Sickle cell disease (SCD) is one of the most common monogenic diseases in humans with multiple phenotypic expressions that can manifest as both acute and chronic complications. Although described more than a century ago, challenges in comprehensive disease management and collaborative research on this disease are compounded by the complex molecular and clinical phenotypes of SCD, environmental and psychosocial factors, limited therapeutic options and ambiguous terminology. This ambiguous terminology has hampered the integration and interoperability of existing SCD knowledge, and SCD research translation. The SCD Ontology (SCDO), which is a community-driven integrative and universal knowledge representation system for SCD, overcomes this issue by providing a controlled vocabulary developed by a group of experts in both SCD and ontology design. SCDO is the first and most comprehensive standardized human- and machine-readable resource that unambiguously represents terminology and concepts about SCD for researchers, patients and clinicians. It is built around the central concept ‘hemoglobinopathy’, allowing inclusion of non-SCD haemoglobinopathies, such as thalassaemias, which may interfere with or influence SCD phenotypic manifestations. This collaboratively developed ontology constitutes a comprehensive knowledge management system and standardized terminology of various SCD-related factors. The SCDO will promote interoperability of different research datasets, facilitate seamless data sharing and collaborations, including meta-analyses within the SCD community, and support the development and curation of data-basing and clinical informatics in SCD.
Manually, based on terms in existing ontologies and in collaboration with sickle cell disease (SCD) experts where necessary.
As necessary. Not currently following a fixed frequency.
Terms/classes are added as they are identified as necessary by the sickle cell disease (SCD) community.
Researchers in Hemoglobinopathy and/or sickle cell disease (SCD), SCD patients and clinicians.
First draft was made available in BioPortal in May 2017
The field of sickle cell disease (SCD) research and care.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
For external terms/classes, the ontology from which the term was imported.
metadata complete - requires restrictions and relationships
Use on obsolete terms, relating the term to another term that can be used as a substitute.
An administrative note of use for a curator but of no use for a user.
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.
An assertion of whether or not the term/class description is an adaptation of the description in the description source.
Requested inclusion of this property into RO. Check details here again after inclusion.
'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.
This property is required unless dc:creator is "SCDO".
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.
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?
A relation between a measure (e.g. a survey) and how the measure has been adapted cross-culturally.
Requested inclusion of this property into RO. Check details here again after inclusion. Should be restricted to all measure/questionnaire classes.
A relationship between a condition/disease and a description of how the condition/disease is staged/graded.
Staging provided is disease/phenotype specific.
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.
Requested inclusion of this property into RO. Check details here again after inclusion. To be applied to "Measurement", "Test, Method or Assay", "Therapeutics"
A relation between a measure or measurement and the recommended procedure used by the measure or used to obtain the measurement.
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.
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)
A relation between a measure (e.g. a survey) and the population that the measure was designed to target.
Possible values used in the SCDO: Healthy Population; Clinic Patients (Children and/or Adults with SCD); Family Members; and/or Health Care Provider
An account of known translations of a measure into other languages (other than English).
A relation between a planned process and an objective it can be used to achieve.
This property is originally an object property.
Eventually to be replaced by "is caused by" object property
A relationship between a condition (a phenotype or disease) and a description of distinctive characteristics or essential features.
Description inherent in name (not provided by source)
Used for properties, not classes. For classes, use "has curation status" object property.
A relation between a selected entity and the predefined criteria that were met by the entity and that made it eligible for selection.
A relation between a measure and the age ranges for which the measure has been validated.
A relation between a measure (e.g. a survey) and an indication of whether the measure is freely available.
'yes' indicates that the measure is freely available. 'no' indicates that the measure is not freely available.
Records the slider label used by REDCap for a data element that uses a slider to collect data.
An indication of whether or not a clinical code requires an additional code to be specified with it. Annotation is either "yes", "no" or "if applicable, X", where X is the name of a diagnosis for which a code should be provided if it is applicable.
An indication of whether a term/class already exists in other ontologies. Only used for term (descriptions) that were not taken directly from an existing ontology.
Annotation options: Negligable Not relevant to context of sickle cell Few but definitions not freely available Suggest update to description Suggest update to label None
Records the answer options text for input in Redcap for a data element that provides answer options.
Records the field label of a data element.
Records the variable of the associated data element from a REDCap data capture instrument.
Records the section of a CRF in which a data element occurs.
Records the calculation used to automatically calculate the value for a data element in REDCap.
Records a data element's field note (a note provided below the answer field).
Records the order in which a data element appears in a specific section of a specific CRF/questionnaire/instrument. This is provided in the form of a number which is relative to the order numbers of other data elements of the section.
Used to provide a list of sections present in a questionnaire/instrument.
Records the type of validation used for a data element in REDCap.
Records the branching logic applied to a data element in REDCap.
Records the mainimum value that is accepted for a data element that has validation applied to it in REDCap.
Records the maximum value that is accepted for a data element that has validation applied to it in REDCap.
Records the field annotations of a data element in REDCap.
Used to show if a data element is considered an "identifier" (meaning it contains identifying information).
Used to show if a data element is a required field. "y" is assigned to it if the data element is a required field.
Records the custom alignment of a data element in REDCap.
Records a data element's field type, as per REDCap.
Used to record the matrix group that a data element occurs in.
An indication of whether or not a data element with a dropdown field should be autocompleted. Annotation is either "yes" or "no".
An indication of whether or not a data element with a slider field should display the slider's number values. Annotation is either "yes" or "no".
Used to record the identifier that had been used previously but is no longer in use.
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.
A legal document giving official permission to do something with a Resource.
Information about who can access the resource or an indication of its security status.
The method by which items are added to a collection.
The frequency with which items are added to a collection.
The policy governing the addition of items to a collection.
A class of entity for whom the resource is intended or useful.
Date (often a range) that the resource became or will become available.
An established standard to which the described resource conforms.
The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant.
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 or a curator.) The SCDO uses this especially to apply to term descriptions.
A related resource that references, cites, or otherwise points to the described resource.
Date of formal issuance (e.g., publication) of the resource.
Recommended best practice is to use a controlled vocabulary such as RFC 4646 [RFC4646].
A legal document giving official permission to do something with the resource.
A related resource from which the described class/term's annotations are derived.
An alias in which the alias is broader than the primary class name. Example: cell division is a broad synonym of cytokinesis.
A database cross-reference. An annotation which directs one to information contained within a database.
An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle.
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.
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.
An annotation property used to further annotate synonym axioms.
Additional information describing the class/term.
A human-readable name for the class/term.
Further information about the class/term.
The annotation property that indicates that a given entity has been deprecated.
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).
Inverse of "has phenotype" object property.
If required later, specify as inverse of "has phenotype" in Protege.
A relation that holds between a disease or an organism and a phenotype that is a symptom (subjective evidence of disease perceived by the patient).
Description adapted from RO. Suggest this description be updated in RO.
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.
A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.
A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.
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)
A relationship between a condition (phenotype or disease) and a relevant ICD-10-CM Diagnosis Code.
A relation between a device (diagnostic device) and the recording of the output (diagnostic measurement) of the device.
A relation between a process (e.g. a form of therapy) and a medical device, where the medical device is used in the process.
A relationship between a condition (a phenotype or disease) and an entity (a genotype or genetic variation) where the entity has a causal role for the condition.
A relation between a phenotype that is a diagnosis and a diagnostic tool used in making the diagnosis.
A relation between a condition (phenotype or disease) and a type of treatment or a specific treatment, where the condition can be treated with the treatment.
If required later, specify as inverse of "treats".
A relationship between a phenotype and a disease modifier, where the disease modifier modifies the mortality (due to the phenotype) of the SCD sufferer.
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)
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.
Essential measures have been attributed according to information in PhenX.
A relation between a particular genotype or disorder and the pattern in which the particular genotype or disorder is passed from one generation to the next.
A relationship between a condition (phenotype or disease), entity (aspect of quality of life) or process (therapy) and a disease modifier, where the condition, entity or process is modified by the disease modifier in some way.
A relationship between a disease modifier and a condition (phenotype or disease), entity (aspect of quality of life) or process (therapy), where the disease modifier modifies the condition, entity or process in some way.
A relation between a type of treatment or a specific treatment and a condition (phenotype or disease), where the type of treatment or specific treatment treat the condition.
If required later, specify as inverse of "treated with".
A relation between a Diagnostic Tool (test, method, assay, etc.) or the Diagnostic Measurement obtained from such a tool and a specific Diagnostic Device, where the Diagnostic Device is used in the application of the Diagnostic Tool or to obtain the Diagnostic Measurement.
A relation between a condition (hemoglobinopathy) and the genotype that causes the condition.
An object property that specifies the type of an ICD-10-CM code, whether Billable or Non-Billable.
A relationship that holds between a phenotype (i.e. manifestation) and a condition such as a disease (hemoglobinopathy), wherein the phenotype is evidence of the condition.
A relation between a phenotype that is a symptom (subjective evidence of disease perceived by the patient) and a disease.
A relationship between 'a' and 'b', where 'a' has some causal role for 'b'.
A relationship between an entity (e.g. genetic variation such as mutation or specific allele) and a genotype, where the entity contributes to the genotype.
A relation between a condition (Hemoglobinopathy) and a form of research (type of study) that the condition was studied in.
A relation between a condition (disease or phenotype) and a type of linking association (e.g. age of onset association).
A relationship between a diagnostic measurement and the diagnostic tool used to produce the measurement.
A relationship between a diagnostic device and the diagnostic tool by which the device is used.
A relation between a diagnostic tool (test, method, assay, etc.) and a diagnostic device, where the diagnostic device is used in the application of the diagnostic tool.
A relation between a diagnostic measurement and a diagnostic device, where the diagnostic measurement is the output of the diagnostic device.
A relation between a diagnostic tool and the diagnostic measurement that it measures.
A relation between a genotype and a genetic variation (e.g. mutation or genetic recombination), where the genetic variation contributes to the genotype.
A condition (phenotype or disease) or event (adverse event) induced by an entity (e.g. a drug) or activity (e.g. exercise).
The "developmentally induced by" object property in RO has the alternative term "induced by".
A relationship between a condition (a phenotype or disease) and an entity (e.g. environment) or condition (phenotype or disease) which could be an existing condition or an event, where the entity or second condition has a causal role for the condition being described.
A relation between a condition (disease or phenotype) and an aspect of an individual's life (personal attribute), behavior, an environmental exposure, or an inborn or inherited characteristic that increases the likelihood of the condition.
A relation between an aspect of an individual's life (personal attribute), behavior, an environmental exposure, or an inborn or inherited characteristic that increases the likelihood of a condition and the condition (disease or phenotype) that it increases the likelihood of.
A relation between a condition (disease or phenotype) or an entity (molecular phenotype) and a genetic variation (e.g. mutation or genetic recombination), where the genetic variation has some causal or contributing role that influences the condition or entity.
has causal or contributing genetic variation
A relation between an entity (genotype) and a molecular phenotype, where the entity has some causal or contributing role that influences the molecular phenotype.
causes or contributes to molecular phenotype
A relationship that holds between a condition such as a disease (hemoglobinopathy) and a phenotype (i.e. manifestation), where the phenotype is evidence of the condition.
A relation between a condition that is a diagnosis and a phenotype used in making the diagnosis.
A relation between an Abnormal Phenotype that is a diagnosis and a Diagnostic Measurement or Diagnostic Device Visual Output used in making the diagnosis.
A relation between a genotype and a molecular phenotype, where the genotype has a causal role for the molecular phenotype.
A relation between a condition (disease such as a Hemoglobinopathy) and a molecular phenotype, where the molecular phenotype is evidence of the condition.
A relationship between a Clinical or Research Assessment Data Element and a Clinical or Research Assessment Question Type.
A relationship between a multiple choice data element and an answer option or a group of answer options that are provided to the respondent by the data element.
A relationship between a data element and the type of information that is collected by that data element.
A relationship between a data element and the unit of measurement used, as a standard, for the information that is collected by the data element.
A relationship between a Diagnostic Measurement and a Phenotype, where the Phenotype is a possible finding of the Diagnostic Measurement, depending on the value recorded for the Diagnostic Measurement.
A relationship between an Abnormal Phenotype that is a diagnosis of a condition and a Phenotype that is a finding from a Diagnostic Measurement, where the Phenotype that is a finding is used as evidence to diagnose patients with the Abnormal Phenotype that is a diagnosis.
A relationship between a Diagnostic Measurement and the Unit of Measurement used for the values provided by the data properties that specify upper (ULN) or lower (LLN) limit of normal for the Diagnostic Measurement.
A relationship between a clinical code (such as ICD10 code) and a Phenotype, where the code can only be applied in instances where the phenotype is present.
A relation between an entity (phenotypic, therapeutic or diagnostic concept) and a guideline or directive.
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).
Used to record the lowest value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for particular laboratory result or other quantitative parameter.
Used to record the top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for particular laboratory result or other quantitative parameter.
Records the minimum number of selections that a respondent is allowed to make from a list of multiple answer options provided for a data element.
Records the maximum number of selections that a respondent is allowed to make from a list of multiple answer options provided for a data element.
Used to record the lowest value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for males for a particular laboratory result or other quantitative parameter.
Used to record the lowest value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for females for a particular laboratory result or other quantitative parameter.
Used to record the lowest value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for children for a particular laboratory result or other quantitative parameter.
Used to record the top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for males for a particular laboratory result or other quantitative parameter.
Used to record the top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for females for a particular laboratory result or other quantitative parameter.
Used to record the top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for children for a particular laboratory result or other quantitative parameter.
A spatiotemporal region encompassing some part of the life cycle of an organism.
See specific stages in the "Human Developmental Stages Ontology"
An information content entity specifying the upper and lower limit of a range of ages of continuants.
Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited.
Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.
Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.
Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances.
Add sub-class "Iron Chelator" with sub-classes "Deferoxamine" and "Deferiprone" (see wikipedia page for "Beta Thalassemia"...mentions how they're used to treat beta thalassemia major). Also add "Deferoxamine" and "Deferiprone" below "Iron Chelation Therapy".
An anti-inflammatory drug that is not a steroid. In addition to anti-inflammatory actions, non-steroidal anti-inflammatory drugs have analgesic, antipyretic, and platelet-inhibitory actions. They act by blocking the synthesis of prostaglandins by inhibiting cyclooxygenase, which converts arachidonic acid to cyclic endoperoxides, precursors of prostaglandins.
A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood.
A drug that prevents or reduces fever by lowering the body temperature from a raised state. An antipyretic will not affect the normal body temperature if one does not have fever. Antipyretics cause the hypothalamus to override an interleukin-induced increase in temperature. The body will then work to lower the temperature and the result is a reduction in fever.
A gamma-amino acid that is cyclohexane substituted at position 1 by aminomethyl and carboxymethyl groups. Used for treatment of neuropathic pain and restless legs syndrome.
A natural or synthetic analogue of the hormones secreted by the adrenal gland.
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.
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.
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.
A member of the class of imidazoles substituted at C-1, -2 and -5 with 2-hydroxyethyl, nitro and methyl groups respectively. It has activity against anaerobic bacteria and protozoa, and has a radiosensitising effect on hypoxic tumour cells. It may be given by mouth in tablets, or as the benzoate in an oral suspension. The hydrochloride salt can be used in intravenous infusions. Metronidazole is a prodrug and is selective for anaerobic bacteria due to their ability to intracellularly reduce the nitro group of metronidazole to give nitroso-containing intermediates. These can covalently bind to DNA, disrupting its helical structure, inducing DNA strand breaks and inhibiting bacterial nucleic acid synthesis, ultimately resulting in bacterial cell death.
A semisynthetic derivative of codeine that acts as a narcotic analgesic more potent and addicting than codeine.
An extended-release (ER) form of oxycodone (Xtampza ER) was approved for the management of daily, around-the-clock pain management in April, 2016.
Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small particles and the inlet pressure is relatively high.
Perhaps change label to "Hemoglobin by High Performance Liquid Chromatography"? See dc:source provided.
A test which produces colour change in the sample.
Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels.
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.
There are many more specific sub-classes in the CMO. Are there any we want to include here?
Morphological measurement involving the entire body of an organism.
Measurement of the structure or forms of the entire body or parts of the body of an organism.
Include the term "Body Composition" from PhenX? -- -- Any other relevant terms missing as sub-classes here?
A quantification of a parameter of the chemical composition of blood.
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.
The number of white blood cells in a specified volume of blood.
The number of platelets (thrombocytes) in a specified volume of blood, usually expressed as platelets per cubic millimeter of whole blood.
The number of granulocytes categorized as neutrophils in a specified volume of blood. A neutrophil is, or is in the process of becoming, a granular leucocyte having a nucleus with three to five lobes connected by threads of chromatin, cytoplasm containing very fine granules, and which is readily stainable with neutral dyes.
A measurement of the blood, it's contents, cells or other factors contained within the blood.
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.
Perhaps include missing sub-classes of "Blood Cell Measurement" from the Clinical Measurement Ontology?
Percentage of total blood volume that is made up of red blood cells.
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.
The amount of creatinine, a catabolic product of creatine phosphate used in skeletal muscle contraction found in a specified volume of serum.
Link to "Glomerular Filtration Rate"... which object property? Create a new one and suggest to RO? "used to calculate"?
A measurement to assess the morphological or physiological state of the respiratory system or portion of the respiratory system.
The number of granulocytes (polymorphonuclear leukocytes) in a specified volume of blood, usually 1 cubic millimeter.
The amount of bilirubin found in a specific volume of blood.
Any measurement of the movement of blood through the heart and blood vessels.
Add any more from below "circulation measurement" in the CMO? Suggest to CMO "Blood Flow Measurement" be an exact synonym of "Circulation Measurement", as we have made it here. Suggest to CRISP that their "blood flow measurement" instead be "Blood Flow Test".
Measurement to assess the sequential process through which multiple factors of the blood interact to form an insoluble fibrin clot.
Add other sub-classes of "Blood Coagulation Measurement" from the CMO? blood fibrinogen level? thrombin time? activated clotting time (ACT)? platelet aggregation measurement? bleeding time (BT)?
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.
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.
Any measurement of a gas or gases dissolved in arterial blood, that is, blood which has absorbed oxygen in the lungs, including oxygen, nitrogen carbon dioxide and/or hydrogen.
Any measurement of urine, the fluid waste product excreted by the kidneys, or its components.
The force per unit area attributable to the carbon dioxide, a colorless, odorless, incombustible gas formed during respiration and composed of one atom of carbon and two atoms of oxygen, dissolved in a specified volume of blood, defined as the force per unit area exerted by carbon dioxide in a mixture of gases in equilibrium with such a sample of blood at the same temperature.
Partial Pressure of Blood Carbon Dioxide
Partial Pressure of Blood Carbon Dioxide (Pco2)
Partial Pressure of Carbon Dioxide (PaCO2)
The average amount of hemoglobin per red blood cell calculated by dividing the total mass of hemoglobin by the number of red blood cells in a volume of blood.
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.
Add the sub-class "mean corpuscular sickle hemoglobin concentration (MCSHC)"? (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC290884/pdf/jcinvest00309-0076.pdf)
Mean Corpuscular Haemoglobin Concentration
Mean Corpuscular Hemoglobin Concentration
The calculation of the cellular elements of the blood, usually including cell counts for white and red blood cells and platelets.
PhenX protocol: Complete Blood Count #220501
The total number of leukocytes in 1 cubic millimeter of peripheral venous blood.
The number of each type of leukocyte present in a specific volume of blood, usually 1 cubic millimeter.
Perhaps add sub-classes from "Clinical Measurement Ontology"?
Blood Differential White Blood Cell Count
The complete or entire amount of bilirubin in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Bilirubin is the bile pigment produced by breakdown of heme and reduction of biliverdin.
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.
The optical density as calculated from the intensity of light at a specified wavelength as it passes through a solution of lysed red blood cells.
A measure of the oxygen carrying pigment of erythrocytes.
Pressure exerted by the heart muscle in its maximally contracted state.
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.
Any measurement of a gas or gases dissolved in the blood, including oxygen, nitrogen carbon dioxide and/or hydrogen.
The amount of oxygen bound to hemoglobin in the blood expressed as a percentage of the maximal binding capacity.
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.
The heaviness or degree to which the entire body of an organism at the point of or shortly after birth is drawn to the earth by gravity.
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.
Measurement of the amount of haptoglobin in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Haptoglobin is a serum alpha2 globulin glycoprotein, produced by the liver, that functions to bind free plasma hemoglobin, which allows degradative enzymes to gain access to the hemoglobin, while at the same time preventing loss of iron through the kidneys and protecting the kidneys from damage by hemoglobin.
The amount of N-terminal (NT)-pro hormone BNP (Nppb) in a specified volume of blood.
Value given as 1 Decimal Place Nanogram per Liter (according to PhenX https://www.phenxtoolkit.org/protocols/view/810501) associated with acute congestive heart failure (http://www.ebi.ac.uk/efo/EFO_0004745)
Blood NH2-Terminal pro-B-Type Natriuretic Peptide Level
N-Terminal Prohormone of Brain Natriuretic Peptide Level
N-Terminal Pro-Brain Natriuretic Peptide Level
A vitamin metabolic disorder that results from low blood levels of vitamin B12.
A colitis caused by inadequate blood supply to the colon.
Is diagnosed by: abdominal computed tomography scan
A hemochromatosis characterized by a predisposition to iron loading that is exacerbated by excessive intake of dietary iron, commonly related to consumption of tradition beer brewed in non-galvanized steel drums.
A neuropathy that is characterized by damage to a single nerve, which results in loss of movement, sensation, or other function of that nerve.
A lung disease that involves a vasoocclusive crisis of the pulmonary vasculature seen in patients with sickle cell anemia. The crisis is initiated by a lung infection, and the resulting inflammation and loss of oxygen tension leads to sickling of red cells and further vasoocclusion.
This definition was given by the WG: '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." With this definition source:The acute chest syndrome in sickle cell disease: incidence and risk factors. The Cooperative Study of Sickle Cell Disease. O. Castro, D. J. Brambilla, B. Thorington, C. A. Reindorf, R. B. Scott, P. Gillette, J. C. Vera, P. S. Levy Blood. 1994 Jul 15; 84(2): 643–649. However, the definition did not seem to come from this source, so the DO term was used instead.
Acute Chest Syndrome in Sickle Cell Disease
From the DO: The disease has_symptom fever, has_symptom pleuritic chest pain, has_symptom tachypnea, has_symptom cough, has_symptom hypoxemia, has_symptom marked leukocytosis, has_symptom marked leukocytosis, and has_symptom diffuse infiltrates on chest radiograph.
A brain disease that is characterized by the occurrance of at least two unprovoked seizures resulting from a persistent epileptogenic abnormality of the brain that is able to spontaneously generate paroxysmal activity and typically manifested by sudden brief episodes of altered or diminished consciousness, involuntary movements, or convulsions.
A gastrointestinal system infectious disease that involves inflammation of the lining of the stomach and small and large intestines, which is caused by viruses, bacteria, or parasites. Chemicals and drugs also cause gastroenteritis. The symptoms include diarrhea, loss of appetite, nausea, vomiting, cramps, and discomfort in the abdomen.
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
An arthritis that involves infection by a pathogen located in a joint.
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.
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.
This requirement indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.
This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community.
This could be coupled with a string describing the primary study investigator(s).
This requirement indicates that the requestor must provide documentation of local IRB/ERB approval.
This should be coupled with an ontology term describing the geographical location the restriction applies to.
This should be coupled with a date specified as ISO8601
This should be coupled with an integer value indicating the number of months.
This requirement indicates that use is limited to use by approved users.
This requirement indicates that use is limited to use within an approved project.
This requirement indicates that use is limited to use within an approved institution.
This requirement indicates that the requestor must return derived/enriched data to the database/resource.
An environmental system process that results in the introduction of contaminants into an environment.
A genotype information which is about the presence and degree of alpha-thalassemia, a form of thalassemia involving the number of functional HBA1 and HBA2 genes.
A clinical visit that is primarily for a regular examination.
An anemia with hemoglobin levels less than 5 gm/dL.
An information content entity that is about a clinical visit.
A scalar measurement datum of the concentration of urea in blood that is a specified output of a blood test.
An individual attribute that is the usual or principal work or business of an individual.
Human-made surroundings that provide the setting for human activity, ranging in scale from personal shelter and buildings to neighborhoods and cite, and can often include their supporting infrastructure, such as water supply or energy networks.
A reference to a place on the Earth, by its name or by its geographical location.
Intersex is an umbrella term with a complex history. It is usually used to refer to persons with congenital conditions which involve differences in the many intertwined processes of sexual development.
Principles which provide a framework within which ethical dilemmas and other problems may be analyzed.
The pattern in which a particular genetic trait or disorder is passed from one generation to the next.
A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele.
A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals with two pathogenic alleles, either homozygous (two copies of the same mutant allele) or compound heterozygous (whereby each copy of a gene has a distinct mutant allele).
Absence of any measurable level of sperm in a male's semen.
Hypogonadotropic hypogonadism is characterized by reduced function of the gonads (testes in males or ovaries in females) and results from the absence of the gonadal stimulating pituitary hormones: follicle stimulating hormone (FSH) and luteinizing hormone (LH).
An abnormal functionality of the genital system.
Abnormality of Reproductive System Physiology
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.
May be Acute (acute kidney injury) or chronic (chronic kidney disease).
Has a variety of causes - dependent upon acuity - see definitions for acute kidney injury (acute renal failure) and chronic kidney disease.
Treatment is dependent upon etiology and acuity. If refractory to medical therapy, renal replacement or dialysis may be indicated.
Scarring and fibrosis within the glomerulus.
Any form of injury to the kidney can lead to glomerulosclerosis.
Histologically noted by scarring and fibrosis in the glomerulus.
Segmental accumulation of scar tissue in individual (but not all) glomeruli.
Focal and Segmental Glomerular Sclerosis
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.
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.
A nonspecific term referring to disease or damage of the kidneys.
A phenotype that shows detectable differences from normal.
The presence of inflammation affecting the kidney.
May be caused by autoimmune disease, allergic responses, toxic injury, infectious causes.
May be associated with loss of kidney function, pyuria or hematuria, and proteinuria dependent upon cause.
Prolonged and/or excessive menses at regular intervals in excess of 80 ml or lasting longer than 7 days.
Abnormally Heavy Bleeding During Menstruation
Inflammation or infection of the middle ear.
Source needed for additional information.
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
Any abnormality of the eye, including location, spacing, and intraocular abnormalities.
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.
Blindness is the condition of lacking visual perception defined as visual perception below 3/60 and/or a visual field of no greater than 10 degress in radius around central fixation.
An abnormality of mental functioning including various affective, behavioural, cognitive and perceptual abnormalities.
Include "Poor School Performance" as a sub-class.
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.
Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info.
Peripheral neuropathy affecting the sensory nerves.
Reduced count of spermatozoa in the semen, defined as a sperm count below 20 million per milliliter semen.
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.
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.
A group of abnormalities characterized by hyperglycemia and glucose intolerance.
The presence of chronic increased pressure in the systemic arterial system.
Passing the age when puberty normally occurs with no physical or hormonal signs of the onset of puberty.
Delayed Development of Secondary Sex Characteristics
Insufficient production of growth hormone, which is produced by the anterior pituitary gland. Growth hormone is a major participant in control of growth and metabolism.
An abnormality of the parathyroid gland.
A condition caused by a deficiency of parathyroid hormone characterized by hypocalcemia and hyperphosphatemia.
Abnormality of the adrenal glands, i.e., of the endocrine glands located at the top of the kidneys.
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).
An increased concentration of insulin in the blood.
Excessive production of parathyroid hormone (PTH) by the parathyroid glands.
Elevated Blood Parathyroid Hormone Level
Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels.
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).
Infrequent menses (less than 6 per year or more than 35 days between cycles).
Osteopenia is a term to define bone density that is not normal but also not as low as osteoporosis. By definition from the World Health Organization osteopenia is defined by bone densitometry as a T score -1 to -2.5.
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 criteria, osteoporosis is defined as a BMD that lies 2.5 standard deviations or more below the average value for young healthy adults (a T-score below -2.5 SD).
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.
Bone pain, backache, gradual loss of height, stooped posture, fractures.
Yellow pigmentation of the skin or sclera due to bilirubin, which in turn is the result of increased bilirubin concentration in the bloodstream.
A darkening of the skin related to an increase in melanin production and deposition.
Bluish discoloration of the skin and mucosa due to poor circulation or inadequate oxygenation of arterial or capillary blood.
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.
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. This term refers to an abnormally increased susceptibility to developing petechiae.
An abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body.
Any manifestation of a skin disease associated with the production of pus.
A reduction of skin color related to a decrease in melanin production and deposition.
An abnormal reduction in the amount of pigmentation (reduced or absent) of skin, hair and eye (iris and retina).
Raised, well-circumscribed areas of erythema and edema involving the dermis and epidermis. Urticaria is intensely pruritic, and blanches completely with pressure.
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).
Hard, pebble-like deposits that form within the gallbladder.
Add here "bilirubin gallstones" (see paper "Liver involvement in sickle cell disease" by Emel GÜRKAN et al.). in HP these are called "Pigment Gallstones".
An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities.
Abnormality of Prenatal Development or Birth
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. The term epilepsy is used to describe chronic, recurrent seizures.
A state of disinterestedness, listlessness, and indifference, resulting in difficulty performing simple tasks or concentrating.
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.
- 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 relevant object property
Reduction of neurologic reflexes such as the knee-jerk reaction.
Loss of strength in the arm, leg, and sometimes face on one side of the body. Hemiplegia refers to a complete loss of strength, whereas hemiparesis refers to an incomplete loss of strength.
A generalized disorder of peripheral nerves.
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.
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.
Syncope refers to a generalized weakness of muscles with loss of postural tone, inability to stand upright, and loss of consciousness. Once the patient is in a horizontal position, blood flow to the brain is no longer hindered by gravitation and consciousness is regained. Unconsciousness usually lasts for seconds to minutes. Headache and drowsiness (which usually follow seizures) do not follow a syncopal attack. Syncope results from a sudden impairment of brain metabolism usually due to a reduction in cerebral blood flow.
Lack of clarity and coherence of thought, perception, understanding, or action.
-- Perhaps move below "Behavioral Abnormality"?
A term that means brain disease, damage, or malfunction. In general, it is manifested by an altered mental state.
-- Provide source for additional info. -- -- Specify which Blood Tests and Which Imaging Tests are used to diagnose.
Hemorrhage into the parenchyma of the brain.
Damage to cerebral nuclei caused in infants by highly increased levels of unconjugated bilirubin. The basal ganglia and brainstem nuclei could be shown to have a yellow staining historically in infants who died of kernicterus, that is, kernicterus is strictly speaking a pathological diagnosis. The presence of kernicterus may be inferred in infants with characteristic acute or chronic bilirubin-induced neurological dysfunction.
Infection (bacteria), ischemia, joint injury (trauma, surgery), degeneration.
Joint pain, joint swelling, stiffness, lack of function.
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.
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.
The ability of a joint to move beyond its normal range of motion.
A chronic disorder of the liver in which liver tissue becomes scarred and is partially replaced by regenerative nodules and fibrotic tissue resulting in loss of liver function.
Scar Tissue Replaces Healthy Tissue in the Liver
The presence of excessive fibrous connective tissue in the liver. Fibrosis is a reparative or reactive process.
Impairment of bile flow due to obstruction in the small bile ducts within the liver.
Is managed by: analgesia, hydration, antibiotics, and in severe cases exchange transfusion may be needed.
Simultaneous enlargement of the liver and spleen.
Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm.
An abnormal restriction of fetal growth with fetal weight below the tenth percentile for gestational age.
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.
An abnormality of the integument, which consists of the skin and the superficial fascia.
The birth of a baby of less than 37 weeks of gestational age.
Any abnormality of the cardiovascular system.
Abnormality of the Cardiovascular System
The presence of an abnormality of cardiac function that is responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction.
Necrosis of the myocardium caused by an obstruction of the blood supply to the heart and often associated with chest pain, shortness of breath, palpitations, and anxiety as well as characteristic EKG findings and elevation of serum markers including creatine kinase-MB fraction and troponin.
Inflammation of the sac-like covering around the heart (pericardium).
Enlargement or increased size of the heart left ventricle.
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.
The abnormal accumulation of fluid in two or more fetal compartments, including ascites, pleural effusion, pericardial effusion, and skin edema.
An abnormality of the hematopoietic system.
Abnormality of Blood and Blood-Forming Tissues
An abnormality of platelets. Platelets, also known as thrombocytes, are non-nucleated disk-shaped cells mainly involved in blood coagulation.
A reduction in the number of circulating thrombocytes.
Neutrophils are the most abundant leukocytes in blood and are considered to be the first line of defense during inflammation and infections. They are myeloid granulocytes and their names is derived from the fact that their cytoplasm contains granules that stain with acidic dye as well as granules that stain with basic dye. Their nuclei consist of three to five lobes connected by slender threads of chromatin. Mature neutrophils live for approximately one day.
An abnormally low number of neutrophils in the peripheral blood.
Any structural abnormality of erythrocytes (red-blood cells).
A type of anemia caused by premature destruction of red blood cells (hemolysis).
An abnormal decreased number of leukocytes in the blood.
Anemia characterized by the presence of erythroblasts that are larger than normal (megaloblasts).
Thrombocythemia and thrombocytosis are conditions with a higher than normal number of platelets. The term "thrombocythemia" is preferred when the cause of a high platelet count isn't known. The condition sometimes is called primary or essential thrombocythemia. Increased numbers of platelets in the peripheral blood.
A reduced number of reticulocytes in the peripheral blood.
A reduction in erythrocytes volume or hemoglobin concentration.
A cancer of the blood and bone marrow characterized by an abnormal proliferation of leukocytes.
Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia).
There is conflicting positioning of this term in different ontologies. Need an expert to decide descriptions and positioning of this and related terms.
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.
The presence of stenosis of the renal artery.
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.
May be caused by atherosclerotic disease, fibromuscular dysplasia.
Reduced blood flow through the renal arteries, large and branching vessels.
An elevation in the number of reticulocytes (immature erythrocytes) in the peripheral blood circulation.
Increased Number of Immature Red Blood Cells
A type of anemia characterized by an abnormally low concentration of hemoglobin in the erythrocytes.
A kind of anemia in which the volume of the red blood cells is reduced.
In normocytic anemia, the mean corpuscular volume (MCV) is below normal limits (>80 fl in adults).
A decreased concentration of glucose in the blood.
A type of diabetic metabolic abnormality with an accumulation of ketone bodies.
A form of inflammation of the kidney affecting the interstitium of the kidneys surrounding the tubules.
An abnormal increase in the number of leukocytes in the blood.
Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis).
An abnormal morphology (form) of the face or its components.
Bilateral bulging of the lateral frontal bone prominences with relative sparing of the midline.
Abnormally increased frequency of loose or watery bowel movements.
Infrequent or difficult evacuation of feces.
Atrophy (wasting, decrease in size of cells or tissue) affecting the cerebrum.
An abnormality of the telencephalon, which is also known as the cerebrum.
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).
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).
Abnormality of Extrapyramidal Motor Function
Migraine is a chronic neurological disorder characterized by episodic attacks of headache and associated symptoms.
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.
An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles.
Curation completed by the SCDO curator team: Amy and Khuthala.
Inflammation of any part of the lung parenchyma.
Difficulty in breathing. The physical presentation of respiratory distress is generally referred to as labored breathing, while the sensation of respiratory distress is called shortness of breath or dyspnea.
Hemorrhage occurring between the arachnoid mater and the pia mater.
Subarachnoid hemorrhage may occur spontaneously, usually from a ruptured cerebral aneurysm, or may result from head injury.
An abnormally high level of uric acid in the blood.
An increased concentration of nitrogen compounds in the blood.
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.
The presence of developmental dysplasia of the nail.
Abnormal accumulation of fluid in the brain.
An embolus (that is, an abnormal particle circulating in the blood) located in the pulmonary artery and thereby blocking blood circulation to the lung. Usually the embolus is a blood clot that has developed in an extremity (for instance, a deep venous thrombosis), detached, and traveled through the circulation before becoming trapped in the pulmonary artery.
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.
Impairment of expressive language and relative preservation of receptive language abilities. That is, the patient understands language (speech, writing) but cannot express it.
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
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).
Experience difficulties with understanding or expressing language.
An increase of the pressure inside the cranium (skull) and thereby in the brain tissue and cerebrospinal fluid.
The presence of an abnormal lateral curvature of the spine.
Congenital vertebral anomalies, idiopathic, result of a neuromuscular condition.
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to bone.
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.
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
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.
A cancer originating in lymphocytes and presenting as a solid tumor of lymphoid cells.
Include as sub-class: Acquired Immunodeficiency Syndrome (term in NCIT)
A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys, and serosal membranes.
Exaggerated anterior convexity of the thoracic vertebral column.
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.
Microscopic hematuria detected by dipstick or microscopic examination of the urine.
Any disease characterized by the formation of numerous granulomas.
Has disease stages: Allergic (Churg-strauss syndrome), eosinophilic (langerhan cell histiocytosis), langerhans (langerhan cell histiocytosis), lymphomatoid, siderotica, wegeners. Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation.
An elevated lipid concentration in the blood.
An abnormality of the composition of urine or the levels of its components.
An abnormality detectable by sonography of the heart (echocardiography).
Excretion in urine of proteins of a size smaller than albumin (molecular weight 69 kD).
Abnormally increased serum levels of alkaline phosphatase activity.
Decreased Circulating Alkaline Phosphatase Level
An abnormally low urinary specific gravity, i.e., reduced concentration of solutes in the urine.
Could this be a synonym for 'Impaired Urinary Concentration' (SCDO:0000621)?
Urine specific gravity is lower than that of plasma < 1.008.
A disorder of muscle unrelated to impairment of innervation or neuromuscular junction.
A type of hyperbilirubinemia with neonatal onset.
Abnormally reduced serum levels of alkaline phosphatase.
Complete bilateral fractures of the pars interarticularis resulting in the anterior slippage of the vertebra.
Spondylolysis, arthritis, degeneration, trauma, metastases or metabolic bone disease, congenital.
Displacement of One Backbone Compared to Another
Sudden and involuntary contractions of one or more muscles.
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the back.
muscle strain, trauma, surgery, fracture, osteoporosis, fibromialgia, spinal disc herniation.
Abnormal results of investigations using electromyography (EMG).
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.
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.
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.
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.
Decreased Circulating Low-Density Lipoprotein Levels
Reduced Circulating LDL Cholesterol Level
Decreased Circulating LDL Cholesterol Level
Increased concentration of total (conjugated and unconjugated) bilirubin in the blood.
Anomalous concentrations of fat-soluble substances (molecules composed of carbon and hydrogen and are characteristically insoluble in water) in the blood.
Abnormal Circulating Lipid Concentration
The presence of free hemoglobin in the urine.
If, following hemolysis, haptoglobins (hemoglobin-binding proteins) are saturated, then free hemoglobin appears in the urine.
A skin abnormality characterized by redness and irritation, with thick, red skin that displays flaky, silver-white patches (scales).
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.
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.
Elevated serum creatinine, uremia, acidosis, hyperkalemia, hyperphosphatemia, secondary hyperpararthyroidism, anemia, hypertension, fluid retention.
Any deviation from the normal concentration of a nitrogen compound in the blood circulation.
Abnormal Circulating Nitrogen Compound Concentration
An abnormality of alkaline phosphatase level.
Abnormality of Alkaline Phosphatase Activity
Note that the alkaline phosphatase family has four isoenzymes in humans, each of which additionally can have different isoforms. The primary clinical importance of measuring alkaline phosphatase is to check the possibility of bone disease or liver disease.
Abnormality of Alkaline Phosphatase Level
The presence of abnormally shaped erythrocytes.
Exaggerated concavity of the anterior or posterior surface of the vertebral body, i.e., the upper and lower vertebral endplates are hollowed inward.
A defect in the ability to concentrate the urine.
Notable within the first decade of life.
Can be caused by tubular damage in the kidney; can be seen in sickle cell disease and sickle cell trait.
A tachycardia originating in the ventricles characterized by rapid heart rate (over 100 beats per minute) and broad QRS complexes (over 120 ms).
Ventricular tachycardia (VT) is a potentially life-threatening ventricular arrhythmia that presents as a wide QRS complex tachycardia, and is defined as three or more consecutive QRS complexes with a duration longer than 120 milliseconds (ms) and a rate of 100 beats per minute or more, whereby the complexes have a ventricular origin. VT can be subdivided as follows: (i) sustained VT persists for 30 seconds or more; (ii) non-sustained VT lasts less than 30 seconds; (iii) monomorphic VT displays a uniform QRS morphology; and (iv) polymorphic VT displays QRS morphologies that variy from beat to beat. VT is observed most commonly in individuals with structural heart disease or acute myocardial infarction (MI). VT may also be observed in in the setting of drug toxicity or electrolyte abnormalities or in individuals with Mendelian disease.
An abnormal increase in the binding affinity of hemoglobin for oxygen.
Inability of the left ventricle to perform its normal physiologic function. Failure is either due to an inability to contract the left ventricle or the inability to relax completely and fill with blood during diastole.
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 before the 20th week of pregnancy.
Formation of a blood clot (thrombus) inside a cerebral vein, causing the obstruction of blood flow.
Add "Cerebral Venous Sinus Thrombosis" (in the Stroke Ontology) as a sub-class
Inflammation of the blood vessels within the brain.
Larger than normal size of erythrocytes. Macrocytosis refers to a mean cell volume (MCV) greater than 100 fL. If macrocytosis is an isolated abnormality, the amount of hemoglobin in the cell increases proportionately, so the mean cell hemoglobin concentration (MCHC) remains within normal limits.
Normal hemoglobin synthesis is characterized by production of equal amounts of alpha and beta globins. This term refers to a deviation from this pattern and is the main characteristic of the various forms of thalassemia.
A bacterial infection of the endocardium, the inner layer of the heart, which usually involves the heart valves.
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.
Attention Deficit-Hyperactivity Disorder
Childhood Attention Deficit/Hyperactivity Disorder
Attention Deficit Hyperactivity Disorder
Inability to perform rapid, alternating movements.
Bleeding within the vitreous compartment of the eye.
A type of hypothyroidism that results from a defect in thyroid-stimulating hormone secretion.
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.
Acute death of renal tubular cells that usually results from prolonged renal ischemia, nephrotoxins, or sepsis.
The clinical course of acute tubular necrosis may be divided into initiation, maintenance, and recovery phases.
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.
Loss of kidney function, reduced urine output, elevated serum creatinine.
Peripheral neuropathy is a general term for any disorder of the peripheral nervous system.
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.
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.
Facial Muscle Weakness of Muscles Innervated by CN VII
An abnormal level of a circulating protein in the blood.
Abnormality of Circulating Protein Level
A disease where there is cellular death (necrosis) of bone components due to interruption of the blood supply.
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.
The interruption of the blood supply may have many different causes such as rapid growth, heredity causes, trauma or overuse, anatomic conformation, dietary imbalances or secondary effects of other diseases.
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.
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.
An increased whiteness (density) of affected bones.
The age group in which disease manifestations appear.
Abnormal functionality of the cardiovascular system.
Abnormal Cardiovascular System Physiology
A decrease in the amount of intravascular fluid, particularly in the volume of the circulating blood.
Any morphological abnormality of the skin.
Any abnormality of the physiological function of the skin.
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.
Abnormal Tendency to Infections of the Skin
Delivery of a fetus through surgical incisions made through the abdominal wall (laparotomy) and the uterine wall (hysterotomy).
Shoulder dystocia occurs when the fetal anterior shoulder impacts against the maternal symphysis following delivery of the vertex.
Any cardiac rhythm other than the normal sinus rhythm. Such a rhythm may be either of sinus or ectopic origin and either regular or irregular. An arrhythmia may be due to a disturbance in impulse formation or conduction or both.
Hemorrhage into the parenchyma of the cerebellum.
Need to include this term mentioned here to the SCDO: -- obstructive hydrocephalus
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.
Pain in the lower back and hip radiating in the distribution of the sciatic nerve.
Provide source for additional info. Terms to add to therapeutics for linking via "is treated with" obj property: Local heat, acupuncture, physical therapy, surgery
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.
Abnormal number of platelets per volume of blood. In a healthy adult, a normal platelet count is between 150,000 and 450,000 per microliter of blood.
Bleeding in the anterior chamber of the eye.
Number of leukocytes per volume of blood beyond normal limits.
Increased number of neutrophils circulating in blood.
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.
A reduction in the ratio of production of beta globin to that of alpha globin. This is the major abnormality in the various forms of beta thalassemia.
A reduction in the ratio of production of alpha globin to that of beta globin. This is the major abnormality in the various forms of alpha thalassemia.
A deviation from the normal range of neutrophil cell counts in the circulation.
An abnormal concentration of creatinine in the blood.
An abnormally reduced amount of creatinine in the blood.
A fungal infection of the toenails or fingernails that tends to cause the nails to thicken, discolor, disfigure, and split.
Medscape: Onychomycosis: Author: Antonella Tosti, MD; Chief Editor: Dirk M Elston, MD et al..
has disease stage: Distal lateral subungual onychomycosis (DLSO), White superficial onychomycosis (WSO), Proximal subungual onychomycosis (PSO), Endonyx onychomycosis (EO), Candidal onychomycosis. Is characterised by: Disfigured nails, pain, paraesthesia, loss of dexterity, difficulty walking, standing, exercise.
An increased white blood cell count in the cerebrospinal fluid.
A structural or developmental anomaly of any of the tissues involved in the genital system.
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.
A morbilliform rash is said to resemble the rash of measles, rubella or scarlet fever, thus mimicking viral and bacterial exanthemas.
An inflammation of the kidney involving the parenchyma of kidney, the renal pelvis and the kidney calices.
An altered ability of any enzyme or their cofactors to act as catalysts. This term includes changes due to altered levels of an enzyme.
An abnormally low level of blood oxygen.
Partial or complete wasting (loss) of brain tissue that was once present.
An increased level of iron in liver tissues.
This abnormality can be measured by liver biopsy or by hepatic magnetic resonance imaging. Equivalents
Persistent pain, usually defined as pain that has lasted longer than 3 to 6 months.
Increased numbers of mesangial cells per glomerulus, defined as four or more nuclei in a peripheral mesangial segment.
Hematuria that is visible upon inspection of the urine.
The presence of mildly increased concentrations of albumin in the urine (in adults, 30-150 mg per day).
Chronic kidney disease: early identification and management of chronic kidney disease in adults in primary and secondary care; NICE Clinical Guidelines (July 2014)
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.
A functional anomaly of the nervous system.
Abnormality of Nervous System Physiology
A structural anomaly of the nervous system.
Abnormality of Nervous System Morphology
A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation.
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.
Myocarditis can be caused by a variety of bacterial and viral infections. Enteroviruses, especially coxsackievirus B, are often associated with acute myocarditis. However, with the advent of genetic analysis, adenovirus and parvovirus B19 have also been found to be frequent causes of myocarditis. Exposure to drug treatment, physical stimuli such as radiation and heat, metabolic disorders, immune disorders, and pregnancy are also causes of myocarditis. Many cases of myocarditis are idiopathic. Myocarditis presents with non-specific symptoms including chest pain, dyspnoea, and palpitations, and thus often mimics more common disorders such as coronary artery disease. In some patients, cardiac MRI and endomyocardial biopsy can help identify myocarditis, predict risk of cardiovascular events, and guide treatment.
Any functional abnormality of erythrocytes (red-blood cells).
Any deviation from the normal number of red blood cells per volume in the circulation.
An abnormal elevation above the normal number of red blood cells per volume in the circulation.
An abnormal reduction below the normal number of red blood cells per volume in the circulation.
Any deviation from the normal concentration of hemoglobin in the blood.
It might seem wrong to place this class here, but note that a change in hemoglobin concentration affects the size/volume and hence morphology of erythrocytes. Perhaps add sub-classes "Increased hemoglobin concentration" and "Decreased hemoglobin concentration" from HPO...their descriptions don't seem quite right though (should it not rather be "in the erythrocytes", not "in the circulation"?
An abnormal reduction below normal hemoglobin concentration in the circulation.
An abnormal elevation above normal hemoglobin concentration in the circulation.
Any anomaly of the digestive system, a collection of organs that is made up of the gastrointestinal tract and the liver, pancreas, and gallbladder. The gastrointestinal tract is a series of hollow organs joined in a long, twisting tube from the mouth to the anus, including the mouth, esophagus, stomach, small intestine, large intestine and anus.
Kaeda JS, Roper D, Srivastava P, et al. Severe hemolytic anemia associated with the homozygous state for an unstable hemoglobin variant (Hb Bushwick). Blood 1995; 86:1977.
A deviation from normal of the mean corpuscular volume, or mean cell volume (MCV) of red blood cells, usually taken to be 80 to 100 femtoliters.
A reduction from normal of the mean corpuscular volume, or mean cell volume (MCV) of red blood cells (usually defined as an MCV below 80 femtoliters).
A symptom or manifestation indicating a systemic or general effect of a disease and that may affect the general well-being or status of an individual.
An elevated level of the enzyme lactate dehydrogenase in serum.
Deviation from the normal Hgb/Hct; the average hemoglobin concentration in a given volume of packed red cells, calculated from the hemoglobin therein and the hematocrit, in erythrocyte indices.
Abnormal Mean Cell Haemoglobin Concentration
Abnormal Mean Cell Hemoglobin Concentration
Abnormal Mean Corpuscular Haemoglobin Concentration
Abnormal Mean Corpuscular Hb Concentration
Abnormal Mean Corpuscular Hemoglobin Concentration
Less than the normal Hgb/Hct; the average hemoglobin concentration in a given volume of packed red cells, calculated from the hemoglobin therein and the hematocrit, in erythrocyte indices.
Decreased Mean Corpuscular Haemoglobin Concentration
Low Mean Corpuscular Haemoglobin Concentration
Low Mean Corpuscular Hemoglobin Concentration
Reduced Mean Corpuscular Haemoglobin Concentration
Reduced Mean Corpuscular Hemoglobin Concentration
Decreased Mean Corpuscular Hemoglobin Concentration
Greater than the normal Hgb/Hct; the average hemoglobin concentration in a given volume of packed red cells, calculated from the hemoglobin therein and the hematocrit, in erythrocyte indices.
High Mean Corpuscular Haemoglobin Concentration
High Mean Corpuscular Hemoglobin Concentration
Increased Mean Corpuscular Haemoglobin Concentration
Increased Mean Corpuscular Hemoglobin Concentration
Inflammation of the inner lining of the uterus
Local accumulation of fluid, plasma proteins, and leukocytes in the endometrium.
A collection of pus, immune cells, and other material in the brain.
Brain abscess usually results from a bacterial or fungal infection.
An abnormal phenomenon characterized by a classic tetrad of excessive daytime sleepiness with irresistible sleep attacks, cataplexy (sudden bilateral loss of muscle tone), hypnagogic hallucination, and sleep paralysis.
An irreversible distortion of the morphology of an erythrocyte such that the cells are elongated and curved, resembling the blade of a sickle (the hand-held agricultural tool traditionally used to harvest grains).
The growth of endometrial tissue outside the uterus.
An obstruction in the veins of the liver caused by a blood clot (thrombosis).
A clot that obstructs blood flow in a mesenteric vein (the superior and the inferior mesenteric vein drain blood from the small and large intestine).
Any structural anomaly of the heart and great vessels.
Abnormal Cardiovascular System Morphology
A hole (perforation) in the wall of the intestine.
A pregnancy in which the fertilized egg inserts in a location outside of the main cavity of the uterus (usually in the Fallopian tube).
An abnormally high concentration in the circulation of aspartate aminotransferase (AST).
Elevated Serum Glutamic Oxaloacetic Transaminase
Elevated Serum Aspartate Aminotransferase
An abnormally high concentration in the circulation of alanine aminotransferase (ALT), which is an enzyme that catalyzes the transfer of amino groups to form the hepatic metabolite oxaloacetate. ALT is found abundantly in the cytosol of the hepatocyte. ALT activity in the liver is about 3000 times that of serum activity. Thus, in the case of hepatocellular injury or death, release of ALT from damaged liver cells increases measured ALT activity in the serum. Although it is generally thought to be specific to the liver, it is also found in the kidney, and, in much smaller quantities, in heart and skeletal muscle cells.
Elevated Serum Glutamic-Pyruvic Transaminase
An abnormal level of an analyte measured in the blood.
Abnormal Circulating Metabolite Concentration
The ABO histo-blood group consists of two antigens (A and B antigens) and four blood types (types A, B, AB, and O). The A and B antigens are the product of the ABO gene and are autosomal codominant. The group O phenotype is an autosomal-recessive phenotype due to the homozygous inheritance of two null ABO alleles. Group O individuals express the H antigen, the biosynthetic precursor to A and B antigens. ABO, therefore, is the blood type, whereas A, B, and H refer to the antigens. The ABO system consists of A and B antigens and antibodies against these antigens.
A deviation from the normal serum concentration/activity of lactate dehydrogenase (LDH), which catalyzes the reduction of pyruvate to form lactate.
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.
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.
Pregnancy-induced hypertension in association with significant amounts of protein in the urine.
A general term for inflammation of the muscles without respect to the underlying cause.
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the chest.
Excessive growth or abnormal thickening of bone tissue.
Severe systemic inflammatory response to infection.
Perhaps remove here and only keep below "Abnormality of the Immune System"? Source needed for additional information. Perhaps include different types of sepsis (see under D018805 in MESH)?
caused by: Bacteria and fungus mainly characterised by: Systematic manifestations of inflammation has disease stage: Mild, moderate, severe
Inflammatory or noninflammatory diseases affecting the glomeruli of the nephron.
A discontinuity of the skin exhibiting loss of the epidermis and often portions of the dermis and subcutaneous fat.
Abnormal test result of cardiovascular physiology.
A date specification that designates when an informed consent form was signed.
An informed consent by the parent/guardian of a child or a minor to consent to give permission for the child/minor to be included in research.
An informed consent for an unspecified range of future research subject to a few content and/or process restrictions.
A planned process in which data possessed by one person or organization is shared with one or more other persons or organizations.
A directive information entity that prescribes some process for withdraw from another planned process.
A descriptive information content entity that describes how biospecimens will be used.
A directive information entity that prescribes the information that is permitted to be shared or the processes for sharing that information.
A descriptive information content entity that describes how data will be used.
A descriptive information content entity that describes future use of material or information.
The use of antimalarial drugs for the prevention of infection.
Any process carried out to determine the condition of a patient's spleen.
Needs relating to Splenomegaly phenotype.
A permanent change in the DNA sequence of a gene that alters the genetic message carried by that gene.
Perhaps include here an "Alpha Thalassemia Mutation" sub-class? Could use the current description for "Alpha-Globin Locus Deletion" and instead give "Alpha-Globin Locus Deletion" a description similar to that of "Beta-Globin Locus Deletion"
An organism population whose members are particpating in non-parasitic symbiosis with a particular host.
A material entity bearing an antifungal disposition.
A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population.
Perhaps use Bacterial Infection and Viral Infection as modifiers? Include here "transfusion-related hepatitis infections" and or "viral hepatitis" (See paper "Liver involvement in sickle cell disease" by Emel GÜRKAN et al.)
Focal pathological and/or inflammatory changes characterized by alteration in the size, shape and organization of the cellular components of the skin.
Anomalies in the average levels of hemoglobin contained in an erythrocyte.
Abnormal Mean Corpuscular Hemoglobin Level
Increased volume of urine produced and excreted.
Clinicians sometimes mistakenly label increased urinary frequency as polyuria (increased urine output); Though rarely used, pollakisuria (or pollakiuria) is the correct term for increased frequency of urination.
Reduced ability or inability to self-repair and close wounds.
Death anytime within the perinatal period.
Anomaly in the processes involved in the maintenance of an internal equilibrium of lipids in the fluids and tissues.
Anomaly in the amount of oxygen and carbon dioxide in the blood.
Greater likelihood that an organism will develop ill effects from a bacterial infection or from components of or toxins produced by bacteria.
Decreased Resistance to Bacterial infection
Characterised by: Repeated/recurrent local or systemic bacterial infections. Caused by: Multifactorial generally factors ultimately cause impaired immunity.
Increased Susceptibility to Bacterial Infection
A retrogressive impairment of function or destruction of the functional cells of the nervous system that receive, conduct, and transmit impulses.
Usually in the elderly persons. Aging associated with most disorders
Multifactorial causes such as program cell death, genetic mutations, protein misfolding and intracellular mechanisms
Multiple disease entities such as alzhiemers disease, parkinsons disease , huntington's disease and amylotrophic lateral sclerosis
The observable morphological and physiological characteristics related to a state of equilibrium in the body with respect to various functions and to chemical composition of the fluids and tissues or the processes that cause many of the chemical changes in living mammalian organisms that are manifested through development and lifespan.
Greater than the level of heat natural to a living being.
Less than the level of heat natural to a living being.
Deviation in the level of heat natural to a living being.
Greater than the average levels of hemoglobin contained in an erythrocyte.
Less than the average levels of hemoglobin contained in an erythrocyte.
A measure (DImax) related to cell surface area, of the changeability of the membrane of circulating oxygen transporting cells as a function of physiologically relevant osmolality at a constant applied shear stress.
Anomaly in the processes involved in the maintenance of an internal equilibrium of various functions or chemical or protein composition of the blood.
An anomaly in the coefficient of variance (reference range) of the red blood cell volume for an organism.
Abnormal Red Blood Cell Distribution Width
Higher than normal coefficient of variance (reference range) of the red blood cell volume for an organism.
Increased Erythrocyte Distribution Width
Increased Red Blood Cell Distribution Width
Lower than normal coefficient of variance (reference range) of the red blood cell volume for an organism.
Decreased Erythrocyte Distribution Width
Reduced Red Blood Cell Distribution Width
Decreased Red Blood Cell Distribution Width
Destruction of erythrocytes such that hemoglobin is released from the cells; may occur by many different causal agents such as antibodies, bacteria, chemicals, temperature, and changes in tonicity.
Any anomaly in the amount in the urine of a carboxylic acid containing one or more amino groups (-NH2) and a carboxyl (-COOH) group.
Any change in the amount of creatinine in the urine
An increased amount of creatinine in the urine compared to the normal state.
a reduced amount of creatinine in the urine compared to the normal state
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.
Urine specific gravity is similar to that of plasma (1.008-1.012).
A drinking behavior associated with the intake of alcohol.
A drug used to treat depression and peripheral neuropathy (pain, numbness, tingling, burning, or weakness in the hands or feet) that can occur with diabetes.
An examination of the retina of the eye using an ophthalmoscope.
A finding indicating the presence of an inflammatory or neoplastic cellular infiltrate in the lung parenchyma.
A project to develop standards for the collection and analysis of patient-reported health status data using a system of highly reliable, precise measures for physical, mental, and social well-being. Patients are asked a series of rigorously reviewed questions covering common domains and metrics across differing conditions and treatments. The questions can be administered in short forms or adaptively through computerized adaptive testing and reports can be generated to allow clinicians to better understand how treatments might affect the quality of life of their patients.
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.
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.
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.
Patient Reported Outcomes Measurement Information System
Patient Reported Outcomes Measurement Information System (PROMIS)
The kind of visit undertaken by the subject within a study, such as inpatient, outpatient, telephone, etc.
The release from the requirement to obtain informed consent during a study that is granted by Human Subject Protection committee for a research institution for a protocol that is being reviewed by the Institutional Review Board.
International Ethical Guidelines for Health-related Research Involving Humans, Fourth Edition. Geneva. Council for International Organizations of Medical Sciences (CIOMS); 2016.
Waiver of the requirement of a signed consent form from potential participants or parents of children who are potential participants may be approved by a Research Ethics Committee if the research carries no more than minimal risk (i.e., risk that is no more likely and not greater than that attached to routine medical or psychological examination) and if the procedures to be used are only those for which signed consent forms are not customarily required outside the research context. Such waivers may also be approved when existence of a signed consent form would be an unjustified threat to the participant's confidentiality.
A 9-item scale using each of the 9 DSM-IV criteria with self-reported frequency of "0" (not at all) to "3" (nearly every day). One of the most widely used instruments to assess depression, PHQ-9 scores of 5, 10, 15, and 20 represent mild, moderate, moderately severe, and severe depression, respectively.
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.
Hemoglobin that has a nitric oxide bound to the cysteine at position 93 in the beta-globin chain.
The cessation of menstruation for six months or more in a female that is not pregnant, breastfeeding or menopausal.
Hemoglobin where the heme group has formed a stable complex with carbon monoxide (CO). This complex is produced after CO has been inhaled or as a byproduct of hemoglobin, protoporphyrin or dichloromethane catabolism. The heme-CO complex is approximately 200 times more stable than heme-oxygen complexes. Thus, high levels of carboxyhemoglobin in the circulation can lead to tissue hypoxia and death.
A severe hypersensitivity-like reaction occurring during dialysis due to exposure to the dialysis membrane.
A crack or break in a dialysis catheter caused by material weakness or mechanical compression.
Any heart or vascular disorder occurring as a consequence of injury to the cardiovascular system.
Any disorder of the liver occurring as a consequence of injury to the liver parenchyma.
Any eye disorder occurring as a consequence of injury to the eye.
Any issue that arises as a consequence of a problem with a patient's dialysis access.
A type of high-throughput, multiplex PCR method used to determine abnormal DNA copy number changes of up to 50 genomic DNA or RNA sequences with a single pair of PCR primers. It is frequently used in the detection of genetic aberrations in tumors, and can distinguish sequences differing in only a single nucleotide.
Multiplex Ligation-Dependent Probe Amplification
Failure to meet, or late achievement of developmental milestones.
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.
Tissue death resulting from an interruption to the blood supply.
This is a synonym for osteonecrosis in our ontology (SCDO:0000841), which is controversial between different literature. Please check with a clinician if these two terms refer to the same condition.
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.
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.
PhenX protocol: Intelligence Scale - 16 to 90 years #820501
Wechsler Adult Intelligence Scale - Fourth Edition
Wechsler Adult Intelligence Scale 4th Edition
Wechsler Adult Intelligence Scale, Fourth Edition
Wechsler Adult Intelligence Scale, Fourth Edition (WAIS-IV)
A battery of tests that allow an investigator to conduct a comprehensive evaluation of a child or adolescent's cognitive ability.
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.
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.
PhenX protocol: Intelligence Scale - 6 to 16 years 11 months #820503
Wechsler Intelligence Scale for Children-Fifth Edition
Wechsler Intelligence Scale for Children-Fifth Edition (WISC-V)
Intelligence Scale - 6 to 16 years 11 months
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.
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.
PhenX protocol: Intelligence Scale - 2 years, 6 months to 7 years, 7 months #820502
Wechsler Preschool & Primary Scale of Intelligence 4th Edition
Wechsler Preschool and Primary Scale of Intelligenc-Fourth Edition
Wechsler Preschool and Primary Scale of Intelligenc-Fourth Edition (WPPSI-IV)
Wechsler Preschool and Primary Scale of Intelligence IV
Intelligence Scale - 2 years, 6 months to 7 years, 7 months
An assessment tool designed to measure an individual's cognitive capabilities. It may be general or it may assess abilities in more discrete cognitive domains.
A diagnostic technique that uses pulsed Doppler ultrasound to both identify blood vessels in the brain and measure the velocity of blood flow through those vessels. It allows a more accurate estimation of stroke risk because it allows outlining of parenchymal structures and visualization of the examined vessels.
Imaging Transcranial Doppler Ultrasonography
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.
A standardized rating scale developed by Ziad Nasreddine in 1996 to screen for mild cognitive dysfunction and impairment. This instrument assesses the following cognitive domains: attention and concentration, executive functions, memory, language, visuoconstructional skills, conceptual thinking, calculations, and orientation
PhenX protocol: Global Mental Status Screener - Adult #130701
Montreal Cognitive Assessment Functional Test
Montreal Cognitive Assessment Questionnaire
A chest X-ray finding indicating the presence of a radio-opaque area in the lung. The opacification is caused by fluid or solid material within the airways or lung parenchyma.
Described in the Tanzania guidelines as 'reduced air entry, increased tactile vocal fremitus, and dull percussion at lung bases, usually bilateral'.
A measurement of the concentration of iron in the liver as an estimate of body iron load.
A circumferential measurement of the largest part of the upper arm.
Hemoglobin where the heme group has formed a reversible complex with oxygen (O2) in the lungs. This molecule is found in the systemic arteries and transports O2 from the lungs to the tissues where it is readily released.
Hemoglobin containing a heme group that is not bound to oxygen (O2). This molecule is normally found in the systemic veins following transit through capillaries and release of O2 into the tissues. Excess deoxyhemoglobin can be associated with hypoxia.
The persistence of substantial fetal hemoglobin production into adulthood, usually associated with hemoglobinopathies due to mutations in the alpha and/or beta chain of hemoglobin.
Hereditary Persistence of Foetal Haemoglobin
Hereditary Persistence of Fetal Hemoglobin
A variant of sickle cell disease due to homozygosity of the E6V mutation, amino acid substitution of valine for glutamic acid in the sixth position of the beta chain, resulting in the production of hemoglobin S from both alleles.
A humanized monoclonal immunoglobulin G1 anti-P-selectin antibody with vaso-protective and anti-vaso-occlusive properties. Upon administration, crizanlizumab binds to P-selectin and blocks its interaction with P-selectin glycoprotein ligand-1 (PSGL-1; SELPLG) on neutrophils and monocytes. P-selectin, a glycoprotein that functions as a cell adhesion molecule (CAM), translocates to the surface of activated endothelial cells and platelets, upon stimulation, where it binds to its ligand and mediates the rolling of platelets and neutrophils on activated endothelial cells. Therefore, blockade of p-selectin may inhibit platelet aggregation, maintain blood flow and minimize sickle cell-related pain crises (SCPC).
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.
To maintain data by placing the data, or a copy of the data, onto an electronically accessible device for preservation (either in plain-text or encrypted format).
An independent group that comprises medical, scientific, and non-scientific members, and is tasked with the continuing review and approval of research, including clinical trials, with respect to the protocols, methods, and informed consent process to ensure the protection of the rights, safety, and wellbeing of participants.
The interval of time during which subjects are to be enrolled in a clinical study.
An orally bioavailable modulator and stabilizer of sickle cell hemoglobin (HbS), with potential use in the treatment of sickle cell disease (SCD). Upon administration, voxelotor targets and covalently binds to the N-terminal valine of the alpha chain of HbS. This stabilizes HbS, thereby improving oxygen binding affinity. The binding of voxelotor to HbS prevents HbS polymerization, reduces sickling, decreases red blood cell (RBC) damage and increases the half-life of RBCs. This improves blood flow and decreases hemolytic anemia.
Is an accepted therapy for adults and pediatric patients 12 years of age and older with sickle cell disease.
Application of genetic material (usually DNA) into cells in order to permanently correct an inherited disease or acquired disease.
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.
Review current sub-classes in light of and include relevant classes from "EDDA Study Designs Taxonomy" to be added as sub-classes.
A patient-reported outcome measurement system designed to evaluate and monitor the physical, mental, and social well-being of adults with sickle cell disease.
Cross-cultural adaptation underway in Brazil. ASCQ-Me's development using modern measurement theory facilitates cross cultural adaptation.
PhenX protocol: Adult Sickle Cell Quality of Life Measurement Information System (ASCQ-Me) #820201
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).
Rigor in development, using modern measurement theory and aligned with PROMIS measurement development.
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.
Adult Sickle Cell Quality of Life Measurement Information System
Adult Sickle Cell Quality-of-Life Measurement Information System
It includes questions that enable adults with SCD to describe their functioning and well-being. Its 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; and Pain Frequency.
Adult Sickle Cell Quality-of-Life Measurement Information System (ASCQ-Me)
An evaluation of the perfusion of blood through the brain.
A variant of sickle cell disease due to heterozygosity for hemoglobin S and hemoglobin D mutations. Patients present with the symptoms of sickle cell disease but the symptoms are less frequent and severe compared to patients with hemoglobin SS disease.
A pulmonary complication of sickle cell disease characterized by radiographic interstitial abnormalities and impaired pulmonary function. In severe cases, pulmonary hypertension is present.
Restricive lung disease often associated with chest pain and hypoxemia. May also be associated with pulmonary hypertension.
Powars et al 1988 Medicine (Baltimore), Knight-Madden et al 2010 Lung.
Sickle Cell Chronic Restrictive Lung Disease
A clinician-assessed rating of psychological and social functioning in children ages six to seventeen that was developed by Shaffer et al. in 1983. The numerical scale, which is an adaptation of the adult Global Assessment Scale (GAS) developed by Endicott et al in 1976, is scored from 0 to 100 based on behaviors and life situations that are applicable to children.
PhenX protocol: Global Mental Status Screener - Older Children and Adolescents #130703
Children’s Global Assessment Scale (CGAS)
Global Mental Status Screener - Older Children and Adolescents
A person who is separated from their spouse, whether or not there is a legal arrangement.
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.
Note: "Genetic Test" is a SNOMED CT term. Include NCIT's "Presymptomatic Testing" as a sub-class?
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.
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.
The date on which a diagnosis of disease was made.
A set of people with some shared element. The substance of shared element varies widely, from geography to a situation to interest to lives and values. The term is widely used to evoke sense of collectivity.
The statistical characterization of human populations or segments of human populations (e.g., characterization by age, sex, race, or income).
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.
Include other Ethnic groups that are sub-classes of "Ethnic Group" in ERO.
Activity that requires physical or mental exertion, especially when performed to develop or maintain fitness.
A person who belongs to the sex that normally produces ova. The term is used to indicate biological sex distinctions, or cultural gender role distinctions, or both.
A functional unit of heredity which occupies a specific position on a particular chromosome and serves as the template for a product that contributes to a phenotype or a biological function.
Any demarcated area of the Earth; may be determined by both natural and human boundaries.
The red respiratory protein of erythrocytes, consisting of approximately 3.8% heme and 96.2% globin (64.5 KD), which as oxyhemoglobin (HbO2) transports oxygen from the lungs to the tissues where the oxygen is readily released and HbO2 becomes Hb.
Laboratory test involving interaction of antigens with specific antibodies.
A systematic means of communicating by the use of sounds, symbols, or gestures.
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.
The year when a diagnosis was assigned to an individual's condition.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site to large nucleotide sequences visible at a chromosomal level.
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.
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.
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?
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.
Laboratory analysis of urine, commonly used to aid in the diagnosis of disease or to detect the presence of a specific substance. It involves examination of the urine by physical or chemical means as well as microscopic examination that helps to screen for urinary tract infections, renal disease, and diseases of other organs, that result in abnormal metabolites (break-down products) appearing in the urine.
Other urine tests to be added as sub-classes? There are many in the NCIT.
The rate of blood flow through the cerebral arteries.
The assemblage of properties that distinguish people on the basis of the societal roles expected for the two sexes.
An account of all reproductive events and problems a person has experienced. An important aggregate factor in epidemiological studies of women's health. The concept usually includes the number and timing of pregnancies and their outcomes, the incidence of breast feeding, and may include age of menarche and menopause, regularity of menstruation, fertility, gynecological or obstetric problems, or contraceptive usage.
Having to do with the physical, psychological, cognitive, and social consequences of disease, including stigmatization of persons affected.
A single base pair substitution that alters the genetic code in a way that produces an amino acid that is different from the usual amino acid at that position. Some missense mutations will alter the function of the protein.
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.
An instrument used to measure an event involving emission, absorption, or refraction of light.
Any rearrangement to the genomic content that results in the loss of one or more nucleotides of DNA. Deletions are generally irreversible rearrangements. They may alter the reading frame of a gene, or may result in loss of large chromosomal regions.
The distinguishing qualities or prominent aspects of an individual person.
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.
Analysis of the RNA expression pattern in a tissue sample using molecular techniques.
A person who belongs to the sex that normally produces sperm. The term is used to indicate biological sex distinctions, cultural gender role distinctions, or both.
A point mutation occurring within the protein-coding region of a gene, and which codes for the same amino acid as expected.
This gene plays a role in transcriptional regulation and is involved in several signal transduction pathways.
How long something has existed; elapsed time since birth.
Could add many sub-classes of "Age" from NCIT.
A word or group of words indicating the identity of a person usually consisting of a first (personal) name and a last (family) name with an optional middle name. In some cultural traditions the family name comes first.
The maximum pressure exerted into the systemic arterial circulation during the contraction of the left ventricle of the heart.
The minimum pressure exerted into the systemic arterial circulation during cardiac ventricular relaxation and filling.
A collective generic term that refers here to a wide variety of dependencies, areas of special sovereignty, uninhabited islands, and other entities in addition to the traditional countries or independent states.
A collection or single item of factual or reported information, derived from measurement or research, from which conclusions may be drawn.
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.
A protein, RNA or a complex that contains proteins and/or RNA.
If additional gene products are included in the future, they can be categorised according to those below this term in the "National Cancer Institute Thesaurus" (NCIT)
Lack of coordination of muscle movements resulting in the impairment or inability to perform voluntary activities. Causes include peripheral nerve disorders, posterior column injuries, cerebral and cerebellar disorders, basal ganglia disorders, and thalamic disorders.
Perhaps add "Cerebellar Ataxia" subclass?
Abnormally high level of bilirubin in the blood. Excess bilirubin is associated with jaundice.
A balloon type pouch or bulge in the wall of a cerebral blood vessel.
System of classification based on nation from which a person originates, regardless of the nation in which he/she currently resides.
The totality of characteristics of reproductive structure, functions, phenotype, and genotype, differentiating the male from the female organism.
A severe acute inflammatory response affecting the hands and feet of individuals with sickle cell disease, sickle cell-hemoglobin C disease or sickle cell-beta-thalassemia. It is caused by vaso-occlusive episodes leading to ischemia and finally infarction of the distal portions of the extremities. Clinical signs of pain, swelling and tenderness of digits usually begin in early childhood and may be the initial manifestations of sickle cell anemia. Clinical course is self-limited with instances typically lasting a few weeks and occurring during sickling crises. An initial episode before the age of 1 strongly correlates with a more severe disease course.
An acute infectious disorder caused by gram positive or gram negative bacteria. Representative examples include pneumococcal, streptococcal, salmonella and meningeal infections.
Increase in the number of hematopoietic cells in the bone marrow. It may involve all or individual hematopoietic cell lines.
A non-infectious mixture containing recombinant hepatitis B surface antigen (HBsAg) in a liquid vehicle. Immunization with the hepatitis B vaccine induces the formation of specific anti-hepatitis B antibodies and an active immunity against hepatitis B infection.
A sterile liquid preparation infused into a vein. IV fluid is prescribed as a replacement of fluid, electrolytes, calories, vitamins, and other nutritional substances. In addition, IV fluids are used to administer blood products and medications such as chemotherapy. Examples of IV fluids include Normal Saline, Ringers Solution, and Lactated Ringers Solution.
Any disease or disorder that occurs during the course of, or because of, another disease, treatment, or procedure.
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.
An account of all experiences related to the receipt of blood, WBC, platelets, and/or other blood components.
Perhaps use as Disease Modifier? Add these sub-classes: Hepatitis C Infection (term in NCIT) Hepatitis B Infection (term in NCIT) HIV Infection (term in NCIT)
An acute or chronic inflammation involving the gallbladder wall. It may be associated with the presence of gallstones.
A sensation of discomfort secondary to surgery.
The co-occurrence of pregnancy and a disease. The disease may precede or follow conception and it may or may not have a deleterious effect on the pregnant woman or fetus.
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.
Cholecystitis that is persistent and long-standing.
Acute infection of the bile ducts caused by bacteria ascending from the small intestine.
Necrotic changes in the bone tissue of the femoral head due to interruption of blood supply.
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
Avascular Necrosis of the Capital Femoral Epiphysis
Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity.
A test performed by an ophthalmologist or optometrist assessing vision and ability to focus on and discern objects, as well as other tests and examinations pertaining to the eyes.
A non-invasive method that provides estimates of arterial oxyhemoglobin saturation by utilizing selected wavelengths of light to determine the saturation of oxyhemoglobin.
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.
Heptavalent Pneumococcal Conjugate Vaccine
Pneumococcal 7-Valent Conjugate Vaccine (Diphtheria CRM197 Protein)
Seven Valent Pneumococcal PS Meningococcal OMPC Conjugate Vaccine
Seven-Valent Pneumococcal PS-Meningococcal OMPC Conjugate Vaccine
Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction.
An increase in the viscosity of blood resulting from an increase in the proportion of cellular elements of the blood, a change in the mechanical properties of the cellular elements of the blood, and/or an alteration in plasma viscosity.
A decrease in the amount of oxygen in the body. Symptoms range from mild (impaired judgment, memory loss, impaired motor coordination) to severe (seizures and coma). In SCD patients, this is considered as saturated oxygen < 95% on air.
Have merged the definition of hypoxia from NCIT and the Tanzanian Management Guidelines. Not sure if the SaO2 value is specific to SCD patients - please get a clinician to review. This is a symptom of acute chest syndrome.
The probability of benefit to individuals in a defined population from a medical technology applied for a given medical problem under ideal conditions of use. Efficacy is a measure of effect of therapy among appropriate patients in whom treatment is tolerated and effectively administered, under the condition of sufficient patients' compliance, usually determined in randomized trials.
The philosophical study of moral values and rules. Ethics is a general term for what is often described as the "science of morality". The Western tradition of ethics is sometimes called moral philosophy. This is one of the three major branches of philosophy, alongside metaphysics and logic.
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.
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.
A sequence of decimal digits (0-9) that is used for identifying a destination telephone line or other device in a telephone network.
An area or portion of something with more or less definite boundaries designed or specified according to some established biological, administrative, economic, demographic, etc. criteria.
It didn't have sense to have this term as a sub-class of "Major Area", which has also been deprecated.
A unit of temperature of the temperature scale designed so that the freezing point of water is 0 degrees and the boiling point is 100 degrees at standard atmospheric pressure. The current official definition of the Celsius sets 0.01 C to be at the triple point of water and a degree to be 1/273.16 of the difference in temperature between the triple point of water and absolute zero. One degree Celsius represents the same temperature difference as one Kelvin.
An association is a non-hierarchical, named relationship between a source and target concept that does not affect classification and is not inherited by child concepts during classification. Associations are bidirectional and have a stated inverse. Unlike roles, associations do not have a domain or range.
Determination of a value is not relevant in the current context.
A diagnostic test used to examine and define microscopic tissue structure, composition, or etiology. The test results are often used by a clinician to diagnose disease or disordered function.
The number of breaths (inhalation and exhalation) taken per minute time.
A bacterial infectious process affecting any part of the urinary tract, most commonly the bladder and the urethra. Symptoms include urinary urgency and frequency, burning sensation during urination, lower abdominal discomfort, and cloudy urine.
Removal of tissue from the liver for microscopic examination.
Use relevant object property to link to "Elevated Hepatic Iron Concentration".
Indicates a person currently joined in a legally binding matrimonial union. Classify common law marriage as married. Includes married couples living together and not living together.
Indicates a person who has never been married or whose marriages have been annulled.
Indicates a person who is no longer married because of the death of his/her spouse and has not remarried.
Indicates a person whose marriage has been legally dissolved and has not remarried.
A broad-spectrum aminoglycoside antibiotic produced by fermentation of Micromonospora purpurea or M. echinospora. Gentamicin is an antibiotic complex consisting of four major (C1, C1a, C2, and C2a) and several minor components. This agent irreversibly binds to the bacterial 30S ribosomal subunit. Specifically, this antibiotic is lodged between 16S rRNA and S12 protein within the 30S subunit. This leads to interference with translational initiation complex, misreading of mRNA, thereby hampering protein synthesis and resulting in bactericidal effect. Aminoglycosides are mostly ineffective against anaerobic bacteria, fungi and viruses.
Administration of antibiotics with the intent of preventing bacterial infection.
Is recommended, particularly up to the age of 5 years, to prevent bacterial infections in SCD patients.
A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus.
A propionic acid derivate and nonsteroidal anti-inflammatory drug (NSAID) with anti-inflammatory, analgesic, and antipyretic effects. Ibuprofen inhibits the activity of cyclo-oxygenase I and II, resulting in a decreased formation of precursors of prostaglandins and thromboxanes. This leads to decreased prostaglandin synthesis, by prostaglandin synthase, the main physiologic effect of ibuprofen. Ibuprofen also causes a decrease in the formation of thromboxane A2 synthesis, by thromboxane synthase, thereby inhibiting platelet aggregation.
2-[4-(2-methylpropyl)phenyl]propanoic acid
A cyclohexanone derivative with analgesic and anesthetic properties. Although its mechanism of action is not well understood, ketamine appears exerts complex pharmacological actions including inhibition of biogenic amine uptake, binding to opioid receptors, and inhibition of N-methyl D-aspartate (NMDA) receptors. Because of the involvement of spinal NMDA receptors in the process of central sensitization, this agent may reduce pain perception and induce sedation.
A derivative of dibenzocycloheptadiene and a tricyclic antidepressant. Amitriptyline inhibits the re-uptake of norepinephrine and serotonin by the presynaptic neuronal membrane in the central nervous system (CNS), thereby increasing the synaptic concentration of norepinephrine and serotonin. Due to constant stimulation to these receptors, amitriptyline may produce a downregulation of adrenergic and serotonin receptors, which may contribute to the antidepressant activity.
A point mutation occurring within the protein-coding region of a gene, and which codes for a stop that can truncate the protein.
A small scale mutation caused by the substitution of a single nucleotide for another nucleotide.
A way of denoting the collective genotype of a number of closely linked loci on a chromosome.
A unit of concentration (molarity unit) equal to one millimole of solute per liter of solution.
A metric unit of mass concentration defined as the concentration of one gram of a substance per unit volume of the mixture equal to one cubic meter. The concept also refers to the metric unit of mass density (volumic mass) defined as the density of a substance which mass equal to one gram occupies the volume of one cubic meter.
A 3-isobutyl derivative of gamma-amino butyric acid (GABA) with anti-convulsant, anti-epileptic, anxiolytic, and analgesic activities. Although the exact mechanism of action is unknown, pregabalin selectively binds to alpha2delta (A2D) subunits of presynaptic voltage-dependent calcium channels (VDCCs) located in the central nervous system (CNS). Binding of pregabalin to VDCC A2D subunits prevents calcium influx and the subsequent calcium-dependent release of various neurotransmitters, including glutamate, norepinephrine, serotonin, dopamine, and substance P, from the presynaptic nerve terminals of hyperexcited neurons; synaptic transmission is inhibited and neuronal excitability is diminished. Pregabalin does not bind directly to GABA-A or GABA-B receptors and does not alter GABA uptake or degradation.
A unit of mass concentration defined as the concentration of one gram of a substance per unit volume of the mixture equal to one deciliter (100 milliliters). The concept also refers to the metric unit of mass density (volumic mass) defined as the density of substance which mass equal to one gram occupies the volume one deciliter.
A unit of mass concentration defined as the concentration of one milligram of a substance in unit volume of the mixture equal to one cubic deciliter or 100 cubic centimeters. It is also a unit of mass density (volumic mass) defined as the density of substance which mass equal to one milligram occupies the volume one cubic deciliter or 100 cubic centimeters.
A unit of cell concentration expressed as a number of cells in thousands per unit volume equal to one microliter.
A unit of cell concentration expressed as a number of cells in millions per unit volume equal to one microliter.
Unit of arbitrary substance concentration (biologic activity concentration) defined as the concentration of one international unit per one liter of the system volume.
The calendar date on which a person was born.
A unique identifier for a subject in a study.
The unique identification of a subject in a specified context. NOTE(S): This class is a resolution of the requirement for noting the type of an identifier which is not handled by the purely technical HL7 II data type.; A unique symbol that establishes identity of the subject. EXAMPLE(S): study subject number 7 on a specific study OTHER NAME(S): NOTE(S):; Unique Identifier of patient or fetus who is the subject of observations.; The unique identification of a subject in a specified context.
A unique identifier assigned to each clinical trial subject to protect the subject's identity and used in lieu of the subject's name when the investigator reports adverse events and/or other trial-related data.
Clinical Study Subject Unique Identifier
Clinical Trial Subject Unique Identifier
The formal plan of an experiment or research activity, including the objective, rationale, design, materials and methods for the conduct of the study; intervention description, and method of data analysis.
A method of ultrasound imaging in which the ultrasound probe is pressed against the skin of the abdomen in order to create an image of the abdominal organs.
Difficulties related to an apparatus used to gain access to arteries and veins.
Having no known name or identity or known source.
Of your own free will or design; not forced or compelled; controlled by individual volition.
The quantitative measurement of liver enzymes in the blood, which is useful in assessing the functional state of a patient's liver. Liver function tests include the measurement of albumin, alanine transaminase, aspartate transaminase, alkaline phosphatase, bilirubin, and gamma glutamyl transferase.
Other LFTs to be added here? There are more in NCIT
PhenX protocol: Liver Function - Assay #190801
Hemoglobin subunit alpha (142 aa, ~15 kDa) is encoded by both the human HBA1 and human HBA2 genes. This protein plays a role in the distribution of oxygen from the lungs to other organs and tissues.
Examination of the anterior segment of the eye using a medical instrument called a slit lamp.
Any problem arising from the use of a medical device.
Accumulation of iron in the tissues. It may be a manifestation of an inherited disorder (e.g., hemochromatosis) or acquired (in patients with repeated blood transfusions). Symptoms include hepatomegaly, arthritis, diabetes mellitus, and bronzed skin. If untreated it has a progressive course and may lead to death.
Perhaps suggest that NCIT merges this term with "Hemochromatosis", which they have as a separate term. Sub-classes need to be worked on further. Consider sub-classes of "hemochromatosis" in the DO. Include Hemosiderosis as a sub-class?
An acute or subacute reversible condition characterized by headaches, mental status changes, visual disturbances, and seizures associated with imaging findings of posterior leukoencephalopathy. It has been observed in association with hypertensive encephalopathy, eclampsia, and immunosuppressive and cytotoxic drug treatment.
Reversible Posterior Leukoencephalopathy Syndrome
Posterior Reversible Leukoencephalopathy
The development of a blood clot in a catheter.
A parent report or patient self report for measuring health-related quality of life (HRQOL) in healthy children and adolescents and those with acute and chronic health conditions. The PedsQL Measurement Model uses a modular approach that integrates both generic core scales and disease-specific modules into one measurement system. (Copyright 1998-2008 James W. Varni, Ph.D.)
Many measures available in Spanish, French and Portuguese
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.
Pediatric Quality of Life Inventory (PedsQL)
A sample of blood applied in a thin film to a microscope slide for study under a microscope.
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.
A description of an individual's current and past experience with alcoholic beverage consumption.
Add other terms in the PhenX "Alcohol Use" collection?
An identifying number within an institution that is used to reference a subject's medical information.
Anemia not associated with symptoms of fatigue, headaches, palpitations, or shortness of breath. In asymptomatic anemia the hematocrit levels usually range from 32 to 35%.
An inherited metabolic disorder characterized by iron accumulation in the tissues.
Hemoglobin subunit epsilon (147 aa, ~16 kDa) is encoded by the human HBE1 gene. This protein plays a role in the transport of oxygen to tissues of the embryo.
A type of polypeptide chain that when in combination with alpha globin polypeptide chains forms adult hemoglobin 2 (HbA2). HbA2 comprises around 3% of adult hemoglobin. 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.
Hemoglobin subunit beta (147 aa, ~16 kDa) is encoded by the human HBB gene. This protein plays a role in the transport of oxygen to tissues of the adult body.
Measurement of the breathing capacity of the lung by means of a spirometer.
A product of hemoglobin produced by oxidation of the iron atom from the ferrous to the ferric state.
An instrument consisting of a predetermined set of questions for a clinical or research assessment.
Clinical or Research Assessment Questionnaire
A statement (either spoken or written) that is made in reply to a clinical research assessment question.
Clinical or Research Assessment Response
The biopsy of placental tissue containing the chorionic villi from the maternal uterus in early pregnancy to diagnose fetal genetic defects.
Testing to determine if there is a predisposition or indication of a possible genetic or a chromosomal abnormality.
Hemorrhage defined as a blood loss in excess of 500 mL after vaginal delivery or more than 1000 mL after a cesarean delivery.
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.
An acute inflammatory process that leads to necrosis of the pancreatic parenchyma. Signs and symptoms include severe abdominal pain, nausea, vomiting, diarrhea, fever, and shock. Causes include alcohol consumption, presence of gallstones, trauma, and drugs.
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.
A condition in which a person is heterozygous for a globin gene, with one normal allele and one defective allele.
NCIT includes this class below "Hemoglobinopathy", hence its inclusion here.
A condition in which a person has reduced protein production from two of the four alpha-globin alleles.
-/- alpha/alpha or -/alpha -/alpha. It can exist in two forms: (1) alpha-thal-1 (alpha alpha/--), involves cis deletion of both alpha genes on the same chromosome; (2) alpha-thal-2 (alpha-/alpha-), involves trans deletion of alpha genes this occurs on different (homologous) chromosomes.
A condition in which a person has reduced protein production from one of the four alpha-globin alleles.
A compound heterozygous state in which a person has a hemoglobin S allele along with a beta-thalassemia allele. The severity of the condition is determined to a large extent by the quantity of normal hemoglobin produced by the beta-thalassemia gene.
Sickle Cell-Beta-Thalassemia Disease Syndrome
A morphologic finding indicating enlargement of the glomeruli in a kidney specimen.
A conjugate vaccine of meningococcal polysaccharide used for active immunization against invasive meningococcal disease caused by Neisseria meningiditis serogroups A, C, Y, and W-135.
Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugated Vaccine
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.
Pneumococcal 10-Valent Conjugate Vaccine
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.
Pneumococcal 13-Valent Conjugate Vaccine
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.
Methemoglobinemia that is caused by exposure to certain drugs (xylocaine and benzene) and nitrate-rich foods.
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.
Sickle Cell Disease-S Beta Zero Thalassemia
The formation of a thrombus in the renal vein.
Ischemic necrosis of the spinal cord caused by occlusion of the arteries that supply blood to the spinal cord. Signs and symptoms include intermittent back pain, pain in the legs, paralysis, and incontinence.
Can be treated with exchange transfusion (SCDO:0001303)
An assay that produces a picture of an entity.
Perhaps replace this term with "Diagnostic Imaging" from NCIT?
A sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
Add sub-class "beta-globin gene sequencing" as per the "Diagnostic Methods" section of the term "Dominant beta-thalassemia" in Orphanet.
A material entity bearing the disposition to infect an organism
A microscope that produces an image of an object by targeting it with an electron beam.
It is capable of much higher magnifications and has a greater resolving power than a light microscope, allowing it to see much smaller objects in finer detail.
A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs.
A device that is used to generate X-rays.
An assay to determine the temperature of an evaluant.
An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens.
The window period for antibody tests in most people is somewhere between 3 to 12 weeks from the time of infection.
A value specifcation that specifies the youngest age when specifying an age range.
A value specifcation that specifies the oldest age when specifying an age range.
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).
Example of usage: A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS.
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.
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).
A disease characterized by abnormal and uncontrolled cell division.
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.
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) -- Add the sub-class "Clinical Phenotype" from Ontology for General Medical Science
A clinically abnormal phenotype that is characteristic of a single disease.
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.
A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome.
A genetic disorder inherited during conception that is part of all cells in the organism.
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?
A communication from a patient about something they perceive as being abnormal about their body or life.
An answer to question where the answer is Yes.
An answer to question where the answer is No.
An answer to question that indicates the response to the specified question is unknown.
An answer to question where one declines to answer the specified question.
An answer to question that is not enumerated in the list and then may be entered with free text in a separate text box
A protein that is a translation product of the human SELL gene or a 1:1 ortholog thereof. It is a leukocyte adhesion receptor that play an important role in regulating the inflammatory response by mediating leukocyte tethering and rolling on adherent leukocytes.
L-selection is a serum marker for neutrophil activation.
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).
The performance of the basic activities of self care, such as dressing, ambulation, or eating.
Ability to Carry Out Activities of Daily Living
A structurally abnormal hemoglobin that occurs in one or more forms of Sickle Cell Disease (SCD).
Probably too specific to SCD be included in other ontologies.
Structurally Abnormal Hemoglobin Present in SCD
Abnormality in structure and function of the Red Blood Cell.
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".
Analgesic antipyretic derivative of acetanilide. It has weak anti-inflammatory properties and is used as a common analgesic, but may cause liver, blood cell, and kidney damage.
A condition that co-exists or follows from sickle cell disease and that has a severe and rapid onset of symptoms with short duration.
Probably too specific to warrant inclusion into anther ontology.
Acute Complications of Sickle Cell Disease
An acute onset of wheezing in a person with SCD who has no co-morbid asthma.
Cohen et al 2011 Am J Hematol., Glassberg et al 2014 Curr Opin Pediatr., Knight-Madden et al 2014 Ped Resp Rev
Etiology may be unclear. May be related to inflammation of SCD and/or viral lower respiratory tract infection.
Too specific to SCD to be included in other ontologies? PFTs may be done to asses for airway hyper-responsiveness.
Sickle cell pain management that aims to heal the acute process.
Request inclusion into MESH below "Pain Management" / "Sickle Cell Pain Management" (also to be suggested for inclusion)
An acute respiratory illness with no lower respiratory tract signs or infiiltrate on chest radiograph.
Request inclusion into relevant ontology
Few but definitions not freely available
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.
Suggest update to description for "Patient Compliance" in MESH.
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.
Suggest update to label in PhenX (from "Migraine - Adult") as we have done.
PhenX protocol: Migraine - Adult #130501
An adverse event that occurs after a drug administration.
Should this be a sub-class of "Environmental Disease Modifier"?
Electrophoresis in which agar or agarose gel is used as the diffusion medium.
A rare congenital disorder characterized by a partial or complete absence (agenesis) of an area of the brain that connects the two cerebral hemispheres. It can be the result of a failure in any one of the multiple steps of callosal development including cellular proliferation and migration, axonal growth or glial patterning at the midline.
Suggest update to description in HPO. Include links to relevant Therapeutics.
A quantitative measurement of alanine aminotransferase present in a blood sample.
Suggest update to description in NCIT (from "Alanine Aminotransferase Measurement")
Serum Glutamic-Pyruvic Transaminase Test
The amount of alanine aminotransferase present in a specified volume of blood.
Serum Glutamic-Pyruvic Transaminase Level
Increased concentration of albumin in the urine; more than 30mg in 24hours or urine albumin creatinine ratio (ACR) >3 mg/mmol.
Because albuminuria may be affected by non-pathological factors (exercise, menstruation contamination, biological variability, etc.), abnormal values should be confirmed within 1-2 months.
An indication of whether the respondent has ever consumed any alcoholic beverage during his or her entire life.
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. A hemoglobinopathy with two clinically significant forms: hemoglobin Bart hydrops fetalis (deletion of all 4 alpha-globin genes; --/--) which is severe and often results in neonatal death; and hemoglobin H disease (most commonly caused by deletion of 3 alpha-globin genes; --/-alpha) which results in hemolytic anemia, splenomegaly and bone changes.
Curation completed by the SCDO curator team: Clair.
Origa R, Moi P. Alpha-Thalassemia. 2005 Nov 1 [Updated 2016 Dec 29]. In: Adam MP, Ardinger HH, Pagon RA, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle 1993-2018. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1435/
Drugs that selectively bind to and activate alpha adrenergic receptors.
A region of chromosome 16 that includes five functional genes and two pseudogenes. The order of genes is: 5' - zeta - pseudozeta - mu - pseudoalpha-1 - alpha-2 -alpha-1 - theta1 - 3'. It is responsible for the creation of the alpha parts (roughly half) of the oxygen transport protein Hemoglobin.
Request inclusion into relevant ontology perhaps below "Genetic Locus"/"Globin Locus" (also to be included) in MESH.
Methods of pain relief that may be used with or in place of analgesics.
A compound capable of relieving pain without the loss of consciousness.
An adverse drug event that results in unexpected and unwanted events due to anesthetic drug treatment.
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.
Suggest update to description in DO. Currently no 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.
Angiotensin Converting Enzyme Inhibitors
Angiotensin-Converting Enzyme Inhibitors
The respondent's total family income from the last calendar year.
Request inclusion into MESH below "Income". The PhenX protocol is U.S. specific. Is there one relevant to the African setting?
PhenX protocol: Annual Family Income #11101
Substance that reduces or suppresses inflammation.
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.
Used in the treatment of acute or chronic vascular hypertension regardless of pharmacological mechanism. Among the antihypertensive agents are diuretics; (especially diuretics, thiazide); adrenergic aeta-antagonists; adrenergic alpha-antagonistics; angiotensin-converting enzyme inhibitors; calcium channel blockers; ganglionic blockers; and vasodilator agents.
This gene encodes a secreted high density lipoprotein which binds to apolipoprotein A-I. Variants in the APOL1 gene can influence susceptibility to end-stage renal disease and Trypanosomiasis (African Sleeping Sickness).
Exists in other ontologies but we have provided a description more relevant to its relationship with SCD.
Exercises performed in or underwater for conditioning or rehabilitation (e.g., in injured athletes or patients with joint diseases).
A hematology assay that measures the acidity (pH) and the levels of oxygen and carbon dioxide in the blood from an artery. This test is used to check how well the lungs are able to move oxygen into the blood and remove carbon dioxide from the blood.
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.
A water-soluble, semi-synthetic derivative of the sesquiterpene lactone artemisinin with anti-malarial, anti-schistosomiasis, antiviral, and potential anti-neoplastic activities.
The score obtained from the Adult Sickle Cell Quality-of-Life Measurement Information System (ASCQ-Me).
Is this term acceptable? If so, request inclusion into relevant ontology
Sickle Cell Disease Adult Quality of Life Questionnaire Assessment Score
A bioassay to measure levels of aspartate aminotransferase (AST), which is released into the blood following tissue damage.
Suggest update to PhenX label ("Aspartate Aminotransferase Level") also to NCIT label (from "Aspartate Aminotransferase Measurement")
The amount of aspartate aminotransferase present in a specified volume of blood.
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.
Suggest update to label in PhenX (from "Quality of Care")
PhenX protocol: Quality of Care - Adults #820101
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).
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
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.
Possibly too specifiic to this ontology to be included in another ontology? 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.
Diagnostic Technique, Method, Test or Assay
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.
Request inclusion into relevant ontology. Perhaps in the CPT.
Assessment of Short-Axis Cardiac Function by MRI
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.
Further work: is caused by links to be moved to object property links
Include a copy of this term below "Comorbid Disease" and/or below "Respiratory System".
It is characterized by spasmodic contraction of airway smooth muscle, wheezing and dyspnea.
A chronic inflammatory genetically determined disease of the skin marked by increased ability to form reagin (IgE), with increased susceptibility to allergic rhinitis and asthma, and hereditary disposition to a lowered threshold for pruritus. It is manifested by lichenification, excoriation, and crusting, mainly on the flexural surfaces of the elbow and knee. In infants it is known as infantile eczema.
This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. During hematopoietic cell differentiation, this gene is down-regulated. It is possibly involved in lymphoma pathogenesis since translocations associated with B-cell malignancies also deregulates its expression. Multiple transcript variants encoding several different isoforms have been found for this gene.
Link to "Hereditary Persistence of fetal hemoglobin".
B-cell CLL/lymphoma 11A (zinc finger protein)
BAF Chromatin Remodeling Complex Subunit BCL11A Gene
Fetal Hemoglobin Quantitative Trait Locus 5
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. 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. Bacteria can be classified by their response to oxygen: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or phototrophy (via light reaction); for chemotrophs by their source of chemical energy: chemolithotrophy (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for carbon; nitrogen; etc.; heterotrophy (from organic sources) or autotrophy (from carbon dioxide). They can also be classified by whether or not they stain (based on the structure of their cell walls) with crystal violet dye: gram-negative or gram-positive.
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.
Request inclusion into relevant ontology. Could be as a child of "Symptom Specific Assessment Tool" in the NCIT.
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.
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.
Behavior Rating Inventory of Executive Function
The actions or reactions of a person in response to a situation or stimuli.
Personal or collective understanding of what the causes (could be predisposing factors, enabling factors, precipitating factors, reinforcing factors, and/or risk factors) are of a certain illness.
Cultural beliefs, such as re-incarnation and witchcraft, may influence notions on causality of sickle cell disease.
Personal or collective understanding of what can remedy or treat illness.
Request inclusion into relevant ontology, perhaps MESH.
A beta-thalassemia caused by the reduced (beta-) synthesis of the beta globin chains of the hemoglobin (Hb) tetramer.
Request inclusion into relevant ontology, perhaps DOID.
A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed
A hemoglobinopathy 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.
Suggest update to description in DOID. Include a "Dominant Beta-Thalassemia" sub-class? (see Orphanet)
Origa R. Beta-Thalassemia. 2000 Sep 28 [Updated 2018 Jan 25]. In: Adam MP, Ardinger HH, Pagon RA, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle 1993-2018. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1426/
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.
A severe early-onset form of beta thalassemia characterized by severe anemia requiring regular red blood cell transfusions.
The inheritance of only one mutated beta-globin allele (beta+ or beta0).
Request inclusion into relevant ontology. Perhaps below "clinical subtype" in Orphanet. The exact synonym "B+/B" has been changed to "B-/B", as per the change in convention from "Beta Plus Thalassemia" to "Beta Minus Thalassemia".
Beta-zero thalassemia is a form of beta-thalassemia in which beta-globin chain synthesis is absent. The clinical phenotype is often that of transfusion-dependant beta thalassemia major, however modifying factors may ameliorate the symptoms of severe anemia (Cao & Gallanelo, 2010).
A globin locus composed of five genes located on a short 45 kb region of chromosome 11. The order of genes in this cluster is: 5' - epsilon - gamma-G - gamma-A - delta - beta - 3'. It is responsible for the creation of the beta parts (roughly half) of the oxygen transport protein Hemoglobin.
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.
A bioassay to measure levels of bilirubin, a yellow substance found in bile produced when the liver breaks down old red blood cells.
Suggest update to label in PhenX (from "Bilirubin Level").
An analytical in vitro procedure used to detect, quantify and/or study the binding or activity of a biological molecule, such as an enzyme.
A biological factor that modifies one or more aspects of a disease, such as sickle cell disease (SCD) (e.g. aspects such as temporal pattern, age of onset and mortality), for specific phenotype(s) of the disease.
The country in which the respondent was born.
The country in which the respondent's biological father was born.
The country in which the respondent's biological mother was born.
The country or countires in which the respondent's biological grandparents were born.
Request inclusion into relevant ontology There is a protocol in PhenX but it is US specific.
The country in which the respondent's biological maternal (on the mother's side of the family) grandfather was born.
The country in which the respondent's biological maternal (on the mother's side of the family) grandmother was born.
The country or countires in which the respondent's biological parents were born.
The country in which the respondent's biological paternal (on the father's side of the family) grandfather was born.
The country in which the respondent's biological paternal (on the father's side of the family) grandmother was born.
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.
Test used in the analysis of the hemic system.
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.
Test to determine the presence of blood infection (e.g. sepsis; bacteremia).
The introduction of whole blood or blood component directly into the blood stream. (Dorland, 27th ed)
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
The major and unavoidable complication of transfusions in sickle cell disease is iron overload. 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.
The distance from the sole to the crown of the head with body standing on a flat surface and fully extended.
The mass or quantity of heaviness of an individual. It is expressed by units of pounds or kilograms.
Add these terms from PhenX?: -- - Weight Loss/Gain
An abnormal hardening or increased density of bone tissue.
Segen's Medical Dictionary. S.v. "bone sclerosis." Retrieved April 30 2019 from https://medical-dictionary.thefreedictionary.com/bone+sclerosis
The bone is more radiopaque than normal on a plain film.
A noninvasive method to assess the endothelial dysfunction in the brachial artery.
Voltages between parts of the brain that are detectable with an electroencephalograph.
An episode of severe pain that occurs with rapid onset even when pain-control medication is being used. Breakthrough pain can occur spontaneously or in relation to a specific activity, and can last from a few seconds to a few hours.
Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
There are currently no data that clearly describe or can be used to define breakthrough pain in SCD.
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.
Request inclusion into NCIT below "Research or Clinical Assessment Tool".
Broadbent E, Petrie KJ, Main J, Weinman, J. (2006). The brief illness perception questionnaire. Journal of Psychosomatic Research, 60, 631-637.
Good psychometric properties, widely used, has been translated into several languages.
Brief Illness Perception Questionnaire (B-IPQ)
Brief RCOPE is a 14-item instrument that measures religious coping with major life stressors. 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.
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.
The improvement of forced expiratory volume in 1 second (FEV1) after inhalation of beta2-agonists and is typically measured as the change in airflow after the administration of short-acting beta2-adrenergic agonists (SABAs).
Suggest that the description be updated in PhenX (https://www.phenxtoolkit.org/protocols/view/90301)
Bauer S, Park HN, Seo HS, et al. Assessment of bronchodilator responsiveness following methacholine-induced bronchoconstriction in children with asthma. Allergy Asthma Immunol Res. 2011;3(4):245-50.
A test to assess an individual's change in pulmonary function in response to inhaled bronchodilator medications.
Suggest update to label in PhenX (from "Bronchodilator Responsiveness (BDR)") Can also suggest inclusion in MESH below "Respiratory Function Tests"
PhenX protocol: Bronchodilator Responsiveness (BDR) #90301
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)
An instrument which, by means of a cathode-ray oscillograph, projects an electrocardiographic record on a luminous screen.
'Anatomical system that has as its parts the heart and blood vessels. [Curator team: []]'
'Clinical presentations that may be followed by evaluative studies that eventually lead to a diagnosis. [Curator team: []]'
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.
A flexible, tubular device that is used to carry fluids into or from a blood vessel, hollow organ, or body cavity.
Add info (rdfs:comment) about how catheters are used in different therapeutics. -- -- Link relevant Therapeutics term(s) to this term via "has medical device".
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.
Suggest definition replaced in OAE. Currenlty it's shown as the definition editor.
A causal adverse drug event that is induced by a drug-drug interaction.
Causal Adverse Drug Event Due to Drug-Drug Interaction
A causal adverse drug event that is induced by a food-drug interaction.
Causal Adverse Drug Event Due to Food-Drug Interaction
A causal adverse drug event that is induced by genetic predisposition.
Causal Adverse Drug Event Due to Genetic Predisposition
A causal adverse drug event due to genetic predisposition that is specifically induced by SNP.
The determination of the amount of free hemoglobin present in a sample.
Suggest update to label in NCIT (from "Free Hemoglobin Measurement")
The level of hemoglobin external to erythrocytes in a biological specimen.
Request inclusion into relevant ontology If wanting to include "Plasma Hemoglobin Level" in the future, see CMO:0000588 for a description. synonyms: Plasma Free Hemoglobin (PFHb) Level, Plasma Hemoglobin Level.
Cerebral collateral circulation is a subsidiary vascular network which is dynamically recruited after arterial occlusion and may provide residual blood flow to ischemic areas.
The description doesn't actually describe the term. Needs revision. Perhaps: Blood flow through cerebral collateral circulation, a subsidiary vascular network which is dynamically recruited after arterial occlusion and which may provide residual blood flow to ischemic areas. Suggest inclusion into CMO, below "circulation measurement".
Cerebral collateral circulation in experimental ischemic stroke. Elisa Cuccione, Giada Padovano, Alessandro Versace, Carlo Ferrarese, Simone Beretta. Exp Transl Stroke Med. 2016; 8: 2. Published online 2016 Mar 1. doi: 10.1186/s13231-016-0015-0 PMCID: PMC4772465
A test of how well the cerebrum is functioning.
The movement and the forces involved in the movement of the blood through the blood vessels in the brain.
Request inclusion into relevant ontology. Perhaps replace with "cerebral blood flow measurement" from the EFO?
The analysis of a sample material, called an analyte, using a set of chemical procedures.
A medical imaging assessment of the chest wall, airways, lungs, pulmonary vessels, heart, mediastinum, and pleura.
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).
Healthy Children; Children with Medical Conditions
French, isiXhosa, isiZulu, Portuguese, Punjabi, Sesotho, Temil, Telugu, Gujarati
Demonstrated validity with SCD populations; at least two publications using the measure in SCD.
5 to 18 years (child report 10 - 18 years; parent report 5 - 18 years)
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.
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.
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.
A parent's highest level of education obtained, as reported by the child.
Request inclusion into MESH below "Current Educational Attainment" (also to be suggested), below "Socioeconomic Factors". Also suggest inclusion in the EFO, below measurement.
PhenX protocol: Child-Reported Parental Education Attainment #210201
Child-Reported Parental Education Attainment
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.
Check and show which source was used for the description and whether the description was adapted from the source.
Kovacs, M. (1985). The Children's Depression, Inventory (CDI). Psychopharmacology Bulletin, 21, 995-998.
Children's Depression Inventory 2 (CDI 2)
A measure that seeks to determine the extent to which 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.
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.
Deaux EB. Health Locus of Control in Chukotka children. Alaska Med. 1992 Jul-Sep; 34(3):135-9.
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.
English, Russian, a 9- item shorter Egyptian version
Has adequate reliability, construct validity and internal consistency.
Children's Health Locus of Control Scale
Children's Health Locus of Control Scale (CHLC)
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.
Used info in "Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014" to link to relevant phenotypes.
Chronic Complications of Sickle Cell Disease
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.
Suggest update to description in DO (currently no definition).
When assessed by albuminuria, often presents in second decade of life in sickle cell disease and prevalence increases with age.
CKD is classified using a combination of GFR and ACR categories
Sickle cell disease, hypertension, diabetes, polycystic kidney disease, glomerulonephritis, various other causes.
Reduced glomerular filtration, elevated creatinine, anemia, bone disease, uremia.
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.
Is a long-term condition where the kidneys don't work as well as they should.
Chronic pain caused by damage to nerve fibers. It is usually associated with tissue injury. 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.
This pain occurs in a specific tissue or organ and is usually described as constant and deep, nagging, and achy in nature.
Chronic Pain in a Specific Tissue or Organ
The only complaint is the patient's self-report of pain that does not go away.
Intractable Chronic Pain Without Obvious Pathology
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.
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.
The description does not seem complete as it does not address the "chronic" aspect. Request inclusion into relevant ontology 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?
Persistent pain in sickle cell disease. In sickle cell disease, persistent pain (pain that has lasted longer than 3 to 6 months) no longer serves as a warning sign. However, the time distinction is arbitrary and the condition may be difficult to distinguish from frequently recurring acute pain. Chronic pain may occur with objective signs of avascular necrosis, arthropathy, arthritis, leg ulcers or vertebral body collapse, or without objective signs, due to neuroplasticity of the peripheral nervous system.
Sickle cell pain management that aims to restore function and improve the quality of life.
An indication of a person's current cigarette use as well as some indication of cigarette smoking history.
Request inclusion below "smoking status" in Exposure Ontology
Meteorological conditions, including temperature, precipitation, and wind, that characteristically prevail in a particular region; includes regions of the earth having particular meteorological conditions.
Process of substituting a symbol or code for a term such as a diagnosis or procedure. (from Slee's Health Care Terms, 3d ed.)
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-)
The capability to perform acceptably those duties directly related to patient care.
'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. [Curator team: []]'
'A quick and accurate way of assessing the patient health states using well defined set of questions and analyzed for an optimal clinical decision for the patient. [Curator team: Gaston K. Mazandu]'
obsolete Clinical Diagnostic Questionnaire
A physician administered examination to assess peripheral neuropathy.
PhenX protocol: Neuropathy - Clinical Assessment #130201
Can be used to assess 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.
Abnormal clinical manifestations of beta thalassemia that are as a result of the underlying genotype.
Could this not rather be "Clinical Subtype of Beta Thalassemia"? See "clinical subtype" in Orphanet.
'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. [Curator team: []]'
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.
Term to be adapted as necessary to match EDDA Study Designs Taxonomy
'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. [Curator team: []]'
'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. [Curator team: []]'
'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. [Curator team: []]'
'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. [Curator team: []]'
'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. [Curator team: []]'
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.
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.
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.
A profound state of unconsciousness associated with depressed cerebral activity from which the individual cannot be aroused. Coma generally occurs when there is dysfunction or injury involving both cerebral hemispheres or the brain stem reticular formation.
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 may indicate infection. Anatomic causes of coma are diagnosed from CT (computed tomography) or MRI (magnetic resonance imaging) scans.
A co-existing or additional disease with reference to an initial diagnosis or with reference to the index condition that is the subject of study.
Request inclusion into relevant ontology 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
Comparison of outcomes, results, responses, etc for different techniques, therapeutic approaches or other inputs.
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).
'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. [Curator team: []]'
obsolete Compound Heterozygous Hemoglobinopathy
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.
'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. [Curator team: []]'
obsolete Consensus Development Conference
'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. [Curator team: []]'
obsolete Consensus Development Conference, NIH
A tool for collecting standardized information on enrollees' experiences with health plans and their services.
PhenX protocol: Quality of Care - Children #820102
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).
Children and adolescents, ages 17 and younger
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.
Consumer Assessment of Healthcare Providers and Systems (CAHPS) Health Plan Survey 4.0 Child Medicaid Questionnaire
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.
'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. [Curator team: []]'
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.
A state of harmony between internal needs and external demands and the processes used in achieving this condition.
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.
Abrams M.R., Phillips G. and Keefe F.J. (1989). Sickle cell disease pain: Relation of coping strategies
Demonstrated validity with SCD populations USA and UK; several publications.
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.
Coping Strategies Questionnaire revised for Sickle Cell Disease
Coping Strategies Questionnaire revised for Sickle Cell Disease (CSQ-SCD)
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.
Coping Strategies Questionnaire revised for Sickle Cell Disease Children (CSQ-SCD Children)
A causal adverse drug event that is induced by a corticosteroid.
Request inclusion into OAE below "Causal Adverse Drug Event".
A corticosteroid-induced adverse event that has the outcome of vaso-occlusion.
Request inclusion into OAE below "Corticosteroid-Induced Adverse Event" (also suggested by us for inclusion).
Corticosteroid-Induced Vaso-Occlusive Adverse Event
The personal cost of disease which may be economic, social, or psychological. 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, the societal cost of providing services related to the delivery of health care.
The extent to which a health intervention can be regarded as providing value for money, based on a cost-effectiveness analysis that compares the costs and health effects of the intervention. This informs decision-makers who have to determine where to allocate limited healthcare resources.
Request inclusion into relevant ontology, possibly into MESH, perhaps in an appropriate place below "Quality of Health Care".
A bioassay to measure the serum concentration of creatinine, a metabolite of muscle creatine that is filtered out of blood by the kidneys.
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)
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.
A collective expression for all behaviour patterns acquired and socially transmitted through symbols. Culture includes customs, traditions, and language.
Therapeutics relating to or used in the cure of diseases.
The length of time that a person has lived since their birth up until the current day.
Few but available definitions not adequate
The respondent's highest level of education at the current time.
Request inclusion into MESH below "Socioeconomic Factors".
The respondent's current employment status.
PhenX protocol: Current Employment Status #11301
The respondent's current marital status.
Can add sub-classes of "Marital Status" from MESH.
PhenX protocol: Current Marital Status #10902
The amount of the protein cystatin C (formerly gamma trace, post-gamma-globulin or neuroendocrine basic polypeptide) found in a specified sample of blood. This extracellular cystatin subtype is abundantly expressed in bodily fluids.
This class is used as a biomarker of kidney function and kidney disease.
A blood disorder characterized by the appearance of sickle-shaped red blood cells and anemia.
Broad term used to describe several different acute conditions occurring with sickle cell disease, including aplastic crisis, hemolytic crisis, and vasoocclusive crisis.
Sickle cell anemia with vasoocclusive pain
Sickle cell anemia with acute chest syndrome
Sickle cell anemia, acute chest syndrome
D57.01 Hb-SS disease with acute chest syndrome
Acute sickle cell splenic sequestration crisis
Hb-SS disease with splenic sequestration
Sickle cell anemia acute crisis splenic sequestration
D57.02 Hb-SS disease with splenic sequestration
D57.1 Sickle-cell disease without crisis
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.
D57.20 Sickle-cell/Hb-C disease without crisis
D57.21 Sickle-cell/Hb-C disease with crisis
Acute chest syndrome due to sickle cell-hemoglobin c disease crisis
Acute chest syndrome sickle cell hb-c crisis
Sickle Cell Disease-SC with acute chest syndrome
Sickle-cell/Hb-C disease with acute chest syndrome
D57.211 Sickle-cell/Hb-C disease with acute chest syndrome
Sickle Cell Disease-SC with splenic sequestration
Sickle-cell/Hb-C disease with splenic sequestration
D57.212 Sickle-cell/Hb-C disease with splenic sequestration
Sickle Cell Disease-SC with crisis, unspecified
Sickle Cell Disease-SC with vasoocclusive pain NOS
Sickle cell-hemoglobin c disease with crisis
Sickle-cell/Hb-C disease with crisis NOS
Sickle-cell/Hb-C disease with crisis, unspecified
Sickle-cell/Hb-C disease with vasoocclusive pain NOS
D57.219 Sickle-cell/Hb-C disease with crisis, unspecified
The condition of being heterozygous for hemoglobin S.
Hemolytic anemia, in which patients are heterozygous for both the sickle cell gene and a thalassemia gene.
D57.40 Sickle-cell thalassemia without crisis
Sickle-cell thalassemia with (painful) crisis
Sickle-cell thalassemia with vasoocclusive pain
D57.41 Sickle-cell thalassemia, unspecified, with crisis
Sickle-cell thalassemia, unspecified, with acute chest syndrome
D57.411 Sickle-cell thalassemia, unspecified, with acute chest syndrome
Sickle cell thalassemia with splenic sequestration
Sickle-cell thalassemia, unspecified, with splenic sequestration
D57.412 Sickle-cell thalassemia, unspecified, with splenic sequestration
Sickle-cell thalassemia with (painful) crisis NOS
Sickle-cell thalassemia with vasoocclusive pain NOS
Sickle-cell thalassemia, unspecified, with crisis
D57.419 Sickle-cell thalassemia, unspecified, with crisis
D57.80 Other sickle-cell disorders without crisis
D57.81 Other sickle-cell disorders with crisis
D57.811 Other sickle-cell disorders with acute chest syndrome
D57.812 Other sickle-cell disorders with splenic sequestration
D57.819 Other sickle-cell disorders with crisis, unspecified
'Protein molecule are large, complex molecules that play many critical roles in the body. They do most of the work in cells and are required for the structure, function, and regulation of the body's tissues and organs. [Curator team: []]'
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.
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.
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.
'The system pertaining to teeth, oral cavity, and associated structures. [Curator team: []]'
Terms that are no longer being used in the ontology.
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.
Skill in performing tasks, especially with the hands.
A medical device used to diagnose medical conditions.
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.
A non-steroidal anti-inflammatory agent (NSAID) with antipyretic and analgesic actions. It is primarily available as the sodium salt.
2-((2,6-dichlorophenyl)amino)benzeneacetic acid
[2-(2,6-dichloroanilino)phenyl]acetic acid
Concepts involved with nutritional physiology, including categories of substances eaten for sustenance, nutritional phenomena and processes, eating patterns and habits, and measurable nutritional parameters.
Should this term rather be replaced by more specific terms such as Dietary Intake? Or have such terms as sub-classes?
obsolete Diffusion Capacity by Biochemical Methods
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.
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.
Suggest update to label in PhenX (from "Lung Function - Diffusion Capacity") Need to add equipment used for this test under "Devices" and link to them below.
PhenX protocol: Lung Function - Diffusion Capacity #810301
One DALY can be thought of as one lost year of "healthy" life. The sum of these DALYs across the population, or the burden of disease, can be thought of as a measurement of the gap between current health status and an ideal health situation where the entire population lives to an advanced age, free of disease and disability.
WHO Global Burden of Disease assessment, also used in SCD studies
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.
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.
A factor that modifies one or more aspects of a disease, such as sickle cell disease (SCD) (e.g. aspects such as temporal pattern, age of onset and mortality), for specific phenotype(s) of the disease.
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.
A diagnostic ultrasound-based imaging technique operating at the frequency range of 2 megahertz. This machine makes use of the doppler effect to measure and visualise blood flow for possible pathology or lesions within blood vessels.
Doppler Ultrasound Machine - 2 Megahertz
An adverse event that has an outcome of a decreased amount of the drug excreted by the body.
An adverse drug event that results in the development of a dependence on the drug.
The amount of drug substances taken into the body.
This seemed an obvious addition to the modifier class?
A drug AE that has an outcome of lower threshold to the normal pharmacologic action of a drug.
An adverse event that results in symptoms that occur after the discontinuation of the use of a certain drug.
A neuropathy AE that is induced by a drug administration.
'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. [Curator team: []]'
A small hemorrhagic spot, larger than a petechia, in the skin or mucous membrane forming a nonelevated, rounded or irregular, blue or purplish patch.
Suggest update to description. The term in the HPO was not detailed enough.
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.
A machine used for ultrasonic recording of the size, motion, and composition of the heart and surrounding tissues.
Acquisition of knowledge as a result of instruction in a formal course of study.
The visual output that an electrocardiograph produces.
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.
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.
Request that MESH removes ECG, EKG and Elecrocardiogram as synonyms.
A graphic record of the electrical activity of the brain as recorded by an electroencephalograph.
An instrument that measures electrical potentials on the scalp and generates a record of the electrical activity of the brain.
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.
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.
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.
Perhaps change label to "Hemoglobin Electrophoresis"? Exactsynonym "Hb ELP". See dc:source provided.
The system pertaining to the stomach, intestines, and associated organs including liver, gallbladder, and pancreas.
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.
Request inclusion into relevant ontology Perhaps include MESH term "Life Change Events" as a main sub-class, with "Disaster" (under Physical Environment) copied below it?
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. Many classical enzymatic assay methods involve the use of synthetic colorimetric substrates and measuring the reaction rates using a spectrophotometer.
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.
Types and formulations of studies used in epidemiological and clinical research.
deprecated Epidemiologic Study Characteristics as Topic
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).
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.
Add the different versions of this questionnaire, as listed in the description here.
Goldberg, David; Hillier, Valerie (1979). "A scaled version of the General Health Questionnaire". Psychological Medicine. Cambridge University Press. 9 (01): 139–145.
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.
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.
Generalised Anxiety Disorder Questionnaire
Generalised Anxiety Disorder Questionnaire (GAD-7)
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.
A biological disease modifier that is of a genetic nature.
Organized services to provide diagnosis, treatment, and prevention of genetic disorders.
Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.
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).
Request inclusion into relevant ontology as more specific type (sub-class) of glaucoma.
Glaucoma (Secondary to Presence of Blood in the Anterior Chamber of the Eye)
A test to assess the respondent's overall mental capability.
A genetic locus responsible for the encoding of globins.
Request inclusion into relevant ontology, perhaps below "Genetic Locus" in MESH.
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.
This gene encodes glucose-6-phosphate dehydrogenase. This protein is a cytosolic enzyme encoded by a housekeeping X-linked gene whose main function is to produce NADPH, a key electron donor in the defense against oxidizing agents and in reductive biosynthetic reactions. G6PD is remarkable for its genetic diversity. Many variants of G6PD, mostly produced from missense mutations, have been described with wide ranging levels of enzyme activity and associated clinical symptoms. G6PD deficiency may cause neonatal jaundice, acute hemolysis, or severe chronic non-spherocytic hemolytic anemia. Two transcript variants encoding different isoforms have been found for this gene.
Glucose-6-Phosphate 1-Dehydrogenase Gene
A deficiency or slowing down of growth pre- and postnatally greater than two standard deviations from the age- and sex-related normal.
A bioassay to measure haptoglobin, which is produced by the liver and transports hemoglobin to the liver for recycling.
Suggest update to label in PhenX (from "Haptoglobin Level").
Individual lifestyle and behavior which may or may not enhance or maintain good health.
Suggest the NCIT updates their description for this term to include negative /risk inreasing behaviour? Include: -- gaining better control of your diabetes -- lowering cholesterol -- lowering blood pressure -- maintaining a healthy body weight -- eating a balanced diet -- Include these from MESH: -- Treatment Refusal -- Vaccination Refusal
People's beliefs about health problems, perceived benefits of action and barriers to action, and self-efficacy.
The health belief model suggests that health beliefs explain engagement (or lack of engagement) in health-promoting behaviour.
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.
Whether the respondent is covered by health insurance or some other form of health care coverage at the time of the interview.
Suggest inclusion into MESH. The phenX term is actually referring to a protocol for collecting data on Health Insurance Coverage. The protocol is somewhat U.S. specific. Should probably be modified to be more relevant to the African setting.
PhenX protocol: Health Insurance Coverage #11502
Also applicable to a population not just to an individual.
Degree to which individuals have the capacity to obtain, process and understand basic health information and services needed to make appropriate health decisions.
Health data accessible to the patient and others.
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.
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.
Suggest update to description in Medline Plus Health Topics
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.
The ease with which an individual can obtain needed medical services.
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
The WHO Constitution envisages "...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.
Dietary patterns which have been found to be important in reducing disease risk.
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.
Examinations used to diagnose and treat heart conditions.
The number of times the heart ventricles contract per unit of time, usually per minute.
Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart valves.
Request inclusion into relevant ontology. Perhaps below "Heart Measurement" in the CMO. Can add sub-classes as per the measurements given in the Diagnostic Criteria below the Protocol section in PhenX for "Heart Valve Function". Sub-classes that are also morphological measurements can be included below "Body Morphological Measurement"
A measurement device used to perform complete blood counts, erythrocyte sedimentation rates (ESRs), or coagulation tests.
A test to detect potential blood disorders or diseases in people who do not have any symptoms of disease.
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.
The blood-making organs and tissues, principally the bone marrow and lymph nodes.
This gene encodes the enzyme, heme oxygenase 1, an essential enzyme in heme catabolism and cellular homeostasis.
Suggest update to description in NCIT (for "HMOX1 Gene")
Organs involved in the production of BLOOD, including the cellular and the molecular components essential in providing defense against foreign organisms or substances.
A commonly occurring abnormal hemoglobin in which lysine replaces a glutamic acid residue at the sixth position of the beta chains. It results in reduced plasticity of erythrocytes.
An abnormal hemoglobin resulting from the substitution of valine for glutamic acid at position 6 of the beta chain of the globin moiety. The heterozygous state results in sickle cell trait, the homozygous in sickle cell anemia.
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.
An abnormal hemoglobin, composed of four gamma globin chains, causing it to have an extremely high affinity for oxygen, resulting in almost no oxygen delivery to the tissues.
Additional info from the definition in HPO: "Hb Barts (Hemoglobin Barts) 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."
Suggest update to description in HP as we have done.
The most severe form of alpha-thalassemia and is almost always lethal, and characterized by fetal onset of generalized edema, pleural and pericardial effusions, and severe hypochromic anemia. It is caused by the presence of Hemoglobin Barts, a hemoglobin with four gamma chains, which has an extremely high affinity for oxygen, resulting in almost no oxygen delivery to the tissues
Suggest update to description in ORDO as we have done.
Hemoglobin Barts Hydrops Fetalis Syndrome
An autosomal recessive disorder resulting from the production of hemoglobin C, secondary to an amino acid substitution of lysine for glutamic acid in the sixth position of the beta chain (E6K), and characterized by mild hemolytic anemia and occasionally jaundice, though most patients are asymptomatic.
The inheritance of the gene for hemoglobin C from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent.
Request inclusion into NCIT below "Hemoglobin Trait".
'A form of beta-thalassemia with a phenotype of mild to moderate hemolytic anemia. Patients are often asymptomatic but if present symptoms include anemia and enlarged spleen.'
deprecated Hemoglobin C-Beta Thalassemia
A test to measure the presence and amount of a variant of hemoglobin in the blood.
Many terms below "Hemoglobin Variant Test" in SNOMED CT could be added.
Suggest update to label and description in NCIT (from "Hemoglobin Variant Measurement" and "A test to measure the variants of hemoglobin.") It is not clear whether this term was is in fact a synonym of "Hemoglobin Profile Assay". We assumed it wasn't. If it actually is, we need to address the ambiguity caused.
An autosomal recessive hemoglobinopathy characterized by production of abnormal variant hemoglobin known as hemoglobin D, with no or mild clinical manifestations (splenomegaly, very mild anemia).
The inheritance of the gene for hemoglobin D from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent.
'Hemoglobin D/xcexb2xc2xb0 thalassemia is a form of beta-thalassemia which results in a mild to moderate clinical picture. The severity of the condition depends on the degree of thalassemia and how it affects production of Hemoglobin A, however this condition is often considered fairly benign.'
deprecated Hemoglobin D-Beta Thalassemia
An unusual hemoglobin that shows all the electrophoretic features of Hb D, but has no inherited disability. This hemoglobin has a beta 87 Thr > Lys mutation.
Request inclusion into NCIT below "Hemoglobin"/"Hemoglobin Variant"/"Unusual Hemoglobin".
An abnormal hemoglobin (one of the types of hemoglobin D) in which glutamine replaces glutamic acid at codon 121 of beta globin.
Request inclusion in the HPO, below "Abnormal Hemoglobin"/"Hemoglobin D".
A disease caused by atypical hemoglobins molecules other than hemoglobin C,D,E, F, H, O-Arab and S.
adapted from description under ID SCDO:0001065
deprecated Hemoglobin Disease Other than C,D,E,F,H,O-Arab,S
An autosomal recessive haemoglobinopathy characterized by an abnormal form of haemoglobin called haemoglobin E, which disrupts the oxygen-carrying ability of red blood cells. The condition can lead to mild or moderate hemolytic anemia; however, this condition often has no clinical manifestations. with a generally benign, asymptomatic presentation.
The inheritance of the gene for hemoglobin E from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent.
Hb E-carriers generally do not have any signs or symptoms related to abnormal hemoglobin.
'Hemoglobin E/xcexb2+ thalassemia is a form of beta-thalassemia that is often, but not always, milder than hemoglobin E/xcexb2xc2xb0 thalassemia. This condition shows a marked clinically diverse picture whereby abnormalities of xcexb2-globin chain synthesis result almost asymptomatic anemia to more severe transfusion-dependant anemia (Vichinsky, 2007).'
deprecated Hemoglobin E-Beta Thalassemia
The score of fetal hemoglobin (Hb F) in the blood of an individual.
A variant of Hemoglobin Lepore Syndrome.
A variant of Hemoglobin Lepore Syndrome. Crossover occurs between glutamine at position 87 of delta chain and histidine at position 116 of beta chain. It is associated with unusual high levels of Hb F. This is the only one of the three variants of described in association with HbS.
Hemoglobin Lepore Washington-Boston Syndrome
The inheritance of the gene for hemoglobin Lepore from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent.
'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. [Curator team: []]'
Add HBD to Disease Modifiers (below Gene Product)? And link to it.
Hemoglobin Lepore-Beta Thalassaemia Syndrome
deprecated Hemoglobin Lepore-Beta Thalassaemia
A type of dominant hereditary methemoglobinemia resulting from the production of hemoglobin M, which is readily oxidised to yield excess methemoglobin which leads to cyanosis.
Autosomal Dominant Congenital Methemoglobinemia Type II
Autosomal Dominant Hereditary Methemoglobinemia Type II
Hemoglobin M Disease is autosomal dominant, thus does not seem to have a "trait" condition.
A very rare autosomal recessive hemoglobinopathy characterized by an abnormal form of hemoglobin called hemoglobin O-Arab. It is associated with a mild to moderate anemia.
The inheritance of hemoglobin O-Arab from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent.
The type and relative amounts of various normal and abnormal hemoglobin types.
A bioassay that measures and identifies the different types of hemoglobin in the bloodstream. It can be used to identify and characterize the different variants in structure and synthesis of hemoglobin that cause sickle cell disease.
PhenX protocol: Hemoglobin Characterization #830301
Hemoglobin Electrophoresis plus Solubility
Hemoglobinopathy Evaluation Profile Blood Test
Hemoglobinopathy Fractionation Profile Blood Test
A test to quantify the presence of hemoglobin S in the blood and therefore determine whether a person has sickle cell trait or sickle cell disease.
In SNOMED CT this term is "Sickle cell identification". Request inclusion into relevant ontology.
The inheritance of one of the faulty genes that causes thalassemia.
An inherited disorder of the structure and/or synthesis of hemoglobin, with a variable phenotype expression ranging from benign to severe.
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.
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.
The description needs to be reviewed by an expert. Request inclusion into Clinical Measurement Ontology, below "liver size measurement".
Which Hepatitis B Test is to be referred to here? (There are various different types below "Immunology Test" in the "Sage Bionetworks Synapse Ontology")
Is this test for viral load measurement or or antibody measurement? (See terms below "Immunology Test" in the "Sage Bionetworks Synapse Ontology")
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).
A study that compares a group of participants receiving an intervention with a similar group from the past who did not.
A questionnaire to determine whether an individual has had a traumatic brain injury (TBI).
Suggest update to label as we have done. We are using "History of Head Trauma" below Personal Attribute.
PhenX protocol: History of Head Trauma #130601
History of Head Trauma Diagnostic Instrument
A questionnaire to determine if the respondent has a history of kidney failure.
Link to? -- Kidney Failure -- Personal Attribute---> Personal medical history --> History of Kidney Failure
Suggest update to label as we have done. We are using "History of Kidney Failure" below Personal Attribute.
PhenX protocol: Personal History of Kidney Failure #140601
History of Kidney Failure Diagnostic Instrument
A questionnaire to determine if the respondent has had an ischemic infarction (i.e. stroke) and/or any symptoms related to this event.
Suggest update to label as we have done. We are using "History of Stroke" below Personal Attribute.
PhenX protocol: History of Stroke - Ischemic Infarction and Hemorrhage #130301
History of Stroke - Ischemic Infarction and Hemorrhage - Questionnaire
History of Stroke - Ischemic Infarction and Hemorrhage - Diagnostic Instrument
A questionnaire to determine a respondent's history of type 1 or type 2 diabetes.
Link to? -- Personal Attribute---> Personal medical history --> History of Type I and Type 2 Diabetes
Suggest update to label as we have done. We are using "History of Type I and Type 2 Diabetes" below Personal Attribute.
PhenX protocol: Personal History of Type 1 and Type 2 Diabetes #140501
History of Type I and Type 2 Diabetes Diagnostic Instrument
A bioassay to measure human immunodeficiency virus (HIV) antibodies and/or HIV antigens in order to determine whether an individual has an HIV infection.
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 are obtained by adding up the ratings of the items on each subscale. A score above 8 in any of the subscales indicates that the patient has experienced clinically significant anxiety or depression over the past week.
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
Widely used around the world, also used in SCD
Hospital Anxiety and Depression Scale Questionnaire
Hospital Anxiety and Depression Scale Questionnaire (HADS)
Hospital Anxiety and Depression Scale (HADS)
The confinement of a patient in a hospital.
Perhaps "Hospital Utilization" would be better here?
A record of those living in the respondent's household and about his or her relationship with them.
Request inclusion into MESH below "Social Conditions"?
PhenX protocol: Household Roster-Relationships #11402
A unique treatment that administers electrolyte-packed IV fluids directly into a patient's bloodstream. Depending on the patient's needs, the fluid may be enhanced with additives such as calcium, magnesium sulfate or a Vitamin B complex. It is a far more efficient method of absorption when compared to the traditional method of drinking liquids/electrolytes.
Suggest update to description in NCIT (currently no description)
An antineoplastic agent that inhibits DNA synthesis through the inhibition of ribonucleoside diphosphate reductase.
A causal adverse drug event that is induced by hydroxyurea.
A hydroxyurea-induced adverse event that has an outcome relating to or affecting the skin.
Request inclusion into OAE below "Hydroxyurea-Induced Adverse Event" (also suggested by us for inclusion). Or Obsolete and use an object property (has adverse events) to link Hydroxyea to Cutaneous.
Hydroxyurea-Induced Cutaneous Adverse Event
A hydroxyurea-induced adverse event that has the outcome of splenomegaly.
Request inclusion into OAE below "Hydroxyurea-Induced Adverse Event" (also suggested by us for inclusion). Or Delete and use an object property (has adverse events) to link Hydroxyea to Splenomegaly.
Hydroxyurea-Induced Splenomegaly Adverse Event
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).
Excessive pigmentation of the skin, usually as a result of increased epidermal or dermal melanin pigmentation, hypermelanosis. Hyperpigmentation can be localized or generalized. The condition may arise from exposure to light, chemicals or other substances, or from a primary metabolic imbalance.
Drugs used to induce drowsiness or sleep or to reduce psychological excitement or anxiety.
The ICD-10-CM diagnosis classification system developed by the Centers for Disease Control and Prevention for use in all U.S. health care treatment settings. Diagnosis coding under this system uses a different number of digits and some other changes, but the format is very much the same as ICD-9-CM. The National Center for Health Statistics (NCHS), the Federal agency responsible for use of the International Statistical Classification of Diseases and Related Health Problems, 10th revision (ICD-10) in the United States, has developed a clinical modification of the classification for morbidity purposes. The ICD-10 is used to code and classify mortality data from death certificates, having replaced ICD-9 for this purpose as of January 1, 1999. ICD-10-CM is the replacement for ICD-9-CM, volumes 1 and 2, effective October 1, 2015.
Request inclusion into relevant ontology, perhaps below "Clinical Coding" in MESH.
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.
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.
Good psychometric properties, widely used around the world, has been translated into several languages.
Illness Perception Questionnaire Revised
Illness Perception Questionnaire Revised (IPQ-R)
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.
An assay that identifies a substance (especially a protein) by its action as an antigen.
A drug adverse event that has an outcome of decreased levels of immunosuppressant drugs in the patient's body.
Immunosuppressant Drug Level Decreased AE
An assay that employs 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.
Request inclusion into relevant ontology. NCIT contains "Immunoturbidimetry", but not "Immunoturbidimetry Assay". Do we rather want to have this term as "Immunoturbidimetry"?
Substances causing insects to turn away from them or reject them as food.
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).
Suggest update to description in NCIT (we're not using their description, but their description says "from one to twenty-four months of age")
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.
PhenX protocol: Intelligence Scale - Birth to 3.5 years #820504
Bayley Scales of Infant and Toddler Development, Third Edition
Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III)
An adverse drug event that results in the intentional use of a drug in the wrong way (recreationally etc).
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.
Intracerebral hemorrhage (ICH) is when blood suddenly bursts into brain tissue, causing damage to the brain.
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.
CSF pressure less than 6 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.
Suggest update to description in DOID (currently no description)
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.
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.
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.
The hydrostatic pressure of venous blood in the marrow of bones.
Term should be requested for inclusion into the "Ontology of Biological Attributes", perhaps in an appropriate location under "organ system trait". Or perhaps below "bone measurement" or "bone marrow measurement" in the CMO?
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.
Should this be under "Abnormal Cardiovascular System Morphology" or ""Abnormal Cardiovascular System Physiology"?
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.
Perhaps change label to "Hemoglobin Isoeletcric Focusing"? Exactsynonym "Hb IEF". See dc:source provided.
Laboratory tests used to evaluate how well the kidneys are working through examination of blood and urine.
A specialized area of medicine in which exercise and movement are used as the primary form of rehabilitation.
Collections of facts, assumptions, beliefs and practices that health professionals hold about the aetiology, pathophysiology, quality management of SCD and related social support systems based on global standards.
Probably too specific to SCD to be included in other ontologies.
The level of lactate dehydrogenase, an enzyme released during tissue damage and injury, found in a specified biological specimen.
Request inclusion into relevant ontology Should this term's name be changed to "L-Lactate Dehydrogenase Level"?
Normal and abnormal ranges given here: https://www.healthline.com/health/lactate-dehydrogenase-test#results
A bioassay to measure levels of lactate dehydrogenase, an enzyme released during tissue damage and injury.
Suggest update to label in PhenX (from "Lactate Dehydrogenase Level").
Ulceration of the skin and underlying structures of the lower extremity. About 90% of the cases are due to venous insufficiency (varicose ulcer), 5% to arterial disease, and the remaining 5% to other causes.
Typical way of life or manner of living characteristic of an individual or group. (From APA, Thesaurus of Psychological Index Terms, 8th ed).
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)
Any process carried out to determine the condition of a patient's liver.
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.
Studies in which variables relating to an individual or group of individuals are assessed over a period of time.
A sampling methodology using small sample sizes when conducting surveys in small geographical or population-based areas or lots.
Measurement of the amount of air that the lungs may contain at various points in the respiratory cycle.
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 or sub-classes of "Lung Volume Measurements" in MESH.
Clinical assessment to determine the volume of gas within an individual's lung.
Suggest update to label in PhenX (from "Lung Function - Lung Volume") 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). SNOMED has more terms below "Lung Volume Test" Link to necessary medical device.
PhenX protocol: Protocol - Lung Function - Lung Volume #810401
'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. [Curator team: []]'
The use of drugs or other agents to prevent malarial infection. Examples: Proguanil, mefloquine, artesunate, insect repellant, insecticide-treated-bednet.
An instrument that is used for measuring the pressure of liquids and gases.
Request inclusion into "Eagle-I Research Resource Ontology", below the "instrument" term. Perhaps the specific manometer used for measuring "Intraosseous Pressure" should be added as a sub-class and linked to directly.
The American Heritage Science Dictionary. Retrieved October 20, 2016 from Dictionary.com website
The current marital status of the respondent's caregiver (i.e. family member or another individual who takes primary responsibility for the respondent).
Request inclusion into MESH below "Family Characteristics".
PhenX protocol: Marital Status of Primary Caregiver #840101
A questionnaire to capture the frequency of acute pain episodes within a defined time frame due to sickle cell disease (SCD). It includes three self-administered questions from the Cooperative Study of Sickle Cell Disease (CSSCD) that capture number of painful episodes that required visits to the emergency room or hospital or interfered with daily activities.
Suggest update to label in PhenX as we have done here because we have used "Frequency of Sickle Cell Pain Episodes Per Year" for the Diagnostic Instrument Measurement.
PhenX protocol: Frequency of Sickle Cell Pain Episodes Per Year #830101
Measure of Frequency of Sickle Cell Pain Episodes
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.
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
The weight of the participant in kilograms.
An information entity used in the diagnosis of medical conditions. It could be the recording of the output of a diagnostic device or the outcome of a diagnostic tool.
The MOS Social Support Survey is a self-administered questionnaire 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.
Suggest update to description in NCIT for "Medical Outcomes Study Social Support Survey".
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.
Medical Outcomes Study Social Support Survey
Medical Outcomes Study (MOS) Social Support Survey
Recording of pertinent information concerning patient's illness or illnesses.
Voluntary cooperation of the patient in taking drugs or medicine as prescribed. This includes timing, dosage, and frequency.
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.
Request inclusion into relevant ontology Would it also be appropriate to add this to "Diagnostic Instrument" below "Diagnostics"?
PhenX protocol: Medication Inventory #140301
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)
A phospholipid-interacting antimalarial drug (antimalarials). It is very effective against plasmodium falciparum with very few side effects.
A type of glomerulonephropathy characterized by histology with thickening of the basement membrane and deposition of immune complexes in the subepithelial space.
Typically seen in adult population; rare in children.
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.
Nephrotic syndrome with histologic features specific to membranous nephropathy.
Emotional, psychological, and social well-being of an individual or group.
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.
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.
Request inclusion into relevant ontology. Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? (from SNOMED CT)
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)
'Any procedure or test to diagnose a disease or disorder. [Curator team: []]'
Perhaps move other sibling classes below this class? (Imaging Test/Diagnostic Imaging, -- -- Include sub-class "Biopsy" and include specific types below that?
A questionnaire to assess migraines and headaches.
Suggest update to label in PhenX (from "Migraine") as we have done.
Transportable radiographic equipment allowing imaging services to be brought to the patient.
Difficulty moving from place to place or from one position to another without assistance.
The biological processes, properties, and objects that are involved in maintaining, expressing, and transmitting from one organism to another, genetically encoded traits.
obsolete Modifying the Home Environment and Making it Safer For the Patient
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.
'A work that reports on a study executed by several cooperating institutions. [Curator team: []]'
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.
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.
Healthy population and patients with specific medical conditions
Has adequate construct validity and acceptable metric properties
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.
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.
Multidimensional Health Locus of Control Scales
Multidimensional Health Locus of Control Scales (MHLC)
The presence of skeletal muscular atrophy, reduction in the muscle bulk.
Suggest update to description in HPO. Provide source for additional info.
Anatomical system that consists of the muscular and skeletal systems.
The process of identifying carriers/heterozygotes of a genetic mutation that can result in a severe recessive condition. Carrier screening is done using various laboratory techniques.
Request inclusion into relevant ontology (MESH) or suggest inclusion of description in NCIT.
Alswaidi, F.M. and O'brien, S.J., 2009. Premarital screening programmes for haemoglobinopathies, HIV and hepatitis viruses: review and factors affecting their success. Journal of medical screening, 16(1), pp.22-28.
This term is very similar to but different (more specific) from the term "Genetic Carrier Screening" in MESH.
This gene encodes a protein with three HTH DNA-binding domains that functions as a transcription regulator. This protein plays an essential role in the regulation of hematopoiesis. This gene may be aberrently expressed or rearranged or undergo translocation in leukemias and lymphomas, and is considered to be an oncogene. Alternative splicing results in multiple transcript variants.
MYB Proto-Oncogene, Transcription Factor
A bioassay to determine an individual's level of N-terminal pro-brain natriuretic peptide (NT-proBNP).
Label different from source's "N-terminal Pro-brain Natriuretic Peptide (NT-proBNP)"
Equipment needed: Phlebotomy supplies, centrifuge for serum separation, and freezer for sample storage is required.
N-terminal Pro-brain Natriuretic Peptide Test
A specific opiate antagonist that has no agonist activity. It is a competitive antagonist at mu, delta, and kappa opioid receptors.
Are the synonyms included relevant to SCD? Should other synonyms from the description source be included?
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)
'A subspecialty of internal medicine concerned with the anatomy, physiology, and pathology of the kidney. [Curator team: []]'
Nephrotic syndrome is a collection of findings resulting from glomerular dysfunction with an increase in glomerular capillary wall permeability associated with pronounced 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.
Suggest update to description in the HPO
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.
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.
Heavy proteinuria, edema, hyperlipidemia. May also be associated with hypertension and increased risk of venous thrombosis.
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.
In sickle cell disease, seen primarily in adult population but may develop in childhood if secondary cause occurs.
Glomerular diseases that lead to protein loss in the urine (See Nephrotic Syndrome).
Is diagnosed by assessment of proteinuria (see Proteinuria) by 24hr urine collection or by urine protein-creatinine ratio on spot urine sample [KDIGO 2012].
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.
An invisible complication of sickle cell anemia (SSA) 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.
Physician-supervised programs designed to rehabilitate people with diseases, trauma, or disorders of the nervous system.
Testing of neonates to identify those with major sickling diseases.
Link to "Hb isoelectric focusing" and "HPLC fractionation" ? Request inclusion into relevant ontology. Perhaps in SNOMED CT below "Screening for sickle cell disease"?
Newborn Screening for Sickle Cell Disease and Other Hemoglobinopathies. JAMA. 1987;258(9):1205–1209. doi:10.1001/jama.1987.03400090089040
Newborn Infant Screening for Sickle Cell
A physical assessment of the various symptoms associated with a stroke, consisting of 11 categories. For each category, 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.
PhenX protocol: NIH Stroke Scale (NIHSS) #820801
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.
Patients who do not turn up for scheduled healthcare appointments.
Frequent urination at night that interrupts sleep. It is often associated with outflow obstruction, diabetes mellitus, or bladder inflammation (cystitis).
Often occuring as a result of heart insufficiency.
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.
A gene that does not encode a globin family protein.
Perhaps too specific to the SCDO to be included in other ontologies?
Sickle retinopathy caused by direct damage or remodeling of the small blood vessels supplying the retina secondary to vaso-occlusion and local ischemia.
Request inclusion into HPO below "Retinopathy/Sickle Retinopathy".
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.
Request inclusion into relevant ontology Provide source for additional info.
Several possible etiologies including infections by various classes of microorganisms, pulmonary fat emobolism, infarction and pulmonary embolism.
Acute onset of respiratory symptoms and signs including cough, coryza +/- fever.
Non-specific Acute Lower Respiratory Tract Episode
'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). [Curator team: []]'
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).
Skilled treatment that helps individuals achieve independence in all facets of their lives. It assists in the development of skills needed for independent living.
Low output of urine, defined as an output below 5mL/kg/hr over 6 hours.
Surgery performed on the eye or any of its parts.
Device for examining the interior of the eye, permitting the clear visualization of the structures of the eye at any depth.
Examination of the interior of the eye with an ophthalmoscope.
Include "Direct Ophthalmoscopy" and "Indirect Ophthalmoscopy" from NCIT as sub-classes? (Direct could be used to diagnose "Conjunctival Comma Sign")
A general term for bone weakness owing to a defect in mineralization of the protein framework known as osteoid. This defective mineralization is mainly caused by lack in vitamin D. Osteomalacia in children is known as rickets.
Suggest update to description in HPO. (remove "Osteomalacia" from start of definitiion) Provide source for additional info.
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.
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.
An inflammatory process accompanied by bone destruction and caused by an infecting microorganism.
Suggest update to description in HPO (remove "Osteomyelitis is" from the start of the definition. Provide source for additional info.
Bacteria, blunt trauma, fracture, bone surgery.
Tenderness, redness, and warmth in the area of infection, fever, fatigue, bone pain, swelling around the affected bone, lost range of motion.
Osteomyelitis can be acute or chronic and can be caused by a variety of microbial agents.
The amount of oxygen bound to hemoglobin in arterial blood expressed as a percentage of the maximal binding capacity, as determined by an arterial blood gas test.
Request inclusion into CMO below "Oxygen Saturation"
Oxyhemoglobin to Total Hemoglobin Ratio Measurement
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.
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.
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.
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.
A method of determining the shape and consistency of the liver by feeling with the fingers or hands.
Invertebrate organisms that live on or in another organism (the host), and benefit at the expense of the other. Traditionally excluded from definition of parasites are pathogenic bacteria; fungi; viruses; and plants; though they may live parasitically.
Voluntary cooperation of the patient in following a prescribed regimen.
A headache disability questionnaire which 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). It 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.
Suggest update to label in PhenX (from "Migraine - Children") as we have done.
PhenX protocol: Migraine - Children #130502
Pediatric Migraine Disability Assessment
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.
PhenX protocol: Pediatric NIH Stroke Scale (PedNIHSS) #820802
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.
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.
A questionnaire to assess educational performance and learning accommodations.
Suggest update to label in PhenX as we have done.
PhenX protocol: Pediatric School Performance #840201
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.
A generic symptom-specific instrument to measure fatigue across pediatric populations.
Request inclusion into NCIT below "Pediatric Quality of Life Inventory".
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
Children 2 - 18 (child report ages 5 - 18 years; parent proxy report of children ages 2 - 18 years)
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.
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.
PhenX protocol: PedsQL Sickle Cell Disease Module #820202
No. The PedsQ Sickle Cell Disease Module is a proprietary instrument and administration requires permission and a license from the MAPI Research Trust.
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.
Use of penicillin for the prevention of infections with penicillin-susceptible organisms, e.g. Streptococcus pneumoniae.
A method of determining the size of the liver by tapping on the surface of the abdomen.
To be requested for inclusion into SNOMED CT, below "Diagnostic procedure on liver".
An estimation of the oxygen saturation level usually measured with a pulse oximeter device.
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.
Probably too specific to warrant inclusion into anther ontology. Make sure complications as described in "Definitions of the Phenotypic Manifestations of Sickle Cell Disease" (Ballas, 2010) are included in Phenotype.
The physical method (technology) used to measure / readout the effect caused by a perturbagen in the assay environment.
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.
Physical Environment. Merriam-Webster.com. Merriam-Webster, n.d. Web. 9 Nov. 2016.
Systematic and thorough inspection of the patient for physical signs of disease or abnormality.
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.
Determine and specify the description source. -- -- Include a term to do with level of independence?
An organismal assay designed to capture information pertaining to the organic processes and phenomena of an organism or any of its parts or of a particular bodily process.
A therapeutic intervention that remediates impairments and promotes mobility, function, and quality of life through examination, diagnosis, and physical intervention.
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.
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.
The process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As the process 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.
'Works about randomized clinical trials that compare interventions in clinical settings and which look at a range of effectiveness outcomes and impacts. [Curator team: []]'
Prenatal detection of a fetus affected with Sickle Cell Disease using appropriate laboratory techniques. Detection of affected fetuses allows couples to make informed decisions regarding the pregnancy.
Request inclusion into relevant ontology. Perhaps in SNOMED CT below "Screening for sickle cell disease".
Activities to prevent Sickle Cell Disease or its complications.
Probably too specific to SCD to be included in other ontologies. Consider making the description more generic (e.g. "Activities to prevent a disease or its complications.")
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.
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.
This term is not below Quality of Health Care in MESH, but below "Health Services Administration" ---> "Patient Care Management" ---> "Comprehensive Health Care
A biguanide compound which metabolizes in the body to form cycloguanil, an anti-malaria agent. Cycloguanil stops 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.
N-(4-Chlorophenyl)-n'-(isopropyl)-imidodicarbonimidic diamide
Sickle retinopathy that involves the upregulation of vascular growth factors due to chronic changes of local hypoxia and ischemia.
Retinopathy due to SCD Characterized by Neovascularization
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.
PhenX protocol: Quality of Life - Adult #221302
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.
PhenX protocol: Quality of Life - Pediatric #221301
A planned process that has the objective to reduce the risk of acquiring one or more infections.
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.
Increased amounts of any protein (including albumin) in the urine - typically more than 300mg in a 24hr period.
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]).
At most severe form - lead to nephrotic syndrome.
Caused by a variety of kidney diseases, including sickle cell disease, diabetes, glomerular disease, arteriosclerosis.
Elevated amounts of protein in the urine - typically greater than 300mg in 24 hrs.
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.
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.
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.
Demonstrated validity with SCD populations in the US
Provider Attitudes Toward Patients with Sickle Cell Disease
Pruritus, or itch, is defined as an unpleasant sensation that provokes the desire to scratch.
Suggest update to description. The current description seems to be describing two different things in the same description.
Stress wherein emotional factors predominate.
The absence of appropriate stimuli in the physical or social environment which are necessary for the emotional, social, and intellectual development of the individual.
This term is placed below "Culture" in MESH.
A generic term for the treatment of mental illness or emotional disturbances primarily by verbal or nonverbal communication.
'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. [Curator team: []]'
Measurement of the various processes involved in the act of respiration: inspiration, expiration, oxygen and carbon dioxide exchange, lung volume and compliance, etc.
An elevation of mean pulmonary arterial systolic pressure (mPASP) (>20 mmHg at rest or >30 mmHg with exercise). The 6th World Symposium on PH reduced it from >25mmHg to >20mmHg for at rest, but did not adjust the definition for PH with exercise.
Simonneau et al 2013 J Am Coll Cardiol; Ataga et al.
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.
Increased Blood Pressure in Blood Vessels of Lungs
Pulmonary hypertension can be secondary to known cardiac, pulmonary, or hepatic disease. If no cause is identifiable, the term primary pulmonary hypertension is used.
A measurement device, usually attached to the earlobe or fingertip, that measures the oxygen saturation of arterial blood.
This consists of 2 parts, the "pulse oximeter monitor" and the "pulse oximeter probe". Perhaps can be included as sub-classes or siblings? See "Pulse Oximetry (Rest)" in PhenX.
The application of pulse oximetry to measure a patient's saturation of oxyhemoglobin when the patient is at rest.
Suggest update to description in PhenX Suggest inclusion of term below "Pulse Oximetry" in the CMO.
PhenX protocol: Pulse Oximetry (Rest) #91102
The systemic measurement of the quality of health care that includes a broad set of perfomance measures such as the quality of services and the outcomes analysis for particular diseases and conditions, mortality and morbidity, patient safety, data on maternal and child health, as well as evaluation of quality of diagnosis, care accessibility, implementation of proven evidence-based practices, quality of reporting systems for errors and adverse events, reliability and accessibility of health and health care-related information, and health care organizations infrastructure.
Suggest update to description in EDDA (replace "excessability" with "accessibility".
The levels of excellence which characterize the health service or health care provided based on accepted standards of quality.
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.
Request inclusion into relevant ontology. Include the term "Transition from pediatric care" somewhere...see the source provided here.
A measurement tool that is useful in aiding routine clinical practice with regard to quality of life and/or quality of care.
Quality of Life and Care Measurement Scales
A questionnaire to assess the physical, emotional, and social impact of chronic conditions, such as sickle cell disease (SCD).
Quality of Life in Sickle Cell Disease Measure
A measurement tool with eight potential uses in aiding routine clinical practice. It can be used to prioritise problems, facilitate communication, screen for potential problems, identify preferences, monitor changes or response to treatment, and train new staff. It can also be used in clinical audit and in clinical governance. The first five of these can be used in the clinical encounter, while the last three contribute to training, reviewing care, and improving care in the future.
Sickle cell symptoms where there is evidence of some relation with quality of life.
Probably too specific to be included in other ontologies.
Quality of Life Related SCD Symptoms and Complications
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.
Standard global assessment of health interventions, also used in SCD studies
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 x 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.
'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. [Curator team: []]'
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).
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.
'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. [Curator team: []]'
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.
Request inclusion into NCIT below "Research or Clinical Assessment Tool". Add these annotation properties: -- has cross-cultural adaptation -- freely available -- has translations
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.
Rapid Estimate of Adolescent Literacy in Medicine
Rapid Estimate of Adolescent Literacy in Medicine (REALM-Teen)
A questionnaire that assesses recovery and recurrence of stroke in children. It is completed by a parent about their child.
PhenX protocol: Recovery and Recurrence Questionnaire (RRQ) - Pediatrics #820702
Recovery and Recurrence Questionnaire (RRQ) - Pediatrics
Recovery and Recurrence Questionnaire (RRQ)
Recurrent episodes of wheezing in persons with SCD who have no co-morbid asthma.
Other markers of severity of SCD- eg complications of SCD, high LDH.
The amount of red blood cell derived microparticles in a specific volume of blood.
Request inclusion into relevant ontology More info can be taken from the dc:source provided. Perhaps add MeSH term "Cell-Derived Microparticles" as a superclass of this term?
Erythrocyte-Derived Microparticles Level
Red Blood Cell Derived Microparticles Level
Hemoglobin A (HbA) contains two alpha-globin chains and two beta-globin chains. HbA is normally the main adult hemoglobin, representing about 96-98 percent of all hemoglobin. This term represents a decrease in the proportion of HbA below this limit, and can be seen in various forms of thalassemia.
Restoration of human functions to the maximum degree possible in a person or persons suffering from disease or injury.
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.
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.
Therapy for the insufficient cleansing of the BLOOD by the kidneys based on dialysis and including hemodialysis, peritoneal dialysis, and hemodiafiltration.
Include types of renal dialysis as sub-classes: -- Peritoneal dialysis -- Hemodialysis -- Pediatric dialysis? -- Hemofiltration -- Hemodiafiltration
Inadequate blood flow to one or both kidneys, or nephrons, usually due to functional constriction or actual obstruction of blood vessels.
Suggest update to description in Mammalian Phenotype ontology. Provide source for additional info.
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.
Usually associated with kidney injury as noted by decrease in urine output and/or elevation in serum creatinine.
The transference of a kidney from one human or animal to another.
Acidosis owing to malfunction of the kidney tubules with accumulation of metabolic acids and hyperchloremia.
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.
Defects in the kidneys in reabsorption of bicarbonate (HCO3), the excretion of hydrogen ions (H+), or both.
A relatively normal GFR and a metabolic acidosis accompanied by hyperchloremia and a normal plasma anion gap.
Accumulation of Acid in Body Due to Kidney Problem
A questionnaire to assess either male or females' pregnancy history. Females are asked about the number of pregnancies, description of pregnancies and smoking during pregnancy. Males are asked whether they have ever fathered a pregnancy and, if so, the description of the pregnancy.
Suggest update to labels of as we have done. We are using "Reproductive History" below Personal Attribute. Also suggest update to description as we have done.
Reproductive History Diagnostic Instrument
'Anatomical system that has as its parts the organs concerned with reproduction. [Curator team: []]'
'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 team: []]'
Consider other sub-classes of this in NCIT.
The number of times an organism breathes with the lungs (respiration) per unit time, usually per minute.
Lungs and respiratory system of the body.
Root of all terms in the Sickle Cell Disease Ontology, an effort of unambiguously describing all concepts and unifying up-to-date knowledge in sickle cell disease.
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.
Henrik Berg Rasmussen (April 4th 2012). Restriction Fragment Length Polymorphism Analysis of PCR-Amplified Fragments (PCR-RFLP) and Gel Electrophoresis - Valuable Tool for Genotyping and Genetic Fingerprinting, Gel Electrophoresis Sameh Magdeldin, IntechOpen, DOI: 10.5772/37724. Available from: https://www.intechopen.com/books/gel-electrophoresis-principles-and-basics/restriction-fragment-length-polymorphism-analysis-of-pcr-amplified-fragments-pcr-rflp-and-related-te
Restriction Fragment Length Polymorphism - Polymerase Chain Reaction
Restriction Fragment Length Polymorphism PCR
The number of reticulocytes per unit volume of blood. The values are expressed as a percentage of the erythrocyte count or in the form of an index ("corrected reticulocyte index"), which attempts to account for the number of circulating erythrocytes.
PhenX protocol: Reticulocyte Count #810601
A reticulocyte count that was performed with an electronic haematology analyzer.
Reticulocyte Count by Hematology Analyzer
A reticulocyte count that was performed with microscopy.
A procedure that uses intense cold to induce a chorioretinal scar and to destroy retinal or choroidal tissue.
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.
We provided a more SCD specific description than the generic descriptions provided in existing ontologies.
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.
An open swath of land that has few homes or other buildings, and not very many people.
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.
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.
Pain resulting from the presence of Sickle Cell Disease (SCD). Such pain can be acute, chronic or a mixture of the two.
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
An operation for retinal detachment which reduces the size of the globe by indenting the sclera so that it approximates the retina.
Specialized healthcare delivered as a follow-up or referral from a primary care provider.
Usual level of physical activity that is less than 30 minutes of moderate-intensity activity on most days of the week.
Caring for self when ill or positive actions and adopting behaviors to prevent illness.
Cognitive mechanism based on expectations or beliefs about one's ability to perform actions necessary to produce a given effect.
The weight in kilograms or pounds as reported by the participant.
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.
The amount of the HDL cholesterol, the small lipoprotein:cholesterol complex that transports cholesterol out of the arteries and to the liver for reprocessing or excretion, in a specified volume of serum.
Blood High Density Lipoprotein Cholesterol Amount
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.
Add these annotation properties: -- has cross-cultural adaptation -- freely available -- has translations
Suggest update to label in PhenX (from "Physical, Social, and Mental Health Functioning (SF-36V2)")
Demonstrated validity with SCD populations; multiple publications using the measure in SCD; very widely used with healthy populations and those with chronic conditions
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.
Request inclusion into NCIT below "Research or Clinical Assessment Tool". Add these annotation properties: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations
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.
Sickle Cell Disease Health-Related Stigma Scale
Sickle Cell Disease Health-Related Stigma Scale (SCD-HRSS)
The SCPBI-Y is a brief clinical interview designed to assess pain burden for children and adolescents with SCD.
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.
Sickle Cell Disease Pain Burden Interview - Youth
Sickle cell tests are used to help diagnose sickle cell anemia (also called sickle cell disease) and to identify those who may have sickle cell trait. Sickle cell anemia is an inherited disorder that leads to the production of an abnormal hemoglobin called hemoglobin S (Hb S or Hgb S). Sickle cell tests determine the presence and relative amount of hemoglobin S in a blood sample.
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.
PhenX protocol: Self-efficacy in Sickle Cell Disease #820401
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).
Scale of Self-efficacy in Sickle Cell Disease
A variant form of sickle cell disease that results from inheriting the sickle mutation in combination with another beta-globin gene mutation. These hemoglobinopathies may have different clinical severity compared to the homozygous form of sickle cell disease (HbSS).
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.
Request inclusion into MESH below "Pain Management".
Pain lasting at least two hours that requires an unscheduled emergency room visit or hospitalization or that disrupts daily activities.
Could be categorised as a phenotype "Finding".
A cancer that is almost exclusively associated with sickle cell trait and/or sickle cell disease.
A mild form of sickle cell thalassemia characterized by the presence of hemoglobin S and a reduced amount of hemoglobin A in the red blood cells. It is characterized by the presence of small red blood cells and mild anemia.
Suggest update to label in NCIT from "Sickle Beta Plus Thalassemia" to "Sickle Beta Minus Thalassemia"
Sickle Cell Disease-S Beta Minus Thalassemia
A rare compound heterozygous hemoglobinopathy characterised by the presence of two beta globin gene variants: that of hemoglobin S (beta-6(GAG-->GTG)) and that of hemoglobin D-Punjab (beta-121(GAA-->CAA)).
Request inclusion into relevant ontology. Perhaps as sub-class of "Sickle Cell-Hemoglobin D Disease" in the NCIT.
Rahimah Ahmad*, Syahira Lazira Omar*, Siti Hida H M Arif*, Faidatul Syazlin A Hamid*, Nur Aisyah Aziz*, Nik Hafidzah N Mustapha**, Zubaidah Zakaria*Haemoglobin Sickle D Punjab: - A Case Report. Med J Malaysia. 2014. Vol 69 No 1.
A variant of sickle cell disease due to heterozygosity for hemoglobin S and hemoglobin E mutations, which can cause mild hemolytic anemia.
Suggest update to description of "Sickle Cell-Hemoglobin D Disease" in the NCIT.
Sickle cell-Hb Lepore Boston syndrome is a type of sickle cell disease 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 Hb Lepore variants described in association with HbS.
Sickle Cell-Hemoglobin Lepore Boston Syndrome
Hb Lepore Washington, also known as Hb Lepore Boston or Hb Lepore Washington-Boston; most common in Italians from Southern Italy.
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.
'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. [Curator team: []]'
obsolete Sickle Cell-Hemoglobin Other than A,C,D,E,O-Arab
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.
Request inclusion into HPO below "Retinopathy". Use the scielo source to add info on diagnosis and treatment.
A qualitative screening test for sickling haemoglobins, especially HbS. In the SCT, sodium metabisulfite or sodium dithionate is used to desolubilise haemoglobin S to the crystallised deoxygenated form, which causes the abnormal RBCs to sickle, as detected by light microscopy.
In SNOMED CT this term seems to be both "Sickle cell identification, slide method" and "Sickling Test". Request they merge these terms?
Segen's Medical Dictionary. © 2012 Farlex, Inc.
Sickle Cell Identification, Slide Method
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.
Too specific to SCD to be included in other ontologies. 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
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.
'The bodily system consisting of the skin and its associated structures, such as the hair, nails, sweat glands, and sebaceous glands. [Curator team: []]'
integumentary system. (n.d.) The American Heritage Medical Dictionary. (2007). Retrieved December 14 2016
An abnormal change in skin color, appearance, or texture.
An intrinsic sleep disorder characterized by breathing abnormalities.
An interviewer-administered questionnaire which captures routine sleep schedule, sleep deprivation, morningness-eveningness, insomnia, narcolepsy, cataplexy and associated distress.
Suggest update to label in PhenX (from "Suggest update to label") as we have done.
PhenX protocol: Sleep Disorders Screener #121001
National Institute of Mental Health (NIMH) Sleep Patterns and Problems Instrument
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.
Inhaling and exhaling the smoke of burning tobacco (Cigar, Cigarette, Hookah, Pipe, Smoking, Waterpipe).
The aggregate of social and cultural institutions, forms, patterns, and processes that influence the life of an individual or community.
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.
Request inclusion into relevant ontology Include terms for social relationships; social activities?
Compr Psychiatry. 2000 Jan-Feb;41(1):63-9. Assessment of social functioning in depression.
PROMIS Domain Frameworks/Definitions nih.promis.org
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.
A role that is ascribed to individuals in a community.
An extent/ degree to which an individual fulfills the expectations of his/her social role.
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.
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.
Abstract standards or empirical variables in social life which are believed to be important and/or desirable.
Social and economic factors that characterize the individual or group within the social structure.
Maybe include some sub-classes of this term in MESH? There would be overlap with terms in QOL, so would need to work around that.
The combination of one's social class and income level. Includes socioeconomic differences between individuals or groups.
A basic first line test that looks for the presence of abnormal Hemoglobin S in a blood sample. Sodium metabisulfite is added to the blood sample which causes Hb S polymerisation and sickling of red blood cells if Hb S is present. A positive result means that a person has either Sickle Cell Disease or Sickle Cell Trait. Confirmatory tests are needed to distinguish which form of SCD the patient has.
In SNOMED CT this term is "Hemoglobin S Solubility Test" Commonly used tests include hemoglobin electrophoresis, isoelectric focusing (IEF), high performance liquid chromatography (HPLC), and DNA analysis.
Instruments for measuring arterial blood pressure consisting of an inflatable cuff, inflating bulb, and a gauge showing the blood pressure.
Sensitivity or attachment to religious values, or to things of the spirit as opposed to material or worldly interests.
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.
A form of nephrotic syndrome that does not respond to treatment with steroid medication after 8 weeks, specifically in children.
Suggest update to description in HPO Provide source for additional info.
May represent underlying focal segmental glomerulosclerosis, minimal change disease, or other underlying cause. Can be subseqeunt to known mutations.
Persistence of nephrotic syndrome despite appropriate treatment with corticosteroids.
A perceived attribute that is deeply discrediting and is considered to be a violation of social norms.
An oversimplified perception or conception, especially or persons, social groups, etc.
A group of pathological conditions characterized by sudden loss of neurological function due to brain ischemia or intracranial hemorrhages. 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.
Types of stroke relevant to SCD to be added as children of this class.
This measure is a physical assessment to determine neurological deficits due to a stroke.
This measure is used to describe the consequences of a stroke and to monitor the effects of treatment and recovery.
This questionnaire includes 59 proxy- or self-report items in 8 domains that assess multidimensional stroke outcomes in adults.
PhenX protocol: Stroke Impact Scale (SIS) - Adults #820701
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.
Include below "Cerebral Flow Test"? -- Include below "Vascular Endothelial Function Test"?
Stroke Risk Test in Children with Sickle Cell Disease
The occurrence of multiple self-limited episodes of unwanted, often painful erections lasting <4 hours.
Request inclusion into relevant ontology, perhaps below "Priapism" in MESH.
Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014
Assessment with the goal to obtain a relevant drug and alcohol history and perform a physical examination in order to establish whether there is a diagnosis of a substance use disorder.
If substance use disorder diagnosed, the patient’s readiness to change should be categorized and information from the assessment should be used to formulate a management plan based on the individual’s needs.
An indication of whether the respondent has ever used a drug during his or her entire life.
Frequent thinking about or preoccupation with killing oneself.
Suggest update to description in HPO (correct typo in "oneself")
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.
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.
A computerized test for the assessment of visual attention problems in individuals ages 8 years old and older.
PhenX protocol: Sustained and Selective Attention #821201
Conners Continuous Performance Test 3rd Edition
Conners Continuous Performance Test 3rd Edition (Conners CPT 3)
Sustained and Selective Attention Diagnostic Instrument
Therapeutics that ease the symptoms without addressing the basic cause of the disease.
Refers to a worsening, over a short period of time, of the symptoms and signs of SCD; usually associated with pain and/or shortage of blood (anaemia). Can be suspected in a person with sickle cell disease who presents with a sudden onset of pain, infection, anemia or other symptoms such as stroke or priapism. Acute pain frequently occurs spontaneously, but may be precipitated by infections, skin cooling, dehydration or stress.
This is a difficult one to describe, as I think it can also be referred to as an 'acute painful crisis' (this is not clear from the literature). Have tried to merge descriptions from different sources - please review.
Rees, D. C., Olujohungbe, A. D., Parker, N. E., Stephens, A. D., Telfer, P. and Wright, J. (2003), Guidelines for the management of the acute painful crisis in sickle cell disease. British Journal of Haematology, 120: 744-752. doi:10.1046/j.1365-2141.2003.04193.x
'Affecting a number of tissues relating to the entire organism as distinguished from and of its individual parts. [Curator team: []]'
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.
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).
Request inclusion into NCIT below "Research or Clinical Assessment Tool". Still must add these annotation properties: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available
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.
Test of Functional Health Literacy in Adults
Test of Functional Health Literacy in Adults (TOFHLA)
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).
Request inclusion into NCIT below "Research or Clinical Assessment Tool". Also requires these properties: -- has cross-cultural adaptation -- has translations
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.
A medical device used to prevent and treat medical conditions, or to alleviate pain or injury.
The washing of a body cavity or surface by flowing water or solution for therapy or diagnosis.
Procedures, agents or devices concerned with the remedial treatment or prevention of diseases.
Chemotherapy to be added in this class? If so, would have to be specific types of chemotherapy relevant to the type of therapeutics class.
Include as subclasses: -- Prosthesis -- Phototherapy (therapy for Jaundice) -- Risk Reduction? Copy relevant disease modifiers below this.
A mutation named with the blend of insertion and deletion. It refers to a length difference between two alleles where it is unknowable if the difference was originally caused by a sequence insertion or by a sequence deletion. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a frameshift mutation.
Ending the tobacco habits of smoking, chewing, or snuff use.
A person who practices the art of healing using traditional medicine, a system 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.
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.
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.
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.
Percutaneous Electrical Nerve Stimulation
Percutaneous Electrical Neuromodulations
Transcutaneous Electrical Nerve Stimulation
Temporary loss of vision in one eye due to a lack of blood flow to the retina.
Request inclusion into HP below "Blindness".
'Work consisting of reporting using a method of detecting genetic causes in human traits and genetic factors in behavior using sets of twins. [Curator team: []]'
Works about methods of detecting genetic etiology in human traits. The basic premise of twin studies is that monozygotic twins carry identical genes, while zygotic twins are genetically no more similar than two siblings born after separate pregnancies. (Last, J.M., A Dictionary of Epidemiology, 2d ed)
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. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The preferred substrate of this enzyme is bilirubin, although it also has moderate activity with simple phenols, flavones, and C18 steroids. Mutations in this gene result in Crigler-Najjar syndromes types I and II and in Gilbert syndrome.
UDP Glucuronosyltransferase Family 1 Member A1
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.
A bioassay to measure urine concentration of albumin, which is produced by the liver and is the most abundant protein in the blood.
Label different from source's "Urinary Microalbumin - Assay"
PhenX protocol: Urinary Microalbumin Assay #141501
In the protocol provided, albumin concentration is measured according to a fluorescent immunoassay (FIA). The protocol also lists reference ranges for healthy adults. 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. 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.
A bioassay to measure urine concentration of creatinine, a muscle metabolite that is filtered out of blood by the kidneys.
PhenX protocol: Urinary Creatinine - Assay #141601
Any measurement of protein present in urine.
Suggest update to description (currently no description provided).
The organs and passageways concerned with the production and excretion of urine, including the kidneys, ureters, urinary bladder, and urethra.
The amount of albumin in a specified volume of urine.
Suggest that the CMO removes the second part of the definition and puts as comment, as we have done. Also suggest the change to this second part.
Urine albumin levels which are above normal but not detectable with routine protein testing are referred to as low level albuminuria (the old term is microalbuminuria). Because albuminuria may be affected by non-pathological factors (exercise, menstruation contamination, biological variability, etc.), abnormal values should be confirmed within 1-2 months.
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 low level albuminuria (the old term is microalbuminuria).
A 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 the amount of creatinine in a specified volume of urine. Often expressed as albumin concentration divided by creatinine concentration times 1000 mg per gram.
Suggest update to description as we have done.
Albumin To Creatinine Protein Ratio Measurement
Urine Albumin Level to Urine Creatinine Level Ratio
The concentration of creatinine in a urine specimen.
Request inclusion below "urine creatinine measurement" in the CMO.
Urine Creatinine Concentration Measurement Datum
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.
Urine Turbidimetry with Sulfosalicylic Acid
Urine Protein Sulfosalicylic Acid Precipitation Test
The medical specialty concerned with the study, diagnosis, and treatment of diseases of the genitourinary tract.
Works consisting of research using processes by which the reliability and relevance of a procedure for a specific purpose are established.
Smoking vapors produced from electronic nicotene delivery systems.
A measure of vascular endothelial cell response to stimulation, for example, by vasoactive substances released by or those that interact with the vascular endothelium.
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.
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.
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).
PhenX protocol: Adaptive Behavior/Adaptive Function #820601
This measure can be used to identify individuals with developmental disabilities or delays, perform diagnostic evaluations, monitor progress, and develop programs.
Vineland Adaptive Behavior Scales, Second Edition (Vineland-II)
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.
Add sub-classes: Hepatitis C Virus (term in NCIT) Hepatitis B Virus (term not found in other ontologies)
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.
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.
Can this term also be below "Immunological Assay"?
An acute onset of wheezing in a person with SCD and co-morbid asthma.
Glassberg, Jeffrey A., Robert Strunk, and Michael R. DeBaun. “Wheezing in Children with Sickle Cell Disease.” Current opinion in pediatrics 26.1 (2014): 9–18. PMC. Web. 2 Aug. 2017.
Synergistic inflammatory response due to both SCD and asthma.
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).
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.
Request inclusion into NCIT below "Research or Clinical Assessment Tool". Still must add these annotation properties: -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations
Demonstrated validity with SCD populations; at least two publications using the measure
WHOQOL Group (1993). Measuring quality of life: The development of the World Health Organisation quality of life instrument (WHOQOL). Geneva: WHO.
World Health Organisation Quality of Life Instrument
World Health Organisation Quality of Life Instrument (WHOQOL)
The visual output that an X-ray machine produces.
The visual output that an X-ray machine produces when imaging the chest.
Medical treatment involving the use of controlled amounts of X-Rays.
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.
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).
The EuroQol Group. EuroQol-a new facility for the measurement of health-related quality of life. Health Policy. 1990; 16(3):199-208.
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.
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.
EuroQol Five Dimension Self-Report Questionnaire
European Quality of Life Five Dimension Five Level Scale Questionnaire
EuroQol Five Dimensions Questionnaire (EQ-5D)
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.
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.
Functional Assessment of Chronic Illness Therapy-Spirituality Scale
Functional Assessment of Chronic Illness Therapy-Spirituality (FACIT-Sp) Scale
The application of modern theories of learning and conditioning in the treatment of behavior disorders.
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.
Hb-SS disease with vasoocclusive pain NOS
Hemoglobin S sickling disorder with crisis
D57.00 Hb-SS disease with crisis, unspecified
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.
The transfer of erythrocytes from a donor to a recipient or reinfusion to the donor.
Works consisting of studies determining the effectiveness or utility of processes, personnel, and equipment.
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.
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.
The organ of vision that consists of the eyeball and the optic nerve.
Facial paralysis is loss of facial movement because of nerve damage.
Is this not the same thing as "Facial Nerve Palsy"?
Inability to function due to tiredness related to sickle cell disease.
Use the literature cited here to link to other phenotypes.
Studies to determine the advantages or disadvantages, practicability, or capability of accomplishing a projected plan, study, or project.
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.
Were these specific synonyms selected form the long list in the description source because of specific relevance to SCD?
A bioassay to measure the serum concentration of ferritin (i.e., iron).
Suggest update to label in PhenX (from "Serum or Plasma Ferritin")
The amount of ferritin found in a specified volume of serum.
Suggest update to description and label of "ferritin measurement" in the EFO.
Blood Serum Ferritin Concentration Measurement Datum
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.
Not sure whether this can be classified as a "Medical Device".
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.
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.
A rare neurologic movement disorder characterized by sustained muscle contractions of a single body region, usually producing twisting and repetitive movements or abnormal postures or positions.
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.
L-Glutamic acid, N-(4-(((2-amino-1,4-dihydro-4-oxo-6-pteridinyl)methyl)amino)benzoyl)-
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.
An observable characteristic of disease that is persistent and long standing.
Terms deprecated in the "Phenotype" class.
A questionnaire to measure the health status of individuals who had a stroke.
Functionality After Stroke Diagnostic Instrument
'The system concerned with the function and disorders of the gastrointestinal tract, including stomach, intestines, and associated organs including liver, pancreas and gall bladder. [Curator team: []]'
Combined effects of genotypes and environmental factors together to affect phenotypic characteristics.
Deviation(s) in the nucleotide sequence of the genetic material of an individual from that typical of the group to which the individual belongs, or deviation(s) in the nucleotide sequence of the genetic material of offspring from that of its parents.
'To be defined by an expert [Curator team: []]'
This gene provides instructions for making a protein called alpha-globin, which is involved in oxygen transport. This protein is also produced from a nearly identical gene called HBA2.
This gene provides instructions for making a protein called alpha-globin, which is involved in oxygen transport. This protein is also produced from a nearly identical gene called HBA1.
Gamma Globin is a type of polypeptide chain that when in combination with alpha globin chains forms fetal hemoglobin. Beta-Hemoglobin subunits gamma-1 (147 aa, ~16 kDa) and gamma-2 (147 aa, ~16 kDa) are encoded by the human HBG1 and HBG2 gene respectively, in the beta-globin gene cluster. These proteins play a role in the transport of oxygen to tissues of the fetal body.
A reduction in the ratio of production of alpha globin to that of gamma globin.
Request inclusion into the HPO below "Imbalanced Hemoglobin Synthesis".
The state, in utero or shortly after birth, in which all four alpha globin genes are deleted or inactivated resulting in absent alpha globin synthesis. If gamma globin synthesis persists, then the resulting phenotype is hemoglobin Barts (four gamma chains) and hemoglobin Bart hydrops fetalis.
Request inclusion into HPO below "Reduced Alpha/Gamma Synthesis Ratio" (also requested for inclusion).
Marengo-Rowe, A.J., 2007, January. The thalassemias and related disorders. In Baylor university medical center proceedings (Vol. 20, No. 1, pp. 27-31). Taylor & Francis.
Absence of Alpha Globin Synthesis with Gamma Globin Synthesis
A deletion in or of the HBA1 or HBA2 gene that can result in some form of alpha thalassemia.
Still need to add one sub-class: the complete deletion of the HBA1 and HBA2 genes on one chromosome 16, combined with a defect (deletional or nondeletional) in either the HBA1 or HBA2 gene on the other chromosome 16, leaving one functioning gene present (https://www.snpedia.com/index.php/Alpha_Thalassemia)
Deletion of all four alpha-globin genes resulting in the most severe form of alpha thalassemia, Hemoglobin Barts Hydrops Fetalis.
Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt genetic translation of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.
The administration of oxygen to an individual. It is of paramount importance in the peri-operative care of SCD patients as hypoxaemia predisposes to sickling.
Renal medullary carcinoma is a rare, aggressive subtype of renal cell carcinoma characterized by a large, white or tan, firm, infiltrative tumor with microabscess-like foci centered in the renal medulla, typically presenting with hematuria, abdominal/flank pain, weight loss and fever. It is associated with sickle cell trait and disease and metastasis to the bones and lungs is common at time of diagnosis.
Shetty A, Matrana MR. Renal medullary carcinoma: a case report and brief review of the literature. Ochsner J. 2014;14(2):270-5.
A part of anthropological linguistics concerned with the interrelation between a language and the cultural behavior of those who speak it.
That period when the patient with sickle cell anaemia is free of infection, pain, or other disease processes.
Juwah, A. I., Nlemadim, E. U., & Kaine, W. (2004). Types of anaemic crises in paediatric patients with sickle cell anaemia seen in Enugu, Nigeria. Archives of disease in childhood, 89(6), 572-576.
A reduction in the level of performance of the kidneys in areas of function comprising the concentration of urine, removal of wastes, the maintenance of electrolyte balance, homeostasis of blood pressure, and calcium metabolism.
Not anemic, i.e. no reduction in erythrocytes volume and/or hemoglobin concentration.
An amino acid-specifying codon that has been converted to a stop codon by mutation. Its occurance is abnormal causing premature termination of protein translation and results in production of truncated and non-functional proteins. A nonsense mutation is one that converts an amino acid-specific codon to a stop codon.
This term already exists in the ontology as 'Chronic Neuropathic Pain' (SCDO:0000228), however when searching other ontologies, the term 'chronic' is included in the definition. I have therefore edited the definition to include the term 'chronic'. Please review as to whether we need to change the label that currently exists in SCDO. Is treated with: amitriptyline, duloxetine, gabapentin, or pregabalin.
Deletion of both HBA2 genes, which results in an alpha-thal-2 (alpha-/alpha-) form of alpha thalassemia trait. With this deletion there is nearly normal production of red blood cells, but there may be a mild anemia.
A mutation in the beta-globin gene, HBB, that results in reduced beta globin synthesis.
A rapid heartrate that exceeds the range of the normal resting heartrate for age, gender or patient population.
Suggest update to description in HPO. The original description stated 'A rapid heartrate that exceeds the range of the normal resting heartrate for age', however I think it should be recommended that gender and patient population be included.
The process whereby a mutation in a hemoglobin molecule causes conformational changes in the hemoglobin molecule, which cause increased hydrophobicity of the molecule, which result in the formation of crystals consisting of the mutated hemoglobin molecules. This type of crystallisation is observed in hemoglobins with the HbC mutation.
A deficiency of the essential metal Zinc; an essential cofactor for many enzymes. Zinc deficiency is caused by a lack of zinc in the diet, loss of zinc after absorption, for example through loss through burns, inability to absorb Zinc, or increased loss through exercise.
Insufficiency of arterial or venous blood supply to the spleen due to emboli, thrombi, vascular torsion, or pressure that produces a macroscopic area of necrosis.
This represents the phenotypic feature of mutational effects on a given property of an organism biological system [Gaston K. Mazandu, []].
The privacy of information and its protection against unauthorized disclosure.
The pattern of gene expression at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.
The presence and extensiveness of a disease in the body. It is objectively evaluated through diagnostic testing and physiological examination of the impaired biological organs or tissues, in cases in which disease severity can be distinguished from other realms of health, as in heart disease.
Request inclusion into relevant ontology. This exists in the Influenza Ontology, but their definition is not ideal.
Reimbursement of research participants for costs directly incurred during the research, such as travel costs and reasonable compensation for their inconvenience and time spent. Compensation can be monetary or non-monetary.
Request inclusion into relevant ontology The label for this term has been changed to be more specific than the original "Compensation".
International Ethical Guidelines for Health-related Research Involving Humans, Fourth Edition. Geneva, Council for International Organizations of Medical Sciences (CIOMS); 2016.
Research participants should be reasonably reimbursed for costs directly incurred during the research, such as travel costs, and compensated reasonably for their inconvenience and time spent. Compensation can be monetary or non-monetary. Compensation must not be so large as to induce potential participants to consent to participate in the research against their better judgment ("undue inducement"). A local research ethics committee must approve reimbursement and compensation for research participants.
A mutation wholly or partly responsible for causing Hemoglobin D Disease.
The abiding by applicable principles such as 1. compliance by research institutions; 2. obtaining and documenting informed consent; 3. Research Ethics Committee membership function, operations, review of research, and record keeping; 4. additional protection for certain vulnerable research subjects - pregnant women, prisoners, and children
National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research. The Belmont Report: Ethical Principles and Guidelines for the Protection of Human Subjects of Research. [Bethesda, Md.]
Research ethics committees: Basic concepts for capacity building. International Ethical Guidelines for Health-related Research Involving Humans, Fourth Edition. Geneva. Council for International Organizations of Medical Sciences (CIOMS); 2016.
The Commission, 1978. World Health Organization. Geneva: WHO Document Production Services; 2009.
A mutation in the beta-globin gene, HBB, that results in absent beta globin synthesis.
An abnormality of the body's metabolism or homeostasis.
Suggest update to description in HPO. Currenlty the HPO does not have a description.
Naturally occurring genetic variations associated with drug response. While these variants are not markers for genetic predisposition to disease, they influence pharmacokinetics and pharmacodynamics and often occur on genes encoding drug metabolism enzymes and transporters (e.g., angiotensin converting enzyme; cytochrome P-450 CYP2D6).
'The hemoglobin molecule that transports oxygen in the blood is made up of a number of components. Human hemoglobin is a tetramer: in adults it is made up of two alpha globins and two beta globins; in the fetus, of two alpha and two g globins; and in the embryo, two e and two z globins. The sequences of these five globin types are similar and the genes that code for them occur in clusters on the chromosomes. In humans, there are two main clusters of globin genes: the alpha globin cluster on chromosome 16 and the beta globin cluster on chromosome 11. [Curator team: []]'
A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a material) to be used for testing, analysis, inspection, investigation, demonstration, or trial use.
Deoxygenated malfunctioning or mutated hemoglobins which clump together and form a long polymer in a process called polymerisation.
Request inclusion in the HPO, below "Abnormal Hemoglobin". Description still needs work.
A person's ethnic status, whether conserved or mixed ethnicity.
Genetic variation in the structure leading to the abnomality of protein structure in non-sickle cell disease hemoglobin.
Documents describing a medical treatment or research project, including proposed procedures, risks, and alternatives, that are to be signed by an individual, or the individual's proxy, to indicate his/her understanding of the document and a willingness to undergo the treatment or to participate in the research.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
A procedure in which a sample of peripheral blood is viewed under a microscope to count different circulating blood cells (red blood cells, white blood cells, platelets, etc.) and see whether the cells look normal.
A legal representation or family member of the participant gives consent on behalf of the patient.
Request inclusion into the Informed Consent Ontology. MESH has the term Third-party consent, but the description's not suitable.
Dynamic consent is a personalised, communication interface to enable greater participant engagement in clinical and research activities.The interface facilitates two-way communication to stimulate a more engaged, informed and scientifically literate participant population where individuals can tailor and manage their own consent preferences. It has the potential to be applied more broadly to situations where there are multiple and varied uses of data requiring different kinds of consent over a period of time.
Request inclusion into ICO below "Informed Consent".
Surgical procedure involving either partial or entire removal of the spleen.
Hemoglobin characterized by structural alterations within the molecule that confer an inherited health condition phenotype. The alteration can be either absence, addition or substitution of one or more amino acids in the globin part of the molecule at selected positions in the polypeptide chains.
Suggest HPO to update their term description and to move terms related to hemoglobin concentration below "Abnormal Hemoglobin Concentration". Include as a sub-class "Hemoglobin S-Providence"?
The polymerase chain reaction (PCR) is the most common method to detect the deletional thalassaemias. Gap-PCR amplifies the deleted DNA sequence using the primers flanking the deleted region 10. Three primers are designed for each deletion to amplify the normal (undeleted) and deleted gene sequences.
Kho SL, Chua KH, George E, Tan JA. A novel gap-PCR with high resolution melting analysis for the detection of α-thalassaemia Southeast Asian and Filipino β°-thalassaemia deletion. Sci Rep. 2015;5:13937. Published 2015 Sep 14. doi:10.1038/srep13937
The genetic constitution of the individual, comprising the alleles present at each genetic locus.
Characterized by an established ileus, with vomiting, a silent distended abdomen and distended bowel loops and fluid levels on abdominal x-ray. Some hepatic enlargement is common, and it is often associated with bilateral basal lung consolidation (chest syndrome).
Request inclusion into relevant ontology Can be treated with analgesia, IV fluids, and antibiotics if patient is febrile.
The most common and normal adult human hemoglobin tetramer, comprising over 97% of the total red blood cell hemoglobin and consisting of two alpha chains and two beta chains.
Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin". Suggest update to description in MESH.
May be caused by an acute VOC, malarial infection or oxidant drug exposure in individuals with concomitant glucose-6-phosphate dehydrogenase (G6PD) deficiency. Haemolytic crisis may be distinguished from aplastic crisis by the finding of a reticulocytosis as opposed to a reticulocytopenia.
SCD Management guidelines - South Africa
A term used to express willingness to participate in research by persons who are by definition too young to give informed consent but who are old enough to understand the proposed research in general, its expected risks and possible benefits, and the activities expected of them as subjects.
The source term seems to be deprecated in the ICO.
The protein product of the fusion of the gene products of the HBD and HBB genes that causes the mutation which causes the Hemoglobin Lepore Trait.
Crossover between delta and beta globin gene loci
Chronic splenic sequestration associated with enlarged spleen and cytopaenia with anaemia and reduction in white blood cells and platelets. The anaemia is usually chronic in nature and patients rarely present with signs of heart failure.
Request inclusion into the HPO below "Hypersplenism".
Management of Sickle Cell Disease - The United Republic of Tanzania (By Ministry of Health)
The sequential set of three nucleotides in transfer RNA that interacts with its complement in messenger RNA, the Codon, during translation in the ribosome.
Also known as sense codon, a set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (terminator codon). Most codons are universal, but some organisms do not produce the transfer RNAs complementary to all codons. These codons are referred to as unassigned codons (nonsense codons).
Add "Terminator Codon" as a parent of "Nonsense Codon" as in MESH?
A codon that directs initiation of protein translation (Translation, Genetic) by stimulating the binding of initiator tRNA (RNA, TRANSFER, MET). In prokaryotes, the codons AUG or GUG can act as initiators while in eukaryotes, AUG is the only initiator codon.
Brief reversible episodes of focal, nonconvulsive ischemic dysfunction of the brain having a duration of less than 24 hours, and usually less than one hour, caused by transient thrombotic or embolic blood vessel occlusion or stenosis. Events may be classified by arterial distribution, temporal pattern, or etiology (e.g., embolic vs. thrombotic).
A chest pain that is caused when your heart muscle doesn't get enough oxygen-rich blood.
A rarely recognized complication of vaso-occlusive crisis. It is characterized by a presentation of right upper quadrant pain in the liver. A smooth, tender, enlarged liver is noted on physical exam. The lab values show a decrease in the hemoglobin/hematocrit. An increase in reticulocyte count is also seen.
Norris, W. E. (2004). Acute hepatic sequestration in sickle cell disease. Journal of the National Medical Association, 96(9), 1235-1239. The Management of Sickle Cell Disease. 1984. (Revised June 2002). NIH publication 02-2117. Available at http:/www.nhlbi.nih.gov/health/prof/blood/sickle/sc.
'A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-(4-hydroxyphenyl)acetamido group. [Curator team: []]'
An acquired disorder caused by several hematological and immunological diseases and characterized by impairment of splenic function.
Request inclusion into relevant ontology, perhaps below "Abnormality of the Spleen" in the HPO.
Kirkineska L, Perifanis V, Vasiliadis T. Functional hyposplenism. Hippokratia. 2014;18(1):7–11.
Vijay, V., Cavenagh, J.D. and Yate, P., 1998. The anaesthetist's role in acute sickle cell crisis. British journal of anaesthesia, 80(6), pp.820-828.
Deletion of a part of the beta-globin locus.
Request inclusion into relevant ontology No online description for this term exists, would it be sufficient to say 'Long lasting form of anemia'? or is there a better definition specific for sickle cell anemia?
An increase in the rate of hemolysis, in conjunction with specific clinical complications of sickle cell disease.
Request inclusion into Mammalian Phenotype ontology below "Hemolysis". Info also provided by the definition source: 'Hyperhemolysis should be typified by an acute reduction in hemoglobin level associated with higher than usual reticulocyte counts and perhaps an unaccountable and sudden increase in LDH.'
Disorders of Hemoglobin: Genetics, Pathophysiology, and Clinical Management. Martin H. Steinberg, Bernard G. Forget, Douglas R. Higgs, David J. Weatherall. Cambridge University Press, 17 Aug 2009
A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.
An abnormally high number of reticulocytes per unit volume of blood. The normal fraction of reticulocytes in the blood depends on the clinical situation but is usually 0.5% to 2.5% in adults and 2% to 6% in infants.
Request inclusion into relevant ontology Symptom of splenic sequestration, or increased haemolysis.
The physical characteristics of the globin polypeptides that form hemoglobins.
Work consisting of a structured file of information or a set of logically related data stored and retrieved using computer-based means.
The major component of hemoglobin in the fetus. This hemoglobin has two alpha and two gamma polypeptide subunits in comparison to normal adult hemoglobin, which has two alpha and two beta polypeptide subunits. Fetal hemoglobin concentrations can be elevated (usually above 0.5%) in children and adults affected by leukemia and several types of anemia.
Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin", for completion sake.
A disorder of cardiac function caused by insufficient blood flow to the muscle tissue of the heart. The decreased blood flow may be due to narrowing of the coronary arteries (coronary artery disease), to obstruction by a thrombus (coronary thrombosis), or less commonly, to diffuse narrowing of arterioles and other small vessels within the heart. Severe interruption of the blood supply to the myocardial tissue may result in necrosis of cardiac muscle (myocardial infarction).
Avascular necrosis of femoral head (ANFH) is a severely disabling disease characterised by progressive groin pain, a limping gait, leg length discrepancy, collapse of the subchondral bone, limitation of hip function and eventual degeneration of the hip joint requiring total hip arthroplasty.
deprecated-Avascular Necrosis of the Femoral Head
The meaning ascribed to the base sequence with respect to how it is translated into amino acid sequence. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons.
Deletion of the HBB and HBD genes that results in delta-beta thalassemia.
A biological object that contains genetic information and that is involved in transmitting genetically encoded traits from one organism to another.
An ethical principle that obligates one to treat people fairly. Distributive justice refers to allocating benefits and harms fairly; procedural justice refers to using fair processes to make decisions that affect people; formal justice refers to treating similar cases in the same way. In human subjects research, the principle of justice implies that subjects should be selected equitably.
Elevated body temperature due to failed thermoregulation, or inflammation or immune responses.
Merged the two descriptions from NCIT and HP Suggest update to description in NCIT and HP.
A person who has not attained the age at which full civil rights are accorded.
An ethnic group that includes persons with significant ethnic contributions from more than one group.
Critical and exhaustive investigation or experimentation, having for its aim the discovery of new facts and their correct interpretation, the revision of accepted conclusions, theories, or laws in the light of newly discovered facts, or the practical application of such new or revised conclusions, theories, or laws.
An uncommon complication of cholecystitis and refers to a situation where the gallbladder lumen is filled and distended by purulent material (pus).
Aplasia or hemolysis may be precipitated by another illness/infection in sickle cell disease patients. Acutely severe anemia is defined as Hb < 5g/dl or a recent acute drop in HB > 2g/dl below the individual's steady state value. If no steady state value is available, it can be detected by the presence of acutely symptomatic anemia (i.e. tachycardia, cardiac failure, shock).
Request inclusion into relevant ontology. Please check with the working group as to how they feel about the label for this term.
Research involving the collection, storage, or use of private data or biological samples from living individuals by means of interactions, interventions, surveys, or other research methods or procedures.
The collecting of fetal blood samples typically via endoscopic ultrasound guided fine needle aspiration from the umbilical vein, followed by examination of the blood to detect fetal abnormalities.
Percutaneous Umbilical Cord Blood Sampling
A material transfer agreement (MTA) is a type of legally enforceable contract employed by research institutions and companies to set the terms under which their materials and associated data may be obtained and used by others.
Henderson J (2007) Counterpoint: MTAs are a practical necessity. Nat Biotechnol 25: 722–724.
A branch of applied ethics that studies the value implications of practices and developments in life sciences, medicine, and health care.
A condition due to a dietary deficiency of ascorbic acid (vitamin C), characterized by malaise, lethargy, and weakness. As the disease progresses, joints, muscles, and subcutaneous tissues may become the sites of hemorrhage. Ascorbic acid deficiency frequently develops into SCURVY in young children fed unsupplemented cow's milk exclusively during their first year. It develops also commonly in chronic alcoholism. (Cecil Textbook of Medicine, 19th ed, p1177)
A rare intracranial arteriopathy involving progressive stenosis of the cerebral vasculature located at the base of the brain causing transient ischemic attacks or strokes.
Hemoglobin that presents no inherited health condition phenotype.
Request inclusion into NCIT below "Hemoglobin".
An acute form of acquired red cell aplasia. A significant change in blood picture is observed, characterised by a precipitous fall in the haemoglobin level (>20 g/l beyond steady state level) and reduced (<1%) or absent reticulocytes in the peripheral blood. The total white blood cell or platelet counts may or may not be affected. In addition, there is no significant increase in the unconjugated fraction of serum bilirubin.The most common cause is infection by parvovirus B19, a DNA virus that replicates inside immature red blood cells in the bone marrow, resulting in severe anaemia (hemoglobin levels well below steady state) and low reticulocyte count. It is rarely recurrent.
Mutations in the HBG1 and/or HBG2 genes. Such mutations can lead to variably increased levels of fetal hemoglobin (Hb) (Hb F, alpha2gamma2) in the syndrome of hereditary persistence of fetal Hb (HPFH).
Request inclusion into relevant ontology. Perhaps add sub-classes of specific mutations as in the dc:source.
Condition characterized by splenomegaly, some reduction in the number of circulating blood cells in the presence of a normal or hyperactive bone marrow, and the potential for reversal by splenectomy.
Al-Salem, A. H. (2011). Splenic Complications of Sickle Cell Anemia and the Role of Splenectomy. ISRN Hematology, 2011, 864257. http://doi.org/10.5402/2011/864257
Significant change in blood picture characterised by a precipitous fall in the haemoglobin level associated with jaundice, marked reticulocytosis, and polychromasia on the blood smear, increased unconju- gated hyperbilirubinaemia, and increased urobilinogen content in urine above the steady state level for each individual patient.
An ethnic group that includes persons with ethnic contributions from only one ethnic group.
Hemoglobin with altered structural and biochemical properties.
Voluntary authorization, by a patient or research subject, with full comprehension of the risks involved, for diagnostic or investigative procedures, and for medical and surgical treatment.
Significant change in blood picture characterised by a precipitous fall in the haemoglobin level of at least 20 g/l and accompanied by a rapidly enlarging spleen or liver (greater than 2 cm from the steady state level) and reticulocytosis above the steady state level for each individual patient. Signs of acute circulatory insufficiency such tachypnoea, tachycardia, and hypotension may or may not be present. It is the earliest life-threatening complication seen in patients with SCD besides pneumococcal infections.
A hemoglobinopathy caused by a reduced or imbalanced synthesis of a normal globin chain or by a defect in the switch between synthesis of different types of normal hemoglobin.
'Other molecules are complexes which do not contain protein or RNA, including lipids, carbohydrates, etc.'
Insufficient production of steroid hormones (primarily cortisol) by the adrenal glands as a result of a primary defect in the glands themselves.
Suggest update to description. Not sure if they changed their description or if we adapted it.
The probability that an event will occur. It encompasses a variety of measures of the probability of a generally unfavorable outcome.
A process of inclusive participation that supports mutual respect of values, strategies, and actions for authentic partnership of people affiliated by geographic location, shared interest, or similar circumstances to address issues affecting community wellbeing.
This term was too general. Was replaced by "Geographic Area".
Information or a description of consent (hypothetical or obtained) or any aspect involved in or captured in the consent process.
Request inclusion into relevant ontology, perhaps the ICO.
In situ death of bone within the humeral head due to disruption of blood supply.
Has synonym: Osteonecrosis of the humeral head
deprecated-Avascular necrosis of the humeral head
The molecular characteristics of a cell of tissue including expressed coding and non-coding RNAs, proteins and their post-translational modifications, lipids, carbohydrates and small molecules that characterize the state in a cell or tissue and that result from the interaction of its genotype and the environment.
HBB genetic variants that result in reduced or absent hemoglobin subunit beta production.
Hemolytic anemia, in which patients are compound or double heterozygous for both the sickle cell gene and a thalassemia gene.
A document containing the determination of the Research Ethics Committee (REC) that the clinical study with human subject participation has been reviewed and may be conducted at a particular study site within the constraints set forth by the REC and other institutional and federal requirements. The regulations require that an REC conduct continuing review of research at intervals appropriate to the degree of risk, but not less than once a year.
Hemoglobin produced in the blood islands in the embryonic yolk sac during the mesoblastic stage of gestation. There are four different embryonic hemoglobins, Hemoglobin Gower 1, Hemoglobin Gower 2, Hemoglobin Portland 1 and Hemoglobin Portland 2.
Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin". Add sub-classes: Hemoglobin Gower 1 Hemoglobin Gower 2 Hemoglobin Portland 1 Hemoglobin Portland 2
R Al-Mufti, H Hambley, F Farzaneh, KH Nicolaides Haematologica Jan 2000, 85 (7) 690-693;
A seizure that occurs in the context of a brain insult (systemic, toxic, or metabolic) and may not recur when the underlying cause has been removed or the acute phase has elapsed. It is often associated with infections, infarctions, and severe metabolic or sickle cell complications.
Deletion of both HBA1 genes, which results in an alpha-thal-2 (alpha-/alpha-) form of alpha thalassemia trait. With this deletion there is nearly normal production of red blood cells, but there may be a mild anemia.
A hemoglobinopathy caused by the presence of structurally abnormal hemoglobins.
Persistence of an inflammatory event in the articulation overtime.
The obstruction of blood vessels by altered erythrocytes that can result in pain, anemia and tissue ischemia.
Characterized by pain and discomfort in the right upper quadrant (RUQ) of the abdomen caused by a number of possible aetiologies in sickle cell disease. Causes of RUQ pain may be divided into pain originating from the liver or gall bladder versus other origins of abdominal pain in that region.
A biobank is a collections of samples of biological substances (e.g. tissue, blood, DNA) which are linked to data about the samples and their donors. They have a dual nature as collections of samples and data and usually require investigators or institutions to agree to certain conditions as a condition for sharing samples or data with them.
Suggest update to description in OMIABIS
The concurrence of sickle cell anemia and alpha-thalassemia. This condition is thought to result in less severe hemolytic anemia due to reduced concentration of hemoglobin S and its polymerization within red blood cells.
Co-Inheritance of Alpha-Thalassemia and Sickle Cell Anemia
Co-Inheritance of Sickle Cell Anemia and Alpha-Thalassemia
Sickle Cell Anemia Associated with Coexistent Alpha Thalassemia
Sickle Cell Anemia Associated with Alpha Thalassemia
A radiograph of dental structures made on x-ray film or stored as a digital image. The radiographs may be extraoral or intraoral. Three common types of intraoral dental images are periapical, interproximal, and occlusal radiographs.
"dental radiograph." Mosby's Medical Dictionary, 8th edition. 2009. Elsevier 7 Nov. 2018 https://medical-dictionary.thefreedictionary.com/dental+radiograph
The removal of excess iron from the body with special drugs.
Request inclusion into MESH below "Chelation Therapy"
The capacity for self-governance, i.e. the ability to make reasonable decisions.
Blockage of blood flow in the central retinal artery. Results in sudden painless loss of vision and occurs in children and young adults. Thrombus formation in the retinal artery occurs spontaneously or in association with hyphema, Moyamoya and acute chest sydrome. There is no associated pain and it may be unilateral or bilateral.
Occurs where there is infarction of vertebral bone marrow, leading to collapse of the vertebrae with a typical 'fish mouth' appearance. It is often asymptomatic, but may cause acute and/or long term pain requiring analgesia and mechanical support such as a brace. Can be an acute or chronic bone problem in SCD.
Suggest update to description in HPO (currently no description).
Principle dictating that harm should not come to individuals as a result of their participation in a research project.
Shamoo AE and Resnik DB, Responsible Conduct of Research, 3rd ed. (New York: Oxford University Press, 2015).
A nutritional condition produced by a deficiency of folic acid in the diet.
Alcohol interferes with its intermediate metabolism and absorption. Folic acid deficiency may develop in long-term anticonvulsant therapy or with use of oral contraceptives.
This deficiency causes anemia, macrocytic anemia, and megaloblastic anemia. It is indistinguishable from vitamin B 12 deficiency in peripheral blood and bone marrow findings, but the neurologic lesions seen in B 12 deficiency do not occur. (Merck Manual, 16th ed)
A hemoglobinopathy caused by compound heterozygous inheritance of one hemoglobin S allele and one hemoglobin allele that produces structurally abnormal hemoglobin.
Hemoglobin with decreased solubility in the red cell due to substitutions in the primary sequence of globin which alters the tertiary or quaternary structure of the molecule and results in a globin polypeptide/hemoglobin tetramer that is unstable and precipitates intracellularly, reducing the red blood cell lifespan.
Request inclusion in the HPO, below "Abnormal Hemoglobin".
An acute condition of intrasplenic pooling of large amounts of blood.
Suggest update to description in the Radiology Lexicon, or use their description "Splenic sequestration occurs in sickle cell disease when sickled red blood cells become trapped in the spleen, causing it to enlarge."
A complication of kidney diseases characterized by cell death involving kidney papilla in the kidney medulla. Damages to this area may hinder the kidney to concentrate urine resulting in polyuria. Sloughed off necrotic tissue may block kidney pelvis or ureter. Necrosis of multiple renal papillae can lead to kidney failure.
'Any single chemical entity that is an electrically neutral entity consisting of more than one atom. Each atom carries a certain number of electrons that orbit around the nucleus.[Curator team: []]'
Effort made to secure the well-being of persons, maximizing possible benefits and minimizing possible harms.
The physical characteristics and levels of proteins that characterize the state in a cell or tissue and that result from the interaction of its genotype and the environment.
Request inclusion into BioAssay Ontology below "biochemical phenotype". Can all sub-classes of the "Gene Product" class not be included here? Can this class not be removed but its sub-classes kept?
An abnormally low number of reticulocytes per unit volume of blood.
Request inclusion into relevant ontology Symptom of aplastic crisis, possibly due to parvovirus B19 infection. Is there a certain value below which is considered a low reticulocyte count?
'The aplastic crisis is temporary cessation of red cell production. This usually affect sickle cell patients, because of the markedly shortened red cell survival time in patients with sickle cell disease, a precipitous drop in hemoglobin occurs in the absence of adequate reticulocytosis. [Curator team: []]'
Pain resulting from tissue ischemia as a result of blockage of mesenteric blood vessels.
Akingbola TS, Kolude B, Aneni EC, et al. ABDOMINAL PAIN IN ADULT SICKLE CELL DISEASE PATIENTS: A NIGERIAN EXPERIENCE. Annals of Ibadan Postgraduate Medicine. 2011;9(2):100-104.
Abdominal distension with generalised abdominal tenderness (no rebound tenderness) and reduced bowel sounds. Abdomen moves with respiration. Vomiting/diarrhoea are not common.
A mutation in the beta-globin gene, HBB, that causes decreased or absent beta-globin synthesis.
A genetic mutation in the HBB gene that results in absent or decreased hemoglobin subunit beta or an abnormal hemoglobin other than Hb S.
Too specific to SCD to be included in other ontologies.
The proteins and their post-translational modifications, lipids, carbohydrates and small molecules that characterize the state in a cell or tissue and that result from the interaction of its genotype and the environment.
'Genotypes which are not specific to sickle cell trait.'
The moral obligations governing the conduct of research. Used for discussions of research ethics as a general topic.
Elements, types, descriptions and formulations of a research study.
Revealing of information, by oral or written communication.
Reporting to parents or guardians about care to be provided to a minor (minors).
A legal requirement that designated types of information acquired by professionals or institutions in the course of their work be reported to appropriate authorities.
Making information permanently non-identifiable that is associated with the identity of specific entities via encryption or other methods.
An observable characteristic of disease that has a severe and rapid onset of symptoms with short duration.
A unique identifier generated either manually or electronically when adding a subject to a study.
Procedures which temporarily or permanently remedy insufficient cleansing of body fluids by the kidneys.
Could this and it's sub-classes not fall below any of the other main Therapeutics classes? Symptomatic?
An abnormal hemoglobin caused by various point mutations within the HBB gene. This form of hemoglobin prevents red blood cells from carrying oxygen effectively. There are at least 8 different types of hemoglobin D.
A group of abnormal hemoglobins in which amino acid substitutions take place in either the alpha, beta or gamma chains but near the heme iron. This results in facilitated oxidation of the hemoglobin to yield excess methemoglobin which leads to cyanosis.
Suggest update to description in MESH (to include "gamma chains") Suggest this term replaces "Methemoglobinemia" below "Abnormal Hemoglobin" in the HPO.
An abnormal hemoglobin that results from the substitution of lysine for glutamic acid at position 26 of the beta chain. It is most frequently observed in southeast Asian populations.
Request inclusion in the HPO, below "Abnormal Hemoglobin", for the sake of completion.
A group of disorders caused by large deletions of the beta-globin gene complex; typically 30% fetal haemoglobin.
Hereditary Persistence of Fetal Hemoglobin-Sickle Cell Disease Syndrome
Sickle Cell Disease Syndrome-Hereditary Persistence of Fetal Hemoglobin
Sickle Cell Disease-S/Persistence of Fetal Hemoglobin
Sickle Cell-Hereditary Persistence of Fetal Hemoglobin
Members of the beta-globin family. In humans, they are encoded in a gene cluster on chromosome 11. They include hemoglobin subunit epsilon, hemoglobin subunit gamma, hemoglobin subunit delta and hemoglobin subunit beta. 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.
This gene encodes the hemoglobin subunit beta and is located on chromosome 11 mapped at 11p15.5.
This gene encodes the hemoglobin subunit delta, which is a component of hemoglobin A2, which plays a role in the transport of oxygen to tissues of the adult body, but exists only in small amounts in all adult humans (1.5-3.1% of all hemoglobin molecules).
An abnormal hemoglobin that results from the substitution of glutamic acid with lysine at position 121 of the beta chain.
MESH and Zimmerman SA. Am J Hematol. 1999 Apr; 60(4) 279-84
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.
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.
'Every annotation must be attributed to a source, which may be a literature reference, another database or a computational analysis. The annotation must indicate what kind of evidence is found in the cited source to support the association between the gene product and the GO term. A simple controlled vocabulary is used to record evidence; and the evidence codes are simply the three-letter codes used to signify the type of evidence cited. [Curator team: Exact []]'
The information in this class and its sub-classes will be migrated to evidence code properties.
'Used for annotations that depend directly on computation or automated transfer of annotations from a database, particularly when the analysis is performed internally and not published. A key feature that distinguishes this evidence code from others is that it is not made by a curator; use IEA when no curator has checked the specific annotation to verify its accuracy. [Curator team: Exact []]'
obsolete IEA (inferred from electronic annotation)
'This should be used for information extracted from articles in the medical literature. [Curator team: []]'
'Can be used for annotations based on individual clinical experience. [Curator team: []]'
obsolete ICE (individual clinical experience)
'Usually reviews or disease entries (e.g. OMIM) that only refers to the original publication. [Curator team: []]'
obsolete TAS (traceable author statement)
'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. [Curator team: []]'
obsolete NAS (non-traceable author statement)
'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. [Curator team: []]'
Terms deprecated in the "Personal Attribute" class.
A diagnostic instrument, technique, laboratory assay or test, or method of patient examination used for differential diagnosis.
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.
Terms deprecated in the "Diagnostics" class.
Terms deprecated in the "Therapeutics" class.
When the abnormal hemoglobin, hemoglobin C (HbC), has been detected in a blood sample.
An abnormality of the cerebral vasculature.
Abnormality of the Cerebral Blood Vessels
A mutation wholly or partly responsible for causing a sickle cell disease.
Request inclusion into relevant ontology 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
The glutamic acid in position 6 in the primary sequence of a beta-chain produced by the HBB gene is replaced by valine.
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 lysine. This mutation is found as a single alteration in Hemoglobin O-Arab and is one of the two contributing mutations to the production of Hemoglobin S-Oman.
A mutation where the glutamic acid in position 6 in the primary sequence of a beta-chain produced by the HBB gene is replaced by lysine. This mutation results in the production of Hemoglobin C and confers resistance to malaria.
A mutation in the HBB gene causing substitution of glutamic acid for lysine at the 26th position of the beta-globin chain.
A person's concept of self as being male and masculine or female and feminine, or ambivalent, based in part on physical characteristics, parental responses, and psychological and social pressures. It is the internal experience of gender role.
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. This mutation is found as a single alteration in Hemoglobin Korle Bu and is one of the two contributing mutations to the production of Hemoglobin C-Harlem.
A mutation where the valine in position 23 in the primary sequence of a beta-chain produced by the HBB gene is replaced by isoleucine. When compounded with the HbS mutation in the same gene, the sickling Hemoglobin S-Antilles is produced.
A mutation where the threonine in position 87 in the primary sequence of a beta-chain produced by the HBB gene is replaced by isoleucine. This mutation is found as a single alteration in Hemoglobin Quebec-Chori. Compound heterozygosity for Hb Quebec-chori and Hb S results in sickle cell disease.
Witkowska, H. E., Lubin, B. H., Beuzard, Y., Baruchel, S., Esseltine, D. W., Vichinsky, E. P., Kleman, K. M., Bardakdjian-Michau, J., Pinkoski, L., Cahn, S., Roitman, E., Green, B. N., Falick, A. M., Shackleton, C. H. L. Sickle cell disease in a patient with sickle cell trait and compound heterozygosity for hemoglobin S and hemoglobin Quebec-Chori. New Eng. J. Med. 325: 1150-1154, 1991.
A mutation where the leusine residue in position 6 in the primary sequence of a beta-chain produced by the HBB gene is replaced by phenylalanine. This mutation on its own produces a stable hemoglobin that does not result in hemolysis (Hb Rockford), but when in combination with the Hb S mutation (HBB, GLU6VAL), the symptomatic Hb Jamaica Plain is produced.
Perrault, J., Fairbanks, V. F., McCormick, D. J., Kubik, K., Madden, B. J., Holmes, M. W., Hoyer, J. D. Hemoglobin Rockford, beta68(E12)leu-to-phe: a new HB variant associated with mild anemia. (Abstract) Blood 90 (Suppl. 1): 30b, 1997.
The alleles, or variant forms of the HBB gene, that are carried by an SCD sufferer.
Probably too specific to be included in other ontologies. 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?
The genotype when an individual has the Hb C gene from one parent and the Hb S gene from the other. Individuals with Hb SC have similar symptoms to individuals with Hb SS, however, the anemia is less severe.
Compound heterozygosity for the hemoglobin S (HBB Glu6Val) and hemoglobin D-Punjab (HBB Glu121Gln) variants.
Torres LS, Okumura JV, Silva DG, Bonini-Domingos CR. Hemoglobin D-Punjab: origin, distribution and laboratory diagnosis. Rev Bras Hematol Hemoter. 2015;37(2): 120–126. pmid:25818823
Compound heterozygosity for the hemoglobin S (HBB Glu6Val) and hemoglobin O-Arab (HBB GluU121Lys) variants.
Compound heterozygosity for the hemoglobin S (HBB Glu6Val) and hemoglobin E (HBB Glu26Lys) variants.
The homozygous genotype that involves a substitution of glutamic acid for a valine at position 6 of beta-globin chains produced by both beta-globin gene (HBB) alleles.
Compound heterozygous inheritance of Hb S and Hb D mutations. Hb S occurs from substitution of valine for glutamic acid in the beta-6 position (beta6Glu>Val). Hb D generally results from substitution of glutamic acid for glutamine at beta-121 (beta121Glu>Gln); such as the Hb D-Punjab/Hb D-Los Angeles variants. There are several other Hb D variants, including Hb D-Iband where threonine is substituted by lysine at beta-87 (beta87Thr>Lys) and Hb D-Iran where glutamic acid is substituted by glutamine at beta-22 (beta22Glu>Gln).
Compound heterozygous inheritance of Hb S and Hb C-Harlem mutations. Hb S occurs from substitution of valine for glutamic acid in the beta-6 position (beta6Glu>Val). Hb C-Harlem involves two substitutions in each beta-chain: the first being identical to that found in Hb S, and the second being a substitution of aspartic acid at position 73 by asparagine (beta73Asp>Asn).
beta6Glu>Val/beta6Glu>Val, beta73Asp>Asn
An abnormal hemoglobin in which two mutations occur 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.
Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions".
The inheritance of the gene for hemoglobin D-Punjab from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent.
Hemoglobin D-Punjab Trait causes no clinical or hematological alterations
The underlying molecular makeup resulting in sickle cell disease.
Probably too specific to warrant inclusion into anther ontology. 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?: -- J, M, Methemoglobin?
An altered level of normal hemoglobin (Hemoglobin A (Hb A), Hemoglobin A2 (Hb A2) or Hemoglobin F (Hb F, fetal hemoglobin) in the blood, which may be seen in those suffering with Sickle Cell Disease (SCD).
Altered Level of Normal Hemoglobin in SCD
A rare type of sickle cell disease with the compound heterozygous genotype involving the mutations for Hemoglobin S and Hemoglobin C-Harlem. This condition is described to have a clinical course similar to sickle cell anemia.
Moo-Penn, W., Bechtel, K., Jue, D., Chan, M.S., Hopkins, G., Schneider, N.J., Wright, J. and Schmidt, R.M., 1975. The presence of hemoglobin S and C Harlem in an individual in the United States. Blood, 46(3), pp.363-367.
A 106-kb deletion of the beta globin gene cluster.
A consent model in which participants are given a set of options allowing them to select how they want to participate in the research.
Request inclusion into the Informed Consent Ontology.
Requires that consent to the use of human samples be specific to the 'purpose' for which the sample is to be used and that where previously collected samples are to be used for a different 'research purpose' further consent should generally be obtained.
Request inclusion into the ICO below "Informed Consent".
The determination of the amount of hemoglobin F present in a sample.
Suggest update to label in NCIT (from "Hemoglobin F Measurement") Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT?
When one beta-globin gene carries the hemoglobin S mutation (beta6Glu>Val) whereas the other carries a null mutation, called beta-zero, because of the resulting inability to synthesize any beta-globin chain.
Hemoglobin Genotype S/Beta Zero Thalassaemia
'Genotype where a person is a compound heterozygote for the hemoglobin S mutation and a severe beta plus thalassemia mutation. Source: CLAIR [Curator team: []]'
Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031.
Severe S/Beta-Plus-Thalassaemia Genotype
Genotype whereby a person is heterozygous for a hemoglobin S mutation and heterozygous for a mutation that causes persistant fetal hemoglobin production into adulthood. HPFH causative mutations are largely due to deletions in the beta-globin locus, but also by point mutations in the gamma-globin gene promoters.
Stamatoyannopoulos, G. (2005). Control of globin gene expression during development and erythroid differentiation. Experimental Hematology, 33(3), 259. http://doi.org/10.1016/j.exphem.2004.11.007
A compound heterozygous genotype, involving the mutations for Hemoglobin S (beta6Glu>Val) and Hemoglobin Lepore Boston.
Stevens MC, Lehmann H, Mason KP, Serjeant BE, Serjeant GR. 1982. Sickle cell Hb Lepore Boston syndrome. Uncommon differential diagnosis to homozygous sickle cell disease. Am J Dis Child. 136(1):19-22.
A genotype that involves a double mutation in one beta-globin gene that results in hemoglobin with low oxygen affinity, which results in the polymerisation of the hemoglobin variant (hemoglobin Jamaica Plain) and thus sickling of erythorcytes.
A sickling hemoglobin with reduced oxygen affinity that causes severe hemolytic anemia and sickling of erythrocytes.
A form of hemoglobin caused by two mutations in its beta-chains, the classic beta S mutation (beta 6 Glu>Val) and beta 23 Val>Ile. Hemoglobin S-Antilles has the same electrophoretic mobility as Hemoglobin S but a distinct isoelectric focus and produces sickling in the carriers of the Hb A/S Antilles trait.
A form of hemoglobin caused by two mutations in a beta-globin chain, the classic beta S mutation (beta6 Glu> Val) and a beta121 Glu > Lys mutation identical to that of Hb-O Arab. The hemoglobin variant has reduced solubility and there is an apparent increase in red cell sickling tendency. It is reported to cause a rare dominant form of sickle cell disease, Sickle Cell Disease A/S-Oman.
Nagel, R.L., Daar, S., Romero, J.R., Suzuka, S.M., Gravell, D., Bouhassira, E., Schwartz, R.S., Fabry, M.E. and Krishnamoorthy, R., 1998. HbS-Oman heterozygote: a new dominant sickle syndrome. Blood, 92(11), pp.4375-4382.
Dominant heterozygosity for the double HBB Glu6Val and Glu121Lys mutation.
A form of sickle cell thalassemia, with a mild clinical phenotype, characterized by the presence of hemoglobin S and a small amount of hemoglobin A in the red blood cells.
Mild Sickle Cell Disease-S Beta Minus Thalassaemia
Mild Sickle Cell-Beta Minus Thalassaemia
Mild Sickle Cell Disease-S Beta Minus Thalassemia
A form of sickle cell thalassemia, with a moderate clinical phenotype, characterized by the presence of hemoglobin S and a small amount of hemoglobin A in the red blood cells.
Moderate Sickle Cell Disease-S Beta Minus Thalassaemia
Moderate Sickle Cell-Beta Minus Thalassaemia
Moderate Sickle Cell-Beta Minus Thalassemia
Moderate Sickle Cell Disease-S Beta Minus Thalassemia
A form of sickle cell thalassemia, with a severe clinical phenotype, characterized by the presence of hemoglobin S and a small amount of hemoglobin A in the red blood cells.
Severe Sickle Cell Disease-S Beta Minus Thalassaemia
Severe Sickle Cell-Beta Minus Thalassaemia
Severe Sickle Cell-Beta Minus Thalassemia
Severe Sickle Cell Disease-S Beta Minus Thalassemia
'Genotype where a person is a compound heterozygote for the hemoglobin S mutation and a moderate beta plus thalassemia mutation. Source: CLAIR [Curator team: []]'
Compound heterozygosity for the hemoglobin C (HBB Glu6Lys) mutation and the double HBB Glu6Val, Val23Ile mutation of hemoglobin S-Antilles.
beta6Glu>Lys/beta6Glu>Val, beta23Val>Ile
A hemoglobin that sickles due to the presence of two beta-globin gene mutations within the same HBB gene.
Request inclusion into the HPO, below "Abnormal Hemoglobin".
Sickling Hemoglobin with Two Beta-Globin Gene Substitutions
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 lysine in position 132 is replaced by asparagine.
Luo, H.Y., Adewoye, A.H., Eung, S.H., Skelton, T.P., Quillen, K., McMahon, L., Steinberg, M.H. and Chui, D.H., 2004. A novel sickle hemoglobin: Hemoglobin S-South End. Journal of pediatric hematology/oncology, 26(11), pp.773-776.
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.
Pediatr Blood Cancer. 2007 Aug;49(2):207-10.
An abnormal hemoglobin in which a threonine is replaced by an isoleucine residue at the eighty-seventh position of beta chains. It migrates like HbA but promotes sickling.
Suggest update to description in MESH (the term in MESH doesn't currently have a description). Also request inclusion in the HPO, below "Abnormal Hemoglobin", for the sake of completion.
Witkowska, H.E., Lubin, B.H., Beuzard, Y., Baruchel, S., Esseltine, D.W., Vichinsky, E.P. et al. Sickle cell disease in a patient with sickle cell trait and compound heterozygosity for hemoglobin S and hemoglobin Quebec-Chori. N Engl J Med. 1991; 325: 1150–1154
A severe compound heterozygous sickling disorder characterized by the presence of both hemoglobin S and hemoglobin Quebec Chori.
Sickle Cell-Hemoglobin Quebec Chori Disease
A mutation where the lysine residue in position 132 in the primary sequence of a beta-chain produced by the HBB gene is replaced by asparagine. This mutation on its own produces Hb Yamagata which has reduced oxygen affinity, but no distinctive clinical abnormalities. However, when present in the same gene as the Hb S mutation (HBB, GLU6VAL), the sickling HbS-South End is produced.
A compound heterozygous genotype, involving the mutations for hemoglobin S and hemoglobin S-South End.
beta Glu6Val, GAG>GTG/beta Glu6Val, GAG>GTG; beta Lys132Asn, AAA>AAC
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.
Suggest inclusion in the HPO, below "Abnormal Hemoglobin". Hb Lepore is produced at a reduced rate and this is why the disease is related to the Β-thalassemic syndromes. Quantity in heterozygotes 7-13%; found in combination with Hb S, Hb C, beta+-thal, and in the homozygous state. 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
A rare, reported severe, type of sickle cell disease with the compound heterozygous genotype involving the mutations for Hemoglobin S and Hemoglobin S-South End.
Sickle Cell-Hemoglobin S-South End Disease
'Sb+ thalassemia is an inherited condition. Hemoglobin S comes from one parent and Beta plus thalassemia comes from the other parent. Instead of appearing round (like donuts), red blood cells are somewhat small, pale and misshapen. [Curator team: []]'
Ask a clinician if this is different to a cluster headache?
A medically undesirable event occurring in a research subject, such as an abnormal sign, symptom, worsening of a disease, injury, etc. A serious adverse event (SAE) results in death, hospitalization (or increased hospital stay), persistent disability, birth defect, or any other outcome that seriously jeopardizes the subject's health.
A desirable research outcome or state of affairs, such as medical treatment, clinically useful information, or self-esteem. In the oversight of human subjects research, money is usually not treated as a benefit.
A situation in which an individual or their close associates might benefit personally from official or professional actions. It includes a conflict between a person's private interests and official responsibilities in a position of trust.The concept refers both to actual conflict of interest and the appearance or perception of conflict.
An homo sapiens that bears an experimental subject role which is realized through his/her participation in a scientific technique as the subject of interest (ie as the subject about which data is generated in an assay or study, or the entity that is transformed or modified in a material processing technique).
A paper or electronic questionnaire specifically used in research by the sponsor of the research to collect data from each research participant. All data on each participant in the study are held and/or documented in the CRF, including adverse events.
Request inclusion into relevant ontology, perhaps as parent of "electronic case report form" in the Ontology for Biomedical Investigations (OBI)
Debbie Kennedy, CRF Designer, Canary Publications, ISBN 0-9531174-7-2
Genes with alleles that affect the phenotype associated with a nonallelic gene.
The type of ICD-10-CM code, in terms of a code's usability for reimbursement purposes.
A specific region that is mapped within a genome. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or hereditary disease.
The protein subunits that comprise multimeric hemoglobins.
Members of the alpha-globin family. In humans, they are encoded in a gene cluster on chromosome 16. They include hemoglobin subunit zeta and hemoglobin subunit alpha. 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.
Sickle cell disease (SCD) is a pleiotropic inherited disorder of the blood, characterised by the appearance of sickle-shaped red blood cells and anemia. It results from homozygosity for the sickle beta-globin gene mutation at position 6 (glu > val), or compound heterozygosity for the sickle gene and either another mutation for a different hemoglobin variant or one of numerous beta-thalassemia mutations.
Suggest update to description in NCIT. 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.
The combination of the hemoglobin S mutation (beta6Glu>Val) and a beta-thalassemia mutation.
A mutation where the serine in position 9 in the primary sequence of a beta-chain produced by the HBB gene is replaced by tyrosine. This mutation is one of 2 amino acid substitutions in the same beta chain that produces the asymptomatic Hemoglobin D-Agri, the other mutation being HBB, GLU121GLN, which on its own produces Hemoglobin D-Punjab.
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.
Derived from a point mutation in the beta-globin gene (HBB: c.364G>C; rs33946267).
A mutation where the glycine in position 16 in the primary sequence of a beta-chain produced by the HBB gene is replaced by arginine.
A mutation where the asparargine acid in position 19 in the primary sequence of a beta-chain produced by the HBB gene is replaced by lysine.
A mutation where the glutamic acid in position 22 in the primary sequence of a beta-chain produced by the HBB gene is replaced by glutamine.
A mutation where the glutamic acid in position 22 in the primary sequence of a beta-chain produced by the HBB gene is replaced by valine.
A mutation where the threonine in position 87 in the primary sequence of a beta-chain produced by the HBB gene is replaced by lysine.
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 alanine.
The Adja ethnic group are mostly farmers and live in the southern part of Benin Republic. They make up 15% of the general country population. This group of people migrated into Benin between the 12th and 13th centuries from River Mono. The primary language is Aja-Gbe with a majority of the people being trilingual.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
Demographic and Health Surveys Program (2011-2012)
Bariba is the ethnic group dominating the northern side of Benin, who constitute 9% of the population. They are the first inhabitants of Benin and are concentrated in the capital city, Nikki. One of their leading practices is horse riding, which is a practice that has been enjoyed from generation to generation. With agriculture being their dominant occupation, Bariba people have a diverse range of produce such as corn, rice and palm oil.
The largest ethnic group in Benin is Fon/Dahomey which constitutes 39% of the total population. Established in 1600 by the Fon, a group that came about through the intermarriage between the Adja and local Gedevi.
The Embu are a Bantu-speaking people who are closely related to the Gikuyu of Ndia and Gicugu to the west, the Mbeere and the Kamba to the southeast, and the Chuka and the Meru to the north in Kenya.
Demographic and Health Surveys Program (2015)
The Kalenjin ethnic group are one of the five largest ethnic groups in Kenya. They are a Nilotic ethnic group and they are mainly farmers.
The Kamba ethnic group, also known as Akamba is one of the five largest ethnic groups in Kenya. They are Bantu-speaking people and primarily agriculturists.
The Kikuyu are the largest single ethnic tribe in Kenya, making up 22% of the country's population. It is believed that the Kikuyu people migrated from Lake Chad to East Africa in 1000 AD, settling in the fertile central highlands of Kenya and engaging in farming.
The Kisii tribe (also known as the Gusii tribe) is a Bantu ethnic group who occupy the Kisii highlands in Nyanza, Western Kenya. The Kisiis constitute the sixth largest ethnic group, comprising about seven percent of the national population. Kisii, which is their ethnic language, is also traditionally known as Ekegusii.
The Luhya ethnic group, also known as the Abaluhya, Baluhya, or Abaluyia, is a Bantu tribe living in Kenya's agriculturally fertile western region. They are the second largest tribe in Kenya and neighbors to some of the Nilotic tribes, including the Luo, Kalenjin, Maasai and Teso (Iteso).
Luo, also called Joluo or Kavirondo constitute the fourth largest ethnic group in Kenya. The Luo speak a Nilotic language of the Nilo-Saharan language family.
A smaller ethnic group, accounting for only about 0.7 percent of Kenya's population, with a similar number living in Tanzania. Maasais speak Maa, a Nilotic ethnic language from their origin in the Nile region of North Africa.
Yoruba is an ethnic group coming from Nigeria and well settled along the eastern boundary of Benin. They are more than 18% of the population. The majority of the Yoruba people in Benin are descendants of the Ife tribe, and the Yoruba people are predominantly of the Muslim religion.
The Meru tribe or Merus is a Bantu ethnic group. They reside on Mount Kenya's agriculturally rich northeastern slopes, in Kenya's Eastern Province. The name Meru refers to both the people and the location. Merus are primarily agrarian, raising a few domestic animals.
The Mijikenda tribe is a Kenyan coastal Bantu tribe that consists of nine closely related sub-tribes. "Mijikenda" literally means nine homes or nine homesteads (in Swahili), referring to the common ancestry of the Mijikenda people. The nine Mijikenda sub-tribes are believed to be nine different homes of the same tribe. Each sub-tribe speaks its own dialect of the Mijikenda language.
A Cushitic speaking people comprising a small minority of Kenya's population. The Somali tend large herds of cattle, goats, sheep, and camels in the dry, arid lands of Northern Kenya. They are politically well organized and are united by both family allegiances and political treaties. The Somali also produce exquisitely carved headrests and woven artifacts.
The Taita people are a Bantu tribe living in the Taita Hills on Kenya's southwest, near the Tanzania border and surrounding plains. Taita tribe actually consists of three separate but closely-related tribes: Wadawida (or Taita), Wasaghala (Sagalla) and Wataveta (Taveta).
Perhaps change label to "Taveta"? Include the Wadawida (or Taita), Wasaghala (Sagalla) and Wataveta (Taveta) as sub-classes? Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
Demographic Health and Surveys Program (2015)
The Borana are a branch of the populous Oromo people found in southern Ethiopia and northern Kenya.
It is the second largest sub-tribe of the Luhya ethnic group in Kenya.
The Pokot are a Kalenjin-speaking people whose language incorporates words from the neighboring Karamojong and Turkana. The Pokot live in an ecologically complex region that extends from the plains of eastern Uganda across the highlands of northwestern Kenya to the plains of Lake Baringo.
The Turkana tribe is a nomadic pastoralist people that inhabit the Turkana district in Kenya's Rift Valley Province. Turkana tribe is part of the Nilotic tribes and constitutes the second largest pastoralist community in Kenya after the Maasais. They speak the Turkana language, which is Nilotic and similar to the Maasai language.
Bassa is a Niger-Congo Kru language. Historians have traced the Bassa's origins back to Egypt nearly six thousand years ago. Due to their migration from Egypt to other parts of Africa, the Bassa in Liberia share a similar history with Bassa groups in other parts of the continent such as Nigeria (Bassa Nge), The Democratic Republic of the Congo (Bassaa la Mpasu), Togo (Basa'r), Senegal (Bassa-Ri), and Cameroon (Basaa Mpoo).
Demographic and Health Surveys Program (2013)
Spectrophotometry involves the use of a spectrophotometer to measure the amount of light that a sample absorbs. The instrument operates by passing a beam of light through a sample and measuring the intensity of light reaching a detector.
A recommendation on the appropriate treatment and care of people with a specific disease or condition, based on the best available evidence, designed to help healthcare professionals in their work.
Management protocols for the purposes of consistency and standardisation, which could also facilitate sharing of resources between centers for maximal utility. These recommendations have been developed for the South African setting, and it is intended to update them regularly to meet new demands and challenges.
Probably not necessary to include in other ontologies.
N A Alli, M Patel, H D Alli, et al. Recommendations for the management of sickle cell disease in South Africa. SAMJ. 2014, Vol. 104, No. 11.
Recommendations for the Management of Sickle Cell Disease in South Africa
Guidelines for the management of specific clinical problems and protocols for various therapeutic procedures for patients with sickle cell disease and thalassaemia; to facilitate uniformity and standardization of care across different disciplines.
National guideline for the control and management of sickle cell disease. 2014.
National Guideline for the Control and Management of Sickle Cell Disease
Guidelines for health care professionals for management of sickle cell disease in patients in the Tanzanian context.
Management of Sickle Cell Disease - The United Republic of Tanzania
A booklet with information and standard guidelines to help parents learn about sickle cell disease and how to take care of their children with sickle cell disease.
A parent's guide to managing sickle cell disease. Brent Sickle Cell and Thalassaemia Centre. 3rd Edition 2012.
A Parental Guide to Managing Sickle Cell Disease
A document that includes standards and guidelines for clinical care and recommendations for how care for adults with sickle cell disease should be delivered.
Standards for Clinical Care of Adults with Sickle Cell Disease in the UK, 2nd Edition. 2018, Sickle Cell Society.
Standards for Clinical Care of Adults with Sickle Cell Disease in the UK
The second edition of the Clinical Care Guidelines of the Sickle Cell Unit, containing revised and expanded guidelines for the management of sickle cell disease. It outlines a standard of care that is informed by best practice, taking into account resource limitations locally and regionally. It also contains patient information leaflets.
Sickle Cell Disease: The Clinical Care Guidelines of the Sickle Cell Unit, 2015
Sickle Cell Disease: The Clinical Care Guidelines of the Sickle Cell Unit
Standard of care guidelines that promote excellence in sickle cell care, and that lead to improved patient experiences around care and treatment.
Segbefia C, Pendergrast J, Amid A, et al. 2015. Consensus Statement on the Care of Patients with Sickle Cell Disease in Canada. The Canadian Haemoglobinopathy Association.
Consensus Statement on the Care of Patients with Sickle Cell Disease in Canada
A document that include standards and guidelines for clinical care and recommendations for how care for children with sickle cell disease should be delivered.
Sickle cell disease in children, standards and guidelines for clinic care. 2nd edition. October 2010
Sickle Cell Disease in Children, Standards and Guidelines for Clinic Care
Guidelines providing the best science-based recommendations to guide practice decisions for primary care providers and other clinicians, nurses, and staff who provide emergency or continuity care to individuals with sickle cell disease (SCD). They assist health care professionals in the management of common issues, including routine health maintenance, the recognition and treatment of common acute and chronic complications and comorbidities of SCD, as well as the indications for and monitoring of hydroxyurea and blood transfusion therapy. The guidelines address the care of infants, children, adolescents, and adults with SCD, with the goal of facilitating high-quality and appropriate care for all individuals with this disease.
Evidence-Based Management of Sickle Cell Disease: Expert Panel Report, 2014
Evidence-Based Management of Sickle Cell Disease
A review of service delivery across Europe to children with sickle cell disease (SCD), reporting on the available minimum standards of care and future perspectives.
Colombatti R and Sainati L. Management of children with sickle cell disease in Europe: current situation and future perspectives. EMJ Hematol. 2016;4[1]:129-135.
Management of Children with Sickle Cell Disease in Europe: Current Situation and Future Perspectives
A document that describes various ways in which sickle cell disease can be managed and its complications can be prevented in children.
European document for children with SCD (Montalambert)
ENERCA Clinical Recommendations for Disease Management and Prevention of Complications of Sickle Cell Disease in Children
Research conducted on members of families, examining the affects of genetics, the environment, or twin offspring.
The distinguishing qualities or prominent aspects of an individual person that have some relation with quality of life.
Probably too specific to SCDO to be included in other ontologies?
Quality of Life Related Personal Attribute
Hemoglobin that has undergone conformational changes resulting in increased hydrophobicity that results in the formation of solid crystals consisting of hemoglobin particles.
When one beta-globin gene carries the hemoglobin S mutation (beta6Glu>Val) whereas the other carries a mutation that reduces the amount of beta-globin chain synthesised.
Hemoglobin Genotype S/Beta Minus Thalassaemia
Work consisting of a set of statements, directions, or principles presenting current or future rules or policy. Guidelines may be developed by government agencies at any level, institutions, organizations such as professional societies or governing boards, or by the convening of expert panels. The text may be cursive or in outline form, but it is generally a comprehensive guide to problems and approaches in any discipline or activity. This concept relates to the general conduct and administration of health care activities rather than to specific decisions for a particular clinical condition.
Do we rather want to use the more specific MESH term "Practice Guideline"?
A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains of hemoglobin S. Individuals with this genotype are known to be carriers of the sickle cell trait.
The condition in which an individual with sickle cell trait shows symptoms of sickle cell disease such as anemia or acute chest syndrome.
Clinical Sickle Cell Disease in the Heterozygous State
Often these individuals have co-inherited another hemoglobin mutation that decreases hemoglobin solubility (eg, HbS-Antilles; Hb-Quebec-Chori; HbS-Oman; Hb Jamaica Plain). Other rare causes of symptomatic sickle cell trait include: mosaicism for cells in which only the sickle mutation was expressed due to post-zygotic uniparental disomy, and when sickle cell trait coexists with pyruvate kinase deficiency, which lowers the hemoglobin oxygen affinity, resulting in hemoglobin S polymerization and sickling.
deprecated-Symptomatic Sickle Cell Trait
A hemoglobinopathy in which the sickle mutation (HBB, Glu6Val) is inherited in combination with another beta-globin gene mutation, other thanHBB, Glu6Val.
Compound Heterozygous Sickle Cell Disease
Sickle cell disease caused by two mutations in the same beta globin allele, specifically the sickle cell mutation beta6 Glu > Val and a second beta68 Leu > Phe mutation.The other beta globin allele produces normal beta globin chains.
Sickle cell disease caused by two mutations in the same beta globin allele, specifically the sickle cell mutation (beta6 Glu > Val) and the hemoglobin O-Arab mutation (beta121 Glu > Lys). The other beta globin allele produces normal beta globin chains.
Sickle cell disease caused by two mutations in the same beta globin allele, specifically the sickle cell mutation beta6 Glu > Val and a second beta 23 Val>Ile mutation. The other beta globin allele produces normal beta globin chains.
A directive information entity that specifies how to establish a diagnosis based on clinical findings.
An ICD-10-CM code that can be used to indicate a diagnosis for reimbursement purposes as there are no codes with a greater level of specificity under each code.
An ICD-10-CM diagnosis code that is not billable as there are more specific codes below it that contain a greater level of detail.
Priapism due to disease classified elsewhere
N48.32 Priapism due to disease classified elsewhere
A data element in the SickleInAfrica Extended Demographics data capture instrument.
SickleInAfrica Extended Demographics Data Element
When the abnormal hemoglobin, hemoglobin E (HbE), has been detected in a blood sample.
When the level of hemoglobin A2 detected in a sample of blood falls in the normal range for HbA2.
A test to detect both HIV antibodies and HIV antigens (a part of the virus) in blood.
It can take 2 to 6 weeks for a person’s body to make enough antigens and antibodies for a combination test to detect HIV infection.
A test to detect HIV in a person's blood.
Request inclusion into relevant ontology. The more specific term "HIV-1 nucleic acid testing" is found in the OBI.
NATS can detect HIV infection about 7 to 28 days after a person has been infected with HIV. NATs are very expensive and not routinely used for HIV screening unless the person had a high-risk exposure or a possible exposure with early symptoms of HIV infection.
An abnormal albumin excretion rate of more than 300 mg/g urine creatinine.
A clinically severe form of sickle cell disease resulting when a person is homozygous for Hemoglobin C-Harlem.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, crossing over; gene conversion; genetic transformation; genetic conjugation; genetic transduction; or mixed infection of viruses.
An exchange of DNA between matching or similar sequences.
The reciprocal exchange of segments at corresponding positions along pairs of homologous chromosomes by symmetrical breakage and crosswise rejoining forming cross-over sites (Holliday junctions) that are resolved during chromosome segregation. Crossing-over typically occurs during meiosis but it may also occur in the absence of meiosis, for example, with bacterial chromosomes, organelle chromosomes, or somatic cell nuclear chromosomes.
The homologous recombination event that occurs during meiosis and results in the delta beta globin fusion chains that replace hemoglobin subunit beta chains in the abnormal hemoglobin, Hemoglobin Lepore.
Crossover between delta (HBD) and beta globin (HBB) gene loci
Clinical sickle cell disease in the heterozygous state due to an additional mutation on the same allele as the beta S mutation.
Hemoglobin Jamaica Plain is an example of an abnormal hemoglobin structure caused by a double mutation in 1 Hb allele.
deprecated Disease Caused by A/Jamaica Plain Genotype
deprecated Disease Caused by A/S-Oman Genotype
deprecated Disease Caused by C/S Antilles Genotype
A hemoglobinopathy involving the presence of structurally abnormal hemoglobins and defects in the quantity of hemoglobins synthesised.
Probably too specific to the SCDO to be included in other ontologies.
Structural and Quantitative Hemoglobinopathy
A genotype whereby one of the four alpha-globin genes is faulty, either as a result of a single nucleotide variant (SNP) or of a deletion.
Suggest update to label of HPO's "Bruising Susceptibility". "Bruising Susceptibility" and "Easy Bruisability" are not actually the same thing.
Bruisability, Bruising susceptibility, Easy bruising
A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains for hemoglobin C. Individuals with this genotype are known to be carriers of the hemoglobin C trait.
A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains for hemoglobin D. Individuals with this genotype are known to be carriers of the hemoglobin D trait.
A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains for hemoglobin E. Individuals with this genotype are known to be carriers of the hemoglobin E trait.
A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains for hemoglobin O-Arab. Individuals with this genotype are known to be carriers of the hemoglobin O-Arab trait.
The homozygous genotype that involves a substitution of glutamic acid for a lysine at position 26 of beta-globin chains (hemoglobin E mutation) produced by both beta-globin gene (HBB) alleles.
The homozygous genotype that involves a hemoglobin D mutation in both beta-globin gene (HBB) alleles.
The homozygous genotype that involves a substitution of glutamic acid for a lysine at position 121 of beta-globin chains (hemoglobin O-Arab mutation) produced by both beta-globin gene (HBB) alleles.
The homozygous genotype that involves a substitution of glutamic acid for a lysine at position 6 of beta-globin chains (hemoglobin C mutation) produced by both beta-globin gene (HBB) alleles.
The presence of an amino acid substitution in either an alpha-, beta-, or gamma-globin chain such that its proximity to the heme iron in the hemoglobin molecule results in facilitated oxidation of the hemoglobin to yield excess methemoglobin. This can occur in either one or both alleles of the effected gene.
Either homozygosity or heterozygosity for the HPFH1 mutation, a 106-KB deletion in the beta globin gene cluster.
Hereditary Persistence of Fetal Hemoglobin Genotype
The homozygous genotype for Hemoglobin Lepore Boston that involves a crossover between both sets of delta (HBD) and beta globin (HBB) gene loci during meiosis.
The inheritance of one normal HBB gene along with an abnormal HBB gene that contains two amino acid substitutions, namely Glu6Val (HbS) and Asp73Asn.
Erythrocytes from persons with Hb CH trait show some sickling in hypertonic saline without deoxygenation; this finding and the renal functional abnormalities are similar to those seen in persons with sickle cell trait and suggest that the renal concentrating defects in the two disorders have similar pathogeneses.
A mutation in the NADH-Cytochrome b5 Reductase 3 gene, CYB5R3, that contributes to the presence of methemoglobinemia (type I or II).
Deletion of one alpha-globin gene, either an HBA1 or HBA2 gene, which results in Alpha Thalassemia Silent (the person with the mutation is a silent carrier).
Either a decrease in the proportion of hemoglobin A to below 96-98% of all hemoglobin, or a complete lack of hemoglobin A production.
Probably too specific to be added to existing ontologies?
A lack of production of normal adult hemoglobin.
Request inclusion into HPO below "Abnormal Hemoglobin Concentration".
A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals that are homozygotes (having two copies of the same mutant allele).
Autosomal Homozygous Recessive Inheritance
A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals that are compound heterozygotes (whereby each copy of a gene has a distinct mutant allele).
Autosomal Recessive Compound Heterozygous Inheritance
Autosomal Recessive Compound Heterozygous
A sickle cell disease phenotype in which an individual heterozygous for hemoglobin S also has a severe pyruvate kinase deficiency, which lowers the hemoglobin oxygen affinity, resulting in hemoglobin S polymerization and sickling.
Sickle Cell Trait with a Severe Pyruvate Kinase Deficiency
A powder form of the optically active form of glutamine having L-configuration; to be administered orally.
Suggest update to description in the Drug Ontology (DRON) for "Glutamine Oral Powder" (currently no description provided).
Oral administration of L-glutamine oral powder is approved by the FDA to reduce the acute complications of sickle cell disease and sickle beta zero-thalassemia in adult and pediatric patients.
A phenotype in which a specific molecular function is abnormal.
An increase in red blood cell sensitivity to change in osmotic pressure. More specifically, the degree or proportion of hemolysis that occurs when a sample of red blood cells are subjected to osmotic stress by being placed in a hypotonic solution.
What is normal osmotic fragility? Perhaps this can be included in the description. Suggest update to description in the HPO. Currently no description given. Include "Osmotic Fragility Test" in an appropriate location below "Diagnostics Tools" and link to this term.
Is this not the same as "Increased Red Cell Osmotic Fragility"? See dc:source provided. What is normal osmotic resistance? Perhaps this can be included in the description. Suggest update to description in the HPO. Currently no description given. Include "Osmotic Fragility Test" in an appropriate location below "Diagnostics Tools" and link to this term.
A situation in which a specific biological process within an organism is abnormal.
Include here "Intrahepatic Sinusoidal Sickling"? See paper "Liver involvement in sickle cell disease" by Emel GÜRKAN et al.
When deoxygenated, malfunctioning or mutated hemoglobins clump together and form a long polymer.
Guidelines that examine current available evidence on indications for transfusion in sickle cell disease.
Guidelines on Red Cell Transfusion in Sickle Cell Disease - Part II: Indications for Transfusion
This guideline addresses the management of an acute painful sickle cell episode in patients presenting to hospital until discharge. This includes the use of pharmacological and non-pharmacological interventions, identifying the signs and symptoms of acute complications, skills and settings for managing an acute painful episode, and the information and support needs of patients.
Sickle Cell Acute Painful Episode - Management of an Acute Painful Sickle Cell Episode in Hospital
A factsheet that shares steps to improve care in emergency departments (ED) of hospitals and clinics for people with sickle cell disease (SCD). It was created to help improve healthcare in the ED for patients with SCD.
Three Tips About Sickle Cell Disease Every Emergency Provider Needs to Know
A comprehensive guideline to aid physicians and other health care professionals in the management of patients with acute and chronic pain associated with sickle cell disease (SCD). The guideline covers the following information: an overview of the disease, the types and characteristics of pain associated with the disease, recommendations for pain assessment, methods for treatment of pain and a discussion of pain in the various developmental stages. It also includes discussions of pain assessment instruments.
Practice Guidelines: Management of Pain in Sickle Cell Disease
A hemoglobin that shows characteristics of an abnormal hemoglobin, but its inheritance does not accompany any disability.
Request inclusion into NCIT below "Hemoglobin"/"Hemoglobin Variant".
Any feeling of illness or physical or mental change that results from strenuous exercise.
Suggest update to description in OMIM (currently no description provided).
A condition due to a deficiency of one or more essential vitamins. (Dorland, 27th ed)
Abnormality originating in one or more muscles of the set of muscles in the body.
An abnormal level of hemoglobin that occurs in one or more forms of Sickle Cell Disease (SCD).
Hemochromatosis that results from repeated blood transfusions.
An acquired metabolic disorder characterized by iron accumulation in the tissues.
Suggest inclusion into existing ontology.
When the abnormal hemoglobin, hemoglobin D-Punjab (Hb D-Punjab), has been detected in a blood sample.
When the abnormal hemoglobin, hemoglobin G-Philadelphia (Hb G-Philadelphia), has been detected in a blood sample.
When the abnormal hemoglobin, hemoglobin O-Arab (Hb O-Arab), has been detected in a blood sample.
When the level of hemoglobin F detected in a sample of blood falls in the normal range for HbF.
The score obtained from a quality of life-related diagnostic instrument.
The score obtained from the Adult Sickle Cell Quality-of-Life Measurement Information System (ASCQ-Me) diagnostic instrument.
A diagnostic instrument that involves an assessment of quality of life- and/or quality of care-related elements.
Quality of Life and Care Diagnostic Instrument
A deteremination of the presence of hepatitis B virus surface antigen.
Suggest update to label in NCIT (from "Hepatitis B Virus Surface Antigen Measurement")
Hepatitis B Virus Surface Antigen Measurement
If a person tests “positive,” then further testing is needed to determine if this is a new “acute” infection or a “chronic” hepatitis B infection. A positive HBsAg test result means that you are infected and can spread the hepatitis B virus to others through your blood.
The determination of the surface antibody reaction of a sample to the Hepatitis B virus.
Suggest update to label in NCIT (from "Hepatitis B Surface Antibody Measurement")
The determination of the amount of Hepatitis B virus core antibody present in a sample.
Suggest update to label in nCIT (from "Hepatitis B Virus Core Antibody Measurement")
A "positive" or "reactive" anti-HBc (or HBcAb) test result indicates a past or current hepatitis B infection. The core antibody does not provide any protection against the hepatitis B virus (unlike the surface antibod). This test can only be fully understood by knowing the results of the HBsAg and anti-HBs tests. A positive anti-HBc (or HBcAb) test result requires talking to your health care provider for a complete explanation of your hepatitis B status.
A set of three blood tests (Hepatitis B Core Antibody Test, Hepatitis B Surface Antibody Test, and Hepatitis B Virus Surface Antigen Test) needed to fully understand whether a person is infected with Hepatitis B or not.
The determination of the amount of hepatitis B virus antibody present in a sample.
Suggest update to label in NCIT (from "Hepatitis B Virus Antibody Measurement")
The determination of the amount of hepatitis B virus core IgG antibody in a biological specimen.
Suggest update to label in NCIT (from "Hepatitis B Virus Core IgG Antibody Measurement")
Hepatitis B Virus Core IgG Antibody Test
The determination of the amount of Hepatitis B virus core IgM antibody present in a sample.
Suggest update to label in NCIT (from "Hepatitis B Virus Core IgM Antibody Measurement")
Hepatitis B Virus Core IgM Antibody Test
Exercise testing for evaluation of hypoxemia and/or desaturation that occurs on exertion.
Suggest inclusion of term below "Pulse Oximetry" in the CMO.
PhenX protocol: Pulse Oximetry (Exercise) #91001
The determination of the amount of hepatitis C virus antigen present in a sample.
Suggest update to label in NCIT (from "Hepatitis C Virus Antigen Measurement"
A determination of the presence of the hepatitis C virus antibody in a biological specimen.
Suggest update to label and description in NCIT (from "Hepatitis C Antibody Measurement")
The determination of the amount of hepatitis C virus core antigen in a biological sample.
Suggest update to label in NCIT (from "Hepatitis C Virus Core Antigen Measurement")
Hepatitis C Virus Core Antigen Measurement
The determination of the surface antibody reaction of a sample to the Hepatitis C virus.
Suggest update to label in NCIT (from "Hepatitis C Surface Antibody Measurement")
Hepatitis C Surface Antibody Measurement
The determination of the amount of cystatin C present in a sample.
Suggest update to label in NCIT (from "Cystatin C Measurement")
The visual output that a specific diagnostic device produces.
A bioassay to measure levels of red blood cell microparticles.
A quantitative measurement of the amount of HDL cholesterol present in a sample of serum.
Suggest update to label in NCIT (from "Serum HDL Cholesterol Measurement")
A technique used to measure velocity and amount of blood flow and circulation in the living system.
Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart.
Suggest this description for this term in the CMO (it was recently described separately from another similar term" but's it's definition has not yet been ascribed).
An information entity, used in the diagnosis of medical conditions, that is a recording of the output of a diagnostic instrument.
Request inclusion into relevant ontology Add terms/Variables obtained from: History of Head Trauma Diagnostic Instrument
Questions asking the respondent about smoking status in his or her entire life.
Cigarette Smoking Status Diagnostic Instrument
Questions asking an adult respondent about smoking status in his or her entire life.
PhenX protocol: Cigarette Smoking Status - Adult #30604
Cigarette Smoking Status Diagnostic Instrument - Adult
Questions asking an adolescentt respondent about smoking status in his or her entire life.
PhenX protocol: Cigarette Smoking Status - Adolescent #30603
Cigarette Smoking Status Diagnostic Instrument - Adolescent
A person who has never smoked a cigarette, not even one or two puffs.
Other ontologies define this as "A person who was not smoking at the time of the interview and has smoked less than 100 cigarettes in their life."
A person who was smoking on a daily basis at the time of the interview.
Other ontologies define this as "Indicates a person who has smoked at least 100 cigarettes in his or her lifetime and who currently smokes every day."
A person who had smoked a cigarette in the past, and was smoking on some days, but not daily, at the time of the interview.
Other ontologies define this as "Indicates a person who has smoked at least 100 cigarettes in his or her lifetime, who smokes now, but does not smoke every day."
A person who was not smoking at the time of the interview but has smoked a cigarette in the past, even if just one or two puffs
Other ontologies define this as "A person who was not smoking at the time of the interview but has smoked at least 100 cigarettes in their life."
A person who has smoked a cigarette in the past, even if just one or two puffs, but was unable to or refused to answer when asked when the last time was that they smoked a cigarette, even one or two puffs.
A person who had smoked in the past 30 days at the time of the interview, but who had not smoked every day of the past 30 days.
A person who had smoked every day of the past 30 days at the time of the interview.
Question asking the respondent if s/he has ever consumed any alcoholic beverage during his or her entire life.
Alcohol - Lifetime Use Diagnostic Instrument
A nine-item, interviewer-administered questionnaire to screen for the presence of epilepsy in adults.
Request inclusion into "PhenX Phenotypic Terms". This is in the PhenX toolkit but not in the ontology in BioPortal. It should probably be included there.
A nine-item, interviewer-administered questionnaire to screen for the presence of epilepsy in family members, including children and those who are deceased.
Family History of Epilepsy Screening Interview
Ottman Brief Epilepsy Screener - Proxy-reported Version
A disruption to the efficacy of the executive functions, which is a group of cognitive processes that regulate, control, and manage other cognitive processes.
Request inclusion into relevant ontology. Perhaps below "Behavioral Abnormality" in the HPO.
A series of 21 age-specific questionnaires and scoring sheets designed to screen a child's skills in five developmental areas: fine motor, gross motor, problem solving, communication, and personal-social. A child's scores for each area are compared to cut-off scores to determine a need for monitoring or further assessment.
Request inclusion into relevant ontology. Maybe below "Clinical or Research Assessment Questionnaire" in the NCIT.
Global Mental Status Screener - Child #130702
The Ages & Stages Questionnaires, Third Edition (ASQ-3)
The frequency of acute pain episodes due to sickle cell disease (SCD).
Request inclusion into relevant ontology Add as sub-classes: (from protocol questions) - a term for the number of times an emergency room was visited because of a sickle cell painful event in the last 6 months - a term for the number of times the person was admitted to a hospital because of a sickle cell painful event in the last 12 months
Not relevant to context of sickle cell. This term in PhenX currently refers to a diagnostic instrument.
Questions from the National Epidemiologic Survey on Alcohol and Related Conditions-III (NESARC-III) related to their lifetime use of illicit and prescribed substances.
PhenX protocol: Substances - Lifetime Use #31102
Substances - Lifetime Use Diagnostic Instrument
A 26-item, self-administered scale completed by the parent that assesses the child's sleep behaviors in the past 6 months. The scale includes six subscales: disorders of initiating and maintaining sleep (items 1, 2, 3, 4, 5, 10, 11); sleep breathing disorders (items 13, 14, 15); disorders of arousal (items 17, 20, 21); sleep-wake transition disorders (items 6, 7, 8, 12, 18, 19); disorders of excessive somnolence (items 22, 23, 24, 25, 26); and sleep hyperhidrosis (score of the items 9, 16). Each item is rated on a 5-point, Likert-type scale (1 = Never; 5 = Always [daily]). Scores from individual items of each subscale are added together to give a subscale score, with higher scores indicating greater symptoms. Scores from the individual subscales can be added together to give a total score.
Request inclusion into relevant ontology. Separate adult vs children instruments not shown in "PhenX Phenotypic Terms".
PhenX protocol: Sleep Disorders Screener - Children #121002
A record of an individual's background in regard to head trauma.
Request inclusion into relevant ontology. Perhaps as a sub-class of "History of Trauma" in "The Stroke Ontology"? PhenX uses this as their label for a questionnaire, but we're going to suggest they change that. Otherwise, don't see it in other ontologies.
A record of an individual's history of stroke(s) and associated symptoms such as slurred speech, double vision, loss of vision, and paralysis.
Request inclusion into NCIT below "Personal Medical History". Note: Is present in The Stroke Ontology.
A record of an individual's history of kidney failure.
Request inclusion into NCIT as a sub-class of "Personal Medical History". PhenX uses this as their label for a questionnaire, but we're going to suggest they change that. Otherwise, don't see it in other ontologies.
A questionnaire to assess history of transfusion.
Suggest update to label as we have done. We are using "History of Transfusion" below Personal Attribute.
PhenX protocol: History of Transfusion #830201
History of Transfusion Diagnostic Instrument
A record of an individual's history of type 1 and type 2 diabetes.
A questionnaire to assess males' pregnancy history.
Suggest update to label and description in PhenX as we have done. We are using "Reproductive History" below Personal Attribute.
PhenX protocol: Reproductive History - Male #101302
Suggest update to label and description.
Reproductive History Diagnostic Instrument - Male
A questionnaire to assess females' pregnancy history.
PhenX protocol: Reproductive History - Female #101301
Reproductive History Diagnostic Instrument - Female
A questionnaire to assess sleep disorders, a broad group of disorders that can be caused by endogenous disturbances in the sleep-wake or timing cycles (American Psychiatric Association, 2000).
A test to assess the structure and function of the heart valves.
Suggest update to label in PhenX (from "Heart Valve Function")
PhenX protocol: Heart Valve Function #40501
Measurement of the breathing capacity of an adult's lung by means of a spirometer.
Suggest update to description in PhenX (currently the same for both adult and child protocols)
PhenX protocol: Spirometry - Adult #91601
Measurement of the breathing capacity of a child's lung by means of a spirometer.
PhenX protocol: Spirometry - Child #91602
Pattern of behavior which predisposes certain individuals to increased risk for contracting disease or sustaining personal injury. These behaviors may cluster into a risky lifestyle.
Physical surroundings or conditions of a hospital or other health facility and influence of these factors on patients and staff.
Height above sea level or above the earth's surface.
A measure of educational progress reported using a questionnaire based approach, often used as a proxy for cognitive performance as the two are correlated.
PhenX protocol: Current Educational Attainment #11001
A gene that encodes one of the globin family proteins, which are globular heme-containing proteins and include androglobin, cryoglobin, hemoglobin subunits, myoglobin and neuroglobin.
A gene that provides instructions for making a protein called alpha-globin.
A gene located in the beta-globin locus (or gene cluster) on chromosome 11.
Include sub-classes?: HBE1 (encodes hemoglobin subunit epsilon) HBG1 HBG2 HBM HBQ1 HBZ
Should this perhaps rather be something like "Beta-Globin Locus Gene"? To prevent confusion with the HBB Gene. Request inclusion into relevant ontology.
A member of the alpha-globin family. In humans, it is encoded in the alpha-globin gene cluster or locus, located on chromosome 16. Two hemoglobin subunit zeta chains combine with two hemoglobin subunit epsilon chains to form the embryonic Hemoglobin Gower 1.
An adult hemoglobin component normally present in hemolysates from human erythrocytes in concentrations of about 3%. The hemoglobin is composed of two alpha chains and two delta chains. The percentage of HbA2 varies in some hematologic disorders, but is about double in beta-thalassemia.
Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin".
A mutation that contributes to decreased or absent synthesis of the delta- and beta-globin chains with a compensatory increase in expression of fetal gamma-chain synthesis.
A health abnormality in a woman during pregnancy.
Suggest update to description in HP. Currently no description.
Request inclusion into NCIT as sub-class of "Avascular Necrosis of Humerus".
Health care services that are respectful of and responsive to the health beliefs, practices and cultural and linguistic needs of diverse patients. 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.
Any kidney disorder occurring as a consequence of injury to the kidney.
Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES.
A gene component is a component of a gene.
A gene regulatory component is a gene component that exerts a regulatory function.
A gene enhancer is a short region of DNA that can be bound with proteins to enhance transcription levels of genes in a gene cluster.
A gene promoter is a region of DNA that initiates transcription of a particular gene.
A characteristic that further describes the nature of data.
The predominant publication type for articles and other items indexed for NLM databases.
A characteristic or directive that further describes the nature of data sharing.
Requirements indicate additional conditions set for use of data.
The standard method of providing feedback to study participants regarding their information (data, biological samples, genetic material) that has been shared.
Policy for Returning Results to Participant
An element or information entity that is required to be provided in consent forms.
The policy regarding participants' right to withdraw their participation in a study.
A course or principle of action adopted or proposed by a study.
A statement of what the key investigational purpose of the study is.
A statement about how the researcher is obligated by law to report if the participant is found to have a communicable disease.
Communicable Disease - Report by Law Statement
The principles of professional conduct concerning the rights and duties of the physician, relations with patients and fellow practitioners, as well as actions of the physician in patient care and interpersonal relations with patient families.
Concepts related to ethics, excluding types of ethics.
A protein expressed in enterocytes of the small intestine and released into the systemic circulation when there is intestinal damage. This protein plays a role in binding to saturated long-chain fatty acids with a high affinity and to unsaturated long-chain fatty acids with less affinity.
Intestinal-Type Fatty Acid-Binding Protein
The level of intestinal fatty-acid binding protein in the systemic circulation (serum).
Used to provide the evidence for intestinal injury due to VOC affecting the splanchnic vasculature.
Serum Intestinal Fatty-Acid Binding Protein Level
Adverse functional, metabolic, or structural changes in ischemic tissues resulting from the restoration of blood flow to the tissue (reperfusion), including swelling; hemorrhage; necrosis; and damage from free radicals. The most common instance is myocardial reperfusion injury.
An increased circulating blood concentration of the intestinal fatty-acid binding protein.
Significantly high serum iFABP levels is evidence of intestinal injury.
The level of L-selectin in the systemic circulation (serum).
The number of aged neutrophils in a specified volume of blood, usually 1 cubic millimeter.
A medication that is typically used for indications other than pain control but provides control of pain in some painful diseases.
An infusion of ketamine at a low dose (up to 5 µg/kg/min).
Low-dose ketamine infusion may be considered as an adjunct analgesic agent in patients with vaso-occlusive episodes who report continued severe pain despite high-dose opioid therapy, particularly those experiencing opioid-induced adverse effects.
Pain that may be caused by or related to cellular, tissue, and systemic changes that occur during neoplasm growth, tissue invasion, and metastasis.
The current age of a patient, calculated using the current date and the patient's date of birth and provided in years.
A type of consent that includes an aspect of timing (i.e. an indication of when consent was acquired).
Consent that is taken later after enrollment into study especially in emergency situations.
Informed consent given prior to enrollment.
Consent obtained at a population level through public/community engagement where individual consenting is not feasible. This is normally done for low risk studies and/or in case of emergencies.
A decision made by a research ethics committee.
When a research ethics committee approves a study's application for approval of their proposed research.
When a research ethics committee declines a study's application for approval of their proposed research.
A method in which a patient or their legal representative provides consent.
When the participant or a legal representative or family member provides consent by filling out and/or signing a written form.
When the participant communicates consent orally rather than by filling out and signing a written form. Normally a witness is present when verbal consent is given.
A unique identifier assigned to a study participant's data when it is registered in the SickleInAfrica data registry.
The name of the country where the sample or data was collected.
The rules by which data are described and recorded.
A data element used to capture or facilitate the capture of data in a clinical or research assessment.
Clinical or Research Assessment Data Element
A type of question pertaining to a clinical or research assessment data element.
Clinical or Research Assessment Question Type
deprecated Dropdown Multiple Choice Field Type
deprecated Dropdown Single Choice Field Type
The situation, with regard to obtaining consent from a respondent, at a particular stage during a process.
A question that provides the respondent with specific answer options to choose from.
A question that allows the respondent to give their own answer instead of selecting an answer from answer options.
A close-ended question that provides two possible answers.
A close-ended question that provides multiple answers for respondents to select from and allows for the selection of multiple options.
Multiple Choice Multiple Selection Question
A close-ended question that provides multiple answers for respondents to select from but allows for the selection of only one option.
Multiple Choice Single Selection Question
A dichotomous question that has answer options "true" and "false".
A dichotomous question that has answer options "yes" and "no".
A open ended question that restricts the nature of the text answer that can be provided by the respondent.
A open ended question that allows the respondent to respond in free text, without any restrictions on the nature of the text answer provided.
A data element in a SickleInAfrica data capture instrument.
A data element in the SickleInAfrica core data capture instrument.
The Sickle in Africa core data element that collects the concentration of albumin in the respondent's urine.
Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise)
SickleInAfrica CDE - Urinary Albumin Concentration Question
The Sickle in Africa core data element that records whether the respondent has consented as necessary.
SickleInAfrica CDE - Informed Consent Obtained Question
An indication of whether informed consent was obtained from the respondent and/or their proxy.
Voluntary authorization given by a respondent and/or their proxy to be enrolled into a study as a research subject.
Voluntary authorization given by a study respondent and/or their proxy to have their specimen(s) stored.
Voluntary authorization given by a study paticipant to have their genetic material stored.
The Sickle in Africa core data element that records the type(s) of informed consent obtained from the participant.
1, Study Enrollment Consent 2, Specimen Storage Consent 3, Genetic Material Storage Consent 4, Broad Consent
SickleInAfrica CDE - Type of Informed Consent Obtained Question
An indication of the type of informed consent that was obtained from the respondent and/or their proxies.
Time-related information that can be observed and is related to consent.
The current age of a patient, calculated using the current date and the patient's date of birth.
The Sickle in Africa core data element that records the date on which the respondent signed the consent form for the relevant study.
Date subject signed consent (dd/mm/yyyy)
SickleInAfrica CDE - Date of Signing Consent Question
The Sickle in Africa core data element that records the name of the person who managed the process of consenting the respondent.
SickleInAfrica CDE - Consented By Question
An indication of whether the respondent has had a blood transfusion since their last hospital visit. This is any transfusion before enrolment if it is the patient's first hospital visit.
An indication of whether the consent form used for obtaining informed consent from the respondent has been uploaded to the relevant electronic system.
The name of the person who conducted consenting of the respondent.
Time-related information that can be observed.
Time-related information that can be observed and is related to a diagnosis.
The Sickle in Africa core data element that records the visit date, in the format dd/mm/yyyy.
SickleInAfrica CDE - Visit Date Question
The Sickle in Africa core data element that records the site-specific unique identifier that was assigned to the study participant by the data collectors at the data collection site.
Site-specific ID eg. GH20181234 for Ghana, NG20184321 for Nigeria or TZ20180001 for Tanzania
SickleInAfrica CDE - Site Participant Number Question
The Sickle in Africa core data element that records the respondent's date of birth in the format dd/mm/yyyy.
SickleInAfrica CDE - Date of Birth Question
The current age of a patient, calculated using the current date and the patient's date of birth and provided in months.
The length of time that a person has lived since their birth up until the current day, as reported in years by the respondent.
The Sickle in Africa core data element that records the respondent's age, as reported by the respondent in years.
SickleInAfrica CDE - Self-Reported Age Question
The Sickle in Africa core data element that records the respondent's current marital status.
1, Married 2, Widowed 3, Divorced 4, Separated 5, Never been married/Annulled
SickleInAfrica CDE - Current Marital Status Question
The Sickle in Africa core data element that records the date on which the respondent last received a blood transfusion.
SickleInAfrica CDE - Date of Transfusion Question
The Sickle in Africa core data element that records the type of SCD test that was used to diagnose the respondent, in the case where the type of test was not listed as an answer option in a previous data element.
SickleInAfrica CDE - SCD Other Test Question
The Sickle in Africa core data element that records the respondent's sex.
1, Male 2, Female 3, Intersex -7, Refused
The Sickle in Africa core data element that records whether the respondent knows the date of their SCD diagnosis.
SickleInAfrica CDE - Date of Diagnosis Known Question
Information or a description that further describes a diagnosis.
An indication of whether the date of the respondent's diagnosis of a disease is known by the respondent or the respondent's guardian.
An indication of whether the date of the respondent's SCD diagnosis is known by the respondent or the respondent's guardian.
The Sickle in Africa core data element that records the respondent's date of diagnosis in the format dd/mm/yyyy.
SickleInAfrica CDE - Date of Diagnosis Question
The date on which a diagnosis of sickle cell disease was made.
The date on which a patient received a blood transfusion.
The year in which a sickle cell disease diagnosis was made.
The month when a diagnosis was assigned to an individual's condition.
The month when a sickle cell disease diagnosis was made.
The Sickle in Africa core data element that records the month of the year in which the respondent was diagnosed with SCD.
SickleInAfrica CDE - Month of Diagnosis Question
A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.
The Sickle in Africa core data element that records the respondent's SCD test result.
SS = Sickle Cell Disease-SS | SBThal = Sickle Beta Thalassemia | SC = Sickle Cell Disease-SC | AS = Sickle Cell Trait
SickleInAfrica CDE - SCD Test Result Question
The result of a medical investigation to identify the type of sickle cell disease that a person has.
The Sickle in Africa core data element that records the type of SCD test that was used to diagnose the respondent.
1, HPLC 2, HBE 3, IEF 4, Basique 5, Acide 6, Sickle SCAN rapid test 7, Other
HPLC = High-Performance Liquid Chromatography| HBE = Hemoglobin Electrophoresis | IEF = Isoelectric Focusing| Basique = Basique SCD Test | Acide = Acide SCD Test
SickleInAfrica CDE - Type of SCD Test Question
A piece of information that further describes a diagnostic measurement.
The type of test that was used to obtain a sickle cell disease diagnosis.
The Sickle in Africa core data element that records the respondent's SCD test result, in the case where the specific result was not listed as an answer option in a previous data element.
If other SCD test result, please specify:
SickleInAfrica CDE - SCD Test Other Result Question
The Sickle in Africa core data element that records the respondent's ABO Blood Group.
SickleInAfrica CDE - Blood Group Question
A blood test that uses the principles of gel electrophoresis to separate out the various types of hemoglobin in order to determine the level of different types of hemoglobin in the blood.
Placed as sub-class here according to position in the "Read Codes, Clinical Terms Version 3 (CTV3)" Ontology
A blood type containing type A red blood cell surface markers, with the presence of a protein called rhesus (Rh) factor.
A blood type containing type A red blood cell surface markers, with the absence of a protein called rhesus (Rh) factor.
A blood type containing type B red blood cell surface markers, with the presence of a protein called rhesus (Rh) factor.
A blood type containing type B red blood cell surface markers, with the absence of a protein called rhesus (Rh) factor.
A blood type containing no surface markers on red blood cells, with the presence of a protein called rhesus (Rh) factor.
A blood type containing no surface markers on red blood cells, with the absence of a protein called rhesus (Rh) factor.
A blood type containing both type A and B red blood cell surface markers, with the presence of a protein called rhesus (Rh) factor.
A blood type containing both type A and B red blood cell surface markers, with the absence of a protein called rhesus (Rh) factor
Information about how a patient's SCD is being managed.
The Sickle in Africa core data element that records the respondent's hydroxyurea use status (i.e. an indication of whether the respondent is using hydroxyurea).
SickleInAfrica CDE - Hydroxyurea Use Question
An indication of whether the respondent is using hydroxyurea.
The Sickle in Africa core data element that records the date on which the respondent started hydroxyurea therapy, in the format dd/mm/yyyy.
Date of initiation of hydroxyurea therapy (dd/mm/yyyy)
SickleInAfrica CDE - Hydroxyurea Initiation Date Question
The date on which hydroxyurea therapy was initiated.
The Sickle in Africa core data element that records whether the respondent is using penicillin V as a prophylaxis against bacterial infections.
SickleInAfrica CDE - Penicillin V Use Question
An indication of whether the respondent is using penicillin V prophylaxis.
The Sickle in Africa core data element that records the respondent's folic acid use status (i.e. an indication of whether the respondent is using folic acid).
SickleInAfrica CDE - Folic Acid Use Question
An indication of whether the respondent is using folic acid.
An indication of whether the respondent is using malaria prophylaxis.
The Sickle in Africa core data element that records whether the respondent is using malaria chemoprophylaxis (drugs that prevent malaria).
SickleInAfrica CDE - Malaria Prophylaxis Question
The Sickle in Africa core data element that records whether the respondent's pneumococcal vaccination is up to date.
SickleInAfrica CDE - Pneumococcal Vaccination Question
An indication of whether the respondent is up to date with their pneumococcal vaccinations.
The person who recorded the information about how a patient's condition is being managed.
Any assay which measures the amount, level or concentration of urea in whole blood.
The date on which the respondent's management details were added/recorded.
The Sickle in Africa core data element that collects the red blood cell count in the respondent's blood, as measured by a complete blood count.
Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise)
SickleInAfrica CDE - Red Blood Cell Count Question
The Sickle in Africa core data element that collects the white blood cell count in the respondent's blood, as measured by a complete blood count.
SickleInAfrica CDE - White Blood Cell Count Question
Any structural abnormality of leukocytes (nucleated cells of the myeloid or lymphoid lineages, found in blood or other tissue).
Suggest the HPO update their definition. Theirs currently is "An abnormality of leukocytes."
The Sickle in Africa core data element that collects the platelet count in the respondent's blood, as measured by a complete blood count.
SickleInAfrica CDE - Platelet Count Question
The Sickle in Africa core data element that collects the concentration of hemoglobin in the respondent's blood, as measured by a complete blood count.
SickleInAfrica CDE - Hemoglobin - CBC Question
The Sickle in Africa core data element that collects the respondent's mean cell volume (MCV), as measured by a complete blood count.
SickleInAfrica CDE - Mean Cell Volume Question
The Sickle in Africa core data element that collects the respondent's mean cell hemoglobin (MCH), as measured by a complete blood count.
SickleInAfrica CDE - Mean Cell Hemoglobin Question
The Sickle in Africa core data element that collects the respondent's mean cell hemoglobin concentration (MCHC), as measured by a complete blood count.
Mean cell hemoglobin concentration (MCHC)
SickleInAfrica CDE - Mean Cell Hemoglobin Concentration Question
The Sickle in Africa core data element that collects the respondent's red cell distribution width, as measured by a complete blood count.
SickleInAfrica CDE - Red Cell Distribution Width Question
Red blood cell distribution width (RDW or RDW-CV or RCDW and RDW-SD) is a measure of the range of variation of red blood cell (RBC) volume that is reported as part of a standard complete blood count. Usually red blood cells are a standard size of about 6-8 μm in diameter. Certain disorders, however, cause a significant variation in cell size. Higher RDW values indicate greater variation in size. Normal reference range of RDW-CV in human red blood cells is 11.5-14.5%.[1] If anemia is observed, RDW test results are often used together with mean corpuscular volume (MCV) results to determine the possible causes of the anemia. It is mainly used to differentiate an anemia of mixed causes from an anemia of a single cause.
The Sickle in Africa core data element that collects the level of serum creatinine in the respondent's blood.
SickleInAfrica CDE - Serum Creatinine Concentration Question
An abnormally increased amount of creatinine in the blood.
Suggest update to description in HPO (include the word "abnormally")
The Sickle in Africa core data element that collects the concentration of creatinine in the respondent's urine.
SickleInAfrica CDE - Urinary Creatinine Concentration Question
The Sickle in Africa core data element that collects the level of alanine aminotransferase in the respondent's blood.
Liver Function Assay (PhenX protocol PX190801 unless stated otherwise)
SickleInAfrica CDE - Alanine Aminotransferase Level Question
The Sickle in Africa core data element that collects the level of aspartate aminotransferase in the respondent's blood.
SickleInAfrica CDE - Aspartate Aminotransferase Level Question
The Sickle in Africa core data element that collects the level of alkaline phosphatase in the respondent's blood.
SickleInAfrica CDE - Alkaline Phosphatase Level Question
A quantitative measurement of alkaline phosphatase present in a blood sample.
A multiplexed qualitative point-of-care immunoassay used for the rapid diagnosis of sickle cell disorders. The test is made up of three indicators which detect the presence of hemoglobins A, S, and C, allowing the user to rapidly distinguish between normal, carrier, and sickle cell samples.
An indication of a person's current status in terms of living with a person as though married (in a romantic relationship and living together but not married).
An indication of whether a person has previously lived with someone as though married (in a romantic relationship and lived together but were not married).
The Sickle in Africa core data element that collects the level of billirubin in the respondent's blood.
Laboratory Results: Bilirubin Level (PhenX protocol PX0810901 unless stated otherwise)
SickleInAfrica CDE - Total Bilirubin Concentration Question
The Sickle in Africa core data element that collects the level of lactate dehydrogenase in the respondent's blood.
Laboratory Results: Lactate Dehydrogenase Level (PhenX protocol PX0811001 unless stated otherwise)
SickleInAfrica CDE - Lactate Dehydrogenase Level Question
A decreased or reduced level of the enzyme lactate dehydrogenase in serum.
The current label in HPO is "Reduced lactate dehydrogenase B level". Seems the "B" in the label and the comment that refers to the B subunit should be removed.
The Sickle in Africa core data element that collects the reticulocyte count in the respondent's blood, as measured by a complete blood count.
Laboratory Results: Reticulocyte Count (PhenX protocol PX0810601 unless stated otherwise)
SickleInAfrica CDE - Reticulocyte Count Question
A test used to measure the reticulocyte count (number of reticulocytes in a given volume of blood).
The Sickle in Africa core data element that records the hemoglobins for which assay results were recorded.
1, Hb A 2, Hb F 3, Hb S 4, Hb C 5, Hb E 6, Hb A2 7, Hb D-Punjab 8, Hb G-Philadelphia 9, Hb O-Arab
For which hemoglobins were assay results recorded?
Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise)
SickleInAfrica CDE - Hb Assay Results Recorded Question
The hemoglobins for which assay results were recorded.
Hemoglobin G Philadelphia (HbG Phil) is a structural variant of the hemoglobin molecule that involves the alpha chain rather than the beta chain. It has a frequency of about 1 in 5,000 African Americans, but has been reported in other ethnic groups in the Mediterranean region as well, HbG Phil itself has no clinical consequences. The only finding of clinical interest is the mild microcytosis. While this molecule has no clinical consequences, the presence helps to distinguish HbG from HbD that shares its electrophoretic migration on HPLC and gel electrophoresis and which does have consequences when it occurs with sickle trait.
The amount of hemoglobin A present in a specified volume of blood.
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin A.
SickleInAfrica CDE - Hemoglobin A Level Question
The amount of hemoglobin S present in a specified volume of blood.
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin S.
SickleInAfrica CDE - Hemoglobin S Level Question
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin C.
SickleInAfrica CDE - Hemoglobin C Level Question
The amount of hemoglobin C present in a specified volume of blood.
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin E.
SickleInAfrica CDE - Hemoglobin E Level Question
The amount of hemoglobin E present in a specified volume of blood.
The amount of hemoglobin A2 present in a specified volume of blood.
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin A2.
SickleInAfrica CDE - Hemoglobin A2 Level Question
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin D-Punjab.
Record the levels of Hb D-Punjab if measured.
SickleInAfrica CDE - Hemoglobin D-Punjab Level Question
The amount of hemoglobin D-Punjab present in a specified volume of blood.
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin G-Philadelphia.
Record the levels of Hb G-Philadelphia if measured.
SickleInAfrica CDE - Hemoglobin G-Philadelphia Level Question
The amount of hemoglobin G-Philadelphia present in a specified volume of blood.
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin O-Arab.
Record the levels of Hb O-Arab if measured.
SickleInAfrica CDE - Hemoglobin O-Arab Level Question
The amount of hemoglobin O-Arab present in a specified volume of blood.
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin F.
SickleInAfrica CDE - Hemoglobin F Level Question
The amount of hemoglobin F present in a specified volume of blood.
The sex of the respondent's spouse, as provided by the respondent.
The sex of the respondent's partner (where the partner is not a spouse), as provided by the respondent.
The Sickle in Africa core data element that collects the respondent's body temperature.
SickleInAfrica CDE - Body Temperature Question
The Sickle in Africa core data element that collects the respondent's respiratory rate.
SickleInAfrica CDE - Respiratory Rate Question
The Sickle in Africa core data element that collects the respondent's partial pressure of carbon dioxide in their arterial blood, as measured by an arterial blood gas test.
Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise)
SickleInAfrica CDE - Partial Pressure CO2 Question
The Sickle in Africa core data element that collects the respondent's partial pressure of oxygen their arterial blood, as measured by an arterial blood gas test.
SickleInAfrica CDE - Partial Pressure O2 Question
The pressure exerted by oxygen dissolved in the blood, indicating how well oxygen is able to move from the airspace of the lungs into the blood.
The Sickle in Africa core data element that collects the respondent's arterial oxygen saturation (oxyhemoglobin saturation), as measured by an arterial blood gas test.
SickleInAfrica CDE - Oxyhemoglobin Saturation Question
The Sickle in Africa core data element that collects the respondent's carboxyhemoglobin to total hemoglobin ratio, as measured by an arterial blood gas test.
SickleInAfrica CDE - Carboxyhemoglobin Question
The Sickle in Africa core data element that collects the respondent's methemoglobin to total hemoglobin ratio, as measured by an arterial blood gas test.
SickleInAfrica CDE - Methemoglobin Question
The ratio of methemoglobin compared to total hemoglobin present in a sample. The measurement may be expressed as a ratio or percentage.
Used term from existing ontology but will suggest they update their label and description to ours.
Methemoglobin to Total Hemoglobin Ratio Measurement
The ratio of carboxyhemoglobin compared to total hemoglobin present in a sample. The measurement may be expressed as a ratio or percentage.
Carboxyhemoglobin to Total Hemoglobin Ratio
An elevated concentration in the blood of methemoglobin, which is the ferric (Fe(3+)) form of hemoglobin.
Injury or toxic agents can convert a larger proportion of hemoglobin to methemoglobin, which does not function reversibly as an oxygen carrier and thus less oxygen is made available to the tissues.
A site-specific unique identifier assigned to a study participant by the data collectors at the data collection site.
A unique identifier provided on SCD passports.
The Sickle in Africa core data element that records the unique identifier that was assigned to the study participant's data when it was registered in the SickleInAfrica data registry.
SickleInAfrica CDE - SickleInAfrica Participant Number
The Sickle in Africa core data element that calculates the respondent's age in months, using the visit date and birth date collected by other core data elements.
datediff([date_today],[date_of_birth], "M","dmy")
SickleInAfrica CDE - Age In Months Calculation
A data capture instrument designed and applied by the Sickle In Africa Consortium.
Consent Demographics SCD Diagnosis Details Management Details Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) Liver Function Assay (PhenX protocol PX190801 unless stated otherwise) Laboratory Results: Bilirubin Level (PhenX protocol PX0810901 unless stated otherwise) Laboratory Results: Lactate Dehydrogenase Level (PhenX protocol PX0811001 unless stated otherwise) Laboratory Results: Reticulocyte Count (PhenX protocol PX0810601 unless stated otherwise) Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise)
SickleInAfrica Core Data Element Instrument
The Sickle in Africa core data element that collects the total concentration of hemoglobin in the respondent's blood.
SickleInAfrica CDE - Total Hemoglobin Question
An assay to determine the body temperature of an evaluant using an oral thermometer.
PhenX protocol: Body Temperature - Oral Thermometers #810102
Body Temperature - Oral Measurement Assay
An assay to determine the body temperature of an evaluant using a tympanic (i.e. ear) thermometer.
PhenX protocol: Body Temperature - Tympanic Thermometers #810101
Body Temperature - Tympanic Measurement Assay
The temperature of the external acoustic tube.
The temperature of the lumen of the rectum.
The Sickle in Africa core data element that records the type of body temperature that was taken for the respondent.
1, Oral Temperature 2, Tympanic (ear) Temperature 3, Axillary (armpit) Temperature 4, Rectal Temperature
SickleInAfrica CDE - Type of Temperature Question
An answer to a question where the answer is a year between 1900 and the current year, selected from a provided list of years.
An answer to a question where the answer is a month between 1 - 12, selected form a list of months.
Hb-SS disease with cerebral vascular involvement
Sickle cell anemia with cerebral vascular involvement
D57.03 Hb-SS disease with cerebral vascular involvement
Hb-SS disease with crisis with other specified complication
Sickle cell anemia with crisis with other specified complication
D57.09 Hb-SS disease with crisis with other specified complication
When there is no deviation from the normal concentration of hemoglobin in the blood.
Sickle Cell Disease-SC with cerebral vascular involvement
Sickle-cell/Hb-C disease with cerebral vascular involvement
D57.213 Sickle-cell/Hb-C disease with cerebral vascular involvement
Sickle Cell Disease-SC with crisis with other specified complication
Sickle-cell/Hb-C disease with crisis with other specified complication
D57.218 Sickle-cell/Hb-C disease with crisis with other specified complication
D57.413 Sickle-cell thalassemia, unspecified, with cerebral vascular involvement
Sickle-cell thalassemia, unspecified, with crisis with other specified complication
D57.418 Sickle-cell thalassemia, unspecified, with crisis with other specified complication
Sickle-cell thalassemia beta zero without crisis
D57.42 Sickle-cell thalassemia beta zero without crisis
Sickle-cell thalassemia beta zero with crisis
D57.43 Sickle-cell thalassemia beta zero with crisis
Sickle-cell thalassemia beta zero with acute chest syndrome
D57.431 Sickle-cell thalassemia beta zero with acute chest syndrome
Sickle-cell thalassemia beta zero with splenic sequestration
D57.432 Sickle-cell thalassemia beta zero with splenic sequestration
Sickle-cell thalassemia beta zero with cerebral vascular involvement
D57.433 Sickle-cell thalassemia beta zero with cerebral vascular involvement
Sickle-cell thalassemia beta zero with crisis with other specified complication
D57.438 Sickle-cell thalassemia beta zero with crisis with other specified complication
Sickle-cell thalassemia beta zero with crisis, unspecified
D57.439 Sickle-cell thalassemia beta zero with crisis, unspecified
Sickle-cell thalassemia beta minus without crisis
Sickle-cell thalassemia beta plus without crisis
D57.44 Sickle-cell thalassemia beta plus without crisis
Sickle-cell thalassemia beta minus with crisis
Sickle-cell thalassemia beta plus with crisis
D57.45 Sickle-cell thalassemia beta plus with crisis
Sickle-cell thalassemia beta minus with acute chest syndrome
Sickle-cell thalassemia beta plus with acute chest syndrome
D57.451 Sickle-cell thalassemia beta plus with acute chest syndrome
Sickle-cell thalassemia beta minus with splenic sequestration
Sickle-cell thalassemia beta plus with splenic sequestration
D57.452 Sickle-cell thalassemia beta plus with splenic sequestration
Sickle-cell thalassemia beta minus with cerebral vascular involvement
Sickle-cell thalassemia beta plus with cerebral vascular involvement
D57.453 Sickle-cell thalassemia beta plus with cerebral vascular involvement
Sickle-cell thalassemia beta minus with crisis with other specified complication
Sickle-cell thalassemia beta plus with crisis with other specified complication
D57.458 Sickle-cell thalassemia beta plus with crisis with other specified complication
Sickle-cell thalassemia beta minus with crisis, unspecified
Sickle-cell thalassemia beta plus with crisis, unspecified
D57.459 Sickle-cell thalassemia beta plus with crisis, unspecified
D57.818 Other sickle-cell disorders with crisis with other specified complication
D57.813 Other sickle-cell disorders with cerebral vascular involvement
An elevated concentration in the blood of carboxyhemoglobin, which is the form of hemoglobin where the heme group has formed a stable complex with carbon monoxide (CO).
An abnormal reduction in the amount of oxygen bound to hemoglobin in arterial blood expressed as a percentage of the maximal binding capacity.
Decreased Arterial Oxyhemoglobin Saturation
Decreased Oxygen Saturation of Arterial Blood
Decreased Oxyhemoglobin/Total Hemoglobin
A phenotype of the body's metabolism or homeostasis that is not clinically abnormal.
When the degree to which oxygen is bound to hemoglobin in arterial blood is in the normal range.
When the level of carboxyhemoglobin detected in a sample of blood falls in the normal range for carboxyhemoglobin.
When the level of methemoglobin detected in a sample of blood falls in the normal range for methemoglobin.
A lack of production of hemoglobin D-Punjab.
A lack of production of hemoglobin G-Philadelphia.
A lack of production of hemoglobin O-Arab.
An abnormal reduction in the pressure exerted by oxygen dissolved in the blood.
Arterial Oxygen Partial Pressure Decreased
Decreased Partial Pressure of Blood Oxygen
The observable morphological and physiological characteristics of the human blood cells or the organs associated with the development and formation of blood cells that are manifested through development and lifespan.
A phenotype of the body's hematopoietic system that is not clinically abnormal.
When the number of red blood cells in a specified volume of blood falls in the normal range.
When the number of white blood cells in a specified volume of blood falls in the normal range.
When the number of platelets in a specified volume of blood falls in the normal range.
When the average volume or size of a single red blood cell falls in the normal range.
When the average amount of hemoglobin per red blood cell (calculated by dividing the total mass of hemoglobin by the number of red blood cells in a volume of blood) falls in the normal range.
Mean Corpuscular Hemoglobin Level Normal
Normal Mean Corpuscular Hemoglobin Level
When the amount of hemoglobin in a given volume of packed red blood cells falls in the normal range.
Mean Corpuscular Hemoglobin Concentration Normal
Normal Mean Cell Hemoglobin Concentration
Normal Mean Corpuscular Hemoglobin Concentration
When the range of variation of red blood cell (RBC) volume falls in the normal range.
Red Blood Cell Distribution Width Normal
Normal Red Blood Cell Distribution Width
When the level of serum creatinine is in the normal range.
When the level of serum alanine aminotransferase is in the normal range.
Normal Serum Alanine Aminotransferase Level
Serum Alanine Aminotransferase Level Normal
When the level of serum aspartate aminotransferase is in the normal range.
Normal Serum Aspartate Aminotransferase Level
When the level of serum alkaline aminotransferase is in the normal range.
When the level of the enzyme lactate dehydrogenase in the serum is in the normal range.
When the number of reticulocytes in a specified volume of blood falls in the normal range.
When the total bilirubin level in the serum is in the normal range.
When the concentration of urinary albumin falls in the normal range.
When the concentration of urine creatinine falls in the normal range.
When the pressure exerted by oxygen dissolved in the blood falls in the normal range.
When the pressure exerted by carbon dioxide dissolved in the blood falls in the normal range.
Normal Partial Pressure of Blood Carbon Dioxide
Partial Pressure of Blood Carbon Dioxide Normal
Partial Pressure of Carbon Dioxide Normal
Normal Partial Pressure of Carbon Dioxide
An abnormal reduction in the pressure exerted by carbon dioxide dissolved in the blood.
Decreased Partial Pressure of Blood Carbon Dioxide
Partial Pressure of Blood Carbon Dioxide Decreased
Decreased Partial Pressure of Carbon Dioxide
An abnormal increase in the pressure exerted by carbon dioxide dissolved in the blood.
Elevated Partial Pressure of Carbon Dioxide
Increased Partial Pressure of Blood Carbon Dioxide
Partial Pressure of Carbon Dioxide Increased
Raised Partial Pressure of Carbon Dioxide
Increased Partial Pressure of Carbon Dioxide
Clinical manifestation consisting of a deficiency of carbon dioxide in arterial blood.
A clinical manifestation of abnormal increase in the amount of carbon dioxide in arterial blood.
When the abnormal hemoglobin, hemoglobin S (HbS), has been detected in a blood sample.
The Sickle in Africa core data element that records the type of visit undertaken by a patient.
1, Routine 2, Acute 3, Review 4, First visit
SickleInAfrica CDE - Type of Visit Question
A clinical visit occuring because of an acute (severe with sudden onset) health condition.
The Sickle in Africa core data element that records the patient's medical record number.
SickleInAfrica CDE - Medical Record Number Question
The Sickle in Africa core data element that records the name of the hospital that a patient visited.
SickleInAfrica CDE - Hospital Name Question
The name of the hospital visited by a patient.
The Sickle in Africa core data element that records a respondent's first name.
SickleInAfrica CDE - First Name Question
The Sickle in Africa core data element that records a respondent's middle name.
SickleInAfrica CDE - Middle Name Question
A first name is a name that denotes a specific individual between members of a group of individuals, whose members usually share the same surname.
A middle name is a name assigned to an individual that is not the first or last name.
A last name (surname) is a name added to a given name and is part of a personal name and is often the family name.
The Sickle in Africa core data element that records a respondent's last name.
The Sickle in Africa core data element that records a respondent's height.
The Sickle in Africa core data element that records a respondent's measured weight.
The Sickle in Africa core data element that records the ethnic group to which a respondent belongs.
SickleInAfrica CDE - Ethnic Group Question
The Sickle in Africa core data element that records the religion of a respondent.
The Sickle in Africa core data element that records the region in which the respondent lives.
A street name is the token given to identify a particular street.
The Sickle in Africa core data element that records the name of the street in which the respondent lives.
The Sickle in Africa core data element that records the landmark that is nearest to where the participant lives.
SickleInAfrica CDE - Nearest Landmark Question
A recognizable natural or artificial geographic feature, used for navigation (often visible from long distances), that is nearest to where the participant lives.
The Sickle in Africa core data element that records the participant's primary telephone number.
SickleInAfrica CDE - Telephone 1 Question
The Sickle in Africa core data element that records the participant's secondary telephone number.
SickleInAfrica CDE - Telephone 2 Question
The Sickle in Africa core data element that records the name of the participant's next of kin.
SickleInAfrica CDE - Next of Kin Name Question
The Sickle in Africa core data element that records the telephone number of the participant's next of kin.
SickleInAfrica CDE - Next of Kin Number Question
The Sickle in Africa core data element that records the participant's next of kin's relationship to the participant.
SickleInAfrica CDE - Relationship to Participant Question
A respondent's primary telephone number.
A respondent's secondary telephone number.
The telephone number of a respondent's next of kin.
The relationship that the participant's next of kin has with the participant.
The Sickle in Africa core data element that records whether the participant was given a blood transfusion.
SickleInAfrica CDE - Blood Transfusion Question
The Sickle in Africa core data element that records the number of units of blood that a participant was given during a blood transfusion.
SickleInAfrica CDE - Units Transfused Question
The number of units of blood that a patient received during a blood transfusion.
The Sickle in Africa core data element that records whether a participant has difficulty in breathing.
SickleInAfrica CDE - Difficulty in Breathing Question
The Sickle in Africa core data element that records a participant's systolic blood pressure.
SickleInAfrica CDE - Systolic Blood Pressure Question
The Sickle in Africa core data element that records a participant's diastolic blood pressure.
SickleInAfrica CDE - Diastolic Blood Pressure Question
The Sickle in Africa core data element that records whether a participant has priapism.
The Sickle in Africa core data element that records whether a participant has chest pain.
SickleInAfrica CDE - Chest Pain Question
The Sickle in Africa core data element that records whether a participant has anaemia.
The Sickle in Africa core data element that records whether a participant has jaundice.
The Sickle in Africa core data element that collects the concentration of urea in the respondent's blood.
A clinical visit that is the patient's first clinical visit.
A clinical visit that is a follow-up for a previous visit.
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.
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.
Muscle pain is a pain characterized by pain in one or more muscles.
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).
A standardized quantity of a physical quality.
A unit which is a standard measure of the distance between two points.
A unit which is a standard measure of the amount of matter/energy of a physical object.
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
A mass unit which is equal to 10^[-12] g.
A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
A volume unit which is equal to 10^[-15] L.
A unit which is a standard measure of the force applied to a given area.
A concentration unit which is a standard measure of the mass of a substance in a given volume (density).
A unit which is a standard measure of physical quantity consisting of only a numerical number without any units.
A dimensionless ratio unit which denotes numbers as fractions of 100.
A dimensionless unit which denotes an amount or magnitude of one quantity relative to another.
A concentration unit which denotes the average cell number in a given volume.
A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth.
A unit which represents a standard measurement occurrence of a process per unit time.
A unit of cell concentration which is equal to one cell in a volume of 1 microliter.
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.
A viral vaccine that protects against infection with influenza virus.
A Streptococcal vaccine that is used against S. pneumoniae infection, which causes pneumococcal diseases.
The amount of alkaline phosphatase present in a specified volume of blood.
The proportion, quantity, or volume in whole blood, serum, or plasma of this enzyme, which hydrolyzes orthophosphoric monoesters.
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 into a detailed three-dimensional image of your brain Other tests: Some of the other tests you may have to help diagnose ataxia and determine how severe it is can include: a lumbar puncture – where a sample of cerebrospinal fluid is taken from the base of the spine to check it for infection and any other abnormalities. nerve conduction studies and electromyography (EMG) – tests used to assess the electrical activity in nerves and muscles. videofluoroscopy – a continuous moving X-ray taken while you swallow different types of food and drink. an electrocardiogram (ECG) – an assessment of the electrical activity of the heart. an echocardiogram – an ultrasound scan of the heart.
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
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.
May be Acute (acute kidney injury) or chronic (see chronic kidney disease).
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].
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
Biologic therapy, Antibody therapy, Stem-cell transplantation, Splenectomy, Steroid treatment, Radioimmunotherapy, Surgery, chemotherapy, and radiation therapy,
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.
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
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
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.
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 into a detailed three-dimensional image of your brain Other tests: Some of the other tests you may have to help diagnose ataxia and determine how severe it is can include: a lumbar puncture – where a sample of cerebrospinal fluid is taken from the base of the spine to check it for infection and any other abnormalities. nerve conduction studies and electromyography (EMG) – tests used to assess the electrical activity in nerves and muscles. videofluoroscopy – a continuous moving X-ray taken while you swallow different types of food and drink. an electrocardiogram (ECG) – an assessment of the electrical activity of the heart. an echocardiogram – an ultrasound scan of the heart.
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.