants).

Health Literacy
type: Class
subclass of: Coping Skill
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Degree to which individuals have the capacity to obtain, process and understand basic health information and services needed to make appropriate health decisions.
database cross reference: MESH:D057220
definition source: D057220
description adapted from source: no
hasExactSynonym: Knowledge about Sickle Cell Disease
hasNarrowSynonym: Genetic Counseling
comment: See also: Genetic Counseling

Health Records
type: Class
subclass of: Medical Records
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Health data accessible to the patient and others. Longitudinal patient-maintained records of individual health history and tools that allow individual control of access.
database cross reference: MESH:D055991
definition source: D055991
description adapted from source: no
hasExactSynonym: Health Records, Personal
hasExactSynonym: Personal Health Information
hasExactSynonym: Personal Health Record
hasExactSynonym: Personal Health Records
hasExactSynonym: Personal Medical Record
hasExactSynonym: Personal Medical Records

Health Service Utilization
type: Class
subclass of: Quality of Health Care
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The measure of the population's use of the health care services available to them. This includes the utilization of Hospital resources, Personal Care Home (PCH) resources, and physician resources. Health care utilization and health status are used to examine how efficiently a health care system produces health in a population.
dc:source: http://mchp-appserv.cpe.umanitoba.ca/viewDefinition.php
description adapted from source: Only label adapted
hasExactSynonym: Health Care Utitlization
hasExactSynonym: Healthcare Utitlization
comment: (Patient/provider relationship; communication (including respect, courtesy); stigma: special issues related to pain and pain medications; adherence with medications and treatments (provider responsible to educate and support patient/family; provider adherence with guidelines and best practices). (Stigma; prejudice; barriers). (Stigma; prejudice; barriers)

Health System
type: Class
subclass of: Quality of Health Care
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A system responsible for delivering services that improve, maintain or restore the health of individuals and their communities. This includes the care provided by hospitals and family doctors, but also less visible tasks such as the prevention and control of communicable disease, health promotion, health workforce planning and improving the social, economic or environmental conditions in which people live.
curator note: Perhaps this should be separate from Quality of Health Care?
definition source: health-systems
description adapted from source: yes
hasExactSynonym: Health Care Delivery
hasExactSynonym: Health Care Systems
hasExactSynonym: Healthcare Delivery

Health Utility
type: Class
subclass of: Quality of Health Care
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Utility measures of health related quality of life are preference values that patients attach to their overall health status. In clinical trials, utility measures summarize both positive and negative effects of an intervention into one value between 0 (equal to death) and 1 (equal to perfect health). These measures allow for comparison of patient outcomes of different diseases, and for comparison between various health care interventions. There are 2 different approaches to utility measurement.
definition source: http://www.ncbi.nlm.nih.gov/pubmed/7674256
description adapted from source: no
hasExactSynonym: Health Utility Index
comment: Health states are defined and then value placed upon those health states.

Healthcare Access
type: Class
subclass of: Quality of Health Care
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Access to health care refers to the ease with which an individual can obtain needed medical services. The WHO Constitution enshrines "...the highest attainable standard of health as a fundamental right of every human being." The right to health includes access to timely, acceptable, and affordable health care of appropriate quality.
dc:source: health-care-access.html
dc:source: en
curator note: Check which source was used to obtain the description and change it's property to "description source". Additional WG note: organization of health system [insurance]; electronic (portable) health records; special issues related to pain and pain medications; levels of care (primary, secondary, tertiary) (Location – [rural/urban; mobile units]; hours; affordability; timeliness). Availability of personnel. Equipment treatments other resources
description adapted from source: yes
hasExactSynonym: Access to Healthcare
hasExactSynonym: Health Care Access

Healthy Diet
type: Class
subclass of: Healthy Lifestyle
subclass of: Lifestyle Therapy
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Dietary patterns which have been found to be important in reducing disease risk.
database cross reference: MESH:D000072001
definition source: http://purl.bioontology.org/ontology/MESH/D000072001
description adapted from source: no
hasExactSynonym: Healthy Eating

Healthy Lifestyle
type: Class
subclass of: Health Behaviour
subclass of: Lifestyle
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A pattern of behavior involving lifestyle choices which ensure optimum health. Examples are eating right; maintaining physical, emotional, and spiritual wellness, and taking preemptive steps against communicable diseases.
database cross reference: MESH:D000070497
definition source: http://purl.bioontology.org/ontology/MESH/D000070497
description adapted from source: no
hasExactSynonym: Healthy Life Style

Heart Contraction Pressure
type: Class
subclass of: Cardiovascular Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Pressure exerted by the heart muscle in its maximally contracted state.
database cross reference: CMO:0000665
definition source: CMO_0000665
description adapted from source: no

Heart Function Test
type: Class
subclass of: Physiological Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Examinations used to diagnose and treat heart conditions.
database cross reference: D006334
definition source: D006334
description adapted from source: Only label adapted
hasExactSynonym: Heart Function Tests
hasExactSynonym: Pulmonary Function Test

Heart Rate
type: Class
subclass of: Cardiovascular Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The number of times the heart ventricles contract per unit of time, usually per minute.
dc:source: 003399.htm
database cross reference: EFO:0004326
definition source: EFO_0004326
description adapted from source: no
has recommended procedure: The pulse can be measured at areas where an artery passes close to the skin. These areas include the: back of the knees; groin; neck; temple; top or inner side of the foot; wrist. To measure the pulse at the wrist, place the index and middle finger over the underside of the opposite wrist, below the base of the thumb. Press with flat fingers until you feel the pulse. To measure the pulse on the neck, place the index and middle fingers just to the side of the Adam's apple, in the soft, hollow area. Press gently until you locate the pulse. Note: Sit or lie down before taking the neck pulse. The neck arteries in some people are sensitive to pressure. Fainting or slowing of the heartbeat can result. Also, do not take the pulses on both sides of the neck at the same time. Doing so can slow the flow of blood to the head and lead to fainting. Once you find the pulse, count the beats for 1 full minute. Or count the beats for 30 seconds and multiply by 2. This will give the beats per minute.
has_application_toward: Measuring the pulse gives important information about your health. Any change from your normal heart rate can indicate a health problem. Fast pulse may signal an infection or dehydration. In emergency situations, the pulse rate can help determine if the patient's heart is pumping. Pulse measurement has other uses as well. During or immediately after exercise, the pulse rate gives information about your fitness level and health.
hasBroadSynonym: Cardiac Chronotropy
hasExactSynonym: Heart Beat
hasExactSynonym: Pulse
hasExactSynonym: Pulse Rate
comment: Normal results for resting heart rate: Newborns 0 to 1 month old: 70 to 190 beats per minute; Infants 1 to 11 months old: 80 to 160 beats per minute; Children 1 to 2 years old: 80 to 130 beats per minute; Children 3 to 4 years old: 80 to 120 beats per minute; Children 5 to 6 years old: 75 to 115 beats per minute; Children 7 to 9 years old: 70 to 110 beats per minute; Children 10 years and older, and adults (including seniors): 60 to 100 beats per minute; Well-trained athletes: 40 to 60 beats per minute. Abnormal results: Resting heart rates that are continually high (tachycardia) may mean a problem. Resting heart rates that are below the normal values (bradycardia) may also mean a problem. A pulse that is very firm (bounding pulse) and that lasts for more than a few minutes, or an irregular pulse can also indicate a problem. A pulse that is hard to locate may mean blockages in the artery. These blockages are common in people with diabetes or hardening of the artery from high cholesterol. A Doppler study may be ordered to check the blockages.

Heart Valve Function Measure
type: Class
subclass of: Heart Function Test
subclass of: Restriction
  on property: has medical device
  some values from: Echocardiography Machine
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Echocardiogram
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Measure to assess the structure and function of the heart valves.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX40500
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Heart Valve Function #040501
has_application_toward: To determine the function of the heart valves in order to assess risk factors for stenosis or insufficiency of the mitral, aortic, pulmonary or tricuspid valves of the heart.

Hematocrit
type: Class
subclass of: Red Blood Cell Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Percentage of total blood volume that is made up of red blood cells.
abbreviation: Hct
database cross reference: CMO:0000037
definition source: CMO_0000037
description adapted from source: no
hasExactSynonym: Hct
hasExactSynonym: Packed Cell Volume
hasExactSynonym: Packed Red Blood Cell Volume

Hematology Analyzer
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has measurement
  some values from: Complete Blood Count
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: A measurement device used to perform complete blood counts, erythrocyte sedimentation rates (ESRs), or coagulation tests.
database cross reference: ERO:0000494
definition source: ERO_0000494
description adapted from source: no
hasExactSynonym: Haematology Analyser

Hematology Screening Test
type: Class
subclass of: Blood Test
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
curator note: In SNOMED CT
hasExactSynonym: Haematology Screening Test

Hematopoietic Stem Cell Transplantation
type: Class
subclass of: Curative Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Transfer of hematopoietic stem cells from bone marrow or blood between individuals within the same species (transplantation, homologous) or transfer within the same individual (transplantation, autologous). Hematopoietic stem cell transplantation has been used as an alternative to bone marrow transplantation in the treatment of a variety of neoplasms.
dc:source: sickle-cell-disease-report.pdf
database cross reference: MESH:D018380
definition source: D018380
description adapted from source: no
hasExactSynonym: BMT
hasExactSynonym: Bone Marrow Transplant
hasRelatedSynonym: Bone Marrow Transplantation
comment: Hematopoietic stem cell transplantation (HSCT) is a treatment option for an increasing but still small number of people with SCD. The procedure involves “conditioning” therapy, utilizing myelosuppressive and/or immune-modifying drugs, followed by infusion of histocompatible stem cells (derived from bone marrow, peripheral blood, or umbilical cord blood). Substantial risks are involved with the procedure, and it is not yet feasible in the majority of people with SCD. Although clinical trials have provided promising results, and cure appears to be possible in a large proportion of patients receiving HSCT, additional research is still needed that addresses the potential risks of this therapy (e.g., failure of engraftment and chronic graft-versus-host disease) before HSCT can become a widely used therapy.

Hematopoietic System
type: Class
subclass of: Hemic and Immune Systems
description: The blood-making organs and tissues, principally the bone marrow and lymph nodes.
database cross reference: MESH:D006413
definition source: D006413
description adapted from source: no
hasRelatedSynonym: Hematology

Hematuria
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Presence of blood in the urine.
curator note: Perhaps move this out from below "Nephrology"?
database cross reference: MeSH:D006417
definition source: D006417
description adapted from source: no
hasExactSynonym: Blood in Urine

Heme Oxygenase 1
type: Class
subclass of: Non-Globin Loci
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: This gene encodes the enzyme, heme oxygenase 1, an essential enzyme in heme catabolism.
abbreviation: HMOX1
abbreviation: HO1
definition source: http://www.ncbi.nlm.nih.gov/gene/3162
description adapted from source: yes
hasExactSynonym: HO1
hasExactSynonym: Haemoxygenase 1
hasExactSynonym: Hemeoxygenase 1
hasExactSynonym: Hemoxygenase-1
comment: Official Full Name: heme oxygenase 1; Gene ID: 3162; Chromosome: 22; Position: 35381067..35394214 (GRCh38.p2); Variants
preferred label: HMOX1

Hemic and Immune Systems
type: Class
subclass of: from phenotype
description: Organs involved in the production of BLOOD, including the cellular and the molecular components essential in providing defense against foreign organisms or substances.

Hemochromatosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: caused by
  some values from: Blood Transfusion
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A metal metabolism disorder characterized by the accumulation of iron in various organs of the body.
database cross reference: DOID:2352
definition source: DOID 2352
description adapted from source: no
hasExactSynonym: Diabetes Bronze
hasExactSynonym: Haemochromatosis
hasExactSynonym: Iron Overload
hasExactSynonym: Iron Storage Disorder

Hemoglobin C
type: Class
subclass of: Abnormal Hemoglobin Structure Present in SCD
subclass of: Restriction
  on property: phenotype of
  some values from: Hemoglobin C Disease
subclass of: Restriction
  on property: phenotype of
  some values from: Hemoglobin C Trait
subclass of: Restriction
  on property: phenotype of
  some values from: Sickle Cell Disease-SC
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6LYS
subclass of: Restriction
  on property: has curation status
  has value: accepted by SCDO WG (WS2)
description: An abnormal hemoglobin in which lysine replace a glutamic acid residue at the sixth position of beta chains.
dc:source: uk-HbC.pdf
database cross reference: MESH:D006444
definition source: D006444
description adapted from source: yes
has disease stage: Mild
hasExactSynonym: Hb C
hasExactSynonym: HbC

Hemoglobin S
type: Class
subclass of: Abnormal Hemoglobin Structure Present in SCD
subclass of: Restriction
  on property: phenotype of
  some values from: Sickle Cell Disease-SS
subclass of: Restriction
  on property: phenotype of
  some values from: Sickle Cell Disease Variant
subclass of: Restriction
  on property: phenotype of
  some values from: Sickle Cell Trait
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has curation status
  has value: accepted by SCDO WG (WS2)
description: An abnormal hemoglobin resulting from the substitution of valine for glutamic at position 6 of the beta globin.
dc:source: HP_0045047
database cross reference: HP:0045047
database cross reference: MESH:D006451
definition source: D006451
definition source: HP_0045047
description adapted from source: yes
hasExactSynonym: Hb S
hasExactSynonym: HbS
hasExactSynonym: Sickle Hemoglobin
comment: HbS can be identified by multiple methodologies including hemoglobin electrophoresis and high-performance liquid chromatography.
comment: The heterozygous state results in sickle cell trait, the homozygous in sickle cell anemia.

Hemoglobin H
type: Class
subclass of: Gene Product
subclass of: Restriction
  on property: phenotype of
  some values from: Hemoglobin H Disease
subclass of: Restriction
  on property: has curation status
  has value: accepted by SCDO WG (WS2)
description: An abnormal hemoglobin composed of four beta chains. It is caused by the reduced synthesis of the alpha chain. This abnormality results in alpha-thalassemia.
database cross reference: HP:0011903
database cross reference: MESH:D006447
definition source: D006447
definition source: HP_0011903
description adapted from source: no
hasExactSynonym: Hb H
hasExactSynonym: HbH

Hemoglobin A2 Profile
type: Class
subclass of: Hemoglobin Profile Assay
subclass of: Restriction
  on property: has curation status
  has value: uncurated
curator note: Is this term necessary?

Hemoglobin Bart's
type: Class
subclass of: from phenotype
subclass of: Restriction
  on property: phenotype of
  some values from: Hemoglobin Bart Syndrome
subclass of: Restriction
  on property: has curation status
  has value: accepted by SCDO WG (WS2)
description: An abnormal hemoglobin composed of four gamma globin.
database cross reference: HP:0005507
definition source: HP_0005507
description adapted from source: yes
hasExactSynonym: Hb Bart's
hasExactSynonym: Hemoglobin Bart's

Hemoglobin Bart Syndrome
type: Class
subclass of: Alpha Thalassemia
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin Bart's
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Is a tetramer with four gamma globin chains, and is essentially pathognomonic for one or another form of alpha thalassemia. Hb Barts has an extremely high affinity for oxygen, resulting in almost no oxygen delivery to the tissues.
database cross reference: HP:0005507
definition source: HP_0005507
description adapted from source: no
hasExactSynonym: Hb Bart
hasExactSynonym: Hb Bart syndrome
hasExactSynonym: Hemoglobin Bart
hasExactSynonym: Hemoglobin Bart Hydrops Fetalis Syndrome

Hemoglobin C Disease
type: Class
subclass of: Hemoglobinopathy Occuring in Heterozygous State in Sickle Cell Disease Variants
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin C
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An autosomal recessive hemoglobinopathy characterized by an abnormal form of hemoglobin called hemoglobin C, which disrupts the oxygen-carrying ability of red blood cells. This condition has a mild clinical course, with most patients being asymptomatic. When symptoms appear, they include mild to moderate hemolytic anemia, splenomegaly, and occasionally jaundice.
dc:source: 200853-overview
abbreviation: Hb C
database cross reference: NCIT:C34675
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
definition source: Hb-F-C
description adapted from source: yes
hasExactSynonym: Hb C-disease
comment: Affected gene: HBB gene (with an autosomal recessive pattern of inheritance) Affected protein: Hemoglobin subunit beta (UniProt Number: P68871)
comment: Originated on the west coast of Africa. Hb C is found in diverse populations in Africa, southern Europe, and South and Central America, though its exact allelic distribution across these varied populations remains unclear.

Hemoglobin C Trait
type: Class
subclass of: Hemoglobin Trait
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin C
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The inheritance of the gene for hemoglobin C from one parent and a gene for normal adult hemoglobin (hemoglobin A) form the other parent.
abbreviation: Hb AC
definition source: haemoglobinc.aspx
description adapted from source: yes
hasExactSynonym: Haemoglobin C-A Disorder
hasExactSynonym: Hemoglobin C-A Disorder
hasExactSynonym: Heterozygous for Hb C
hasRelatedSynonym: Hb C-Carrier
hasRelatedSynonym: Hemoglobin C-Carrier

Hemoglobin C-Beta-Thalassemia
type: Class
subclass of: Compound Heterozygous Hemoglobinopathy
subclass of: Restriction
  on property: has phenotype
  some values from: Beta Thalassemia
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Hemoglobin C
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A form of beta-thalassemia in which the patient is compound heterozygous for hemoglobin C and beta-thalassemia, resulting in moderate hemolytic anemia.
dc:source: Hb-F-C-A
dc:source: http://www.orpha.net/consor/cgi-bin/OC_Exp.php
abbreviation: HbC - BT
curator note: The description could be more detailed.
definition source: http://www.orpha.net/consor/cgi-bin/OC_Exp.php
description adapted from source: yes
hasExactSynonym: Hb C-Beta Thalassemia Syndrome
hasExactSynonym: Hemoglobin C Beta-Thalassemia
comment: Prevalence of this form is not known but it is predominant in African populations.

Hemoglobin Characterization
type: Class
subclass of: Blood Test
subclass of: Restriction
  on property: essential measure
  some values from: Complete Blood Count
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: History of Transfusion
subclass of: Restriction
  on property: essential measure
  some values from: Medication Inventory
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A test to measure the variants of hemoglobin that cause sickle cell disease.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Many terms below this term in SNOMED CT should be added.
database cross reference: PX830300
definition source: http://bioportal.bioontology.org/ontologies/NCIT
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Hemoglobin Characterization #830301
has_application_toward: This PhenX protocol can be used to identify and characterize the different variants in structure and synthesis of hemoglobin that cause sickle cell disease.
hasExactSynonym: Haemoglobin Variant Observation
hasExactSynonym: Haemoglobin Variant Test
hasExactSynonym: Haemoglobinopathy Screen
hasExactSynonym: Hemoglobin Variant Observation
hasExactSynonym: Hemoglobin Variant Test
hasExactSynonym: Hemoglobinopathy Screen

Hemoglobin Concentration
type: Class
subclass of: Hemoglobin Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The amount of hemoglobin, the red oxygen-carrying pigment of erythrocytes, in a specified volume of blood, as calculated from the optical density of a solution of lysed red cells in which hemoglobin has been converted to cyanomethemoglobin and measured with a spectrophotometer.
dc:source: CMO_0000506
dc:source: 003645.htm
database cross reference: CMO:0000506
description adapted from source: no
has_application_toward: The hemoglobin test is a commonly ordered blood test and is almost always done as part of a complete blood count (CBC). Common reasons or conditions for ordering the hemoglobin test include:Symptoms such as fatigue, feelings of poor health, or unexplained weight loss; Signs of bleeding are present; Before and after major surgery; During pregnancy; Presence of chronic kidney disease or many other chronic medical problems; Monitoring of anemia and its cause; Monitoring during treatment for cancer; Monitoring medicines that may cause anemia or low blood counts.
hasExactSynonym: Hemoglobin level
hasExactSynonym: hemoglobin absorbance
comment: The reference ranges for hemoglobin concentration in adults are as follows: Men: 14.0-17.5 (mean 15.7) g/dL; Women: 12.3-15.3 (mean 13.8) g/dL The reference ranges for hemoglobin concentration in children are as follows: Birth: mean 16.5 g/dL (-2SD: 13.5 g/dL); 1-3 days: mean 18.5 g/dL (-2SD: 14.5 g/dL); 1 week: mean 17.5 g/dL (-2SD: 13.5 g/dL); 2 weeks: mean 16.5 g/dL (-2SD: 12.5 g/dL); 1 month: mean 14.0 g/dL (-2SD: 10.0 g/dL); 2 months: mean 11.5 g/dL (-2SD: 9.0 g/dL); 3-6 months: mean 11.5 g/dL (-2SD: 9.5 g/dL); 0.5-2 years: mean 12.0 g/dL (-2SD: 11.0 g/dL); 2-6 years: mean 12.5 g/dL (-2SD: 11.5 g/dL); 6-12 years: mean 13.5 g/dL (-2SD: 11.5 g/dL); 12-18 years female: mean 14.0 g/dL (-2SD: 12.0 g/dL); 12-18 years male: mean 14.5 g/dL (-2SD: 13.0 g/dL)

Hemoglobin D Disease
type: Class
subclass of: Hemoglobinopathy Occuring in Heterozygous State in Sickle Cell Disease Variants
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin D
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An autosomal recessive hemoglobinopathy characterized by an abnormal form of hemoglobin called hemoglobin D, which disrupts the oxygen-carrying ability of red blood cells.
dc:source: FactSheet Provider HbDD En.pdf
dc:source: HbDFactSheet.pdf
definition source: HbDFactSheet.pdf
description adapted from source: yes
hasExactSynonym: Hb DD
comment: Affected gene: HBB gene (with an autosomal recessive pattern of inheritance) Affected protein: Hemoglobin subunit beta (UniProt Number: P68871)
comment: Hemoglobin D is the fourth most common hemoglobin variant, which developed as a response to the selective pressure of malaria. It is most often found in people living in India, Pakistan, England, Ireland, Holland, Australia, China, Iran, Turkey and their descendants. However, they are also found in people of European descent, especially British and Irish. Homozygous Hb DD is rare and a relatively mild disease. Heterozygous Hb D/β-thal is more common and more serious.
comment: It is most often found in people living in India, Pakistan, England, Ireland, Holland, Australia, China, Iran, Turkey and their descendants.

Hemoglobin D Trait
type: Class
subclass of: Hemoglobin Trait
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin D
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The inheritance of the gene for hemoglobin D from one parent and a gene for normal adult hemoglobin (hemoglobin A) form the other parent.
definition source: HbDFactSheet.pdf
description adapted from source: yes
hasExactSynonym: Hb AD
hasRelatedSynonym: Hb D-Carrier
hasRelatedSynonym: Hemoglobin D-Carrier

Hemoglobin D-Beta Thalassemia
type: Class
subclass of: Compound Heterozygous Hemoglobinopathy
subclass of: Restriction
  on property: has phenotype
  some values from: Beta Thalassemia
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Hemoglobin D
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A form of beta-thalassemia in which the patient is compound heterozygous for hemoglobin D and beta-thalassemia, which results in a mild to moderate clinical presentation, depending upon the degree of thalassemia affecting the hemoglobin A gene.
description: A form of beta-thalassemia in which the patient is compound heterozygous for hemoglobin D and beta-thalassemia, which results in a mild to moderate presentation of.
definition source: HbDFactSheet.pdf
description adapted from source: yes
is caused by: This condition is caused by mutations in the HBB gene. One copy of the gene has a mutation leading to an abnormal form of hemoglobin known as hemoglobin D.
hasExactSynonym: HbD - BT
hasExactSynonym: Hemoglobin D Beta-Thalassemia
comment: A mild hemolytic anemia usually develops in the first few months of life as the amount of fetal hemoglobin decreases and hemoglobin D increases. Splenomegaly and other complications can occur but in general it is considered a fairly benign condition. Also, because the red blood cell indices are abnormal in hemoglobin D/B thalassemia, iron deficiency, if suspected, may need to be assessed more directly through serum iron levels, iron binding capacity, and percent saturation.

Hemoglobin D-Ibadan
type: Class
subclass of: from phenotype
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin D
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A variant of Hemoglobin D Disease (Hb D) that substitutes lysine for the normal threonine at codon 7 of the B-chain.
dc:source: http://www.ncbi.nlm.nih.gov/pubmed/12144055
abbreviation: Hb D-Ibadan
definition source: FactSheet Provider HbDD En.pdf
description adapted from source: yes
comment: Hb D-Ibadan [beta87(F3)Thr-->Lys] is a common variant in the Nigerian population

Hemoglobin D-Punjab
type: Class
subclass of: Abnormal Hemoglobin Structure Present in SCD
subclass of: Restriction
  on property: phenotype of
  some values from: Sickle Cell Disease-S/D-Punjab
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU121GLN
subclass of: Restriction
  on property: has curation status
  has value: accepted by SCDO WG (WS2)
description: Abnormal hemoglobin in which glutamine replaces glutamic acid at codon 121 of beta globin.
dc:source: Hemoglobin D-Punjab
dc:source: Abnormal haemoglobins
dc:source: PMC4382585
abbreviation: Hb D-Punjab
definition source: FactSheet Provider HbDD En.pdf
description adapted from source: yes
hasExactSynonym: Hb D-Los Angelese
hasExactSynonym: Hemoglobin D (Chicago)
hasExactSynonym: Hemoglobin D (Los Angeles)
hasExactSynonym: Hemoglobin D (North Carolina)
hasExactSynonym: Hemoglobin D (Portugal)
hasExactSynonym: Hemoglobin D (Punjab)
hasExactSynonym: Hemoglobin Oak Ridge
comment: Hemoglobin D-Punjab is harmless alone, even in homozygous state, but is the only Hb of the “D family” which leads to a severe form of sickle cell disease when associated with Hb S.
comment: Is a rare variant often observed in populations from Northwestern India but also found in many individuals from Balkan region, Turkey, North and West Africa.

Hemoglobin Disease Other than C,D,E,F,H,O-Arab,S
type: Class
subclass of: from phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
subclass of: Restriction
  on property: has curation status
  has value: example likely to be removed
definition source: Hb-F-and-other-than-A-C-D-E-F-H-O-Arab-S
description adapted from source: yes

Hemoglobin E Disease
type: Class
subclass of: Hemoglobinopathy Occuring in Heterozygous State in Sickle Cell Disease Variants
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin E
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An autosomal recessive hemoglobinopathy characterized by an abnormal form of hemoglobin called hemoglobin E, which disrupts the oxygen-carrying ability of red blood cells. The condition has no or mild clinical manifestations (hemolytic anemia).
dc:source: Bachir, D; Galacteros, F (November 2004), Hemoglobin E disease. Orphanet Encyclopedia, retrieved January 13, 2014.
definition source: Hb-F-E
definition source: http://www.orpha.net/consor/cgi-bin/OC_Exp.php
description adapted from source: yes
hasExactSynonym: Hb E-Disease
comment: Affected gene: HBB gene (with an autosomal recessive pattern of inheritance) Affected protein: Hemoglobin subunit beta (UniProt Number: P68871)
comment: Hemoglobin E is most prevalent in Southeast Asia (Thailand, Myanmar, Cambodia, Laos, Vietnam).

Hemoglobin E Trait
type: Class
subclass of: Hemoglobin Trait
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin E
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The inheritance of the gene for hemoglobin E from one parent and a gene for normal adult hemoglobin (hemoglobin A) form the other parent.
definition source: Hb-F-A-E
description adapted from source: yes
hasExactSynonym: Hb AE
hasExactSynonym: Hb E Trait
hasRelatedSynonym: Hb E-carrier

Hemoglobin E-Beta Thalassemia
type: Class
subclass of: Compound Heterozygous Hemoglobinopathy
subclass of: Restriction
  on property: has phenotype
  some values from: Beta Thalassemia
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Hemoglobin E
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A form of beta-thalassemia in which the patient is compound heterozygous for hemoglobin E and beta-thalassemia, which results in a mild to severe clinical presentation ranging from a condition indistinguishable from beta-thalassemia major to a mild form of beta-thalassemia intermedia.
dc:source: Hb-F-E-A
dc:source: http://www.orpha.net/consor/cgi-bin/Disease_Search.php
abbreviation: HbE - BT
definition source: http://www.orpha.net/consor/cgi-bin/Disease_Search.php
description adapted from source: yes
hasExactSynonym: Hemoglobin E Beta-Thalassemia
comment: Prevalence of this form is not known but HbE - beta-thalassemia is predominant in Southeast Asia.

Hemoglobin F Profile
type: Class
subclass of: Hemoglobin Profile Assay
subclass of: Restriction
  on property: has curation status
  has value: uncurated
curator note: Is this term necessary?

Hemoglobin H Disease
type: Class
subclass of: Alpha Thalassemia
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin H
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A form of alpha thalassemia that results from reduced protein production from three of the four alpha-globin genes. Clinically it is characterized by chronic hemolytic anemia.
dc:source: Hb-F-H
dc:source: http://www.orpha.net/consor/cgi-bin/OC_Exp.php
abbreviation: HbH Disease
database cross reference: NCIT:C95504
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Alpha-Thalassemia Intermedia
hasExactSynonym: Hb H-disease
comment: Affected gene: HBA1 gene HBA2 gene Affected protein: Hemoglobin subunit alpha 1 (UniProt Number: P69905) Hemoglobin subunit alpha 2 (UniProt Number: P69905)
comment: Patients have variable microcytic hypochromic hemolytic anemia, splenomegaly (50 to 80%) and less commonly hepatomegaly (50%), mild jaundice (20-40%), and mild-to-moderate beta-thalassemia major (see this term)-like skeletal changes mainly affecting the face (30%). Hypersplenism and gallstones are also found, as well as acute episodes of hemolysis in response to oxidant drugs and infections. Hydrops fetalis (see this term) is present in very rare cases. Iron overload is common in older patients, even in the absence of transfusion, and is attributed to iron hyperabsorption. Growth retardation has been reported in children. (orpha.net; 10/2017)
comment: Predominantly seen in Southeast Asia, the Middle East and the Mediterranean. (orpha.net; 10/2017)
comment: The severity of the disease is related to its molecular basis: patients with non-deletional types of HbH disease, such as Constant Spring mutation, are more severely affected than those with the common deletional types. (orpha.net; 10/2017)

Hemoglobin Lepore Baltimore
type: Class
subclass of: from phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A variant of Hemoglobin Lepore Syndrome.
dc:source: Hemoglobin Lepore syndrome
definition source: Hemoglobin Lepore syndrome
description adapted from source: yes
hasExactSynonym: Hb Lepore Baltimore
comment: Most common in people from the Balkan countries, Albanians Croats, Serbs, Slovenes and Romanians. It has also been described in Turks and in regions of Spain and Portugal. A rare case of the Baltimore variety was discovered in an African American woman in the Bronx, New York and dubbed Hn Lepore-Bronx and another variety was discovered in the city of Saskatoon, Saskatchewan, Canada and dubbed Hb E-Lepore Saskatoon.

Hemoglobin Lepore Boston Disease
type: Class
subclass of: Hemoglobin Lepore Syndrome
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A variant of Hemoglobin Lepore Syndrome. This is the only one of the three variants described in association with HbS.
dc:source: Hemoglobin Lepore syndrome
definition source: Hemoglobin Lepore syndrome
description adapted from source: yes
hasExactSynonym: Hb Lepore Boston Syndrome
hasExactSynonym: Hb Lepore Washington Syndrome
hasExactSynonym: Hb Lepore Washington-Boston Syndrome
hasExactSynonym: Hemoglobin Lepore Washington Syndrome
hasExactSynonym: Hemoglobin Lepore Washington-Boston Syndrome
comment: Most common in Italians from Southern Italy.

Hemoglobin Lepore Hollandia
type: Class
subclass of: from phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A variant of Hemoglobin Lepore Syndrome.
dc:source: Hemoglobin Lepore syndrome
definition source: Hemoglobin Lepore syndrome
hasExactSynonym: Hb Hollandia
comment: Was identified in Papua New Guinea and Bangladesh.

Hemoglobin Lepore Syndrome
type: Class
subclass of: Delta Beta Thalassaemia
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A rare autosomal recessive hemoglobinopathy, caused by the presence of two deltabeta globin fusion chains, which occurs due to a "crossover" between the delta (HBD) and beta globin (HBB) gene loci during meiosis.
dc:source: http://ltd.aruplab.com/Tests/Pdf/252
definition source: Hemoglobin Lepore syndrome
description adapted from source: yes
hasExactSynonym: Hb Lepore
hasExactSynonym: Hb Lepore Syndrome
hasExactSynonym: Homozygous Hb Lepore
hasExactSynonym: Homozygous Hemoglobin Lepore

Hemoglobin Lepore Trait
type: Class
subclass of: Hemoglobin Trait Other than C,D,E,S,O-Arab
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The inheritance of the gene for hemoglobin Lepore from one parent and a gene for normal adult hemoglobin (hemoglobin A) form the other parent.
dc:source: Hemoglobin Lepore syndrome
dc:source: haemoglobin-lepore
definition source: Hemoglobin Lepore syndrome
description adapted from source: yes
hasExactSynonym: Heterozygous Hb Lepore
comment: Individuals heterozygous for the Hb Lepore request no particular treatment. There is no anemia or, if there is, it is very mild. ("Hemoglobin Lepore syndrome", Wikipeadia, 01/2017)
comment: People heterozygous for haemoglobin Lepore (Hb ALepore) have no symptoms and a normal life expectancy. At the examination of their blood, one can see that the red blood cells are smaller and paler. It should be distinguished from an iron deficiency. (Enerca, 01/2017)

Hemoglobin Lepore-Beta Thalassaemia
type: Class
subclass of: Compound Heterozygous Hemoglobinopathy
subclass of: Restriction
  on property: has phenotype
  some values from: Beta Thalassemia
subclass of: Restriction
  on property: treated with
  some values from: Blood Transfusion
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A form of beta-thalassemia in which the patient is compound heterozygous for hemoglobin lepore and beta-thalassemia, which results in beta-thalassemia intermedia to beta-thalassemia major.
dc:source: Epidemiology
dc:source: hemoglobin lepore beta thalassemia syndrome
curator note: Add HBD to Disease Modifiers (below Gene Product)? And link to it.
description adapted from source: yes
hasExactSynonym: Hb Lepore-B-Thalassaemia
hasExactSynonym: Hemoglobin Lepore-B-Thalassaemia
hasExactSynonym: Hemoglobin Lepore-Beta Thalassaemia Syndrome
comment: An important gene associated with Hemoglobin Lepore-Beta-Thalassemia Syndrome is HBD (Hemoglobin Subunit Delta),
comment: The Hb Lepore trait has a worldwide distribution and may affect individuals of various ethnicities however the three main varieties which been defined tend to be more prevalent among specific ethnic groups, typically Caucasians of the Southern regions Central and Eastern Europe.
comment: Transfusion therapy might be required.

Hemoglobin M Disease
type: Class
subclass of: Hereditary Methemoglobinemia
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin M
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Hemoglobin M Disease is a blood disorder in which an abnormal amount of methemoglobin is produced.
dc:source: http://www.orpha.net/consor/cgi-bin/Disease_Search.php
curator note: This seems to be a type of "Hereditary Methemoglobinemia", so should perhaps be added below that term?
definition source: 000562.htm
description adapted from source: no
hasBroadSynonym: Congenital Methemoglobinemia
hasExactSynonym: M Hemoglobinopathy
hasExactSynonym: Methemoglobinemia
hasRelatedSynonym: Blue Baby Syndrome
comment: Autosomal dominant inheritance.

Hemoglobin M Trait
type: Class
subclass of: Hemoglobin Trait Other than C,D,E,S,O-Arab
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A group of abnormal hemoglobins in which amino acid substitutions take place in either the alpha or beta chains but near the heme iron. This results in facilitated oxidation of the hemoglobin to yield excess methemoglobin which leads to cyanosis.
database cross reference: MESH:D006449
definition source: D006449
description adapted from source: no

Hemoglobin Measurement
type: Class
subclass of: Blood Cell Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A measure of the oxygen carrying pigment of erythrocytes.
database cross reference: CMO:0000508
definition source: CMO_0000508
description adapted from source: no

Hemoglobin O-Arab Disease
type: Class
subclass of: Hemoglobinopathy Occuring in Heterozygous State in Sickle Cell Disease Variants
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin O-Arab
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A very rare autosomal recessive hemoglobinopathy characterized by an abnormal form of hemoglobin called hemoglobin O-Arab.
dc:source: http://onlinelibrary.wiley.com/doi/10.1002/pbc.24414/pdf
definition source: http://onlinelibrary.wiley.com/doi/10.1002/pbc.24414/pdf
description adapted from source: yes
hasExactSynonym: Hb O-Arab
hasExactSynonym: Homozygous Hb O-Arab
hasExactSynonym: Homozygous Hemoglobin O-Arab
comment: Affected gene: HBB gene (with an autosomal recessive pattern of inheritance) Affected protein: Hemoglobin subunit beta (UniProt Number: P68871) Amino acid substitution: 121 Glu --> Lys
comment: Found in people from the Balkans, the Middle East, and Africa.
comment: Mostly found in people from the Balkans, the Middle East, and Africa.

Hemoglobin O-Arab Trait
type: Class
subclass of: Hemoglobin Trait
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The inheritance of hemoglobin O-Arab from one parent and a gene for normal adult hemoglobin (hemoglobin A) form the other parent.
dc:source: http://onlinelibrary.wiley.com/doi/10.1002/pbc.24414/pdf
definition source: http://onlinelibrary.wiley.com/doi/10.1002/pbc.24414/pdf
description adapted from source: yes
hasExactSynonym: Hb A/O-Arab
hasExactSynonym: Heterozygous Hb O-Arab
hasExactSynonym: Heterozygous Hemoglobin O-Arab
comment: Patients with this trait will not suffer from associated health problems except for minor anemia and microcytosis.

Hemoglobin Profile
type: Class
subclass of: Hemoglobin Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Hemoglobin Profile Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The type and relative amounts of various normal and abnormal hemoglobin types.
definition source: test
description adapted from source: yes

Hemoglobin Profile Assay
type: Class
subclass of: Molecular Profiling Assay
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Electrophoresis
subclass of: Restriction
  on property: has diagnostic tool
  some values from: High-Performance Liquid Chromatography
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A bioassay for hemoglobin classification.
dc:source: http://www.phenxtoolkit.org/index.php
dc:source: hemoglobinopathy-fractionation-profile-blood-test.html
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Hemoglobin Characterization #830301
has_application_toward: The PhenX protocol provided here can be used to identify and characterize the different variants in structure and synthesis of hemoglobin that cause sickle cell disease.
hasExactSynonym: Hb Electrophoresis Plus Solubility
hasExactSynonym: Hemoglobin Characterization
hasExactSynonym: Hemoglobin Electrophoresis
hasExactSynonym: Hemoglobin Electrophoresis plus Solubility
hasExactSynonym: Hemoglobin Fractionation
hasExactSynonym: Hemoglobinopathy Evaluation Profile Blood Test
hasExactSynonym: Hemoglobinopathy Fractionation Profile Blood Test
preferred label: Hemoglobin Profiling

Hemoglobin S Test
type: Class
subclass of: Hemoglobin Characterization
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
curator note: In SNOMED CT this term is "Sickle cell identification"
hasExactSynonym: Sickle cell identification

Sickle Cell Disease-SS
type: Class
subclass of: Sickle Cell Disease
subclass of: Restriction
  on property: has clinical code
  some values from: D57.0 Hb-SS disease with crisis
subclass of: Restriction
  on property: has clinical code
  some values from: D57.1 Sickle-cell disease without crisis
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin S
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A disease characterized by chronic hemolytic anemia, episodic painful crises, and pathologic involvement of many organs. It is the clinical expression of homozygosity for hemoglobin S.
dc:source: Hb-F-S
abbreviation: SCD-SS
database cross reference: MESH:D000755
definition source: D000755
description adapted from source: no
hasExactSynonym: Hb SS Disease
hasExactSynonym: Hb SS-Disease
hasExactSynonym: Hemoglobin SS Disease
hasExactSynonym: Homozygous Sickle Cell Disease
hasExactSynonym: SS and S/Beta-Zero Thalassemia
hasExactSynonym: Severe SCD
hasExactSynonym: Sickle Cell Anemia
hasExactSynonym: Sickle Cell Disease
hasExactSynonym: Sickle Cell Disease SS
hasExactSynonym: Sickle Cell Hemoglobin S Disease
comment: Affected gene: HBB gene (with an autosomal recessive pattern of inheritance) Affected protein: Hemoglobin subunit beta (UniProt Number: P68871)

Hemoglobin Trait
type: Class
subclass of: Hemoglobinopathy
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A condition in which a person is heterozygous for a globin gene, with one normal allele and one defective allele.
database cross reference: NCIT:C95534
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: yes
hasExactSynonym: Heterozygous Hemoglobinopathy

Hemoglobin Trait Other than C,D,E,S,O-Arab
type: Class
subclass of: Hemoglobin Trait
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The inheritance of some normal hemoglobin (hemoglobin FA) and some abnormal hemoglobin other than hemoglobin C,D,E,S or O-Arab.
definition source: Hb-F-A-and-other-than-C-D-E-S-O-Arab
description adapted from source: yes

Hemoglobinopathy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An inherited disorder characterized by structural alterations of a globin chain within the hemoglobin molecule.
dc:source: simple-facts-about-sickle-cell
curator note: Hemoglobin-disorders-newborn-screen-interpretation
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: yes
comment: Sickle cell diseases include inheritance of the gene for sickle hemoglobin from one parent and one of the following: A gene for sickle hemoglobin from the other parent (Hb SS), A gene for another abnormal hemoglobin from the other parent (Hb SC, HbSD Punjab, HbSO Arab, HbS Leopore, or Hb SE), A gene that limits hemoglobin production from the other parent (sickle beta +/0 thalassemia). In S beta (+) thalassemia there is some production of beta globin, and in S beta (0) thalassemia there is no production of beta globin.

Hemoglobinopathy Toms River
type: Class
subclass of: from phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://www.orpha.net/consor/cgi-bin/Disease_Search.php
hasExactSynonym: Transient neonatal cyanosis
hasExactSynonym: anemia due to Toms River Hemoglobin
comment: Hemoglobinopathy Toms River, is also known as transient neonatal cyanosis and anemia due to toms river hemoglobin An important gene associated with Hemoglobinopathy Toms River is HBG2 (Hemoglobin Subunit Gamma 2).

Hemoglobinuria
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Test
subclass of: Restriction
  on property: treated with
  some values from: Supportive Therapeutics
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Acute Kidney Injury
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The presence of free hemoglobin in the urine.
dc:source: HP_0003641
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0003641
description adapted from source: no
is caused by: Presence of free hemoglobin in the urine, typically seen in setting of significant hemolysis.
is characterised by: Discoloration of the urine without blood cells noted in the urine.
hasExactSynonym: Increased Urine Hemoglobin Level

Hepatic Iron Concentration
type: Class
subclass of: Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Liver Biopsy
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A measurement of the concentration of iron in the liver as an estimate of body iron load.
dc:source: liver-iron-concentration-LIC
database cross reference: NCIT:C124065
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no
hasExactSynonym: Hepatic Iron
hasExactSynonym: Liver Iron
hasExactSynonym: Liver Iron Concentration

Hepatic Span
type: Class
subclass of: Body Morphological Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Palpation of Liver
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Percussion of Liver
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
subclass of: Restriction
  on property: has curation status
  has value: to be replaced with external ontology term
description: The distance between the lower border of the liver in the mid-clavicular line, and the upper border of the liver in the mid-clavicular line.
curator note: The description needs to be reviewed by an expert. Also possibly request inclusion into Clinical Measurement Ontology, below "liver size measurement".
definition source: Liver span
description adapted from source: yes
hasExactSynonym: Liver Span

Hepatitis B Test
type: Class
subclass of: Immunochemical Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A test for Hepatitis B Virus.
curator note: Which Hepatitis B Test is to be referred to here? (There are various different types below "Immunology Test" in the "Sage Bionetworks Synapse Ontology")

Hepatitis C Test
type: Class
subclass of: Immunochemical Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A test for Hepatitis C Virus.
curator note: Is this test for viral load measurement or or antibody measurement? (See terms below "Immunology Test" in the "Sage Bionetworks Synapse Ontology")

Hereditary Methemoglobinemia
type: Class
subclass of: Methemoglobinemia
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Hereditary methemoglobinemia (HM) is a rare red cell disorder classified principally into two clinical phenotypes: autosomal recessive congenital (or hereditary) methemoglobinemia types I and II (RCM/RHM type 1; RCM/RHM type 2).
dc:source: http://www.orpha.net/consor/cgi-bin/Disease_Search.php
dc:source: Francois. A case of congenital cyanosis without an apparent cause. Bull Acad Roy Med Belg 1845; 4:698.
definition source: http://www.orpha.net/consor/cgi-bin/Disease_Search.php
description adapted from source: no
hasExactSynonym: Congenital Methemoglobinemia
comment: The first case of congenital methemoglobinemia was probably reported by Francois in 1845 when he described one of his patients with chronic congenital cyanosis without obvious cardiac or pulmonary disease .

Hereditary Persistence of Fetal Hemoglobin
type: Class
subclass of: Hemoglobinopathy Occuring in Heterozygous State in Sickle Cell Disease Variants
subclass of: Restriction
  on property: has phenotype
  some values from: Increased Hemoglobin F
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, 106-KB DEL
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Hereditary persistence of fetal hemoglobin (HPFH, BrE: Hereditary persistence of foetal haemoglobin) is a benign condition in which significant fetal hemoglobin (hemoglobin F) production continues well into adulthood, disregarding the normal shutoff point after which only adult-type hemoglobin should be produced.
dc:source: 261.full.pdf
abbreviation: HPFH
definition source: Hereditary persistence of fetal hemoglobin
description adapted from source: no
hasExactSynonym: HPFH
comment: It was first discovered in Nigeria. Hereditary persistence of fetal hemoglobin has been encountered in Negroes in Uganda, Jamaica, United States, and in a single Caucasian family in Greece.

High-Performance Liquid Chromatography
type: Class
subclass of: Chemical Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small particles and the inlet pressure is relatively high.
dc:source: test
abbreviation: HPLC
curator note: Perhaps change label to "Hemoglobin by High Performance Liquid Chromatography"? Exactsynonym "HPLC". See dc:source provided.
definition source: CHMO_0001009
description adapted from source: no
has_application_toward: Used to measure percentage of globin in the blood.
hasExactSynonym: HPLC
hasExactSynonym: High Performance Liquid Chromatography
hasExactSynonym: High Pressure Liquid Chromatography
hasExactSynonym: High-Pressure Liquid Chromatography

Hip Replacement Arthroplasty
type: Class
subclass of: Supportive Therapeutics
subclass of: Symptomatic Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Replacement of the hip joint.
database cross reference: MESH:D019644
definition source: D019644
description adapted from source: no
hasExactSynonym: Hip Prosthesis Implantation
hasExactSynonym: Hip Replacement Arthroplasty
hasExactSynonym: Hip Replacements, Total
hasExactSynonym: Replacement Arthroplasties, Hip
hasExactSynonym: Total Hip Replacement

Historically Controlled Study
type: Class
subclass of: Epidemiologic Studies
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A study that compares a group of participants receiving an intervention with a similar group from the past who did not.
database cross reference: MESH:D065386
definition source: D065386

History of Head Trauma
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A questionnaire to determine whether an individual has had a traumatic brain injury (TBI).
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX130600
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: History of Head Trauma #130601
has respondents: Self
has_application_toward: This measure is used to screen an individual for a past traumatic brain injury. Traumatic brain injury can lead to a variety of psychiatric, cognitive, and physical problems.
validated for age ranges: Adult, aged 18 or older

History of Kidney Failure
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: essential measure
  some values from: Blood Pressure Measurement
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: History of Type I and Type 2 Diabetes
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A questionnaire to determine if the respondent has a history of kidney failure.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Link to? Kidney Failure Personal Attribute---> Personal medical history
database cross reference: PX140600
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has protocol: PhenX protocol: Personal History of Kidney Failure #140601
has_application_toward: The risk of developing kidney disease is correlated with family history of kidney disease as well as several conditions (e.g., hypertension) and diseases (e.g., diabetes).

History of Stroke - Ischemic Infarction and Hemorrhage
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A questionnaire to determine if the respondent has had an ischemic infarction (i.e. stroke) and/or any symptoms related to this event.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX130300
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: History of Stroke - Ischemic Infarction and Hemorrhage #130301
has respondents: Self
has_application_toward: This measure is used to determine whether an individual has had a stroke and to assess the associated complications. Stroke, a loss of brain function due to disrupted blood flow, is the most common debilitating neurological condition in the United States and is the third leading cause of death. Stroke etiology is influenced both by genetic and environmental factors and risk factors include increasing age, systolic blood pressure, diabetes, atrial fibrillation, male gender, smoking and cardiovascular disease (Aminoff et al., 2005, Wolf et al., 1991).
validated for age ranges: Adult, aged 18 or older

History of Transfusion
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A questionnaire to assess history of transfusion.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX830200
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: History of Transfusion #830201
has_application_toward: Blood transfusions, which are used to treat various medical conditions such as hemophilia, cancer, and sickle cell disease, expose patients to risks of infectious agents (e.g., HIV and hepatitis), iron overload, alloimmunization and hyperviscosity. Transfusion therapy can also impact the results of bioassays, such as complete blood count, reticulocyte count, cell-free hemoglobin, haptoglobin, aspartate aminotransferase, and measurements such as transcranial Doppler ultrasonography (TCD).

History of Type I and Type 2 Diabetes
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Reproductive History
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A questionnaire to determine a respondent’s history of type 1 or type 2 diabetes.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Link to? Personal Attribute---> Personal medical history
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has protocol: PhenX protocol: Personal History of Type 1 and Type 2 Diabetes #140501
has_application_toward: This measure can be used to stratify a study population into those with diabetes and those without diabetes.

HIV Test
type: Class
subclass of: Blood Test
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: This is a bio-assay to measure human immunodeficiency virus (HIV) antibodies.
curator note: Also below "Immunochemical Assay"?
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has_application_toward: The measure determines whether a participant has human immunodeficiency virus (HIV) infection.
hasExactSynonym: Human Immunodeficiency Virus Test

Hospital Anxiety and Depression Scale (HADS)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The HADS consists of 2 subscales each with 7 items for measuring anxiety, and 7 items for depression rated from 0 - 3. Anxiety and depression scores were obtained by adding up the ratings of the items on each subscale. A score above 8 in any of the subscales indicates clinically significant anxiety or depression.
dc:source: Zigmond A.S. and Snaith R.P. (1983). The hospital anxiety and depression scale. Acta Psychiatry Scandinavia, 67, 361-370. Anie, K.A.; Green, J.; Tata, P.; Fotopoulos, C. E.; Oni, L. and Davies, S. C. (2002) Self-help manual-assisted cognitive behavioural therapy for sickle cell disease. Behavioural and Cognitive Psychotherapies, 30, 451-458
abbreviation: HADS
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: multiple
has respondents: Patient Reported Outcome
has target population: Clinic Patients
selection criteria met: Widely used around the world, also used in SCD
validated for age ranges: Adults (18 to 91 years)
hasExactSynonym: HADS
hasExactSynonym: Hospital Anxiety and Depression Scale

Hospitalization
type: Class
subclass of: Health Service Utilization
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The confinement of a patient in a hospital.
database cross reference: MESH:D006760
definition source: D006760
description adapted from source: no
hasExactSynonym: Hospital Admission
hasExactSynonym: Hospitalisation
hasExactSynonym: Hospitalisations
hasExactSynonym: Hospitalizations
comment: Hospitalization refers to being in a hospital or being placed in a hospital. It should not be confused with patient admission or patient re-admission.

Household Roster-Relationships
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Current Marital Status
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A record of those living in the respondent's household and about his or her relationship with them.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Include under QoL?
database cross reference: PX11400
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Household Roster - Relationships #011402
has_application_toward: Household rosters enumerate the people who live in the household and record some of the characteristics of those people (such as age and sex) and how they are related to one another. The data can be used to describe household size, structure, and composition. Household characteristics have an effect on the socioeconomics and lifestyles of the household inhabitants. Researchers are able to constitute family and nonfamily households from a household roster. This information also illustrates whether multiple generations of a family share the same residence.

Hydration
type: Class
subclass of: Preventative Therapeutics
subclass of: Lifestyle Therapy
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The quality or state of being hydrated; especially: the condition of having adequate fluid in the body tissues.
curator note: This definition should probably be altered to be more suitable as a therapy.
definition source: hydration
description adapted from source: no

Hydromorphone
type: Class
subclass of: Opioid
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An opioid analgesic derived from morphine and used mainly as an analgesic. It has a shorter duration of action and is more potent than morphine.
database cross reference: DB00327
definition source: DB00327
description adapted from source: no
hasExactSynonym: 3-hydroxy-17-methyl-4,5alpha-epoxymorphinan-6-one
hasRelatedSynonym: (-)-(5R)-4,5-Epoxy-3-hydroxy-9alpha-methylmorphinan-6-one
hasRelatedSynonym: 6-Deoxy-7,8-dihydro-6-oxomorphine
hasRelatedSynonym: Dihydromorfinon
hasRelatedSynonym: Dimorphone
hasRelatedSynonym: Hydromorphonum
hasRelatedSynonym: Idromorfone

Hydrops Fetalis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Blood Transfusion
subclass of: Restriction
  on property: treated with
  some values from: Exchange Transfusion, Whole Blood
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Spontaneous Abortion
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The abnormal accumulation of fluid in two or more fetal compartments, including ascites, pleural effusion, pericardial effusion, and skin edema.
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0001789
definition source: HP_0001789
description adapted from source: no
is caused by: Fetal: severe fetal anemia, hemolytic anemias (Rh disease, alpha thalassemia), heart failure, tumors, twin to twin transfusions, deficiency of enzyme beta-glucuronidase, Niemann-Pick Disease, Gaucher Disease, Turner Syndrome, fetal cardiac defects and skeletal defects, Noonan Syndrome. Maternal: some vertically transmitted infections (syphilis, Parvovirus B19, citomegalovirus), hyperthyroidism.
is characterised by: Edema, heart failure, pleural effusion, pericardial effusion, ascites, pallor, underactive fetus and newborn.

Hydroxyurea
type: Class
subclass of: Preventative Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An antineoplastic agent that inhibits DNA synthesis through the inhibition of ribonucleoside diphosphate reductase.
database cross reference: DB01005
definition source: DB01005
description adapted from source: no
comment: Absorption: Well absorbed from the gastrointestinal tract.
comment: Half Life: 3-4 hours
comment: Indication: Hemoglobin SS Disease
comment: Mechanism of Action: Hydroxyurea is converted to a free radical nitroxide (NO) in vivo, and transported by diffusion into cells where it quenches the tyrosyl free radical at the active site of the M2 protein subunit of ribonucleotide reductase, inactivating the enzyme. The entire replicase complex, including ribonucleotide reductase, is inactivated and DNA synthesis is selectively inhibited, producing cell death in S phase and synchronization of the fraction of cells that survive. Repair of DNA damaged by chemicals or irradiation is also inhibited by hydroxyurea, offering potential synergy between hydroxyurea and radiation or alkylating agents. Hydroxyurea also increases the level of fetal hemoglobin, leading to a reduction in the incidence of vasoocclusive crises in sickle cell anemia. Levels of fetal hemoglobin increase in response to activation of soluble guanylyl cyclase (sGC) by hydroxyurea-derived NO.
comment: Metabolism: Hepatic
comment: Pharmacodynamics: Hydroxyurea has dose-dependent synergistic activity with cisplatin in vitro. In vivo Hydroxyurea showed activity in combination with cisplatin against the LX-1 and CALU-6 human lung xenografts, but minimal activity was seen with the NCI-H460 or NCI-H520 xenografts. Hydroxyurea was synergistic with cisplatin in the Lewis lung murine xenograft. Sequential exposure to Hydroxyurea 4 hours before cisplatin produced the greatest interaction.
comment: Route of Elimination: Renal excretion is a pathway of elimination.
comment: Toxicity: Oral, mouse: LD50 = 7330 mg/kg; Oral, rat: LD50 = 5760 mg/kg Teratogenicity: Teratogenic effects have occurred in experimental animals.Hydroxyurea use during a small number of human pregnancies has been reported. Adverse effects have not been observed in any of the exposed newborns. Reproductive Effects: Adverse reproductive effects have occurred in experimental animals. Mutagenicity: Mutagenic effects have occurred in experimental animals.Mutagenic effects have occurred in humans.

Hydroxyurea-Induced Adverse Event
type: Class
subclass of: Causal Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete

Hydroxyurea-Induced Cutaneous Adverse Event
type: Class
subclass of: Hydroxyurea-Induced Adverse Event
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://jamanetwork.com/journals/jamadermatology/fullarticle/478284

Hydroxyurea-Induced Splenomegaly Adverse Event
type: Class
subclass of: Hydroxyurea-Induced Adverse Event
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: https://www.ncbi.nlm.nih.gov/pubmed/14508799

Hypergonadotropic Hypogonadism
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Depression
subclass of: Restriction
  on property: results_in
  some values from: Infertility
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Reduced function of the gonads (testes in males or ovaries in females) associated with excess pituitary gonadotropin secretion and resulting in delayed sexual development and growth delay.
curator note: Provide source for additional info.
database cross reference: HP:0000815
definition source: HP_0000815
description adapted from source: no
is caused by: In males: Congenital abnormalities ( Klinefelter's syndrome, Other chromosomal abnormalities); Mutation in the FSH and LH receptor genes, Cryptorchidism, Disorders of androgen biosynthesis, Myotonic dystrophy, Congenital anorchia, Varicocele. Acquired causes: infections; radiation; Alkylating and antineoplastic agent; Suramin; Ketoconazole; Glucocorticoids; Environmental toxins; trauma; Testicular torsion; Bilateral orchiectomy; Autoimmune damage; Chronic systemic diseases: Cirrhosis, Chronic renal failure, HIV, idiophathic. In females: genetic ( Turner Syndrome), chemotherapy, radiation, autoimmune primary ovarian insufficiency, premature ovarian failure.
hasExactSynonym: Hypergonadotrophic Hypogonadism
preferred label: Primary Hypogonadism

Hyperinsulinemia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Exercise
subclass of: Restriction
  on property: results_in
  some values from: Diabetes Mellitus
subclass of: Restriction
  on property: results_in
  some values from: Hypoglycemia
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An increased concentration of insulin in the blood.
curator note: Provide source for additional info.
database cross reference: HP:0000842
definition source: HP_0000842
description adapted from source: no
is caused by: Obesity, neoplasms, pancreatic cancer, polycystic ovary syndrome, trans-unsaturated fatty acids.
hasExactSynonym: Elevated insulin level

Hyperkalemia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Abnormally high potassium concentration in the blood, most often due to defective renal excretion. It is characterized clinically by electrocardiographic abnormalities (elevated T waves and depressed P waves, and eventually by atrial asystole). In severe cases, weakness and flaccid paralysis may occur. (Dorland, 27th ed).
database cross reference: MeSH:D006947
definition source: D006947
description adapted from source: no
hasExactSynonym: High Blood Potassium Levels
hasExactSynonym: Hyperkalemias
hasExactSynonym: Hyperpotassemia
hasExactSynonym: Hyperpotassemias

Hyperkeratosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Hyperkeratosis is thickening of the outer layer of the skin, the stratum corneum, which is composed of large, polyhedral, plate-like envelopes filled with keratin which are the dead cells that have migrated up from the stratum granulosum.
dc:source: HP_0000962
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000962
description adapted from source: no
is caused by: Inherited (epidermolytic, follicular, hyperkeratosis lenticula ris per stan) or acquired (chronic inflammation, infection, chemical irrtiants, radiations sunlight.
is characterised by: Corns, calluses, warts, chronic eczema, lichen planus, actinic keratoses, seborrheic keratoses.

Hyperlipidemia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An elevated lipid concentration in the blood.
database cross reference: HP:0003077
definition source: HP_0003077
description adapted from source: no

Hyperostosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: treated with
  some values from: Anti-Inflammatory Agent
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: results_in
  some values from: SCD Related Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Excessive growth or abnormal thickening of bone tissue.
curator note: Provide source for additional info.
database cross reference: HP:0100774
definition source: HP_0100774
description adapted from source: no
is caused by: May be inherited, or due to excess of growth hormone, Paget's disease,Virchow's disease, Crouzon disease.
is characterised by: Benign overgrowth of the bone.
hasExactSynonym: Bone Hypertrophy
hasExactSynonym: Bone Overgrowth

Hyperparathyroidism
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Osteomalacia
subclass of: Restriction
  on property: results_in
  some values from: Osteoporosis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Excessive production of parathyroid hormone (PTH) by the parathyroid glands.
curator note: Provide source for additional info.
database cross reference: HP:0000843
definition source: HP_0000843
description adapted from source: no
is caused by: Primary: adenoma, hyperplasia or carcinoma of the gland. Secondary: hypocalcemia, vitamin D deficiency, chronic kidney failure.
is characterised by: Hyperfunction of the parathyroid glands that may produce any or non-specific symptoms. They can be: weakness , fatigue, depression, bone pain, decreased appetite, nausea, vomiting, constipation, polyuria, polydipsia.
hasExactSynonym: Elevated Blood Parathyroid Hormone Level

Hyperpigmentation
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Hyperpigmentation is a common, usually harmless condition in which patches of skin become darker in color than the normal surrounding skin, the darkening occurs when an excess of melanin, the brown pigment that produces normal skin color, forms deposits in the skin.
dc:source: MP_0001188
dc:source: www.aocd.org
curator note: Perhaps merge with "Cutaneous Hyperpigmentation"? Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: MP:0001188
description adapted from source: yes
is caused by: Inherited e.g freckles or acquired (sun damage, harmonal, trauma, skin disease such as acne).
is characterised by: Freckles, chloasma spots, acne, lentigines.

Hyperthyroidism
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Depression
subclass of: Restriction
  on property: results_in
  some values from: Osteoporosis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An abnormality of thyroid physiology characterized by excessive secretion of the thyroid hormones thyroxine (i.e., T4) and/or 3,3',5-triiodo-L-thyronine zwitterion (i.e., triiodothyronine or T3).
curator note: Provide source for additional info.
database cross reference: HP:0000836
definition source: HP_0000836
description adapted from source: no
is caused by: Autoimmune diseases (Graves', Hashitoxicosis), toxic adenoma, toxic multinodular goiter, TSH-producing pituitary adenoma, Non-neoplastic TSH-mediated hyperthyroidism, Hyperemesis gravidarum, Trophoblastic disease. Tyroiditis: ( Subacute granulomatous (de Quervain's); Painless thyroiditis - silent thyroiditis, lymphocytic thyroiditis; Postpartum thyroiditis; Amiodarone; Radiation; Palpation. Exogenous: Excessive replacement therapy, Intentional suppressive therapy, Factitious hyperthyroidism, Ectopic hyperthyroidism: Struma ovarii, Metastatic follicular thyroid cancer.
is characterised by: Anxiety, emotional lability, weakness, tremor, palpitations, heat intolerance, increased perspiration, and weight loss despite a normal or increased appetite. Milder symptoms may appear. Enlargement of the Thyroid gland may be present depending on the cause.
hasExactSynonym: Overactive Thyroid

Hyperuricemia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Kidney Failure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An abnormally high level of uric acid in the blood.
dc:source: HP_0002149
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0002149
description adapted from source: no
is caused by: Genetic background, insulin resistance, hypertension, renal insufficiency, obesity, purin-rich diet, use of diuretics, salycilates, pyrazinamide, ethambutol, nicotinic acid, cyclosporin, cytotoxic agents, consumption of alcohol, tumor lysis syndrome, starvation, very low calorie diet.
hasExactSynonym: High blood uric acid level
hasExactSynonym: Hyperuricaemia

Hyphema
type: Class
subclass of: Ophthalmologic Complication
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Glaucoma (Secondary to Presence of Blood in the Anterior Chamber of the Eye)
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Bleeding in the anterior chamber of the eye.
dc:source: Ballas et al 2010 Am J Hematol
dc:source: Gharaibeh et al 2013 Cochrane Database Syst Rev
dc:source: Mowatt et al 2010 Eur J Ophthalmol
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0011886
definition source: HP_0011886
description adapted from source: no
is caused by: Often follows trauma, which may be minimal, risk increased in people with sickle cell trait and sickle cell disease.
is characterised by: History of trauma or surgery.
comment: Diagnostic Criteria: Simple inspection of the anterior chamber through the transparent cornea. A very bright focal beam of light is usually sufficient for visualization of blood. The presence of sickling of the erythrocytes within the anterior chamber's fluid cannot be determined by visual inspection, even with the magnification afforded by the slit lamp biomicroscope.
comment: Hyphema in patients with SCD and in individuals with sickle cell trait may lead to mechanical obstruction of the flow of aqueous humor, culminating in increasing the pressure of the entire eye. If the blood flow is substantially compromised in the retina or optic nerve at the back of the eye, as a result of the events in the front of the eye, irreversible blindness may occur quickly and without warning. Hyphema, therefore, should be considered an emergency in patients with SCD or in individuals with sickle cell trait.

Hypnotics and Sedatives
type: Class
subclass of: Supportive Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Drugs used to induce drowsiness or sleep or to reduce psychological excitement or anxiety.
database cross reference: MESH:D006993
definition source: D006993
description adapted from source: no
hasExactSynonym: Sedatives and Hypnotics
hasNarrowSynonym: Hypnotics
hasNarrowSynonym: Sedatives
hasRelatedSynonym: Effect, Hypnotic
hasRelatedSynonym: Effects, Hypnotic
hasRelatedSynonym: Hypnotic Effect
hasRelatedSynonym: Hypnotic Effects
hasRelatedSynonym: Sedative Effect

Hypoglycemia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Coma
subclass of: Restriction
  on property: results_in
  some values from: Seizure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A decreased concentration of glucose in the blood.
curator note: Provide source for additional info.
database cross reference: HP:0001943
definition source: HP_0001943
description adapted from source: no
is caused by: Use of certain medications ( insulin, sulfonilureas, biguanides), some drugs (alcohol), kidney failure, certain tumors, liver disease, hypothyroidism, starvation, inborn error of metabolism, severe infections, reactive hypoglicemia, hormone deficiency ( Addison's disease).
is characterised by: May occur: shakiness, palpitations, sweating, pallor, mydriasis, hunger, borborygmus, nausea, vomiting, headache, weakness,irritability, confusion, double vision.
hasExactSynonym: Low Blood Sugar

Hypopigmentation
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A reduction of skin color related to a decrease in melanin production and deposition.
dc:source: HP_0001010
dc:source: Mini review: Acta Derm Venereol 2010; 90: 6-11. A Practical Classification of Childhood Hypopigmentation Disorders.
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0001010
description adapted from source: no
is caused by: Genetic or acquired.
is characterised by: Generalized or loclaized decreased pigmentation of the skin.

Hyporeflexia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Absence of neurologic reflexes such as the knee-jerk reaction.
dc:source: HP_0001265
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0001284
description adapted from source: no
is caused by: Some of the common causes may include: myxedema; cretinism; cerebral palsy; Parkinsonism; lower motor neuron lesions; antidepressants.
hasExactSynonym: Depressed tendon reflexes

Hypothyroidism
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Arthralgia
subclass of: Restriction
  on property: results_in
  some values from: Infertility
subclass of: Restriction
  on property: results_in
  some values from: Obesity
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Deficiency of thyroid hormone.
curator note: Provide source for additional info.
database cross reference: HP:0000821
definition source: HP_0000821
description adapted from source: no
is caused by: Dysfuncion of the Tyroid glane due to Thyroiditis, inflammation, viral infection, Radiation Therapy, medications, Thyroid Surgery, too little iodine in the diet, pregnancy.
is characterised by: Fatigue, changes in the menstrual cicle, constipation, depression, dry hair, hair loss, dry skin, high sensitivity to cold, slow heart rate, unexplained weight gain or difficulty loosing weight, swelling of the thyroid gland (goiter), carpal tunnel syndrome.
hasExactSynonym: Low T4
hasExactSynonym: Underactive Thyroid

Hypoxemia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An abnormally low level of blood oxygen.
database cross reference: HP:0012418
definition source: HP_0012418
description adapted from source: no
hasExactSynonym: Low Blood Oxygen Level

Ibuprofen
type: Class
subclass of: Anti-Inflammatory Agent
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Ibuprofen, a propionic acid derivative, is a prototypical nonsteroidal anti-inflammatory agent (NSAIA) with analgesic and antipyretic properties.
curator note: Were these specific synonyms selected form the long list in the description source because of specific relevance to SCD?
database cross reference: DB01050
definition source: DB01050
description adapted from source: no
hasExactSynonym: 2-[4-(2-methylpropyl)phenyl]propanoic acid
hasRelatedSynonym: (+-)-alpha-methyl-4-(2-methylpropyl)benzeneacetic acid
hasRelatedSynonym: (+-)-ibuprofen
hasRelatedSynonym: (+-)-p-isobutylhydratropic acid
hasRelatedSynonym: Adran
hasRelatedSynonym: Ibumetin
hasRelatedSynonym: Liptan
hasRelatedSynonym: alpha-(p-isobutylphenyl)propionic acid

ICD-10-CM Diagnosis Codes
type: Class
subclass of: Clinical Coding
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Illness Perception Questionnaire Revised (IPQ-R)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The IPQ-R is an 84-item self-completed instrument developed to provide a quantitative measurement of the components of illness representations, as described by Leventhal's Common-Sense Model (CSM) of selfregulation it is divided into 3 sections: identity subscale (14 symptoms), causal subscale (18 causes), and a third section which contains 7 subscales, including consequences, timeline acute/chronic and cyclical, personal and treatment control/cure, illness coherence, and emotional representations. The questionnaire wording can be adapted to the specific illness by replacing the word illness with the name of the condition. For the identity subscale, respondents are asked if they have experienced a number of symptoms since their illness, and if they feel the symptoms are related to their current illness. Response is by circling ‘yes’ or ‘no’ to each question. Responses are then summed to give an overall score. For the causal subscale, respondents are asked what they perceive to be the cause of their illness and are asked to respond to each of the listed causes using a 5-point Likert style scale, ranging from strongly disagree to strongly agree. Respondents are also asked to rank the 3 most important factors believed to be the cause of their illness. The third section (7 subscales) is scored by summing responses to each item is on a 5-point Likert style scale, ranging from strongly disagree to strongly agree. All items for each of the subscales are summed to give an overall score. High scores on the identity, consequences, timeline acute/chronic and cyclical subscales represent strongly held beliefs about the number of symptoms attributed, the negative consequences, and the chronicity and cyclical nature of the illness. High scores on the personal and treatment control and coherence subscales represent positive beliefs about controllability and a personal understanding of the illness.
dc:source: Moss-Morris R, Weinman J, Petrie KJ, Horne R, Cameron LD, Buick D (2002). The Revised Illness Perception Questionnaire (IPQ-R). Psychol Health 17:1-16.
abbreviation: IPQ-R
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: multiple
has respondents: Patient Reported Outcome
has target population: Clinic Patients
has translations: many
selection criteria met: Good psychometric properties, widely used around the world, has been translated into several languages.
validated for age ranges: Adults
hasExactSynonym: IPQ-R
hasExactSynonym: Illness Perception Questionnaire Revised

Imaging Assay
type: Class
subclass of: Diagnostic Technique, Method, Test or Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: An imaging assay is an assay to produce a picture of an entity.
curator note: Perhaps replace this term with "Diagnostic Imaging" from NCIT?
database cross reference: OBI:0000185
definition source: OBI_0000185
description adapted from source: no
preferred label: Imaging Test

Imaging Transcranial Doppler Ultrasonography
type: Class
subclass of: Cerebral Blood Flow Assay
subclass of: Ultrasonography Test
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: TCDi
hasExactSynonym: TCDi

Ultrasonography Test
type: Class
subclass of: Imaging Assay
subclass of: Restriction
  on property: has medical device
  some values from: Ultrasound Machine
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A test that employs ultrasonography, a technique in which high-frequency sound waves are bounced off internal organs and the echo pattern is converted into a 2 dimensional picture of the structures beneath the transducer.
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: yes
hasBroadSynonym: Ultrasonography
hasExactSynonym: Immaging by Ultrasonography

Immune System
type: Class
subclass of: Hemic and Immune Systems
description: The body's defense mechanism against foreign organisms or substances and deviant native cells. It includes the humoral immune response and the cell-mediated response and consists of a complex of interrelated cellular, molecular, and genetic components.
database cross reference: MESH:D007107
definition source: D007107
description adapted from source: no

Immunochemical Assay
type: Class
subclass of: Immunological Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Methods for the quantitative analysis of chemical substances, such as proteins, that utilize the highly specific binding between an antigen or hapten and homologous antibodies.
definition source: immunochemical+assay
description adapted from source: yes

Immunological Assay
type: Class
subclass of: Biochemical Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Laboratory test involving interaction of antigens with specific antibodies.
definition source: http://bioportal.bioontology.org/ontologies/SYN/
description adapted from source: Only label adapted
hasExactSynonym: Immunoassay
hasExactSynonym: Immunological Laboratory Method
hasExactSynonym: Immunology Test

Immunosuppressant Drug Level Decreased AE
type: Class
subclass of: Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A drug adverse event that has an outcome of decreased levels of immunosuppressant drugs in the patient's body.
database cross reference: OAE:0001071
definition source: OAE_0001071
description adapted from source: no

Immunoturbidimetry Assay
type: Class
subclass of: Immunological Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: An assay employing immunoturbidimetry, a method that measures the absorbance of light from a sample which is used for quantifying an amount of analyte based on the level of turbidity produced by the formation and precipitation of an immune complex containing the analyte.
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: yes
hasBroadSynonym: Immunoturbidimetry

Impaired Urinary Concentration
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Blood Transfusion
subclass of: Restriction
  on property: results_in
  some values from: Enuresis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A defect in the ability to concentrate the urine.
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0004727
definition source: HP_0004727
description adapted from source: no
has age of onset: Notable within the first decade of life.
is caused by: Can be caused by tubular damage in the kidney; can be seen in sickle cell disease and sickle cell trait.
is characterised by: Excretion of urine of which the specific gravity is similar to that of plasma ; isosthenuria - pathologic consequence, urine specific gravity is similar to that of plasma (1.008-1.012) ; hyposthenuria urine specific gravity is lower than that of plasma < 1.008.
hasExactSynonym: Urinare Concentrating Defect
hasExactSynonym: Urinare Concentration Defect

Impaired Wound Healing
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Infection
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Reduced ability or inability to self-repair and close wounds.
dc:source: MP_0001792
dc:source: Medscape: Chronic wound: Author: Jorge I de la Torre, MD, FACS; Chief Editor: Joseph A Molnar, MD, PhD, FACS more
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: MP:0001792
description adapted from source: no
has disease stage: Diabetic sores, pressure soure, venous stasis ulcers.
is caused by: Impaired immunity, infection, foreign body, neuropathic impairment, pressure over bony prominences, hypoxia in areas of venous congestion.
is characterised by: Wounds that take longer than normal to self repair.
hasExactSynonym: Delayed Wound Healing
hasExactSynonym: Impaired Wound Repair

Increased Bone Mineral Density
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An abnormal increase of bone mineral density, that is, of the amount of matter per cubic centimeter of bones which is often refered to as osteosclerosis. Osteosclerosis can be detected on radiological examination as an increased whiteness (density) of affected bones.
curator note: Provide source for additional info.
database cross reference: HP:0011001
definition source: HP_0011001
description adapted from source: no
is caused by: Ischemia, chronic infection, and tumor formation, osteoarthritis, osteoma, hepatitis C, . May be caused by faulty bone resorption as a result of some abnormality involving osteoclasts.
is characterised by: An increased whiteness (density) of affected bones.
hasExactSynonym: Bone Sclerosis
hasExactSynonym: Increased Bone Density
hasExactSynonym: Osteosclerosis of Bones
preferred label: Osteosclerosis

Increased Hemoglobin A2
type: Class
subclass of: Abnormal Hemoglobin Level Present in SCD
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An elevated concentration in the blood of hemoglobin A2 (HbA2), which is a normal variant of hemoglobin A that consists of two alpha and two delta chains and is normally present at low levels in adults but may be increased in beta thalassemia.
database cross reference: HP:0045048
definition source: HP_0045048
description adapted from source: Only label adapted

Increased Susceptibility to Bacterial Infection
type: Class
subclass of: Infection
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: treated with
  some values from: Infection Prophylaxis
subclass of: Restriction
  on property: results_in
  some values from: Sepsis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Greater likelihood that an organism will develop ill effects from a bacterial infection or from components of or toxins produced by bacteria.
curator note: Source needed for additional info and this term must be included under "Immune System".
database cross reference: MP:0002412
definition source: MP_0002412
description adapted from source: no
is caused by: Multifactorial generally factors ultimately cause impaired immunity.
is characterised by: Repeated/recurrent local or systemic bacterial infections.
hasExactSynonym: Decreased Resistance to Bacterial infection

Infection
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Invasion of the host organism by microorganisms that can cause pathological conditions or diseases.
dc:source: D007239
dc:source: Farlex Partner Medical Dictionary Farlex 2012
curator note: Perhaps use Bacterial Infection and Viral Infection as modifiers? Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: MESH:D007239
description adapted from source: no

Infectious Agent
type: Class
subclass of: Environmental Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: An organism that has an infectious disposition.
dc:source: http://www.ontobee.org/ontology/OBI
database cross reference: OBI:0000925
description adapted from source: yes
hasRelatedSynonym: Infection

Infertility
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Inability to produce live offspring
dc:source: MP_0001924
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: MP:0001924
description adapted from source: no
is caused by: Drugs, endocrine diseases, genetic.
is characterised by: Lack of capacity
hasRelatedSynonym: Sterile

Influenza Virus Vaccine
type: Class
subclass of: Vaccine
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A viral vaccine that protects against infection with influenza virus.
database cross reference: VO:0000642
definition source: VO_0000642
description adapted from source: no

Insect Repellents
type: Class
subclass of: Malaria Prophylaxis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Substances causing insects to turn away from them or reject them as food.
database cross reference: MESH:D007302
definition source: D007302
description adapted from source: no

Insulin Resistance
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Healthy Diet
subclass of: Restriction
  on property: treated with
  some values from: Healthy Lifestyle
subclass of: Restriction
  on property: treated with
  some values from: Exercise
subclass of: Restriction
  on property: results_in
  some values from: Chronic Kidney Disease
subclass of: Restriction
  on property: results_in
  some values from: Diabetes Mellitus
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels.
curator note: Provide source for additional info.
database cross reference: HP:0000855
definition source: HP_0000855
description adapted from source: no
is caused by: Diet high in fats and carbohydrates, obesity, genetic predispositon, sedentary lifestyle, protease inhibitors.
is characterised by: May have no symptoms, or: brain fogginess and inability to focus, high glucose levels, intestinal bloating, sleepiness, weight gain, increased trygliceride levels, increased blood pressure, acanhosis nigricans, increased hunger, depression.

Intelligence Scale
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: This measure provides an estimate of an individual’s overall global intellectual function.
curator note: Should these also/rather be included below QoL?
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has_application_toward: Impairments in general cognitive function, as measured by the intelligence quotient (IQ), are associated with some genetic diseases (e.g., Down’s syndrome, Fragile X syndrome, sickle cell disease [SCD]), stroke, prematurity, nutritional deficiencies, and use of drugs and alcohol.

Intelligence Scale - 16 to 90 years
type: Class
subclass of: Intelligence Scale
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A standardized tool designed to assess an individual’s cognitive abilities. It consists of a battery of tests that allow an investigator to conduct a comprehensive cognitive evaluation of IQ.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Intelligence Scale - 16 to 90 years #820501
validated for age ranges: 16 to 90 years old
freely available: This is a proprietary instrument and is available online from Pearson.
hasExactSynonym: WAIS-IV
hasExactSynonym: Wechsler Adult Intelligence Scale, Fourth Edition
hasExactSynonym: Wechsler Adult Intelligence Scale, Fourth Edition (WAIS-IV)
comment: Life stage: Adolescent, Adult
comment: The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the WAIS-IV and the Wechsler Intelligence Scale for Children-Fifth Edition (WISC-V). The Working Group recommends providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for the WAIS-IV and the WISC-V for guidance on selecting an age-appropriate test for individuals.

Intelligence Scale - 2 years, 6 months to 7 years, 7 months
type: Class
subclass of: Intelligence Scale
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A standardized tool designed to assess the cognitive development in preschool and young children (up to age 7 years and 7 months). It consists of a battery of tests that allow an investigator to conduct a comprehensive evaluation of IQ.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Intelligence Scale - 2 years, 6 months to 7 years, 7 months #820502
validated for age ranges: 2 years and 6 months to 7 years and 7 months
freely available: This is a proprietary instrument and is available online from Pearson
hasExactSynonym: WPPSI-IV
hasExactSynonym: Wechsler Preschool and Primary Scale of Intelligenc-Fourth Edition
hasExactSynonym: Wechsler Preschool and Primary Scale of Intelligenc-Fourth Edition (WPPSI-IV)
comment: Life stage: Toddler, Child
comment: The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the WPPSI-IV and the Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III) and between the WPPSI-IV and the Wechsler Intelligence Scale for Children-Fifth Edition (WISC-V). The Working Group recommends that providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for the WPPSI-IV, Bayley-III, and the WISC-V for guidance on selecting an age-appropriate test.

Intelligence Scale - 6 to 16 years 11 months
type: Class
subclass of: Intelligence Scale
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A battery of tests that allow an investigator to conduct a comprehensive evaluation of a child or adolescent’s cognitive ability.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Intelligence Scale - 6 to 16 years 11 months #820503
has translations: Spanish
validated for age ranges: 6 years to 16 years and 11 months
freely available: This is a proprietary instrument and is available online from Pearson.
hasExactSynonym: WISC-V
hasExactSynonym: Wechsler Intelligence Scale for Children-Fifth Edition
hasExactSynonym: Wechsler Intelligence Scale for Children-Fifth Edition (WISC-V)
comment: It consists of a core battery of subtests, which focus on five specific domains (verbal comprehension, processing speed, visual spatial, working memory, and fluid reasoning), as well as optional ancillary subtests. These ancillary subtests measure areas that are important to areas of academic achievement.
comment: Life stage: Child, Adolescent
comment: The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the Wechsler Intelligence Scale for Children®-Fifth Edition (WISC-V) and Wechsler Preschool and Primary Scale of Intelligence-Fourth Edition (WPPSI-IV), as well as between the WISC-V and the Wechsler Adult Intelligence Scale, Fourth Edition (WAIS-IV). The Working Group recommends that providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for WISC-V, WPPSI-IV, and WAIS-IV for guidance on selecting an age-appropriate test.

Intelligence Scale - Birth to 3.5 years
type: Class
subclass of: Intelligence Scale
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A standardized tool designed to assess a child’s development as compared to same-age peers. It has components that involve both direct observation and interaction with a child as well as caregiver questionnaires. It consists of five domains (cognitive, motor, language, social-emotional, and adaptive behavior).
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Intelligence Scale - Birth to 3.5 years #820504
validated for age ranges: birth to age 3 years, 6 months
freely available: Bayley-III is a proprietary instrument and is available online from Pearson. A fee is associated with the Bayley-III, and this fee is dependent upon various factors, such as if the Bayley-III is purchased as a kit (i.e., questionnaires, manuals, or forms) or in individual components.
hasExactSynonym: Bayley Scales of Infant and Toddler Development, Third Edition
hasExactSynonym: Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III)
hasExactSynonym: Bayley-III
comment: Life stage: Infant, Toddler, Child
comment: The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the Bayley-III and the Wechsler Preschool and Primary Scale of Intelligence-Fourth Edition (WPPSI - IV). The Working Group recommends that providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for Bayley-III and the WPPSI-IV for guidance on selecting an age-appropriate test.

Intentional Drug Misuse AE
type: Class
subclass of: Adverse Drug Event
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An adverse drug event that results in the intentional use of a drug in the wrong way (recreationally etc).
database cross reference: OAE:0001093
definition source: OAE_0001093
description adapted from source: no

Interrupted Time Series Analysis
type: Class
subclass of: Epidemiologic Studies
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A study that uses observations at multiple time points before and after an intervention (the "interruption"), in an attempt to detect whether the intervention has had an effect significantly greater than any underlying trend over time.
definition source: D065186

Interstitial Nephritis
type: Class
subclass of: Nephritis
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Test
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Chronic Kidney Injury
subclass of: Restriction
  on property: results_in
  some values from: Kidney Failure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A form of inflammation of the kidney affecting the interstitium of the kidneys surrounding the tubules.
dc:source: HP_0001970
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0001970
description adapted from source: no
is caused by: May have a variety of causes, most often caused by drugs (NSAIDs, Proton pump inhibitors, antibiotics), infections (Legionella, TB, many others), toxic (heavy metals, etc.) or associated with systemic disease (Sjogrens, sarcoidosis).
is characterised by: Nonspecific findings of kidney injury (elevated creatinine), may have symptoms related to underlying cause - drug induced may present with allergic type symptoms including rash, fever. Other autoimmune causes may present with symptoms of underlying disease.
hasExactSynonym: Tubulointerstitial

Intracerebral Haemorrhage
type: Class
subclass of: Intracranial Hemorrhage
subclass of: Restriction
  on property: diagnosed by
  some values from: Imaging Assay
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Confusion
subclass of: Restriction
  on property: results_in
  some values from: Depression
subclass of: Restriction
  on property: results_in
  some values from: Neurocognitive Impairment
subclass of: Restriction
  on property: results_in
  some values from: Seizure
subclass of: Restriction
  on property: results_in
  some values from: Fatigue
subclass of: Restriction
  on property: results_in
  some values from: Visual Impairment
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
subclass of: Restriction
  on property: has curation status
  has value: example likely to be removed
description: Intracerebral hemorrhage (ICH) is when blood suddenly bursts into brain tissue, causing damage to the brain.
dc:source: Overview1
curator note: Should this term be merged with "Cerebral Hemorrhage" and "Intracerebral Haemorrhage" made a synonym of "Cerebral Hemorrhage"? Specify description source and source for additional info.
description adapted from source: no
is caused by: High blood pressure is the most common cause of intracerebral hemorrhage. In younger people, another common cause is abnormally formed blood vessels in the brain. Other causes include: head injury or trauma, ruptured cerebral aneurysm (weak spot in a blood vessel that bursts), arteriovenous malformation (a grouping of malformed blood vessels in the brain that disrupts normal blood flow), use of blood thinners, bleeding tumours, cocaine use (can cause severe hypertension and lead to hemorrhage), bleeding disorders (e.g., hemophilia, sickle cell anemia).
is characterised by: Symptoms of ICH include: sudden weakness, tingling, or paralysis in the face, arm, or leg, especially if it occurs on only one side of the body, sudden onset of severe headache, trouble swallowing, trouble with vision in one or both eyes, loss of balance and coordination, dizziness,trouble with language skills (reading, writing, speaking, understanding), nausea, vomiting, apathy, sleepiness, lethargy, loss of consciousness, confusion, delirium.
hasExactSynonym: Intracerebral Bleeding

Intracranial Hemorrhage
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: diagnosed by
  some values from: X-Ray Image
subclass of: Restriction
  on property: diagnosed by
  some values from: Fluorescein Angiography
subclass of: Restriction
  on property: treated with
  some values from: Antihypertensive Agents
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Intracerebral hemorrhage (ICH) is a type of stroke caused by bleeding within the brain tissue itself.
dc:source: PE-ICH.HTM
abbreviation: ICH
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
description adapted from source: yes
has age of onset: Ten percent of strokes are caused by ICH (approximately 70,000 new cases each year). ICH is twice as common as subarachnoid hemorrhage (SAH) and has a 40% risk of death. ICH occurs slightly more frequently among men than women and is more common among young and middle-aged African Americans and Japanese. Advancing age and hypertension are the most important risk factors for ICH. Approximately 70% of patients experience long-term deficits after an ICH.
is caused by: Hypertension: an elevation of blood pressure that may cause tiny arteries to burst inside the brain. Blood thinner therapy: drugs such as coumadin, heparin, and warfarin used to treat heart and stroke conditions. AVM: a tangle of abnormal arteries and veins with no capillaries in between. Aneurysm: a bulge or weakening of an arterial wall. Head trauma: fractures to the skull and penetrating wounds (gunshot) can damage an artery and cause bleeding. Bleeding disorders: hemophilia, sickle cell anemia, DIC, thrombocytopenia. Tumors: highly vascular tumors such as angiomas and metastatic tumors can bleed into the brain tissue. Amyloid angiopathy: a degenerative disease of the arteries. Drug usage: cocaine and other illicit drugs can cause ICH. Spontaneous: ICH by unknown causes.
is characterised by: Symptoms usually come on suddenly and can vary depending on the location of the bleed. Common symptoms include: headache, nausea, and vomiting; lethargy or confusion; sudden weakness or numbness of the face, arm or leg, usually on one side; loss of consciousness; temporary loss of vision; seizures.

Intracranial Hypertension
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An increase of the pressure inside the cranium (skull) and thereby in the brain tissue and cerebrospinal fluid.
database cross reference: HP:0002516
definition source: HP_0002516
description adapted from source: no
hasExactSynonym: Intracranial Hypertension

Intracranial Hypotension
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Intracranial hypotension, also known as craniospinal hypotension is defined as CSF pressure less than 7 cm of H2O in patients with clinical presentation compatible with intracranial hypotension, which are postural headache, nausea, vomiting, neck pain, visual and hearing disturbances, and vertigo It most commonly results from CSF leaks somewhere along the neuraxis.
dc:source: intracranial-hypotension-1
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
description adapted from source: no
has age of onset: Spontaneous intracranial hypotension is typically encountered in middle age (30-50 years of age) and has a predilection for women (F:M 2:1). Of interest, this is a similar demographic to pseudotumour cerebri, which is believed to be an unrecognised predisposing factor. Epidemiology of secondary intracranial hypotension is variable and matches that of the underlying cause.
has disease stage: Intracranial hypotension can broadly be divided into: 1.Primary: usually referred to as spontaneous intracranial hypotension. 2. Secondary: iatrogenic (LP or surgery), over shunting due to diversion devices or traumatic.
is caused by: It most commonly results from CSF leaks somewhere along the neuraxis, and leads to alterations in the equilibrium between the volumes of intracranial blood, CSF, and brain tissue (Monro-Kellie hypothesis). A decrease in CSF volume leads to compensatory dilatation of the vascular spaces, mostly venous side due to its higher compliance. Spontaneous intracranial hypotension (SIH) is usually the result of a CSF leak in the spine due to spontaneous dural dehiscence of meningeal diverticulums (perineural cyst), secondary to degenerative dural tears (typically related to calcified thoracic disc protrusions) or rarely due to congenital focal absence of dura (nude nerve root). Much less frequently, but increasingly recognised, SIH can result from small medial sphenoid meningocoeles, often in patients with undiagnosed pseudotumour cerebri. It is also more commonly seen in connective tissue disorders, including Marfan syndrome Ehlers-Danlos syndrome (type II), and autosomal dominant polycystic kidney disease (ADPKD). In many instances, the manifestation of these syndromes may be subtle or not fit into defined syndromes. CSF leaks can also be iatrogenic, following lumbar puncture, surgery, secondary to over shunting, or trauma.
is characterised by: Generally, there are no localising symptoms forms directly from the leak, as CSF is absorbed into tissues. The condition often presents as a positional headache which is relieved by a recumbent position, usually within 15-30min. It is confirmed by assessing opening pressure on LP (less than 7 cm CSF). Note that when this is done fluoroscopically, it should be performed in a lateral position to allow for accurate measurement of pressure. Occasionally presentation is more sinister, with even decreased level of consciousness and coma reported.

Intraosseous Pressure
type: Class
subclass of: Measurement
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
subclass of: Restriction
  on property: has curation status
  has value: to be replaced with external ontology term
description: The hydrostatic pressure of blood in the marrow of long bones.
dc:source: 24200532 Sickle-cell hip necrosis and intraosseous pressure
curator note: Term should be requested for inclusion into the "Ontology of Biological Attributes", perhaps in an appropriate location under "organ system trait".
definition source: intraosseous
definition source: http://www.ncbi.nlm.nih.gov/pubmed/6456552
description adapted from source: yes
hasExactSynonym: IOP

Intrauterine Growth Restriction
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Neurodevelopmental Abnormality
subclass of: Restriction
  on property: results_in
  some values from: Preterm Delivery
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An abnormal restriction of fetal growth with fetal weight below the tenth percentile for gestational age.
abbreviation: IUGR
curator note: Provide source for additional info.
database cross reference: HP:0001511
definition source: HP_0001511
description adapted from source: no
is caused by: Maternal: malnutrition, lack of adequate oxygen supply to the fetus, anemia, smoking, alcohol and/or drug use, recent pregnancy, gestacional diabetes, pulmonary or cardiovascular disease, renal disease, hypertension, other chronic diseases; uteroplacental: preeclampsia, multiple gestation, uterine malformations, placental insufficiency; fetal: chromosomal abnormalities, vertically transmitted infections.
is characterised by: Insufficient growth of the foetus.
hasExactSynonym: IUGR
hasExactSynonym: Intrauterine Growth Retardation
hasExactSynonym: Prenatal Growth Retardation
hasExactSynonym: Prenatal-Onset Growth Retardation
hasExactSynonym: Small for Gestational Age Infant

Ischemia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A hypoperfusion of the blood through an organ or tissue caused by a pathologic constriction or obstruction of its blood vessels, or an absence of blood circulation.
database cross reference: MESH:D007511
definition source: D007511
description adapted from source: no
hasExactSynonym: Ischemias

Isoeletcric Focusing
type: Class
subclass of: Electrophoresis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Electrophoresis in which a pH gradient is established in a gel medium and proteins migrate until they reach the site (or focus) at which the pH is equal to their isoelectric point.
dc:source: test
curator note: Perhaps change label to "Hemoglobin Isoeletcric Focusing"? Exactsynonym "Hb IEF". See dc:source provided.
database cross reference: D007525
definition source: D007525
description adapted from source: no
hasExactSynonym: Electrofocusing

Isosthenuria
type: Class
subclass of: Impaired Urinary Concentration
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Inability of the kidneys to produce either a concentrated or a dilute urine; refers to a state in chronic renal disease in which the kidney cannot form urine with a higher or a lower specific gravity (concentration) than that of protein-free plasma; the specific gravity of the urine becomes fixed, irrespective of the fluid intake.
database cross reference: MP:0013305
definition source: MP_0013305
description adapted from source: no
hasExactSynonym: Impaired Urine-Concentrating Ability
hasExactSynonym: Urine Concentrating Defect

Jaundice
type: Class
subclass of: Phenotype
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Kernicterus
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Yellow pigmentation of the skin or sclera due to bilirubin, which in turn is the result of increased bilirubin concentration in the bloodstream.
database cross reference: HP:0000952
definition source: HP_0000952
description adapted from source: no
is caused by: Hemolysis and inflammation of the liver.
is characterised by: Yellowing of the sclera and/or the skin.
hasExactSynonym: Icterus
hasExactSynonym: Yellow Skin
hasExactSynonym: Yellowing of the Skin
hasNarrowSynonym: Cholestatic Jaundice
hasNarrowSynonym: Scleral Icterus

Joint Hypermobility
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: treated with
  some values from: Anti-Inflammatory Agent
subclass of: Restriction
  on property: treated with
  some values from: Exercise
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: results_in
  some values from: SCD Related Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The ability of a joint to move beyond its normal range of motion.
curator note: Provide source for additional info.
database cross reference: HP:0001382
definition source: HP_0001382
description adapted from source: no
is caused by: Misaligned joints, abnormally shaped ends of one or more bones at a joint, a Type 1 collagen or other connective tissue defect (as found in Ehlers-Danlos syndrome, Loeys-Dietz syndrome and Marfan syndrome).
hasExactSynonym: Hyperextensible Joints
hasExactSynonym: Increased Mobility of Joints
hasExactSynonym: Joint Hyperextensibility

Kernicterus
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A term used pathologically to describe BILIRUBIN staining of the BASAL GANGLIA; BRAIN STEM; and CEREBELLUM and clinically to describe a syndrome associated with HYPERBILIRUBINEMIA. Clinical features include athetosis, MUSCLE SPASTICITY or hypotonia, impaired vertical gaze, and DEAFNESS. Nonconjugated bilirubin enters the brain and acts as a neurotoxin, often in association with conditions that impair the BLOOD-BRAIN BARRIER (e.g., SEPSIS). This condition occurs primarily in neonates (INFANT, NEWBORN), but may rarely occur in adults. (Menkes, Textbook of Child Neurology, 5th ed, p613)
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
definition source: D007647

Kidney Failure
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Serum Creatinine Level
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin Excretion Rate
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Test
subclass of: Restriction
  on property: treated with
  some values from: Renal Replacement Therapy
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Azotaemia
subclass of: Restriction
  on property: results_in
  some values from: Edema
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Failure of the kidneys to adequately filter toxins and waste products from the blood; classified as acute (as in acute kidney injury) or chronic (as in chronic kidney disease); a number of other diseases or health problems may cause either form of renal failure to occur.
curator note: Some sources give "Renal Insufficiency" as an exact synonym.
curator note: Source needed for additional info.
database cross reference: MP:0003606
definition source: MP_0003606
description adapted from source: no
has age of onset: Variable
has disease stage: May be Acute (acute kidney injury) or chronic (chronic kidney disease).
is caused by: Has a variety of causes - dependent upon acuity - see definitions for acute kidney injury (acute renal failure) and chronic kidney disease.
hasBroadSynonym: Renal Insufficiency
hasExactSynonym: Renal Failure
comment: Treatment is dependent upon etiology and acuity. If refractory to medical therapy, renal replacement or dialysis may be indicated.

Kidney Function Test
type: Class
subclass of: Physiological Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Laboratory tests used to evaluate how well the kidneys are working through examination of blood and urine.
database cross reference: MESH:D007677
definition source: D007677
description adapted from source: no
hasExactSynonym: Kidney Function Tests
hasExactSynonym: Renal Function Test
hasExactSynonym: Renal Function Tests

Kinesiotherapy
type: Class
subclass of: Rehabilitation
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A specialized area of medicine in which exercise and movement are used as the primary form of rehabilitation.
definition source: kinesiotherapy
description adapted from source: no

Knowledge about Sickle Cell Disease
type: Class
subclass of: Clinical Competence
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Collections of facts, assumptions, beliefs and practices that health professionals hold about the aetiology, pathophysiology, quality management of SCD and related social support system based on global standards.
definition source: https://www.ncbi.nlm.nih.gov/mesh/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/20353928
description adapted from source: yes

Kyphosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Exercise
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Back Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Exaggerated anterior convexity of the thoracic vertebral column.
curator note: Provide source for additional info.
database cross reference: HP:0002808
definition source: HP_0002808
description adapted from source: no
is caused by: Vertebral fractures, Low bone density, Short vertebral height, Degenerative disc disease, Postural changes, Muscle weakness, loss of elastic tissues of the Intervertebral ligaments, Genetic/metabolic conditions: osteogenesis imperfecta, Ehlers Danlos Syndrome, Marfan syndrome, cystic fibrosis, mucopolysaccharidoses, spondylo-epiphyseal dysplasia, and Scheuermann's disease. Other causes: congenital kyphosis and neurofibromatosis, spondylolisthesis, ankylosing spondylitis, spinal tuberculosis, post laminectomy syndrome and other complications from spinal surgical procedures.
is characterised by: Sagittal convexity, or forward curvature, of the normal thoracic spine which can range from normal to abnormal.
hasExactSynonym: Gibbus Deformity
hasExactSynonym: Hunched Back
hasExactSynonym: Hyperkyphosis
hasExactSynonym: Round Back

Lactate Dehydrogenase Level
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Lactate Dehydrogenase Test
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Venipuncture
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A quantitative measurement of the amount of lactate dehydrogenase present in a sample of serum.
database cross reference: NCIT:C61026
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: Only label adapted
hasExactSynonym: LD Measurement
hasExactSynonym: LDH Measurement
hasExactSynonym: Lactate Dehydrogenase Measurement
hasExactSynonym: Lactic Acid Dehydrogenase Measurement
hasExactSynonym: Serum Lactate Dehydrogenase Measurement

Lactate Dehydrogenase Test
type: Class
subclass of: Blood Test
subclass of: Restriction
  on property: has measurement
  some values from: Lactate Dehydrogenase Level
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A bioassay to measure levels of lactate dehydrogenase, an enzyme released during tissue damage and injury.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX811000
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Lactate Dehydrogenase Level #811001
has_application_toward: Elevated lactate dehydrogenase (LDH) levels are reflective of increased hemolysis in sickle cell disease. Additionally, elevated LDH levels are associated with cancer, tissue damage, hemolysis and anemia, and infectious diseases such as HIV and bacterial meningitis.
hasExactSynonym: LDH Test
hasExactSynonym: Lactate Dehydrogenase Level Test
hasExactSynonym: Lactic Acid Dehydrogenase Test

Leg Ulcer
type: Class
subclass of: Skin Ulcer
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Open sore on lower extremity that is slow to heal. Such sores are debilitating due to severe pain, swelling, disfiguration.
database cross reference: MESH:D007871
definition source: D007871
description adapted from source: yes
hasBroadSynonym: Skin Ulcer
hasBroadSynonym: Skin Ulcers
hasExactSynonym: Leg Ulcers

Leg Weakness
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A weakness affecting lower or hind limbs.
dc:source: MP_0009434
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: MP:0009434
is caused by: Myopathy, malnutrition, inherited metabolic diseases, metabolic disturbances, muscle atrophy.
hasExactSynonym: Hindlimb Weakness

Leukaemia
type: Class
subclass of: Cancer
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A cancer of the blood and bone marrow characterized by an abnormal proliferation of leukocytes.
database cross reference: HP:0001909
definition source: HP_0001909
description adapted from source: no
hasExactSynonym: Blood Cancer

Lifestyle
type: Class
subclass of: Environmental Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Typical way of life or manner of living characteristic of an individual or group. (From APA, Thesaurus of Psychological Index Terms, 8th ed)
database cross reference: MESH:D008019
definition source: D008019
description adapted from source: no
hasExactSynonym: Life Style

Light Coagulation
type: Class
subclass of: Ophthalmologic Surgical Procedure
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The coagulation of tissue by an intense beam of light, including laser (LASER COAGULATION). In the eye it is used in the treatment of retinal detachments, retinal holes, aneurysms, hemorrhages, and malignant and benign neoplasms. (Dictionary of Visual Science, 3d ed)
database cross reference: MESH:D008028
definition source: D008028
description adapted from source: no
hasExactSynonym: Photocoagulations
hasNarrowSynonym: Laser Coagulation

Liver Biopsy
type: Class
subclass of: Diagnostic Technique, Method, Test or Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
curator note: Use relevant object property to link to "Elevated Hepatic Iron Concentration".
has_application_toward: Detecting "Elevated Hepatic Iron Concentration".

Liver Examination
type: Class
subclass of: Physical Examination
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Any process carried out to determine the condition of a patient's liver.
database cross reference: IDODEN:0003652
definition source: http://bioportal.bioontology.org/ontologies/IDODEN
description adapted from source: no

Liver Function Assay
type: Class
subclass of: Physiological Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: This is a measure to assess liver functionality and cellular integrity.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX190800
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Liver Function Assay #190801
has_application_toward: This is a screener to detect the presence and type of liver disease and determine the extent of damage to the liver.
preferred label: Liver Function Test

Locus of Control
type: Class
subclass of: Health Beliefs
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Personality construct referring to an individual's perception of the locus of events as determined internally by his or her own behaviour versus fate, luck, or external forces.
database cross reference: MESH:D007389
definition source: D007389
description adapted from source: no
hasExactSynonym: Health Locus of Control
hasRelatedSynonym: Perception
hasRelatedSynonym: Self-confidence
hasRelatedSynonym: Social Control

Longitudinal Studies
type: Class
subclass of: Cohort Studies
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Studies in which variables relating to an individual or group of individuals are assessed over a period of time.
definition source: D008137

Lot Quality Assurance Sampling
type: Class
subclass of: Sampling Studies
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A sampling methodology using small sample sizes when conducting surveys in small geographical or population-based areas or lots.
database cross reference: MESH:D055810
definition source: D055810

Low LDL-Cholestrol Levels
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Reduced amount in the blood of the lipoprotein:cholesterol complex that transports cholesterol out of the arteries and around the body, for use by various tissues in normal bodily functions
database cross reference: MP:0000183
definition source: MP:0000183
description adapted from source: no
hasExactSynonym: low circulating LDL cholesterol level

Lung Volume Measurement
type: Class
subclass of: Respiratory System Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Spirometry
subclass of: Restriction
  on property: essential measure
  some values from: Body Height
subclass of: Restriction
  on property: essential measure
  some values from: Body Weight
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Measurement of the amount of air that the lungs may contain at various points in the respiratory cycle.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Perhaps use the "DEFINITIONS AND SUBDIVISIONS OF LUNG VOLUME" section in the "Lung Function - Lung Volume #810401" protocol source in PhenX to include types of lung volume as subclasses. Can also use subclasses of Experimental Factor Ontology (EFO) term "pulmonary function measurement".
definition source: D008176
description adapted from source: no
has_application_toward: Lung volume can be used to differentiate obstructive and restrictive pulmonary conditions and to detect and quantify symptoms associated with conditions that impact the lung, such as sickle cell disease, cystic fibrosis, and obstructive airway disease.
hasExactSynonym: Lung Capacities
hasExactSynonym: Lung Capacity
hasExactSynonym: Lung Volume
hasExactSynonym: Lung Volume Measurements

Lung Volume Test
type: Class
subclass of: Pulmonary Function Test
subclass of: Restriction
  on property: has measurement
  some values from: Lung Volume Measurement
subclass of: Restriction
  on property: has medical device
  some values from: Spirometer
subclass of: Restriction
  on property: essential measure
  some values from: Body Height
subclass of: Restriction
  on property: essential measure
  some values from: Body Weight
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Clinical assessment to determine the volume of gas within an individual's lung.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Link to necessary medical device.
curator note: Perhaps use the protocol source in PhenX to include different ways of measuring FRC (functional residual capacity) as subclasses (e.g. Measurement of FRC using body plethysmography, Measurement of FRC using nitrogen washout, Measurement of FRC using helium dilution, Measurement of lung volume using imaging techniques).
database cross reference: PX810400
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has protocol: PhenX protocol: Lung Function - Lung Volume #810401
has recommended procedure: The American Thoracic Society (ATS) and the European Respiratory Society (ERS) Task Force recommendations for standardisation of the measurement of lung volume testing outline how to obtain measurement of functional residual capacity (FRC) using body plethysmography, nitrogen washout, helium dilution, and imaging techniques. In addition, this source contains details regarding the assessment of total lung capacity (TLC), vital capacity (VC), reserve volume (RV), expiratory reserve volume (ERV), and inspiratory capacity (IC). These recommendations for standardization of the measurement of lung volume testing are part of a series of recommendations by the ATS/ERS Task Force for the standardization of lung function testing, which can be found on the ATS website. Detailed information regarding patient preparation is included in the general considerations document for lung function testing in this series.
has_application_toward: Lung volume can be used to differentiate obstructive and restrictive pulmonary conditions and to detect and quantify symptoms associated with conditions that impact the lung, such as sickle cell disease, cystic fibrosis, and obstructive airway disease.
hasExactSynonym: Lung Function - Lung Volume
hasExactSynonym: Lung Volume Assay
hasExactSynonym: Pulmonary Volume Assay
hasExactSynonym: Pulmonary Volume Test
comment: The American Thoracic Society (ATS) and the European Respiratory Society (ERS) Task Force recommendations for standardisation of the measurement of lung volume testing outline how to obtain measurement of functional residual capacity (FRC) using body plethysmography, nitrogen washout, helium dilution, and imaging techniques. In addition, this source contains details regarding the assessment of total lung capacity (TLC), vital capacity (VC), reserve volume (RV), expiratory reserve volume (ERV), and inspiratory capacity (IC). These recommendations for standardization of the measurement of lung volume testing are part of a series of recommendations by the ATS/ERS Task Force for the standardization of lung function testing, which can be found on the ATS website. Detailed information regarding patient preparation is included in the general considerations document for lung function testing in this series.

Lymphoid System
type: Class
subclass of: from phenotype
description: The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system.
database cross reference: UBERON:0002465
definition source: UBERON_0002465
description adapted from source: no
hasRelatedSynonym: Lymphatic Drainage System

Lymphoma
type: Class
subclass of: Cancer
subclass of: Restriction
  on property: treated with
  some values from: Hematopoietic Stem Cell Transplantation
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A cancer originating in lymphocytes and presenting as a solid tumor of lymphoid cells.
database cross reference: HP:0002665
definition source: HP_0002665
description adapted from source: no
is characterised by: Painless swelling of the lymph nodes (glands), often in the neck or armpits where these nodes are concentrated. Swelling may also occur in the groin and abdomen.

Magnetic Resonance Imaging
type: Class
subclass of: Imaging Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Imaging that uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders.
description: Techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body.
dc:source: default.htm
dc:source: 003335.htm
database cross reference: NCIT:C16809
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no
has recommended procedure: You may be asked to wear a hospital gown or clothing without zippers or snaps (such as sweatpants and a t-shirt). Certain types of metal can cause blurry images. You will lie on a narrow table, which slides into a large tunnel-shaped scanner. Some exams require a special dye (contrast). Most of the time, the dye will be given through a vein (IV) in your hand or forearm before the test. The dye helps the radiologist see certain areas more clearly. Small devices, called coils, may be placed around the head, arm, or leg, or around other areas to be studied. These help send and receive the radio waves, and improve the quality of the images. During the MRI, the person who operates the machine will watch you from another room. The test lasts about 30 to 60 minutes, but may take longer.
has_application_toward: Having MRIs with other imaging methods can often help your doctor make a diagnosis. MRI images taken after a special dye (contrast) is delivered into your body may provide extra information about the blood vessels. A magnetic resonance angiogram (MRA), is a form of magnetic resonance imaging that creates 3-dimensional pictures of blood vessels. It is often used when traditional angiography cannot be done.
hasExactSynonym: MRI
hasExactSynonym: MRT
hasExactSynonym: Magnetic Resonance Tomography
hasExactSynonym: NMR Imaging
hasExactSynonym: NMRI
hasExactSynonym: Nuclear Magnetic Resonance Imaging
comment: A normal result means the body area being studied looks normal.

Malaria Prophylaxis
type: Class
subclass of: Infection Prophylaxis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The use of drugs or other agents to prevent malarial infection. Examples: Proguanil, mefloquine, artesunate, insect repellant, insecticide-treated-bednet.
definition source: drugs.html
description adapted from source: yes
hasExactSynonym: Malaria Prevention

Manometer
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has measurement
  some values from: Intraosseous Pressure
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
subclass of: Restriction
  on property: has curation status
  has value: to be replaced with external ontology term
description: An instrument that is used for measuring the pressure of liquids and gases.
dc:source: 24200532 Sickle-cell hip necrosis and intraosseous pressure-
curator note: Request inclusion into "Eagle-I Research Resource Ontology", below the "instrument" term.
definition source: manometer
definition source: The American Heritage Science Dictionary. Retrieved October 20, 2016 from Dictionary.com website
description adapted from source: no

Marital Status of Primary Caregiver
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: http://www.phenxtoolkit.org/index.php
description: The marital status of the respondent’s primary caregiver (i.e. family member or another individual who takes primary responsibility for the respondent).
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Include under QoL?
database cross reference: PX840100
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Marital Status of Primary Caregiver #840101
has_application_toward: Marital status of the primary caregiver is associated with socioeconomic status, academic achievement, health status and outcomes, insurance coverage, and health care utilization.

Mean Corpuscular Hemoglobin Concentration
type: Class
subclass of: Red Blood Cell Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The amount of hemoglobin in a given volume of packed red blood cells and is often calculated by dividing the hemoglobin concentration by the hematocrit.
abbreviation: MCHC
database cross reference: CMO:0000291
definition source: CMO_0000291
description adapted from source: no
hasExactSynonym: MCHC
hasExactSynonym: Mean Corpuscular Haemoglobin Concentration

Mean Corpuscular Hemoglobin Level
type: Class
subclass of: Red Blood Cell Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The average amount of hemoglobin per red blood cell caculated by dividing the total mass of hemoglobin by the number of red blood cells in a volume of blood.
abbreviation: MCH
database cross reference: CMO:0000290
definition source: CMO_0000290
description adapted from source: no
hasExactSynonym: MCH
hasExactSynonym: Mean Corpuscular Haemoglobin
hasExactSynonym: Mean Corpuscular Haemoglobin Level
hasExactSynonym: Mean Corpuscular Hemoglobin

Mean Corpuscular Volume
type: Class
subclass of: Red Blood Cell Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A mean corpuscular volume is the result of calculation of the mean volume of erythrocytes in a blood sample.
description: A measure of the average volume or size of a single red blood cell. It is derived by dividing the total volume of packed red blood cells by the total red blood cell count.
database cross reference: CMO:0000038
definition source: CMO_0000038
description adapted from source: no
hasExactSynonym: MCV
hasExactSynonym: Mean Cell Volume

Measure of Frequency of Sickle Cell Pain Episodes
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A questionnaire to capture the frequency of acute pain episodes per year due to sickle cell disease (SCD).
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX830100
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Label and description adapted
has protocol: PhenX protocol: Frequency of Sickle Cell Pain Episodes Per Year #830101
has respondents: Self
has target population: Clinic Patients (Adults with SCD)
has_application_toward: Frequency of acute sickle cell pain episodes is correlated with disease severity and early mortality.
validated for age ranges: 18 and older
freely available: yes
comment: The Sickle Cell Disease Research and Scientific Panel (SRSP) notes that a pain episode is pain lasting at least two hours that requires an unscheduled emergency room visit or hospitalization or that disrupts daily activities. The SRSP suggests that this protocol could be administered to adolescents younger than 18 and to young children via a proxy.

Measure of Sickle Cell Stigma (MoSCS)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Measure of disease specific stigma based on patient reported outcome measurements that assesses 4 MoSCS factors: Social exclusion, Internalized Stigma, Expected Discrimination and Disclosure concerns. Measure includes stigma scores; perceived disease severity, acute care service utilization, hospital admission levels. N=262
dc:source: Bediako, Shawn M et al. “The Measure of Sickle Cell Stigma: Initial Findings from the Improving Patient Outcomes through Respect and Trust Study.” Journal of health psychology (2014): 1359105314539530. PMC. Web. 13 Mar. 2016. PMCID: PMC4627860
abbreviation: MoSCS
definition source: J Health Psychol. 2016 May; 21(5): 808–820.
description adapted from source: yes
has cross-cultural adaptation: African-Americans
has respondents: Patient Reported Outcome
has target population: Adults with Sickle Cell Disease
validated for age ranges: Adults 18 years and older
hasExactSynonym: Measure of Sickle Cell Stigma
hasExactSynonym: MoSCS

Measured Weight
type: Class
subclass of: Body Weight
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The weight of the participant in kilograms.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX21500
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Weight - Measured Weight #021501

Measurement
type: Class
subclass of: Diagnostics
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: A measurement is an information entity that is a recording of the output of a measurement such as produced by an instrument.
curator note: Perhaps change name to "Diagnostic Measurement" and change description accordingly?
database cross reference: EFO:0001444
definition source: EFO_0001444
description adapted from source: no

Medical Outcomes Study (MOS) Social Support Survey
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The MOS Social Support Survey is a self-administered questionnaire that that includes 19 items across four functional support subscales: emotional/informational support (8 items), tangible/instrumental support (4 items), affectionate support (3 items), and positive social interaction (3 items). Each item is scored on a 5-point Likert style scale (1 = None of the Time; 5 = All of the Time) to indicate how often that type of support is available to them. A score for each social support subscale can be computed by averaging across the individual items or by adding scores individual items together. Higher scores indicate more support.
dc:source: Sherbourne CD, Stewart A. The MOS Social Support Survey. Social Science and Medicine, v. 32, 1991, pp. 705-714. Sherbourne, Cathy D. and Anita Stewart. The MOS Social Support Survey. Santa Monica, CA: RAND Corporation, 1993.
dc:source: www.phenxtoolkit.org
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self
has target population: Clinic patients
validated for age ranges: Adults 18 years and older
freely available: no
hasExactSynonym: MOS Social Support Survey
hasExactSynonym: Medical Outcomes Study Social Support Survey

Medical Records
type: Class
subclass of: Quality of Health Care
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Recording of pertinent information concerning patient's illness or illnesses.
database cross reference: MESH:D008499
definition source: D008499
description adapted from source: no

Medication Adherence
type: Class
subclass of: Patient Compliance
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Voluntary cooperation of the patient in taking drugs or medicine as prescribed. This includes timing, dosage, and frequency.
database cross reference: MESH:D055118
definition source: D055118
description adapted from source: yes

Medication Inventory
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A record of the type and dosage of all prescription and over-the-counter medications as well as dietary supplements currently being taken by the individual.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Would it also be appropriate to add this to "Diagnostic Instrument" below "Diagnostics"?
database cross reference: PX140300
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Medication Inventory #140301

Meditation
type: Class
subclass of: Behavior Therapy
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A state of consciousness in which the individual eliminates environmental stimuli from awareness so that the mind can focus on a single thing, producing a state of relaxation and relief from stress. A wide variety of techniques are used to clear the mind of stressful outside interferences. It includes meditation therapy. (Mosby's Medical, Nursing, and Allied Health Dictionary, 4th ed)
database cross reference: MESH:D019122
definition source: D019122
description adapted from source: no
hasNarrowSynonym: Meditation, Transcendental
hasNarrowSynonym: Transcendental Meditation

Mefloquine
type: Class
subclass of: Malaria Prophylaxis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A phospholipid-interacting antimalarial drug (antimalarials). It is very effective against plasmodium falciparum with very few side effects.
database cross reference: DB00358
definition source: DB00358
description adapted from source: no

Membranous Nephropathy
type: Class
subclass of: Nephropathy
subclass of: Restriction
  on property: diagnosed by
  some values from: Electron Microscope
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: End Stage Kidney Disease
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A form of nephrotic syndrome characterized by histology with thickening of the basement membrane and deposition of immune complexes in the subepithelial space.
dc:source: HP_0012578
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0012578
description adapted from source: yes
has age of onset: Typically seen in adult population; rare in children.
is caused by: Idiopathic - may be related to M-type phosplipase A2 receptor antibodies; secondary forms may be related to autoimmune disease, underlying maligancies, drugs or infections. Has been reported in patients with sickle cell disease.
is characterised by: Nephrotic syndrome with histologic features specific to membranous nephropathy.
hasExactSynonym: Membranous glomerulonephritis

Meningitis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: results_in
  some values from: Neurocognitive Impairment
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Meningitis is an infection of the meninges, the membranes that surround the brain and spinal cord.
dc:source: encephalitis meningitis.htm
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
description adapted from source: yes
is caused by: Causes include viruses, bacteria, fungus, and parasites.
is characterised by: Symptoms of meningitis, which may appear suddenly, often include high fever, severe and persistent headache, stiff neck, nausea, sensitivity to bright light, and vomiting. Changes in behavior such as confusion, sleepiness, and difficulty waking up may also occur. In infants, symptoms of meningitis or encephalitis may include fever, vomiting, lethargy, body stiffness, unexplained irritability, and a full or bulging fontanel (the soft spot on the top of the head).
comment: Diagnosis made by lumbar puncture. Additional brain imaging such as CT scan/MRI may be required to exclude other causes.

Menorrhagia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Anti-Inflammatory Agent
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: results_in
  some values from: SCD Related Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Prolonged and/or excessive menses at regular intervals.
curator note: Provide source for additional info.
database cross reference: HP:0000132
definition source: HP_0000132
description adapted from source: yes
is caused by: Endometrial polyps, ademomyosis, leiomyoma, malignancy, hyperplasia, coagulopathy, ovulatory disfunction, endometrial, infection, inflammation, iatrogenic, other.
hasExactSynonym: Abnormally Heavy Bleeding During Menstruation
hasExactSynonym: Hypermenorrhea
comment: Treatment depends on the underlying condition.

Mental Health
type: Class
subclass of: Quality of Life
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Mental health includes our emotional, psychological, and social well-being. It affects how we think, feel and act as we cope with life. It also helps determine how we handle stress, relate to others, and make choices. Mental health is important at every stage of life, from childhood and adolescence through adulthood.
definition source: http://purl.bioontology.org/ontology/MEDLINEPLUS/C0025353
description adapted from source: no
hasExactSynonym: Emotional Health
hasExactSynonym: Mental Hygiene
hasRelatedSynonym: Mental Disturbance
hasRelatedSynonym: Psychological Resilience
comment: Related concept: Psychological resilience: The human ability to adapt in the face of tragedy, trauma, adversity, hardship, and ongoing significant life stressors.

Meta-Analysis
type: Class
subclass of: Publication Type
description: Works consisting of studies using a quantitative method of combining the results of independent studies (usually drawn from the published literature) and synthesizing summaries and conclusions which may be used to evaluate therapeutic effectiveness, plan new studies, etc. It is often an overview of clinical trials. It is usually called a meta-analysis by the author or sponsoring body and should be differentiated from reviews of literature.
database cross reference: MESH:D017418
definition source: D017418
description adapted from source: no

Metabolic State
type: Class
subclass of: Biological Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The state of the chemical reactions that occur within the cells, tissues, or an organism. These processes include both the biosynthesis (anabolism) and the breakdown (catabolism) of organic materials utilized by the living organism.
database cross reference: MESH:D008660
definition source: D008660
description adapted from source: yes
hasRelatedSynonym: Metabolics
hasRelatedSynonym: Metabolome

Methadone
type: Class
subclass of: Opioid
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A synthetic opioid that is used as the hydrochloride. It is an opioid analgesic that is primarily a mu-opioid agonist. It has actions and uses similar to those of morphine. It also has a depressant action on the cough center and may be given to control intractable cough associated with terminal lung cancer. Methadone is also used as part of the treatment of dependence on opioid drugs, although prolonged use of methadone itself may result in dependence.
curator note: Were these specific synonyms selected from the description source because of specific relevance to SCD?
database cross reference: DB00333
definition source: DB00333
description adapted from source: no
hasExactSynonym: 6-(dimethylamino)-4,4-diphenylheptan-3-one
hasRelatedSynonym: (+-)-methadone
hasRelatedSynonym: 6-Dimethylamino-4,4-diphenyl-3-heptanone
hasRelatedSynonym: methadonum

Methemoglobinemia
type: Class
subclass of: Genetic Disorder
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The presence of methemoglobin in the blood, resulting in cyanosis. A small amount of methemoglobin is present in the blood normally, but injury or toxic agents convert a larger proportion of hemoglobin into methemoglobin, which does not function reversibly as an oxygen carrier. Methemoglobinemia may be due to a defect in the enzyme NADH methemoglobin reductase (an autosomal recessive trait) or to an abnormality in hemoglobin M (an autosomal dominant trait). (Dorland, 27th ed)
database cross reference: MESH:D008708
definition source: D008708
description adapted from source: no

Diagnostic Method
type: Class
subclass of: from diagnostics
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: Any procedure or test to diagnose a disease or disorder.
curator note: Perhaps move other sibling classes below this class? (Imaging Test/Diagnostic Imaging, Include sub-class "Biopsy" and include specific types below that?
database cross reference: NCIT:C18020
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Diagnostic Procedure

Microbiome
type: Class
subclass of: Biological Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: An organism population whose members are particpating in non-parasitic symbiosis with a particular host.
database cross reference: IDO:0000515
definition source: IDO_0000515
description adapted from source: no
hasExactSynonym: Normal Resident Microflora Population

MicroRNA
type: Class
subclass of: Gene Product
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Single-stranded RNA molecules thought to regulate the expression of other genes. miRNAs are encoded by genes that are transcribed from DNA but not translated into protein (non-coding RNA).
abbreviation: miRNA
database cross reference: SBO:0000316
definition source: SBO_0000316
description adapted from source: no
hasExactSynonym: miRNA

Microscope
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope).
dc:source: OBI_0400169
database cross reference: OBI:0400169

Mid Upper Arm Circumference
type: Class
subclass of: Body Morphological Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A circumferential measurement of the largest part of the upper arm.
dc:source: http://www.phenxtoolkit.org/index.php
abbreviation: MUAC
abbreviation: MUARMCIR
database cross reference: C124475
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no
has protocol: PhenX protocol: Mid-Upper Arm Circumference #021101
hasExactSynonym: MUAC
hasExactSynonym: MUARMCIR

Migraine
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Patient Symptom Report
subclass of: Restriction
  on property: treated with
  some values from: Antihypertensive Agents
subclass of: Restriction
  on property: treated with
  some values from: Diet, Food, and Nutrition
subclass of: Restriction
  on property: treated with
  some values from: Healthy Diet
subclass of: Restriction
  on property: treated with
  some values from: Exercise
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Migraine is a chronic neurological disorder characterized by episodic attacks of headache and associated symptoms.
dc:source: HP_0002076
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0002076
description adapted from source: no
is caused by: Roughly one-third of affected individuals can predict the onset of a migraine because it is preceded by an "aura," visual disturbances that appear as flashing lights, zig-zag lines or a temporary loss of vision. People with migraine tend to have recurring attacks triggered by a number of different factors, including stress, anxiety, hormonal changes, bright or flashing lights, lack of food or sleep, and dietary substances. Migraine in some women may relate to changes in hormones and hormonal levels during their menstrual cycle. For many years, scientists believed that migraines were linked to the dilation and constriction of blood vessels in the head. Investigators now believe that migraine has a genetic cause.
hasExactSynonym: Migraine headache

Migraine Questionnaire
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A questionnaire to assess migraines and headaches.
database cross reference: PX130500
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has_application_toward: This measure is used to screen a general population for the presence of headaches and migraines and to assess some of the associated symptoms.

Miscarriage
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Depression
subclass of: Restriction
  on property: results_in
  some values from: Infection
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Accidental or natural termination of a clear pregnancy at a stage where the fetus is incapable of surviving independently of the mother.
curator note: Provide source for additional info.
database cross reference: MP:0013172
definition source: MP_0013172
description adapted from source: no
is caused by: Smoking, obesity, diabetes, drug and alcohol use, infections, trauma, stress, uterine or hormonal abnormalities, multiple pregnancy, chronic maternal diseases, chromosomal abnormalities .
is characterised by: Vaginal bleeding with or without pain, sadness, anxiety may occur.

Mobile Radiographic Unit
type: Class
subclass of: X-Ray Machine
subclass of: Restriction
  on property: has curation status
  has value: uncurated
dc:source: http://purl.bioontology.org/ontology/SNOMEDCT/68080007
definition source: hospt equip 26.pdf

Mobility Limitation
type: Class
subclass of: Physical Health
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Difficulty moving from place to place or from one position to another without assistance.
database cross reference: MESH:D051346
definition source: D051346
description adapted from source: yes
hasExactSynonym: Ambulation Difficulty
hasExactSynonym: Ambulatory Difficulty
hasExactSynonym: Difficulty Ambulation
hasExactSynonym: Difficulty Walking
hasExactSynonym: Mobility Limitations

Moderately Increased Albuminuria
type: Class
subclass of: Albuminuria
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin Concentration
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin Excretion Rate
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin-Creatinine Ratio
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A small or moderate increase of albumin excretion in the urine.
dc:source: microalbuminuria
dc:source: HP_0012594
database cross reference: HP:0012594
definition source: microalbuminuria
description adapted from source: no
hasExactSynonym: Low Level Albuminuria
hasExactSynonym: Microalbuminuria
hasExactSynonym: Mildly Increased Albuminuria
comment: A confirmed albumin:creatinine ratio (ACR) of 3 mg/mmol or more should be regarded as clinically significant.
comment: In adults, an increase of albumin in the urine of 30-150 mg per day constitutes the presence of mildly increased albuminuria.
comment: The criteria for clinically significant proteinuria have been changed from an albumin-creatinine ratio (ACR) of 30 mg/mmol or more to 3 mg/mmol or more. This is because there is evidence that the risk of adverse outcomes is a continuum and starts at an ACR well below 30 mg/mmol.

Modifier Gene
type: Class
subclass of: Genetic Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Genes with alleles that affect the phenotype associated with a nonallelic gene.
database cross reference: MESH:D060045
definition source: D060045
description adapted from source: no
hasExactSynonym: Gene, Modifier
hasExactSynonym: Modifier Genes

Modifying the Home Environment and Making it Safer For the Patient
type: Class
subclass of: from therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
definition source: http://bioportal.bioontology.org/ontologies/ADO/
description adapted from source: no

Molecular Profiling Assay
type: Class
subclass of: Diagnostic Technique, Method, Test or Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
curator note: Is this term needed? If we only have "Hemoglobin Profiling" below it then maybe we remove it and instead just have "Hemoglobin Profiling"?
hasExactSynonym: Molecular Profiling

Mononeuropathy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Radiography
subclass of: Restriction
  on property: treated with
  some values from: Occupational Therapy
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: results_in
  some values from: Paralysis
subclass of: Restriction
  on property: results_in
  some values from: SCD Related Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Mononeuropathy is damage to a single nerve, which results in loss of movement, sensation, or other function of that nerve.
dc:source: 000780.htm
curator note: Perhaps replace with description in existing ontology? (HP?) Provide source for additional info.
description adapted from source: no
is caused by: Mononeuropathy is a type of damage to a nerve outside the brain and spinal cord (peripheral neuropathy).
hasExactSynonym: Single Damaged Nerve

Morbilliform Rash
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Infection
subclass of: Restriction
  on property: results_in
  some values from: Skin Ulcer
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An exanthema consisting of widespread pink-to-red macules (flat spots of 2-10 mm in diameter) or papules (red bumps) that blanch with pressure. The macules and papules may cluster and merge to form sheets over several days.
dc:source: HP_0012282
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0012282
description adapted from source: no
is caused by: Infections, hypersensitivity drug reaction.
is characterised by: Looks like measles, macular lesions that are red and usually 2-10 mm in diameter but may be confluent in places.

Morphine
type: Class
subclass of: Opioid
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The principal alkaloid in opium and the prototype opiate analgesic and narcotic. Morphine has widespread effects in the central nervous system and on smooth muscle.
curator note: Were these specific synonyms selected from the description source because of specific relevance to SCD?
database cross reference: DB00295
definition source: DB00295
description adapted from source: no
hasExactSynonym: 17-methyl-7,8-didehydro-4,5alpha-epoxymorphinan-17-ium-3,6alpha-diol
hasRelatedSynonym: (5alpha,6alpha)-17-methyl-7,8-didehydro-4,5-epoxymorphinan-3,6-diol
hasRelatedSynonym: (5alpha,6alpha)-didehydro-4,5-epoxy-17-methylmorphinan-3,6-diol
hasRelatedSynonym: Morfina
hasRelatedSynonym: Morphia
hasRelatedSynonym: morphium

Motor Aphasia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Anxiety
subclass of: Restriction
  on property: results_in
  some values from: Depression
subclass of: Restriction
  on property: results_in
  some values from: Social Isolation
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Is a condition that affects the brain and leads to problems using language correctly.
dc:source: Introduction.aspx
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
description adapted from source: no
has age of onset: Aphasia is one of the most common communication disorders to affect the brain. Although there are no official figures, the Stroke Association estimates more than 376,000 stroke survivors in the UK are living with aphasia. Aphasia can affect people of all ages, including children. It's most common in people over 65 years old as stroke and common progressive neurological conditions tend to affect older adults
is caused by: Aphasia is caused by damage to parts of the brain responsible for understanding and using language. Common causes include:stroke, thought to be the most common cause, around one in three people experience some degree of aphasia after having a stroke.severe head injury. brain tumour.progressive neurological conditions (conditions that over time cause progressive brain and nervous system damage).
is characterised by: Experience difficulties with understanding or expressing language.
hasExactSynonym: Broca's Aphasia
hasExactSynonym: Expressive Aphasia
hasExactSynonym: Loss of Expressive Speech
comment: Diagnosis: A speech and language therapist (SLT) usually diagnoses the condition by testing your language capabilities.

Multicenter Study
type: Class
subclass of: Publication Type
description: A work that reports on a study executed by several cooperating institutions.
database cross reference: MESH:D016448
definition source: D016448
description adapted from source: no

Multicenter Studies as Topic
type: Class
subclass of: Study Design
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Works about controlled studies which are planned and carried out by several cooperating institutions to assess certain variables and outcomes in specific patient populations, for example, a multicenter study of congenital anomalies in children.

Multidimensional Health Locus of Control Scales (MHLC)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The multidimensional health locus of control (MHLC) scale is a widely used measure of the factors that people believe exert some measures of control over their health. The MHLC originally developed by Wallston and colleagues contained 3 subscales describing various types of control-related cognitions an individual may have about the current state of his or her health. These were: Internal Health Locus of Control (IHLC), Powerful Others Health Locus of Control (PHLC) and Chance Health Locus of Control (CHLC). Subsequently, a fourth subscale, the God Locus of Health Control (G LHC) scale was developed to assess the extent of an individual's belief that God controls his or her health status was added to the measure. Thus, the expanded MHLC Consists of 4 sub-scales: one Internal and 3 external subscales namely, powerful others, chance and God. Each of the 4 sub-scales has 6 items making a total of 24 items. The two original versions of the MHLC (forms A & B) deal with the general health status whereas the third version (Form C) assesses control-related cognitions about a specific disease state.
dc:source: Wallston K., Wallston B. and De Vellis R. (1978). Development of the multidimensional health locus of control (MHLC) scales. Health Education Monographs, 6, 160-169.
dc:source: Wallston KA, Malcarne VL, Flores L, Hansdottir I, Smith CA, Stein MJ, Weisman MH, Clements PJ. Does God Determine Your Health? The God Locus of Health Control Scale. Cognitive Therapy and Research . April 1999, Volume 23 (2):131-142.
abbreviation: MHLC
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self
has target population: Healthy population and patients with specific medical conditions
has translations: Spanish; Chinese; Persian
selection criteria met: Has adequate construct validity and acceptable metric properties
validated for age ranges: 15 years and above
freely available: no
hasExactSynonym: MHLC
hasExactSynonym: MHLC Scales
hasExactSynonym: Multidimensional Health Locus of Control Scales

Muscle Atrophy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Quality of Life
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The presence of skeletal muscular atrophy, reduction in the muscle bulk.
curator note: Provide source for additional info.
database cross reference: HP:0003202
definition source: HP_0003202
description adapted from source: Label and description adapted
is caused by: Cancer, AIDS, congestive heart failure, chronic obstructive pulmonary disease, renal failure, burns, cachexia, starvation, prolonged immobilization, neurogenic atrophy.
is characterised by: Muscle weakness, reduction in muscle size.
hasExactSynonym: Amyotrophy
hasExactSynonym: Neurogenic Muscle Atrophy
hasExactSynonym: Skeletal Muscle Atrophy

Muscle Cramps
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Anxiety
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: results_in
  some values from: Quality of Life
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Sudden and involuntary contractions of one or more muscles.
dc:source: HP_0003394
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0003394
description adapted from source: no
is caused by: Hyperflexion, hypoxia, exposure to large changes in temperature, dehydration, or low blood salt, hypokalemia, hypocalcemia, medications: raloxifen, statins.

Muscle Pain
type: Class
subclass of: Pain
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: treated with
  some values from: Anti-Inflammatory Agent
subclass of: Restriction
  on property: treated with
  some values from: Cognitive Therapy
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Muscle pain is a pain characterized by pain in one or more muscles.
curator note: Provide source for additional info. Perhaps include below "Pain" under "Nervous System"?
database cross reference: SYMP:0019161
definition source: SYMP_0019161
description adapted from source: no
is caused by: Over-stretching of one muscle or a group of muscles, trauma, infections ( influenza, Lyme, Ebola, Dengue fever, Chicungunya fever, Babesiosis, Malaria, Toxoplasmosis, Hemorrhage fever, polio, Rocky Mountain spotted fever, Trichinosis), vaccines, muscle hematoma, autoimmune disorders ( lupus, polymyalgia, polymyositis, nutricional deficiencies, chronic fatigue syndrome, acute rejection after heart transplant surgery, rhabdomyolysis, severe potassium deficiency, fibromialgia, muscle abscess , reaction to drugs ( statins, fibrates, ACE inhibitors, cocaine), repetitive strain injury,withdrawal syndrome of certain drugs ( corticosteroids, opioids, barbiturates, benzodiazepines, caffeine, alcohol).
is characterised by: Pain of a muscle or a group of muscles.
hasExactSynonym: Myalgia

Musculoskeletal System
type: Class
subclass of: from phenotype
description: Anatomical system that consists of the muscular and skeletal systems.
database cross reference: UBERON:0002204
definition source: UBERON_0002204
description adapted from source: no
hasExactSynonym: Musculo-Skeletal System

Mutation Carrier Screening
type: Class
subclass of: Genetic Testing
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://bioportal.bioontology.org/ontologies/NCIT/

MYB proto-oncogene, transcription factor
type: Class
subclass of: Non-Globin Loci
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: This gene encodes a protein with three HTH DNA-binding domains that functions as a transcription regulator.
abbreviation: MYB
curator note: Link to "Hereditary Persistence of fetal hemoglobin".
definition source: http://www.ncbi.nlm.nih.gov/gene/4602
description adapted from source: yes
hasExactSynonym: MYB-HSP1
comment: Official Full Name: MYB proto-oncogene, transcription factor; Gene ID: 4602; Chromosome: 6; Position: 135180981..135219173
preferred label: MYB

Myoglobinuria
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Renal Dialysis
subclass of: Restriction
  on property: treated with
  some values from: Supportive Therapeutics
subclass of: Restriction
  on property: results_in
  some values from: Acute Kidney Injury
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Presence of myoglobin in the urine.
dc:source: HP_0002913
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0002913
description adapted from source: no
is caused by: Occurs in setting of rhabdomyolysis (muscle breakdown).
is characterised by: Presence of myoglobin in the urine, may have positive dipstick testing for blood with no red blood cells seen on microscopy.
hasExactSynonym: Increased Urine Myoglobin Level

Myopathy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: treated with
  some values from: Anti-Inflammatory Agent
subclass of: Restriction
  on property: treated with
  some values from: Supportive Therapeutics
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Leg Weakness
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A disorder of muscle unrelated to impairment of innervation or neuromuscular junction.
curator note: Provide source for additional info.
database cross reference: HP:0003198
definition source: HP_0003198
description adapted from source: no
is caused by: Inherited: dystrophies ( degeneration/ progressive), myotonia/ neuromyotonia, congenital myophaties , mithochondrial, familial periodic, inflammatory, metabolic ( lipid or glycogen storage diseases). Acquired: drugs ( corticosteroids, statins, alcohol), dermatomyositis, polymyositis, myositis ossificans, rhabdomyolysis.
is characterised by: Muscle weakness, cramps, stiffness, tetany.
hasExactSynonym: Muscle Tissue Disease
hasExactSynonym: Myopathic Changes
hasExactSynonym: Myopathies

Myositis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A general term for inflammation of the muscles without respect to the underlying cause.
curator note: Provide source for additional info.
database cross reference: HP:0100614
definition source: HP_0100614
description adapted from source: no
is caused by: Autoimmune diseases, infections, some drugs (statins).
is characterised by: Inflammation of the muscle with or without weakness, pain or some degree of atrophy, high blood levels of creatine kinase.
hasExactSynonym: Muscle Inflammation

N-Terminal Pro-Brain Natriuretic Peptide Level
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A quantification of N-terminal prohormone of brain natriuretic peptide (NT-proBNP) which is associated with acute congestive heart failure.
dc:source: http://www.phenxtoolkit.org/index.php
dc:source: Hall, C. (2004), Essential biochemistry and physiology of (NT-pro)BNP. European Journal of Heart Failure, 6: 257–260. doi:10.1016/j.ejheart.2003.12.015
abbreviation: NT-proBNP
database cross reference: EFO:0004745
definition source: EFO_0004745
description adapted from source: Label and description adapted
has_application_toward: Levels of NT-proBNP can be used as a screening tool to evaluate an individual’s left and right ventricular function. Elevated NT-proBNP levels can be used diagnostically in decompensated congestive heart failure and they can be followed longitudinally to understand response to therapy. In patients with pulmonary hypertension and acute pulmonary embolism, elevated levels reflect an increased risk of morbidity and mortality. Additionally, in patients with sickle cell disease, levels of NT-proBNP levels > 160 pg/ml predict increased mortality risk. (PhenX)
has_application_toward: This adverse prognostic marker might be considered as a potential eligibility criterion for investigational or high-risk interventions, such as haematopoietic stem cell transplantation or gene therapy. (Hall, 2004)
hasExactSynonym: N-Terminal Prohormone of Brain Natriuretic Peptide
hasExactSynonym: NT-proBNP
hasExactSynonym: NT-proBNP Measurement
comment: N-terminal pro-brain natriuretic peptide (NT-proBNP) is the N-terminal inactive protein fragment (76 amino acids) that is cleaved from the brain natriuretic peptide (BNP) prohormone, proBNP, to release the biologically active BNP. NT-proBNP is released from the right or left ventricle of the heart when it is under increased strain related to volume or pressure overload.

N-terminal Pro-brain Natriuretic Peptide Test
type: Class
subclass of: Blood Test
subclass of: Restriction
  on property: has measurement
  some values from: N-Terminal Pro-Brain Natriuretic Peptide Level
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A bioassay to determine an individual’s level of N-terminal pro-brain natriuretic peptide (NT-proBNP).
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Equipment needed: Phlebotomy supplies, centrifuge for serum separation, and freezer for sample storage is required.
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has protocol: PhenX protocol: N-terminal Pro-brain Natriuretic Peptide (NT-proBNP) #810501
hasExactSynonym: NT-proBNP Test
comment: The PhenX protocol provides instructions for drawing, processing, and storing blood according to the National Health and Nutrition Examination Survey (NHANES) methods. Because there are many comparable assays for ascertaining levels of N-terminal-pro-brain natriuretic peptide (NT-proBNP), the protocol also provides basic guidelines to aid comparability among different studies. The National Health and Nutrition Examination Survey (NHANES) instructions for drawing, processing, and storing blood provide a standard methodology used successfully for many years to ensure comparable results across study sites. However, the Sickle Cell Disease Working Group 1 (Cardiovascular, Pulmonary, and Renal) notes that certain aspects (e.g., exclusion criteria) of the NHANES protocol are study specific and might not be applicable to all types of studies (e.g., sickle cell disease). Investigators who want to include participants that have hemophilia or have received cancer chemotherapy in the last 4 weeks will need to implement special venipuncture procedures.

Nail Dystrophy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: treated with
  some values from: Antifungal
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Onychodystrophy (nail dystrophy) refers to nail changes apart from changes of the color (nail dyschromia) and involves partial or complete disruption of the various keratinous layers of the nail plate.
dc:source: HP_0008404
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0008404
is caused by: Infections, trauma, nutrient deficiency, overexposure to harsh chemicals.
is characterised by: Peeling, slit, brittle, discoloured nails.
hasExactSynonym: Onychodystrophy
hasExactSynonym: Poor nail formation

Naloxone
type: Class
subclass of: Opioid
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A specific opiate antagonist that has no agonist activity. It is a competitive antagonist at mu, delta, and kappa opioid receptors.
curator note: Are the synonyms included relevant to SCD? Should other synonyms from the description source be included?
database cross reference: DB01183
definition source: DB01183
description adapted from source: no
hasExactSynonym: 3,14-dihydroxy-17-(prop-2-en-1-yl)-4,5alpha-epoxymorphinan-6-one
hasRelatedSynonym: 1-N-Allyl-14-hydroxynordihydromorphinone
hasRelatedSynonym: 17-allyl-3,14-dihydroxy-4,5alpha-epoxymorphinan-6-one
hasRelatedSynonym: Naloxonum

Narcolepsy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Patient Symptom Report
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Narcolepsy is a rare, long-term brain disorder that causes a person to suddenly fall asleep at inappropriate times.
dc:source: Introduction.aspx
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
description adapted from source: no
has age of onset: Narcolepsy is a fairly rare condition. It is difficult to know exactly how many people have narcolepsy because many cases are thought to go unreported. However, it is estimated that the condition affects at least 25,000 people in the UK. Men and women are thought to be affected equally by narcolepsy, although some studies have suggested the condition may be more common in men. The symptoms often begin during adolescence, although the condition is usually diagnosed between the ages of 20 and 40.
is caused by: Many cases of narcolepsy are caused by a lack of the brain chemical orexin (also known as hypocretin), which regulates sleep.This deficiency is thought to result from the immune system mistakenly attacking parts of the brain that produce this chemical.However, this does not explain all cases of narcolepsy, and the exact cause of this problem is often unclear. Factors that have been suggested to trigger narcolepsy include hormonal changes (which can occur during puberty or themenopause), major psychological stress, a sudden change in sleep patterns and an infection (such as flu).
is characterised by: Symptoms can range from getting a few words mixed up to having difficulty with all forms of communication, such as reading, writing, naming objects and understanding speech.Some people are unaware their speech makes no sense and get frustrated when others don't understand.

Nasal Decongestants
type: Class
subclass of: Supportive Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Drugs designed to treat inflammation of the nasal passages, generally the result of an infection (more often than not the common cold) or an allergy related condition, e.g., hay fever. The inflammation involves swelling of the mucous membrane that lines the nasal passages and results in inordinate mucus production. The primary class of nasal decongestants are vasoconstrictor agents. (From PharmAssist, The Family Guide to Health and Medicine, 1993)
database cross reference: MESH:D014663
definition source: http://www.ncbi.nlm.nih.gov/mesh/68014663
description adapted from source: no
hasBroadSynonym: Decongestant
hasBroadSynonym: Decongestants
hasRelatedSynonym: Nasal Vasoconstrictor Agents
hasRelatedSynonym: Vasoconstrictor Agents

National Origin
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: System of classification based on nation from which a person originates, regardless of the nation in which he/she currently resides.
curator note: Include list of nations below.
database cross reference: NCIT:C28407
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no

Nephritis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Test
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Nonspecfic term referring to inflammation affecting the kidney.
dc:source: HP_0000123
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000123
description adapted from source: yes
has disease stage: no
is caused by: May be caused by autoimmune disease, allergic responses, toxic injury, infectious causes.
is characterised by: May be associated with loss of kidney function, pyuria or hematuria, and proteinuria dependent upon cause.
hasExactSynonym: Kidney Inflammation

Nephrology
type: Class
subclass of: Urinary System
description: A subspecialty of internal medicine concerned with the anatomy, physiology, and pathology of the kidney.
database cross reference: MeSH:D009398
definition source: D009398
description adapted from source: no
hasRelatedSynonym: Kidney Diseases

Nephropathy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Serum Creatinine Level
subclass of: Restriction
  on property: diagnosed by
  some values from: Urinary Albumin Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Urinary Creatinine Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin Concentration
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Creatinine Concentration
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Test
subclass of: Restriction
  on property: treated with
  some values from: Angiotensin-Converting Enzyme Inhibitors
subclass of: Restriction
  on property: treated with
  some values from: Blood Transfusion
subclass of: Restriction
  on property: treated with
  some values from: Hydroxyurea
subclass of: Restriction
  on property: results_in
  some values from: Albuminuria
subclass of: Restriction
  on property: results_in
  some values from: End Stage Kidney Disease
subclass of: Restriction
  on property: results_in
  some values from: Hematuria
subclass of: Restriction
  on property: results_in
  some values from: Impaired Urinary Concentration
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A nonspecific term referring to disease or damage of the kidneys.
dc:source: HP_0000112
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000112
description adapted from source: no
is caused by: Nonspecific but may arise due to variety of conditions including but not limited to sickle cell disease, hypertension, diabetes mellitus, glomerular disease, hereditary diseases, cystic kidney disease.
is characterised by: Sickle cell nephropathy a complication of sickle cell disease associated with tubular and medullary dysfunction. Renal histology is often characterised by glomerular hypertrophy, perihilar focal segmental glomerulosclerosis, and global sclerosis.
hasExactSynonym: Kidney Damage

Nephrotic Syndrome
type: Class
subclass of: Nephropathy
subclass of: Restriction
  on property: diagnosed by
  some values from: Urinary Albumin Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Urinary Creatinine Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Urinary Protein Measurement
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin Excretion Rate
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin-Creatinine Ratio
subclass of: Restriction
  on property: treated with
  some values from: Angiotensin-Converting Enzyme Inhibitors
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: End Stage Kidney Disease
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Nephrotic syndrome is a collection of findings resulting from glomerular dysfunction with an increase in glomerular capillary wall permeability associated with pronounced proteinuria greater than 3.5g pre 24 hours. Nephrotic syndrome refers to the constellation of clinical findings that result from severe renal loss of protein, with Proteinuria >3.5 g per 24 hours (in children, >40 mg/m2/hr or PCR >2000 mg/g [>200 mg/mmol] or >300 mg/dl or 3+ on urine dipstick) plus hypoalbuminemia (<3gm/dl) and edema.
dc:source: HP_0000100
dc:source: KDIGO
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000100
description adapted from source: yes
has age of onset: Nephrotic syndrome related to sickle cell disease typically occurs in adulthood and preceded by lesser degree of proteinuria, other forms may occur at any age with different histologic lesions occurring at different ages.
has disease stage: no
is caused by: Variety of causes - in sickle cell disease, most common lesion is focal segmental glomerulosclerosis (FSGS). Other causes may be other forms of primary glomerular disease including membranous nephropathy, minimmal change disease, membranoproliferative glomerulonephritis. Secondary forms may result from diabetes, amyloidosis.
is characterised by: Heavy proteinuria, edema, hyperlipidemia. May also be assocaited with hypertension and increased risk of venous thrombosis.
hasExactSynonym: Nephrosis
comment: Is diagnosed by assessment of proteinuria (see Proteinuria) by 24hr urine collection or by urine protein-creatinine ratio on spot urine sample [KDIGO 2012].

Nephrotic-Range Proteinuria
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Urinary Albumin Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Urinary Creatinine Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Urinary Protein Measurement
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin Excretion Rate
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin-Creatinine Ratio
subclass of: Restriction
  on property: treated with
  some values from: Angiotensin-Converting Enzyme Inhibitors
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Hyperlipidemia
subclass of: Restriction
  on property: results_in
  some values from: Kidney Failure
subclass of: Restriction
  on property: results_in
  some values from: Nephrotic Syndrome
subclass of: Restriction
  on property: results_in
  some values from: Edema
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Severely increased amount of excretion of protein in the urine, defined as 3.5 grams per day or more in adults and 40 mg per meter-squared body surface area per hour in children, or urine protein to creatinine ratio >2000 mg/g [>200 mg/mmol] in children.
dc:source: HP_0012593
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0012593
description adapted from source: yes
has age of onset: in sickle cell disease, seen primarily in adult population but may develop in childhood if secondary cause occurs.
is caused by: Glomerular diseases that lead to protein loss in the urine (See nephrotic syndrome).
is characterised by: Severely increased amount of excretion of protein in the urine, defined as 3.5 grams per day or more in adults and 40 mg per meter-squared body surface area per hour in children, or urine protein to creatinine ratio >2000 mg/g [>200 mg/mmol] in children.
comment: Is diagnosed by assessment of proteinuria (see Proteinuria) by 24hr urine collection or by urine protein-creatinine ratio on spot urine sample [KDIGO 2012].

Nervous System
type: Class
subclass of: from phenotype
description: The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior.
database cross reference: UBERON:0001016
definition source: UBERON_0001016
description adapted from source: no
hasExactSynonym: Neurological System
hasNarrowSynonym: Nerve Net
hasRelatedSynonym: Systema Nervosum

Neurocognitive Impairment
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An invisible complication of sickle cell anemia (SS) that defies detection by imaging and other routine diagnostic methods. Impaired neurocognitive function in seemingly neurologically intact patients is not related to vasoocclusion or hemolysis. It is detected by neuropsychiatric and neurobehavioral testing and is associated with anemia and age.
definition source: PMC3415156
description adapted from source: no

Neurodevelopmental Abnormality
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A deviation from normal of the neurological development of a child, which may include any or all of the aspects of the development of personal, social, gross or fine motor, and cognitive abilities. This term should be used to describe abnormalities with onset in the developmental period.
database cross reference: HP:0012759
definition source: HP_0012759
description adapted from source: no

Neurological Rehabilitation
type: Class
subclass of: Rehabilitation
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Physician-supervised programs designed to rehabilitate people with diseases, trauma, or disorders of the nervous system.
database cross reference: MESH:D000066530
definition source: http://purl.bioontology.org/ontology/MESH/D000066530
description adapted from source: no
hasExactSynonym: Neurologic Rehabilitation
hasExactSynonym: Neurorehabilitation
hasExactSynonym: Rehabilitation, Neurologic
hasExactSynonym: Rehabilitation, Neurological

Neuron Degeneration
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Umbrella term for the progressive loss of structure or function of neurons, including death of neurons.
curator note: Provide source for additional info.
definition source: what
description adapted from source: yes
has age of onset: Usually in the elderly persons. Aging associated with most disorders
is caused by: Multifactorial causes such as program cell death, genetic mutations, protein misfolding and intracellular mechanisms
is characterised by: Multiple disease entities such as alzhiemers disease, parkinsons disease , huntington's disease and amylotrophic lateral sclerosis
hasExactSynonym: Nerve Degeneration
hasExactSynonym: Nerve Degenerations
hasExactSynonym: Neuron Degenerations

Newborn Screening for Sickle Cell
type: Class
subclass of: Genetic Screening
subclass of: Hematology Screening Test
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: test
curator note: Link to "Hb isoelectric focusing" and "HPLC fractionation" via "Test, Method or Assay" object property. Remove from " Genetic Screening".
comment: As an infant with sickle cell trait/disease grows and develops, the amount of Hb S will increase as the amount of hemoglobin F decreases. At about age 2, the levels stabilize.

NIH Stroke Scale (NIHSS)
type: Class
subclass of: Stroke Impact Measure
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A physical assessment of the various symptoms associated with a stroke, consisting of 11 categories.
dc:source: http://www.phenxtoolkit.org/index.php
abbreviation: NIHSS
database cross reference: PX820801
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: NIH Stroke Scale (NIHSS) #820801
validated for age ranges: 18 years and older
freely available: Examiners must be trained to administer, score, and interpret the NIH Stroke Scale (NIHSS). The National Institute of Neurological Disorders and Stroke (NINDS) provides a comprehensive interactive training DVD for the NIHSS. Information and purchasing details for this training are available on the NINDS website.
hasExactSynonym: NIH Stroke Scale
hasExactSynonym: NIHSS
comment: For each category of the NIHSS, the test administrator asks the respondent to perform an activity or respond to stimuli. Respondents receive a score for each category based upon their ability to complete the activity or respond to the action. Each score typically ranges from 0 to 3. Each category of the NIHSS is designed to determine the respondent’s level of consciousness (LOC), visual, motor, or language ability.

No-Show Patient
type: Class
subclass of: Patient Compliance
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Patients who do not turn up for scheduled healthcare appointments. Do not confuse with PATIENT DROPOUTS.
database cross reference: MESH:D000067455
definition source: http://purl.bioontology.org/ontology/MESH/D000067455
description adapted from source: no
hasExactSynonym: No Show Patient
hasExactSynonym: Patient No Show
hasExactSynonym: Patient No-Show

Nocturia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Frequent urination at night that interrupts sleep. It is often associated with outflow obstruction, diabetes mellitus, or bladder inflammation (cystitis).
dc:source: Nocturia
database cross reference: MeSH:D053158
definition source: D053158
description adapted from source: no
is caused by: Hormone imbalances and vesical problems.
hasExactSynonym: Nycturia

Non Opioid
type: Class
subclass of: Analgesics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A subclass of analgesic agents that typically do not bind to opioid receptors and are not addictive. Many non-narcotic analgesics are offered as nonprescription drugs.
database cross reference: MESH:D018712
definition source: D018712
description adapted from source: no
hasExactSynonym: Non-Narcotic
hasExactSynonym: Nonnarcotic
hasExactSynonym: Nonnarcotic Analgesic
hasExactSynonym: Nonnarcotic Opioid
hasExactSynonym: Nonopioid

Non-Globin Loci
type: Class
subclass of: Modifier Gene
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
creator: SCDO
description: A gene that is not a member of the alpha- or beta-globin family (see Alpha-globin or beta-globin).

Non-Proliferative Sickle Retinopathy
type: Class
subclass of: Sickle Retinopathy
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Sickle retinopathy caused by direct damage or remodeling of the small blood vessels supplying the retina secondary to vaso-occlusion and local ischemia.
abbreviation: NPSR
definition source: Retinopathy
definition source: Sickle Cell Retinopathy
description adapted from source: yes

Non-specific Acute Lower Respiratory Tract Episode
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: treated with
  some values from: Blood Transfusion
subclass of: Restriction
  on property: treated with
  some values from: Hydration
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Includes acute respiratory episodes with lower respiratory tract signs that do not meet the criteria for other diagnoses. May include episodes which would have been diagnosed as ACS were radiographic facilities available.
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
is caused by: Several possible etiologies including infections by various classes of microorganisms, pulmonary fat emobolism, infarction and pulmonary embolism.
is characterised by: Acute onset of respiratory symptoms and signs including cough, coryza +/- fever.

Obesity
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Healthy Diet
subclass of: Restriction
  on property: treated with
  some values from: Behavior Therapy
subclass of: Restriction
  on property: results_in
  some values from: Diabetes Mellitus
subclass of: Restriction
  on property: results_in
  some values from: Dyslipidemia
subclass of: Restriction
  on property: results_in
  some values from: Obstructive Sleep Apnea
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Body weight that is grossly above the acceptable or desirable weight, usually due to accumulation of excess fats in the body. The standards may vary with age, sex, genetic or cultural background. In the body mass index (BMI), a BMI greater than 30.0 kg/m2 is considered obese, and a BMI greater than 40.0 kg/m2 is considered morbidly obese.
curator note: Provide source for additional info.
database cross reference: HP:0001513
definition source: HP_0001513
description adapted from source: no
is caused by: Genetic predisposition, nutritional error, sedentary lifestyle.
is characterised by: Overweight, high body mass index.

Observational Study
type: Class
subclass of: Clinical Study
description: A work that reports on the results of a clinical study in which participants may receive diagnostic, therapeutic, or other types of interventions, but the investigator does not assign participants to specific interventions (as in an interventional study).
database cross reference: MESH:D064888
definition source: D064888
description adapted from source: no

Observational Studies as Topic
type: Class
subclass of: Clinical Studies as Topic
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Works about clinical studies in which participants may receive diagnostic, therapeutic, or other types of interventions, but the investigator does not assign participants to specific interventions (as in an interventional study).
definition source: D064887

Obstructive Sleep Apnea
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Electrocardiogram
subclass of: Restriction
  on property: diagnosed by
  some values from: Electrocardiographic Monitor
subclass of: Restriction
  on property: diagnosed by
  some values from: Electrocardiography
subclass of: Restriction
  on property: diagnosed by
  some values from: Electroencephalogram
subclass of: Restriction
  on property: diagnosed by
  some values from: Electroencephalograph
subclass of: Restriction
  on property: diagnosed by
  some values from: Electroencephalography
subclass of: Restriction
  on property: diagnosed by
  some values from: Pulse Oximeter
subclass of: Restriction
  on property: diagnosed by
  some values from: Pulse Oximetry (Rest)
subclass of: Restriction
  on property: diagnosed by
  some values from: Electrocardiograph
subclass of: Restriction
  on property: treated with
  some values from: Healthy Lifestyle
subclass of: Restriction
  on property: treated with
  some values from: Lifestyle
subclass of: Restriction
  on property: results_in
  some values from: Fatigue
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A condition characterized by obstruction of the airway and by pauses in breathing during sleep occurring many times during the night. Obstructive sleep apnea is related to a relaxation of muscle tone (which normally occurs during sleep) leading to partial collapse of the soft tissues in the airway with resultant obstruction of the air flow.
curator note: Provide source for additional info.
database cross reference: HP:0002870
definition source: HP_0002870
description adapted from source: no
has age of onset: 2-8 years
has disease stage: The severity is staged using the apnoea-hypopnoea index (AHI)Staged as 1. Mild 2. Moderate 3. Severe
is caused by: Overweight or obese, large neck, medicines, unusual structure in the neck such as narrow airway, large tonsils, adenoids or tongue or a small lower jaw, drinking and smoking.
is characterised by: Apnoea and hypopnoea
hasExactSynonym: Obstructive Sleep Apnoea

Occupation
type: Class
subclass of: Quality of Life
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An individual attribute that is the usual or principal work or business of an individual.
database cross reference: ExO:0000034
definition source: ExO_0000034
description adapted from source: no
hasExactSynonym: Career
hasExactSynonym: Employment
hasExactSynonym: Job
hasExactSynonym: Vocation
hasNarrowSynonym: Entrepreneurship

Occupational Therapy
type: Class
subclass of: Rehabilitation
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Skilled treatment that helps individuals achieve independence in all facets of their lives. It assists in the development of skills needed for independent living.
database cross reference: MESH:D009788
definition source: D009788
description adapted from source: no
hasBroadSynonym: Physical Therapy
hasBroadSynonym: Physiotherapy
hasExactSynonym: Occupational Therapies
hasExactSynonym: Therapies, Occupational
hasExactSynonym: Therapy, Occupational

Edema
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body.
database cross reference: HP:0000969
definition source: HP_0000969
description adapted from source: no
hasExactSynonym: Fluid Retention
hasExactSynonym: Oedema

Oligospermia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Reduced count of spermatozoa in the semen, defined as a sperm count below 20 million per milliliter semen.
dc:source: HP_0000798
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000798
description adapted from source: no
is caused by: Hypopituitarism, hyperprolactinemia, testosterone, chemotherapy, abnormalities of the testes, physical obstruction of the posttesticular genital tracts.
hasExactSynonym: Low Sperm Count

Oliguria
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Measurement
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Low output of urine, defined as an output below 5mL/kg/hr over 6 hours.
dc:source: HP_0100520
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0100520
description adapted from source: yes
is caused by: May be caused by any form of acute kidney injury, including volume depletion, ischemic injury, obstruction and intrinsic renal disease.
is characterised by: Low output of urine, defined as an output below 5mL/kg/hr over 6 hours.
hasExactSynonym: Reduced Urine Output

Onychodysplasia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The presence of developmental dysplasia of the nail.
dc:source: HP_0002164
dc:source: Medscape: Congenital Onychodysplasia: Author: Gregory J Raugi, MD, PhD; Chief Editor: William D James, MD et al.
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0002164
description adapted from source: no
is caused by: A genetic mechanism most likely underlies the pathophysiology of congenital onychodystrophy of the index finger. Two other proposed theories are (1) in utero ischemic injury and (2) in utero exposure to teratogens.
is characterised by: Anonychia, micronychia, polynychia, hemionychogryphosis, malaligned and deformed nails.
hasExactSynonym: Dysplastic nails

Onychomycosis
type: Class
subclass of: Infection
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: treated with
  some values from: Antifungal
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Onychomycosis is a fungal infection of the toenails or fingernails that may involve any component of the nail unit, including the matrix, bed, or plate.
dc:source: HP_0012203
dc:source: Medscape: Onychomycosis: Author: Antonella Tosti, MD; Chief Editor: Dirk M Elston, MD et al..
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0012203
description adapted from source: yes
has disease stage: Distal lateral subungual onychomycosis (DLSO), White superficial onychomycosis (WSO), Proximal subungual onychomycosis (PSO), Endonyx onychomycosis (EO), Candidal onychomycosis.
is caused by: Fungal infection.
is characterised by: Disfigured nails, pain, paraesthesia, loss of dexterity, difficulty walking, standing, exercise.

Ophthalmologic Complication
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Transient Monocular Blindness
subclass of: Restriction
  on property: results_in
  some values from: Blindness
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Any eye disorder occurring as a consequence of injury to the eye.
dc:source: Ballas et al 2010 Am J Hematol
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no
is characterised by: Insiduous nature in some cases, acute onset in others. Unusual in 1st decade of life.
hasExactSynonym: Ophthalmologic Manifestations
comment: These are relatively common and may occur in all segments of the eye and may not be detected at their early stages unless an eye examination is performed annually.

Ophthalmologic Surgical Procedure
type: Class
subclass of: Symptomatic Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Surgery performed on the eye or any of its parts.
database cross reference: MESH:D013508
definition source: D013508
description adapted from source: no

Ophthalmoscope
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Retinal Examination
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Device for examining the interior of the eye, permitting the clear visualization of the structures of the eye at any depth.
database cross reference: MESH:D019721
definition source: D019721
description adapted from source: yes
hasExactSynonym: Funduscope
hasExactSynonym: Ophthalmoscopes

Ophthalmoscopy
type: Class
subclass of: Eye Examination
subclass of: Restriction
  on property: has medical device
  some values from: Ophthalmoscope
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Examination of the interior of the eye with an ophthalmoscope.
curator note: Include "Direct Ophthalmoscopy" and "Indirect Ophthalmoscopy" as sub-classes? (Direct could be used to diagnose "Conjunctival Comma Sign")
database cross reference: MESH:D009887
definition source: D009887
description adapted from source: no

Opioid
type: Class
subclass of: Analgesics
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Any agent that acts on an opioid receptor or affects the life cycle of an opioid transmitter. Synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood.
curator note: Differences between Opioid Agent and Opioid Analgesic need to be checked. Then sub-classes of this term need to be checked for further classification.
database cross reference: CHEBI:35482
database cross reference: CHEBI:60598
definition source: CHEBI_35482
definition source: CHEBI_60598
description adapted from source: yes

Optical Instrument
type: Class
subclass of: Microscope
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Osteomalacia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Osteomalacia is a general term for bone weakness owing to a defect in mineralization of the protein framework known as osteoid.
dc:source: HP_0002749
curator note: Provide source for additional info.
database cross reference: HP:0002749
definition source: HP_0002749
description adapted from source: no
is caused by: Abnormal vitamin D metabolism: 1) Deficient intake or absorption;2) Defective 25-hydroxylation due to biliary cirrhosis- alcoholic cirrhosis- anticonvulsants; 3) Loss of vitamin D binding protein- nephrotic syndrome; 4) Defective 1-alpha 25-hydroxylation: Hypoparathyroidism, Renal failure, Vitamin D-dependent rickets type 1; 5) Defective target organ response to calcitriol: Vitamin D-dependent rickets, type II (Hereditary vitamin D resistant rickets, HVDRR). Mineralization defects: 1) Abnormal matrix: Chronic renal failure, Osteogenesis imperfecta, Fibrogenesis imperfecta, Axial osteomalacia; 2) Enzyme deficiency: Hypophosphatasia; 3) Mineralization inhibitors: bisphosphonates, Aluminum, fluoride. Phosphate deficiency: 1) Decreased intake ( antiacids); 2) Impaired renal reabsorption, that can be Primary defects = X-linked hypophosphatemic rickets (vitamin D resistant rickets, VDRR), Hereditary hypophosphatemic rickets with hypercalciuria, Sporadic acquired hypophosphatemic rickets, Fanconi syndrome, Wilson disease, cystinosis, multiple myeloma; or can be Secondary defects = 2) Secondary hyperparathyroidism (renal tubular acidosis, type 1 and disorders of vitamin D metabolism), 2) Oncogenic osteomalacia.
is characterised by: May be asymptomatic and present radiologically as osteopenia. Or it may present as diffuse bone and joint pain, muscle weakness, and difficulty walking, Fractures, Muscle spasms, cramps.
comment: Osteomalacia in children is known as rickets.

Osteomyelitis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Sepsis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An infection of bone.
curator note: Provide source for additional info. Move/copy below Infection?
database cross reference: HP:0002754
definition source: HP_0002754
description adapted from source: no
is caused by: Bacteria, blunt trauma, fracture, bone surgery.
is characterised by: Tenderness, redness, and warmth in the area of infection, fever, fatigue, bone pain, swelling around the affected bone, lost range of motion.
hasExactSynonym: Bone Infection

Osteonecrosis
type: Class
subclass of: Phenotype
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: caused by
  some values from: Ischemia
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: results_in
  some values from: SCD Related Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A disease where there is cellular death (necrosis) of bone components due to interruption of the blood supply.
dc:source: http://purl.bioontology.org/ontology/MEDLINEPLUS/C0029445
curator note: This term replaced "Avascular Necrosis" in QoL.
definition source: http://purl.bioontology.org/ontology/MEDLINEPLUS/C0029445
description adapted from source: yes
is characterised by: Local pain. Typical images on X-ray.
hasExactSynonym: AVN
hasExactSynonym: Aseptic Bone Necrosis
hasExactSynonym: Avascular Bone Necrosis
hasExactSynonym: Avascular Necrosis
hasExactSynonym: Avascular Necrosis (AVN)
hasExactSynonym: Bone Infarction
hasExactSynonym: Bone Infarcts
hasExactSynonym: Bone Necrosis
hasExactSynonym: Ischemic Bone Necrosis
hasExactSynonym: Osteochondronecrosis
comment: It is most common in the upper leg. Other common sites are your upper arm and your knees, shoulders and ankles.
comment: No one is sure what causes the disease. Risk factors include: Long-term steroid treatment Alcohol abuse Joint injuries Having certain diseases, including arthritis and cancer Doctors use imaging tests and other tests to diagnose osteonecrosis. Treatments include medicines, using crutches, limiting activities that put weight on the affected joints, electrical stimulation and surgery.

Osteonecrosis of the Femoral Head
type: Class
subclass of: Osteonecrosis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Necrotic changes in the bone tissue of the femoral head due to interruption of blood supply.
dc:source: http://www.ncbi.nlm.nih.gov/pubmed/1944426
dc:source: 24200532 Sickle-cell hip necrosis and intraosseous pressure
abbreviation: ONFH
curator note: Add description. See HPO term "Avascular necrosis of the capital femoral epiphysis". Perhaps add "Bone decompression by drilling" to therapeutics and link to it with "is treated with"
database cross reference: SNOMEDCT:203476003
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: Only label adapted
hasExactSynonym: Avascular Necrosis of Femoral Head
hasExactSynonym: Avascular Necrosis of the Capital Femoral Epiphysis
hasExactSynonym: Avascular Necrosis of the Femoral Head
hasExactSynonym: Avascular Necrosis of the Head of Femur
hasExactSynonym: ONFH
comment: Osteonecrosis of the femoral head is common in patients with sickle cell disease, with an incidence ranging from about 2 to 4.5 cases per 100 patient-years. Patients with the hemoglobin SS genotype and alpha-thalassemia and those with frequent painful crises are at highest risk. The overall prevalence is about 10 percent. The results of hip arthroplasty are poor.

Osteopenia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Diet, Food, and Nutrition
subclass of: Restriction
  on property: treated with
  some values from: Healthy Diet
subclass of: Restriction
  on property: treated with
  some values from: Healthy Lifestyle
subclass of: Restriction
  on property: treated with
  some values from: Exercise
subclass of: Restriction
  on property: results_in
  some values from: Osteoporosis
subclass of: Restriction
  on property: results_in
  some values from: SCD Related Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Osteopenia refers to a reduction in bone mineral density (BMD) below normal peak BMD but not low enough to be classified as osteoporosis. According to the WHO, osteopenia is characterized by a value of BMD more than 1 standard deviation below the young adult mean, but less than 2 standard deviations below this value.
curator note: Provide source for additional info.
database cross reference: HP:0000938
definition source: HP_0000938
description adapted from source: no
is caused by: Genetic predisposition, low calcium diet, getting little exercise, smoking, decrease in estrogen at the menopause, steroid medicine use for a long time, Vitamin D insufficiency.
is characterised by: Bone pain, backache, gradual loss of height, stooped posture, fractures.
hasExactSynonym: Decreased Bone Mineral Density
hasExactSynonym: Generalized osteopenia

Osteoporosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Exercise
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO, osteoporosis is characterized by a value of BMD 2.5 standard deviations or more below the young adult mean, based on age and sex.
curator note: Provide source for additional info.
database cross reference: HP:0000939
definition source: HP_0000939
description adapted from source: yes
is caused by: Genetic predisposition, low calcium diet, getting little exercise, smoking, decrease in estrogen at the menopause, steroid medicine use for a long time, Vitamin D insufficiency.
is characterised by: Bone pain, backache, gradual loss of height, stooped posture, fractures.

Otitis Media
type: Class
subclass of: Infection
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: treated with
  some values from: Antifungal
subclass of: Restriction
  on property: results_in
  some values from: Meningitis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Inflammation or infection of the middle ear.
curator note: Source needed for additional information.
database cross reference: HP:0000388
definition source: HP_0000388
description adapted from source: no
is caused by: Usually bacterial but can be caused by fungus or virus infection.
is characterised by: Pain or discharge from one or both ears

Oxycodone
type: Class
subclass of: Opioid
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A semisynthetic derivative of codeine that acts as a narcotic analgesic more potent and addicting than codeine.
database cross reference: DB00497
definition source: DB00497
description adapted from source: yes
hasExactSynonym: 14-hydroxy-3-methoxy-17-methyl-4,5alpha-epoxymorphinan-6-one
hasRelatedSynonym: (-)-14-Hydroxydihydrocodeinone
hasRelatedSynonym: 4,5-Epoxy-14-hydroxy-3-methoxy-17-methylmorphinan-6-one
hasRelatedSynonym: 4,5alpha-Epoxy-14-hydroxy-3-methoxy-17-methylmorphinan-6-one
hasRelatedSynonym: Dihydro-14-hydroxycodeinone
hasRelatedSynonym: Dihydrohydroxycodeinone
hasRelatedSynonym: Oxicodona
hasRelatedSynonym: Oxycodonum

Oxygen Saturation Measurement
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The determination of oxygen-hemoglobin saturation of blood either by withdrawing a sample and passing it through a classical photoelectric oximeter or by electrodes attached to some translucent part of the body like finger, earlobe, or skin fold. It includes non-invasive oxygen monitoring by pulse oximetry.
dc:source: Oxygen saturation (medicine)
database cross reference: NCIT:C60832
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: SO2

Oxygen Saturation of Arterial Blood
type: Class
subclass of: Oxygen Saturation Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Arterial Blood Gas Test
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Arterial oxygen saturation, as determined by an arterial blood gas test.
dc:source: Oxygen saturation (medicine)
definition source: Oxygen saturation (medicine)
description adapted from source: yes
hasExactSynonym: SaO2
hasExactSynonym: sats
comment: A value below 60% causes hypoxemia (which can also be caused by anemia). Hypoxemia due to low SaO2 is indicated by cyanosis.

Pain
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Transcutaneous Electrical Nerve Stimulation
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An unpleasant sensory and emotional experience triggered in the nervous system, associated with actual or potential tissue damage, or described in terms of such damage.
curator note: Include "Bone Pain" (from below "Musculoskeletal System") as sub-class? Provide source for additional info.
database cross reference: HP:0012531
definition source: HP_0012531
description adapted from source: yes
is caused by: Somatic pain is caused by injury to skin, muscles, bone, joint, and connective tissues. Deep somatic pain is usually described as dull or aching, and localized in one area. Visceral pain refers to pain that originates from ongoing injury to the internal organs or the tissues that support them. Somatic pain from injury to the skin or the tissues just below it often is sharper and may have a burning or pricking quality.
is characterised by: Nociceptive pain is believed to be caused by the ongoing activation of pain receptors in either the surface or deep tissues of the body. There are two types: "somatic" pain and "visceral" pain. Neuropathic pain is believed to be caused by changes in the nervous system that sustain pain even after an injury heals. "Psychogenic" pain is a simple label for all kinds of pain that can be best explained by psychological problems.

Pain Status
type: Class
subclass of: Physical Health
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
creator: SCDO
description: The impact of sickle cell pain on the daily activities of patients. The degree to which pain interferes with their quality of life. This pain is related to the unique features of Sickle Cell Disease.
hasExactSynonym: Pain Burden
hasExactSynonym: Pain Disability
hasExactSynonym: Pain Impact
hasExactSynonym: Pain Interference

Pallor
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Abnormally pale skin.
dc:source: HP_0000980
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000980
description adapted from source: no
has disease stage: Mild, moderate, severe.
is caused by: Anaemia, extreme cold
is characterised by: Whitening of the skin, loss of red colour in the skin or mucous membrane.
hasRelatedSynonym: Paleness

Palpation of Liver
type: Class
subclass of: Liver Examination
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
subclass of: Restriction
  on property: has curation status
  has value: to be replaced with external ontology term
dc:source: liver.html
curator note: Needs description.
definition source: http://purl.bioontology.org/ontology/SNOMEDCT/172488004
has_application_toward: Approximation of liver size. Feeling for tenderness and masses.

Paralysis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Paralysis of voluntary muscles means loss of contraction due to interruption of one or more motor pathways from the brain to the muscle fibers. Motor paralysis is often accompanied by an impairment in the facility of movement.
curator note: Provide source for additional info.
database cross reference: HP:0003470
definition source: HP_0003470
description adapted from source: yes
is caused by: Most paralysis is due to strokes or injuries such as spinal cord injury or a broken neck. Other causes of paralysis include: Nerve diseases such as amyotrophic lateral sclerosis, Autoimmune diseases such as Guillain-Barre syndrome, Bell's palsy, which affects muscles in the face, Polio used to be a cause of paralysis, but polio no longer occurs in the U.S.
is characterised by: Paralysis can be complete or partial. It can occur on one or both sides of your body. It can also occur in just one area, or it can be widespread. Paralysis of the lower half of your body, including both legs, is called paraplegia. Paralysis of the arms and legs is quadriplegia.
hasExactSynonym: Inability to Move

Parasite
type: Class
subclass of: Infectious Agent
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Invertebrate organisms that live on or in another organism (the host), and benefit at the expense of the other.
database cross reference: MESH:D010271
definition source: D010271
description adapted from source: Both label and description adapted
hasExactSynonym: Parasites

Patient Compliance
type: Class
subclass of: Health Behaviour
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Voluntary cooperation of the patient in following a prescribed regimen.
database cross reference: MESH:D010349
definition source: D010349
description adapted from source: no
hasExactSynonym: Patient Adherence
hasExactSynonym: Patient Cooperation

Patient Health Questionnaire-9 (PHQ-9)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The PHQ-9 is a multipurpose instrument for screening, diagnosing, monitoring and measuring the severity of depression. It incorporates DSM-IV depression diagnostic criteria with other leading major depressive symptoms into a brief self-report tool, and rates the frequency of the symptoms, which factors into the scoring severity index. The PHQ-9 is completed by the patient in minutes and is rapidly scored by the clinician.
abbreviation: PHQ-9
definition source: Kroenke K, Spitzer R, Williams W. The PHQ-9: Validity of a brief depression severity measure. Journal of General Internal Medicine. 2001; 16: 606-616.
description adapted from source: yes
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self
has target population: Clinic patients
has translations: Swahili; multiple languages for India; Portuguese; French; Spanish
selection criteria met: Widely used around the world, also used in SCD.
validated for age ranges: Adults 18 years and older
freely available: no
hasExactSynonym: PHQ-9
hasExactSynonym: Patient Health Questionnaire-9

Patient Reported Outcomes Measurement Information System (PROMIS)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Consists of 4 sub-scales: one Internal and 3 external subscales namely, powerful others, chance and God. Each of the 4 sub-scales has 6 items making a total of 24 items. The two original versions of the MHLC (forms A & B) deal with the general health status whereas the third version (Form C) assesses control-related cognitions about a specific disease state.
dc:source: http://www.phenxtoolkit.org/index.php
dc:source: Bevans, M., Ross, A., & Cella, D. (2014). Patient-Reported Outcomes Measurement Information System (PROMIS): Efficient, standardized tools to measure self-reported health and quality of life. Nursing Outlook, 62, 339-345.
dc:source: Dampier C, Barry V, Gross HE, Lui Y, Thornburg CD, DeWalt DA, Reeve BB. (2016). Initial Evaluation of the Pediatric PROMIS® Health Domains in Children and Adolescents With Sickle Cell Disease. Pediatric Blood & Cancer. Feb 19. doi: 10.1002/pbc.25944.
dc:source: DeWitt, E. M., Barnett, K., Farrell, J., Revicki, D., Carle, A., Cook, K., Sherry, D. D. (2014). A164: Development of pediatric item banks to measure pain behavior in the Patient-Reported Outcomes Measurement Information System. Arthritis & Rheumatology, 66(Suppl. 11), S212-S2121.
abbreviation: PROMIS
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: The development of PROMIS using modern measurement theory facilitates cross cultural adaptation. Translations use universal approach so do not have to be country specific.
has respondents: Self; Proxy (Parent report)
has target population: Clinic patients
has translations: French; Spanish; Portuguese
selection criteria met: Rigor in development, using modern measurement theory; used in multiple SCD studies
validated for age ranges: Children 5 - 17 years; Adults 18 years and older
freely available: no
hasExactSynonym: PROMIS
hasExactSynonym: Patient Reported Outcomes Measurement Information System

Patient Symptom Report
type: Class
subclass of: Medical Records
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A communication from a patient about something they perceive as being abnormal about their body or life.
database cross reference: OGMS:0000088
definition source: OGMS_0000088
description adapted from source: no

Pediatric Migraine Disability Assessment
type: Class
subclass of: Migraine Questionnaire
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The Pediatric Migraine Disability Assessment (PedMIDAS) headache disability questionnaire is completed by the patient and his/her parent and is reviewed with the clinician or study staff. It captures the impact of headaches on school performance (three questions), activities at home (one question on homework or chores), and social and/or sports functions (two questions). The PedMIDAS is scored by summing the answers across the six questions. If a range is provided as an answer, either use the high end of the range or prompt for a single answer. The frequency and severity are not scored but can be used for clinical reference.
dc:source: http://www.phenxtoolkit.org/index.php
abbreviation: PedMIDAS
database cross reference: PX130502
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Pediatric Migraine Disability Assessment #130502
hasExactSynonym: PedMIDAS

Pediatric NIH Stroke Scale (PedNIHSS)
type: Class
subclass of: Stroke Impact Measure
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A physical assessment of the various symptoms associated with a stroke, consisting of eleven categories. The PedNIHSS was developed by a panel of pediatric and adult stroke experts and is a modification of the adult NIH stroke scale (NIHSS). Modifications were made to allow individuals age 18 or younger to be assessed and are identified in the PedNIHSS by bold italic text.
dc:source: http://www.phenxtoolkit.org/index.php
abbreviation: PedNIHSS
database cross reference: PX820802
definition source: http://www.phenxtoolkit.org/index.php
has protocol: PhenX protocol: Pediatric NIH Stroke Scale (PedNIHSS) #820802
validated for age ranges: 2-18 years old
freely available: Examiners must be trained to administer, score, and interpret the NIHSS. The National Institute of Neurological Disorders and Stroke (NINDS) provides a comprehensive interactive training DVD for the National Institutes of Health Stroke Scale (NIHSS). Information and purchasing details for this training is available on the NINDS website.
hasExactSynonym: PedNIHSS
hasExactSynonym: Pediatric NIH Stroke Scale
comment: For each category of the PedNIHSS, the examiner asks the respondent to perform an activity or respond to an action by the provider. Respondents receive a score for each category based upon their ability to complete the activity or respond to the action. Each score typically ranges from 0 to 3. Each category of the PedNIHSS is designed to determine the respondent’s level of consciousness (LOC), visual, motor, or language ability.
comment: Life stage: Toddler, Child, Adolescent

Pediatric Quality of Life Inventory (PedsQL)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The MHLC scales consist of three forms of A, B and C. A and B are parallel forms and either one can be used, while Form C is applied for either the sick or to measure HLC under special conditions.
dc:source: Varni, J. W., Seid, M., and Kurtin, P. S. (2001). PedsQL 4.0: Reliability and validity of the 86 pediatric quality of life inventory version 4.0 generic core scales in healthy and patient populations. Medical Care, 39, 800-812.
abbreviation: PedsQL
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has respondents: Self; Proxy (Parent report)
has target population: Clinic patients
has translations: Many measures available in Spanish, French and Portuguese
validated for age ranges: Toddlers; Children; Adolescents
freely available: yes
hasExactSynonym: Pediatric Quality of Life Inventory
hasExactSynonym: PedsQL

Pediatric School Performance
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: An assessment of the respondent's educational performance and learning accommodations.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Include under QoL?
database cross reference: PX840200
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Pediatric School Performance #840201
has_application_toward: Many rare genetic conditions (e.g., sickle cell disease) and other diseases are associated with developmental delays, damage to the central nervous system, and frequent absences from school due to illness, all of which can impact school performance.

PedsQL Multidimensional Fatigue Scale
type: Class
subclass of: Pediatric Quality of Life Inventory (PedsQL)
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The 18-item PedsQL Multidimensional Fatigue Scale encompasses three domains: 1) General Fatigue, 2) Sleep/Rest Fatigue and 3) Cognitive Fatigue. The format, instructions, Likert response scale, and scoring method are identical to the PedsQL 4.0 Generic Core Scales [16], with higher scores indicating better HRQOL (lower fatigue symptoms). The instructions ask how much of a problem each item has been during the past one month.
dc:source: Panepinto JA, Torres S, Bendo CB, McCavit TL, Dinu B, Sherman-Bien S, Bemrich-Stolz C, Varni JW (2014). PedsQL Multidimensional Fatigue Scale in sickle cell disease: feasibility, reliability, and validity. Pediatric Blood & Cancer, 61,171-177
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has respondents: Self; Proxy (Parent report)
has target population: Clinic patients
selection criteria met: Validation study in SCD
validated for age ranges: Children 2 - 18 (child report ages 5 - 18 years; parent proxy report of children ages 2 - 18 years)

PedsQL Sickle Cell Disease Module
type: Class
subclass of: Pediatric Quality of Life Inventory (PedsQL)
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The PedsQL Sickle Cell Disease Module includes 43 items from 9 subscales: Pain and Hurt (9 items); Pain Impact (10 items); Pain Management and Control (2 items); Worry (5 items); Worry II (2 items); Emotions (2 items); Treatment (7 items); Communication I (3 items); and Communication II (3 items). For all ages, each item asks how much of a problem there has been in the past month. There are self- or parent-reported forms for ages 8 to 18, and responses are scored on a 5-point Likert-style scale (0 = never a problem; 1 = almost never a problem; 2 = sometimes a problem; 3 = often a problem; 4 = almost always a problem). Forms for children ages 5 to 7 are interviewer-administered, and responses include a 3-point Likert-style scale (0 = not at all a problem; 2 = sometimes a problem; 4 = a lot of a problem). Items are reversed-scored and converted to a 100-point scale (0 = 100, 1 = 75, 2 = 50, 3 = 25, 4 = 0) with higher scores indicating better quality of life. Scores for individual subscales are the sum of items divided by the total number or items answered. The total score for the PedsQL Sickle Cell Disease Module is the sum of the items divided by the number of items answered.
dc:source: http://www.phenxtoolkit.org/index.php
dc:source: Panepinto JA, Torres S, Bendo CB, McCavit TL, Dinu B, Sherman-Bien S, Bemrich-Stolz C, Varni JW (2013).PedsQL sickle cell disease module: feasibility, reliability, and validity.Pediatric Blood & Cancer, 60,1338-1344.
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has respondents: Self; Proxy (Parent report)
has target population: Children with SCD
has target population: Clinic Patients (Children with SCD)
validated for age ranges: Ages 2 to 18
freely available: The PedsQL™ Sickle Cell Disease Module is a proprietary instrument and administration requires permission and a license from the MAPI Research Trust.
comment: Life Stage: Toddler, Child, Adolescent
comment: Life stage: Toddler; Child; Adolescent

Penicillin
type: Class
subclass of: Preventative Therapeutics
subclass of: Symptomatic Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Any member of the group of substituted penams containing two methyl substituents at position 2, a carboxylate substituent at position 3 and a carboxamido group at position 6.
database cross reference: CHEBI:17334
definition source: CHEBI_17334
description adapted from source: no
hasExactSynonym: Penicillins

Penicillin Prophylaxis
type: Class
subclass of: Infection Prophylaxis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
creator: SCDO
description: Use of penicillin for the prevention of infections with penicillin-susceptible organisms, e.g. Streptococcus pneumoniae.
curator note: This term is in SNOMEDCT.

Percussion of Liver
type: Class
subclass of: Liver Examination
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
subclass of: Restriction
  on property: has curation status
  has value: to be replaced with external ontology term
dc:source: liver.html
curator note: Needs description.
curator note: To be requested for inclusion into SNOMED CT, below "Diagnostic procedure on liver".
has_application_toward: Measuring the liver size.

Perinatal Death
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Death anytime within the perinatal period.
dc:source: MP_0002081
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: MP:0002081
description adapted from source: yes
is caused by: Preterm birth, infant respiratory distress syndrome, birth defects, infections.
hasExactSynonym: perinatal death

Peripheral Neuropathy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Microscope
subclass of: Restriction
  on property: diagnosed by
  some values from: Patient Symptom Report
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: treated with
  some values from: Diet, Food, and Nutrition
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: results_in
  some values from: SCD Related Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Peripheral neuropathy is a general term for any disorder of the peripheral nervous system.
dc:source: 000593.htm
database cross reference: HP:0009830
definition source: HP_0009830
description adapted from source: yes
is characterised by: Symptoms depend on which nerve is damaged, and whether the damage affects one nerve, several nerves, or the whole body. Pain and numbness: Tingling or burning in the arms and legs may be an early sign of nerve damage. These feelings often start in your toes and feet. You may have deep pain. This often happens in the feet and legs. You may lose feeling in your legs and arms. Because of this, you may not notice when you step on something sharp. You may not notice when you touch something that is too hot or cold, like the water in a bathtub. You may not know when you have a small blister or sore on your feet. Numbness may make it harder to tell where your feet are moving and can cause a loss of balance. Muscle problems: Damage to the nerves can make it harder to control muscles. It can also cause weakness. You may notice problems moving a part of your body. You may fall because your legs buckle. You may trip over your toes. Doing tasks such as buttoning a shirt may be harder. You may also notice that your muscles twitch or cramp. Your muscles may become smaller. Problems with body organs: People with nerve damage may have problems digesting food. You may feel full or bloated and have heartburn after eating only a little food. Sometimes you may vomit food that has not been digested well. You may have either loose stools or hard stools. Some people have problems swallowing. Damage to the nerves to your heart may cause you to feel light-headed, or faint, when you stand up. Angina is the warning chest pain for heart disease and heart attack. Nerve damage may "hide" this warning sign. You should learn other warning signs of a heart attack. They are sudden fatigue, sweating, shortness of breath, nausea, and vomiting.
hasBroadSynonym: Neuropathy
hasExactSynonym: Peripheral Nerve Damage
hasExactSynonym: Peripheral Neuritis

Peripheral Oxygen Saturation
type: Class
subclass of: Oxygen Saturation Measurement
subclass of: Restriction
  on property: has medical device
  some values from: Pulse Oximeter
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Pulse Oximetry (Rest)
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An estimation of the oxygen saturation level usually measured with a pulse oximeter device.
definition source: Oxygen saturation (medicine)
description adapted from source: yes
hasExactSynonym: SpO2

Increased Hemoglobin F
type: Class
subclass of: Abnormal Hemoglobin Level Present in SCD
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Hemoglobin F (HbF) contains two globin alpha chains and two globin gamma chains. It is the main form of hemoglobin in the fetus during the last seven months of intrauterine development and in the half year of postnatal life. In adults it normally makes up less than one percent of all hemoglobiin. This term refers to an increase in HbF above this limit. In beta thalassemia major, it may represent over 90 percent of all hemoglobin, and in beta thalassemia minor it may make up between 0.5 to 4 percent.
database cross reference: HP:0011904
definition source: HP_0011904
description adapted from source: Only label adapted
hasExactSynonym: Persistence of Hemoglobin F
hasExactSynonym: Raised Hemoglobin F

Personal Attribute
type: Class
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The distinguishing qualities or prominent aspects of an individual person.
curator note: Populate this class with demographic terms from PhenX and elsewhere. Some terms will be duplicated in QoL. Add these from PhenX?: - Acculturation - Residential History Also look at other sub-classes in NCIT.
database cross reference: NCIT:C19332
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no

Personal Medical History
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A record of a patient's background regarding health and the occurrence of disease events of the individual. In addition, personal medical history may be a variable in epidemiologic studies.
curator note: Sub-classes in NCIT to be added here.
database cross reference: NCIT:C18772
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Medical History
hasExactSynonym: Past Medical History

Petechiae
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Ecchymosis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Petechiae are pinpoint-sized reddish/purple spots, resembling a rash, that appear just under the skin or a mucous membrane when capillaries have ruptured and some superficial bleeding into the skin has happened.
dc:source: HP_0000967
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000967
description adapted from source: yes
is caused by: Local injury and trauma, allergic reactions, autoimmune diseases, viral infections, thrombocythemia (an abnormally low platelet level), certain medical treatments such as radiation, chemotherapy, anticoagulants, cortisone, aspirin, idiopathic thrombocytopenic purpura (ITP), leukemia and other bone marrow malignancies that may lower the number of platelets, and sepsis (bloodstream infection).
is characterised by: Pinpoint-sized reddish/purple (bleeding )spots that appear just under the skin or a mucous membrane.

Phenotype
type: Class
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
curator note: Sub-classes to be added?: increased lactate dehydrogenase level (in Ontology of Adverse Events AOE) decreased lactate dehydrogenase level (Mammalian Phenotype Ontology) Splenomegaly (link this to Spleen Examination) Obstructive Hydrocephalus (see "Cerebellar Hemorrhage") Failure to Thrive (MeSH) Cardiac Output, Low (MeSH) Cardiac Output, High (MeSH) Properties to be used to link phenotypes to Disease Modifiers: - temporal pattern modified by - age of onset modified by - mortality modified by
database cross reference: OGMS:0000023
definition source: http://bioportal.bioontology.org/ontologies/OGMS
description adapted from source: no

Phenotype of Sickle Cell Disease
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A (combination of) quality(ies) of some or all sickle cell disease individuals, determined by the interaction of the genetic make-up of these individuals (with regard to sickle cell disease) and their environment.
dc:source: PMC5046828
dc:source: Hemoglobin. 2011;35(5-6):511-9. doi: 10.3109/03630269.2011.610477. Epub 2011 Sep 20.
curator note: Make sure complications as described in "Definitions of the Phenotypic Manifestations of Sickle Cell Disease" (Ballas, 2010) are included in Phenotype.
definition source: http://bioportal.bioontology.org/ontologies/OGMS
description adapted from source: Label and description adapted
has_application_toward: It is essential that the phenotypic manifestations of sickle cell disease be defined accurately so that communication among providers and researchers facilitates the implementation of appropriate and cost-effective diagnostic and therapeutic modalities.
comment: Although sickle cell disease arises due to a single gene mutation, the sickle cell gene is pleiotropic in nature and thus has multiple phenotypic expressions that constitute the complications of sickle cell disease.

Physical Detection Method
type: Class
subclass of: Diagnostic Technique, Method, Test or Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The physical method (technology) used to measure / readout the effect caused by a perturbagen in the assay environment.
curator note: Not sure if we want this term?
database cross reference: bao:BAO_0000035
definition source: BAO_0000035
description adapted from source: no

Physical Environment
type: Class
subclass of: Environmental Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The part of the human environment that consists of purely physical factors, including the natural environment (such as soil, climate, water supply) and the built environment.
definition source: "Physical Environment." Merriam-Webster.com. Merriam-Webster, n.d. Web. 9 Nov. 2016.
description adapted from source: yes

Physical Examination
type: Class
subclass of: Diagnostic Technique, Method, Test or Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Systematic and thorough inspection of the patient for physical signs of disease or abnormality.
dc:source: Overview1
database cross reference: MESH:D010808
definition source: D010808
description adapted from source: no
hasExactSynonym: Physical Assessment
comment: A primary care provider (PCP) performs this examination. A PCP may be a doctor, a nurse practitioner, or a physician assistant. The exam is also known as a wellness check.

Physical Health
type: Class
subclass of: Quality of Life
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: One's ability to carry out activities that require physical actions, ranging from self-care (activities of daily living) to more complex activities that require a combination of skills, often within a social context. "Physical Function" is inclusive of the term "disability" and includes the full spectrum of physical functioning from severe impairment to exceptional physical abilities.
dc:source: PROMIS Domain Frameworks/Definitions nih.promis.org
curator note: Determine and specify the description source. Include a term to do with level of independence?
curator note: The name of this term was changed from "Physical Functioning" to "Physical Health" so that it is named similarly to the "Mental Health" class.
description adapted from source: no
hasExactSynonym: Mobility
hasExactSynonym: Physical Function
hasExactSynonym: Physical Functioning
hasExactSynonym: Physical Health
hasRelatedSynonym: Disability
comment: Patient Reported Outcomes measure the effect of the disease as well as the positive and negative consequences of treatment on health and functioning from the patient’s perspective.

Physiological Assay
type: Class
subclass of: Diagnostic Technique, Method, Test or Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: An organismal assay designed to capture information pertaining to the the organic processes and phenomena of an organism or any of its parts or of a particular bodily process.
database cross reference: ERO:0001292
definition source: ERO_0001292
description adapted from source: no
preferred label: Physiological Test

Physiotherapy
type: Class
subclass of: Rehabilitation
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A therapeutic intervention that remediates impairments and promotes mobility, function, and quality of life through examination, diagnosis, and physical intervention.
database cross reference: OAE:0002476
definition source: OAE_0002476
description adapted from source: no
hasExactSynonym: Physical Therapy

Pica
type: Class
subclass of: Behavioral Abnormality
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An appetite for and the persistent ingestion of non-food substances such as clay. In order to diagnose pica, this behavior must have persisted over a period of at least one month.
dc:source: http://www.bloodjournal.org/content/116/21/4807
dc:source: http://www.ncbi.nlm.nih.gov/pubmed/11695934
database cross reference: HP:0011856
definition source: HP_0011856
description adapted from source: no
comment: Pica may be more prevalent in SCD compared with the general population but is an area in need of further study.

Pilot Projects
type: Class
subclass of: Study Design
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Small-scale tests of methods and procedures to be used on a larger scale if the pilot study demonstrates that these methods and procedures can work.
definition source: D010865

Platelet Count
type: Class
subclass of: Platelet Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The number of platelets (thrombocytes) in a specified volume of blood, usually expressed as platelets per cubic millimeter of whole blood.
database cross reference: CMO:0000029
definition source: CMO_0000029
description adapted from source: no
hasExactSynonym: Blood Platelet Number
hasExactSynonym: Blood Platelet count
hasExactSynonym: Platelet Number

Platelet Measurement
type: Class
subclass of: Blood Cell Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Any measurement of platelets, the disk-shaped structures found in the blood of mammals which play a vital role in blood coagulation. Platelets lack nuclei and DNA but contain active enzymes and mitochondria.
database cross reference: CMO:0000921
definition source: CMO_0000921
description adapted from source: no

Pneumatic Retinopexy
type: Class
subclass of: Symptomatic Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A nonincisional procedure that has become a well-accepted alternative to scleral buckling and vitrectomy for the repair of selected cases of rhegmatogenous retinal detachment.
abbreviation: PR
definition source: 1844217-overview
description adapted from source: yes
comment: Pneumatic retinopexy is a 2-step procedure. In the first step, an expanding gas bubble is injected into the vitreous cavity and the patient is positioned so that the bubble closes the retinal break, permitting resorption of subretinal fluid. The second step entails induction of a chorioretinal adhesion around all retinal breaks with cryopexy, laser, or both.

Pneumococcal 10-Valent Conjugate Vaccine
type: Class
subclass of: Conjugate Pneumococcal Vaccine
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An active immunizing vaccine used to prevent infection by the bacterium Streptococcus pneumoniae. It is indicated for disease caused by serotypes 1, 5, 4, 6B, 7, 9V, 14, 18C, 19F, and 23F.
abbreviation: PCV 10
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: PCV 10

Pneumococcal 13-Valent Conjugate Vaccine
type: Class
subclass of: Conjugate Pneumococcal Vaccine
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A pneumococcal conjugate vaccine containing 13 different strains of the bacterium Streptococcus pneumoniae, used in children and studied in immunocompromised patients for the prevention of pneumococcal disease. The pneumococcal 13-valent conjugate vaccine contains capsular antigen polysaccharides derived from the S. pneumoniae serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F and 23F that are individually conjugated to a nontoxic diphtheria cross-reactive material (CRM) carrier protein (CRM197). Upon vaccination, pneumococcal 13-valent conjugate vaccine induces active immunization against 13 different serotypes of S. pneumoniae and protects against pneumococcal disease.
dc:source: http://www.cdc.gov/vaccines/vpd-vac/pneumo/default.htm
abbreviation: PCV 13
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: PCV 13
hasExactSynonym: PCV13 Vaccine
hasExactSynonym: Prevnar 13
comment: The pneumococcal conjugate vaccine, PCV13 is currently recommended for all children younger than 5 years old, all adults 65 years or older, and people 6 through 64 years old with certain medical conditions.

Pneumococcal 7-Valent Conjugate Vaccine
type: Class
subclass of: Conjugate Pneumococcal Vaccine
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An active immunizing agent used to prevent infection by the bacterium Streptococcus pneumoniae. Pneumococcal 7-valent conjugate vaccine consists of a solution of saccharides of the capsular antigens of Streptococcus serotypes 4, 6B, 9V, 14, 18C, 19F, and 23F individually conjugated to diphtheria CRM 197 protein.
abbreviation: PCV 7
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: 7 Valent PncOMPC Vaccine
hasExactSynonym: 7-Valent PncOMPC Vaccine
hasExactSynonym: Heptavalent Pneumococcal Conjugate Vaccine
hasExactSynonym: PCV 7
hasExactSynonym: PCV7 Vaccine
hasExactSynonym: Pneumococcal 7-Valent Conjugate Vaccine (Diphtheria CRM197 Protein)
hasExactSynonym: Prevenar
hasExactSynonym: Prevnar
hasExactSynonym: Seven Valent Pneumococcal PS Meningococcal OMPC Conjugate Vaccine
hasExactSynonym: Seven-Valent Pneumococcal PS-Meningococcal OMPC Conjugate Vaccine

Pollution
type: Class
subclass of: Physical Environment
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: An environmental system process that results in the introduction of contaminants into an environment.
database cross reference: ENVO:02500036
definition source: ENVO_02500036
description adapted from source: no
hasExactSynonym: Environmental Pollution

Polymerase Chain Reaction
type: Class
subclass of: Genetic Technique
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
abbreviation: PCR
database cross reference: OBI:0000415
definition source: OBI_0000415
description adapted from source: no
hasExactSynonym: PCR

Polyneuropathy
type: Class
subclass of: Peripheral Neuropathy
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: diagnosed by
  some values from: Spirometry
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Test
subclass of: Restriction
  on property: treated with
  some values from: Occupational Therapy
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A generalized disorder of peripheral nerves.
dc:source: polyneuropathy
dc:source: overview-of-polyneuropathy
database cross reference: HP:0001271
definition source: HP_0001271
is caused by: Acute polyneuropathy has many causes: Infections involving a toxin produced by bacteria, as occurs in diphtheria,An autoimmune reaction (when the body attacks its own tissues), as occurs in Guillain-Barré syndrome (see Guillain-Barré Syndrome), Drugs, including the anticonvulsant phenytoin, some antibiotics (such as chloramphenicol, nitrofurantoin, and sulfonamides), some chemotherapy drugs (such as vinblastine and vincristine), and some sedatives (such as barbital and hexobarbital), Cancer (such as multiple myeloma), which damages nerves by directly invading or putting pressure on them or by triggering an autoimmune reaction, Certain toxins, such as organophosphate insecticides, triorthocresyl phosphate (TOCP), and thallium The cause of chronic polyneuropathy is often unknown. Known causes include the following: Diabetes Mellitus, Excessive use of alcohol, Nutritional deficiencies (such as thiamin deficiency), an uncommon cause in the United States, except among alcoholics who are malnourished, Vitamin B12 deficiency, which causes subacute combined degeneration of the spinal cord (see Subacute Combined Degeneration) and often pernicious anemia (see Inadequate absorption), An underactive thyroid gland (hypothyroidism), Toxic substances, including heavy metals such as lead and mercury, Kidney failure, Certain cancers, such as lung cancer, Rarely, vitamin B6 (pyridoxine) taken in excessive amounts.
is characterised by: Acute polyneuropathy (as occurs in Guillain-Barré syndrome) begins suddenly in both legs and progresses rapidly upward to the arms. Symptoms include weakness and a pins-and-needles sensation or loss of sensation. The muscles that control breathing may be affected, resulting in respiratory failure.In the most common form of chronic polyneuropathy, only sensation is affected. Usually, the feet are affected first, but sometimes the hands are. A pins-and-needles sensation, numbness, burning pain, and loss of vibration sense and position sense (knowing where the arms and legs are) are prominent symptoms. Because position sense is lost, walking and even standing become unsteady. Consequently, muscles may not be used. Eventually, they may weaken and waste away. Then, muscles may become stiff and permanently shortened (called contractures). Diabetic neuropathy commonly causes painful tingling or burning sensations in the hands and feet-a condition called distal polyneuropathy. Pain is often worse at night and may be aggravated by touch or by a change in temperature. People may lose the senses of temperature and pain, so they often burn themselves and may have open sores caused by prolonged pressure or other injuries. Without pain as a warning of too much stress, joints are susceptible to injuries. This type of injury is called neurogenic arthropathy (Charcot joints) Polyneuropathy often affects the nerves of the autonomic nervous system, which controls involuntary functions in the body (such as blood pressure, heart rate, digestion, salivation, and urination). Typical symptoms are constipation, sexual dysfunction, and fluctuating blood pressure-most notably a sudden fall in blood pressure when a person stands up (orthostatic hypotension). The skin may become pale and dry, and sweating may be reduced. Much less often, control of bowel movements or urination is lost, leading to fecal or urinary incontinence.
hasExactSynonym: Peripheral Nerve Disease

Polyvalent Pneumococcal Vaccine
type: Class
subclass of: Streptococcus Pneumoniae Vaccine
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An polyvalent vaccine used to prevent infection by the bacterium Streptococcus pneumoniae. Pneumococcal polyvalent vaccine contains highly purified capsular antigens from the 23 most prevalent or invasive pneumococcal types of Streptococcus pneumoniae to ensure cross-protection. Following vaccination, protective capsular type-specific antibody levels typically develop by the third week; serotype-specific antibody levels generally decline after 5-10 years.
dc:source: index.html
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: Only label adapted
hasBroadSynonym: Pneumococcal vaccine
hasExactSynonym: PPSV
hasExactSynonym: Pneumococcal Polysaccharide Vaccine
hasExactSynonym: Pneumococcal Polyvalent Vaccine
hasNarrowSynonym: Pneumovax 23
comment: Pneumococcal polysaccharide vaccine is recommended for all adults 65 years or older, people 2 through 64 years old who are at increased risk for disease due to certain medical conditions, and adults 19 through 64 years old who smoke cigarettes.

Postpartum Hemorrhage
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Blood Transfusion
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Significant maternal haemorrhage/blood loss following deilvery of a child.
dc:source: HP_0011891
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0011891
description adapted from source: no
is caused by: Atonia, trauma, coagulopathy.
is characterised by: Hemorrhage after delivery, with loss of more than 500 to 1000 mL of blood, causing hemodinamic instability.
hasExactSynonym: Bleeding post-delivery

Pragmatic Clinical Trial
type: Class
subclass of: Randomized Controlled Trial
description: Works about randomized clinical trials that compare interventions in clinical settings and which look at a range of effectiveness outcomes and impacts.
database cross reference: MESH:D065007
definition source: D065007
description adapted from source: no

Preeclampsia
type: Class
subclass of: Comorbid Disease
subclass of: Restriction
  on property: results_in
  some values from: Coma
subclass of: Restriction
  on property: results_in
  some values from: Eclampsia
subclass of: Restriction
  on property: results_in
  some values from: Kidney Failure
subclass of: Restriction
  on property: results_in
  some values from: Preterm Delivery
subclass of: Restriction
  on property: results_in
  some values from: Seizure
subclass of: Restriction
  on property: results_in
  some values from: Stroke
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Pregnancy-induced hypertension in association with significant amounts of protein in the urine.
database cross reference: HP:0100602
definition source: HP_0100602
description adapted from source: no
is caused by: Abnormal development of placental vessels, low flow blood of the placental vessels.
is characterised by: Edema, hypertension, proteinuria, headache, visual abnormalities, abdominal pain, nausea, vomiting.
hasExactSynonym: Pre-eclampsia

Prenatal Screening for Sickle Cell
type: Class
subclass of: Genetic Screening
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: test

Preterm Delivery
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Hospitalization
subclass of: Restriction
  on property: results_in
  some values from: Infection
subclass of: Restriction
  on property: results_in
  some values from: Neurodevelopmental Abnormality
subclass of: Restriction
  on property: results_in
  some values from: Seizure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The birth of a baby of less than 37 weeks of gestational age.
dc:source: HP_0001622
curator note: Provide source for additional info.
database cross reference: HP:0001622
definition source: HP_0001622
description adapted from source: Only label adapted.
is caused by: Preeclampsia, chronic condition of the mother, twin pregnancy, infection, some gynecologic diseases, smoking, drug use, stress, physical injury or trauma, maternal age less than 17 years or greater than 35 years, some defect in the fetus, placental abnormality.
is characterised by: Birth ahead of schedule
hasExactSynonym: Premature Birth
hasExactSynonym: Premature Delivery
hasExactSynonym: Premature Delivery of Affected Infants
hasExactSynonym: Preterm Birth

Preventative Therapeutics
type: Class
subclass of: Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
creator: SCDO
description: Activities to prevent Sickle Cell Disease or its complications.
hasExactSynonym: Preventive Therapeutics
hasExactSynonym: Prophylactic Therapeutics

Priapism
type: Class
subclass of: Phenotype
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A prolonged painful erection that may last hours and is not associated with sexual activity. It is seen in patients with sickle cell anemia, advanced malignancy, spinal trauma, and certain drug treatments.
dc:source: Nelson, Winter. Priapism: evolution of management in 48 patients in a 22 year series. J Urology 1977;117:455-58
database cross reference: MESH:D011317
definition source: D011317
description adapted from source: no
comment: Patients with known etiology should be treated specifically for the primary disease and usually more conservatively for priapism.
comment: Priapism can affect sexual relations and reproductive potential for men.

Primary Healthcare
type: Class
subclass of: Health System
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Care which provides integrated, accessible health care services by clinicians who are accountable for addressing a large majority of personal health care needs, developing a sustained partnership with patients, and practicing in the context of family and community.
curator note: This term is not below Quality of Health Care in MESH, but below "Health Services Administration" ---> "Patient Care Management" ---> "Comprehensive Health Care"
database cross reference: MESH:D011320
definition source: D011320
description adapted from source: no
hasExactSynonym: Primary Care
hasExactSynonym: Primary Health Care

Proguanil
type: Class
subclass of: Malaria Prophylaxis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Proguanil is a prophylactic antimalarial drug, which works by stopping the malaria parasite, Plasmodium falciparum and Plasmodium vivax, from reproducing once it is in the red blood cells. It does this by inhibiting the enzyme, dihydrofolate reductase, which is involved in the reproduction of the parasite.
database cross reference: DB01131
definition source: DB01131
description adapted from source: no
hasExactSynonym: 1-(P-Chlorophenyl)-5-isopropylbiguanide
hasExactSynonym: Chlorguanide
hasExactSynonym: Chloroguanide
hasExactSynonym: N-(4-Chlorophenyl)-n'-(isopropyl)-imidodicarbonimidic diamide

Proliferative Sickle Retinopathy
type: Class
subclass of: Sickle Retinopathy
subclass of: Restriction
  on property: diagnosed by
  some values from: Retinal Examination
subclass of: Restriction
  on property: diagnosed by
  some values from: Slit-Lamp Examination
subclass of: Restriction
  on property: diagnosed by
  some values from: Fluorescein Angiography
subclass of: Restriction
  on property: results_in
  some values from: Blindness
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Sickle retinopathy that involves the upregulation of vascular growth factors due to chronic changes of local hypoxia and ischemia.
dc:source: Sickle Cell Retinopathy
dc:source: Ballas et al 2010 Am J Hematol
dc:source: Bonanomi et al 2013 Arq Bras Oftalmol
abbreviation: PSR
definition source: Sickle Cell Retinopathy
description adapted from source: yes
is caused by: Sickle Cell Disease
is characterised by: Neovascularization and formation of sea fans.
hasExactSynonym: Retinopathy due to SCD Characterized by Neovascularization
hasExactSynonym: Sickle Cell Proliferative Retinopathy
comment: Diagnostic Criteria: Eye exam using direct and indirect ophthalmoscopy, slit lamp biomicroscopy, and fluorescein angiography. Ophthalmoscopic inspection is usually sufficient to detect the five clinical stages listed under the "Severity Index" below. Severity Index: Stage I: peripheral arteriolar occlusion(s). Stage II: vascular remodeling with arteriovenous anastomoses at the boundary between perfused and nonperfused peripheral retina. Stage III: peripheral retinal neovascularization that assumes a frond-like configuration resembling the marine invertebrate Gorgonia flabellum (sea fan). Most sea fan formations are found at the interface between perfused and non-perfused peripheral retina growing toward the ischemic pre-equatorial retina. Stage IV: defined by the presence of vitreous hemorrhage. As sea fans grow into the vitreous cavity, traction on their delicate vascular channels results in bleeding at irregular intervals for years. Stage V: retinal detachment.
comment: Involves neovascular fronds that emerge from the retinal vasculature at the interface of perfused and non-perfused retina in response to vascular growth factors produced by ischemic retina. The neovascular tissue is predisposed to hemorrhage and vitreoretinal traction forces. Although these preretinal neovascular formations, which may resemble and are called sea fans, are bright red when viable, they appear white when autoinfarcted or caused to involute by laser photocoagulation.
comment: The ocular complications of PSR are more characteristically seen in HbC (SC) and SThal disease, rather than in SS disease.

PROMIS Adult Profile 29
type: Class
subclass of: Patient Reported Outcomes Measurement Information System (PROMIS)
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: This protocol includes 29 self-administered quality of life-type questions from the PROMIS Profile 29 for adults. The quality of life questions include physical function, anxiety, depression, fatigue, sleep disturbance, ability to participate in social roles and activities, and pain intensity over the past 7 days. Each question, except for the pain intensity question, is measured on a 5-point scale.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Quality of Life - Adult #221302
has respondents: Self
has_application_toward: Information collected from this questionnaire can be used to assess the individual’s current quality of life, which may influence emotional and physical problems.
validated for age ranges: 18 years and older
hasExactSynonym: PROMIS 25 Profie v2.0
comment: Life stage: Adult

PROMIS Pediatric Profile 25
type: Class
subclass of: Patient Reported Outcomes Measurement Information System (PROMIS)
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: This protocol includes 25 quality of life-type questions relating to physical function mobility, anxiety, depressive symptoms, fatigue, peer relationships, pain interference, and pain intensity over the past 7 days.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Quality of Life - Pediatric #221301
has respondents: Self; Proxy (Parent report)
has_application_toward: Information collected from this questionnaire can be used to assess the individual’s current quality of life, which may influence emotional and physical problems.
validated for age ranges: Children age 8-17 years old (parent proxy for children age 5-17 years old)
hasExactSynonym: PROMIS 25
hasExactSynonym: PROMIS 25 Profie
comment: Life Stage: Child, Adolescent
comment: This measure consists of seven item banks. There is one bank for physical function mobility, anxiety, depressive symptoms, fatigue, peer relationships, pain interference, and pain intensity. For each question, the respondent is asked to reflect on the past 7 days. The pain intensity item bank contains one question with a 10-point answer scale. The other banks each contain four questions, and each question has a 5-point answer scale.

Infection Prophylaxis
type: Class
subclass of: Preventative Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A planned process that has the objective to reduce the risk of acquiring one or more disorders.
database cross reference: OGMS:0000103
definition source: OGMS_0000103
description adapted from source: no

Prospective Studies
type: Class
subclass of: Cohort Studies
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Observation of a population for a sufficient number of persons over a sufficient number of years to generate incidence or mortality rates subsequent to the selection of the study group.
definition source: D011446

Proteinuria
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Serum Creatinine Level
subclass of: Restriction
  on property: diagnosed by
  some values from: Urinary Protein Measurement
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin Concentration
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin Excretion Rate
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Albumin-Creatinine Ratio
subclass of: Restriction
  on property: treated with
  some values from: Angiotensin-Converting Enzyme Inhibitors
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Chronic Kidney Disease
subclass of: Restriction
  on property: results_in
  some values from: Nephrotic Syndrome
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Increased amounts of any protein (including albumin) in the urine - typically more than 300mg in a 24hr period.
dc:source: sickle-cell-disease-guidelines
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000093
definition source: HP_0000093
description adapted from source: yes
has age of onset: In sickle cell disease, overt proteinuria (distinguised from albuminuria) may be noted in childhood although less common (4.5% in ages 2-21 [Wigfall 2000] v. 26% in adults [Guasch 2006]).
has disease stage: At most severe form - lead to nephrotic syndrome.
is caused by: Caused by a variety of kidney diseases, including sickle cell disease, diabetes, glomerular disease, arteriosclerosis.
is characterised by: Elevated amounts of protein in the urine - typically greater than 300mg in 24 hrs.
hasExactSynonym: High Urine Protein Levels
comment: Screening Recommendations: Screen all individuals with SCD, beginning by age 10, for proteinuria. If the result is negative, repeat screening annually. If the result is positive, perform a first morning void urine albumin-creatinine ratio and if abnormal, consult with or refer to a renal specialist.

Prothrombin Time
type: Class
subclass of: Blood Coagulation Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Measurement of the clotting ability of fibrinogen, prothrombin, proaccelerin, proconvertin and Stuart factor, usually given in seconds to formation of clot after the addition of a tissue factor or thromboplastin.
dc:source: CMO_0000211
database cross reference: CMO:0000211
description adapted from source: no
hasExactSynonym: PTT

Provider Attitudes Toward Patients with Sickle Cell Disease
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: This is a 17-item scale, separated into 4 subscales with good psychometric properties. Negative Attitudes Scale comprises six items grouped together (Mean=36.5, SD=21.9, Potential range = 0 to 100). Higher scores on this scale indicate an endorsement of more negative views about SCD patients. Positive Attitudes Scale comprises four items grouped together (Mean=45.7, SD=24.3, Potential range = 0 to 100). Higher scores indicate an endorsement of more positive views about SCD patients. Concern Raising Behaviors Scale comprises four items grouped together (Mean = 53.7, SD = 22.0, Potential range = 0 to 100). Higher scores indicate greater endorsement of the belief that certain SCD patient behaviors raise clinician concern that the patient is inappropriately drug-seeking. Red-Flag Behaviors Scale comprises three items grouped together (Mean = 58.7, SD = 22.7, Potential range = 0 to 100). Higher scores on this scale indicate greater endorsement of the belief that certain SCD patient behaviors raise clinician concern about patient drug-seeking.
dc:source: Haywood, Jr., C., Lanzkron, S., Hughes, MD3, Brown, R., Massa, M., Ratanawongsa, N., and Beach, MC. (2010). A Video-Intervention to Improve Clinician Attitudes Toward Patients with Sickle Cell Disease: The Results of a Randomized Experiment. J Gen Intern Med 26(5):518–23.
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: African Americans
has respondents: Self
has target population: Heath care providers
selection criteria met: Demonstrated validity with SCD populations in the US
validated for age ranges: Adults
freely available: no

Pruritus
type: Class
subclass of: Cyanosis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Pruritus, or itch, is defined as an unpleasant sensation that provokes the desire to scratch.
dc:source: HP_0000989
dc:source: Pruritus and Systemic Disease by Author: David F Butler, MD; Chief Editor: William D James, MD Medscape
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000989
description adapted from source: yes
has disease stage: Localized or systemic.
is caused by: Renal, cholestatic, hematologic, endocrine and idiopathic.
is characterised by: Itchiness.
hasExactSynonym: Itchy skin

Psoriasis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A skin abnormality characterized by redness and irritation, with thick, red skin that displays flaky, silver-white patches (scales).
dc:source: HP_0003765
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0003765
description adapted from source: no
is caused by: Genetic predispostion with enviromental triggers.
is characterised by: Skin characterized by redness, irritation, with thick, red skin that displays flaky, silver-white patches (scales).

Psychological Stress
type: Class
subclass of: Mental Health
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Social, psychological, and environmental occurrences, which require an adjustment or effect a change in an individual's pattern of living.
database cross reference: MESH:D008016
definition source: D008016
description adapted from source: Label and description adapted
hasExactSynonym: Emotional Stress
hasExactSynonym: Life Stress

Psychosocial Deprivation
type: Class
subclass of: Mental Health
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The absence of appropriate stimuli in the physical or social environment which are necessary for the emotional, social, and intellectual development of the individual.
curator note: This term is placed below "Culture" in MESH.
database cross reference: MESH:D011610
definition source: D011610
description adapted from source: no
hasExactSynonym: Psychosocial Deprivations

Psychosocial Effect
type: Class
subclass of: Mental Health
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Having to do with the physical, psychological, cognitive, and social consequences of disease, including stigmatization of persons affected.
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no
hasExactSynonym: Psychosocial
hasExactSynonym: Psychosocial Effects
hasExactSynonym: Psychosocial Effects/Treatment
hasExactSynonym: Treatment/Psychosocial Effects

Psychotherapy
type: Class
subclass of: Supportive Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A generic term for the treatment of mental illness or emotional disturbances primarily by verbal or nonverbal communication. Branch of psychotherapy associated with Victor Frankl.
database cross reference: MESH:D011613
definition source: D011613
description adapted from source: no
hasBroadSynonym: Psychiatry
hasBroadSynonym: Therapy
hasExactSynonym: Logotherapy
hasExactSynonym: Psycho-Therapy

Publication Type
type: Class
subclass of: Evidence Code
description: Describes the type of material the article represents (e.g., Review, Clinical Trial, Retracted Publication, Letter); see the PubMed Publication Types, e.g., review[pt]. Publication Types are arranged hierarchically with more specific terms arranged beneath broader terms.
definition source: http://bioportal.bioontology.org/ontologies/EDDA_PT
description adapted from source: no

Pulmonary Function Test
type: Class
subclass of: Physiological Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A test that measures breathing and how well the lungs are functioning. There are three different measures of lung function: spirometry, lung volumes, and diffusion capacity.
dc:source: 003853.htm
abbreviation: PFT
definition source: 003853.htm
definition source: pft.htm
description adapted from source: yes
has_application_toward: Pulmonary function tests are done to: Diagnose certain types of lung disease (such as asthma, bronchitis, and emphysema); Find the cause of shortness of breath; Measure whether exposure to chemicals at work affects lung function; Check lung function before someone has surgery. Assess the effect of medication; Measure progress in disease treatment.
hasExactSynonym: Lung Function Test
hasExactSynonym: PFT
hasExactSynonym: Respiratory Function Test
comment: Normal values are based upon your age, height, ethnicity, and gender. Normal results are expressed as a percentage. A value is usually considered abnormal if it is less than 80% of your predicted value.

Pulmonary Hypertension
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: N-terminal Pro-brain Natriuretic Peptide Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An elevation of pulmonary arterial systolic pressure (PASP) (>25 mmHg at rest or >30 mmHg with exercise).
dc:source: Simonneau et al 2013 J Am Coll Cardiol; Ataga et al.
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info. Perhaps use description from term in existing ontology?
description adapted from source: yes
is caused by: Multifactorial, including chronic thromboembolism, splenectomy, high cardiac output, left-heart disease, and hyperviscosity; the role of an inactivation of nitric oxide by free plasma hemoglobin due to chronic hemolysis is controversial.
is characterised by: Chest pain and poor exercise tolerance.

Pulse Oximeter
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has measurement
  some values from: Peripheral Oxygen Saturation
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Pulse Oximetry (Rest)
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: A measurement device, usually attached to the earlobe or fingertip, that measures the oxygen saturation of arterial blood.
database cross reference: ERO:0000876
definition source: ERO_0000876
description adapted from source: Only label adapted
hasExactSynonym: Blood Oxygen Monitor
hasExactSynonym: Oxygen Monitor

Pulse Oximetry (Rest)
type: Class
subclass of: Pulmonary Function Test
subclass of: Restriction
  on property: has measurement
  some values from: Peripheral Oxygen Saturation
subclass of: Restriction
  on property: has medical device
  some values from: Pulse Oximeter
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A non-invasive method that provides estimates of arterial oxyhemoglobin saturation by utilizing selected wavelengths of light to determine the saturation of oxyhemoglobin.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no
has protocol: PhenX protocol: Pulse Oximetry (Rest) #091101
has_application_toward: This measure is used to determine if study subject's oxygenation level is unstable.
comment: The pulse oximeter consists of a small device that clips to the body (typically a finger, earlobe or an infants foot) and transfers its readings to a reading meter by wire or wirelessly. The device uses light-emitting diodes in conjunction with a light-sensitive sensor to measure the absorption of red and infrared light in the extremity. The difference in absorption between oxygenated and deoxygenated hemoglobin makes the calculation possible.

Pyoderma
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: results_in
  some values from: Infection
subclass of: Restriction
  on property: results_in
  some values from: Skin Ulcer
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Any manifestation of a skin disease associated with the production of pus.
dc:source: HP_0000999
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0000999
description adapted from source: no
is caused by: Bacterial infection or skin infection.
is characterised by: Impetigo, impetigo contagiosa, ecthyma, folliculitis, Bockhart's impetigo, furuncle, carbuncle, tropical ulcer, pyoderma gangrenos (autoimmune).
hasExactSynonym: Pus-Filled Lesion

Quality of Care Measure
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A measure used to assess patient-reported utilization and perceptions about quality of care for individuals treated for sickle cell disease (SCD).
curator note: Include as sub-classes: ASQE-Me - Quality of Care in SCD Consumer Assessment of Healthcare Providers and Systems (CAHPS) Health Plan Survey 4.0 Child Medicaid Questionnaire
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has_application_toward: These questions are used to assess the patient-reported health care needs and quality of service from health care providers for individuals with chronic conditions such as sickle cell disease (SCD).

Quality of Health Care
type: Class
subclass of: Quality of Life and Care
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: The levels of excellence which characterize the health service or health care provided based on accepted standards of quality.
database cross reference: MESH:D011787
definition source: D011787
description adapted from source: no
hasBroadSynonym: Quality of Care
hasExactSynonym: Health Care Quality
hasExactSynonym: Healthcare Quality
hasExactSynonym: Quality of Healthcare

Quality of Life
type: Class
subclass of: Quality of Life and Care
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The subjective measurement of an individual's sense of well-being and ability to enjoy life. The concept holds varying meanings for different people and may evolve over time. For some individuals it implies autonomy, empowerment, capability, and choice; for others, security, social integration, or freedom from stress or illness.
dc:source: WHOQOL Measuring Quality of LIfe. WHO/MSA/MNH/PSF/97.4
abbreviation: QOL
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Health Related Quality of Life
hasExactSynonym: QOL
hasRelatedSynonym: Health Status
comment: WHO QOL: Individual's perception of their position in life in the context of the culture and value systems in which they live and in relation to their goals, expectations, standards and concerns. It is a broad ranging concept affected in a complex way by the person's physical health, psychological state, level of independence, social relationships, personal beliefs and their relationship to salient features of their environment.

Quality of Life and Care
type: Class
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: The subjective measurement of an individual's sense of well-being and ability to enjoy life, and the levels of excellence which characterize the health service or health care provided to individuals based on accepted standards of quality.
dc:source: http://pediatrics.aappublications.org/content/130/5/926
curator note: Include the term "Transition from pediatric care" somewhere...see the source provided here.

Quality of Life and Care Measure
type: Class
subclass of: Quality of Life and Care
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Quality of Life in Sickle Cell Disease
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A questionnaire to assess the physical, emotional, and social impact of chronic conditions, such as sickle cell disease (SCD).
curator note: Include as sub-classes: PedsQL Sickle Cell Disease Module ASCQ-Me - Quality of Life in SCD
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has_application_toward: This measure can be used to track health status and treatment outcomes and understand the health care requirements of patients with chronic conditions, such as sickle cell disease (SCD).
hasExactSynonym: Quality of Life in SCD

Quality of Life Measure
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: This is a measure to assess quality of life (QOL) based on how the individual has felt over the past 7 days.
curator note: Include as sub-classes: PROMIS Pediatric Profile 25 PROMIS Adult Profile 29 ...and their parent class
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has_application_toward: Information collected from this questionnaire can be used to assess the individual’s current quality of life, which may influence emotional and physical problems.

Quality of Life Related SCD Symptoms and Complications
type: Class
subclass of: Quality of Life
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
creator: SCDO
description: Sickle cell symptoms where there is evidence of some relation with quality of life.

Quality-Adjusted Life Year (QALY)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: QALYs are used primarily to correct a person's life expectancy based on the levels of health-related quality of life they are predicted to experience throughout the course of their life, or part of it. The number of QALYs lived by an individual in one year is simply: QALYs lived in one year = 1 * Q with Q ≤ 1; where Q is the health-related quality of life weight attached to the relevant year of life. I.e. QALY assumes a utility value (quality of life) of 1 = perfect health and a utility value of 0 = dead: Years of Life x Utility Value = Number of QALYs. E.g. If a person lives in perfect health for one year, that person will have 1 QALY (1 Year of Life × 1 Utility Value = 1 QALY), If a person lives in perfect health but only for half a year, that person will have 0.5 QALYs (0.5 Years of Life x 1 Utility Value = 0.5 QALYs) OR if a person lives for 1 year in a situation with 0.5 utility (half of perfect health), that person will also have 0.5 QALYs (1 Year of Life x 0.5 Utility Value = 0.5 QALYs). In cost-effectiveness evaluations the QALY is used to quantify the effectiveness of, for instance, a new medication versus the current one. In other words, the current standard of care is taken as the baseline, and the QALYs gained from the new (improved) intervention are counted in addition.
abbreviation: QALY
curator note: Review description. Perhaps move some info to a comment? Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self; Proxy
has target population: All
selection criteria met: Standard global assessment of health interventions, also used in SCD studies
validated for age ranges: Children and adults
freely available: no
hasExactSynonym: QALY
hasExactSynonym: Quality-Adjusted Life Year

Quality-Adjusted Life Year (QALY) - removed - see Quality of Life and Care Measure
type: Class
subclass of: Health Utility
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete

Questionnaire
type: Class
subclass of: from diagnostics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Collection of data obtained from voluntary subjects. The information usually takes the form of answers to questions, or suggestions. Predetermined sets of questions used to collect data - clinical data, social status, occupational group, etc.
database cross reference: MESH:D011795
definition source: http://bioportal.bioontology.org/ontologies/MESH
description adapted from source: Label and description adapted

Race
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Different relevant racial groups need to be recorded. Perhaps as sub-classes of this class? The PhenX protocol is U.S. specific. Is there one relevant to the African setting?
database cross reference: NCIT:C17049
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no
has_application_toward: Race is used to stratify study populations and to associate those populations with physical, geographic, biological, social, and cultural characteristics (e.g., African Americans). Race is a social and epidemiological factor, and individuals of some races are at greater risk for certain diseases.
hasExactSynonym: Racial Group

Radiography
type: Class
subclass of: Imaging Assay
subclass of: Restriction
  on property: has medical device
  some values from: X-Ray Machine
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Examination of any part of the body for diagnostic purposes by means of X-RAYS or GAMMA RAYS, recording the image on a sensitized surface (such as photographic film).
database cross reference: MESH:D011859
definition source: D011859
description adapted from source: no
hasExactSynonym: Imaging by X-Ray
hasExactSynonym: X-Ray
preferred label: X-Ray Imaging

Radionuclide Imaging
type: Class
subclass of: Imaging Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The production of an image obtained by cameras that detect the radioactive emissions of an injected radionuclide as it has distributed differentially throughout tissues in the body. The image obtained from a moving detector is called a scan, while the image obtained from a stationary camera device is called a scintiphotograph.
curator note: "Scintigraphy" was removed from below this class as it is in fact an exact synonym.
database cross reference: D011877
definition source: D011877
description adapted from source: no
hasExactSynonym: Imaging by Radionuclide
hasExactSynonym: Scintigraphy

Randomized Controlled Trial
type: Class
subclass of: Controlled Clinical Trial
description: A work that reports on a clinical trial that involves at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, such as the use of a random-numbers table.
database cross reference: MESH:D016449
definition source: D016449
description adapted from source: no

Rapid Estimate of Adolescent Literacy in Medicine (REALM-Teen)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The Rapid Estimate of Adolescent Literacy or REALM-Teen is a valid, reliable, easy-to-administer tool that will allow health professionals to screen youth in grades 6-12 for below-grade reading. The REALM-Teen is a reading recognition instrument, modeled after the Rapid Estimate of Adult Literacy in Medicine (REALM), the most commonly used tool to screen adults for low literacy in health care settings. The REALM-Teen is a reading recognition instrument which measures an individual’s ability to pronounce words in ascending order of difficulty. All test words are commonly used adolescent health terms.
dc:source: Davis TC, Wolf MS, Arnold CL, Byrd RS, Long SW, Springer T, Kennen E, Bocchini JA. (2006). Development and validation of the Rapid Estimate of Adolescent Literacy in Medicine (REALM-Teen): a tool to screen adolescents for below-grade reading in health care settings. Pediatrics 118(6):e1707-14.
abbreviation: REALM-Teen
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Also these properties: has cross-cultural adaptation freely available has translations
has respondents: Self
has target population: Adolescents with SCD
selection criteria met: Used in SCD studies
validated for age ranges: Adolescents
hasExactSynonym: REALM-Teen
hasExactSynonym: Rapid Estimate of Adolescent Literacy in Medicine

Recovery and Recurrence Questionnaire (RRQ)
type: Class
subclass of: Functionality After Stroke Measure
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A questionnaire that assesses recovery and recurrence of stroke in children. It is completed by a parent about their child.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX820702
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Recovery and Recurrence Questionnaire (RRQ) - Pediatrics #820702
has respondents: Proxy (Parent)
has target population: Children and adolescents who have a stroke, ages 0-18
validated for age ranges: 0-18
freely available: yes
comment: Life stage: Infant, Toddler, Child, Adolescent

Recurrent Wheeze in Sickle Cell Disease
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Blood Transfusion
subclass of: Restriction
  on property: treated with
  some values from: Hydroxyurea
subclass of: Restriction
  on property: results_in
  some values from: Acute Chest Syndrome
subclass of: Restriction
  on property: results_in
  some values from: Sickle Cell Painful Event
subclass of: Restriction
  on property: results_in
  some values from: Stroke
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Recurrent episodes of wheezing in a persons with SCD who have no co-morbid asthma.
dc:source: Knight-Madden et al 2014 Ped Resp Rev; Glassberg et al 2014 Curr Opin Pediatr.
abbreviation: RWIS
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
is caused by: Likely related to inflammation of SCD.
is characterised by: Other markers of severity of SCD- eg complications of SCD, high LDH.

Red Blood Cell Count
type: Class
subclass of: Red Blood Cell Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The number of red blood cells in a specified volume of blood most commonly 1 cubic millimeter (i.e. 1 microliter) of peripheral venous blood.
database cross reference: CMO:0000025
definition source: CMO_0000025
description adapted from source: no
hasExactSynonym: Erythrocyte Count
hasExactSynonym: Erythrocyte Number
hasExactSynonym: Erythrocyte Numbers

Red Blood Cell Measurement
type: Class
subclass of: Blood Cell Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Any measurement of a single red blood cell, one of the hemoglobin-containing blood cells that transport oxygen and carbon dioxide to and from the tissues, or of all of the red blood cells in a sample of blood.
database cross reference: CMO:0001356
definition source: CMO_0001356
description adapted from source: no
hasExactSynonym: Erythrocyte Measurement

Red Blood Cell Microparticles Level
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Flow Cytometry
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A bioassay to measure levels of red blood cell microparticles.
dc:source: PMC3678264
curator note: More info can be taken from the dc:source provided.
curator note: Perhaps add MeSH term "Cell-Derived Microparticles" as a superclass of this term?
curator note: The description given is actually one for an assay that measures "Red Blood Cell Microparticles Level". It should be used to create the relevant assay term under "Diagnostic Tool" and a more appropriate description needs to be provided fro this term.
has recommended procedure: This protocol provides instructions for drawing, processing, and storing blood according to the National Health and Nutrition Examination Survey (NHANES) methods. Because there are many comparable assays for measuring red blood cell microparticle levels, the protocol also provides basic guidelines to aid comparability among different studies.
has_application_toward: Red blood cell microparticle levels are associated with hemolysis and anemia, sickle cell disease, thrombosis, and cardiovascular disease.
hasBroadSynonym: Cell-Derived Microparticles
hasExactSynonym: EMP Level
hasExactSynonym: Erythrocyte-Derived Microparticles Level

Reduced Hemoglobin A
type: Class
subclass of: Abnormal Hemoglobin Level Present in SCD
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Hemoglobin A (HbA) contains two globin alpha chains and two globin beta chains. HbA is normally the main adult hemoglobin, representing about 96-98 percent of all hemoglobin. This term represents a decreased in the proportion of HbA below this limit, and can be seen in various forms of thalassemia.
database cross reference: HP:0011905
definition source: HP_0011905
description adapted from source: no

Rehabilitation
type: Class
subclass of: Supportive Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Restoration of human functions to the maximum degree possible in a person or persons suffering from disease or injury.
database cross reference: MESH:D012046
definition source: D012046
description adapted from source: no
hasRelatedSynonym: Habilitation

Reincarnation
type: Class
subclass of: Beliefs About Causes of Illness
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Reincarnation is the philosophical or religious concept that an aspect of a living being starts a new life in a different physical body or form after each biological death.
dc:source: reincarnation-best-evidence-2593151
definition source: Reincarnation
description adapted from source: no
hasExactSynonym: Rebirth
hasExactSynonym: Transmigration

Religion
type: Class
subclass of: Culture
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A set of beliefs concerning the nature, cause, and purpose of the universe, especially when considered as the creation of a superhuman agency. It usually involves devotional and ritual observances and often a moral code for the conduct of human affairs.
database cross reference: MESH:D012067
definition source: D012067
description adapted from source: no
hasRelatedSynonym: Religiosity
hasRelatedSynonym: Religious Beliefs

Renal Artery Stenosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Chronic Kidney Disease
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The presence of stenosis of the renal artery.
dc:source: HP_0001920
abbreviation: RAS
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0001920
has age of onset: If due to FMD, presents at younger age, typically between 25-50 (and more common in women); if related to atherosclerotic disase, more likely to present after age 50.
is caused by: May be caused by atherosclerotic disease, fibromuscular dysplasia.
is characterised by: Reduced blood flow through the renal arteries, large and branching vessels.
hasExactSynonym: Narrowing of Kidney Artery

Renal Dialysis
type: Class
subclass of: Renal Replacement Therapy
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Therapy for the insufficient cleansing of the BLOOD by the kidneys based on dialysis and including hemodialysis, peritoneal dialysis, and hemodiafiltration.
curator note: Include types of renal dialysis as sub-classes: Peritoneal dialysis Hemodialysis Pediatric dialysis? Hemofiltration Hemodiafiltration
database cross reference: MESH:D006435
definition source: D006435
description adapted from source: no
hasExactSynonym: Dialyses, Renal
hasExactSynonym: Extracorporeal Dialyses
hasExactSynonym: Extracorporeal Dialysis
hasExactSynonym: Haemodialysis
hasExactSynonym: Hemodialyses
hasExactSynonym: Renal Dialyses

Renal Ischemia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: treated with
  some values from: Supportive Therapeutics
subclass of: Restriction
  on property: results_in
  some values from: Acute Kidney Injury
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Inadequate blood flow to one or both kidneys, or nephrons, usually due to functional constriction or actual obstruction of blood vessels.
dc:source: MP_0011758
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info. Move to below "Ischemia"?
database cross reference: MP:0011758
description adapted from source: no
is caused by: Loss of adequate blood flow may be due to obstruction of blood vessels - large or small or due to low flow states such as prolonged hypotension.
is characterised by: Usually associated with kidney injury as noted by decrease in urine output and/or elevation in serum creatinine.
hasExactSynonym: kidney ischemia

Renal Transplant
type: Class
subclass of: Renal Replacement Therapy
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The transference of a kidney from one human or animal to another.
database cross reference: MESH:D016030
definition source: D016030
description adapted from source: Only label adapted
hasExactSynonym: Kidney Grafting
hasExactSynonym: Kidney Transplantation
hasExactSynonym: Kidney Transplantations
hasExactSynonym: Renal Transplantation
hasExactSynonym: Renal Transplantations

Renal Tubular Acidosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Diuresis
subclass of: Restriction
  on property: results_in
  some values from: Growth Delay
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Acidosis owing to malfunction of the kidney tubules with accumulation of metabolic acids.
dc:source: HP_0001947
abbreviation: RTA
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0001947
description adapted from source: yes
has disease stage: Has multiple types - Type 1 (Distal RTA), Type 2 (Proximal RTA), Type 4 (Hyperkalemic RTA). Sickle cell disease may demonstrate a voltage dependent Type 1 RTA.
is caused by: Defects in the kidneys in reabsorption of bicarbonate (HCO3), the excretion of hydrogen ions (H+), or both.
is characterised by: A relatively normal GFR and a metabolic acidosis accompanied by hyperchloremia and a normal plasma anion gap.
hasExactSynonym: RTA

Reproductive History
type: Class
subclass of: Personal Medical History
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The respondent's pregnancy history. For females it is with regard to their number of pregnancies, description of pregnancies and smoking during pregnancy. For males, it is with regard to whether they have ever fathered a pregnancy and, if so, the description of the pregnancy.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX101300
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Reproductive History - Female #101301
has protocol: PhenX protocol: Reproductive History - Male #101302
has_application_toward: The purpose of this measure is to assess the demonstrated fecundity and fertility of the individual. This measure can also be used for estimating certain in utero exposures if the research subject is an infant.

Reproductive System
type: Class
subclass of: from phenotype
description: Anatomical system that has as its parts the organs concerned with reproduction.
database cross reference: UBERON:0000990
definition source: UBERON_0000990
description adapted from source: no
hasRelatedSynonym: Genital Tract
hasRelatedSynonym: Reproductive Tract

Research Activity
type: Class
subclass of: from personal attribute
description: Systematic investigation into a subject in order to discover facts, establish or revise a theory, or develop a plan of action based on the facts discovered.
curator note: Consider other sub-classes of this in NCIT.
database cross reference: NCIT:C15429
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no

Respiratory Rate
type: Class
subclass of: Respiratory System Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Respiratory rate is the number of breaths an individual takes within a specific amount of time (frequently given in breaths per minute).
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX091400
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Respiratory Rate - Adult Protocol #091403
has protocol: PhenX protocol: Respiratory Rate - Child Protocol #091402
has protocol: PhenX protocol: Respiratory Rate - Infant Protocol #091401
has_application_toward: Respiratory rate is a low-burden, quantitative variable that can be used to distinguish individuals with and without various forms of lung disease.
hasExactSynonym: Breathing Frequency
hasExactSynonym: Pulmonary Ventilation Rate
hasExactSynonym: Respiration Rate

Respiratory System
type: Class
subclass of: from phenotype
description: Lungs and respiratory system of the body.
dc:source: pulmonary+system
description adapted from source: yes
hasExactSynonym: Pulmonary System
comment: Patients with SCD have a unique pathophysiology that puts the microvasculature of the lung at particular risk for complications.

Respiratory System Measurement
type: Class
subclass of: Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A measurement to assess the morphological or physiological state of the respiratory system or portion of the respiratory system.
database cross reference: CMO:0000094
definition source: CMO_0000094
description adapted from source: no

Restriction Fragment Length Polymorphism PCR
type: Class
subclass of: Polymerase Chain Reaction
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: PCR-restriction fragment length polymorphism (RFLP)-based analysis, also known as cleaved amplified polymorphic sequence (CAPS), is a popular technique for genetic analysis. It has been applied for the detection of intraspecies as well as interspecies variation. There exist several techniques that are related with PCR-RFLP and also involve gel electrophoresis including techniques for DNA fingerprinting and expression profiling.
hasExactSynonym: PCR-RFLP
hasExactSynonym: Restriction Fragment Length Polymorphism - Polymerase Chain Reaction

Reticulocyte Count
type: Class
subclass of: Red Blood Cell Count
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A bioassay to measure the number of reticulocytes (immature red blood cells).
description: A reticulocyte count (also known as a retic count, reticulocyte index, or corrected reticulocyte) is a measurement and percentage of how many reticulocytes are in the blood. This count indicates whether enough red blood cells are being produced in the bone marrow.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX810600
description adapted from source: no
has recommended procedure: This protocol provides instructions for drawing, processing, and storing blood according to the National Health and Nutrition Examination Survey (NHANES) methods. Because there are many comparable assays and instruments for measuring reticulocyte count, the protocol also provides basic guidelines to aid comparability among different studies.
has_application_toward: Reticulocyte count measures how fast red blood cells are made. Elevated reticulocyte counts are associated with blood loss, hemolysis and hemolytic anemia, and in response to the anemia of clinical conditions such as sickle cell.

Reticulocyte Count by Hematology Analyzer
type: Class
subclass of: Reticulocyte Count
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: A reticulocyte count that was performed with an electronic haematology analyzer

Reticulocyte Count by Microsocopy
type: Class
subclass of: Reticulocyte Count
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: A reticulocyte count that was performed with microscopy.

Retinal Cryopexy
type: Class
subclass of: Ophthalmologic Surgical Procedure
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A procedure that uses intense cold to induce a chorioretinal scar and to destroy retinal or choroidal tissue.
definition source: Retinal-Cryopexy.html
description adapted from source: yes
hasExactSynonym: Retinal Cryotherapy

Retinal Detachment
type: Class
subclass of: Ophthalmologic Complication
subclass of: Restriction
  on property: diagnosed by
  some values from: Ophthalmoscopy
subclass of: Restriction
  on property: diagnosed by
  some values from: Retinal Examination
subclass of: Restriction
  on property: diagnosed by
  some values from: Slit-Lamp Examination
subclass of: Restriction
  on property: results_in
  some values from: Blindness
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Separation of the retina from the choroid and eye wall due to holes in the retina and traction on the retina by vitreous bands and condensed preretinal membranes (usually as sequelae of proliferative sickle retinopathy). Retinal detachment is the most severe complication (Stage V) of proliferative sickle retinopathy.
dc:source: Ballas et al 2010 Am J Hematol
dc:source: Bonanomi et al 2013 Arq Bras Oftalmol
database cross reference: EFO:0005773
definition source: Ballas et al 2010 Am J Hematol
description adapted from source: no
is caused by: Often a complication of sickle retinopathy.
comment: Classification: If the retinal detachment is confined to the peripheral fundus, visual acuity may not be affected, but if the detachment extends to macula, severe reduction of visual acuity ensues. If no holes are found in the detached retina, the detachment is thought to be tractional in nature. Usually, sickle cell detachments of the retina are caused by traction and not from a hole forming in retinal tissue (serous or rhegmatogenous detachment).
comment: If the retina can be visualized to be elevated from the wall of the eye, the diagnosis of retinal detachment can be made.
comment: Retinal detachment should be considered an ophthalmologic emergency, whether or not visual acuity is affected. Surgery for reattachment should be done as soon as possible.

Retinal Examination
type: Class
subclass of: Eye Examination
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Ophthalmoscopy
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Slit-Lamp Examination
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An examination of the retina of the eye.
database cross reference: NCIT:C101217
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: yes
hasExactSynonym: Fundoscopy
comment: Eye examination with dilated pupils to be able to assess the entire retina.

Retrospective Studies
type: Class
subclass of: Cohort Studies
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Studies used to test etiologic hypotheses in which inferences about an exposure to putative causal factors are derived from data relating to characteristics of persons under study or to events or experiences in their past. The essential feature is that some of the persons under study have the disease or outcome of interest and their characteristics are compared with those of unaffected persons.
definition source: D012189

Rheumatoid Arthritis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Occupational Therapy
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An autoimmune response that primarily affects connective tissue; it also results in chronic inflammation of the joints, especially of the hands and feet and may also cause inflammation of the tissue around the joints, as well as other organs in the body.
curator note: Provide source for additional info.
database cross reference: MP:0003561
definition source: MP_0003561
description adapted from source: no
is caused by: Presence of auto antibodies that attack his or her own body tissues, the exact cause is unknown.
is characterised by: inflammation of the small joints in the hands and feet that produces pain, swelling and stiffness. People can also have fever, tiredness.
hasExactSynonym: Osteoarthrosis Deformans

Right Heart Catheterization
type: Class
subclass of: Heart Function Test
subclass of: Restriction
  on property: has medical device
  some values from: Catheter
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A diagnostic procedure in which a catheter is guided into the right heart, where pressures may be measured and radiocontrast material may be injected to visualize blood flow in and around the right heart.
database cross reference: C80411
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no

Rural Location
type: Class
subclass of: Geographic Location
subclass of: Healthcare Access
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A rural area is an open swath of land that has few homes or other buildings, and not very many people.
curator note: Copied this below "Geographic Location" under "Disease Modifiers".
definition source: rural-area
description adapted from source: no
hasExactSynonym: Rural Area
hasExactSynonym: Rural Setting
comment: Rural is normally about population density. But the definition of rural can have a different meaning depending on the context.

Salmon Patch Hemorrhage
type: Class
subclass of: Ophthalmologic Complication
subclass of: Restriction
  on property: diagnosed by
  some values from: Ophthalmoscopy
subclass of: Restriction
  on property: diagnosed by
  some values from: Slit-Lamp Examination
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Round or oval-shaped intraretinal accumulation of erythrocytes that may be up to 2 mm in diameter. This small intraretinal hematoma is initially red and becomes salmon colored with time.
definition source: Ballas et al 2010 Am J Hematol
description adapted from source: no
hasExactSynonym: Salmon Patch Hemorrhages
comment: Diagnostic Criteria: Eye exam using direct and indirect ophthalmoscopy as well as slit lamp biomicroscopy. With fundus photography, white arterioles may be noted adjacent to the arteriole that is the source of blood. With fluorescein angiography, nonperfusion of the adjacent arteriole may be seen. Severity Index: The blood may spontaneously resolve with time. If not, vitrectomy (removal of vitreous) may be required.

Sampling Studies
type: Class
subclass of: Study Design
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Studies in which a number of subjects are selected from all subjects in a defined population. Conclusions based on sample results may be attributed only to the population sampled.
database cross reference: MESH:D012494
definition source: D012494

SCD Related Pain
type: Class
subclass of: Pain
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
creator: SCDO
description: Pain resulting from the presence of Sickle Cell Disease (SCD). Such pain can be acute, chronic or a mixture of the two.
dc:source: Okpala I., Tawil A. Management of pain in sickle-cell disease. Journal of the Royal Society of Medicine. 2002;95(9):456-458. doi: 10.1258/jrsm.95.9.456
hasExactSynonym: SCD Pain

Sciatica
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: treated with
  some values from: Anti-Inflammatory Agent
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: results_in
  some values from: Quality of Life
subclass of: Restriction
  on property: results_in
  some values from: SCD Related Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Pain in the lower back and hip radiating in the distribution of the sciatic nerve.
curator note: Provide source for additional info. Terms to add to therapeutics for linking via "is treated with" obj property: Local heat, acupuncture, physical therapy, surgery
database cross reference: HP:0011868
definition source: HP_0011868
description adapted from source: no
is caused by: Compression of a spinal nerve root by disc or arthritic spur, degenerative changes involvind main structures, disc protrusion, congenital abnormalities of the bony spinal column, infection, inflammation, neoplasm, vascular diseases.

Scleral Buckling
type: Class
subclass of: Ophthalmologic Surgical Procedure
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An operation for retinal detachment which reduces the size of the globe by indenting the sclera so that it approximates the retina.
database cross reference: MESH:D012591
definition source: D012591
description adapted from source: no
hasExactSynonym: Scleral Buckle Surgery
hasExactSynonym: Scleral Bucklings

Scoliosis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Back Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The presence of an abnormal lateral curvature of the spine.
curator note: Provide source for additional info.
database cross reference: HP:0002650
definition source: HP_0002650
description adapted from source: no
is caused by: Congenital vertebral anomalies, idiopathic, result of a neuromuscular condition.
is characterised by: Spinal tortuosity.
hasBroadSynonym: Curvature of Spine
hasBroadSynonym: Curved Spine

Secondary Healthcare
type: Class
subclass of: Health System
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Specialized healthcare delivered as a follow-up or referral from a primary care provider.
database cross reference: MESH:D063127
definition source: D063127
description adapted from source: no
hasExactSynonym: Secondary Care
hasExactSynonym: Secondary Health Care

Secondary Hypothyroidism
type: Class
subclass of: Hypothyroidism
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A type of hypothyroidism that results from a defect in thyroid-stimulating hormone secretion.
curator note: Provide source for additional info.
database cross reference: HP:0008245
definition source: HP_0008245
description adapted from source: no
is characterised by: Fatigue or a general listless feeling, Unintentional weight gain, Increased sensitivity to cold, Noticeable thinning and brittleness of fingernails or hair, Heavier periods than normal, Pain in muscles or joints, Weakness and overall tired feeling.
hasExactSynonym: TSH deficient hypothyroidism
hasExactSynonym: Thyroid stimulating hormone deficiency
hasExactSynonym: Thyrotropin deficiency

Sedentary Lifestyle
type: Class
subclass of: Lifestyle
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Usual level of physical activity that is less than 30 minutes of moderate-intensity activity on most days of the week.
database cross reference: MESH:D057185
definition source: D057185
description adapted from source: no

Seizure
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Seizures are an intermittent abnormality of the central nervous system due to a sudden, excessive, disorderly discharge of cerebral neurons and characterized clinically by some combination of disturbance of sensation, loss of consciousness, impairment of psychic function, or convulsive movements.
curator note: Provide source for additional info.
database cross reference: HP:0001250
definition source: HP_0001250
description adapted from source: Label and description adapted
is characterised by: Seizures fall into two main groups. Focal seizures, also called partial seizures, happen in just one part of the brain. Generalized seizures are a result of abnormal activity on both sides of the brain.
hasExactSynonym: Seizures
hasRelatedSynonym: Epilepsy

Self Care
type: Class
subclass of: Rehabilitation
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Performance of activities or tasks traditionally performed by professional health care providers. The concept includes care of oneself or one's family and friends.
database cross reference: MESH:D012648
definition source: D012648
description adapted from source: no
hasExactSynonym: Self Management
hasExactSynonym: Self-Care
hasExactSynonym: Self-Management

Self Efficacy
type: Class
subclass of: Coping Skill
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Cognitive mechanism based on expectations or beliefs about one's ability to perform actions necessary to produce a given effect.
dc:source: D020377
database cross reference: MESH:D020377
description adapted from source: yes
hasExactSynonym: Self-Concept

Self-Reported Weight
type: Class
subclass of: Body Weight
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The weight in kilograms or pounds as reported by the participant.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Weight - Self-Reported Weight #021502
comment: Self-reported weight values are considered to be less accurate and are used only when measured weight cannot be obtained.

Sensory Neuropathy
type: Class
subclass of: Peripheral Neuropathy
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Peripheral neuropathy affecting the sensory nerves.
database cross reference: HP:0000763
definition source: HP_0000763
hasExactSynonym: Peripheral Sensory Neuropathy

Sepsis
type: Class
subclass of: Infection
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Culture
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: treated with
  some values from: Antifungal
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Severe systemic inflammatory response to infection.
curator note: Source needed for additional information. Perhaps include different types of sepsis (see under D018805 in MESH)?
database cross reference: HP:0100806
definition source: HP_0100806
description adapted from source: yes
has disease stage: Mild, moderate, severe
is caused by: Bacteria and fungus mainly
is characterised by: Systematic manifestations of inflammation

Seroepidemiologic Studies
type: Class
subclass of: Epidemiologic Studies
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Epidemiologic studies based on the detection through serological testing of characteristic change in the serum level of specific antibodies. Latent subclinical infections and carrier states can thus be detected in addition to clinically overt cases.
definition source: D016036

Serum Creatinine Level
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Creatinine Blood Test
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: History of Kidney Failure
subclass of: Restriction
  on property: essential measure
  some values from: History of Type I and Type 2 Diabetes
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The amount of creatinine, a catabolic product of creatine phosphate used in skeletal muscle contraction found in a specified volume of serum.
dc:source: CMO_0000057
curator note: Link to "Glomerular Filtration Rate"... which object property? Create a new one and suggest to RO? "used to calculate"?
database cross reference: CMO:0000057
description adapted from source: no
has_application_toward: Serum creatinine concentration is the most standardized way to calculate glomerular filtration rate (GFR) as a measure of kidney function.
hasExactSynonym: Creatinine Level

Serum HDL Cholesterol
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The proportion, quantity, or volume in whole blood, serum, or plasma of the small lipoprotein:cholesterol complex that transports cholesterol out of the arteries and to the liver for reprocessing or excretion.
dc:source: VT_0000184
database cross reference: VT:0000184
description adapted from source: no
hasExactSynonym: Blood HDL Cholesterol Amount
hasExactSynonym: Blood High Density Lipoprotein Cholesterol Amount
hasExactSynonym: Circulating HDL Cholesterol Amount
hasExactSynonym: Circulating HDL Cholesterol Level
hasExactSynonym: HDL Cholesterol Level
hasExactSynonym: HDL Level

SF-36v2 Health Survey
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The SF-36v2 Health Survey is a 36-item instrument for measuring health status and outcomes via patient self-report. It is designed for use in surveys of general and specific populations, health policy evaluations, and clinical practice and research. The SF-36v2® measures the following eight health concepts, which are relevant across age, disease, and treatment groups: physical functioning, role limitations due to physical health problems, bodily pain, general health, vitality (energy/fatigue), social functioning, role limitations due to emotional problems, and mental health (psychological distress and psychological well-being). Both standard (4-week) and acute (1-week) recall versions are available. The survey’s standardized scoring system yields a profile of eight health scores and two summary measures (physical and mental health) and a self-evaluated change in health status.
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Also these properties: has cross-cultural adaptation freely available has translations
has respondents: Self
has target population: Healthy people; Clinic patients
selection criteria met: Demonstrated validity with SCD populations; multiple publications using the measure in SCD; very widely used with healthy populations and those with chronic conditions
validated for age ranges: Adults 18 years and older

Shoulder Dystocia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Shoulder dystocia occurs when the fetal anterior shoulder impacts against the maternal symphysis following delivery of the vertex.
dc:source: HP_0011413
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0011413
description adapted from source: no
is caused by: Fetal macrosomia, diabetes, maternal obesity.
is characterised by: Shoulders fail to deliver shortly after the fetal head.

Sickle Cell Chronic Lung Disease
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Arterial Blood Gas Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Chest X-Ray
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: diagnosed by
  some values from: Pulmonary Function Test
subclass of: Restriction
  on property: treated with
  some values from: Blood Transfusion
subclass of: Restriction
  on property: treated with
  some values from: Hydroxyurea
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Chronic restrictive lung disease in SCD.
dc:source: Powars et al 1988 Medicine (Baltimore), Knight-Madden et al 2010 Lung.
curator note: Flesh out description a bit more. Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info. Perhaps move below "Chronic Restrictive Lung Disease"?
description adapted from source: yes
is caused by: Chronic SCD related lung inflammation, with risk increasing with episodes of ACS.
is characterised by: Restricive lung disease often associated with chest pain and hypoxemia. May also be associated with pulmonary hypertension.

Sickle Cell Disease Health-Related Stigma Scale (SCD-HRSS)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A measure of stigma among adults living with Sickle Cell disease. Focus on; depressive symptoms, pain, assertive communication, satisfaction with pain management experience, and health-related stigma.
dc:source: Jenerette C, Brewer CA, Crandell J, Ataga KI. Preliminary validity and reliability of the Sickle Cell Disease Health-Related Stigma Scale.Issues Ment Health Nurs.2012 Jun;33(6):363-9.
abbreviation: SCD-HRSS
curator note: Check whether the description was adapted from the description source. Note: the source is not freely accessable...needs proper referencing. Also these properties: has respondents has target population selection criteria met validated for age ranges has cross-cultural adaptation freely available has translations
curator note: The source require access to the paper and the description source require logins
definition source: http://ezproxy-prd.bodleian.ox.ac.uk:2066/10.3109/01612840.2012.656823
hasExactSynonym: SCD-HRSS
hasExactSynonym: Sickle Cell Disease Health-Related Stigma Scale

Sickle Cell Disease Pain Burden Interview - Youth
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The SCPBI-Y is a brief clinical interview designed to assess pain burden for children and adolescents with SCD.
dc:source: Zempsky WT, O'Hara EA, Santanelli JP, Palermo TM, New T, Smith-Whitley K, Casella JF. Validation of the sickle cell disease pain burden interview-youth. J Pain. 2013 Sep;14(9):975-82.
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Also these properties: has respondents has target population selection criteria met validated for age ranges has cross-cultural adaptation freely available has translations

Sickle Cell Disease Screening Test
type: Class
subclass of: Hematology Screening Test
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Solubility Test
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
curator note: In SNOMED CT

Sickle Cell Disease Self-Efficacy Scale
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A nine-item self-administered questionnaire that measures disease-specific perceptions of the ability to manage day-to-day issues resulting from sickle cell disease (SCD). Items are scores according to a five-point scale ranging from "1 - Not sure at all" to "5 - Very sure." Responses from individual items are summed to give an overall score with higher scores indicating greater self-efficacy.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has respondents: Self
has target population: Clinic Patients (Adults with SCD)
has_application_toward: Self-efficacy, or one’s perceptions that they can exercise control over their behaviors and environment, may play an important role in determining the ability to adjust to chronic conditions such as sickle cell disease (SCD).
validated for age ranges: 18 and older
hasExactSynonym: Self-efficacy in Sickle Cell Disease
comment: Life stage: Adult

Sickle Cell Disease Variant
type: Class
subclass of: Sickle Cell Disease
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Any hemoglobinopathy in which the sickle mutation is inherited in combination with another globin gene mutation (eg, alpha globin, beta globin, gamma globin). These hemoglobinopathies may have different clinical severity compared with homozygous sickle mutation (HbSS).
dc:source: Hemoglobinopathy
dc:source: overview-of-variant-sickle-cell-syndromes
definition source: overview-of-variant-sickle-cell-syndromes
description adapted from source: yes
hasExactSynonym: Variant Sickle Cell Syndromes

Sickle Cell Pain Management
type: Class
subclass of: Symptomatic Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A form of therapy that employs a coordinated and interdisciplinary approach for easing the suffering and improving the quality of life of those experiencing sickle cell related pain.
definition source: D059408
description adapted from source: Label and description adapted
hasExactSynonym: Sickle Cell Pain Managements

Sickle Cell Painful Event
type: Class
subclass of: SCD Related Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Pain lasting at least two hours that requires an unscheduled emergency room visit or hospitalization or that disrupts daily activities.
curator note: Could be categorised as a phenotype "Finding".
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
hasExactSynonym: Pain Episode
hasExactSynonym: Painful Event
hasExactSynonym: Sickle Cell Pain Episode

Sickle Cell Related Cancer
type: Class
subclass of: Cancer
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An aggressive form of non–clear cell kidney cancer that typically affects young adults and is almost exclusively associated with sickle cell trait.
abbreviation: RMC
curator note: Should this not be divided into 2 terms? "Sickle Cell Related Cancer" with "Renal Medullary Cancer" as a subclass?
definition source: PMC4052598
description adapted from source: no
hasExactSynonym: Renal Medullary Cancer
hasExactSynonym: Renal Medullary Carcimoma

Sickle Cell Trait
type: Class
subclass of: Hemoglobin Trait
subclass of: SCD Genotype
subclass of: Restriction
  on property: has clinical code
  some values from: D57.3 Sickle-cell trait
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The condition of being heterozygous for hemoglobin S.
dc:source: Hb-F-A-S
database cross reference: MESH:D012805
definition source: D012805
description adapted from source: no
hasExactSynonym: AS
hasExactSynonym: AS Genotype
hasRelatedSynonym: Hb S-Carrier
comment: A powerful protector against malaria.
comment: Affected gene: HBB gene (with an autosomal recessive pattern of inheritance) Affected protein: Hemoglobin subunit beta (UniProt Number: P68871)

Sickle Cell Disease-S Beta Plus Thalassemia
type: Class
subclass of: Sickle Cell Disease-S Beta Thalassaemia
subclass of: Restriction
  on property: has phenotype
  some values from: Beta Plus Thalassemia
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin S
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A mild form of sickle cell thalassemia characterized by the presence of hemoglobin S and a small amount of hemoglobin A in the red blood cells. It is characterized by the presence of small red blood cells and mild anemia.
abbreviation: SCD-S Beta Plus Thal
curator note: NB to re-examine this term's name.
database cross reference: NCIT:C98837
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Sickle B+ Thalassemia
hasExactSynonym: Sickle Beta Plus Thalassemia
hasExactSynonym: Sickle Cell-B+ Thalassemia
hasExactSynonym: Sickle Cell-Beta Plus Thalassemia
comment: The reduced production of hemoglobin A is due to reduced production of beta globin.

Sickle Cell Disease-S Beta Thalassaemia
type: Class
subclass of: Sickle Cell-Thalassemia
subclass of: Restriction
  on property: has clinical code
  some values from: D57.4 Sickle-cell thalassemia
subclass of: Restriction
  on property: has phenotype
  some values from: Beta Thalassemia
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin S
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Sickle Cell-Beta Thalassaemia is an inherited form of sickle cell disease that affects red blood cells both in the production of abnormal hemoglobin, as well as the decreased synthesis of beta globin chains.
dc:source: Hb-F-S-A
abbreviation: SCD-S Beta Thal
definition source: sickle cell beta thalassemia.htm
description adapted from source: no
hasExactSynonym: HbSBetaThal
hasExactSynonym: S Beta-Thalassemia
hasExactSynonym: Sickle Beta Thalassaemia
hasExactSynonym: Sickle Beta-Thalassaemia
hasExactSynonym: Sickle Cell-Beta Thalassaemia
comment: Not sure about the description

Sickle Cell Disease-S Beta Zero Thalassemia
type: Class
subclass of: Sickle Cell Disease-S Beta Thalassaemia
subclass of: Restriction
  on property: has phenotype
  some values from: Beta Zero Thalassemia
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin S
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A form of sickle cell thalassemia characterized by the absence of hemoglobin A. Patients usually have severe anemia identical to that seen in sickle cell disease.
dc:source: simple-facts-about-sickle-cell
dc:source: PMC4459467
curator note: Requires further refinement.
database cross reference: NCIT:C98835
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Hb S Beta 0 Thalassemia
hasExactSynonym: Hemoglobin S Beta 0 Thalassemia
hasExactSynonym: S Beta 0 Thalassemia
hasExactSynonym: Sickle Beta 0 Thalassemia
hasExactSynonym: Sickle Cell-Beta 0 Thalassemia
hasExactSynonym: Sickle Cell-Beta Zero Thalassemia
comment: A confusing diagnostic problem is the differentiation of Hb S/Beta-Zero Thal from sickle cell anemia associated with alpha-thalassemia. Hematologic and electrophoretic studies are unable to distinguish between the two conditions and so family studies and DNA analysis are needed to confirm the diagnosis
comment: The absence of hemoglobin A is due to no production of beta globin.

Sickle Cell Disease-SC
type: Class
subclass of: Sickle Cell Disease Variant
subclass of: Restriction
  on property: has clinical code
  some values from: D57.2 Sickle-cell/Hb-C disease
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Hemoglobin C
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Hemoglobin S
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: One of the sickle cell disorders characterized by the presence of both hemoglobin S and hemoglobin C. It is similar to, but less severe than sickle cell anemia.
dc:source: Hb-F-S-C
abbreviation: SCD-SC
database cross reference: MESH:D006450
definition source: D006450
description adapted from source: no
hasExactSynonym: Hb SC-disease
hasExactSynonym: Hemoglobin S / Hemoglobin C Disease
hasExactSynonym: Hemoglobin SC Disease
hasExactSynonym: SC Disease
hasExactSynonym: Sickle Cell Disease SC
hasExactSynonym: Sickle Cell Hemoglobin C Disease
hasExactSynonym: Sickle Cell-Haemoglobin C Disease
hasExactSynonym: Sickle Cell-Hemoglobin C Disease
comment: Affected gene: HBB gene (with an autosomal recessive pattern of inheritance) Affected protein: Hemoglobin subunit beta (UniProt Number: P68871)
comment: Hemoglobin S can distort red blood cells into a sickle (crescent) shape. Hemoglobin C prevents red blood cells from carrying oxygen effectively.

Sickle Cell Disease-SD
type: Class
subclass of: Sickle Cell Disease Variant
subclass of: Restriction
  on property: has clinical code
  some values from: D57.8 Other sickle-cell disorders
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Hemoglobin S
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Hemoglobin D
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: One of the sickle cell disorders characterized by the presence of both hemoglobin S and hemoglobin D. It is similar to, but less severe than sickle cell anemia.
dc:source: Hb-F-S-D
dc:source: HbDFactSheet.pdf
abbreviation: SCD-SD
definition source: Hb-F-S-D
description adapted from source: yes
hasExactSynonym: Haemoglobin S-D Disease
hasExactSynonym: Hb SD-Disease
hasExactSynonym: Hemoglobin S-D Disease
hasExactSynonym: Hemoglobin Sickle D Disease
hasExactSynonym: Sickle Cell Disease SD
hasExactSynonym: Sickle Cell Hemoglobin D Disease
hasExactSynonym: Sickle Cell-Haemoglobin D Disease
hasExactSynonym: Sickle Cell-Hemoglobin D Disease
comment: Affected gene: HBB gene (with an autosomal recessive pattern of inheritance) Affected protein: Hemoglobin subunit beta (UniProt Number: P68871)
comment: Hemoglobin S can distort red blood cells into a sickle (crescent) shape. Hemoglobin D prevents red blood cells from carrying oxygen effectively.

Sickle Cell Disease-S/D-Punjab
type: Class
subclass of: Sickle Cell Disease-SD
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Hemoglobin S
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Hemoglobin D-Punjab
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: PMC4382585
abbreviation: SCD-S/D-Punjab
hasExactSynonym: Hemoglobin S/D-Punjab
hasExactSynonym: Sickle Cell-Haemoglobin D-Punjab
hasExactSynonym: Sickle Cell-Hemoglobin D-Punjab Disease
comment: Common hemoglobin variants worldwide, but prevalent in the Punjab region, Northwestern Indian.
comment: It is named Sickle Cell-Hemoglobin D-Punjab, because of its higher prevalence in the Punjab region of India and Pakistan.

Sickle Cell Disease-SE
type: Class
subclass of: Sickle Cell Disease Variant
subclass of: Restriction
  on property: has clinical code
  some values from: D57.8 Other sickle-cell disorders
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Hemoglobin S
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Hemoglobin E
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: One of the sickle cell disorders characterized by the presence of both hemoglobin S and hemoglobin E. It causes mild hemolytic anemia.
dc:source: Hb-F-S-E
dc:source: Ohashi; et al. (2004). "Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection". Am J Hum Genet. 74 (6): 1189–1208. doi:10.1086/421330. PMC 1182083Freely accessible. PMID 15114532
abbreviation: SCD-SE
definition source: Hb-F-S-E
description adapted from source: yes
hasExactSynonym: Hb SE-Disease
hasExactSynonym: Sickle Cell Disease SE
hasExactSynonym: Sickle Cell-Haemoglobin E Disease
hasExactSynonym: Sickle Cell-Hemoglobin E Disease
comment: Affected gene: HBB gene (with an autosomal recessive pattern of inheritance) Affected protein: Hemoglobin subunit beta (UniProt Number: P68871)
comment: Hemoglobin E is most prevalent in Southeast Asia (Thailand, Myanmar, Cambodia, Laos, Vietnam).
comment: Hemoglobin S can distort red blood cells into a sickle (crescent) shape. Hemoglobin D prevents red blood cells from carrying oxygen effectively. When these mutations occur together, they can cause mild hemolytic anemia.

Sickle Cell Disease-S/Lepore Boston
type: Class
subclass of: Sickle Cell-Thalassemia
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin S
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Sickle cell-Hb Lepore Boston syndrome is a type of sickle cell disease (HbS) that differs from homozygous sickle cell disease where both parents carry sickle hemoglobin. In this variant one parent has the sickle cell hemoglobin the second parent has Hb Lepore Boston, the only one of the three variants described in association with HbS.
dc:source: Hemoglobin Lepore syndrome
abbreviation: Hb S, Lepore Boston
abbreviation: SCD-S/Lepore Boston
description adapted from source: no
hasExactSynonym: Sickle Cell Disease-S/Lepore
hasExactSynonym: Sickle Cell-Hb Lepore Boston Syndrome
hasExactSynonym: Sickle Cell-Hemoglobin Lepore Boston Syndrome
comment: Hb Lepore Washington, also known as Hb Lepore Boston or Hb Lepore Washington-Boston; most common in Italians from Southern Italy

Sickle Cell Disease-S/O-Arab
type: Class
subclass of: Sickle Cell Disease Variant
subclass of: Restriction
  on property: has clinical code
  some values from: D57.8 Other sickle-cell disorders
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Hemoglobin S
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Hemoglobin O-Arab
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: One of the sickle cell disorders characterized by the presence of both hemoglobin S and hemoglobin O-Arab. It can cause anemia, repeated infections, and periodic episodes of pain and organ damage.
dc:source: O-Arab.html
dc:source: Hb-F-S-O-Arab
dc:source: https://www.omim.org/entry/141900#0243
abbreviation: SCD-S/O-Arab
definition source: Hb-F-S-O-Arab
description adapted from source: Yes
hasExactSynonym: Hb F,S,O-Arab
hasExactSynonym: Hb S O-Arab disease
hasExactSynonym: Hb S,O-Arab
hasExactSynonym: Hemoglobin S O-Arab Disease
hasExactSynonym: SO(Arab) disease
hasExactSynonym: Sickle Cell-Haemoglobin O-Arab Disease
hasExactSynonym: Sickle Cell-Hemoglobin O-Arab Disease
comment: Affected gene: HBB gene (with an autosomal recessive pattern of inheritance) Affected protein: Hemoglobin subunit beta (UniProt Number: P68871)
comment: Found mainly in Gypsies and in Pomaks (a population group in the Balkan countries) and also in Arabian, Egyptian, and Black families.

Sickle Cell-Hemoglobin Other than A,C,D,E,O-Arab
type: Class
subclass of: from phenotype
subclass of: Restriction
  on property: has clinical code
  some values from: D57.8 Other sickle-cell disorders
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin C
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin D
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin E
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A variant of sickle cell disease in which individuals have atypical hemoglobin molecules called hemoglobin S together with another form of abnormal hemoglobin, other than hemoglobin C,D,E and O-Arab.
definition source: Hb-F-S-and-other-than-A-C-D-E-O-Arab
description adapted from source: yes
hasExactSynonym: Hb S Other than A,C,D,E,O-Arab

Sickle Cell-Thalassemia
type: Class
subclass of: Sickle Cell Disease Variant
subclass of: Restriction
  on property: has phenotype
  some values from: Hemoglobin S
subclass of: Restriction
  on property: has phenotype
  some values from: Thalassemia
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Hemolytic anemia, in which patients are heterozygous for both the sickle cell gene and a thalassemia gene.
database cross reference: NCIT:C61237
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no
comment: Common worldwide due to migration.

Sickle Retinopathy
type: Class
subclass of: Ophthalmologic Complication
subclass of: Restriction
  on property: results_in
  some values from: Blindness
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Retinal changes of sickle cell disease that can be either proliferative or non-proliferative. In both cases, the changes are caused by erythrostasis secondary to sickling.
dc:source: Sickle Cell Retinopathy
dc:source: http://www.scielo.br/scielo.php
dc:source: Bonanomi et al 2013 Arq Bras Oftalmol
curator note: Use the scielo source to add info on diagnosis and treatment
definition source: Bonanomi et al 2013 Arq Bras Oftalmol
description adapted from source: yes
is caused by: Sickle Cell Disease
is characterised by: Lesions such as retinal black sunburst, sea fans and others.
hasExactSynonym: Retinopathy due to SCD
hasExactSynonym: Sickle Cell Retinopathy
comment: The frequency of retinopathy is greatest in adulthood, but retinopathy has also been described in children.
comment: The incidence of proliferative retinopathy is highest in patients with SC or S-Thal (33% and 14% respectively), while patients with SS have a 3% incidence of proliferative retinopathy.

Sickling Test
type: Class
subclass of: Hemoglobin S Test
subclass of: Restriction
  on property: has curation status
  has value: uncurated
curator note: In SNOMED CT this term seems to be both "Sickle cell identification, slide method" and "Sickling Test"
hasExactSynonym: Sickle cell identification, slide method

Sickness Impact Profile (SIP)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A generic measure used to evaluate the impact of SCD on both physical and emotional functioning of an affected person. SIP is designed to measure perceived health status and to be used as an outcome measure for evaluation, program planning, and policy formation related to health care. It is designed in such a way as to reflect sensitivity to changes and/or differences in health status and to be applicable across a broad range of types and severities of the SCD illness, as well as different demographic and cultural groups.
dc:source: Bergner M., Bobbitt R.A., Carter W.B. and Gilson B.S. (1981). The Sickness Impact Profile: development and final revision of a health status measure. Medical Care 19,787-805.
abbreviation: SIP
curator note: Source require access to the article.
curator note: These annotation properties still required: has respondents has target population selection criteria met validated for age ranges has cross-cultural adaptation freely available has translations
definition source: 10.1007/978-0-387-79948-3 1833
definition source: sick.html
definition source: http://www.ncbi.nlm.nih.gov/pubmed/7278416
description adapted from source: yes
hasExactSynonym: SIP
hasExactSynonym: Sickness Impact Profile

Skin
type: Class
subclass of: from phenotype
description: The bodily system consisting of the skin and its associated structures, such as the hair, nails, sweat glands, and sebaceous glands.
definition source: integumentary system. (n.d.) The American Heritage Medical Dictionary. (2007). Retrieved December 14 2016
description adapted from source: Only label adapted
hasExactSynonym: Dermatologic System
hasExactSynonym: Integumentary System

Skin Inflammation
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Infection
subclass of: Restriction
  on property: results_in
  some values from: Skin Ulcer
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The presence of inflammation of the skin. That is, an abnormality of the skin resulting from the local accumulation of fluid, plasma proteins, and leukocytes.
dc:source: HP_0011123
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0011123
description adapted from source: no
is caused by: Infections, chemicals, physical agents such as radiation.
is characterised by: Reddening or hyperpigmentation of the skin with or without swelling.
hasExactSynonym: Abnormal tendency to infections of the skin
hasExactSynonym: Maculopapular Rash
hasRelatedSynonym: Dermatitis
hasRelatedSynonym: Inflammatory skin disease

Skin Lesions
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Focal pathological and/or inflammatory changes characterized by alteration in the size, shape and organization of the cellular components of the skin.
dc:source: MP_0001212
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: MP:0001212
description adapted from source: no
is caused by: Congenital, iatrogenic.
is characterised by: Change in colour, smell, shape, texture of the skin.

Skin Rash
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Antibiotic
subclass of: Restriction
  on property: treated with
  some values from: Antihistamine
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An abnormal change in skin color, appearance, or texture.
dc:source: OAE_0000362
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
description adapted from source: yes
is caused by: Skin inflammation which has many causes
is characterised by: Change in colour or texture of the skin.

Skin Ulcer
type: Class
subclass of: Phenotype
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: results_in
  some values from: Infection
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A discontinuity of the skin exhibiting loss of the epidermis and often portions of the dermis and subcutaneous fat.
curator note: Find source for additional info
database cross reference: HP:0200042
definition source: HP_0200042
description adapted from source: yes
has disease stage: Wagner's grading of ulcer.
is caused by: Wounds from which ulcers arise can be caused by a wide variety of factors, but the main cause is impaired blood circulation and trauma.
is characterised by: Open craters, often round, with layers of skin that have eroded, the skin around the ulcer may be red, swollen, and tender, may cause pain on the skin around the ulcer, and fluid may ooze from the ulcer, in some cases, ulcers can bleed.
hasExactSynonym: Skin Ulcers

Sleep Breathing Disorder
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An intrinsic sleep disorder characterized by breathing abnormalities.
abbreviation: SBD
database cross reference: NBO:0000494
definition source: NBO_0000494
description adapted from source: no
hasExactSynonym: SBD
hasNarrowSynonym: Sleep Apnea
hasNarrowSynonym: Sleep Apnea Syndromes

Sleeping Disordered Breathing
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
creator: SCDO
description: This measure is a clinical assessment of an individual’s sleep and breathing activities.
dc:source: scoringmanual
has_application_toward: This measure is used to evaluate the presence and symptoms of sleep disorders, including obstructive sleep apnea and hypoxemia that may impact medical and psychosocial complications of individuals with sickle cell disease.
freely available: no
comment: The American Academy of Sleep Medicine (AASM) “Manual for the Scoring of Sleep and Associated Events: Rules, Terminology and Technical Specifications” provides instructions for performing and evaluating polysomnograms (PSGs). It contains details regarding electrode placements, standard montages, and digitization parameters, as well as instructions for scoring sleep stages, arousals, movements during sleep, respiratory events during sleep, and cardiac events. The manual is designed to be administered by physicians and technologists who score sleep studies. The manual is a proprietary online publication that is available for a fee at the AASM website: In addition to the manual, the AASM website provides practice parameters regarding respiratory indications for PSG in children. Polysomnography involves comprehensive recording of the biophysiological patterns that occur during sleep. The PSG typically records the following parameters: brain (EEG), eye movements (EOG), muscle activity or skeletal muscle activation (EMG) and heart rhythm (ECG), respiratory airflow and effort, pulse oximetry and carbon dioxide levels during sleep. The American Academy of Sleep Medicine (AASM) “Manual for the Scoring of Sleep and Associated Events” is an online comprehensive guide for polysomnographic evaluations and is available in desktop, tablet, and mobile device formats. The manual was developed by a committee of sleep experts, is periodically updated, and scoring rules revised based upon an extensive literature review and analysis. Access to the manual is available via subscription. (See website for additional subscription information). This manual is a proprietary instrument of the AASM and can be obtained through the American Academy of Sleep Medicine (AASM) website.

Slit Lamp
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Slit-Lamp Examination
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A microscope with a light source that can be projected into a linear beam. It allows cross-sectional viewing of the aqueous humor; conjuncteiva; cornea; eyelids; iris; and lens of the eye.
database cross reference: MESH:D066167
definition source: D066167
description adapted from source: no

Slit-Lamp Examination
type: Class
subclass of: Eye Examination
subclass of: Restriction
  on property: has medical device
  some values from: Slit Lamp
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Examination of the anterior segment of the eye using a medical instrument called a slit lamp.
database cross reference: NCIT:C75583
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: SLIT LAMP
hasExactSynonym: Slit-Lamp Biomicroscopy
hasExactSynonym: Slit-Lamp Eye Exam
comment: Alternative definition: An eye exam using an instrument that combines a low-power microscope with a light source that makes a narrow beam of light. The instrument may be used to examine the retina, optic nerve, and other parts of the eye.

Smoking
type: Class
subclass of: Lifestyle
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Inhaling and exhaling the smoke of burning tobacco (Cigar, Cigarette, Hookah, Pipe, Smoking, Waterpipe).
database cross reference: MESH:D012907
definition source: D012907
description adapted from source: yes

Smoking Cessation
type: Class
subclass of: Tobacco Use Cessation
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Discontinuation of the habit of smoking, the inhaling and exhaling of tobacco smoke.
database cross reference: MESH:D016540
definition source: D016540
description adapted from source: no
hasExactSynonym: Quit Smoking

Smoking History
type: Class
subclass of: Personal Medical History
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A record of an individual's background in regard to smoking tobacco. This would include such factors as start date, end date (if applicable), number of cigarette smoked, attempts to quit, and others.
database cross reference: NCIT:C29719
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no

Social Environment
type: Class
subclass of: Environmental Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The aggregate of social and cultural institutions, forms, patterns, and processes that influence the life of an individual or community.
database cross reference: MESH:D012931
definition source: D012931
description adapted from source: no
hasExactSynonym: Social Ecology

Social Functioning
type: Class
subclass of: Quality of Life
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Social functioning defines an individual's interactions with their environment and the ability to fulfill their role within such environments as work, social activities, and relationships with partners and family.
dc:source: PROMIS Domain Frameworks/Definitions nih.promis.org
curator note: Include terms for social relationships; social activities?
definition source: Compr Psychiatry. 2000 Jan-Feb;41(1):63-9. Assessment of social functioning in depression.
description adapted from source: yes
hasExactSynonym: Social Function
hasExactSynonym: Social Role

Social Isolation
type: Class
subclass of: Social Functioning
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The separation of individuals or groups resulting in the lack of or minimizing of social contact and/or communication. This separation may be accomplished by physical separation, by social barriers and by psychological mechanisms. In the latter, there may be interaction but no real communication.
database cross reference: MESH:D012934
definition source: D012934
description adapted from source: no
hasExactSynonym: Social Isolations

Social Role
type: Class
subclass of: Social Functioning
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A role that is ascribed to individuals in a community.
database cross reference: SIO:000676
definition source: SIO_000676
description adapted from source: no
hasExactSynonym: Social Function

Social Role Fulfillment
type: Class
subclass of: Social Functioning
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An extent/ degree to which an individual fulfills the expectations of his/her social role.
curator note: Needs description source.
comment: This relates to the importance of having children (parents with trait; individuals' concerns about reproduction).

Social Skill
type: Class
subclass of: Social Functioning
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The personal set of abilities required to successfully interact and communicate with others, both verbally and non-verbally through gestures, body language and personal appearance. Possessing the social, emotional, and intellectual skills and behaviors needed to succeed as a member of society.
database cross reference: MESH:D066107
definition source: D066107
description adapted from source: no
hasExactSynonym: Interpersonal Skill
hasExactSynonym: Social Ability
hasExactSynonym: Social Competence

Social Support
type: Class
subclass of: Social Functioning
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Support systems that provide assistance and encouragement to individuals with physical or emotional disabilities in order that they may better cope. Informal social support is usually provided by friends, relatives, or peers, while formal assistance is provided by churches, groups, etc.
dc:source: Malecki CK, Demaray MK. Measuring perceived social support: development of the child and adolescent social support scale (CASSS) Psychol Sch. 2002;39:1–18. doi: 10.1002/pits.10004.
database cross reference: MESH:D012944
definition source: D012944
description adapted from source: no
hasExactSynonym: Psychosocial Support System
hasExactSynonym: Social Network
comment: Can be assessed in children using the child and adolescent social support scale.

Social Values
type: Class
subclass of: Culture
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Abstract standards or empirical variables in social life which are believed to be important and/or desirable.
database cross reference: MESH:D012945
definition source: D012945
description adapted from source: no
hasBroadSynonym: Value Orientations
hasBroadSynonym: Values

Socioeconomic Factors
type: Class
subclass of: Social Environment
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Social and economic factors that characterize the individual or group within the social structure.
curator note: Maybe have the terms referred to in the comment as sub-classes? There would be overlap with terms in QOL, so would need to work around that.
database cross reference: MESH:D012959
definition source: D012959
description adapted from source: no
comment: Includes: 1) Educational Status (Educational attainment or level of education of individuals; MeSH Unique ID: D004522); 2) Employment (The state of being engaged in an activity or service for wages or salary; MeSH Unique ID: D004651); 3) Family Characteristics (Size and composition of the family; MeSH Unique ID: D005191); 4) Income (Revenues or receipts accruing from business enterprise, labor, or invested capital; MeSH Unique ID: D007182); 5) Medical Indigency (The condition in which individuals are financially unable to access adequate medical care without depriving themselves and their dependents of food, clothing, shelter, and other essentials of living; MeSH Unique ID: D008489); 6) Occupations (Crafts, trades, professions, or other means of earning a living; MeSH Unique ID: D009790); 7) Poverty (A situation in which the level of living of an individual, family, or group is below the standard of the community. It is often related to a specific income level, MeSH Unique ID: D011203); 8) Social Change (Social process whereby the values, attitudes, or institutions of society, such as education, family, religion, and industry become modified. It includes both the natural process and action programs initiated by members of the community, MeSH Unique ID: D012922); 9) Social Class (A stratum of people with similar position and prestige; includes social stratification. Social class is measured by criteria such as education, occupation, and income, MeSH Unique ID: D012923); 10) Social Conditions (The state of society as it exists or in flux. While it usually refers to society as a whole in a specified geographical or political region, it is applicable also to restricted strata of a society, MeSH Unique ID: D012924).

Socioeconomic Status
type: Class
subclass of: Social Environment
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The combination of one's social class and income level. Includes socioeconomic differences between individuals or groups.
definition source: http://bioportal.bioontology.org/ontologies/APAONTO/
description adapted from source: no

Solubility Test
type: Class
subclass of: Hemoglobin S Test
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://bioportal.bioontology.org/ontologies/SNOMEDCT/
curator note: In SNOMED CT this term is "Hemoglobin S Solubility Test"
hasExactSynonym: Hemoglobin S Solubility Test

Spectrophotometer
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance.
dc:source: OBI_0400115
database cross reference: OBI:0400115
description adapted from source: no

Sphygmomanometer
type: Class
subclass of: Manometer
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Instruments for measuring arterial blood pressure consisting of an inflatable cuff, inflating bulb, and a gauge showing the blood pressure.
database cross reference: MESH:D019722
definition source: D019722
description adapted from source: no

Spirituality
type: Class
subclass of: Culture
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Sensitivity or attachment to religious values, or to things of the spirit as opposed to material or worldly interests.
database cross reference: MESH:D029181
definition source: D029181
description adapted from source: no
hasExactSynonym: Spritual Beliefs
comment: May influence coping with SCD and its manifestations in a positive or negative way. (SCDO WG)

Spirometer
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has measurement
  some values from: Lung Volume Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Lung Volume Test
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A spirometer is an apparatus for measuring the volume of air inspired and expired by the lungs. It is a precision differential pressure transducer for the measurements of respiration flow rates. The spirometer records the amount of air and the rate of air that is breathed in and out over a specified period of time.
database cross reference: ERO:0000452
definition source: ERO_0000452
description adapted from source: no

Spirometry
type: Class
subclass of: Pulmonary Function Test
subclass of: Restriction
  on property: has medical device
  some values from: Spirometer
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Spirometry is a common Pulmonary Function Test (PFT) measuring the amount (volume) and/or speed (flow) of air being inhaled and exhaled.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: The protocol source given in PhenX can be used to
database cross reference: PX91600
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Spirometry #091601
has_application_toward: Spirometry is a tool used to screen for the presence of obstructive and restrictive lung diseases.

Spleen Examination
type: Class
subclass of: Physical Examination
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Any process carried out to determine the condition of a patient's spleen.
curator note: Needs relating to Splenomegaly phenotype.
definition source: IDOMAL_0000592
description adapted from source: no

Spondylolisthesis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Analgesics
subclass of: Restriction
  on property: treated with
  some values from: Anti-Inflammatory Agent
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: results_in
  some values from: SCD Related Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Complete bilateral fractures of the pars interarticularis resulting in the anterior slippage of the vertebra.
curator note: Provide source for additional info.
database cross reference: HP:0003302
definition source: HP_0003302
description adapted from source: no
is caused by: Spondylolysis, arthritis, degeneration, trauma, metastases or metabolic bone disease, congenital.
hasExactSynonym: Spondylolithesis

Spontaneous Abortion
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A pregnancy that ends at a stage in which the fetus is incapable of surviving on its own, defined as the spontaneous loss of a fetus.
dc:source: HP_0005268
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0005268
description adapted from source: yes
is caused by: Smoking, obesity, diabetes, drug and alcohol use, infections, trauma, stress, uterine or hormonal abnormalities, multiple pregnancy, chronic maternal diseases, chromosomal abnormalities.

Steroid-Resistant Nephrotic Syndrome
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Nephrotic Syndrome
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: End Stage Kidney Disease
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A form of nephrotic syndrome that does not respond to treatment with steroid medication after 8 weeks, specifically in children.
dc:source: HP_0012588
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0012588
description adapted from source: yes
is caused by: May represent underlying focal segmental glomerulosclerosis, minimal change disease, or other underlying cause. Can be subseqeunt to known mutations.
is characterised by: Persistence of nephrotic syndrome despite appropriate treatment with corticosteroids.

Stigma
type: Class
subclass of: Quality of Life
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A perceived attribute that is deeply discrediting and is considered to be a violation of social norms.
database cross reference: MESH:D057545
definition source: D057545
description adapted from source: no
hasExactSynonym: Social Stigma
hasExactSynonym: Social Stigmas
hasExactSynonym: Stigmas

Stigmatization
type: Class
subclass of: Quality of Life
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An oversimplified perception or conception, especially or persons, social groups, etc.
database cross reference: MESH:D013240
definition source: D013240
description adapted from source: no
hasExactSynonym: Stereotyping
comment: Communities may have stereotypes about the appearance of people with SCD, e.g. if they appear healthy they must not have the disease.

Streptococcus Pneumoniae Vaccine
type: Class
subclass of: Vaccine
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A Streptococcal vaccine that is used against S. pneumoniae infection, which causes pneumococcal diseases.
database cross reference: VO:0000675
definition source: VO_0000675
description adapted from source: no

Stroke
type: Class
subclass of: Phenotype
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: treated with
  some values from: Transcranial Doppler Ultrasonography
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A group of pathological conditions characterized by sudden loss of neurological function due to brain ischemia or intracranial hemorrhages.
dc:source: D020521
curator note: Types of stroke relevant to SCD to be added as children of this class.
database cross reference: MESH:D020521
definition source: D020521
description adapted from source: yes
hasExactSynonym: Brain Vascular Accident
hasExactSynonym: Cerebral Vascular Event
hasExactSynonym: Cerebrovascular Accident
hasExactSynonym: Cerebrovascular Stroke
hasNarrowSynonym: Cerebral Stroke
comment: Stroke is classified by the type of tissue necrosis, such as the anatomic location, vasculature involved, etiology, age of the affected individual, and hemorrhagic vs. non-hemorrhagic nature.

Stroke Impact Measure
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: This measure is a physical assessment to determine neurological deficits due to a stroke.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX820800
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has_application_toward: This measure is used to describe the consequences of a stroke and to monitor the effects of treatment and recovery.

Stroke Impact Scale (SIS)
type: Class
subclass of: Functionality After Stroke Measure
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: This questionnaire includes 59 proxy- or self-report items in 8 domains that assess multidimensional stroke outcomes in adults.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX820701
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Stroke Impact Scale (SIS) - Adults #820701
has respondents: Self; Proxy
has target population: Adults who have had a stroke, ages 18 and older.
has translations: Danish, Dutch, French, German, Greek, Hebrew, Italian, Japanese, Norwegian, Portuguese, Russian, Spanish, Swedish, Tagalog, Thai, Turkish
validated for age ranges: 18 and older
freely available: yes
comment: Items 1(a-d) measure strength. Items 2(a-g) measure memory and thinking. Items 3(a-I) measure emotions. Items 4(a-g) measure ease or difficulty of communication. Items 5(a-j) measure activities of daily living/instrumental activities of daily living (ADL/IADL). Items 6(a-I) measure mobility. Items 7(a-e) measure hand function. Items 8(a-h) measure participation/role function. Item responses are scored on a 5-point Likert-style scale. A score of 1 = an inability to complete the item and a score of 5 = no difficulty experienced at all. A standardized score ranging from 0 to 100 is calculated for all domains, with higher scores indicating a higher quality of life. An extra question on stroke recovery asks that the client rate on a scale from 0 to 100 how much the client feels that he/she has recovered from his/her stroke, where 0 = "no recovery" and 100 = "full recovery."
comment: The Stroke Impact Scale (SIS) should be used with caution in individuals with mild impairment as the items in the Communication, Memory, and Emotion domains are considered easy and only capture limitations in the most impaired individuals.

Stroke Risk Test in Children with Sickle Cell Disease
type: Class
subclass of: Physiological Assay
subclass of: Restriction
  on property: has measurement
  some values from: Cerebral Blood Flow Velocity
subclass of: Restriction
  on property: has medical device
  some values from: Doppler Ultrasound Machine - 2 Megahertz
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Imaging Transcranial Doppler Ultrasonography
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Transcranial Doppler Ultrasonography
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A clinical test to measure the blood flow velocities in intracranial arteries. Elevated intracranial arterial blood flow rates are indicative of expanding vessel lesions and a subsequent increased risk of stroke.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Include below "Cerebral Flow Test"? Include below "Vascular Endothelial Function Test"?
database cross reference: PX821000
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has protocol: PhenX protocol: Stroke Risk in Children with Sickle Cell Disease - TCD #821001
has protocol: PhenX protocol: Stroke Risk in Children with Sickle Cell Disease - TCDi #821002
has target population: Children and adolescents aged 2 years and older with hemoglobin SS or beta-zero thalassemia disease and without a history of clinical stroke.
has_application_toward: This measure is used to stratify stroke risk in children to determine eligibility for prophylactic blood transfusion for stroke prevention.
hasExactSynonym: Stroke Risk in Children with Sickle Cell Disease
comment: Blood-flow velocities indicative of stroke risk can be obtained by either TCD or Imaging Transcranial Doppler (TCDi) ultrasonography. The choice of TCD or TCDi depends on the expertise and equipment available to investigators.

Study Design
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A plan detailing how a study will be performed in order to represent the phenomenon under examination, to answer the research questions that have been asked, and defining the methods of data analysis. Study design is driven by research hypothesis being posed, study subject/population/sample available, logistics/resources: technology, support, networking, collaborative support, etc.
curator note: Review current sub-classes in light of and include relevant classes from "EDDA Study Designs Taxonomy" to be added as sub-classes.
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no
hasExactSynonym: Experiment Design
hasExactSynonym: Experimental Design
hasExactSynonym: Research Design
hasExactSynonym: STYPE
hasNarrowSynonym: Study Type

Study Outcome Measurement
type: Class
subclass of: Research Activity
description: Specific key measurement(s) or observation(s) used to measure the effect of experimental variables on the subjects in a study, or for observational studies, to describe patterns of diseases or traits or associations with exposures, risk factors or treatment. The specific measure that receives the most emphasis in assessment.
database cross reference: NCIT:C93407
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Study Outcome Measure

Stuttering Priapism
type: Class
subclass of: Priapism
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The occurrence of multiple self-limited episodes of unwanted, often painful erections lasting <4 hours.
dc:source: Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014
definition source: Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014
description adapted from source: yes
hasExactSynonym: Recurrent Priapism
comment: Stuttering priapism may lead to a major episode of greater than 4 hours’ duration and may adversely affect quality of life and lead to impotence.
comment: Treatment with chronic hormonal therapy, transfusion therapy, and other treatments may reduce or eliminate these episodes; however, there are no data demonstrating improvement in functional outcomes. Therefore, the decision to treat must be balanced against the side effects of interventions, which can include decreased libido.

Subarachnoid Hemorrhage
type: Class
subclass of: Intracranial Hemorrhage
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: treated with
  some values from: Healthy Diet
subclass of: Restriction
  on property: treated with
  some values from: Tobacco Use Cessation
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: modified by
  some values from: Lifestyle
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Bleeding in the space that surrounds the brain, between the arachnoid mater and the pia mater.
dc:source: subarachnoid hemorrhage 134,68
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
description adapted from source: yes
is characterised by: Symptoms of a subarachnoid hemorrhage include: Loss of consciousness, double vision, nausea and/or vomiting, Severe headache - the worst headache pain you've ever had that feels different from other headaches, Trouble speaking, drooping eyelid, confusion and difficulty concentrating, sensitivity to light, neck stiffness, seizures.Before a subarachnoid hemorrhage occurs, a large brain aneurysm that's started to push against nerves in the brain can cause symptoms, such as: pain surrounding the eye, changes in your vision, dilated pupils, weakness or numbness on one side of your body, loss of hearing or trouble with balance, seizures, difficulty with memory
comment: A subarachnoid hemorrhage is a medical emergency, and immediate treatment is essential to help reduce the risk for permanent brain damage. The main goal of treating a subarachnoid hemorrhage is to stop the bleeding. Often, a doctor may perform surgery to place a small clip on the blood vessel to stop blood from leaking into the brain. Alternatively, some types of aneurysms can be treated with an endovascular coil, either by a radiologist or neurosurgeon. This requires making a tiny incision in your thigh and passing a thin catheter through the artery in your leg up to the artery in your head that is bleeding. Recovery times from this type of treatment are much shorter than traditional surgery; however, not all aneurysms can be treated this way. Your doctor can determine if you are a candidate for this treatment after performing your angiogram. Part of the long-term treatment of a subarachnoid hemorrhage also involves addressing any risk factors that may have helped trigger the hemorrhage. This may mean quitting smoking if you're a smoker, gaining better control of your diabetes, lowering cholesterol and blood pressure, maintaining a healthy body weight, and eating a balanced diet.
comment: Diagnosis is made by: CT scan or MRI scan to examine the brain tissue, Angiogram to evaluate the blood vessels in the brain, Spinal tap to analyze the cerebrospinal fluid for the presence of blood.

Substance Use History
type: Class
subclass of: Personal Medical History
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Substances - Lifetime Use
type: Class
subclass of: Substance Use History
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Record of whether or not the respondent has ever used a drug during his or her entire life.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX31100
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Substances - Lifetime Use #031101
has_application_toward: This measure can be used to assess the participant's lifetime use of any drug. The question is often used as a prelude to more detailed questions about substance use to screen out individuals who have ever used these substances.

Suicidal Thoughts
type: Class
subclass of: Depression
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Thinking about, considering, or planning to kill oneself.
definition source: definitions.html
description adapted from source: yes
hasExactSynonym: Suicidal Ideation
hasRelatedSynonym: Suicide

Support Group
type: Class
subclass of: Social Functioning
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Organizations which provide an environment encouraging social interactions through group activities or individual relationships especially for the purpose of rehabilitating or supporting patients, individuals with common health problems, or the elderly. They include therapeutic social clubs.
database cross reference: MESH:D012657
definition source: D012657
description adapted from source: no
hasExactSynonym: Self Help Group
hasExactSynonym: Self-Help Group
hasExactSynonym: Therapeutic Social Club

Supportive Therapeutics
type: Class
subclass of: Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Measures aimed at providing appropriate supportive and rehabilitative services to minimize morbidity and maximize quality of life after a long-term disease or injury is present.
database cross reference: MESH:D055512
definition source: D055512
description adapted from source: no
hasExactSynonym: Supportive Therapy
hasExactSynonym: Tertiary Prevention

Sustained and Selective Attention Measure
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A computerized test for the assessment of visual attention problems in individuals ages 8 years old and older.
dc:source: http://www.phenxtoolkit.org/index.php
abbreviation: Conners CPT 3
database cross reference: PX821200
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Label and description adapted
has protocol: PhenX protocol: Sustained and Selective Attention #821201
has respondents: Self
has_application_toward: Deficits in attention are associated with some psychiatric conditions, (e.g., Attention-Deficit/Hyperactive Disorder-ADHD), genetic diseases (e.g., sickle cell disease), and can be a consequence of stroke.
validated for age ranges: Ages 8 and older
freely available: The Conners Continuous Performance Test 3rd Edition (Conners CPT 3) is a proprietary instrument and administration requires a license from Multi-Health Systems, Inc.
freely available: This is a proprietary instrument and administration requires a license from Multi-Health Systems, Inc.
hasExactSynonym: Conners CPT 3
hasExactSynonym: Conners Continuous Performance Test 3rd Edition
hasExactSynonym: Conners Continuous Performance Test 3rd Edition (Conners CPT 3)
comment: Respondents press the spacebar (or click the mouse) when any letter of the alphabet (except "X") appears on the screen. Commission errors occur when the spacebar is pressed when an "X" is presented. Omission errors occur when the spacebar is not pressed when a letter besides "X" is presented on the screen. Reaction time is the interval between the appearance of the letter on the screen and the response, e.g., pressing the spacebar. The Conners CPT 3™ uses both standardized and raw scores to measure overall visual attention as well as specific aspects of attention in the areas of inattentiveness, impulsivity, sustained attention and vigilance.

Symptomatic Therapeutics
type: Class
subclass of: Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: Therapeutics that ease the symptoms without addressing the basic cause of the disease.
definition source: http://www.medicinenet.com/script/main/art.asp
description adapted from source: yes
hasExactSynonym: Symptomatic Treatment

Systemic
type: Class
subclass of: from phenotype
description: Affecting a number of tissues relating to the entire organism as distinguished from and of its individual parts.
definition source: systemic
description adapted from source: yes

Systemic Lupus Erythematosus
type: Class
subclass of: Comorbid Disease
subclass of: Restriction
  on property: diagnosed by
  some values from: Chest X-Ray
subclass of: Restriction
  on property: diagnosed by
  some values from: Complete Blood Count
subclass of: Restriction
  on property: diagnosed by
  some values from: Urine Test
subclass of: Restriction
  on property: treated with
  some values from: Anti-Inflammatory Agent
subclass of: Restriction
  on property: treated with
  some values from: Malaria Prophylaxis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys, and serosal membranes.
database cross reference: HP:0002725
definition source: HP_0002725
description adapted from source: no
is characterised by: Severe fatigue, joint pain, joint swelling, headaches, a rash on the cheeks and nose, which is called a "butterfly rash", hair loss, anemia, blood-clotting problems, fingers turning white or blue and tingling when cold.

Tandem Mass Spectrometry
type: Class
subclass of: Chemical Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Tandem mass spectrometry is a data transformation that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules).
dc:source: OBI_0200198
abbreviation: MS/MS
hasExactSynonym: MS/MS

Tertiary Healthcare
type: Class
subclass of: Health System
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Care of a highly technical and specialized nature, provided in a medical center, usually one affiliated with a university, for patients with unusually severe, complex, or uncommon health problems.
database cross reference: MESH:D063128
definition source: D063128
description adapted from source: no
hasExactSynonym: Tertiary Care
hasExactSynonym: Tertiary Health Care

Test of Functional Health Literacy in Adults (TOFHLA)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The Test of Functional Health Literacy Assessment (TOFHLA) assesses a patient’s level of comprehension of health-related material. It is available in a full-format (a 22-minute test, with 50 reading comprehension items in three passages and 17 numeracy items), an abbreviated format (a 12-minute test, with 36 reading comprehension items in two passages and four numeracy items) and a shortened version (the S-TOFHLA, a 7-minute test, with 36 reading comprehension items in 2 passages.). The passages on the S-TOFHLA use a modified Cloze procedure where every fifth to seventh word is omitted and subjects select the correct word from among a set of four options. The passages contain information about an upper gastrointestinal tract x-ray procedure, and the “Rights and Responsibilities” section from a Medicaid application, and have Gunning-Fox readability indices of fourth and tenth grade, respectively. In early developmental studies, the reading comprehension passages in the S-TOFHLA had a reliability coefficient (Cronbach’s alpha) of 0.97 and correlation with the Rapid Estimate of Adult Literacy in Medicine (REALM) of 0.81. Each selection is scored a “1” for correct or a “0” for incorrect and scores are summed over items to create a total score. The 36-point scale of the S-TOFHLA is divided into three categories of functional literacy: inadequate (0-16), adequate (17-22) and functional (23-36).
dc:source: Parker RM, Baker DW, Williams MV, Nurss JR. The test of functional health literacy in adults: a new instrument for measuring patients' literacy skills. Journal of General Internal Medicine. 1995;10(10):537-41.
abbreviation: TOFHLA
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Also these properties: has respondents has target population selection criteria met validated for age ranges has cross-cultural adaptation freely available
has translations: Spanish
hasExactSynonym: TOFHLA
hasExactSynonym: Test of Functional Health Literacy in Adults

Thalassemia
type: Class
subclass of: from phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An inherited blood disorder characterized by a decreased synthesis of one of the polypeptide chains that form hemoglobin. Anemia results from this abnormal hemoglobin formation.
dc:source: Hemoglobinopathy
database cross reference: NCIT:C35069
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
comment: Some hemoglobinopathies are also thalassemias, but most are not. Hemoglobinopathies imply structural abnormalities in the globin proteins themselves. Thalassemias, in contrast, usually result in underproduction of normal globin proteins, often through mutations in regulatory genes. ("Hemoglobinopathy", Wikipedia, 01/2017)

The Duke Religion Index (DUREL)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The Duke Religion Index (DUREL) is a five item scale which measures religiosity in three areas: organizational religiosity (OR), non-organizational religiosity (NOR), and intrinsic religiosity. Two of the questions were derived from large epidemiologic studies and have been shown to have a strong predictive value for many health outcomes. OR has been related to less depression, more social support, better physical health, lower resource utilization, and lower mortality. NOR has been shown to be related to poorer physical health, and greater social support. The other three items were taken from the Hoge 10- item religiosity scale (Hodge et al 1972). The DUREL has high test-retest reliability (intra-class correlation = 0.91), high internal consistency (Cronbach’s alpha’s = 0.78–0.91).
dc:source: Koenig, HG and Büssing A. (2010). The Duke University Religion Index (DUREL): A Five-Item Measure for Use in Epidemological Studies. Religions, 1, 78-85.
abbreviation: DUREL
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Also these properties: has cross-cultural adaptation has translations
has respondents: Self
has target population: Adults with SCD
selection criteria met: Used in at least one SCD study
validated for age ranges: Adults
freely available: no
hasExactSynonym: DUREL
hasExactSynonym: The Duke Religion Index

Therapeutic Device
type: Class
subclass of: Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
creator: SCDO
description: A medical device used to prevent and treat medical conditions, or to alleviate pain or injury.
curator note: This term is in the "Read Clinical Terminology Version 2".

Therapeutic Irrigation
type: Class
subclass of: Supportive Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The washing of a body cavity or surface by flowing water or solution for therapy or diagnosis.
database cross reference: MESH:D007507
definition source: D007507
description adapted from source: no
hasExactSynonym: Lavage
hasExactSynonym: Lavages
hasExactSynonym: Therapeutic Irrigations
hasNarrowSynonym: Douching
hasNarrowSynonym: Douchings

Therapeutics
type: Class
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: The treatment and care of a patient for the purpose of both preventing and combating disease or alleviating pain or injury.
curator note: "Chemotherapy" to be added in this class? If so, would have to be specific types of chemotherapy relevant to the type of therapeutics class.
curator note: Include as subclasses: Prosthesis Phototherapy (therapy for Jaundice) Risk Reduction? Copy relevant disease modifiers below this.
definition source: therapeutics
description adapted from source: yes
hasExactSynonym: Therapy
hasExactSynonym: Treatment

Tobacco Use Cessation
type: Class
subclass of: Health Behaviour
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Ending the tobacco habits of smoking, chewing, or snuff use.
database cross reference: MESH:D020340
definition source: D020340
description adapted from source: no
hasExactSynonym: Tobacco Cessation

Total White Blood Cell Count
type: Class
subclass of: White Blood Cell Count
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The total number of leukocytes in 1 cubic millimeter of peripheral venous blood.
database cross reference: CMO:0000365
definition source: CMO_0000365
description adapted from source: no

Traditional Healer
type: Class
subclass of: Beliefs About Remedies and Treatment
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A person who practices the art of healing using traditional medicine, a systems of medicine based on cultural beliefs and practices handed down from generation to generation. The concept includes mystical and magical rituals (spiritual therapies); phytotherapy (plant therapy) and other treatments which may not be explained by modern medicine.
definition source: http://www.ncbi.nlm.nih.gov/mesh/68008519
description adapted from source: yes
hasBroadSynonym: Folk Medicine
hasBroadSynonym: Folk Remedies
hasBroadSynonym: Folk Remedy
hasBroadSynonym: Home Remedies
hasBroadSynonym: Home Remedy
hasBroadSynonym: Indigenous Medicine
hasBroadSynonym: Medicine, Folk
hasBroadSynonym: Medicine, Indigenous
hasBroadSynonym: Medicine, Primitive
hasBroadSynonym: Primitive Medicine
hasBroadSynonym: Remedies, Folk
hasBroadSynonym: Remedies, Home
hasBroadSynonym: Remedy, Folk
hasBroadSynonym: Remedy, Home
hasBroadSynonym: Traditional Medicine
hasExactSynonym: Folk Healer
hasExactSynonym: Healer
hasExactSynonym: Sangoma
hasExactSynonym: Shaman

Trail Making Test
type: Class
subclass of: Executive Function Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: An interviewer-administered, two-part test that requires the respondent to organize numerical and alphabetical sequences that are randomly distributed on a piece of paper. The protocol includes instructions for correcting mistakes and instructions for scoring based on speed and accuracy.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX131101
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Executive Function #131101
has respondents: Self
validated for age ranges: 15 years and older
freely available: The Trail Making Test is a proprietary, fee-based instrument that is available from Reitan Neuropsychology Lab, Inc.
comment: Whereas the Trail Making Test has two parts (Parts A and B), the PhenX Neurology Working Group recommends that part B be used to measure executive function in adults.

Transcranial Doppler Ultrasonography
type: Class
subclass of: Cerebral Blood Flow Assay
subclass of: Ultrasonography Test
subclass of: Supportive Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A non-invasive technique using ultrasound for the measurement of cerebrovascular hemodynamics, particularly cerebral blood flow velocity and cerebral collateral flow. With a high-intensity, low-frequency pulse probe, the intracranial arteries may be studied transtemporally, transorbitally, or from below the foramen magnum.
dc:source: DisertaceMIKULIKpriloha3.pdf
abbreviation: TCD
database cross reference: D017585
definition source: D017585
description adapted from source: no
has_application_toward: To measure: cerebral blood flow velocity or cerebral collateral flow.
hasExactSynonym: TCD
hasExactSynonym: Transcranial Doppler
hasExactSynonym: Ultrasonography, Doppler, Transcranial
comment: This technique is also used to treat ischemic stroke.

Transcutaneous Electrical Nerve Stimulation
type: Class
subclass of: Analgesia
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The use of specifically placed small electrodes to deliver electrical impulses across the skin to relieve pain. It is used less frequently to produce anesthesia.
dc:source: http://www.ncbi.nlm.nih.gov/pubmed/3138879
dc:source: Wang, W. C., S. L. George, and J. A. Wilimas. "Transcutaneous electrical nerve stimulation treatment of sickle cell pain crises." Acta haematologica 80.2 (1988): 99-102.
abbreviation: TENS
curator note: Not sure which dc:source to have (will decide later).
database cross reference: MESH:D004561
definition source: D004561
description adapted from source: no
hasExactSynonym: Percutaneous Electrical Nerve Stimulation
hasExactSynonym: TENS

Transient Monocular Blindness
type: Class
subclass of: Ophthalmologic Complication
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Electrocardiogram
subclass of: Restriction
  on property: diagnosed by
  some values from: Electrocardiographic Monitor
subclass of: Restriction
  on property: diagnosed by
  some values from: Electrocardiography
subclass of: Restriction
  on property: diagnosed by
  some values from: Electrocardiograph
subclass of: Restriction
  on property: diagnosed by
  some values from: Eye Examination
subclass of: Restriction
  on property: treated with
  some values from: Healthy Diet
subclass of: Restriction
  on property: treated with
  some values from: Healthy Lifestyle
subclass of: Restriction
  on property: treated with
  some values from: Exercise
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Stroke
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Temporary loss of vision in one eye due to a lack of blood flow to the retina.
dc:source: 000784.htm
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info. Include this term below "Eye".
description adapted from source: yes
is caused by: Occurs when a blood clot or a piece of plaque blocks an artery in the eye. The blood clot or plaque usually travels from a larger artery, such as the carotid artery in the neck or an artery in the heart, to an artery in the eye. Plaque is a hard substance that forms when fat, cholesterol, and other substances build up in the walls of arteries. Risk factors include: Heart disease, especially irregular heartbeat; Alcohol abuse; Cocaine use; Diabetes; Family history of stroke; High blood pressure; High cholesterol; Increasing age; Smoking (people who smoke one pack a day double their risk of a stroke).
is characterised by: Symptoms include the sudden loss of vision in one eye. This usually lasts for a few seconds to several minutes. Afterwards, vision returns to normal. Some patients describe the loss of vision as a gray or black shade coming down over their eye.If the blockage continues, vision loss may be followed by more serious nervous system symptoms. These symptoms can be similar to those of a stroke, including weakness or speech problems.
hasExactSynonym: Amaurosis Fugax
hasExactSynonym: Temporary Blindness

Tubular Proteinuria
type: Class
subclass of: Proteinuria
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Excretion in urine of proteins of a size smaller than albumin (molecular weight 69 kD).
dc:source: tubular+proteinuria
database cross reference: HP:0003126
definition source: HP_0003126
description adapted from source: no
hasExactSynonym: Low-Molecular-Weight Proteinuria
hasRelatedSynonym: Glomerular Proteinuria

Twin Study
type: Class
subclass of: Publication Type
description: Work consisting of reporting using a method of detecting genetic causes in human traits and genetic factors in behavior using sets of twins.
database cross reference: MESH:D018486
definition source: D018486
description adapted from source: no

Twin Studies as Topic
type: Class
subclass of: Study Design
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Methods of detecting genetic etiology in human traits. The basic premise of twin studies is that monozygotic twins, being formed by the division of a single fertilized ovum, carry identical genes, while dizygotic twins, being formed by the fertilization of two ova by two different spermatozoa, are genetically no more similar than two siblings born after separate pregnancies. (Last, J.M., A Dictionary of Epidemiology, 2d ed)
database cross reference: MESH:D018433
definition source: D018433

UDP Glucuronosyltransferase 1 Family, Polypeptide A1
type: Class
subclass of: Non-Globin Loci
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites.
dc:source: http://www.ncbi.nlm.nih.gov/gene/54658
abbreviation: UGT1A1
description adapted from source: yes
comment: Official Full Name: UDP glucuronosyltransferase 1 family, polypeptide A1; Gene ID: 54658; Chromosome: 2; Position: 233760273..233773299 (GRCh38.p2); Variants
preferred label: UGT1A1

Ultrasound Machine
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs.
dc:source: OBI_0001098
database cross reference: OBI:0001098
description adapted from source: no

Urban Location
type: Class
subclass of: Geographic Location
subclass of: Healthcare Access
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An urban area is the region surrounding a city. Most inhabitants of urban areas have nonagricultural jobs. Urban areas are very developed, meaning there is a density of human structures such as houses, commercial buildings, roads, bridges, and railways.
curator note: Copied this below "Geographic Location" under "Disease Modifiers".
definition source: urban-area
description adapted from source: no
hasExactSynonym: Urban Area
hasExactSynonym: Urban Setting

Urinary Albumin Test
type: Class
subclass of: Kidney Function Test
subclass of: Urine Test
subclass of: Restriction
  on property: has measurement
  some values from: Urine Albumin Concentration
subclass of: Restriction
  on property: essential measure
  some values from: Blood Pressure Measurement
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: History of Kidney Failure
subclass of: Restriction
  on property: essential measure
  some values from: History of Type I and Type 2 Diabetes
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A bioassay to measure urine concentration of albumin, which is produced by the liver and is the most abundant protein in the blood.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX141500
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has protocol: PhenX protocol: Urinary Microalbumin Assay #141501
comment: The Sickle Cell Disease Research and Scientific Panel notes that the terms "microalbuminuria" and "macroalbuminuria" have been used clinically to describe different levels of abnormal albumin excretion rate: 30-299 mg/g urine creatinine, and >300 mg/gr urine creatinine, for microalbuminuria and macroalbuminuria, respectively. Recently, a new terminology has been proposed: "low level albuminuria" instead of microalbuminuia, and "high level albuminuria" for macroalbuminuria, since the older terminology could be interpreted as measuring different molecular forms of albumin. Because albuminuria may be affected by non-pathological factors (exercise, menstruation contamination, biological variability, etc.), abnormal values should be confirmed within 1-2 months.
comment: With the protocol provided, albumin concentration is measured according to a fluorescent immunoassay (FIA). The protocol also lists reference ranges for healthy adults.

Urinary Creatinine Test
type: Class
subclass of: Kidney Function Test
subclass of: Urine Test
subclass of: Restriction
  on property: has measurement
  some values from: Urine Creatinine Concentration
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A bioassay to measure urine concentration of creatinine, a muscle metabolite that is filtered out of blood by the kidneys.
dc:source: http://www.phenxtoolkit.org/index.php
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Urinary Creatinine Assay #141601
has_application_toward: The urinary creatinine measure should be done in conjunction with urinary microalbumin to determine the ratio of urine albumin to urine creatinine, which can predict the risk of nephropathy.
comment: The PhenX protocol provides basic instructions for collecting and processing urine according to National Health and Nutrition Examination Survey (NHANES) methods. Creatinine concentration in a participant’s morning urine sample is measured according to the Jaffe rate method. The protocol also lists reference ranges for healthy adults.

Urinary Protein Measurement
type: Class
subclass of: Urine Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The determination of the amount of protein present in a urine sample.
database cross reference: C74760
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
has_application_toward: Used to diagnose a proteinuria phenotype.
comment: Can be determined using a number of methods including turbidimetric, electrophoresis and dipstick.

Urinary System
type: Class
subclass of: from phenotype
description: The organs and passageways concerned with the production and excretion of urine, including the kidneys, ureters, urinary bladder, and urethra.
database cross reference: BTO:0003092
definition source: BTO_0003092
description adapted from source: no

Urine Albumin Concentration
type: Class
subclass of: Urinary Protein Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Urinary Albumin Test
subclass of: Restriction
  on property: essential measure
  some values from: Blood Pressure Measurement
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: History of Kidney Failure
subclass of: Restriction
  on property: essential measure
  some values from: History of Type I and Type 2 Diabetes
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
creator: SCDO
description: The concentration of albumin in the urine.
dc:source: http://www.phenxtoolkit.org/index.php
comment: Because albuminuria may be affected by non-pathological factors (exercise, menstruation contamination, biological variability, etc.), abnormal values should be confirmed within 1-2 months.

Urine Albumin Excretion Rate
type: Class
subclass of: Urinary Protein Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The amount of albumin excreted into the urine within a specified period of time. If the level of albumin in the urine is above normal but not high enough to be detectable with routine protein testing it is referred to as "microalbumin".
dc:source: EFO_0005667
database cross reference: CMO:0000757
definition source: CMO_0000757
description adapted from source: no
has_application_toward: Urinary albumin is measured as an indicator for kidney malfunctions such as diabetic nephropathy.
hasExactSynonym: Urinary Albumin Excretion Rate

Urine Albumin-Creatinine Ratio
type: Class
subclass of: Urinary Protein Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Comparison of urine microalbumin, that is, a level of albumin in the urine which is above normal but not detectable with routine protein testing, to amount of creatinine in a specified volume of urine. Often expressed as microalbumin concentration divided by creatinine concentration times 1000 mg per gram.
dc:source: http://www.phenxtoolkit.org/index.php
abbreviation: ALBCREAT
database cross reference: CMO:0000384
definition source: CMO_0000384
description adapted from source: no
hasExactSynonym: ACR
hasExactSynonym: ALBCREAT
hasExactSynonym: Albumin To Creatinine Protein Ratio Measurement
hasExactSynonym: Albumin/Creatinine
hasExactSynonym: Microalbumin/Creatinine Ratio
hasExactSynonym: Urine Microalbumin-Creatinine Ratio
comment: The ratio of urine albumin to urine creatinine, is used to predict the risk of nephropathy (National Health and Nutrition Examination Survey and University of Minnesota Laboratory Procedure Manual for Urinary Creatinine, 2008).

Urine Creatinine Concentration
type: Class
subclass of: Urine Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Urinary Creatinine Test
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The concentration of creatinine in the urine.
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes

Urine Measurement
type: Class
subclass of: Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Any measurement of urine, the fluid waste product excreted by the kidneys, or its components.
database cross reference: CMO:0000256
definition source: CMO_0000256
description adapted from source: no

Urine Protein Sulfosalicylic Acid Precipitation Test
type: Class
subclass of: Biochemical Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A method in which sulfosalicylic acid (that is, the SSA reagent) is added to a small and equal volume of clear urine. The acidification causes precipitation of protein in the sample (seen as increasing turbidity), which can be subjectively quantitated visually or more precisely quantitated using photometry.
database cross reference: MMO:0000504
definition source: MMO_0000504
description adapted from source: no
hasExactSynonym: SSA Protein Precipitation Test
hasExactSynonym: Urine SSA Turbidimetry
hasExactSynonym: Urine Sulfosalicylic Acid Turbidimetry
hasExactSynonym: Urine Turbidimetry with Sulfosalicylic Acid

Urine Test
type: Class
subclass of: Physiological Assay
subclass of: Restriction
  on property: has curation status
  has value: uncurated
hasExactSynonym: Urinalysis
hasExactSynonym: Urine Analysis

Urology
type: Class
subclass of: Urinary System
description: The medical specialty concerned with the study, diagnosis, and treatment of diseases of the genitourinary tract.
database cross reference: C17243
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no
hasRelatedSynonym: Urologic
hasRelatedSynonym: Urologic Diseases

Urticaria
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Raised, well-circumscribed areas of erythema and edema involving the dermis and epidermis. Urticaria is intensely pruritic, and blanches completely with pressure.
dc:source: HP_0001025
dc:source: Mediscape: Urticaria Clinical presentation: Author: Henry K Wong, MD, PhD; Chief Editor: Dirk M Elston, MD.
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0001025
description adapted from source: no
is caused by: Infections, allergens, drugs, exercise, pregnancy, autoimmune disease, skin eposure to undue pressure.
is characterised by: Hives, mucous membrane swelling; lips tongue, throat, horse voice.
hasExactSynonym: Hives

Vaccine
type: Class
subclass of: Infection Prophylaxis
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine.
database cross reference: VO:0000001
definition source: VO_0000001
description adapted from source: no

Validation Studies
type: Class
subclass of: Publication Type
description: Works consisting of research using processes by which the reliability and relevance of a procedure for a specific purpose are established.
database cross reference: MESH:D023361
definition source: D023361
description adapted from source: no

Vaping
type: Class
subclass of: Tobacco Use Cessation
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The act of inhaling and exhaling vapors produced from electronic cigarettes.
database cross reference: MESH:D000072137
definition source: http://purl.bioontology.org/ontology/MESH/D000072137
description adapted from source: no
hasExactSynonym: Electronic Cigarrete Use

Vascular Endothelial Function Test
type: Class
subclass of: Physiological Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A measure of vascular endothelial cell response to stimulation—for example, by vasoactive substances released by or those that interact with the vascular endothelium.
definition source: http://circ.ahajournals.org/content/108/17/2054
description adapted from source: yes
hasExactSynonym: Assessment of Endothelial Cell Function
hasExactSynonym: Endothelium Dysfunction Test

Vaso-Occlusive Crisis
type: Class
subclass of: SCD Related Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Pain resulting from tissue ischemia as a result of blockage of blood vessels, occurring in a variety of vascular beds, but most commonly in the bone or bone marrow and requiring analgesic medication.
definition source: http://www.google.co.za/url
definition source: Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
description adapted from source: no
hasExactSynonym: Acute Pain Crisis
hasExactSynonym: Sickle Crisis
hasExactSynonym: VOC
hasExactSynonym: Vaso-Occlusive Crisis
hasExactSynonym: Vaso-Occlusive Episodes

Venipuncture
type: Class
subclass of: Diagnostic Technique, Method, Test or Assay
subclass of: Restriction
  on property: has measurement
  some values from: Complete Blood Count
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Extraction of blood from a vein using a needle. In human, the basilic, cephalic and median cubital veins are most commonly used as well as the femoral vein.
database cross reference: MMO:0000090
definition source: MMO_0000090
description adapted from source: no

Ventricular Hypertrophy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Cluster Headache
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Enlargement of the cardiovascular ventricular muscle tissue with increase in the width of the wall of the ventricle and loss of elasticity. Ventricular hypertrophy is clinically differentiated into left and right ventricular hypertrophy.
curator note: Provide source for additional info.
database cross reference: HP:0001714
definition source: HP_0001714
description adapted from source: no
is characterised by: Often people feel restless and agitated during an attack because the pain is so intense, and may react by rocking, pacing or banging their head against the wall.They commonly also have at least one of the following associated symptoms: a red and watering eye; drooping and swelling of one eyelid; a smaller pupil in one eye; a sweaty face; a blocked or runny nostril; a red ear. These attacks generally last between 15 minutes and three hours, and typically occur between one and eight times a day.
comment: Cluster headache bouts may occur every year over many years and may be lifelong. In general, they become less frequent over time.

Vineland Adaptive Behavior Scales, Second Edition (Vineland-II)
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A parent or caregiver questionnaire administered as part of a structured interview that measures day-to-day performance on communication, daily living, socialization, and motor skills. Standard scores can be derived for communication, daily living, socialization, and motor skills subtests or combined to create an Adaptive Behavior Composite (ABC).
dc:source: http://www.phenxtoolkit.org/index.php
abbreviation: Vineland-II
curator note: Should this also/rather be included below QoL?
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Adaptive Behavior/Adaptive Function #820601
has respondents: Proxy
has_application_toward: This measure can be used to identify individuals with developmental disabilities or delays, perform diagnostic evaluations, monitor progress, and develop programs.
validated for age ranges: All ages from birth through age 90
freely available: This is a proprietary protocol and administration requires a license from Pearson, Inc.
hasBroadSynonym: Adaptive Behavior
hasBroadSynonym: Adaptive Function
hasExactSynonym: Vineland-II
comment: This is considered to be the gold standard for identifying developmental delays. It is a parent- or proxy-structured interview and can be used to assess the function of participants of any age.

Viral Infection
type: Class
subclass of: Infection
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Any disease caused by a virus.
curator note: Remove if subclasses not added below this. Perhaps use as Disease Modifier?
database cross reference: C3439
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Viral Disease
hasExactSynonym: Virus Disease

Virus
type: Class
subclass of: Infectious Agent
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.
database cross reference: MESH:D014780
definition source: D014780
description adapted from source: Only label adapted
hasExactSynonym: Viruses

Vitrectomy
type: Class
subclass of: Ophthalmologic Surgical Procedure
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Removal of the whole or part of the vitreous body in treating endophthalmitis, diabetic retinopathy, retinal detachment, intraocular foreign bodies, and some types of glaucoma.
database cross reference: MESH:D014821
definition source: D014821
description adapted from source: no

Vitreous Hemorrhage
type: Class
subclass of: Ophthalmologic Complication
subclass of: Restriction
  on property: treated with
  some values from: Vitrectomy
subclass of: Restriction
  on property: results_in
  some values from: Transient Monocular Blindness
subclass of: Restriction
  on property: results_in
  some values from: Blindness
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Bleeding into the vitreous cavity caused by mechanical stress (from trauma or normal vitreous movement) on the delicate neovascular fronds growing from the retina into the vitreous chamber.
dc:source: UBERON_0001797
dc:source: Bonanomi et al 2013 Arq Bras Oftalmol, Ballas et al 2010 Am J Hematol.
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: UBERON:0001797
description adapted from source: yes
is caused by: Often a complication of sickle retinopathy
is characterised by: Temporary or permanent blindness.
hasExactSynonym: Hemorrage Within the Vitreous Humor.

Western Blot
type: Class
subclass of: Electrophoresis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
dc:source: D015153
curator note: Can this term also be below "Immunological Assay"?
database cross reference: D015153
description adapted from source: no
hasExactSynonym: Western Immunoblot

Wheezing Episode with Co-Morbid Asthma
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Bronchodilator Responsiveness Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: diagnosed by
  some values from: Pulmonary Function Test
subclass of: Restriction
  on property: results_in
  some values from: Acute Chest Syndrome
subclass of: Restriction
  on property: results_in
  some values from: Sickle Cell Painful Event
subclass of: Restriction
  on property: results_in
  some values from: Stroke
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An acute onset of wheezing in a persons with SCD and co-morbid asthma.
dc:source: Knight-Madden et al 2014 Ped Resp Rev; Glassberg et al 2014 Curr Opin Pediatr.
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
description adapted from source: yes
is caused by: Synergistic inflammatory response due to both SCD and asthma.
is characterised by: Increased severity of episodes.
hasExactSynonym: Asthma Attack

White Blood Cell Count
type: Class
subclass of: White Blood Cell Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The number of white blood cells in a specified volume of blood.
database cross reference: CMO:0000027
definition source: CMO_0000027
description adapted from source: no
hasExactSynonym: Leukocyte Count
hasExactSynonym: White Corpuscle Count

White Blood Cell Measurement
type: Class
subclass of: Blood Cell Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Any value resulting from the quantification of a morphological or physiological parameter of leukocytes, largely colorless blood corpuscles capable of ameboid movement, whose chief function is to protect the body against microorganisms and other disease-causing entities.
database cross reference: CMO:0002341
definition source: CMO_0002341
description adapted from source: no

Whole Body Morphological Measurement
type: Class
subclass of: Body Morphological Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Morphological measurement involving the entire body of an organism.
database cross reference: CMO:0000011
definition source: CMO_0000011
description adapted from source: no

Witchcraft
type: Class
subclass of: Beliefs About Causes of Illness
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An act of employing sorcery (the use of power gained from the assistance or control of spirits), especially with malevolent intent, and the exercise of supernatural powers and alleged intercourse with the devil or a familiar. (From Webster, 3rd Ed).
database cross reference: MESH:D018599
definition source: D018599
description adapted from source: no

World Health Organisation Quality of Life Instrument (WHOQOL)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The WHOQOL is a quality of life assessment developed by the WHOQOL Group with fifteen international field centres, simultaneously, in an attempt to develop a quality of life assessment that would be applicable cross-culturally.
dc:source: WHOQOL Group (1993). Measuring quality of life: The development of the World Health Organisation quality of life instrument (WHOQOL). Geneva: WHO.
abbreviation: WHOQOL
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Also these properties: validated for age ranges has cross-cultural adaptation freely available has translations
has respondents: Self
has target population: Healthy people; Clinic patients
selection criteria met: Demonstrated validity with SCD populations; at least two publications using the measure
hasExactSynonym: WHOQOL
hasExactSynonym: World Health Organisation Quality of Life Instrument

X-Ray Image
type: Class
subclass of: Measurement
subclass of: Restriction
  on property: has medical device
  some values from: X-Ray Machine
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Radiography
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The visual output that an X-ray machine produces.
curator note: Should this rather be below "Diagnostic Device"?

X-Ray Image of Chest
type: Class
subclass of: X-Ray Image
subclass of: Restriction
  on property: has medical device
  some values from: X-Ray Machine
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Chest X-Ray
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The visual output that an X-ray machine produces when imaging the chest.

X-Ray Machine
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Radiography
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A device that is used to generate X-rays.
dc:source: http://purl.bioontology.org/ontology/SNOMEDCT/68080007
database cross reference: A-2C500
database cross reference: OBI:0001138
definition source: OBI_0001138
description adapted from source: Only label adapted
hasBroadSynonym: X-Ray Source
hasExactSynonym: Radiographic unit

X-Ray Therapy
type: Class
subclass of: Supportive Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Medical treatment involving the use of controlled amounts of X-Rays.
dc:source: x-ray+therapy
curator note: Include source of synonyms (dc:source).
database cross reference: MESH:D014964
definition source: D014964
description adapted from source: no
hasExactSynonym: Actinotherapy
hasExactSynonym: Irradiation
hasExactSynonym: Radiation
hasExactSynonym: Radiation Therapy
hasExactSynonym: Radiotherapy
hasExactSynonym: X-ray Beam Therapy
hasNarrowSynonym: Combined Photon Therapy.
hasNarrowSynonym: Combined X-Ray Therapy
hasNarrowSynonym: Deep X-Ray Therapy 150-400 kV.
hasNarrowSynonym: High Dose Rate Electronic Brachytherapy
hasNarrowSynonym: High-Energy Beam Therapy
hasNarrowSynonym: Intracavitary X-ray Therapy
hasNarrowSynonym: Palliative Course of Deep X-Ray Therapy
hasNarrowSynonym: Postoperative Course of Deep X-Ray Therapy
hasNarrowSynonym: Preoperative Course of Deep X-Ray Therapy.
hasNarrowSynonym: Short Distance X-Ray Therapy
hasNarrowSynonym: Ultrahard X-Rays 400-2000 kV

X-Rays
type: Class
subclass of: X-Ray Machine
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Penetrating, high-energy electromagnetic radiation emitted when the inner orbital electrons of an atom are excited and release radiant energy. X-ray wavelengths range from 1 pm to 10 nm. Hard X-rays are the higher energy, shorter wavelength X-rays. Soft x-rays or Grenz rays are less energetic and longer in wavelength. The short wavelength end of the X-ray spectrum overlaps the gamma rays wavelength range. The distinction between gamma rays and X-rays is based on their radiation source.
dc:source: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp
curator note: This should probably be removed.
database cross reference: C17262
database cross reference: D014965
definition source: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp
definition source: D014965
description adapted from source: yes
has_application_toward: In high doses, x-rays are used to treat cancer.
has_application_toward: In low doses, x-rays are used to diagnose diseases by making pictures of the inside of the body.
hasExactSynonym: X-Radiation
hasExactSynonym: X-Ray Electromagnetic Radiation
hasNarrowSynonym: Grenz Rays
comment: Range: 1 pm - 10 nm

Xylometazoline
type: Class
subclass of: Nasal Decongestants
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A nasal vasoconstricting decongestant drug which acts by binding to the same receptors as adrenaline. It is applied as a spray or as drops into the nose to ease inflammation and congestion of the nasal passageways. It binds alpha-adrenergic receptors to activate the adrenal system which causes systemic vasoconstriction, thereby easing nasal congestion.
database cross reference: DB06694
definition source: DB06694
description adapted from source: no
hasExactSynonym: Balminil
hasExactSynonym: Xylomethazoline

EuroQol Five Dimensions Questionnaire (EQ-5D)
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The EQ-5D is a widely-used generic instrument for describing health-related quality of life states in five dimensions scored from 1 to 3 or 1 to 5, and a visual analogue scale to record self-rated health state from 0 to100. These provide a simple descriptive profile and a single index value for health status. The EQ-5D can also be used to calculate health utilities and determine the quality-adjusted life years associated with a health state. There is also a youth version (EQ-5D-Y).
dc:source: Anie KA, Grocott H, White L, Dzingina M, Rogers G, Cho G (2012). Patient self-assessment of hospital pain, mood and health-related quality of life in adults with sickle cell disease. BMJ Open, 2, e001274. doi:10.1136/bmjopen-2012-001274.
dc:source: Howard, J, Malfroy, M, Llewelyn, C et al. The Transfusion Alternatives Preoperatively in Sickle Cell Disease (TAPS) study: a randomised, controlled, multicentre clinical trial. Lancet. 2013; 381(9870):930–938.
dc:source: The EuroQol Group. EuroQol-a new facility for the measurement of health-related quality of life. Health Policy. 1990; 16(3):199-208.
dc:source: www.phenxtoolkit.org
abbreviation: EQ-5D
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has cross-cultural adaptation: Multiple countries and cultural groups
has respondents: Self
has target population: Healthy People; Clinic Patients
selection criteria met: Widely used around the world, also used in SCD
validated for age ranges: Adults and Youth (8 to 18 years)
hasExactSynonym: EQ-5D
hasExactSynonym: EuroQol Five Dimensions Questionnaire

Functional Assessment of Chronic Illness Therapy-Spirituality (FACIT-Sp) Scale
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The FACIT-Sp is a 12-item measure that asks participants to indicate how true various statements are about them on a Likert scale of 0 (‘‘not at all’’) to 4 (‘‘very much’’). Responses on the FACIT-Sp are summed to create a total score, ranging from 0 to 48, with higher scores representing higher levels of spirituality.
dc:source: Peterman AH, Fitchett G, Brady MJ, et al. Measuring spiritual well-being in people with cancer: the functional assessment of chronic illness therapy—Spiritual Well-being Scale (FACIT- Sp). Ann Behav Med. 2002;24:49–58.
abbreviation: FACIT-Sp Scale
curator note: Check and show which source was used for the description and whether the description was adapted from the source.
has respondents: Self; Proxy (Parent report)
has target population: Children with SCD and their parents
selection criteria met: Demonstrated validity in SCD studies.
validated for age ranges: Children and adults
hasExactSynonym: FACIT-Sp Scale
hasExactSynonym: Functional Assessment of Chronic Illness Therapy-Spirituality Scale

Behavior Therapy
type: Class
subclass of: Psychotherapy
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The application of modern theories of learning and conditioning in the treatment of behavior disorders.
database cross reference: MESH:D001521
definition source: D001521
description adapted from source: no
hasExactSynonym: Behavior Modification
hasExactSynonym: Behavior Modifications
hasExactSynonym: Behavior Therapies
hasExactSynonym: Conditioning Therapies
hasExactSynonym: Conditioning Therapy

Cluster Headache
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Patient Symptom Report
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A primary headache disorder that is characterized by severe, strictly unilateral pain which is orbital, supraorbital, temporal or in any combination of these sites, lasting 15-180 min. occurring 1 to 8 times a day. The attacks are associated with one or more of the following, all of which are ipsilateral: conjunctival injection, lacrimation, nasal congestion, rhinorrhea, facial sweating, eyelid edema, and miosis.
dc:source: introduction.aspx
curator note: Include below "Pain"?
database cross reference: MESH:D003027
definition source: D003027
description adapted from source: no
has age of onset: They're estimated to affect around 1 in 500-1,000 people. Anyone of any age can be affected, but they're more common in men and tend to develop in people over the age of 20.
is caused by: It's not clear exactly what causes cluster headaches, but they've been linked to activity in part of the brain called the hypothalamus. People who smoke seem to be at a higher risk. Some cases also appear to run in families, which suggests there may be a genetic link.
is characterised by: Cluster headaches begin suddenly and without warning. The pain is very severe and is often described as a sharp, burning or piercing sensation on one side of the head. The pain is typically felt around the eye, temple and sometimes face, and typically recurs on the same side for each attack.
hasExactSynonym: Cluster Headaches
comment: Cluster headaches aren't life threatening, but they can cause significant suffering and severely affect your quality of life, so it's important to see someone who is familiar with the known effective treatments for the condition. The headaches can't be treated with over-the-counter painkillers such as paracetamol, as these are too slow to take effect. You'll need to have one or more specialist treatments instead.

D57.00 Hb-SS disease with crisis, unspecified
type: Class
subclass of: D57.0 Hb-SS disease with crisis
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
abbreviation: D57.00
definition source: D57.00
hasExactSynonym: D57.00
hasExactSynonym: Hemoglobin S sickling disorder with crisis

Developmental Delay
type: Class
subclass of: Neurodevelopmental Abnormality
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: When a child does not reach their developmental milestones at the expected times. It is an ongoing major or minor delay in the process of development.
curator note: Provide source for additional info.
definition source: devdel.htm
description adapted from source: yes
is caused by: Can have many different causes, such as genetic causes (like Down syndrome), or complications of pregnancy and birth (like prematurity or infections). Often, however, the specific cause is unknown. Some causes can be easily reversed if caught early enough, such as hearing loss from chronic ear infections, or lead poisoning.

Electrocardiograph
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An instrument used in the detection and diagnosis of heart abnormalities that measures electrical potentials on the body surface and generates a record of the electrical currents associated with heart muscle activity.
definition source: electrocardiograph
description adapted from source: no
hasExactSynonym: Cardiograph
hasExactSynonym: Electrocardiographic Instrument
preferred label: Electrocardiographic Device

Erythrocyte Transfusion
type: Class
subclass of: Blood Component Transfusion
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: The transfer of erythrocytes from a donor to a recipient or reinfusion to the donor.
database cross reference: MESH:D017707
definition source: D017707
description adapted from source: no
hasBroadSynonym: Transfusion
hasExactSynonym: Erythrocyte Transfusions
hasExactSynonym: Red Blood Cell Transfusion
hasExactSynonym: Red Blood Cell Transfusions
hasExactSynonym: Transfusion, Erythrocyte
hasExactSynonym: Transfusions, Erythrocyte

Ethnic Group
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A social group characterized by a distinctive social and cultural tradition that is maintained from generation to generation. Members share a common history and origin and a sense of identification with the group. They have similar and distinctive features in their lifestyle habits and shared experiences. They often have a common genetic heritage which may be reflected in their experience of health and disease.
dc:source: http://www.phenxtoolkit.org/index.php
curator note: Different relevant ethnic groups need to be recorded. Perhaps as sub-classes of this class?
database cross reference: NCIT:C16564
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no
has_application_toward: Ethnicity is used to stratify study populations and to associate those populations with physical, geographic, biological, social, and cultural characteristics (e.g., Dominican). Ethnicity is a social and epidemiological factor, and individuals of some ethnicity are at greater risk for disease. By capturing the ethnicity of respondents, the researcher will be able to identify those who are or are not of a certain origin and will be able to stratify the study population accordingly.
hasExactSynonym: Ethnic Origin
hasExactSynonym: Ethnic Origins
hasExactSynonym: Ethnicity

Evaluation Studies
type: Class
subclass of: Publication Type
description: Works consisting of studies determining the effectiveness or utility of processes, personnel, and equipment.
database cross reference: MESH:D023362
definition source: D023362
description adapted from source: no

Exchange Transfusion, Whole Blood
type: Class
subclass of: Blood Transfusion
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Repetitive withdrawal of small amounts of blood and replacement with donor blood until a large proportion of the blood volume has been exchanged. Used in treatment of fetal erythroblastosis, hepatic coma, sickle cell anemia, disseminated intravascular coagulation, septicemia, burns, thrombotic thrombopenic purpura, and fulminant malaria.
dc:source: D005078
database cross reference: MESH:D005078
description adapted from source: no
hasExactSynonym: Exchange Blood Transfusion

Executive Function Measure
type: Class
subclass of: Diagnostic Instrument
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: An interviewer-administered test to measure a respondent’s system of high-level cognitive functions such as abstract thinking, rule acquisition, cognitive flexibility, and goal-oriented behavior.
database cross reference: PX131100
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: Only label adapted
has_application_toward: This measure tests a respondent's total range of function with respect to executive function. It is therefore more specific and sensitive than a measure of global mental status and can be used to assess major problems in executive function as well as minor variations that may be a consequence of normal aging.

Exercise
type: Class
subclass of: Lifestyle
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Physical activity which is usually regular and done with the intention of improving or maintaining physical fitness or health.
database cross reference: MESH:D015444
definition source: D015444
description adapted from source: yes

Exercise-Induced Rhabdomyolysis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Supportive Therapeutics
subclass of: Restriction
  on property: treated with
  some values from: Renal Replacement Therapy
subclass of: Restriction
  on property: results_in
  some values from: Kidney Failure
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Rhabdomyolysis Induced by Exercise.
curator note: Provide source for additional info.
database cross reference: HP:0009045
definition source: HP_0009045
description adapted from source: no.
is caused by: Strenuous exercise performed under high temperatures and humidity; poor hydration levels before, during and after the exercise.
is characterised by: Muscle pain, vomiting, confusion, acute renal failure.
hasExactSynonym: Rhabdomyolysis with Exercise

Extrapyramidal Symptoms
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Genetic Testing
subclass of: Restriction
  on property: diagnosed by
  some values from: Liver Function Assay
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: diagnosed by
  some values from: Ferritin Blood Test
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A neurological condition related to lesions of the basal ganglia leading to typical abnormalities including akinesia (inability to initiate changes in activity and perform volitional movements rapidly and easily), muscular rigidity (continuous contraction of muscles with constant resistance to passive movement), chorea (widespread arrhythmic movements of a forcible, rapid, jerky, and restless nature), athetosis (inability to sustain the muscles of the fingers, toes, or other group of muscles in a fixed position), and akathisia (inability to remain motionless).
dc:source: HP_0002071
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0002071
description adapted from source: no
is caused by: Extrapyramidal symptoms are caused by dopamine blockade or depletion in the basal ganglia; this lack of dopamine often mimics idiopathic pathologies of the extrapyramidal system
is characterised by: Extrapyramidal symptoms include acute dyskinesias and dystonic reactions, tardive dyskinesia, Parkinsonism, akinesia, akathisia, and neuroleptic malignant syndrome
hasExactSynonym: Abnormality of Extrapyramidal Motor Function
hasExactSynonym: Extrapyramidal Dysfunction
hasExactSynonym: Extrapyramidal Signs
hasExactSynonym: Extrapyramidal Syndrome
hasExactSynonym: Extrapyramidal Tract Signs
comment: Diagnosis is made using the following: CT and MRI of the head, Genetic testing, Magnetic resonance angiography to look at the blood vessels in the neck and brain, Positron emission tomography (PET) to look at the metabolism of the brain, Blood tests to check blood sugar, thyroid function, liver function, and iron and copper levels.

Eye
type: Class
subclass of: from phenotype
description: The organ of vision that consists of the eyeball and the optic nerve.
definition source: eye
description adapted from source: yes
hasExactSynonym: Oculus
hasRelatedSynonym: Ophthalmic

Eye Examination
type: Class
subclass of: Physical Examination
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Facial Dysmorphisms
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Depression
subclass of: Restriction
  on property: results_in
  some values from: Quality of Life
subclass of: Restriction
  on property: results_in
  some values from: Visual Impairment
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An abnormal morphology (form) of the face or its components.
curator note: Provide source for additional info.
database cross reference: HP:0001999
definition source: HP_0001999
description adapted from source: Only label adapted
is caused by: Genetic syndromes, fetal alcohol syndrome, hemolytic anemias.
hasBroadSynonym: Malformation of Face
hasExactSynonym: Abnormal Morphology of the Face
hasExactSynonym: Abnormal facial shape
hasExactSynonym: Dysmorphic Facial Features
hasExactSynonym: Unusual Facial Appearance
hasNarrowSynonym: Facial Dysmorphism

Facial Nerve Palsy
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Blood Test
subclass of: Restriction
  on property: diagnosed by
  some values from: Complete Blood Count
subclass of: Restriction
  on property: diagnosed by
  some values from: Magnetic Resonance Imaging
subclass of: Restriction
  on property: diagnosed by
  some values from: Patient Symptom Report
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: diagnosed by
  some values from: Seizure
subclass of: Restriction
  on property: diagnosed by
  some values from: Facial Paralysis
subclass of: Restriction
  on property: treated with
  some values from: Occupational Therapy
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Visual Impairment
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Facial nerve palsy is a dysfunction of cranial nerve VII (the facial nerve) that results in inability to control facial muscles on the affected side with weakness of the muscles of facial expression and eye closure. This can either be present in unilateral or bilateral form.
dc:source: HP_0010628
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
database cross reference: HP:0010628
description adapted from source: no
is caused by: Facial paralysis is almost always caused by: Damage or swelling of the facial nerve, which carries signals from the brain to the muscles of the face. Damage to the area of the brain that sends signals to the muscles of the face . In people who are otherwise healthy, facial paralysis is often due to Bell palsy. This is a condition in which the facial nerve becomes inflamed.Stroke may cause facial paralysis. With a stroke, other muscles on one side of the body may also be involved.Facial paralysis that is due to a brain tumor usually develops slowly. Symptoms can include headaches, seizures, or hearing loss.In newborns, facial paralysis may be caused by trauma during birth. Other causes include: Infection of the brain or surrounding tissues; Lyme disease; Sarcoidosis; Tumor that presses on the facial nerve
hasExactSynonym: Bell's Palsy
hasExactSynonym: Facial Nerve Paralysis
hasExactSynonym: Facial Palsy
hasRelatedSynonym: Facial Muscle Weakness

Facial Paralysis
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: diagnosed by
  some values from: Personal Medical History
subclass of: Restriction
  on property: diagnosed by
  some values from: Physical Examination
subclass of: Restriction
  on property: treated with
  some values from: Physiotherapy
subclass of: Restriction
  on property: treated with
  some values from: Surgery
subclass of: Restriction
  on property: results_in
  some values from: Quality of Life
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Facial paralysis is loss of facial movement because of nerve damage
dc:source: Treatment5
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
description adapted from source: yes
is caused by: According to the National Institute of Neurological Disorders and Stroke, Bell's palsy is the most common form of facial paralysis. Every year, 40,000 Americans experience sudden facial paralysis due to Bell's palsy. This condition causes the muscles on one side of the face to droop noticeably.No one knows exactly why Bell's palsy occurs. It may be related to a viral infection of the facial nerve. The good news is that most patients with Bell's palsy recover completely in about six months. Other causes of facial paralysis or weakness include: skull fracture or injury to the face;head or neck tumor; stroke; chronic middle ear infection or other ear damage; high blood pressure;diabetes;Lyme disease, a bacterial disease transmitted to humans by a tick bite; Ramsay-Hunt Syndrome, a viral infection of the facial nerve; autoimmune diseases such as multiple sclerosis, which affects the brain and spinal cord, and Guillain-Barre syndrome, which affects the nervous system. Birth can cause temporary facial paralysis in some babies. However, 90 percent of babies with this type of injury recover completely without treatment. You can also have facial paralysis at birth due to certain congenital syndromes, such as Moebius syndrome and Melkersson-Rosenthal syndrome.

Fatigue
type: Class
subclass of: Phenotype
subclass of: Quality of Life Related SCD Symptoms and Complications
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Inability to function due to tiredness related to sickle cell disease.
curator note: Use the literature cited here to link to other phenotypes.
database cross reference: MP:0002899
database cross reference: SYMP:0019177
definition source: MP_0002899
definition source: SYMP_0019177
description adapted from source: yes
hasExactSynonym: Fatigability
hasExactSynonym: Fatigable
hasExactSynonym: Lassitude
hasExactSynonym: Tiredness

Feasibility Studies
type: Class
subclass of: Study Design
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Studies to determine the advantages or disadvantages, practicability, or capability of accomplishing a projected plan, study, or project.
definition source: D005240

Fentanyl
type: Class
subclass of: Opioid
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A potent narcotic analgesic, abuse of which leads to habituation or addiction. It is primarily a mu-opioid agonist. Fentanyl is also used as an adjunct to general anesthetics, and as an anesthetic for induction and maintenance.
curator note: Were these specific synonyms selected form the long list in the description source because of specific relevance to SCD?
database cross reference: DB00813
definition source: DB00813
description adapted from source: no
hasExactSynonym: N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide
hasRelatedSynonym: 1-phenethyl-4-N-propionylanilinopiperidine
hasRelatedSynonym: Fentanila
hasRelatedSynonym: N-(1-phenethyl-4-piperidinyl)-N-phenylpropionamide
hasRelatedSynonym: N-(1-phenethyl-4-piperidyl)propionanilide
hasRelatedSynonym: N-phenethyl-4-(N-propionylanilino)piperidine
hasRelatedSynonym: N-phenyl-N-(1-(2-phenylethyl)-4-piperidinyl)propanamide
hasRelatedSynonym: Tentanylum

Ferritin Blood Test
type: Class
subclass of: Blood Test
subclass of: Restriction
  on property: has measurement
  some values from: Ferritin Measurement
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A bioassay to measure the serum concentration of ferritin (i.e., iron).
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX811300
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has protocol: PhenX protocol: Serum or Plasma Ferritin #811301
has recommended procedure: The National Health and Nutrition Examination Survey (NHANES) 2009-2010 Laboratory Procedures Manual for serum/plasma ferritin testing provides comprehensive instructions for processing and storing blood samples to determine an individual’s serum ferritin level. Because there are many comparable assays and instruments for measuring ferritin, the protocol also provides basic guidelines to aid comparability among different studies.
has_application_toward: This measure can be used to evaluate an individual’s iron metabolism, which is important for determining the presence and severity of anemia, and the assessment of iron therapy. Additionally this measure is used to assess iron overload (accumulation of iron in the body), which is associated with hereditary hemochromatosis and with transfusion therapy for many clinical conditions including sickle cell disease, thalassemia, other rare anemias, Hodgkin’s disease, acute leukemia, hemochromatosis, and carcinomas of many tumor types.

Ferritin Measurement
type: Class
subclass of: Blood Chemistry Measurement
subclass of: Restriction
  on property: has diagnostic tool
  some values from: Ferritin Blood Test
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Race
subclass of: Restriction
  on property: essential measure
  some values from: Ethnic Group
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A measurement of ferritin level in serum as an indicator of iron metabolism.
database cross reference: EFO:0004459
definition source: EFO_0004459
description adapted from source: yes

Flexion Contracture
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A flexion contracture is a bent (flexed) joint that cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement of joints.
database cross reference: HP:0001371
definition source: HP_0001371
description adapted from source: no
hasBroadSynonym: Contractures
hasExactSynonym: Flexion Contractures
hasExactSynonym: Flexion Contractures of Joints
hasExactSynonym: Joint Contracture
hasExactSynonym: Joint Contractures

Flow Cytometer
type: Class
subclass of: Diagnostic Device
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: An instrument which is used to count and sort microscopic particles suspended in a buffer. This instrument consists of a flow cell, at least one lamp or laser, a variable number of emission detectors or photomultipliers, a system that converts analog signals to digital, and a computer to run the system and collect and analyze the data output.
curator note: Not sure whether this can be classified as a "Medical Device".
database cross reference: NPO:1769
definition source: NPO 1769
description adapted from source: no

Flow Cytometry
type: Class
subclass of: Physical Detection Method
subclass of: Restriction
  on property: has measurement
  some values from: Red Blood Cell Microparticles Level
subclass of: Restriction
  on property: has medical device
  some values from: Flow Cytometer
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Flow cytometry uses the principles of light scattering and fluorescence from fluorochrome molecules to generate specific multi-parameter data from particles and cells in the size range of 0.5um to 40um diameter.
definition source: BAO_0000005
description adapted from source: no

Fluorescein Angiography
type: Class
subclass of: Imaging Assay
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Visualization of a vascular system after intravenous injection of a fluorescein solution. The images may be photographed or televised. It is used especially in studying the retinal and uveal vasculature.
database cross reference: MESH:D005451
definition source: D005451
description adapted from source: no

Focal Dystonia
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: results_in
  some values from: Pain
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Localized disorder characterized by involuntary muscle contractions that cause slow repetitive movements or abnormal postures.
dc:source: detail dystonias.htm
curator note: Check and show which source was used for the description and whether the description was adapted from the source. Provide source for additional info.
description adapted from source: yes
has age of onset: Early-onset dystonia often begins with symptoms in the limbs and may progress to involve other regions. Some symptoms tend to occur after periods of exertion and/or fluctuate over the course of the day. Adult-onset dystonia usually is located in one or adjacent parts of the body, most often involving the neck and/or facial muscles. Acquired dystonia can affect other regions of the body. Dystonias often progress through various stages. Initially, dystonic movements may be intermittent and appear only during voluntary movements or stress. Later, individuals may show dystonic postures and movements while walking and ultimately even while they are relaxed. Dystonia can be associated with fixed postures and shortening of tendons.
has disease stage: The dystonias can be divided into three groups: idiopathic, genetic, and acquired. Idiopathic dystonia refers to dystonia that does not have a clear cause. Many instances of dystonia are idiopathic. There are several genetic causes of dystonia. Some forms appear to be inherited in a dominant manner, which means only one parent who carries the defective gene is needed to pass the disorder to their child. Each child of a parent having the abnormal gene will have a 50 percent chance of carrying the defective gene. It is important to note the symptoms may vary widely in type and severity even among members of the same family. In some instances, persons who inherit the defective gene may not develop dystonia. Having one mutated gene appears to be sufficient to cause the chemical imbalances that may lead to dystonia, but other genetic or even environmental factors may play a role. Knowing the pattern of inheritance can help families understand the risk of passing dystonia along to future generations. Acquired dystonia, also called secondary dystonia, results from environmental or other damage to the brain, or from exposure to certain types of medications. Some causes of acquired dystonia include birth injury (including hypoxia, a lack of oxygen to the brain, and neonatal brain hemorrhage), certain infections, reactions to certain drugs, heavy metal or carbon monoxide poisoning, trauma, or stroke. Dystonia can be a symptom of other diseases, some of which may be hereditary. Acquired dystonia often plateaus and does not spread to other parts of the body. Dystonia that occurs as a result of medications often ceases if the medications are stopped quickly.
is caused by: The cause of dystonia is not known. Researchers believe that dystonia results from an abnormality in or damage to the basal ganglia or other brain regions that control movement. There may be abnormalities in the brain's ability to process a group of chemicals called neurotransmitters that help cells in the brain communicate with each other. There also may be abnormalities in the way the brain processes information and generates commands to move. In most cases, no abnormalities are visible using magnetic resonance imaging or other diagnostic imaging.
is characterised by: Dystonia can affect many different parts of the body, and the symptoms are different depending upon the form of dystonia. Early symptoms may include a foot cramp or a tendency for one foot to turn or drag-either sporadically or after running or walking some distance-or a worsening in handwriting after writing several lines. In other instances, the neck may turn or pull involuntarily, especially when the person is tired or under stress. Sometimes both eyes might blink rapidly and uncontrollably; other times, spasms will cause the eyes to close. Symptoms may also include tremor or difficulties speaking. In some cases, dystonia can affect only one specific action, while allowing others to occur unimpeded. For example, a musician may have dystonia when using her hand to play an instrument, but not when using the same hand to type. The initial symptoms can be very mild and may be noticeable only after prolonged exertion, stress, or fatigue. Over a period of time, the symptoms may become more noticeable or widespread; sometimes, however, there is little or no progression. Dystonia typically is not associated with problems thinking or understanding, but depression and anxiety may be present.
comment: Botulinum toxin. Botulinum injections often are the most effective treatment for the focal dystonias. Injections of small amounts of this chemical into affected muscles prevents muscle contractions and can provide temporary improvement in the abnormal postures and movements that characterize dystonia. First used to treat blepharospasm, such injections are now widely used for treating other focal dystonias. The toxin decreases muscle spasms by blocking release of the neurotransmitter acetylcholine, which normally causes muscles to contract. The effect typically is seen a few days after the injections and can last for several months before the injections must be repeated. The details of the treatment will vary among individuals.Medications. Several classes of drugs that affect different neurotransmitters may be effective for various forms of dystonia. These medications are used “off-label”, meaning they are approved by the U.S. Food and Drug Administration to treat different disorders or conditions but have not been specifically approved to treat dystonia. The response to drugs varies among individuals and even in the same person over time. These drugs include: Anticholinergic agents block the effects of the neurotransmitter acetylcholine. Drugs in this group include trihexyphenidyl and benztropine. Sometimes these medications can be sedating or cause difficulties with memory, especially at higher dosages and in older individuals. These side effects can limit their usefulness. Other side effects such as dry mouth and constipation can usually be managed with dietary changes or other medications. GABAergic agents are drugs that regulate the neurotransmitter GABA. These medications include the benzodiazepines such as diazepam, lorazepam, clonazepam, and baclofen. Drowsiness is their common side effect. Dopaminergic agents act on the dopamine system and the neurotransmitter dopamine, which helps control muscle movement. Some individuals may benefit from drugs that block t…

Folic Acid
type: Class
subclass of: Preventative Therapeutics
subclass of: Symptomatic Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A member of the vitamin B family that stimulates the hematopoietic system. It is present in the liver and kidney and is found in mushrooms, spinach, yeast, green leaves, and grasses (poaceae). Folic acid is used in the treatment and prevention of folate deficiencies and megaloblastic anemia.
dc:source: DB00158
database cross reference: DB00158
definition source: DB00158
description adapted from source: no
comment: Mechanism of Action: Folic acid, as it is biochemically inactive, is converted to tetrahydrofolic acid and methyltetrahydrofolate by dihydrofolate reductase. These folic acid congeners are transported across cells by receptor-mediated endocytosis where they are needed to maintain normal erythropoiesis, synthesize purine and thymidylate nucleic acids, interconvert amino acids, methylate tRNA, and generate and use formate. Using vitamin B12 as a cofactor, folic acid can normalize high homocysteine levels by remethylation of homocysteine to methionine via methionine synthetase.
comment: Metabolism: Hepatic
comment: Pharmacodynamics: Folic acid, a water-soluble B-complex vitamin, is found in foods such as liver, kidneys, yeast, and leafy, green vegetables. Folic acid is used to diagnose folate deficiency and to treat topical sprue and megaloblastic and macrocytic anemias, hematologic complications resulting from a deficiency in folic acid.
comment: Route of Elimination: Folic Acid is metabolized in the liver to 7, 8-dihydrofolic acid and eventually to 5,6,7,8-tetrahydrofolic acid with the aid of reduced diphosphopyridine nucleotide (DPNH) and folate reductases. A majority of the metabolic products appeared in the urine after 6 hours; excretion was generally complete within 24 hours. Folic Acid is also excreted in the milk of lactating mothers.
comment: Toxicity: IPR-MUS LD50 85 mg/kg,IVN-GPG LD50 120 mg/kg, IVN-MUS LD50 239 mg/kg, IVN-RAT LD50 500 mg/kg, IVN-RBT LD50 410 mg/kg

Follow-Up Studies
type: Class
subclass of: Cohort Studies
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Studies in which individuals or populations are followed to assess the outcome of exposures, procedures, or effects of a characteristic, e.g., occurrence of disease.
definition source: D005500

from phenotype
type: Class
subclass of: deprecated terms

Frontal Bossing
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: treated with
  some values from: Treatment of Precipitating Factors
subclass of: Restriction
  on property: results_in
  some values from: Anxiety
subclass of: Restriction
  on property: results_in
  some values from: Depression
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Bilateral bulging of the lateral frontal bone prominences with relative sparing of the midline.
curator note: Provide source for additional info.
database cross reference: HP:0002007
definition source: HP_0002007
description adapted from source: no
is caused by: Enlargement of the frontal bone, achondroplasia, acromegalia, congenital syphilis, Beta-thalassemia.
hasExactSynonym: Frontal Protruberance
hasExactSynonym: Skull Bossing

Functionality After Stroke Measure
type: Class
subclass of: Quality of Life and Care Measure
subclass of: Restriction
  on property: essential measure
  some values from: Current Age
subclass of: Restriction
  on property: essential measure
  some values from: Gender
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A questionnaire to measure the health status of individuals who had a stroke.
curator note: Should this also/rather be included below Diagnostics?
database cross reference: PX820700
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: no
has_application_toward: This measure is used to assess multidimensional stroke outcomes in both clinical and research settings.

Gastrointestinal System
type: Class
subclass of: from phenotype
description: The system concerned with the function and disorders of the gastrointestinal tract, including stomach, intestines, and associated organs including liver, pancreas and gall bladder.
definition source: gastroenterology
description adapted from source: yes
hasExactSynonym: gastrointestinal tract

Gender
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The respondent's self-conception of being male or female.
dc:source: http://www.phenxtoolkit.org/index.php
database cross reference: PX10700
definition source: http://www.phenxtoolkit.org/index.php
description adapted from source: yes
has protocol: PhenX protocol: Gender #010701
has_application_toward: Gender is one of the most basic variables captured in any biomedical or health-related research study. Differences in the prevalence and severity of a broad range of diseases, disorders, and conditions exist between the sexes.
comment: Gender and sex are often misunderstood, and although they are related there are distinct differences between the two characteristics. Biological sex is a characteristic of living things, and a classification of male or female is given based on the individual's reproductive organs and functions assigned by chromosomal complement. Gender is captured for sociological and epidemiological reasons.

Gene-Environment Interaction
type: Class
subclass of: Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Combined effects of genotypes and environmental factors together on phenotypic characteristics.
database cross reference: MESH:D059647
definition source: D059647
description adapted from source: no

Gene Product
type: Class
subclass of: Genetic Disease Modifier
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: A protein, RNA or a complex that contains proteins and/or RNA.
curator note: If additional gene products are included in the future, they can be categorised according those below this term in the "National Cancer Institute Thesaurus" (NCIT)
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Genome Encoded Entity

Gene Therapy
type: Class
subclass of: Curative Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: Application of genetic material (usually DNA) into cells in order to permanently correct an inherited disease or acquired disease.
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no
hasExactSynonym: DNA Therapy
hasNarrowSynonym: Gene Transfer
hasNarrowSynonym: Gene Transfer Procedure
hasRelatedSynonym: Genetic Intervention
comment: Alternative descriptions: Application of genetic material into cells in order to correct an inherited or acquired disease. Treatment of human disease by gene transfer. Treatment that alters a gene. In studies of gene therapy for cancer, researchers are trying to improve the body's natural ability to fight the disease or to make the cancer cells more sensitive to other kinds of therapy.

Research Subject ID
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Clinic Subject ID
type: Class
subclass of: Personal Attribute
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Renal Replacement Therapy
type: Class
subclass of: Supportive Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Procedures which temporarily or permanently remedy insufficient cleansing of body fluids by the kidneys.
curator note: Could this and it's sub-classes not fall below any of the other main Therapeutics classes? Symptomatic?
database cross reference: MESH:D017582
definition source: D017582
description adapted from source: no

Lifestyle Therapy
type: Class
subclass of: Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Therapy dealing with lifestyle management and includes: behavioral and dietary modifications, exercise, stress management, and addiction control. This therapy must be used as major adjunct to 'standard care' or be applied as alternative treatment to conventional medicine practices.
database cross reference: TRAK:0001203
definition source: TRAK_0001203
description adapted from source: no

Hemoglobin D
type: Class
subclass of: from phenotype
subclass of: Restriction
  on property: phenotype of
  some values from: Hemoglobin D Disease
subclass of: Restriction
  on property: phenotype of
  some values from: Hemoglobin D Trait
subclass of: Restriction
  on property: phenotype of
  some values from: Hemoglobin D-Beta Thalassemia
subclass of: Restriction
  on property: phenotype of
  some values from: Sickle Cell Disease-SD
subclass of: Restriction
  on property: phenotype of
  some values from: Sickle Cell Disease-S/D-Punjab
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Hemoglobin D trait have red blood cells that have normal hemoglobin A and an abnormal hemoglobin.
curator note: Description needs work. This should describe an abnormal hemoglobin.
definition source: hemoglobin-d-trait.html
description adapted from source: no
hasExactSynonym: Hb D
hasExactSynonym: HbD

Hemoglobin M
type: Class
subclass of: from phenotype
subclass of: Restriction
  on property: phenotype of
  some values from: Hemoglobin M Disease
subclass of: Restriction
  on property: phenotype of
  some values from: Hemoglobin M Trait
subclass of: Restriction
  on property: results_in
  some values from: Cyanosis
subclass of: Restriction
  on property: has curation status
  has value: accepted by SCDO WG (WS2)
description: A group of abnormal hemoglobins in which amino acid substitutions take place in either the alpha or beta chains but near the heme iron.
database cross reference: D006449
definition source: D006449
description adapted from source: no
hasExactSynonym: Hb M

Hemoglobin E
type: Class
subclass of: Abnormal Hemoglobin Structure Present in SCD
subclass of: Restriction
  on property: phenotype of
  some values from: Hemoglobin E Disease
subclass of: Restriction
  on property: phenotype of
  some values from: Hemoglobin E Trait
subclass of: Restriction
  on property: phenotype of
  some values from: Hemoglobin E-Beta Thalassemia
subclass of: Restriction
  on property: phenotype of
  some values from: Sickle Cell Disease-SE
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU26LYS
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
description: An abnormal hemoglobin in which lysine replaces glutamic acid at the position 26 of the beta globin.
database cross reference: D006446
definition source: D006446
description adapted from source: yes
hasExactSynonym: Hb E
comment: It is most frequently observed in southeast Asian populations.

Sickle Cell Disease-S/HPFH
type: Class
subclass of: Sickle Cell Disease Variant
subclass of: Restriction
  on property: has molecular phenotype
  some values from: Increased Hemoglobin F
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A group of disorders caused by large deletions of the beta-globin gene complex; typically 30% fetal haemoglobin.
dc:source: http://www.ebi.ac.uk/ols/ontologies/ordo/terms
abbreviation: SCD-S/HPFH
definition source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
description adapted from source: no
hasExactSynonym: HPFH-Sickle Cell Disease Syndrome
hasExactSynonym: Hereditary Persistence of Fetal Hemoglobin-Sickle Cell Disease Syndrome
hasExactSynonym: Sickle Cell Disease Syndrome-Hereditary Persistence of Fetal Hemoglobin
hasExactSynonym: Sickle Cell Disease-S/Persistence of Fetal Hemoglobin
hasExactSynonym: Sickle Cell-Hereditary Persistence of Fetal Hemoglobin

Delta-Globin
type: Class
subclass of: Gene Product
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Hemoglobin subunit delta (147 aa, ~16 kDa) is encoded by the human HBD gene. This protein plays a role in the transport of oxygen to tissues of the adult body.
dc:source: http://bioportal.bioontology.org/ontologies/NCIT
definition source: http://bioportal.bioontology.org/ontologies/NCIT
description adapted from source: no
hasExactSynonym: Hemoglobin Delta Chain
hasExactSynonym: Hemoglobin Subunit Delta
comment: Hemoglobin subunit delta accounts for only ~3% of total hemoglobin in adults.

Beta-Globin
type: Class
subclass of: Gene Product
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: Hemoglobin subunit beta (147 aa, ~16 kDa) is encoded by the human HBB1 gene. This protein plays a role in the transport of oxygen to tissues of the adult body.
definition source: http://bioportal.bioontology.org/ontologies/NCIT/
description adapted from source: no
hasExactSynonym: Hemoglobin Beta Chain
hasExactSynonym: Hemoglobin Subunit Beta

HBB1
type: Class
subclass of: Beta-Globins
subclass of: Restriction
  on property: has curation status
  has value: uncurated
dc:source: http://www.orpha.net/consor/cgi-bin/Disease_Genes.php
hasExactSynonym: Beta-Globin Gene
comment: Disease-causing germline mutation(s) in Beta-thalassemia intermediaAssessed Disease-causing germline mutation(s) in Beta-thalassemia majorAssessed Disease-causing germline mutation(s) in Delta-beta-thalassemiaAssessed Disease-causing germline mutation(s) in Dominant beta-thalassemiaAssessed Disease-causing germline mutation(s) in Heinz body anemiaAssessed Disease-causing germline mutation(s) in Hemoglobin C-beta-thalassemia syndromeAssessed Disease-causing germline mutation(s) in Hemoglobin C diseaseAssessed Disease-causing germline mutation(s) in Hemoglobin D diseaseAssessed Disease-causing germline mutation(s) in Hemoglobin E-beta-thalassemia syndromeAssessed Disease-causing germline mutation(s) in Hemoglobin E diseaseAssessed Disease-causing germline mutation(s) in Hemoglobin M diseaseAssessed Disease-causing germline mutation(s) in Hereditary persistence of fetal hemoglobin-beta-thalassemia syndromeAssessed Disease-causing germline mutation(s) in Hereditary persistence of fetal hemoglobin-sickle cell disease syndromeAssessed Disease-causing germline mutation(s) in Sickle cell anemiaAssessed Disease-causing germline mutation(s) in Sickle cell-beta-thalassemia disease syndromeAssessed Disease-causing germline mutation(s) in Sickle cell-hemoglobin C disease syndromeAssessed Disease-causing germline mutation(s) in Sickle cell-hemoglobin D disease syndromeAssessed Disease-causing germline mutation(s) in Sickle cell-hemoglobin E disease syndromeAssessed Part of a fusion gene in Hemoglobin Lepore-beta-thalassemia syndromeAssessed

HBD
type: Class
subclass of: Beta-Globins
subclass of: Restriction
  on property: modifies
  some values from: Delta Beta Thalassaemia
subclass of: Restriction
  on property: modifies
  some values from: Hemoglobin Lepore-Beta Thalassaemia
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://www.orpha.net/consor/cgi-bin/Disease_Genes.php
hasExactSynonym: Hemoglobin, Delta
comment: Disease-causing germline mutation(s) in Delta-beta-thalassemia
comment: Part of a fusion gene in Hemoglobin Lepore-beta-thalassemia syndrome

Hemoglobin O-Arab
type: Class
subclass of: Abnormal Hemoglobin Structure Present in SCD
subclass of: Restriction
  on property: phenotype of
  some values from: Hemoglobin O-Arab Disease
subclass of: Restriction
  on property: phenotype of
  some values from: Sickle Cell Disease-S/O-Arab
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU121LYS
subclass of: Restriction
  on property: has curation status
  has value: accepted by SCDO WG (WS2)
description: An abnormal hemoglobin that results from the substitution of glutamic acid with lysine at position 121 of the beta chain.
abbreviation: Hb O-Arab
database cross reference: C032031
definition source: MESH and Zimmerman SA. Am J Hematol. 1999 Apr; 60(4) 279-84
description adapted from source: yes
hasExactSynonym: Hb O-Arab
hasExactSynonym: Hb-Arab
hasExactSynonym: Hemoglobin-Arab
comment: Found mainly in Balkans, the Middle East, and Africa. When co-occurring with Hemoglobin S, it can lead to a severe sickling hemoglobinopathy similar to that of homozygous sickle cell anemia.

Surgery
type: Class
subclass of: Symptomatic Therapeutics
subclass of: Restriction
  on property: treats
  some values from: Back Pain
subclass of: Restriction
  on property: treats
  some values from: Bone Pain
subclass of: Restriction
  on property: treats
  some values from: Brain Abscess
subclass of: Restriction
  on property: treats
  some values from: Cancer
subclass of: Restriction
  on property: treats
  some values from: Cerebral Hemorrhage
subclass of: Restriction
  on property: treats
  some values from: Cervical Cord Compression
subclass of: Restriction
  on property: treats
  some values from: Delayed Puberty
subclass of: Restriction
  on property: treats
  some values from: Dysarthria
subclass of: Restriction
  on property: treats
  some values from: Endometriosis
subclass of: Restriction
  on property: treats
  some values from: Glaucoma (Secondary to Presence of Blood in the Anterior Chamber of the Eye)
subclass of: Restriction
  on property: treats
  some values from: Hypergonadotropic Hypogonadism
subclass of: Restriction
  on property: treats
  some values from: Hyperkeratosis
subclass of: Restriction
  on property: treats
  some values from: Hyperostosis
subclass of: Restriction
  on property: treats
  some values from: Hyphema
subclass of: Restriction
  on property: treats
  some values from: Intracerebral Haemorrhage
subclass of: Restriction
  on property: treats
  some values from: Intracranial Hemorrhage
subclass of: Restriction
  on property: treats
  some values from: Intracranial Hypotension
subclass of: Restriction
  on property: treats
  some values from: Kyphosis
subclass of: Restriction
  on property: treats
  some values from: Lymphoma
subclass of: Restriction
  on property: treats
  some values from: Mononeuropathy
subclass of: Restriction
  on property: treats
  some values from: Onychodysplasia
subclass of: Restriction
  on property: treats
  some values from: Onychomycosis
subclass of: Restriction
  on property: treats
  some values from: Ophthalmologic Complication
subclass of: Restriction
  on property: treats
  some values from: Osteomyelitis
subclass of: Restriction
  on property: treats
  some values from: Osteonecrosis
subclass of: Restriction
  on property: treats
  some values from: Peripheral Neuropathy
subclass of: Restriction
  on property: treats
  some values from: Renal Artery Stenosis
subclass of: Restriction
  on property: treats
  some values from: Sciatica
subclass of: Restriction
  on property: treats
  some values from: Scoliosis
subclass of: Restriction
  on property: treats
  some values from: Spondylolisthesis
subclass of: Restriction
  on property: treats
  some values from: Subarachnoid Hemorrhage
subclass of: Restriction
  on property: treats
  some values from: Transient Monocular Blindness
subclass of: Restriction
  on property: treats
  some values from: Facial Nerve Palsy
subclass of: Restriction
  on property: treats
  some values from: Facial Paralysis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A material processing technique that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury or to help improve bodily function or appearance.
database cross reference: ERO:0000378
definition source: ERO_0000378
description adapted from source: no

Antifungal
type: Class
subclass of: Symptomatic Therapeutics
subclass of: Restriction
  on property: treats
  some values from: Bacterial Endocarditis
subclass of: Restriction
  on property: treats
  some values from: Brain Abscess
subclass of: Restriction
  on property: treats
  some values from: Nail Dystrophy
subclass of: Restriction
  on property: treats
  some values from: Onychomycosis
subclass of: Restriction
  on property: treats
  some values from: Otitis Media
subclass of: Restriction
  on property: treats
  some values from: Sepsis
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A material entity bearing an antifungal disposition.
database cross reference: IDO:0000560
definition source: IDO_0000560
description adapted from source: no

Treatment of Precipitating Factors
type: Class
subclass of: Therapeutics
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: Treatment of factors associated with the definitive onset of a disease, illness, accident, behavioral response, or course of action. Usually one factor is more important or more obviously recognizable than others, if several are involved, and one may often be regarded as "necessary". Examples include exposure to specific disease; amount or level of an infectious organism, drug, or noxious agent, etc.
database cross reference: MESH:D015985
definition source: D015985
description adapted from source: no
hasExactSynonym: Management of Precipitating Factors
hasExactSynonym: Management of Underlying Cause
hasExactSynonym: Treatment of Underlying Cause

Blindness
type: Class
subclass of: Visual Impairment
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Blindness is the condition of lacking visual perception due to physiological or neurological factors.
dc:source: HP_0000618
database cross reference: HP:0000618
description adapted from source: no
comment: Various scales have been developed to describe the extent of vision loss and define blindness. Total blindness is the complete lack of form and visual light perception and is clinically recorded as NLP (no light perception). Blindness is frequently used to describe severe visual impairment with residual vision. Those described as having only light perception have no more sight than the ability to tell light from dark and the general direction of a light source.

Visual Impairment
type: Class
subclass of: Ophthalmologic Complication
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: Visual impairment (or vision impairment) is vision loss (of a person) to such a degree as to qualify as an additional support need through a significant limitation of visual capability resulting from either disease, trauma, or congenital or degenerative conditions that cannot be corrected by conventional means, such as refractive correction, medication, or surgery.
dc:source: HP_0000505
database cross reference: HP:0000505
description adapted from source: no
hasExactSynonym: Impaired Vision
hasExactSynonym: Impaired Visual Function
hasExactSynonym: Loss of Eyesight
hasExactSynonym: Poor Vision

Evidence Code
type: Class
subclass of: deprecated terms
curator note: The information in this class and its sub-classes will be migrated to evidence code properties.

IEA (inferred from electronic annotation)
type: Class
subclass of: Evidence Code
dc:source: documentation.html

PCS (published clinical study)
type: Class
subclass of: Evidence Code
description: This should be used for information extracted from articles in the medical literature.
dc:source: documentation.html
comment: Generally, annotations of this type will include the pubmed id of the published study in the DB:Reference field.

ICE (individual clinical experience)
type: Class
subclass of: Evidence Code
description: Can be used for annotations based on individual clinical experience.
dc:source: documentation.html
comment: This may be appropriate for disorders with a limited amount of published data. This must be accompanied by an entry in the DB:Reference field denoting the individual or center performing the annotation together with an identifier.

ITM (inferred by text-mining)
type: Class
subclass of: Evidence Code

TAS (traceable author statement)
type: Class
subclass of: Evidence Code
description: Usually reviews or disease entries (e.g. OMIM) that only refers to the original publication.
dc:source: documentation.html

NAS (non-traceable author statement)
type: Class
subclass of: Evidence Code
description: used in all cases where the author makes a statement that a curator wants to capture but for which there are neither results presented nor a specific reference cited in the source used to make the annotation.
definition source: nas-non-traceable-author-statement

IC (inferred by curator)
type: Class
subclass of: Evidence Code
description: Used for those cases where an annotation is not supported by any direct evidence, but can be reasonably inferred by a curator from other annotations, for which evidence is available.
definition source: ic-inferred-curator

from personal attribute
type: Class
subclass of: deprecated terms

Diagnostic Tool
type: Class
subclass of: Diagnostics
subclass of: Restriction
  on property: has curation status
  has value: pending vetting by the SCDO WG
creator: SCDO
description: A diagnostic instrument, technique, laboratory assay or test, or method of patient examination used for differential diagnosis.

Diagnostic Instrument
type: Class
subclass of: Diagnostic Tool
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A research instrument consisting of a series of questions and other prompts for the purpose of gathering information from respondents to assist with differential diagnosis.
definition source: Questionnaire
description adapted from source: yes
hasExactSynonym: Diagnostic Questionnaire

from diagnostics
type: Class
subclass of: deprecated terms

from therapeutics
type: Class
subclass of: deprecated terms

SCD Causal Mutation
type: Class
subclass of: Thing
subclass of: Restriction
  on property: has curation status
  has value: uncurated
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
curator note: B-Thal mutations: http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.2004.tb00278.x/pdf https://www.ncbi.nlm.nih.gov/pubmed/15153712

HBB, GLU6VAL
type: Class
subclass of: SCD Causal Mutation
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The glutamic acid in position 6 in the primary sequence of a beta-chain produced by the HBB gene is replaced by valine.
definition source: http://www.bloodjournal.org/content/bloodjournal/46/3/363.full.pdf
description adapted from source: yes
hasExactSynonym: E6V

HBB, GLU121LYS
type: Class
subclass of: SCD Causal Mutation
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: A mutation where the

HBB, GLU6LYS
type: Class
subclass of: SCD Causal Mutation
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: A mutation where the

HBB, GLU26LYS
type: Class
subclass of: SCD Causal Mutation
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: A mutation where the

HBB, GLU121GLN
type: Class
subclass of: SCD Causal Mutation
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A mutation where the glutamic acid in position 121 in the primary sequence of a beta-chain produced by the HBB gene is replaced by glutamine.
comment: Derived from a point mutation in the beta-globin gene (HBB: c.364G>C; rs33946267).

HBB, ASP73ASN
type: Class
subclass of: SCD Causal Mutation
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A mutation where the aspartic acid in position 73 in the primary sequence of a beta-chain produced by the HBB gene is replaced by asparagine.
definition source: http://www.bloodjournal.org/content/bloodjournal/46/3/363.full.pdf
description adapted from source: yes
hasExactSynonym: Asp73Asn

HBB, VAL23ILE
type: Class
subclass of: SCD Causal Mutation
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: A mutation where the

HBB, THR87ILE
type: Class
subclass of: SCD Causal Mutation
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: A mutation where the

HBB, LEU68PHE
type: Class
subclass of: SCD Causal Mutation
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: A mutation where the

SCD Genotype
type: Class
subclass of: Thing
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: The alleles, or variant forms of the HBB gene, that are carried by an SCD sufferer. All include at least one copy of the...
curator note: Paper mentioning haplotypes and severity: https://www.nature.com/scitable/topicpage/sickle-cell-anemia-a-look-at-global-8756219 Table of SCD Genotypes: http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.2004.tb00278.x/pdf HBB allelic variants: https://www.omim.org/entry/141900#0243 Perhaps have parent class Hemoglobinopathy Genotype, with Hemoglobinopathy Trait below that?
definition source: genotype-234
description adapted from source: yes

SC
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6LYS
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
hasExactSynonym: SC Genotype
hasExactSynonym: β6Glu>Val/β6Glu>Lys

S/D-Punjab
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU121GLN
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
hasExactSynonym: S/D-Punjab Genotype
hasExactSynonym: β6Glu>Val/β121Glu>Gln

S/O-Arab
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU121LYS
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
hasExactSynonym: S/O-Arab Genotype
hasExactSynonym: β6Glu>Val/β121Glu>Lys

SE
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU26LYS
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
definition source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
hasExactSynonym: SE Genotype
hasExactSynonym: β6Glu>Val/β26Glu>Lys

SS
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
hasExactSynonym: SS Genotype
hasExactSynonym: β6Glu>Val/β6Glu>Val

SD
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has curation status
  has value: uncurated
hasExactSynonym: SD Genotype

Sickle Cell Disease
type: Class
subclass of: Hemoglobinopathy
subclass of: Restriction
  on property: has curation status
  has value: uncurated
definition source: sickle-cell-disease

S/C-Harlem
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, ASP73ASN
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
hasExactSynonym: S/C-Harlem Genotype
hasExactSynonym: β6Glu>Val/β6Glu>Val/β, β73Asp>Asn

Hemoglobin C-Harlem
type: Class
subclass of: Sickling Hemoglobin with Two Beta-Globin Gene Substitutions
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, ASP73ASN
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: An abnormal hemoglobin in which two mutations occurring in its beta-chains results in the sickling of red blood cells containing this hemoglobin. The sickling is the result of the mutation in which glutamic acid in position 6 is replaced by valine, which is not counteracted by the second mutation, in which the aspartic acid in position 73 is replaced by asparagine.
definition source: https://www.omim.org/entry/141900#0243
description adapted from source: yes
hasExactSynonym: HbS-HBC-Harlem
hasExactSynonym: Hemoglobin C-Georgetown
hasExactSynonym: Hemoglobin S-Hemoglobin C-Harlem

SCD Molecular Phenotype
type: Class
subclass of: Phenotype
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Abnormal Hemoglobin Level Present in SCD
type: Class
subclass of: SCD Molecular Phenotype
subclass of: Restriction
  on property: has curation status
  has value: uncurated

Sickle Cell Disease-S/C-Harlem
type: Class
subclass of: Sickle Cell Disease Variant
subclass of: Restriction
  on property: has curation status
  has value: uncurated
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
dc:source: http://www.bloodjournal.org/content/bloodjournal/46/3/363.full.pdf
dc:source: https://www.omim.org/entry/141900#0243
abbreviation: SCD-S/C-Harlem
hasExactSynonym: SC(Harlem) Disease
hasExactSynonym: Sickle Cell-Hemoglobin C-Harlem Disease
comment: Electrophoretically resembles HbSC, but clinically severe; double mutation in beta-globin gene; very rare.

HBB, 106-KB DEL
type: Class
subclass of: SCD Causal Mutation
subclass of: Restriction
  on property: has curation status
  has value: metadata complete
description: A 106-kb deletion of the beta globin gene cluster.
definition source: http://www.omim.org/entry/141900#0202
description adapted from source: yes
hasExactSynonym: HPFH1

Hemoglobinopathy Occuring in Heterozygous State in Sickle Cell Disease Variants
type: Class
subclass of: Hemoglobinopathy
subclass of: Restriction
  on property: has curation status
  has value: uncurated
curator note: Re: diagnosing b-thalassemia --> http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.2004.tb00278.x/pdf

S/Beta -Thal
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: PMC4459467
hasExactSynonym: S/Beta -Thal Genotype
hasExactSynonym: S/Beta -Thalassaemia Genotype
hasExactSynonym: S/Beta -Thalassemia
comment: There is no consensus about the classification of Hb S/β-Thal, but it is usually classified in two types: Hb S/β0-Thal and Hb S/β+-Thal.

Hemoglobin F Measurement
type: Class
subclass of: Hemoglobin Measurement
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The determination of the amount of hemoglobin F present in a sample.
definition source: http://bioportal.bioontology.org/ontologies/SYN
description adapted from source: no
hasExactSynonym: Fetal Hemoglobin
hasExactSynonym: Hemoglobin F

S/Beta-Zero-Thal
type: Class
subclass of: S/Beta -Thal
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
hasExactSynonym: S/Beta-Zero-Thal Genotype
hasExactSynonym: S/Beta-Zero-Thalassaemia Genotype
hasExactSynonym: S/Beta-Zero-Thalassemia

Severe S/Beta-Plus-Thal
type: Class
subclass of: S/Beta-Plus-Thal
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
hasExactSynonym: Severe S/Beta-Plus-Thal
hasExactSynonym: Severe S/Beta-Plus-Thal Genotype
hasExactSynonym: Severe S/Beta-Plus-Thalassaemia Genotype
comment: 1–5% HbA present.

S/HPFH
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has curation status
  has value: uncurated
hasExactSynonym: S/HPFH Genotype

S/Lepore Boston
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has curation status
  has value: uncurated
hasExactSynonym: S/Lepore
hasExactSynonym: S/Lepore Boston Genotype
hasExactSynonym: S/Lepore Genotype

A/Jamaica Plain
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, LEU68PHE
subclass of: Restriction
  on property: has curation status
  has value: uncurated
description: A dominant form of sickle-cell disease involving a double mutation in one beta-globin gene that results in hemoglobin with low oxygen affinity.
definition source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
description adapted from source: yes
comment: Only one case has been described.

Hemoglobin Jamaica Plain
type: Class
subclass of: Sickling Hemoglobin with Two Beta-Globin Gene Substitutions
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, LEU68PHE
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A sickling hemoglobin with reduced oxygen affinity that causes severe hemolytic anemia and sickling of erythrocytes.
definition source: http://www.nejm.org/doi/full/10.1056/NEJMoa040771
description adapted from source: yes
hasExactSynonym: Hb JP
hasExactSynonym: Hb Jamaica Plain
hasExactSynonym: Hemoglobin JP

Hemoglobin S-Antilles
type: Class
subclass of: Sickling Hemoglobin with Two Beta-Globin Gene Substitutions
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, VAL23ILE
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: overview-of-variant-sickle-cell-syndromes

Hemoglobin S-Oman
type: Class
subclass of: Sickling Hemoglobin with Two Beta-Globin Gene Substitutions
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU121LYS
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: overview-of-variant-sickle-cell-syndromes
hasExactSynonym: Hb S-Oman

A/S-Oman
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU121LYS
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: A very rare dominant form of sickle-cell disease caused by double mutation in one beta-globin gene.
dc:source: overview-of-variant-sickle-cell-syndromes
definition source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
description adapted from source: yes

Mild Sickle Cell Disease-S Beta Plus Thalassemia
type: Class
subclass of: Sickle Cell Disease-S Beta Plus Thalassemia
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
abbreviation: Mild SCD-S Beta Plus Thal
hasExactSynonym: Mild Sickle Cell-Beta Plus Thalassaemia

Moderate Sickle Cell Disease-S Beta Plus Thalassemia
type: Class
subclass of: Sickle Cell Disease-S Beta Plus Thalassemia
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
abbreviation: Moderate SCD-S Beta Plus Thal
hasExactSynonym: Moderate Sickle Cell-Beta Plus Thalassaemia

Severe Sickle Cell Disease-S Beta Plus Thalassemia
type: Class
subclass of: Sickle Cell Disease-S Beta Plus Thalassemia
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
abbreviation: Severe SCD-S Beta Plus Thal
hasExactSynonym: Severe Sickle Cell-Beta Plus Thalassaemia

Moderate S/Beta-Plus-Thal
type: Class
subclass of: S/Beta-Plus-Thal
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
hasExactSynonym: Moderate S/Beta-Plus-Thal Genotype
hasExactSynonym: Moderate S/Beta-Plus-Thalassaemia Genotype
comment: 6–15% HbA present.

Mild S/Beta-Plus-Thal
type: Class
subclass of: S/Beta-Plus-Thal
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
hasExactSynonym: Mild S/Beta-Plus-Thal Genotype
hasExactSynonym: Mild S/Beta-Plus-Thalassaemia Genotype
comment: 16–30% HbA present.

C/S Antilles
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6LYS
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, VAL23ILE
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
hasExactSynonym: β6Glu>Lys/β6Glu>Val, β23Val–Ile

Sickling Hemoglobin with Two Beta-Globin Gene Substitutions
type: Class
subclass of: Abnormal Hemoglobin Structure Present in SCD
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://books.google.co.za/books

Hemoglobin S-South End
type: Class
subclass of: Sickling Hemoglobin with Two Beta-Globin Gene Substitutions
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, LYS132ASN
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: https://books.google.co.za/books
comment: Described only in a compound heterozygote with Hemoglobin S.

S/Quebec-Chori
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, THR87ILE
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A compound heterozygous genotype, involving the mutations for Hemoglobin S and Hemoglobin Quebec Chori, which shows an electrophoretic pattern similar to that of the Hb A/S Genotype, but shows sickling.
dc:source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
hasExactSynonym: S/Quebec-Chori Genotype
hasExactSynonym: β6Glu>Val/β87Thr>Ile

Hemoglobin Quebec Chori
type: Class
subclass of: Abnormal Hemoglobin Structure Present in SCD
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, THR87ILE
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: An abnormal hemoglobin in which a threonine replaces an isoleucine residue at the eighty-seventh position of beta chains. It migrates like HbA but promotes sickling.
definition source: http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf
definition source: hb-quebec-chori
description adapted from source: yes

Sickle Cell Disease-S/Quebec Chori
type: Class
subclass of: Sickle Cell Disease Variant
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, THR87ILE
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A severe compound heterozygous sickling disorder.
dc:source: https://www.ncbi.nlm.nih.gov/pubmed/17551985
abbreviation: SCD-S/Quebec Chori
hasExactSynonym: Sickle Cell-Hemoglobin Quebec Chori Disease

HBB, LYS132ASN
type: Class
subclass of: SCD Causal Mutation
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://books.google.co.za/books
hasExactSynonym: LYS132ASN

S/S-South End
type: Class
subclass of: SCD Genotype
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, LYS132ASN
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
description: A compound heterozygous genotype, involving the mutations for Hemoglobin S and Hemoglobin S-South End.
dc:source: http://books.google.co.za/books
hasExactSynonym: S/S-South End Genotype

Hemoglobin Lepore Boston
type: Class
subclass of: Abnormal Hemoglobin Structure Present in SCD
subclass of: Restriction
  on property: has curation status
  has value: metadata complete - requires linking
description: The most common Hemoglobin Lepore type and the only type of the three known variants described in association with HbS. This abnormal hemoglobin consists of two normal alpha globin chains (HBA) and two deltabeta globin fusion chains which occur due to a "crossover" between the delta (HBD) and beta globin (HBB) gene loci during meiosis.
dc:source: Lepore-Boston-Washington.html
dc:source: haemoglobin-lepore
definition source: Homozygous Hb Lepore
definition source: Lepore-Boston-Washington.html
description adapted from source: yes
hasExactSynonym: Hb Lepore-B-W
hasExactSynonym: Hb Lepore-Boston-Washington
hasExactSynonym: Hemoglobin Lepore-Boston-Washington
comment: Hb Lepore is produced at a reduced rate and this is why the disease is related to the Β-thalassemic syndromes.
comment: Quantity in heterozygotes 7-13%; found in combination with Hb S, Hb C, beta+-thal, and in the homozygous state.
comment: the most common Hb Lepore type; found mainly in Italian families; it has also been observed in families from Rumania, Yugoslavia, Turkey, Cyprus, Jamaica, Cuba, Greece, England, Australia, Mexico, etc

Sickle Cell Disease-S/S-South End
type: Class
subclass of: Sickle Cell Disease Variant
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, GLU6VAL
subclass of: Restriction
  on property: has causal mutation
  some values from: HBB, LYS132ASN
subclass of: Restriction
  on property: has curation status
  has value: metadata incomplete
dc:source: http://books.google.co.za/books
abbreviation: SCD-S/S-South End
hasExactSynonym: Sickle Cell-Hemoglobin S-South End Disease
comment: Severe sickle cell disease was present in the adult carrier.

S/Beta-Plus-Thal
type: Class
subclass of: S/Beta -Thal

metadata complete
type: NamedIndividual
type: curation status specification
has curation status: pending vetting by the SCDO developers
description: Class has all required metadata, but is either not guaranteed to be in its final location in the ontology or refers to another class that is not complete.
definition source: IAO_0000120
description adapted from source: yes

metadata complete - requires linking
type: NamedIndividual
type: curation status specification
has curation status: pending vetting by the SCDO developers
creator: SCDO
description: Class has all required metadata, but still needs to be linked to other class(es)

metadata incomplete
type: NamedIndividual
type: curation status specification
has curation status: pending vetting by the SCDO developers
description: Class is being worked on; however, the metadata (including description) are not complete or sufficiently clear to the curators.
definition source: IAO_0000123
description adapted from source: yes

organizational term
type: NamedIndividual
type: curation status specification
has curation status: pending vetting by the SCDO developers
description: Term created to ease viewing/sort terms for development purpose, and will not be included in a release.
definition source: IAO_0000121
description adapted from source: no

pending vetting by the SCDO WG
type: NamedIndividual
type: curation status specification
has curation status: pending vetting by the SCDO developers
description: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by the SCDO working group.
definition source: IAO_0000125
description adapted from source: yes

ready for release
type: NamedIndividual
type: curation status specification
has curation status: pending vetting by the SCDO developers
description: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
dc:source: IAO_0000122
description adapted from source: no

requires discussion
type: NamedIndividual
type: curation status specification
has curation status: pending vetting by the SCDO developers
description: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires curator note(s) to identify the outstanding issues.
definition source: IAO_0000428
description adapted from source: yes

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
has curation status: pending vetting by the SCDO developers
description: Terms with this status should eventually be replaced with a term from another ontology.
definition source: IAO_0000423
description adapted from source: yes

uncurated
type: NamedIndividual
type: curation status specification
has curation status: pending vetting by the SCDO developers
description: Nothing done yet beyond proposing a term name.
definition source: IAO_0000124
description adapted from source: yes

example likely to be removed
type: NamedIndividual
type: curation status specification
has curation status: pending vetting by the SCDO developers
dc:source: IAO_0000002
description adapted from source: Only label adapted

pending vetting by the SCDO developers
type: NamedIndividual
type: curation status specification
creator: SCDO
description: All definitions, placement in the ontology and required minimal metadata are complete. The property is awaiting a final review by the SCDO developers.

accepted by SCDO WG (WS2)
type: NamedIndividual
type: curation status specification
creator: SCDO

R5LNftBfX3J6PgrlXLoxxs
label: Visit your GP if you or your child have unexplained symptomssuch as balance and co-ordination problems or difficulty walking, talking or swallowing. Family and medical history: Your GP may ask whether you have any family history of ataxia. They will also want to know about the progression of your symptoms. They might carry out a simple assessment of your balance, walking and co-ordination. Your GP may also ask how much alcohol you drink and whether you're taking any form of medication. This is because excessive drinking and certain medications can cause ataxia-like symptoms in some people. You may be referred for a series of tests to rule out other possible causes of your symptoms, such as an infection. The tests will probably include blood and urine tests. Further testing: If your symptoms suggest you may have acquired ataxia because of a serious underlying condition, it's likely you'll be admitted immediately to your nearest hospital. Otherwise, you'll be referred to a neurologist (a specialist in brain and nervous system conditions) for further testing or, in the case of children, a paediatrician. Some of the tests you may have are described below. Genetic testing: Genetic testing involves taking a sample of blood and testing the DNA in it for any genetic mutation known to cause ataxia.Currently, tests can detect the mutations responsible for Friedreich's ataxia, ataxia-telangiectasia and most of the spinocerebellar ataxias. Brain scans: Brain scans can be used to check for physical abnormalities in the brain that could be caused by certain types of hereditary ataxia. They can also be used to check for other problems that may affect your brain, such as a brain tumour. The two most widely used brain imaging scans are: magnetic resonance imaging (MRI) scan – this uses a strong magnetic field and radio waves to produce detailed scans of the soft tissue of the brain. computerised tomography (CT) scan – where a series of X-raysare taken and assembled by a computer int…

Surgery

R7hfSAL5e64WUzmSuK5ucF9
label: main treatments are lifestyle changes to ensure you remain as healthy as possible medication to control associated problems such as high blood pressure and high cholesterol dialysis – treatment to replicate some of the kidney's functions; this may be necessary in advanced CKD kidney transplant – this may also be necessary in advanced CKD

R8B2yn4Tm7qG7n6WsVD7ncC
label: Cancer can be caused by genetic factors; lifestyle factors such as tobacco use, diet, and physical activity; certain types of infections; and environmental exposures to different types of chemicals and radiation.

Severely Increased Albuminuria
dc:source: introduction
dc:source: microalbuminuria

Pulse Oximeter

Scintigraphy
description adapted from source: no
database cross reference: D011877
definition source: D011877
description: The production of an image obtained by cameras that detect the radioactive emissions of an injected radionuclide as it has distributed differentially throughout tissues in the body. The image obtained from a moving detector is called a scan, while the image obtained from a stationary camera device is called a scintiphotograph.

May be Acute (acute kidney injury) or chronic (see chronic kidney disease).

Hair-pulling

RBjuh4sGz0f8FVrp6Y9okyR
label: Ddiagnosed by kidney biopsy - Diagnostic features include capillary wall thickening, normal cellularity, IgG and C3 along capillary walls on immunofluorescence, and subepithelial deposits on electron microscopy [KDIGO 2012].

RBtjv0oQvJ6ADwOhywDNCrO
label: Main treatments are lifestyle changes to ensure you remain as healthy as possible medication to control associated problems such as high blood pressure and high cholesterol dialysis – treatment to replicate some of the kidney's functions; this may be necessary in advanced CKD kidney transplant – this may also be necessary in advanced CKD

RBz3vjzQ1Bli4AOzvKzRV0K
label: main treatments are: lifestyle changes to ensure you remain as healthy as possible medication to control associated problems such as high blood pressure and high cholesterol dialysis – treatment to replicate some of the kidney's functions; this may be necessary in advanced CKD kidney transplant – this may also be necessary in advanced CKD

Hemoglobin M Disease

Pain Management

Biologic therapy, Antibody therapy, Stem-cell transplantation, Splenectomy, Steroid treatment, Radioimmunotherapy, Surgery, chemotherapy, and radiation therapy,

essential measures (annotations)
description: A list of essential measures, measures that are critical to the collection of the measure at hand or are necessary for the interpretation of results for the measure at hand. Without such information, the data collected would be incomplete or misleading.
property has curation status: example to be eventually removed

Anti-inflammatory medications for joint pain and stiffness. Steroid creams for rashes. Corticosteroids to minimize the immune response. Antimalarial drugs for skin and joint problems.

Test for Stroke Risk in Children with Sickle Cell Disease - TCD
definition source: http://www.phenxtoolkit.org/index.php

Assessment for Hepatomegaly
description adapted from source: yes
property has curation status: uncurated
definition source: Liver span
description: A measurement performed during physical examination to determine the size of the liver and identify possible hepatomegaly.

Test for Stroke Risk in Children with Sickle Cell Disease - TCDi

RKnp1T8Z6lnu0iMAhHgIiG
label: Peritonitis, intraabdominal abscess, or sepsis, necrotizing myometritis, necrotizing fasciitis of the abdominal wall, septic pelvic thrombophlebitis, and toxic shock syndrome are rare complications, death. Amy be associated to secondary infertility.

RQubaRAap6eVUQ0Po5yQHd
label: Visit your GP if you or your child have unexplained symptomssuch as balance and co-ordination problems or difficulty walking, talking or swallowing. Family and medical history: Your GP may ask whether you have any family history of ataxia. They will also want to know about the progression of your symptoms. They might carry out a simple assessment of your balance, walking and co-ordination. Your GP may also ask how much alcohol you drink and whether you're taking any form of medication. This is because excessive drinking and certain medications can cause ataxia-like symptoms in some people. You may be referred for a series of tests to rule out other possible causes of your symptoms, such as an infection. The tests will probably include blood and urine tests. Further testing: If your symptoms suggest you may have acquired ataxia because of a serious underlying condition, it's likely you'll be admitted immediately to your nearest hospital. Otherwise, you'll be referred to a neurologist (a specialist in brain and nervous system conditions) for further testing or, in the case of children, a paediatrician. Some of the tests you may have are described below. Genetic testing: Genetic testing involves taking a sample of blood and testing the DNA in it for any genetic mutation known to cause ataxia. Currently, tests can detect the mutations responsible for Friedreich's ataxia, ataxia-telangiectasia and most of the spinocerebellar ataxias. Brain scans: Brain scans can be used to check for physical abnormalities in the brain that could be caused by certain types of hereditary ataxia. They can also be used to check for other problems that may affect your brain, such as a brain tumour. The two most widely used brain imaging scans are: magnetic resonance imaging (MRI) scan – this uses a strong magnetic field and radio waves to produce detailed scans of the soft tissue of the brain. computerised tomography (CT) scan – where a series of X-raysare taken and assembled by a computer in…

Neurology
hasNarrowSynonym: Neurological disorders
description adapted from source: no
dc:source: topic 3334
description: The branch of medicine that deals with the anatomy, functions and disorders of the nervous system.

Blood tests, such as antibody tests and a complete blood count, a urinalysis and a chest X-ray.