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.
Anyone can access the resource.
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
OBO Foundry standards.
The field of sickle cell disease (SCD) research and care.
April 2021
English
GPL-3.0
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
no
definition
For external terms/classes, the ontology from which the term was imported.
no
metadata complete - requires restrictions and relationships
IAO:0000412
imported from
Use on obsolete terms, relating the term to another term that can be used as a substitute.
IAO:0100001
term replaced by
An administrative note of use for a curator but of no use for a user.
no
organizational term
IAO:0000232
editor_notes
curator note
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.
yes
metadata complete - requires restrictions and relationships
IAO:0000119
definition source
description source
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.
metadata complete - requires restrictions and relationships
SCDO
'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".
description adapted from source
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?
metadata complete - requires restrictions and relationships
SCDO
has 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.
metadata complete - requires restrictions and relationships
SCDO
has cross-cultural adaptation
A relationship between a condition/disease and a description of how the condition/disease is staged/graded.
Requested inclusion of this property into RO. Check details here again after inclusion.
metadata complete - requires restrictions and relationships
SCDO
Staging provided is disease/phenotype specific.
has disease stage
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"
metadata complete - requires restrictions and relationships
SCDO
has protocol
A relation between a measure or measurement and the recommended procedure used by the measure or used to obtain the measurement.
Requested inclusion of this property into RO. Check details here again after inclusion.
metadata complete - requires restrictions and relationships
SCDO
has recommended procedure
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.
Requested inclusion of this property into RO. Check details here again after inclusion.
Should be restricted to all measure/questionnaire classes.
no
metadata complete - requires restrictions and relationships
SCDO
If the main person of interest responds, "Self" is indicated. If a person other than the main person of interest can respond, "Proxy" is indicated. If the proxy responder has a specific relationship (Family Members; Health Care Provider or Care-giver) to the main person of interest, that relationship should be indicated in brackets after "Proxy", e.g. Proxy (Health Care Provider or Care-giver). If more than one type of proxy responder is relevant, these should be listed and separated by ";", e.g. Proxy (Family Members; Health Care Provider or Care-giver)
has respondents
A relation between a measure (e.g. a survey) and the population that the measure was designed to target.
Requested inclusion of this property into RO. Check details here again after inclusion.
Should be restricted to all measure/questionnaire classes.
metadata complete - requires restrictions and relationships
SCDO
Possible values used in the SCDO: Healthy Population; Clinic Patients (Children and/or Adults with SCD); Family Members; and/or Health Care Provider
has target population
An account of known translations of a measure into other languages (other than English).
Requested inclusion of this property into RO. Check details here again after inclusion.
Should be restricted to all measure/questionnaire classes.
metadata complete - requires restrictions and relationships
SCDO
has translations
A relation between a planned process and an objective it can be used to achieve.
Requested inclusion of this property into RO. Check details here again after inclusion.
This property is originally an object property.
metadata complete - requires restrictions and relationships
has_application_toward
Eventually to be replaced by "is caused by" object property
metadata incomplete
is caused by
A relationship between a condition (a phenotype or disease) and a description of distinctive characteristics or essential features.
Requested inclusion of this property into RO. Check details here again after inclusion.
metadata complete - requires restrictions and relationships
SCDO
is characterised by
Description inherent in name (not provided by source)
Only label adapted
organizational term
Used for properties, not classes.
For classes, use "has curation status" object property.
property has curation status
A relation between a selected entity and the predefined criteria that were met by the entity and that made it eligible for selection.
Requested inclusion of this property into RO. Check details here again after inclusion.
Should be restricted to all measure/questionnaire classes.
metadata complete - requires restrictions and relationships
SCDO
selection criteria met
A relation between a measure and the age ranges for which the measure has been validated.
Requested inclusion of this property into RO. Check details here again after inclusion.
Should be restricted to all measure/questionnaire classes.
metadata complete - requires restrictions and relationships
SCDO
validated for age ranges
A relation between a measure (e.g. a survey) and an indication of whether the measure is freely available.
Requested inclusion of this property into RO. Check details here again after inclusion.
Should be restricted to all measure/questionnaire classes.
metadata complete - requires restrictions and relationships
SCDO
'yes' indicates that the measure is freely available. 'no' indicates that the measure is not freely available.
freely available
Records the slider label used by REDCap for a data element that uses a slider to collect data.
SCDO (Jade Hotchkiss)
has slider label
curation status - complete
curation status - incomplete
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.
SCDO (Jade Hotchkiss)
requires additional code
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.
SCDO (Jade Hotchkiss)
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
existence in other ontologies
Records the answer options text for input in Redcap for a data element that provides answer options.
SCDO (Jade Hotchkiss)
has answer options text
Records the field label of a data element.
SCDO (Jade Hotchkiss)
has field label
Records the variable of the associated data element from a REDCap data capture instrument.
SCDO (Jade Hotchkiss)
has redcap variable
Records the section of a CRF in which a data element occurs.
SCDO (Jade Hotchkiss)
in CRF section
Records the calculation used to automatically calculate the value for a data element in REDCap.
SCDO (Jade Hotchkiss)
has calculation equation
Records a data element's field note (a note provided below the answer field).
SCDO (Jade Hotchkiss)
has field note
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.
SCDO (Jade Hotchkiss)
order in CRF section
Used to provide a list of sections present in a questionnaire/instrument.
SCDO (Jade Hotchkiss)
has sections
Records the type of validation used for a data element in REDCap.
SCDO (Jade Hotchkiss)
has redcap validation
Records the branching logic applied to a data element in REDCap.
SCDO (Jade Hotchkiss)
has branching logic
Records the mainimum value that is accepted for a data element that has validation applied to it in REDCap.
SCDO (Jade Hotchkiss)
has redcap min number validation
Records the maximum value that is accepted for a data element that has validation applied to it in REDCap.
SCDO (Jade Hotchkiss)
has redcap max number validation
Records the field annotations of a data element in REDCap.
SCDO (Jade Hotchkiss)
has redcap field annotation
Used to show if a data element is considered an "identifier" (meaning it contains identifying information).
SCDO (Jade Hotchkiss)
is identifier
Used to show if a data element is a required field. "y" is assigned to it if the data element is a required field.
SCDO (Jade Hotchkiss)
required field
Records the custom alignment of a data element in REDCap.
SCDO (Jade Hotchkiss)
custom alignment
Records a data element's field type, as per REDCap.
SCDO (Jade Hotchkiss)
has field type
Used to record the matrix group that a data element occurs in.
SCDO (Jade Hotchkiss)
in matrix group
An indication of whether or not a data element with a dropdown field should be autocompleted. Annotation is either "yes" or "no".
SCDO (Jade Hotchkiss)
autocomplete
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".
SCDO (Jade Hotchkiss)
show slider
Used to record the identifier that had been used previously but is no longer in use.
SCDO (Jade Hotchkiss)
previous identifier
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.
yes
metadata complete - requires restrictions and relationships
abbreviation
discarded/obsoleted synonym
plural form
layperson term
A legal document giving official permission to do something with a Resource.
no
ontology annotation property
dc:LicenseDocument
License Document
A summary of the resource.
no
ontology annotation property
dc:abstract
Abstract
Information about who can access the resource or an indication of its security status.
no
ontology annotation property
dc:accessRights
Access Rights
The method by which items are added to a collection.
no
ontology annotation property
dc:accrualMethod
Accrual Method
The frequency with which items are added to a collection.
no
ontology annotation property
dc:accrualPeriodicity
Accrual Periodicity
The policy governing the addition of items to a collection.
no
ontology annotation property
dc:accrualPolicy
Accrual Policy
A class of entity for whom the resource is intended or useful.
no
ontology annotation property
dc:audience
Audience
Date (often a range) that the resource became or will become available.
no
ontology annotation property
dc:available
Date Available
An established standard to which the described resource conforms.
no
ontology annotation property
dc:conformsTo
Conforms To
The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant.
no
ontology annotation property
dc:coverage
Coverage
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.
no
ready for release
dc:creator
Creator
A related resource that references, cites, or otherwise points to the described resource.
no
ontology annotation property
dc:isReferencedBy
Is Referenced By
Date of formal issuance (e.g., publication) of the resource.
no
ontology annotation property
dc:issued
Date Issued
A language of the resource.
no
ontology annotation property
Recommended best practice is to use a controlled vocabulary such as RFC 4646 [RFC4646].
dc:language
Language
A legal document giving official permission to do something with the resource.
no
ontology annotation property
dc:license
License
A related resource from which the described class/term's annotations are derived.
yes
pending vetting by the SCDO developers
dc:source
synonym_type_property
An alias in which the alias is broader than the primary class name. Example: cell division is a broad synonym of cytokinesis.
no
pending vetting by the SCDO developers
hasBroadSynonym
A database cross-reference. An annotation which directs one to information contained within a database.
metadata complete - requires restrictions and relationships
SBO:0000554
DbXref
Xref
database cross-reference
database_cross_reference
db xref
hasDbXref
database cross reference
An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle.
no
pending vetting by the SCDO developers
hasExactSynonym
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.
no
pending vetting by the SCDO developers
hasNarrowSynonym
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.
no
pending vetting by the SCDO developers
hasRelatedSynonym
An annotation property used to further annotate synonym axioms.
has_synonym_type
Additional information describing the class/term.
yes
rdfs:comment
A human-readable name for the class/term.
yes
rdfs:label
Further information about the class/term.
yes
rdfs:seeAlso
The annotation property that indicates that a given entity has been deprecated.
deprecated
A preferred label.
yes
pending vetting by the SCDO developers
skos:prefLabel
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).
no
metadata complete - requires restrictions and relationships
RO:0002200
has phenotype
Inverse of "has phenotype" object property.
If required later, specify as inverse of "has phenotype" in Protege.
no
metadata complete - requires restrictions and relationships
phenotype of
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.
RO:0002452
has symptom
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.
RO:0003302
causes or contributes to 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.
RO:0003303
results_in
causes 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.
RO:0003306
contributes to frequency of 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 presence of the entity reduces or eliminates some or all aspects of the condition.
RO:0003307
ameliorates 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.
RO:0003309
exacerbates 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.
RO:0003310
condition ameliorated by
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.
RO:0003311
condition exacerbated by
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)
SCDO (Jade Hotchkiss)
age of onset modified by
A relationship between a condition (phenotype or disease) and a relevant ICD-10-CM Diagnosis Code.
None
SCDO (Jade Hotchkiss)
has clinical code
A relation between a device (diagnostic device) and the recording of the output (diagnostic measurement) of the device.
SCDO (Jade Hotchkiss)
has output measurement
A relation between a process (e.g. a form of therapy) and a medical device, where the medical device is used in the process.
SCDO (Jade Hotchkiss)
uses medical device
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.
SCDO (Jade Hotchkiss)
caused or contributed to by
A relation between a phenotype that is a diagnosis and a diagnostic tool used in making the diagnosis.
SCDO (Jade Hotchkiss)
diagnosed using tool
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".
SCDO (Jade Hotchkiss)
treated with
A relationship between a phenotype and a disease modifier, where the disease modifier modifies the mortality (due to the phenotype) of the SCD sufferer.
SCDO (Jade Hotchkiss)
mortality modified by
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)
SCDO (Jade Hotchkiss)
temporal pattern modified by
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.
SCDO (Jade Hotchkiss)
Essential measures have been attributed according to information in PhenX.
has essential measure
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.
SCDO (Jade Hotchkiss)
has mode of inheritance
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.
SCDO (Jade Hotchkiss)
modified by
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.
SCDO (Jade Hotchkiss)
modifies
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".
SCDO (Jade Hotchkiss)
treats
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.
SCDO (Jade Hotchkiss)
has diagnostic device
A relation between a condition (hemoglobinopathy) and the genotype that causes the condition.
SCDO (Jade Hotchkiss)
has causal genotype
An object property that specifies the type of an ICD-10-CM code, whether Billable or Non-Billable.
SCDO (Jade Hotchkiss)
is ICD-10-CM code type
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.
SCDO (Jade Hotchkiss)
manifestation of
A relation between a phenotype that is a symptom (subjective evidence of disease perceived by the patient) and a disease.
SCDO (Jade Hotchkiss)
symptom of
A relationship between 'a' and 'b', where 'a' has some causal role for 'b'.
SCDO (Jade Hotchkiss)
causes or contributes to
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.
SCDO (Jade Hotchkiss)
contributes to genotype
A relation between a condition (Hemoglobinopathy) and a form of research (type of study) that the condition was studied in.
SCDO (Jade Hotchkiss)
studied in
A relation between a condition (disease or phenotype) and a type of linking association (e.g. age of onset association).
SCDO (Jade Hotchkiss)
associated via
A relationship between a diagnostic measurement and the diagnostic tool used to produce the measurement.
SCDO (Jade Hotchkiss)
obtained via diagnostic tool
A relationship between a diagnostic device and the diagnostic tool by which the device is used.
SCDO (Jade Hotchkiss)
used by diagnostic tool
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.
SCDO (Jade Hotchkiss)
uses diagnostic device
A relation between a diagnostic measurement and a diagnostic device, where the diagnostic measurement is the output of the diagnostic device.
SCDO (Jade Hotchkiss)
output of diagnostic device
A relation between a diagnostic tool and the diagnostic measurement that it measures.
SCDO (Jade Hotchkiss)
measures
A relation between a genotype and a genetic variation (e.g. mutation or genetic recombination), where the genetic variation contributes to the genotype.
SCDO (Jade Hotchkiss)
has contributing genetic variation
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".
SCDO (Jade Hotchkiss)
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.
SCDO (Jade Hotchkiss)
caused by
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.
SCDO (Jade Hotchkiss)
has risk factor
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.
SCDO (Jade Hotchkiss)
risk factor for
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.
SCDO (Jade Hotchkiss)
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.
SCDO (Jade Hotchkiss)
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.
SCDO (Jade Hotchkiss)
has manifestation
A relation between a condition that is a diagnosis and a phenotype used in making the diagnosis.
diagnosed by
A relation between an Abnormal Phenotype that is a diagnosis and a Diagnostic Measurement or Diagnostic Device Visual Output used in making the diagnosis.
SCDO (Jade Hotchkiss)
diagnosed using measurement
A relation between a genotype and a molecular phenotype, where the genotype has a causal role for the molecular phenotype.
SCDO (Jade Hotchkiss)
causes 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.
SCDO (Jade Hotchkiss)
has causal molecular phenotype
A relationship between a Clinical or Research Assessment Data Element and a Clinical or Research Assessment Question Type.
None
SCDO (Jade Hotchkiss)
is 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.
None
SCDO (Jade Hotchkiss)
has answer option
A relationship between a data element and the type of information that is collected by that data element.
None
SCDO (Jade Hotchkiss)
collects
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.
None
SCDO (Jade Hotchkiss)
has answer standard unit
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.
SCDO (Jade Hotchkiss)
has possible finding
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.
SCDO (Jade Hotchkiss)
diagnosed using finding
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.
None
SCDO (Jade Hotchkiss)
has reference range standard unit
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.
SCDO (Jade Hotchkiss)
code requires phenotype
A relation between an entity (phenotypic, therapeutic or diagnostic concept) and a guideline or directive.
SCDO (Jade Hotchkiss)
in guideline
so:associated_with
associated with
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.
None
has lower limit of normal
has lower reference limit
has LLN
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.
None
has upper limit of normal
has upper reference limit
has ULN
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.
SCDO (Jade Hotchkiss)
min number of selections allowed
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.
SCDO (Jade Hotchkiss)
max number of selections allowed
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.
None
has lower limit of normal for males
has LLN male
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.
None
has lower limit of normal for females
has LLN female
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.
None
has lower limit of normal for children
has LLN pediatric
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.
None
has upper limit of normal for males
has ULN male
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.
None
has upper limit of normal for females
has ULN female
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.
None
has upper limit of normal for children
has ULN pediatric
A spatiotemporal region encompassing some part of the life cycle of an organism.
See specific stages in the "Human Developmental Stages Ontology"
http://purl.obolibrary.org/obo/HsapDv_0000000
Sufficient
SCDO:0007384
HsapDv:0000000
Developmental Stage
Human Life Cycle Stage
An information content entity specifying the upper and lower limit of a range of ages of continuants.
Sufficient
SCDO:1000403
APOLLO_SV:00000241
Age Range Category
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.
http://purl.obolibrary.org/obo/ARO_0000006
Sufficient
SCDO:0003119
ARO:0000006
Abomacetin
Emgel
Eritromicina
Erymax
Erythrocin
Erythromycin A
Erythromycine
Erythromycinum
N-methylerythromycin A
Erythromycin
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.
Sufficient
SCDO:0000880
ARO:0000054
PCN
Penicillins
Penicillin
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.
http://purl.obolibrary.org/obo/ARO_0000064
Sufficient
SCDO:0002381
ARO:0000064
AMX
Amolin
Amopenixin
Amoxicilina
Amoxicilline
Amoxicillinum
Clamoxyl
D-Amoxicillin
Moxal
Amoxycillin
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".
Sufficient
SCDO:1000200
CHEBI:23888
Drug
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.
http://purl.obolibrary.org/obo/CHEBI_35475
Sufficient
SCDO:0005809
CHEBI:35475
Non-Steroidal Anti-Inflammatory Agent
Non-Steroidal Anti-Inflammatory Drug
A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood.
http://purl.obolibrary.org/obo/CHEBI_35482
Sufficient
SCDO:0000836
CHEBI:35482
Opioid Analgesic
Opioid
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.
http://purl.obolibrary.org/obo/CHEBI_35493
Sufficient
SCDO:0005335
CHEBI:35493
Anti-Pyretic
Antipyretic
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.
http://purl.obolibrary.org/obo/CHEBI_42797
Sufficient
SCDO:0007493
CHEBI:42797
1-(Aminomethyl)cyclohexaneacetic acid
Neurontin
Gabapentin
A natural or synthetic analogue of the hormones secreted by the adrenal gland.
Sufficient
SCDO:0003901
CHEBI:50858
Corticoides
Corticosteroides
Corticosteroids
Corticosteroid
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.
http://www.drugbank.ca/drugs/DB00327
Sufficient
SCDO:0000577
CHEBI:5790
3-hydroxy-17-methyl-4,5alpha-epoxymorphinan-6-one
Hydromorphone
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.
http://purl.obolibrary.org/obo/CHEBI_60809
Sufficient
SCDO:0000025
CHEBI:60809
Adjuvant Medicine
Adjuvant
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.
http://www.drugbank.ca/drugs/DB00333
Sufficient
SCDO:0000752
CHEBI:6807
6-(dimethylamino)-4,4-diphenylheptan-3-one
Physeptone
Methadone
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.
http://purl.obolibrary.org/obo/CHEBI_6909
Sufficient
SCDO:0002912
CHEBI:6909
Satric
Trichazol
Metronidazole
A semisynthetic derivative of codeine that acts as a narcotic analgesic more potent and addicting than codeine.
http://www.drugbank.ca/drugs/DB00497
Sufficient
SCDO:0000847
CHEBI:7852
14-hydroxy-3-methoxy-17-methyl-4,5alpha-epoxymorphinan-6-one
Dihydrone
An extended-release (ER) form of oxycodone (Xtampza ER) was approved for the management of daily, around-the-clock pain management in April, 2016.
Oxycodone
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.
http://purl.obolibrary.org/obo/CHMO_0001009
Sufficient
SCDO:0000563
CHMO:0001009
HPLC
High Performance Liquid Chromatography
High Pressure Liquid Chromatography
High-Pressure Liquid Chromatography
High-Performance Liquid Chromatography
A test which produces colour change in the sample.
http://purl.obolibrary.org/obo/CHMO_0002580
Sufficient
SCDO:0000264
CHMO:0002580
Colorimetric Test
Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels.
http://purl.obolibrary.org/obo/CMO_0000001
Sufficient
SCDO:0000186
CMO:0000001
Cardiovascular Measurement
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?
http://purl.obolibrary.org/obo/CMO_0000003
Sufficient
SCDO:0000144
CMO:0000003
Blood Pressure Measurement
Morphological measurement involving the entire body of an organism.
http://purl.obolibrary.org/obo/CMO_0000011
Sufficient
SCDO:0001245
CMO:0000011
Whole Body Morphological Measurement
The level of heat in an organism.
Sufficient
SCDO:0000151
CMO:0000015
Body Temperature
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?
http://purl.obolibrary.org/obo/CMO_0000021
Sufficient
SCDO:0000150
CMO:0000021
Anthropometric Measurement
Anthropometrics
Morphometry
Body Morphological Measurement
A quantification of a parameter of the chemical composition of blood.
http://purl.obolibrary.org/obo/CMO_0000023
Sufficient
SCDO:0000136
CMO:0000023
Blood Chemistry Measurement
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.
http://purl.obolibrary.org/obo/CMO_0000025
Sufficient
SCDO:0000973
CMO:0000025
Erythrocyte Count
Erythrocyte Number
Erythrocyte Numbers
Red Blood Count
Red Blood Cell Count
The number of white blood cells in a specified volume of blood.
http://purl.obolibrary.org/obo/CMO_0000027
Sufficient
SCDO:0001243
CMO:0000027
Leukocyte Count
White Corpuscle Count
White Blood Cell Count
The number of platelets (thrombocytes) in a specified volume of blood, usually expressed as platelets per cubic millimeter of whole blood.
http://purl.obolibrary.org/obo/CMO_0000029
Sufficient
SCDO:0000906
CMO:0000029
Blood Platelet Number
Blood Platelet count
Platelet Number
Platelet Count
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.
Sufficient
SCDO:1000442
CMO:0000030
Neutrophil Granulocyte Count
Blood Neutrophil Count
A measurement of the blood, it's contents, cells or other factors contained within the blood.
http://purl.obolibrary.org/obo/CMO_0000035
Sufficient
SCDO:0000143
CMO:0000035
Blood Measurement
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?
http://purl.obolibrary.org/obo/CMO_0000036
Sufficient
SCDO:0000135
CMO:0000036
Blood Cell Measurement
Percentage of total blood volume that is made up of red blood cells.
http://purl.obolibrary.org/obo/CMO_0000037
Sufficient
SCDO:0000503
CMO:0000037
Hct
Packed Cell Volume
Packed Red Blood Cell Volume
Hematocrit
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.
http://purl.obolibrary.org/obo/CMO_0000038
Sufficient
SCDO:0000723
CMO:0000038
MCV
Mean Cell Volume
Mean Corpuscular Volume
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"?
Sufficient
SCDO:0001042
CMO:0000057
Creatinine Level
Serum Creatinine Level
A measurement to assess the morphological or physiological state of the respiratory system or portion of the respiratory system.
http://purl.obolibrary.org/obo/CMO_0000094
Sufficient
SCDO:0000995
CMO:0000094
Respiratory System Measurement
The number of granulocytes (polymorphonuclear leukocytes) in a specified volume of blood, usually 1 cubic millimeter.
Sufficient
SCDO:1000441
CMO:0000111
Blood Granulocyte Count
The amount of bilirubin found in a specific volume of blood.
http://purl.obolibrary.org/obo/CMO_0000123
Sufficient
SCDO:0000134
CMO:0000123
Bilirubin Level
Blood Bilirubin Level
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".
Sufficient
SCDO:0000142
CMO:0000195
Circulation Measurement
Blood Flow Measurement
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)?
http://purl.obolibrary.org/obo/CMO_0000204
Sufficient
SCDO:0000137
CMO:0000204
Blood Coagulation Measurement
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.
Sufficient
SCDO:0000014
CMO:0000210
APTT; Quick
Activated Partial Thromboplastin Time
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.
Sufficient
SCDO:0000933
CMO:0000211
PTT
Prothrombin Time
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.
Sufficient
SCDO:1000718
CMO:0000225
Arterial Blood Gas Measurement
Any measurement of urine, the fluid waste product excreted by the kidneys, or its components.
http://purl.obolibrary.org/obo/CMO_0000256
Sufficient
SCDO:0001214
CMO:0000256
Urine Measurement
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.
Sufficient
SCDO:1000719
CMO:0000283
PaCO2
Partial Pressure of Blood Carbon Dioxide
Partial Pressure of Blood Carbon Dioxide (Pco2)
Partial Pressure of Carbon Dioxide (PaCO2)
Pco2
Partial Pressure of Carbon Dioxide
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.
http://purl.obolibrary.org/obo/CMO_0000290
Sufficient
SCDO:0000722
CMO:0000290
MCH
Mean Cell Hemoglobin
Mean Cell Hemoglobin Level
Mean Corpuscular Haemoglobin
Mean Corpuscular Haemoglobin Level
Mean Corpuscular Hemoglobin
Mean Corpuscular Hemoglobin Level
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)
http://purl.obolibrary.org/obo/CMO_0000291
Sufficient
SCDO:0000721
CMO:0000291
MCHC
Mean Cell Hemoglobin Concentration
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.
http://purl.obolibrary.org/obo/CMO_0000364
PhenX protocol: Complete Blood Count #220501
Sufficient
SCDO:0000270
CMO:0000364
Blood Cell Count
Blood Cell Number
CBC
FBC
Full Blood Count
Complete Blood Count
The total number of leukocytes in 1 cubic millimeter of peripheral venous blood.
http://purl.obolibrary.org/obo/CMO_0000365
Sufficient
SCDO:0001163
CMO:0000365
Total White Blood Cell Count
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"?
http://purl.obolibrary.org/obo/CMO_0000366
Sufficient
SCDO:0000140
CMO:0000366
Blood Differential Leukocyte Count
Blood Differential WBC Count
WBC Differential Count
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.
Sufficient
SCDO:1000500
CMO:0000376
Total Serum Bilirubin Level
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.
Sufficient
SCDO:0000523
CMO:0000506
Hbtotal
Hemoglobin Level
Total Hemoglobin
Total Hemoglobin (Hbtotal)
ctHB
Hemoglobin Concentration
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.
Sufficient
SCDO:1000249
CMO:0000507
Hemoglobin Absorbance
A measure of the oxygen carrying pigment of erythrocytes.
http://purl.obolibrary.org/obo/CMO_0000508
Sufficient
SCDO:0000543
CMO:0000508
Hemoglobin Measurement
Pressure exerted by the heart muscle in its maximally contracted state.
http://purl.obolibrary.org/obo/CMO_0000665
Sufficient
SCDO:0000499
CMO:0000665
Heart Contraction Pressure
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.
http://purl.obolibrary.org/obo/CMO_0000921
Sufficient
SCDO:0000907
CMO:0000921
Platelet Measurement
Any measurement of a gas or gases dissolved in the blood, including oxygen, nitrogen carbon dioxide and/or hydrogen.
Sufficient
SCDO:1000312
CMO:0001321
Blood Gas Measurement
The amount of oxygen bound to hemoglobin in the blood expressed as a percentage of the maximal binding capacity.
Sufficient
SCDO:0000848
CMO:0001324
HbO2
Oxyhemoglobin Saturation
Oxyhemoglobin Saturation (HbO2)
SO2
SaO2
Sats
Oxygen Saturation
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.
http://purl.obolibrary.org/obo/CMO_0001356
Sufficient
SCDO:0000974
CMO:0001356
Erythrocyte Measurement
Red Blood Cell Measurement
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.
Sufficient
SCDO:1000311
CMO:0002079
Body Weight of Neonate
Neonatal Body Weight
Birth Weight
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.
http://purl.obolibrary.org/obo/CMO_0002341
Sufficient
SCDO:0001244
CMO:0002341
White Blood Cell Measurement
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.
Sufficient
SCDO:0000467
CMO:0002520
Haptoglobin Level
Haptoglobin Levels
Serum Haptoglobin Level
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)
Sufficient
SCDO:0000786
CMO:0002876
BNPT Level
Blood NH2-Terminal pro-B-Type Natriuretic Peptide Level
N-Terminal Prohormone of Brain Natriuretic Peptide Level
NT-proBNP Level
NT-proBNP Measurement
N-Terminal Pro-Brain Natriuretic Peptide Level
A vitamin metabolic disorder that results from low blood levels of vitamin B12.
Sufficient
SCDO:0005733
DOID:0050731
Cobalamin Deficiency
Hypocobalaminemia
Vitamin B12 Deficiency
A colitis caused by inadequate blood supply to the colon.
Is diagnosed by: abdominal computed tomography scan
http://purl.obolibrary.org/obo/DOID_0060181
Sufficient
SCDO:0002870
DOID:0060181
Ischemic Cholitis
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.
Sufficient
SCDO:1000282
DOID:0111033
Bantu Siderosis
Iron Overload in Africa
African Iron Overload
A neuropathy that is characterized by damage to a single nerve, which results in loss of movement, sensation, or other function of that nerve.
Sufficient
SCDO:0000769
DOID:1188
Single Damaged Nerve
Mononeuropathy
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.
Sufficient
SCDO:0000015
DOID:1584
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.
Acute Chest Syndrome
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.
http://purl.obolibrary.org/obo/DOID_1826
Sufficient
SCDO:0008484
DOID:1826
Epilepsy
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.
http://purl.obolibrary.org/obo/DOID_2326
Sufficient
SCDO:0007198
DOID:2326
Gastroenteritis
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.
http://purl.obolibrary.org/obo/DOID_4
Sufficient
SCDO:0001365
DOID:4
Disease
An arthritis that involves infection by a pathogen located in a joint.
http://purl.obolibrary.org/obo/DOID_813
Sufficient
SCDO:0002067
DOID:813
Infected Joint
Infectious Arthritis
Septic Arthritis
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.
http://purl.obolibrary.org/obo/DOID_9220
Sufficient
SCDO:0000200
DOID:9220
Primary Central Sleep Apnea
Central Sleep Apnea
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.
http://www.drugbank.ca/drugs/DB06694
Sufficient
SCDO:0001254
DRON:00017565
Balminil
Otrivin
Xylomethazoline
Xylometazoline
This requirement indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.
Sufficient
SCDO:1000413
DUO:0000018
Not for Profit Use Only
This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community.
Sufficient
SCDO:1000416
DUO:0000019
Publication Required
This could be coupled with a string describing the primary study investigator(s).
Sufficient
SCDO:1000409
DUO:0000020
Collaboration Required
This requirement indicates that the requestor must provide documentation of local IRB/ERB approval.
Sufficient
SCDO:1000410
DUO:0000021
Ethics Approval Required
This should be coupled with an ontology term describing the geographical location the restriction applies to.
Sufficient
SCDO:1000411
DUO:0000022
Geographical Restriction
This should be coupled with a date specified as ISO8601
Sufficient
SCDO:1000415
DUO:0000024
Publication Moratorium
This should be coupled with an integer value indicating the number of months.
Sufficient
SCDO:1000418
DUO:0000025
Time Limit on Use
This requirement indicates that use is limited to use by approved users.
Sufficient
SCDO:1000419
DUO:0000026
User Specific Restriction
This requirement indicates that use is limited to use within an approved project.
Sufficient
SCDO:1000414
DUO:0000027
Project Specific Restriction
This requirement indicates that use is limited to use within an approved institution.
Sufficient
SCDO:1000412
DUO:0000028
Institution Specific Restriction
This requirement indicates that the requestor must return derived/enriched data to the database/resource.
Sufficient
SCDO:1000417
DUO:0000029
Return to Database or Resource
An environmental system process that results in the introduction of contaminants into an environment.
http://purl.obolibrary.org/obo/ENVO_02500036
Sufficient
SCDO:0000912
ENVO:02500036
Environmental Pollution
Pollution
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.
Sufficient
SCDO:1000216
EUPATH:0000034
Alpha Thalassemia Genotype
A clinical visit that is primarily for a regular examination.
Sufficient
SCDO:1000848
EUPATH:0000050
Routine Clinical Visit
An anemia with hemoglobin levels less than 5 gm/dL.
http://purl.obolibrary.org/obo/EUPATH_0000215
Sufficient
SCDO:1000055
EUPATH:0000215
Severe Anemia
An information content entity that is about a clinical visit.
Sufficient
SCDO:1000851
EUPATH:0000310
Information on Observation Details
A scalar measurement datum of the concentration of urea in blood that is a specified output of a blood test.
Sufficient
SCDO:1000603
EUPATH:0021227
Serum Urea Concentration
Blood Urea Concentration
An individual attribute that is the usual or principal work or business of an individual.
http://purl.obolibrary.org/obo/ExO_0000034
Sufficient
SCDO:0000821
ExO:0000034
Career
Employment
Job
Vocation
Occupation
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.
Sufficient
SCDO:0000167
ExO:0000048
Built Environment
A reference to a place on the Earth, by its name or by its geographical location.
http://purl.obolibrary.org/obo/GAZ_00000448
Sufficient
SCDO:0000451
GAZ:00000448
Geographic Region
Geographic 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.
Sufficient
SCDO:1000672
GSSO:000109
Intersex
Principles which provide a framework within which ethical dilemmas and other problems may be analyzed.
Sufficient
SCDO:1000427
GSSO:003239
Ethical Principle
The pattern in which a particular genetic trait or disorder is passed from one generation to the next.
http://purl.obolibrary.org/obo/HP_0000005
Sufficient
SCDO:0001367
HP:0000005
Inheritance
Mode of 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 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.
Sufficient
SCDO:1000140
HP:0000006
Autosomal Dominant Form
Autosomal Dominant Inheritance
Autosomal Dominant Predisposition
Autosomal Dominant
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).
http://purl.obolibrary.org/obo/HP_0000007
Sufficient
SCDO:0001368
HP:0000007
Autosomal Recessive Form
Autosomal Recessive Inheritance
Autosomal Recessive Predisposition
Autosomal Recessive
Absence of any measurable level of sperm in a male's semen.
Sufficient
SCDO:0000092
HP:0000027
Absent Sperm in Semen
Azoospermia
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).
Sufficient
SCDO:0002903
HP:0000044
Hypogonadotropic Hypogonadism
Secondary Hypogonadism
Hypogonadotropic Hypogonadism
An abnormality of the kidney.
http://purl.obolibrary.org/obo/HP_0000077
Sufficient
SCDO:0002133
HP:0000077
Abnormal Kidney
Anomaly of the Kidney
Renal Anomaly
Abnormality of the Kidney
An abnormality of the genital system.
Sufficient
SCDO:1000263
HP:0000078
Genital Abnormalities
Genital Abnormality
Genital Anomalies
Genital Defects
Abnormality of the Genital System
An abnormality of the urinary system.
Sufficient
SCDO:0001347
HP:0000079
Anomaly of the Urinary System
Urinary Tract Abnormalities
Urinary Tract Abnormality
Urinary Tract Anomalies
Urinary Tract Anomaly
Abnormality of the Urinary System
An abnormal functionality of the genital system.
Sufficient
SCDO:1000270
HP:0000080
Abnormality of Genital Physiology
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.
http://purl.obolibrary.org/obo/MP_0003606
Variable
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.
Sufficient
SCDO:0000674
HP:0000084
Renal Failure
Renal Insufficiency
Treatment is dependent upon etiology and acuity. If refractory to medical therapy, renal replacement or dialysis may be indicated.
Kidney Failure
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.
Sufficient
SCDO:0000460
NHLBI 2014 Guidelines
HP:0000096
Glomerular Sclerosis
Renal Glomerular Fibrosis
Glomerulosclerosis
Segmental accumulation of scar tissue in individual (but not all) glomeruli.
Sufficient
SCDO:0009968
HP:0000097
Focal Glomerulosclerosis
Focal and Segmental Glomerular Sclerosis
Focal and Segmental Glomerulosclerosis
Focal Segmental Glomerulosclerosis
Inflammation of the renal glomeruli.
Provide source for additional info.
May occur at any age.
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.
Sufficient
SCDO:0000458
HP:0000099
GN
Glomerular Nephritis
Glomerulonephritis
A nonspecific term referring to disease or damage of the kidneys.
Sufficient
SCDO:0000795
HP:0000112
Kidney Damage
Kidney Disease
Nephropathy
A phenotype that shows detectable differences from normal.
http://purl.obolibrary.org/obo/FYPO_0001985
Sufficient
SCDO:0009818
HP:0000118
Phenotypic Abnormality
Abnormal Phenotype
The presence of inflammation affecting the kidney.
Provide source for additional info.
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.
Sufficient
SCDO:0000793
HP:0000123
Kidney Inflammation
Nephritis
Prolonged and/or excessive menses at regular intervals in excess of 80 ml or lasting longer than 7 days.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0000132
Sufficient
SCDO:0000745
HP:0000132
Abnormally Heavy Bleeding During Menstruation
Hypermenorrhea
Menorrhagia
Hemorrhage affecting the gingiva.
http://purl.obolibrary.org/obo/HP_0000225
Sufficient
SCDO:0000452
HP:0000225
Bleeding Gums
Gingival Hemorrhage
Gingivorrhagia
Gingival Bleeding
An abnormality of the face.
http://purl.obolibrary.org/obo/HP_0000271
Sufficient
SCDO:0003024
HP:0000271
Facial Abnormality
Abnormality of the Face
Inflammation or infection of the middle ear.
Source needed for additional information.
http://purl.obolibrary.org/obo/HP_0000388
Sufficient
SCDO:0000846
HP:0000388
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
Otitis Media
Any abnormality of the eye, including location, spacing, and intraocular abnormalities.
Sufficient
SCDO:1000294
HP:0000478
Abnormality of the Eye
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.
Sufficient
SCDO:1000022
HP:0000505
Impaired Vision
Impaired Visual Function
Loss of Eyesight
Poor Vision
Visual Impairment
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.
Sufficient
SCDO:1000021
HP:0000618
Total Vision Loss
Blindness
Any abnormality of the nervous system.
http://purl.obolibrary.org/obo/HP_0000707
Sufficient
SCDO:0009698
HP:0000707
Brain and/or Spinal Cord Issue
Neurologic Abnormalities
Neurological Abnormality
Abnormality of the Nervous System
An abnormality of mental functioning including various affective, behavioural, cognitive and perceptual abnormalities.
Include "Poor School Performance" as a sub-class.
http://purl.obolibrary.org/obo/HP_0000708
Sufficient
SCDO:0000105
HP:0000708
Behavioral Abnormality
Behavioural Abnormality
Behavioural Changes
Behavioural Disorders
Behavioural Disturbances
Behavioural Problems
Behavioural Symptoms
Behavioural/Psychiatric Abnormalities
Behavioural/Psychiatric Abnormality
Psychiatric Disorders
Psychiatric Disturbances
Behavioural Abnormality
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.
Sufficient
SCDO:0000345
HP:0000726
Dementia, Progressive
Progressive Dementia
Dementia
Peripheral neuropathy affecting the sensory nerves.
http://purl.obolibrary.org/obo/HP_0000763
Sufficient
SCDO:0001038
HP:0000763
Peripheral Sensory Neuropathy
Sensory Neuropathy
Inability to produce live offspring.
Sufficient
SCDO:0000639
HP:0000789
Sterility
Infertility
Reduced count of spermatozoa in the semen, defined as a sperm count below 20 million per milliliter semen.
Sufficient
SCDO:0000827
HP:0000798
Low Sperm Count
Oligospermia
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.
http://purl.obolibrary.org/obo/HP_0000805
Sufficient
SCDO:0000434
HP:0000805
Enuresis
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.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0000815
Sufficient
SCDO:0000586
HP:0000815
Hypergonadotrophic Hypogonadism
Primary Hypogonadism
Hypergonadotropic Hypogonadism
An abnormality of the endocrine system.
Sufficient
SCDO:0002780
HP:0000818
Abnormality of the Endocrine System
A group of abnormalities characterized by hyperglycemia and glucose intolerance.
http://purl.obolibrary.org/obo/HP_0000819
Sufficient
SCDO:0000367
HP:0000819
Diabetes Mellitus
An abnormality of the thyroid gland.
Sufficient
SCDO:1000278
HP:0000820
Thyroid Abnormality
Abnormality of the Thyroid Gland
Deficiency of thyroid hormone.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0000821
Sufficient
SCDO:0000603
HP:0000821
Low T4
Underactive Thyroid
Hypothyroidism
The presence of chronic increased pressure in the systemic arterial system.
Sufficient
SCDO:0008801
HP:0000822
Hypertension
Passing the age when puberty normally occurs with no physical or hormonal signs of the onset of puberty.
Sufficient
SCDO:0000342
HP:0000823
Delayed Development of Secondary Sex Characteristics
Delayed Onset of Sexual Maturity
Delayed Pubertal Development
Delayed Sexual Maturation
Delayed Sexual Maturity
Delayed pubertal growth
Pubertal Delay
Delayed Puberty
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.
Sufficient
SCDO:0008218
HP:0000824
Growth Hormone Deficiency
An abnormality of the parathyroid gland.
Sufficient
SCDO:1000279
HP:0000828
Abnormality of the Parathyroid Gland
A condition caused by a deficiency of parathyroid hormone characterized by hypocalcemia and hyperphosphatemia.
Sufficient
SCDO:0007386
HP:0000829
Decreased Parathyroid Hormone Secretion
Low Parathyroid Hormone
Hypoparathyroidism
Abnormality of the adrenal glands, i.e., of the endocrine glands located at the top of the kidneys.
Sufficient
SCDO:0007437
HP:0000834
Adrenal Abnormalities
Adrenal Abnormality
Abnormality of the Adrenal Glands
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).
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0000836
Sufficient
SCDO:0000595
HP:0000836
Overactive Thyroid
Hyperthyroidism
An increased concentration of insulin in the blood.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0000842
Sufficient
SCDO:0000587
HP:0000842
Elevated Insulin Level
Hyperinsulinemia
Excessive production of parathyroid hormone (PTH) by the parathyroid glands.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0000843
Sufficient
SCDO:0000592
HP:0000843
Elevated Blood Parathyroid Hormone Level
Hyperparathyroidism
Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels.
http://purl.obolibrary.org/obo/HP_0000855
Sufficient
SCDO:0000644
HP:0000855
Body Fails to Respond to Insulin
Insulin Resistance
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).
http://purl.obolibrary.org/obo/HP_0000873
Sufficient
SCDO:0000366
HP:0000873
Diabetes Insipidus
Infrequent menses (less than 6 per year or more than 35 days between cycles).
Sufficient
SCDO:0003158
HP:0000876
Light or Infrequent Menstrual Periods
Oligomenorrhea
An abnormality of the skeletal system.
Sufficient
SCDO:0006301
HP:0000924
Skeletal Abnormalities
Skeletal Anomalies
Abnormality of the Skeletal System
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.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0000938
Sufficient
SCDO:0000843
HP:0000938
Decreased Bone Mineral Density
Generalized Osteopenia
Osteopenia
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).
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0000939
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.
Sufficient
SCDO:0000844
HP:0000939
Osteoporosis
An abnormality of the skin.
http://purl.obolibrary.org/obo/HP_0000951
Sufficient
SCDO:0008348
HP:0000951
Abnormal skin morphology
Abnormal skin structure
Dermatopathy
Dermopathy
Skin Abnormality
Abnormality of the Skin
Yellow pigmentation of the skin or sclera due to bilirubin, which in turn is the result of increased bilirubin concentration in the bloodstream.
http://purl.obolibrary.org/obo/HP_0000952
Sufficient
SCDO:0000671
HP:0000952
Icterus
Yellow Skin
Yellowing of the Skin
Jaundice
A darkening of the skin related to an increase in melanin production and deposition.
http://purl.obolibrary.org/obo/HP_0000953
Sufficient
SCDO:0000308
HP:0000953
Hyperpigmentation of the Skin
Increased Skin Pigmentation
Melanoderma
Melanodermia
Skin Hyperpigmentation
Cutaneous Hyperpigmentation
Bluish discoloration of the skin and mucosa due to poor circulation or inadequate oxygenation of arterial or capillary blood.
Sufficient
SCDO:0000309
HP:0000961
Blue Discoloration of the Skin
Cyanotic
Cyanosis
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.
Sufficient
SCDO:0000589
HP:0000962
Hyperkeratosis
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.
Sufficient
SCDO:0000892
HP:0000967
Petechiae
An abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body.
http://purl.obolibrary.org/obo/HP_0000969
Sufficient
SCDO:0000823
HP:0000969
Dropsy
Fluid Retention
Hydrops
Oedema
Water Retention
Edema
Abnormally pale skin.
Sufficient
SCDO:0000863
HP:0000980
Pallor
Any manifestation of a skin disease associated with the production of pus.
Sufficient
SCDO:0000946
HP:0000999
Pus-Filled Lesion
Pyoderma
A reduction of skin color related to a decrease in melanin production and deposition.
Sufficient
SCDO:0000601
HP:0001010
Hypopigmentation of the Skin
Hypopigmented Skin
Skin Hypopigmentation
Hypopigmentation
An abnormal reduction in the amount of pigmentation (reduced or absent) of skin, hair and eye (iris and retina).
Sufficient
SCDO:0000036
HP:0001022
Achromasia
Albinism
Raised, well-circumscribed areas of erythema and edema involving the dermis and epidermis. Urticaria is intensely pruritic, and blanches completely with pressure.
Sufficient
SCDO:0001219
HP:0001025
Hives
Urticaria
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).
Sufficient
SCDO:0000012
HP:0001061
Break Out
Breaking Out
Acne
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".
http://purl.obolibrary.org/obo/HP_0001081
Sufficient
SCDO:0007091
HP:0001081
Gallstones
Cholelithiasis
An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities.
Sufficient
SCDO:1000262
HP:0001197
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.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0001250
Sufficient
SCDO:0001030
HP:0001250
Seizures
Seizure
A state of disinterestedness, listlessness, and indifference, resulting in difficulty performing simple tasks or concentrating.
Sufficient
SCDO:0003089
HP:0001254
Lethargy
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
Sufficient
SCDO:0000403
HP:0001260
Difficulty Articulating Speech
Dysarthric Speech
Dysarthria
Reduction of neurologic reflexes such as the knee-jerk reaction.
Sufficient
SCDO:0000602
HP:0001265
Decreased Reflex Response
Decreased Reflexes
Hyporeflexia
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.
http://purl.obolibrary.org/obo/HP_0001269
Sufficient
SCDO:0008272
HP:0001269
Weakness of One Side of Body
Hemiparesis
A generalized disorder of peripheral nerves.
http://purl.obolibrary.org/obo/HP_0001271
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.
Sufficient
SCDO:0000914
HP:0001271
Peripheral Nerve Disease
Polyneuropathy
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.
http://purl.obolibrary.org/obo/HP_0001279
Sufficient
SCDO:0008553
HP:0001279
Fainting Spell
Syncope
Inflammation of the meninges.
Sufficient
SCDO:0000744
HP:0001287
Meningitis
Lack of clarity and coherence of thought, perception, understanding, or action.
-- Perhaps move below "Behavioral Abnormality"?
Sufficient
SCDO:0000273
HP:0001289
Confusion
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.
Sufficient
SCDO:0000429
HP:0001298
Encephalopathy
Hemorrhage into the parenchyma of the brain.
http://purl.obolibrary.org/obo/HP_0001342
Sufficient
SCDO:0000209
HP:0001342
Bleeding in Brain
Hemorrhagic Stroke
Intracerebral Bleeding
Intracerebral Hemorrhage
Cerebral Hemorrhage
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.
Sufficient
SCDO:0000673
HP:0001343
Kernicterus
Inflammation of a joint.
http://purl.obolibrary.org/obo/HP_0001369
Any age
Infection (bacteria), ischemia, joint injury (trauma, surgery), degeneration.
Joint pain, joint swelling, stiffness, lack of function.
Sufficient
SCDO:0000075
HP:0001369
Joint Inflammation
Arthritis
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.
Provide source for additional info.
http://purl.obolibrary.org/obo/MP_0003561
Sufficient
SCDO:0001011
HP:0001370
Osteoarthrosis Deformans
RA
Rheumatoid Arthritis
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.
http://purl.obolibrary.org/obo/HP_0001371
Sufficient
SCDO:0001324
HP:0001371
Flexion Contractures
Flexion Contractures of Joints
Joint Contracture
Joint Contractures
Flexion Contracture
The ability of a joint to move beyond its normal range of motion.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0001382
Sufficient
SCDO:0000672
HP:0001382
Double-Jointed
Hyperextensible Joints
Increased Mobility of Joints
Joint Hyperextensibility
Joint Hypermobility
An abnormality of the liver.
Sufficient
SCDO:1000272
HP:0001392
Complication of the Liver
Liver Abnormality
Liver Complication
Abnormality of the Liver
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.
Sufficient
SCDO:0001488
HP:0001394
Hepatic Cirrhosis
Scar Tissue Replaces Healthy Tissue in the Liver
Cirrhosis
The presence of excessive fibrous connective tissue in the liver. Fibrosis is a reparative or reactive process.
Sufficient
SCDO:0001493
HP:0001395
Hepatic Fibrosis
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.
http://purl.obolibrary.org/obo/HP_0001406
Sufficient
SCDO:0009774
HP:0001406
Intrahepatic Cholestasis
Simultaneous enlargement of the liver and spleen.
Sufficient
SCDO:0007326
HP:0001433
Hepatosplenomegaly
Abnormality of growth.
Sufficient
SCDO:1000271
HP:0001507
Abnormal Growth
Growth Issue
Growth Abnormality
Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm.
Sufficient
SCDO:0002729
HP:0001508
FTT
Faltering Weight
Poor Weight Gain
Postnatal Failure to Thrive
Undergrowth
Weight Faltering
Failure to Thrive
An abnormal restriction of fetal growth with fetal weight below the tenth percentile for gestational age.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0001511
Sufficient
SCDO:0000658
HP:0001511
IUGR
Intrauterine Growth Retardation
Prenatal Growth Retardation
Prenatal-Onset Growth Retardation
Small for Gestational Age Infant
Intrauterine Growth Restriction
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.
http://purl.obolibrary.org/obo/HP_0001513
Sufficient
SCDO:0000816
HP:0001513
Having too much body fat
Obesity
An abnormality of the integument, which consists of the skin and the superficial fascia.
Sufficient
SCDO:1000274
HP:0001574
Abnormality of the Integument
The birth of a baby of less than 37 weeks of gestational age.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0001622
Sufficient
SCDO:0000920
HP:0001622
Premature Birth
Premature Delivery
Premature Delivery of Affected Infants
Preterm Birth
Preterm Delivery
Any abnormality of the cardiovascular system.
http://purl.obolibrary.org/obo/HP_0001626
Sufficient
SCDO:0002245
HP:0001626
Abnormality of the Cardiovascular System
Cardiovascular Abnormality
Abnormality of 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.
Sufficient
SCDO:0004877
HP:0001635
CHF
Cardiac Insufficiency,
Congestive Heart Failure
Heart Failure
Cardiac Failure
Increased size of the heart.
http://purl.obolibrary.org/obo/HP_0001640
Sufficient
SCDO:0008273
HP:0001640
Enlarged Heart
Increased Heart Size
Cardiomegaly
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.
http://purl.obolibrary.org/obo/HP_0001658
Sufficient
SCDO:0007991
HP:0001658
Myocardial Infarction
Inflammation of the sac-like covering around the heart (pericardium).
Sufficient
SCDO:0003765
HP:0001701
Pericarditis
Enlargement or increased size of the heart left ventricle.
Sufficient
SCDO:0002803
HP:0001712
Heart Left Ventricle Hypertrophy
Left Ventricular Wall Hypertrophy
Left Ventricular Hypertrophy
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.
http://purl.obolibrary.org/obo/HP_0001714
Sufficient
SCDO:0001231
HP:0001714
Ventricular Hypertrophy
An abnormality of the spleen.
Sufficient
SCDO:1000370
HP:0001743
Abnormality of the Spleen
Abnormal increased size of the spleen.
http://purl.obolibrary.org/obo/HP_0001744
Sufficient
SCDO:0005287
HP:0001744
Increased Spleen Size
Results from splenic sequestration
Splenomegaly
An abnormality of the birth process.
Sufficient
SCDO:1000372
HP:0001787
Abnormal Delivery
The abnormal accumulation of fluid in two or more fetal compartments, including ascites, pleural effusion, pericardial effusion, and skin edema.
http://purl.obolibrary.org/obo/HP_0001789
Sufficient
SCDO:0000578
HP:0001789
Hydrops Fetalis
An abnormality of the hematopoietic system.
Sufficient
SCDO:1000264
HP:0001871
Abnormality of the Hematopoietic System
Hematological Abnormality
Hematopoietic System Abnormality
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.
Sufficient
SCDO:1000616
HP:0001872
Platelet Abnormalities
Abnormal Thrombocyte Morphology
A reduction in the number of circulating thrombocytes.
Sufficient
SCDO:0002700
HP:0001873
Thrombocytopenia
A neutrophil abnormality.
Sufficient
SCDO:1000440
HP:0001874
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.
Abnormality of Neutrophils
An abnormally low number of neutrophils in the peripheral blood.
Sufficient
SCDO:0009334
HP:0001875
Decreased Neutrophil Count
Low Blood Neutrophil Count
Low Neutrophil Count
Peripheral Neutropenia
Neutropenia
Any structural abnormality of erythrocytes (red-blood cells).
Sufficient
SCDO:1000285
HP:0001877
Abnormal Erythrocyte Morphology
A type of anemia caused by premature destruction of red blood cells (hemolysis).
http://purl.obolibrary.org/obo/HP_0001878
Sufficient
SCDO:0003844
HP:0001878
Hemolytic Anemia
An abnormal decreased number of leukocytes in the blood.
Sufficient
SCDO:1000614
HP:0001882
Decreased Blood Leukocyte Number
Low White Blood Cell Count
Leukopenia
Anemia characterized by the presence of erythroblasts that are larger than normal (megaloblasts).
http://purl.obolibrary.org/obo/HP_0001889
Sufficient
SCDO:0005864
HP:0001889
Megaloblastic Anemia
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.
Sufficient
SCDO:1000618
HP:0001894
Increased Number of Platelets in Blood
Increased Platelet Count
Thrombocytosis
A reduced number of reticulocytes in the peripheral blood.
Sufficient
SCDO:0001423
HP:0001896
Low Reticulocyte Count
Reduced Number of Reticulocytes
Reduced Reticulocyte Count
Reticulocytopenia
A reduction in erythrocytes volume or hemoglobin concentration.
http://purl.obolibrary.org/obo/HP_0001903
Sufficient
SCDO:0005660
HP:0001903
Anemia
A cancer of the blood and bone marrow characterized by an abnormal proliferation of leukocytes.
http://purl.obolibrary.org/obo/HP_0001909
Sufficient
SCDO:0000687
HP:0001909
Blood Cancer
Leukaemia
Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia).
Further work
Provide source for additional info.
There is conflicting positioning of this term in different ontologies. Need an expert to decide descriptions and positioning of this and related terms.
http://purl.obolibrary.org/obo/HP_0001919
Sufficient
SCDO:0000017
HP:0001919
Acute Kidney Failure
Acute Renal Failure
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.
Acute Kidney Injury
The presence of stenosis of the renal artery.
Provide source for additional info.
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.
Sufficient
SCDO:0000982
HP:0001920
Narrowing of Kidney Artery
RAS
Renal Artery Stenosis
An elevation in the number of reticulocytes (immature erythrocytes) in the peripheral blood circulation.
Sufficient
SCDO:0001272
HP:0001923
High Reticulocyte Count
Increased Immature Red Blood Cells
Increased Number of Immature Red Blood Cells
Increased Reticulocyte Count
Increased Reticulocytes
Reticulocytosis
A type of anemia characterized by an abnormally low concentration of hemoglobin in the erythrocytes.
Sufficient
SCDO:0007371
HP:0001931
Hypochromic Anemia
A kind of anemia in which the volume of the red blood cells is reduced.
Sufficient
SCDO:0008538
HP:0001935
In normocytic anemia, the mean corpuscular volume (MCV) is below normal limits (>80 fl in adults).
Microcytic Anemia
A decreased concentration of glucose in the blood.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0001943
Sufficient
SCDO:0000599
HP:0001943
Low Blood Sugar
Hypoglycemia
A type of diabetic metabolic abnormality with an accumulation of ketone bodies.
http://purl.obolibrary.org/obo/HP_0001953
Sufficient
SCDO:0000369
HP:0001953
Diabetic Ketosis
Diabetic Ketoacidosis
A form of inflammation of the kidney affecting the interstitium of the kidneys surrounding the tubules.
Sufficient
SCDO:0000652
HP:0001970
Tubulointerstitial Nephritis
Interstitial Nephritis
An abnormal increase in the number of leukocytes in the blood.
Sufficient
SCDO:0005790
HP:0001974
Elevated White Blood Count
High White Blood Count
Increased Blood Leukocyte Number
Leukocytosis
Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis).
Sufficient
SCDO:1000287
HP:0001977
Abnormal Thrombosis
An abnormal morphology (form) of the face or its components.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0001999
Sufficient
SCDO:0001314
HP:0001999
Abnormal Morphology of the Face
Abnormal facial shape
Dysmorphic Facial Features
Unusual Facial Appearance
Facial Dysmorphisms
Bilateral bulging of the lateral frontal bone prominences with relative sparing of the midline.
http://purl.obolibrary.org/obo/HP_0002007
Sufficient
SCDO:0001337
HP:0002007
Frontal Protruberance
Skull Bossing
Frontal Bossing
Abnormally increased frequency of loose or watery bowel movements.
Sufficient
SCDO:0008043
HP:0002014
Diarrhoea
Watery stool
Diarrhea
Infrequent or difficult evacuation of feces.
http://purl.obolibrary.org/obo/HP_0002019
Sufficient
SCDO:0003263
HP:0002019
Constipation
Costiveness
Dyschezia
Constipation
Atrophy (wasting, decrease in size of cells or tissue) affecting the cerebrum.
http://purl.obolibrary.org/obo/HP_0002059
Sufficient
SCDO:0000203
HP:0002059
Cortical Atrophy
Degeneration of Cerebrum
Supratentorial Atrophy
Atrophy may be progressive over time.
Cerebral Atrophy
An abnormality of the telencephalon, which is also known as the cerebrum.
http://purl.obolibrary.org/obo/HP_0002060
Sufficient
SCDO:0008895
HP:0002060
Abnormal Cerebral Morphology
Abnormality of the Telencephalon
Abnormality of 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).
http://purl.obolibrary.org/obo/HP_0002067
Sufficient
SCDO:0000158
HP:0002067
Slow Movements
Slowness of Movements
Bradykinesia
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).
Sufficient
SCDO:0001311
HP:0002071
Abnormality of Extrapyramidal Motor Function
Extrapyramidal Dysfunction
Extrapyramidal Signs
Extrapyramidal Syndrome
Extrapyramidal Tract Signs
Extrapyramidal Symptoms
Migraine is a chronic neurological disorder characterized by episodic attacks of headache and associated symptoms.
Sufficient
SCDO:0000759
HP:0002076
Intermittent Migraine Headaches
Migraine Headache
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.
Migraine
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.
http://purl.obolibrary.org/obo/HP_0002086
Sufficient
SCDO:0004899
HP:0002086
Respiratory Abnormality
Abnormality of the Respiratory System
Inflammation of any part of the lung parenchyma.
Sufficient
SCDO:0009838
HP:0002090
Pneumonia
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.
Is a symptom of acute chest syndrome
http://purl.obolibrary.org/obo/HP_0002098
Sufficient
SCDO:0009656
HP:0002098
Breathing Difficulties
Difficulty Breathing
Respiratory Difficulties
Respiratory Distress
Hemorrhage occurring between the arachnoid mater and the pia mater.
Sufficient
SCDO:0001118
HP:0002138
Subarachnoid Haemorrhage
Subarachnoid hemorrhage may occur spontaneously, usually from a ruptured cerebral aneurysm, or may result from head injury.
Subarachnoid Hemorrhage
An abnormally high level of uric acid in the blood.
Sufficient
SCDO:0000596
HP:0002149
High Blood Uric Acid Level
Hyperuricaemia
Hyperuricemia
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.
Sufficient
SCDO:0000093
HP:0002157
Azotemia
Azotaemia
The presence of developmental dysplasia of the nail.
Sufficient
SCDO:0000830
HP:0002164
Dysplastic Nails
Onychodysplasia
Nail Dysplasia
Hemorrhage occurring within the skull.
Sufficient
SCDO:0000654
HP:0002170
Intracranial Hemorrhage
Abnormal accumulation of fluid in the brain.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0002181
Sufficient
SCDO:0000207
HP:0002181
Brain Edema
Brain Oedema
Cerebral Oedema
Cerebral Edema
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.
Sufficient
SCDO:0007912
HP:0002204
Blood Clot in Artery of Lung
Pulmonary Embolism
Abnormally increased size of the liver.
Sufficient
SCDO:0005566
HP:0002240
Hepatomegaly
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.
http://purl.obolibrary.org/obo/HP_0002341
Sufficient
SCDO:0000214
HP:0002341
Cervical Cord Compression Myelopathy
Cervical Spondylotic Myelopathy
Spinal Cord Compression
Cervical Cord Compression
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.
Sufficient
SCDO:0000773
HP:0002427
Broca's Aphasia
Expressive Aphasia
Loss of Expressive Speech
Motor Aphasia
An increase of the pressure inside the cranium (skull) and thereby in the brain tissue and cerebrospinal fluid.
http://purl.obolibrary.org/obo/HP_0002516
Sufficient
SCDO:0000655
HP:0002516
Increased Intracranial Pressure
Intracranial Pressure Elevation
Rise in Pressure Inside Skull
Intracranial Hypertension
An abnormality of the vasculature.
Sufficient
SCDO:1000373
HP:0002597
Abnormality of the Vasculature
The presence of an abnormal lateral curvature of the spine.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0002650
Congenital vertebral anomalies, idiopathic, result of a neuromuscular condition.
Spinal tortuosity.
Sufficient
SCDO:0001026
HP:0002650
Abnormal Curving of the Spine
Scoliosis
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to bone.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0002653
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
Sufficient
SCDO:0000154
HP:0002653
Bone Pain
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.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0002659
Sufficient
SCDO:0000153
HP:0002659
Abnormal Susceptibility to Fractures
Frequent Broken Bones
Increased Bone Fragility
Increased Susceptibility to Fractures
Increased Tendency to Fractures
Bone Fragility
A cancer originating in lymphocytes and presenting as a solid tumor of lymphoid cells.
http://purl.obolibrary.org/obo/HP_0002665
Sufficient
SCDO:0000707
HP:0002665
Cancer of Lymphatic System
Lymphoma
An abnormality of the immune system.
Include as sub-class:
Acquired Immunodeficiency Syndrome (term in NCIT)
Sufficient
SCDO:1000273
HP:0002715
Abnormality of the Immune System
A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys, and serosal membranes.
http://purl.obolibrary.org/obo/HP_0002725
Sufficient
SCDO:0001137
HP:0002725
Systemic Lupus Erythematosus
Exaggerated anterior convexity of the thoracic vertebral column.
http://purl.obolibrary.org/obo/HP_0002808
Sufficient
SCDO:0000679
HP:0002808
Gibbus Deformity
Hunched Back
Hyperkyphosis
Round Back
Kyphosis
Joint pain.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0002829
Sufficient
SCDO:0000074
HP:0002829
Arthralgias
Joint pain
Arthralgia
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.
http://purl.obolibrary.org/obo/HP_0002870
Sufficient
SCDO:0000820
HP:0002870
Obstructive Sleep Apnoea
Obstructive Sleep Apnea
Microscopic hematuria detected by dipstick or microscopic examination of the urine.
http://purl.obolibrary.org/obo/HP_0002907
Sufficient
SCDO:0004833
HP:0002907
Microhematuria
Occult Hematuria
Small Amount of Blood in Urine
Microscopic Hematuria
Presence of myoglobin in the urine.
Sufficient
SCDO:0000783
HP:0002913
Increased Urine Myoglobin Level
Myoglobinuria
Any disease characterized by the formation of numerous granulomas.
Source needed for additional information.
http://purl.obolibrary.org/obo/HP_0002955
Sufficient
SCDO:0000464
HP:0002955
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.
Granulomatosis
An elevated lipid concentration in the blood.
http://purl.obolibrary.org/obo/HP_0003077
Sufficient
SCDO:0000590
HP:0003077
Elevated Lipids in Blood
Hyperlipidemia
An abnormality of the composition of urine or the levels of its components.
Sufficient
SCDO:1000651
HP:0003110
Abnormal Urine Chemistry
Abnormality of Urine Homeostasis
Abnormal Urine Homeostasis
An abnormality detectable by sonography of the heart (echocardiography).
Sufficient
SCDO:1000267
HP:0003116
Abnormal ECG
Abnormal Echocardiography
Abnormal Echocardiogram
Excretion in urine of proteins of a size smaller than albumin (molecular weight 69 kD).
http://purl.obolibrary.org/obo/HP_0003126
Sufficient
SCDO:0001196
HP:0003126
Low-Molecular-Weight Proteinuria
Tubular Proteinuria
Abnormally increased serum levels of alkaline phosphatase activity.
Sufficient
SCDO:1000664
HP:0003155
Blood Alkaline Phosphatase Increased
Decreased Circulating Alkaline Phosphatase Level
Elevated ALP
Elevated Alkaline Phosphatase
High Serum Alkaline Phosphatase
Increased Alkaline Phosphatase
Reduced Circulating ALP
Elevated Serum Alkaline Phosphatase
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)?
http://purl.obolibrary.org/obo/HP_0003158
Sufficient
SCDO:0008046
HP:0003158
Urine specific gravity is lower than that of plasma < 1.008.
Hyposthenuria
A disorder of muscle unrelated to impairment of innervation or neuromuscular junction.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0003198
Sufficient
SCDO:0000784
HP:0003198
Muscle Tissue Disease
Myopathic Changes
Myopathies
Myopathy
A type of hyperbilirubinemia with neonatal onset.
Sufficient
SCDO:0003776
HP:0003265
High Blood Bilirubin Levels in Neonate
Neonatal Hyperbilirubinemia
Abnormally reduced serum levels of alkaline phosphatase.
Sufficient
SCDO:1000667
HP:0003282
Low ALP
Low Alkaline Phosphatase
Reduced Serum Alkaline Phosphatase
Decreased Serum Alkaline Phosphatase
Complete bilateral fractures of the pars interarticularis resulting in the anterior slippage of the vertebra.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0003302
Spondylolysis, arthritis, degeneration, trauma, metastases or metabolic bone disease, congenital.
Sufficient
SCDO:0001102
HP:0003302
Displacement of One Backbone Compared to Another
Slipped Backbone
Spondylolithesis
Spondylolisthesis
Sudden and involuntary contractions of one or more muscles.
Sufficient
SCDO:0000778
HP:0003394
Muscle Spasm
Muscle Cramps
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the back.
Provide source for additional info.
muscle strain, trauma, surgery, fracture, osteoporosis, fibromialgia, spinal disc herniation.
Pain in the lower back.
Sufficient
SCDO:0000095
HP:0003418
Back Pain
Abnormal results of investigations using electromyography (EMG).
Sufficient
SCDO:0000428
HP:0003457
Abnormal EMG
Abnormal Electromyography (EMG).
Abnormal Electromyography Finding
EMG Abnormalities
Electromyogram Abnormal
EMG Abnormality
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.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0003470
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.
Sufficient
SCDO:0000865
HP:0003470
Inability to Move
Paralysis
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.
Sufficient
SCDO:0000703
HP:0003563
Decreased Circulating Low-Density Lipoprotein Levels
Decreased LDL
Decreased LDL Cholesterol Concentration
Decreased LDL Cholesterol Level
Decreased LDLc Concentration
Low Circulating LDL Cholesterol Level
Low LDL-Cholestrol Levels
Reduced Circulating LDL Cholesterol Level
Decreased Circulating LDL Cholesterol Level
Increased concentration of total (conjugated and unconjugated) bilirubin in the blood.
Sufficient
SCDO:1000681
HP:0003573
High Bili Total
High Total Bilirubin
Increased Bilirubin
Increased Total Bilirubin
Anomalous concentrations of fat-soluble substances (molecules composed of carbon and hydrogen and are characteristically insoluble in water) in the blood.
Provide source for additional info.
http://purl.obolibrary.org/obo/MP_0003949
Sufficient
SCDO:0000404
HP:0003611
Abnormal Circulating Lipid Concentration
Abnormal Circulating Lipid Level
Dyslipidaemia
Dyslipidemia
The presence of free hemoglobin in the urine.
Sufficient
SCDO:0000554
HP:0003641
Increased Urine Hemoglobin Level
If, following hemolysis, haptoglobins (hemoglobin-binding proteins) are saturated, then free hemoglobin appears in the urine.
Hemoglobinuria
A skin abnormality characterized by redness and irritation, with thick, red skin that displays flaky, silver-white patches (scales).
Sufficient
SCDO:0000936
HP:0003765
Psoriasiform Dermatitis
Psoriasis
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.
Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info.
Variable
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.
Sufficient
SCDO:0000430
HP:0003774
ESKD
ESRD
End Stage Renal Disease
End Stage Renal Disease (ESRD)
End Stage Renal Failure
End-Stage Renal Disease
End-Stage Renal Failure
Stage 5 Chronic Kidney Disease
End Stage Kidney Disease
A reticulocyte abnormality.
Sufficient
SCDO:1000265
HP:0004312
Abnormality of Reticulocytes
Any deviation from the normal concentration of a nitrogen compound in the blood circulation.
Sufficient
SCDO:1000647
HP:0004364
Abnormal Circulating Nitrogen Compound Concentration
An abnormality of alkaline phosphatase level.
Sufficient
SCDO:1000666
HP:0004379
Abnormality Alkaline Phosphatase Level
Abnormality of ALP Level
Abnormality of Alkaline Phosphatase Activity
Alkaline Phosphatase Abnormal
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.
Sufficient
SCDO:1000245
HP:0004447
Poikilocytosis
Exaggerated concavity of the anterior or posterior surface of the vertebral body, i.e., the upper and lower vertebral endplates are hollowed inward.
Sufficient
SCDO:0000118
HP:0004586
Biconcave Vertebrae
Fish Mouth Deformity
Fish Vertebrae
Step Vertebrae
Biconcave Vertebral Bodies
A defect in the ability to concentrate the urine.
http://purl.obolibrary.org/obo/HP_0004727
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.
Sufficient
SCDO:0000621
HP:0004727
UCD
Urine Concentrating Defect
Urine Concentration Defect
Impaired Renal Concentrating Ability
A tachycardia originating in the ventricles characterized by rapid heart rate (over 100 beats per minute) and broad QRS complexes (over 120 ms).
Sufficient
SCDO:0003769
HP:0004756
VT
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.
Ventricular Tachycardia
An abnormal increase in the binding affinity of hemoglobin for oxygen.
Sufficient
SCDO:1000248
HP:0004825
Increased Haemoglobin Oxygen Affinity
Increased Hemoglobin Oxygen Affinity
A chronic form of hemolytic anemia.
http://purl.obolibrary.org/obo/HP_0004870
Sufficient
SCDO:0001248
HP:0004870
Chronic Hemolytic Anemia
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.
http://purl.obolibrary.org/obo/HP_0005162
Sufficient
SCDO:0002710
HP:0005162
Impaired Left Ventricular Function
Left Ventricular Failure
Left Ventricular Impairment
Left-Sided Heart Failure
Left Ventricular Dysfunction
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.
Sufficient
SCDO:0001103
HP:0005268
Miscarriage
Spontaneous Abortion
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
http://purl.obolibrary.org/obo/HP_0005305
Sufficient
SCDO:0000211
HP:0005305
Blood Clot in Cerebral Vein
Cerebral Thrombosis
Cerebral Vein Thrombosis
Cerebral Venous Thrombosis
Inflammation of the blood vessels within the brain.
http://purl.obolibrary.org/obo/HP_0005318
Sufficient
SCDO:0000210
HP:0005318
Cerebral Vasculitis
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.
Sufficient
SCDO:1000626
HP:0005518
Erythrocyte Macrocytosis
High MCV
Increased MCV
Increased Mean Corpuscular Volume
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.
http://purl.obolibrary.org/obo/HP_0005560
Sufficient
SCDO:0001383
HP:0005560
Imbalanced Hemoglobin Synthesis
A bacterial infection of the endocardium, the inner layer of the heart, which usually involves the heart valves.
Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info.
Sufficient
SCDO:0000099
HP:0006689
Infective Endocarditis
Bacterial Endocarditis
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.
http://purl.obolibrary.org/obo/HP_0007018
Sufficient
SCDO:0000090
HP:0007018
ADHD
Attention Deficit
Attention Deficit Disorder
Attention Deficit-Hyperactivity Disorder
Attention Deficits
Childhood Attention Deficit/Hyperactivity Disorder
Attention Deficit Hyperactivity Disorder
Weakness of the muscles of the legs.
Sufficient
SCDO:0000686
HP:0007340
Hind Limb Weakness
Hindlimb Weakness
Leg Weakness
Lower Extremity Weakness
Lower Limb Muscle Weakness
Lower Limb Weakness
Muscle Weakness in Lower Limbs
Inability to perform rapid, alternating movements.
Leg Weakness
Bleeding within the vitreous compartment of the eye.
Sufficient
SCDO:0001238
HP:0007902
Hemorrage Within the Vitreous Humor
Vitreous Haemorrhage
Vitreous Hemorrhage
A type of hypothyroidism that results from a defect in thyroid-stimulating hormone secretion.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0008245
Sufficient
SCDO:0001028
HP:0008245
TSH Deficient Hypothyroidism
Thyroid Stimulating Hormone Deficiency
Thyrotropin Deficiency
Secondary Hypothyroidism
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.
Sufficient
SCDO:0000788
HP:0008404
Dystrophic Nails
Onychodystrophy
Poor nail formation
Nail Dystrophy
Acute death of renal tubular cells that usually results from prolonged renal ischemia, nephrotoxins, or sepsis.
Provide source for additional info.
Can occur at any age.
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.
Sufficient
SCDO:0000020
HP:0008682
ATN
Renal Tubular Necrosis
Acute Tubular Necrosis
Rhabdomyolysis induced by exercise.
http://purl.obolibrary.org/obo/HP_0009045
Sufficient
SCDO:0001308
HP:0009045
Rhabdomyolysis with Exercise
Exercise-Induced Rhabdomyolysis
Peripheral neuropathy is a general term for any disorder of the peripheral nervous system.
http://purl.obolibrary.org/obo/HP_0009830
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.
Sufficient
SCDO:0000884
HP:0009830
Peripheral Nerve Damage
Peripheral Neuritis
Peripheral Neuropathy
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.
- Provide source for additional info.
Sufficient
SCDO:0001315
HP:0010628
Bell's Palsy
Cranial Nerve VII Palsy
Facial Muscle Weakness of Muscles Innervated by CN VII
Facial Nerve Paralysis
Facial Palsy
Facial Paralysis
Seventh Cranial Nerve Palsy
VIIth Cranial Nerve Palsy
Facial Nerve Palsy
An abnormal level of a circulating protein in the blood.
Sufficient
SCDO:1000438
HP:0010876
Abnormality of Circulating Protein Level
Blood Protein Disease
Serum Protein Abnormality
Abnormal 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.
Sufficient
SCDO:0000841
http://purl.bioontology.org/ontology/MEDLINEPLUS/C0029445
HP:0010885
AVN
Aseptic Bone Necrosis
Aseptic necrosis
Avascular Bone Necrosis
Avascular Necrosis
Avascular Necrosis (AVN)
Bone Infarction
Bone Infarcts
Bone Necrosis
Ischemic Bone Necrosis
Osteochondronecrosis
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.
Osteonecrosis
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.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0011001
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.
Sufficient
SCDO:0000629
HP:0011001
Bone Sclerosis
Increased Bone Density
Osteosclerosis
Osteosclerosis of Bones
Increased Bone Mineral Density
The age group in which disease manifestations appear.
http://purl.obolibrary.org/obo/HP_0011007
Sufficient
SCDO:0003913
HP:0011007
Age of Onset
Abnormality of glucose homeostasis.
Sufficient
SCDO:1000283
HP:0011014
Abnormal Glucose Homeostasis
Abnormal functionality of the cardiovascular system.
Sufficient
SCDO:1000368
HP:0011025
Abnormal Cardiovascular System Physiology
A decrease in the amount of intravascular fluid, particularly in the volume of the circulating blood.
Sufficient
SCDO:0003035
HP:0011106
Depleted Blood Volume
Hypovolemia
Any morphological abnormality of the skin.
Sufficient
SCDO:1000374
HP:0011121
Abnormality of Skin Morphology
Any abnormality of the physiological function of the skin.
Sufficient
SCDO:1000375
HP:0011122
Abnormality of Skin Physiology
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.
Sufficient
SCDO:0001071
HP:0011123
Abnormal Tendency to Infections of the Skin
Dermatitis
Inflammatory Abnormality of the Skin
Inflammatory Skin Disease
Maculopapular Rash
Skin Inflammation
Delivery of a fetus through surgical incisions made through the abdominal wall (laparotomy) and the uterine wall (hysterotomy).
http://purl.obolibrary.org/obo/HP_0011410
Sufficient
SCDO:0000168
HP:0011410
Caesarian Section
Shoulder dystocia occurs when the fetal anterior shoulder impacts against the maternal symphysis following delivery of the vertex.
Sufficient
SCDO:0001045
HP:0011413
Shoulder Dystocia
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.
http://purl.obolibrary.org/obo/HP_0011675
Sufficient
SCDO:0009619
HP:0011675
Abnormal Heart Rate
Abnormality of Cardiac Conduction
Arrhythmias
Cardiac Arrhythmia
Cardiac Arrhythmias
Cardiac Conduction Abnormalities
Cardiac Conduction Defects
Cardiac Rhythm Disturbances
Heart Rhythm Disorders
Irregular Heart Beat
Irregular Heartbeat
Arrhythmia
Hemorrhage into the parenchyma of the cerebellum.
Need to include this term mentioned here to the SCDO: -- obstructive hydrocephalus
Sufficient
SCDO:0000201
HP:0011695
Cerebellar Hemorrhage
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.
http://purl.obolibrary.org/obo/HP_0011856
Sufficient
SCDO:0000904
HP:0011856
Pica
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
http://purl.obolibrary.org/obo/HP_0011868
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.
Sufficient
SCDO:0001024
HP:0011868
Sciatica
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.
Sufficient
SCDO:1000617
HP:0011873
Abnormal Platelet Count
Bleeding in the anterior chamber of the eye.
http://purl.obolibrary.org/obo/HP_0011886
Sufficient
SCDO:0000597
HP:0011886
Hyphema
Number of leukocytes per volume of blood beyond normal limits.
Sufficient
SCDO:1000613
HP:0011893
Abnormal White Blood Cell Count
Abnormal Leukocyte Count
Increased number of neutrophils circulating in blood.
Sufficient
SCDO:1000447
HP:0011897
Neutrophilia
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.
http://purl.obolibrary.org/obo/HP_0011904
Sufficient
SCDO:0000888
HP:0011904
Increased Haemoglobin F
Persistence of Hemoglobin F
Raised Hemoglobin F
Increased Hemoglobin F
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.
http://purl.obolibrary.org/obo/HP_0011906
Sufficient
SCDO:0001709
HP:0011906
Increased Alpha/Beta Synthesis Ratio
Reduced Beta/Alpha Synthesis Ratio
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.
http://purl.obolibrary.org/obo/HP_0011907
Sufficient
SCDO:0006404
HP:0011907
Increased Beta/Alpha Synthesis Ratio
Reduced Alpha/Beta Synthesis Ratio
Inflammation of the bronchioles.
http://purl.obolibrary.org/obo/HP_0011950
Sufficient
SCDO:0005490
HP:0011950
Bronchiolitis
A deviation from the normal range of neutrophil cell counts in the circulation.
Sufficient
SCDO:1000446
HP:0011991
Abnormal Neutrophil Cell Number
Abnormal Neutrophil Count
An abnormal concentration of creatinine in the blood.
Sufficient
SCDO:1000541
HP:0012100
Abnormal Blood Creatinine Level
Abnormal Serum Creatinine Level
Creatinine Levels Abnormal
Abnormal Circulating Creatinine Level
An abnormally reduced amount of creatinine in the blood.
Sufficient
SCDO:1000648
HP:0012101
Low Blood Creatinine
Low Serum Creatinine
Reduced Creatinine Levels
Decreased Serum Creatinine
A fungal infection of the toenails or fingernails that tends to cause the nails to thicken, discolor, disfigure, and split.
Sufficient
SCDO:0000831
Medscape: Onychomycosis: Author: Antonella Tosti, MD; Chief Editor: Dirk M Elston, MD et al..
HP:0012203
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.
Onychomycosis
An increased white blood cell count in the cerebrospinal fluid.
http://purl.obolibrary.org/obo/HP_0012229
Sufficient
SCDO:0000212
HP:0012229
CSF Pleocytosis
Increased Leukocyte Count in CSF
Cerebrospinal Fluid Pleocytosis
A structural or developmental anomaly of any of the tissues involved in the genital system.
Sufficient
SCDO:0009817
HP:0012243
Abnormal Genital System Morphology
Abnormal Reproductive System Morphology
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.
Sufficient
SCDO:0000770
HP:0012282
A morbilliform rash is said to resemble the rash of measles, rubella or scarlet fever, thus mimicking viral and bacterial exanthemas.
Morbilliform Rash
An inflammation of the kidney involving the parenchyma of kidney, the renal pelvis and the kidney calices.
http://purl.obolibrary.org/obo/HP_0012330
Sufficient
SCDO:0005758
HP:0012330
Pyelonephritis
An altered ability of any enzyme or their cofactors to act as catalysts. This term includes changes due to altered levels of an enzyme.
Sufficient
SCDO:1000665
HP:0012379
Abnormal Enzyme/Coenzyme Activity
An abnormally low level of blood oxygen.
http://purl.obolibrary.org/obo/HP_0012418
Sufficient
SCDO:0000604
HP:0012418
Decreased Partial Pressure of Oxygen
Low Blood Oxygen Level
Hypoxemia
Partial or complete wasting (loss) of brain tissue that was once present.
Sufficient
SCDO:0000089
HP:0012444
Brain Atrophy
Brain Degeneration
Brain Wasting
Atrophic Brain
An increased level of iron in liver tissues.
http://purl.obolibrary.org/obo/HP_0012465
Sufficient
SCDO:0000425
HP:0012465
Increased Iron Concentration in Liver
Increased Liver Iron Level
This abnormality can be measured by liver biopsy or by hepatic magnetic resonance imaging.
Equivalents
Elevated Hepatic Iron Concentration
Persistent pain, usually defined as pain that has lasted longer than 3 to 6 months.
Sufficient
SCDO:0001415
HP:0012532
Long-Lasting Pain
Chronic Pain
Increased numbers of mesangial cells per glomerulus, defined as four or more nuclei in a peripheral mesangial segment.
Sufficient
SCDO:0006481
HP:0012574
Mesangial Proliferation
Mesangial Hypercellularity
Hematuria that is visible upon inspection of the urine.
http://purl.obolibrary.org/obo/HP_0012587
Sufficient
SCDO:0008145
HP:0012587
Bloody Urine
Gross Hematuria
Macroscopic Hematuria
The presence of mildly increased concentrations of albumin in the urine (in adults, 30-150 mg per day).
http://patient.info/doctor/microalbuminuria
Sufficient
SCDO:0000764
Chronic kidney disease: early identification and management of chronic kidney disease in adults in primary and secondary care; NICE Clinical Guidelines (July 2014)
HP:0012594
Micro-albuminuria
Microalbuminuria
Mildly Increased Albuminuria
Moderately Increased Albuminuria
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.
Low Level Albuminuria
A functional anomaly of the nervous system.
Sufficient
SCDO:1000765
HP:0012638
Abnormality of Nervous System Physiology
Abnormal Nervous System Physiology
A structural anomaly of the nervous system.
Sufficient
SCDO:1000764
HP:0012639
Abnormal Shape of Nervous System
Abnormality of Nervous System Morphology
Abnormal Nervous System Morphology
A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation.
Sufficient
SCDO:0004069
HP:0012735
Cough
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.
http://purl.obolibrary.org/obo/HP_0012759
Sufficient
SCDO:0000800
HP:0012759
Neurodevelopmental Abnormality
Inflammation of the myocardium.
Sufficient
SCDO:0004203
HP:0012819
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.
Myocarditis
Any functional abnormality of erythrocytes (red-blood cells).
Sufficient
SCDO:1000286
HP:0020054
Abnormal Erythrocyte Physiology
Any deviation from the normal number of red blood cells per volume in the circulation.
Sufficient
SCDO:1000608
HP:0020058
Abnormal RBC Count
Abnormal Red Blood Cell Count
An abnormal elevation above the normal number of red blood cells per volume in the circulation.
Sufficient
SCDO:1000610
HP:0020059
Increased RBC Count
Increased Red Blood Cell Count
An abnormal reduction below the normal number of red blood cells per volume in the circulation.
Sufficient
SCDO:1000609
HP:0020060
Decreased RBC Count
Decreased Red Blood Cell Count
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"?
Sufficient
SCDO:1000186
SCDO (Jade Hotchkiss)
HP:0020061
Abnormal Hemoglobin Concentration
An abnormal reduction below normal hemoglobin concentration in the circulation.
Sufficient
SCDO:1000377
HP:0020062
Decreased Hemoglobin Concentration
An abnormal elevation above normal hemoglobin concentration in the circulation.
Sufficient
SCDO:1000378
HP:0020063
Increased Hemoglobin Concentration
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.
http://purl.obolibrary.org/obo/HP_0025031
Sufficient
SCDO:0000335
HP:0025031
Abnormality of the Digestive System
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.
Sufficient
SCDO:1000624
HP:0025065
Abnormal Erythrocyte Volume
Abnormal MCV
Abnormal Mean Corpuscular Volume
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).
Sufficient
SCDO:1000625
HP:0025066
Decreased MCV
Low MCV
Microcytosis
Reduced Erythrocyte Volume
Decreased Mean Corpuscular Volume
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.
Sufficient
SCDO:1000269
HP:0025142
Systemic Symptom
Constitutional Symptom
An elevated level of the enzyme lactate dehydrogenase in serum.
Sufficient
SCDO:1000652
HP:0025435
High Lactate Dehydrogenase Level
Increased Lactate Dehydrogenase Level
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.
Sufficient
SCDO:1000631
HP:0025546
Abnormal MCHC
Abnormal Mean Cell Haemoglobin Concentration
Abnormal Mean Cell Hb 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.
Sufficient
SCDO:1000635
HP:0025547
Decreased MCHC
Decreased Mean Corpuscular Haemoglobin Concentration
Low MCHC
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.
Sufficient
SCDO:1000636
HP:0025548
High MCHC
High Mean Corpuscular Haemoglobin Concentration
High Mean Corpuscular Hemoglobin Concentration
Increased MCHC
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.
Provide source for additional info.
http://purl.obolibrary.org/obo/MP_0009360
Sufficient
SCDO:0000433
HP:0025636
Endometrial Inflammation
Endometrium Inflammation
Endometritis
A collection of pus, immune cells, and other material in the brain.
http://purl.obolibrary.org/obo/HP_0030049
Sufficient
SCDO:0000159
HP:0030049
Brain abscess usually results from a bacterial or fungal infection.
Brain Abscess
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.
Sufficient
SCDO:0000790
HP:0030050
Narcolepsy
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).
Sufficient
SCDO:1000246
HP:0030058
Banana Cell
Drepanocyte
Sickle Cell
Sickled Erythrocyte
Sickled Red Blood Cell
Sickled Erythrocyte
The growth of endometrial tissue outside the uterus.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0030127
Sufficient
SCDO:0000432
HP:0030127
Endometriosis
An obstruction in the veins of the liver caused by a blood clot (thrombosis).
http://purl.obolibrary.org/obo/HP_0030243
Sufficient
SCDO:0001673
HP:0030243
Blood Clot in Liver Vein
Hepatic Vein Thrombosis
Blood Clot in Liver Vein
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).
Sufficient
SCDO:0004437
HP:0030248
Blood Clot in Mesenteric Vein
Mesenteric Venous Thrombosis
Any structural anomaly of the heart and great vessels.
Sufficient
SCDO:1000369
HP:0030680
Abnormal Cardiovascular System Morphology
A hole (perforation) in the wall of the intestine.
Sufficient
SCDO:1000434
HP:0031368
Intestinal Perforation
A pregnancy in which the fertilized egg inserts in a location outside of the main cavity of the uterus (usually in the Fallopian tube).
Sufficient
SCDO:0000413
HP:0031456
Ectopic Pregnancy
An abnormally high concentration in the circulation of aspartate aminotransferase (AST).
Sufficient
SCDO:1000661
HP:0031956
Aspartate Aminotransferase Increased
Elevated Serum AST
Elevated Serum Glutamic Oxaloacetic Transaminase
Increased Aspartate Aminotransferase
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.
Sufficient
SCDO:1000659
HP:0031964
Alanine Aminotransferase Increased
Elevated Serum Glutamic-Pyruvic Transaminase
Elevated serum ALT
Elevated Serum Alanine Aminotransferase
An abnormal level of an analyte measured in the blood.
Sufficient
SCDO:1000437
HP:0032180
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.
Sufficient
SCDO:1000581
HP:0032224
ABO Blood Group
A deviation from the normal serum concentration/activity of lactate dehydrogenase (LDH), which catalyzes the reduction of pyruvate to form lactate.
Sufficient
SCDO:1000683
HP:0045040
Abnormal Lactate Dehydrogenase Level
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.
http://purl.obolibrary.org/obo/HP_0045048
Sufficient
SCDO:0000630
HP:0045048
Increased HbA2 Hemoglobin
Increased Hemoglobin A2
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.
Sufficient
SCDO:0000411
HP:0100601
Eclampsia
Pregnancy-induced hypertension in association with significant amounts of protein in the urine.
http://purl.obolibrary.org/obo/HP_0100602
Sufficient
SCDO:0000918
HP:0100602
Pre-Eclampsia
Preeclampsia
A general term for inflammation of the muscles without respect to the underlying cause.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0100614
Sufficient
SCDO:0000785
HP:0100614
Muscle Inflammation
Myositis
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the chest.
Sufficient
SCDO:0001988
HP:0100749
Thoracic Pain
Chest Pain
Excessive growth or abnormal thickening of bone tissue.
http://purl.obolibrary.org/obo/HP_0100774
Sufficient
SCDO:0000591
HP:0100774
Bone Hypertrophy
Bone Overgrowth
Hyperostosis
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)?
http://purl.obolibrary.org/obo/HP_0100806
Sufficient
SCDO:0001039
HP:0100806
caused by: Bacteria and fungus mainly
characterised by: Systematic manifestations of inflammation
has disease stage: Mild, moderate, severe
Sepsis
Inflammatory or noninflammatory diseases affecting the glomeruli of the nephron.
http://purl.obolibrary.org/obo/HP_0100820
Sufficient
SCDO:0000459
HP:0100820
Diseased Glomeruli
Glomerulopathies
Glomerulopathy
A discontinuity of the skin exhibiting loss of the epidermis and often portions of the dermis and subcutaneous fat.
Find source for additional info
http://purl.obolibrary.org/obo/HP_0200042
Sufficient
SCDO:0001074
HP:0200042
Open Skin Sore
Skin Ulcers
Skin Ulcer
Abnormal test result of cardiovascular physiology.
Sufficient
SCDO:1000266
HP:0500015
Abnormal Cardiac Test
A date specification that designates when an informed consent form was signed.
Sufficient
SCDO:1000531
ICO:0000036
Date Subject Signed Consent
Informed Consent Form Signing Date
Date of Signing Consent
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.
Sufficient
SCDO:0009293
ICO:0000157
Parental Informed Consent Process
Parental Permission
Parental Permission Consent
Parental Consent
An informed consent for an unspecified range of future research subject to a few content and/or process restrictions.
Sufficient
SCDO:0008115
ICO:0000179
Broad Consent
A planned process in which data possessed by one person or organization is shared with one or more other persons or organizations.
Sufficient
SCDO:0009586
ICO:0000228
Act of Data Sharing
Data Sharing
A directive information entity that prescribes some process for withdraw from another planned process.
Sufficient
SCDO:1000428
ICO:0000255
Withdrawal from Participation Directive
Participant Withdrawal Process
A descriptive information content entity that describes how biospecimens will be used.
Sufficient
SCDO:1000456
ICO:0000278
Description of Future Biospecimen Use
A directive information entity that prescribes the information that is permitted to be shared or the processes for sharing that information.
Sufficient
SCDO:1000407
ICO:0000293
Data Sharing Directive
Data Sharing Agreement
A descriptive information content entity that describes how data will be used.
Sufficient
SCDO:1000453
ICO:0000304
Description of Future Data Use
A descriptive information content entity that describes future use of material or information.
Sufficient
SCDO:1000454
ICO:0000305
Description of Future Use
The use of antimalarial drugs for the prevention of infection.
Sufficient
SCDO:1000668
IDOMAL:0000122
Malaria Chemoprophylaxis
Any process carried out to determine the condition of a patient's spleen.
Needs relating to Splenomegaly phenotype.
http://purl.obolibrary.org/obo/IDOMAL_0000592
Sufficient
SCDO:0001101
IDOMAL:0000592
Spleen Examination
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"
http://purl.obolibrary.org/obo/IDOMAL_50000026
Sufficient
SCDO:0001370
IDOMAL:50000026
Mutation
An organism population whose members are particpating in non-parasitic symbiosis with a particular host.
http://purl.obolibrary.org/obo/IDO_0000515
Sufficient
SCDO:0000755
IDO:0000515
Normal Resident Microbiota Population
Normal Resident Microflora Population
Microbiome
A material entity bearing an antifungal disposition.
http://purl.obolibrary.org/obo/IDO_0000560
Sufficient
SCDO:1000019
IDO:0000560
Antifungal
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.)
Sufficient
SCDO:0000635
IDO:0000586
Infection
Focal pathological and/or inflammatory changes characterized by alteration in the size, shape and organization of the cellular components of the skin.
Sufficient
SCDO:0001072
MP:0001212
Skin Lesions
Anomalies in the average levels of hemoglobin contained in an erythrocyte.
Sufficient
SCDO:1000632
MP:0001589
Abnormal MCH
Abnormal Mean Cell Hemoglobin
Abnormal Mean Cell Hemoglobin Level
Abnormal Mean Corpuscular Hemoglobin Level
Abnormal Mean Corpuscular Hemoglobin
Increased volume of urine produced and excreted.
Provide source for additional info.
http://purl.obolibrary.org/obo/MP_0001762
Sufficient
SCDO:0000395
MP:0001762
Increased Urine Output
Increased Urine Volume
Polyuria
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.
Diuresis
Reduced ability or inability to self-repair and close wounds.
Sufficient
SCDO:0000622
MP:0001792
Delayed Wound Healing
Impaired Wound Repair
Impaired Wound Healing
Death anytime within the perinatal period.
Sufficient
SCDO:0000883
MP:0002081
Perinatal Lethality
Perinatal Death
Anomaly in the processes involved in the maintenance of an internal equilibrium of lipids in the fluids and tissues.
Sufficient
SCDO:1000284
MP:0002118
Abnormal Lipid Homeostasis
Anomaly in the amount of oxygen and carbon dioxide in the blood.
Sufficient
SCDO:1000810
MP:0002329
Abnormal Blood Gas Level
Greater likelihood that an organism will develop ill effects from a bacterial infection or from components of or toxins produced by bacteria.
http://purl.obolibrary.org/obo/MP_0002412
Sufficient
SCDO:0000632
MP:0002412
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.
Provide source for additional info.
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
Sufficient
SCDO:0000802
http://www.neurodegenerationresearch.eu/about/what/
MP:0003224
Nerve Degeneration
Nerve Degenerations
Neuron Degenerations
Neuron Degeneration
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.
Sufficient
SCDO:1000811
MP:0005376
Homeostasis Phenotype
Homeostasis/Metabolism Phenotype
Metabolism/Homeostasis Phenotype
Greater than the level of heat natural to a living being.
Sufficient
SCDO:1000761
MP:0005533
Raised Body Temperature
Increased Body Temperature
Less than the level of heat natural to a living being.
Sufficient
SCDO:1000762
MP:0005534
Reduced Body Temperature
Decreased Body Temperature
Deviation in the level of heat natural to a living being.
Sufficient
SCDO:1000760
MP:0005535
Abnormal Body Temperature
Greater than the average levels of hemoglobin contained in an erythrocyte.
Sufficient
SCDO:1000634
MP:0005561
High MCH
High Mean Corpuscular Hemoglobin
Increased MCH
Increased Mean Cell Hemoglobin
Increased Mean Corpuscular Hemoglobin
Less than the average levels of hemoglobin contained in an erythrocyte.
Sufficient
SCDO:1000633
MP:0005562
Decreased MCH
Decreased Mean Cell Hemoglobin
Low MCH
Low Mean Corpuscular Hemoglobin
Decreased Mean Corpuscular Hemoglobin
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.
Sufficient
SCDO:1000277
MP:0009568
Abnormal Red Blood Cell Deformability
Anomaly in the processes involved in the maintenance of an internal equilibrium of various functions or chemical or protein composition of the blood.
Sufficient
SCDO:1000809
MP:0009642
Abnormal Blood Chemistry
Blood Chemistry Abnormalities
Abnormal Blood Homeostasis
An anomaly in the coefficient of variance (reference range) of the red blood cell volume for an organism.
Sufficient
SCDO:1000639
MP:0010066
Abnormal Erythrocyte Distribution Width
Abnormal RDW
Abnormal Red Blood Cell Distribution Width
Higher than normal coefficient of variance (reference range) of the red blood cell volume for an organism.
Sufficient
SCDO:1000641
MP:0010067
High RCDW
High RDW
High Red Blood Cell Distribution Width
Increased Erythrocyte Distribution Width
Increased RCDW
Increased RDW
Increased Red Blood Cell Distribution Width
Lower than normal coefficient of variance (reference range) of the red blood cell volume for an organism.
Sufficient
SCDO:1000640
MP:0010068
Decreased Erythrocyte Distribution Width
Decreased RCDW
Decreased RDW
Low RCDW
Low RDW
Low Red Blood Cell Distribution Width
Reduced RCDW
Reduced RDW
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.
Sufficient
SCDO:0009017
MP:0010163
Erythrocytolysis
Erythrolysis
Haematolysis
Haemolysis
Hematolysis
Hemolyses
Hemolysis
Any anomaly in the amount in the urine of a carboxylic acid containing one or more amino groups (-NH2) and a carboxyl (-COOH) group.
Sufficient
SCDO:1000653
MP:0011468
Abnormal Urine Amino Acid Level
Any change in the amount of creatinine in the urine
Sufficient
SCDO:1000654
MP:0011469
Abnormal Urine Creatinine Level
An increased amount of creatinine in the urine compared to the normal state.
Sufficient
SCDO:1000656
MP:0011470
Increased Urine Creatinine Level
a reduced amount of creatinine in the urine compared to the normal state
Sufficient
SCDO:1000655
MP:0011471
Low Urine Creatinine Level
Reduced Urine Creatinine Level
Decreased Urine Creatinine Level
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.
http://purl.obolibrary.org/obo/MP_0013305
Sufficient
SCDO:0000667
MP:0013305
Impaired Urine-Concentrating Ability
Urine Concentrating Defect
Urine specific gravity is similar to that of plasma (1.008-1.012).
Isosthenuria
A drinking behavior associated with the intake of alcohol.
http://purl.obolibrary.org/obo/NBO_0000131
Sufficient
SCDO:0000039
NBO:0000131
Alcohol Consumption
Alcohol Intake
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.
http://purl.obolibrary.org/obo/NCIT_C65495
Sufficient
SCDO:0006467
NCIT:65495
Cymbalta
Duloxetine HCl
N-methyl-3-(1-naphthalenyloxy)-3-(2-thiophene)propanamide
Duloxetine
An examination of the retina of the eye using an ophthalmoscope.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C101217
Sufficient
SCDO:0001009
NCIT:C101217
Fundoscopy
Retinal Examination
A finding indicating the presence of an inflammatory or neoplastic cellular infiltrate in the lung parenchyma.
Sufficient
SCDO:0007383
NCIT:C102531
Lung Infiltrate
Pulmonary Infiltrate
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.
Sufficient
SCDO:0000871
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.
NCIT:C102988
PROMIS
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.
Sufficient
SCDO:1000852
NCIT:C103165
Subject Visit Type
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.
Sufficient
SCDO:0005773
International Ethical Guidelines for Health-related Research Involving Humans, Fourth Edition. Geneva. Council for International Organizations of Medical Sciences (CIOMS); 2016.
NCIT:C103270
Consent Waiver
Waiver Of Informed Consent
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.
Waiver of Consent
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.
Sufficient
SCDO:0000870
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.
NCIT:C103526
PHQ-9
PHQ01
Patient Health Questionnaire - 9 Item
Patient Health Questionnaire-9
Patient Health Questionnaire-9 (PHQ-9)
Hemoglobin that has a nitric oxide bound to the cysteine at position 93 in the beta-globin chain.
Sufficient
SCDO:1000169
NCIT:C107564
S-Nitrosated Hemoglobin
S-Nitrosohemoglobin
S-Nitroso-Hemoglobin
The cessation of menstruation for six months or more in a female that is not pregnant, breastfeeding or menopausal.
Sufficient
SCDO:0001447
NCIT:C113340
Secondary Amenorrhea
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.
Sufficient
SCDO:1000168
NCIT:C114300
COHb
Carboxyhemoglobin
COHb
A severe hypersensitivity-like reaction occurring during dialysis due to exposure to the dialysis membrane.
Sufficient
SCDO:1000387
NCIT:C114714
Dialyzer Reaction
Dialysis Membrane Reaction
A crack or break in a dialysis catheter caused by material weakness or mechanical compression.
Sufficient
SCDO:1000386
NCIT:C114717
Dialysis Catheter Fracture
Any heart or vascular disorder occurring as a consequence of injury to the cardiovascular system.
Sufficient
SCDO:1000390
NCIT:C115199
Cardiovascular Complication
Any disorder of the liver occurring as a consequence of injury to the liver parenchyma.
Sufficient
SCDO:1000382
NCIT:C115224
Liver Complication
Hepatic Complication
Any eye disorder occurring as a consequence of injury to the eye.
Sufficient
SCDO:0000832
NCIT:C115319
Ophthalmologic Manifestations
Ophthalmologic Complication
Any issue that arises as a consequence of a problem with a patient's dialysis access.
Sufficient
SCDO:1000391
NCIT:C116081
Dialysis Access Complication
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.
Sufficient
SCDO:0003929
NCIT:C116161
MLPA
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.
Sufficient
SCDO:0001293
http://www.med.umich.edu/yourchild/topics/devdel.htm
NCIT:C116942
Developmental Delay
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.
http://purl.obolibrary.org/obo/NCIT_C118385
Sufficient
SCDO:0004832
NCIT:C118385
AVN
deprecated-Avascular Necrosis
true
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.
Life stage: Adolescent, Adult
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.
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820501
PhenX protocol: Intelligence Scale - 16 to 90 years #820501
Sufficient
SCDO:0000646
NCIT:C120254
WAIS-IV
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)
Intelligence Scale - 16 to 90 years
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.
Life stage: Child, Adolescent
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.
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820503
PhenX protocol: Intelligence Scale - 6 to 16 years 11 months #820503
Sufficient
SCDO:0000648
NCIT:C120255
WISC-V
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.
Life stage: Toddler, Child
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.
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820502
PhenX protocol: Intelligence Scale - 2 years, 6 months to 7 years, 7 months #820502
Sufficient
SCDO:0000647
NCIT:C120256
WPPSI-IV
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.
Sufficient
SCDO:0000645
NCIT:C122920
Intelligence Test
Intelligence Scale
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.
http://purl.obolibrary.org/obo/NCIT_C122931
Sufficient
SCDO:0000613
NCIT:C122931
TCDi
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.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C123446
Sufficient
SCDO:0000281
NCIT:C123446
Continuous Ambulatory ECG
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
Sufficient
SCDO:1000335
NCIT:C123667
MOCA
MOCA01
Montreal Cognitive Assessment
Montreal Cognitive Assessment Functional Test
Montreal Cognitive Assessment Questionnaire
Global Mental Status Screener - Adult
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'.
http://purl.obolibrary.org/obo/NCIT_C124059
Sufficient
SCDO:0006222
NCIT:C124059
Air Space Opacificatio
Air-Space Shadowing
Airspace Consolidation
Airspace Opacification
Consolidation
Pulmonary Consolidation
A measurement of the concentration of iron in the liver as an estimate of body iron load.
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C124065
Sufficient
SCDO:0000555
NCIT:C124065
Hepatic Iron
Liver Iron
Liver Iron Concentration
Hepatic Iron Concentration
A circumferential measurement of the largest part of the upper arm.
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C124475
Sufficient
SCDO:0000758
NCIT:C124475
MUAC
MUARMCIR
Mid-Upper Arm Circumference
Mid Upper Arm Circumference
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.
Sufficient
SCDO:1000275
NCIT:C126120
HbO2
Oxyhemoglobin
Oxygenated Hemoglobin
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.
Sufficient
SCDO:1000057
NCIT:C126121
Deoxyhemoglobin
Deoxygenated Hemoglobin
An abscess within the abdomen.
http://purl.obolibrary.org/obo/NCIT_C128326
Sufficient
SCDO:0008079
NCIT:C128326
Intra-Abdominal Abscess
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.
Sufficient
SCDO:0000560
NCIT:C129072
HPFH
Hereditary Persistence of Foetal Haemoglobin
This is a benign condition.
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.
Sufficient
SCDO:0000549
NCIT:C131682
Hb SS Disease
Hb SS-Disease
Hemoglobin SS Disease
Homozygous Sickle Cell Disease
SCA
SS and S/Beta-Zero Thalassemia
Severe SCD
Sickle Cell Anemia
Sickle Cell Disease SS
Sickle Cell Hemoglobin S Disease
Sickle Cell-SS Disease
Sickle Cell Disease-SS
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).
Sufficient
SCDO:1000380
NCIT:C133543
Adakveo
SEG101
SelG1
Crizanlizumab
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.
http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome
Sufficient
SCDO:0000538
NCIT:C141366
Hb Lepore
Hb Lepore Syndrome
Homozygous Hb Lepore
Homozygous Hemoglobin Lepore
Hemoglobin Lepore Syndrome
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).
Sufficient
SCDO:1000420
NCIT:C142494
Data Storage
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.
Sufficient
SCDO:0009748
NCIT:C142541
Ethics Committee
Human Subject Protection Committee
REC
Research Ethics Committee
Research Ethics Committee
The interval of time during which subjects are to be enrolled in a clinical study.
Sufficient
SCDO:1000400
NCIT:C142664
Recruitment Period
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.
Sufficient
SCDO:1000381
NCIT:C152089
GBT-440
GBT440
Oxbryta
Is an accepted therapy for adults and pediatric patients 12 years of age and older with sickle cell disease.
Voxelotor
Application of genetic material (usually DNA) into cells in order to permanently correct an inherited disease or acquired disease.
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C15238
Sufficient
SCDO:0001344
NCIT:C15238
DNA Therapy
Gene Therapy
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.
Sufficient
SCDO:0001115
NCIT:C15320
Experiment Design
Experimental Design
Research Design
STYPE
Study Design
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
Self
Clinic Patients (Adults with SCD)
Spanish; Portuguese
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.
18 years and older
no
Sufficient
SCDO:0000027
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.
NCIT:C154481
ASCQ-Me
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.
Sufficient
SCDO:0000204
NCIT:C154865
Cerebral Blood Flow Assessment
Cerebral Blood Flow Measurement
Stroke Risk Test
Cerebral Blood Flow Assay
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.
Sufficient
SCDO:0001060
NCIT:C155310
Haemoglobin S-D Disease
Hb SD-Disease
Hemoglobin S-D Disease
Hemoglobin Sickle D Disease
Sickle Cell Disease SD
Sickle Cell Hemoglobin D Disease
Sickle Cell-Haemoglobin D Disease
Sickle Cell-Hemoglobin D Disease
Sickle Cell Disease-SD
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.
Sufficient
SCDO:0001046
Powars et al 1988 Medicine (Baltimore), Knight-Madden et al 2010 Lung.
NCIT:C155312
Sickle Cell Chronic Restrictive Lung Disease
Sickle Cell Chronic 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
Sufficient
SCDO:1000334
NCIT:C155932
CGAS
Children’s Global Assessment Scale
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.
Sufficient
SCDO:1000677
NCIT:C156541
Separated
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?
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C15709
Sufficient
SCDO:0000449
NCIT:C15709
Genetic Analysis
Genetic Examination
Genetic Test
Genetic Testing
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.
Sufficient
SCDO:1000006
NCIT:C15900
Lifestyle Therapy
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.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C1643&jump_to_nav=true
Sufficient
SCDO:0000915
NCIT:C1643
PPSV
Pneumococcal Polysaccharide Vaccine
Pneumococcal Polyvalent Vaccine
Polyvalent Pneumococcal Vaccine
The date on which a diagnosis of disease was made.
Sufficient
SCDO:1000557
NCIT:C164339
Date of Diagnosis
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.
Sufficient
SCDO:0000266
NCIT:C16453
Community
The statistical characterization of human populations or segments of human populations (e.g., characterization by age, sex, race, or income).
Sufficient
SCDO:1000468
NCIT:C16495
Demographic Factors
Demographics
Demography
Population Studies / Demography
Demographic Factor
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.
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C16564
Sufficient
SCDO:0001298
NCIT:C16564
Ethnic Origin
Ethnic Origins
Ethnicity
Ethnic Group
Activity that requires physical or mental exertion, especially when performed to develop or maintain fitness.
Sufficient
SCDO:0001305
NCIT:C16567
Exercise
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.
Sufficient
SCDO:1000560
NCIT:C16576
Female
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.
Sufficient
SCDO:1000359
NCIT:C16612
Gene
Any demarcated area of the Earth; may be determined by both natural and human boundaries.
Sufficient
SCDO:1000367
NCIT:C16632
Geographic Location
Geographic Region
Geographic Area
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.
Sufficient
SCDO:0009453
NCIT:C16676
Hb
Hgb
Hemoglobin
Laboratory test involving interaction of antigens with specific antibodies.
Sufficient
SCDO:0000617
NCIT:C16723
Immunoassay
Immunological Laboratory Method
Immunology Test
Immunological Assay
A systematic means of communicating by the use of sounds, symbols, or gestures.
http://purl.obolibrary.org/obo/NCIT_C16779
Sufficient
SCDO:0005364
NCIT:C16779
Language
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.
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C16809
Sufficient
SCDO:0000708
NCIT:C16809
MIR Scan
MRI
MRT
Magnetic Resonance Imaging Scan
Magnetic Resonance Tomography
NMR Imaging
NMRI
Nuclear Magnetic Resonance Imaging
Magnetic Resonance Imaging
The year when a diagnosis was assigned to an individual's condition.
Sufficient
SCDO:1000567
NCIT:C168823
Year of Diagnosis
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.
Sufficient
SCDO:0004047
NCIT:C17004
Genetic Polymorphism
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.
Sufficient
SCDO:0000949
NCIT:C17047
Health Related Quality of Life
QOL
Quality of Life
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?
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17049
Sufficient
SCDO:0000962
NCIT:C17049
Racial Group
Race
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.
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17230
Sufficient
SCDO:0000614
NCIT:C17230
Immaging by Ultrasonography
Ultrasonography
Ultrasound
Ultrasound Imaging
Ultrasound Test
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.
Sufficient
SCDO:0001216
NCIT:C17241
Urinalysis
Urine Analysis
Urine Test
The rate of blood flow through the cerebral arteries.
Sufficient
SCDO:0000205
NCIT:C173396
CBF Velocity
CBFV
Transcranial Doppler Velocity
Cerebral Blood Flow Velocity
The assemblage of properties that distinguish people on the basis of the societal roles expected for the two sexes.
Sufficient
SCDO:0001341
NCIT:C17357
Gender
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.
Sufficient
SCDO:1000346
NCIT:C17655
Reproductive History
Having to do with the physical, psychological, cognitive, and social consequences of disease, including stigmatization of persons affected.
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17873
Sufficient
SCDO:0000939
NCIT:C17873
Psychosocial Effects
Psychosocial Effects/Treatment
Psychosocial Effect
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.
Sufficient
SCDO:0004314
NCIT:C18133
Missense Mutation
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.
Sub-classes in NCIT to be added here.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C18772
Sufficient
SCDO:0000891
NCIT:C18772
General Medical History
Medical History
PMH
Past Medical History
Personal Medical History
An instrument used to measure an event involving emission, absorption, or refraction of light.
http://purl.obolibrary.org/obo/NCIT_C19228
Sufficient
SCDO:0000837
NCIT:C19228
Optical Instrument
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.
http://purl.obolibrary.org/obo/NCIT_C19296
Sufficient
SCDO:0001371
NCIT:C19296
Deletion Abnormality
Deletion Mutation
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.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C19332
Sufficient
SCDO:0000890
NCIT:C19332
Subject Characteristics
Personal Attribute
Analysis of the RNA expression pattern in a tissue sample using molecular techniques.
Sufficient
SCDO:0000768
NCIT:C19771
Expression Profiling
Molecular Fingerprinting
Molecular Profiling
Molecular Profiling Assay
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.
Sufficient
SCDO:1000559
NCIT:C20197
Male
A point mutation occurring within the protein-coding region of a gene, and which codes for the same amino acid as expected.
Sufficient
SCDO:0005439
NCIT:C20629
Exon Synonymous Mutation
Exonic Synonymous Mutation
Synonymous Mutation
Silent Mutation
This gene plays a role in transcriptional regulation and is involved in several signal transduction pathways.
Sufficient
SCDO:1000393
NCIT:C20711
SP1
Sp1 Transcription Factor Gene
SP1 Gene
How long something has existed; elapsed time since birth.
Could add many sub-classes of "Age" from NCIT.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25150
Sufficient
SCDO:0000030
NCIT:C25150
Aged
Chronological Age
Postnatal Age
Age
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.
Sufficient
SCDO:1000859
NCIT:C25191
Contact Name
Individual's Name
Name
Name of Person
Person.name
Person Name
The maximum pressure exerted into the systemic arterial circulation during the contraction of the left ventricle of the heart.
Sufficient
SCDO:1000892
NCIT:C25298
SYSBP
Systolic Pressure
systolic bp
Systolic Blood Pressure
The minimum pressure exerted into the systemic arterial circulation during cardiac ventricular relaxation and filling.
Sufficient
Vital Signs
6
SCDO:1000893
NCIT:C25299
DIABP
Diastolic Pressure
Diastolic Blood Pressure
Permission to do something.
http://purl.obolibrary.org/obo/NCIT_C25460
Sufficient
SCDO:0001466
NCIT:C25460
Consent
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.
http://purl.obolibrary.org/obo/NCIT_C25464
Sufficient
SCDO:0004140
NCIT:C25464
deprecated Country
true
A collection or single item of factual or reported information, derived from measurement or research, from which conclusions may be drawn.
Sufficient
SCDO:0006670
NCIT:C25474
Data
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.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C258
Sufficient
SCDO:0000059
NCIT:C258
Antibiotic Agents
Antibiotic Drug
Antibiotic Drugs
Antibiotics
Antimicrobial
Antimicrobial Agent
Antibiotic
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)
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C26548
Sufficient
SCDO:0001343
NCIT:C26548
Genome Encoded Entity
Gene Product
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?
Sufficient
SCDO:0000087
NCIT:C26702
Ataxia
Abnormally high level of bilirubin in the blood. Excess bilirubin is associated with jaundice.
Sufficient
SCDO:0003118
NCIT:C27088
High Blood Bilirubin Levels
Hyperbilirubinemia
A balloon type pouch or bulge in the wall of a cerebral blood vessel.
Sufficient
SCDO:0000202
NCIT:C27222
Brain Aneurysm
Cerebral Artery Aneurysm
Dilatation of the Cerebral Artery
Intracranial Aneurysm
Cerebral Aneurysm
System of classification based on nation from which a person originates, regardless of the nation in which he/she currently resides.
Include list of nations below.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C28407
Sufficient
SCDO:0000792
NCIT:C28407
Birth Country
Country of Birth
Country of Origin
National Origin
The totality of characteristics of reproductive structure, functions, phenotype, and genotype, differentiating the male from the female organism.
Sufficient
SCDO:1000671
NCIT:C28421
Participant Sex
Participant's Sex
Respondent's Sex
Sex of Participant
Sex
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.
http://purl.obolibrary.org/obo/NCIT_C28516
Sufficient
SCDO:0000477
NCIT:C28516
Sickle Cell Dactylitis
An acute infectious disorder caused by gram positive or gram negative bacteria. Representative examples include pneumococcal, streptococcal, salmonella and meningeal infections.
Perhaps use as Disease Modifier?
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C2890
Sufficient
SCDO:0000100
NCIT:C2890
Bacterial Infection
Increase in the number of hematopoietic cells in the bone marrow. It may involve all or individual hematopoietic cell lines.
http://purl.obolibrary.org/obo/NCIT_C2905
Sufficient
SCDO:0007438
NCIT:C2905
Hyperplasia of Bone Marrow
Marrow Hyperplasia
Bone Marrow Hyperplasia
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.
http://purl.obolibrary.org/obo/NCIT_C29091
Sufficient
SCDO:0008062
NCIT:C29091
ENGERIX-B
Hepatitis B Vaccine (Recombinant)
RECOMBIVAX HB
Recombinant Hepatitis B Vaccine
Hepatitis B Vaccine
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.
http://purl.obolibrary.org/obo/NCIT_C29107
Sufficient
SCDO:0005247
NCIT:C29107
Intravenous Fluid
IV fluids
Any disease or disorder that occurs during the course of, or because of, another disease, treatment, or procedure.
Sufficient
SCDO:1000384
NCIT:C2959
Complications
Medical Complication
Complication
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.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C29719
Sufficient
SCDO:0001081
NCIT:C29719
Tobacco Smoking History
Smoking History
An account of all experiences related to the receipt of blood, WBC, platelets, and/or other blood components.
Sufficient
SCDO:0000569
NCIT:C30142
Transfusion History
History of Transfusion
An infection caused by a fungus.
Sufficient
SCDO:1000349
NCIT:C3245
Fungal Infection
Any disease caused by a virus.
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)
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C3439
Sufficient
SCDO:0001233
NCIT:C3439
Viral Disease
Virus Disease
Viral Infection
An acute or chronic inflammation involving the gallbladder wall. It may be associated with the presence of gallstones.
http://purl.obolibrary.org/obo/NCIT_C34465
Sufficient
SCDO:0007856
NCIT:C34465
Cholecystitis
A sensation of discomfort secondary to surgery.
Sufficient
SCDO:1000451
NCIT:C34887
Perioperative Pain
Post Surgery Pain
Post-Operative Pain
Postoperative Pain
Peri-Operative Pain
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.
Sufficient
SCDO:1000399
NCIT:C34941
Complication Related to Pregnancy
Pregnancy Complication
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.
Sufficient
SCDO:0001144
NCIT:C35069
Thalassemia
Cholecystitis that is persistent and long-standing.
http://purl.obolibrary.org/obo/NCIT_C35146
Sufficient
SCDO:0009201
NCIT:C35146
Chronic Cholecystitis
Acute inflammation of the gallbladder.
http://purl.obolibrary.org/obo/NCIT_C35152
Sufficient
SCDO:0008927
NCIT:C35152
Acute Cholecystitis
Acute infection of the bile ducts caused by bacteria ascending from the small intestine.
http://purl.obolibrary.org/obo/NCIT_C35372
Sufficient
SCDO:0008766
NCIT:C35372
Ascending Cholangitis
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
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C35447
Sufficient
SCDO:0000842
NCIT:C35447
Avascular Necrosis of Femoral Head
Avascular Necrosis of the Capital Femoral Epiphysis
Avascular Necrosis of the Femoral Head
Avascular Necrosis of the Head of Femur
ONFH
Osteonecrosis of the Femoral Head
Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity.
Sufficient
SCDO:1000435
NCIT:C3671
Trauma
Wound
Injury
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.
http://purl.obolibrary.org/obo/NCIT_C38060
Sufficient
SCDO:0001313
NCIT:C38060
Eye Exam
Eye Examination
A non-invasive method that provides estimates of arterial oxyhemoglobin saturation by utilizing selected wavelengths of light to determine the saturation of oxyhemoglobin.
Sufficient
SCDO:1000351
NCIT:C38085
Pulse Oximetry
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.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C38141
Sufficient
SCDO:0000911
NCIT:C38141
7 Valent PncOMPC Vaccine
7-Valent PncOMPC Vaccine
Heptavalent Pneumococcal Conjugate Vaccine
PCV 7
PCV7 Vaccine
Pneumococcal 7-Valent Conjugate Vaccine (Diphtheria CRM197 Protein)
Prevenar
Prevnar
Seven Valent Pneumococcal PS Meningococcal OMPC Conjugate Vaccine
Seven-Valent Pneumococcal PS-Meningococcal OMPC Conjugate Vaccine
Pneumococcal 7-Valent Conjugate Vaccine
Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction.
Sufficient
SCDO:0004802
NCIT:C3833
No Symptoms
Asymptomatic
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.
http://purl.obolibrary.org/obo/NCIT_C38698
Sufficient
SCDO:0002771
NCIT:C38698
Blood Hyperviscosity
Hypercoagulability
Thrombophilia
Hyperviscosity
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.
SCD Management guidelines - Tanzania
Sufficient
SCDO:0004183
NCIT:C3890
Hypoxia
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.
Sufficient
SCDO:1000156
NCIT:C39547
Clinical Efficacy
Treatment Efficacy
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.
http://purl.bioontology.org/ontology/MESH/D004989
Sufficient
SCDO:0300001
NCIT:C39796
Moral Philosophy
Natural Law
Ethics
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.
Multiple countries and cultural groups
Self
Clinic Patients
Spanish
13 years and older
yes
Sufficient
SCDO:0000103
NCIT:C40438
BDI-II
Beck Depression Inventory
Beck Depression Inventory-II
Beck Depression Inventory-II (BDI-II)
A sequence of decimal digits (0-9) that is used for identifying a destination telephone line or other device in a telephone network.
Sufficient
SCDO:1000881
NCIT:C40978
Phone
Phone Number
Telephone
Telephone Number
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.
http://purl.obolibrary.org/obo/NCIT_C41129
Sufficient
SCDO:0006934
NCIT:C41129
deprecated Region
true
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.
Sufficient
SCDO:1000713
NCIT:C42559
C
Celsius
Celsius Degree
Celsius Temperature
Degree C
Degree Centigrade
Degrees C
Degrees Celsius
Degree Celsius
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.
Sufficient
SCDO:0005031
NCIT:C43646
Association
Determination of a value is not relevant in the current context.
Sufficient
SCDO:1000770
NCIT:C48660
Not Applicable
NA
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.
Sufficient
SCDO:0004740
NCIT:C49131
Histologic Test
Diagnostic Histology Test
The number of breaths (inhalation and exhalation) taken per minute time.
Sufficient
SCDO:1000716
NCIT:C49674
Breaths/Minute
bpm
breaths/min
{BREATHS}/min
{breaths}/min
Breaths per Minute
Abnormal decrease of rate of breathing.
Sufficient
SCDO:1000293
NCIT:C50474
Decreased Respiratory Rate
Bradypnea
Abnormal increase of rate of breathing.
Sufficient
SCDO:1000347
NCIT:C50767
Fast Breathing
Increased Respiratory Rate
Tachypnea
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.
http://purl.obolibrary.org/obo/NCIT_C50791
Sufficient
SCDO:0007744
NCIT:C50791
Urinary Tract Infection
Removal of tissue from the liver for microscopic examination.
Use relevant object property to link to "Elevated Hepatic Iron Concentration".
http://purl.obolibrary.org/obo/NCIT_C51677
Sufficient
SCDO:0000693
NCIT:C51677
Liver Biopsy
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.
Sufficient
SCDO:1000674
NCIT:C51773
Married Status
Married
Indicates a person who has never been married or whose marriages have been annulled.
Sufficient
SCDO:1000678
NCIT:C51774
Never Been Married/Annulled
Never Married
Never Married Status
Never Been Married
Indicates a person who is no longer married because of the death of his/her spouse and has not remarried.
Sufficient
SCDO:1000675
NCIT:C51775
Widowed Status
Widowed
Indicates a person whose marriage has been legally dissolved and has not remarried.
Sufficient
SCDO:1000676
SCDO (Jade Hotchkiss)
NCIT:C51776
Divorced
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.
http://purl.obolibrary.org/obo/NCIT_C519
Sufficient
SCDO:0001259
NCIT:C519
Garamicin
Garamycin
Genoptic
Genoptic S.O.P.
Gentamycin
Gentamycin Complex
U-Gencin
Gentamicin
Administration of antibiotics with the intent of preventing bacterial infection.
http://purl.obolibrary.org/obo/NCIT_C51993
Sufficient
SCDO:0006790
NCIT:C51993
Is recommended, particularly up to the age of 5 years, to prevent bacterial infections in SCD patients.
Antibiotic Prophylaxis
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.
http://purl.obolibrary.org/obo/NCIT_C52009
Sufficient
SCDO:0000048
NCIT:C52009
Amniotic Fluid Testing
Amniocentesis
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.
Sufficient
SCDO:0000606
http://www.drugbank.ca/drugs/DB01050
NCIT:C561
2-[4-(2-methylpropyl)phenyl]propanoic acid
Advil
Ibuprophen
Motrin
Ibuprofen
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.
Sufficient
SCDO:1000450
NCIT:C61797
Ketamine
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.
Used to treat neuropathic pain
http://purl.obolibrary.org/obo/NCIT_C62005
Sufficient
SCDO:0004190
NCIT:C62005
Amitriptyline
A point mutation occurring within the protein-coding region of a gene, and which codes for a stop that can truncate the protein.
Sufficient
SCDO:0003789
NCIT:C62198
Premature Termination Abnormality
Premature Termination Mutation
Nonsense Mutation
A small scale mutation caused by the substitution of a single nucleotide for another nucleotide.
http://purl.obolibrary.org/obo/NCIT_C62200
Sufficient
SCDO:0001372
NCIT:C62200
Point Mutation
A way of denoting the collective genotype of a number of closely linked loci on a chromosome.
Sufficient
SCDO:0007716
NCIT:C63547
Haplotype
A unit of concentration (molarity unit) equal to one millimole of solute per liter of solution.
Sufficient
SCDO:1000899
NCIT:C64387
Millimolar
mM
mmol/L
Millimole per Liter
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.
Sufficient
SCDO:1000505
NCIT:C64572
Gram per Cubic Meter
Microgram per Milliliter
Microgram/Milliliter
Milligram per Cubic Decimeter
Milligram per Liter
Nanogram per Microliter
g/m3
gram(s)/cubic meter
gram/cubic meter
mcg/mL
mg/L
mg/dm3
mg/l
microgram per milliliter
microgram per millilitre
microgram(s)/millilitre
microgram/millilitre
milligram per liter
milligram(s)/litre
ng/uL
ug/mL
ug/ml
µg/mL
microgram per millilitre
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.
http://purl.obolibrary.org/obo/NCIT_C64625
Sufficient
SCDO:0008454
NCIT:C64625
3-(Aminomethyl)-5-methyl-hexanoic Acid
3-Isobutyl GABA
CI 1008
Lyrica
PD 144723
Pregabalin
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.
Sufficient
SCDO:1000620
NCIT:C64783
Gram per Deciliter
Gram/Deciliter
g/dl
gram per deciliter
g/dL
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.
Sufficient
SCDO:1000646
NCIT:C67015
Milligram per Deciliter
Milligram/Deciliter
mg/dl
mg/dL
A unit of cell concentration expressed as a number of cells in thousands per unit volume equal to one microliter.
Sufficient
SCDO:1000511
NCIT:C67244
1000 cells/µL
10E3 Cells/uL
10^3 Cells/uL
10^3{Cells}/uL
Thousand Cells per Microliter
Thousand Cells/cu mm;
thousand cells per microliter
thousand cells/µL
thousands/µL
thousand cells per microliter
A unit of cell concentration expressed as a number of cells in millions per unit volume equal to one microliter.
Sufficient
SCDO:1000504
NCIT:C67251
10E6 cells/uL
10^6 Cells/uL
10^6{Cells}/uL
Million Cells per Microliter
Million Cells/cu mm
million cells per microliter
million cells per microlitre
million cells/µL
million cells per microliter
Unit of arbitrary substance concentration (biologic activity concentration) defined as the concentration of one international unit per one liter of the system volume.
Sufficient
SCDO:1000658
NCIT:C67376
IE/L
International Unit per Liter
International Unit per Litre
International Unit/Liter
International Unit/Litre
Microinternational Unit per Microliter
Milliinternational Unit per Milliliter
IU/L
The calendar date on which a person was born.
Sufficient
SCDO:1000544
NCIT:C68615
BD
DOB
Date of Birth
Birth Date
A unique identifier for a subject in a study.
Sufficient
SCDO:1000469
NCIT:C69256
Participant ID
Participant Identifier
Participant Number
Research Subject ID
Subject ID
Subject Identification Code
Subject Identifier
Subject UID
Subject Unique Identifier
Subject's Unique Identifier
Subject.identifier
SubjectIdentifier
USUBJID
Unique Subject Identifier
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.
Subject Unique Identifier
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.
http://purl.obolibrary.org/obo/NCIT_C70731
Sufficient
SCDO:1000002
NCIT:C70731
Clinical Study Subject Unique Identifier
Clinical Trial 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.
Sufficient
SCDO:1000096
NCIT:C70817
Study Protocol
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.
Sufficient
SCDO:0000005
NCIT:C71375
Abdominal Sonogram
TUS
Transabdominal Ultrasound
Abdominal Ultrasound
Difficulties related to an apparatus used to gain access to arteries and veins.
Sufficient
SCDO:1000389
NCIT:C71746
Vascular Access Device Complications
Having no known name or identity or known source.
Sufficient
SCDO:0007242
NCIT:C71754
Anonymous
Of your own free will or design; not forced or compelled; controlled by individual volition.
Sufficient
SCDO:0001874
NCIT:C74096
Voluntary
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
Sufficient
SCDO:0000695
NCIT:C74954
LFT
Liver Function Assay
Liver Function Assays
Liver Function Tests
Liver Function Test
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.
Sufficient
SCDO:1000365
NCIT:C75434
Alpha Globin
Alpha-Globin
Alpha-Globin Chain
Haemoglobin Alpha Chain
Haemoglobin Subunit Alpha
Hemoglobin Alpha Chain
Hemoglobin Subunit Alpha
Hemoglobin Subunit Alpha
Examination of the anterior segment of the eye using a medical instrument called a slit lamp.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C75583
Sufficient
SCDO:0001078
NCIT:C75583
SLIT LAMP
Slit-Lamp Biomicroscopy
Slit-Lamp Eye Exam
Slit-Lamp Examination
Any problem arising from the use of a medical device.
Sufficient
SCDO:1000385
NCIT:C78254
Device Complication
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?
http://purl.obolibrary.org/obo/NCIT_C78393
Sufficient
SCDO:0001945
NCIT:C78393
Diabetes Bronze
Haemochromatosis
Hemochromatosis
Iron Storage Disorder
Iron Overload
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.
http://purl.obolibrary.org/obo/NCIT_C78598
Sufficient
SCDO:0007836
NCIT:C78598
Reversible Posterior Leukoencephalopathy Syndrome
Posterior Reversible Leukoencephalopathy
The development of a blood clot in a catheter.
Sufficient
SCDO:1000388
NCIT:C78638
Thrombus in 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.)
Self; Proxy (Parent report)
Clinic patients
Many measures available in Spanish, French and Portuguese
Toddlers; Children; Adolescents
yes
Sufficient
SCDO:0000875
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.
NCIT:C78652
Pediatric Quality of Life Inventory
PedsQL
Pediatric Quality of Life Inventory (PedsQL)
A sample of blood applied in a thin film to a microscope slide for study under a microscope.
Sufficient
SCDO:0008915
NCIT:C79903
Blood Smear
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.
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C80411
Sufficient
SCDO:0001012
NCIT:C80411
Pulmonary Artery Catheterization
Swan-Ganz Catheterization
Right Heart Catheterization
A description of an individual's current and past experience with alcoholic beverage consumption.
Add other terms in the PhenX "Alcohol Use" collection?
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C81229
Sufficient
SCDO:0000040
NCIT:C81229
Alcohol Use History
An identifying number within an institution that is used to reference a subject's medical information.
Sufficient
SCDO:1000853
NCIT:C81262
Medical Record Number
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%.
http://purl.obolibrary.org/obo/NCIT_C82909
Sufficient
SCDO:0003672
NCIT:C82909
Mild Anemia
The date on which a visit occurred.
Sufficient
SCDO:1000540
NCIT:C83031
Clinical Visit Date
Visit Date
An inherited metabolic disorder characterized by iron accumulation in the tissues.
Sufficient
SCDO:0000512
NCIT:C84481
Congenital Haemochromatosis
Hereditary Haemochromatosis
Iron Overload Disease
Primary Haemochromatosis
Hereditary Hemochromatosis
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.
http://purl.obolibrary.org/obo/NCIT_C84979
Sufficient
SCDO:0001381
NCIT:C84979
Epsilon-Globin
Haemoglobin Epsilon Chain
Haemoglobin Subunit Epsilon
Hemoglobin Epsilon Chain
Hemoglobin Subunit Epsilon
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.
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C84980
https://www.ncbi.nlm.nih.gov/gene/3045
Sufficient
SCDO:1000011
NCIT:C84980
Delta Globin
Delta-Globin
Haemoglobin Delta Chain
Haemoglobin Subunit Delta
Hemoglobin Delta Chain
Hemoglobin Subunit Delta
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.
Sufficient
SCDO:1000358
NCIT:C84983
Beta Globin
Beta Globin Chain
Beta-Globin
Beta-Globin Chain
HBB
Haemoglobin Beta Chain
Haemoglobin Subunit Beta
Hemoglobin Beta Chain
Hemoglobin Subunit Beta
Measurement of the breathing capacity of the lung by means of a spirometer.
Sufficient
SCDO:0001100
NCIT:C85397
Spirometry
A product of hemoglobin produced by oxidation of the iron atom from the ferrous to the ferric state.
Sufficient
SCDO:1000167
NCIT:C86008
MetHb
Methemoglobin
An instrument consisting of a predetermined set of questions for a clinical or research assessment.
Sufficient
SCDO:1000476
NCIT:C91105
Clinical or Research Assessment Questionnaire
A statement (either spoken or written) that is made in reply to a clinical research assessment question.
Sufficient
SCDO:1000473
NCIT:C91106
Clinical or Research Assessment Response
Clinical or Research Assessment Answer
The biopsy of placental tissue containing the chorionic villi from the maternal uterus in early pregnancy to diagnose fetal genetic defects.
http://purl.obolibrary.org/obo/NCIT_C92755
Sufficient
SCDO:0000223
NCIT:C92755
CVS
Chorionic Villus Sampling
Testing to determine if there is a predisposition or indication of a possible genetic or a chromosomal abnormality.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C92803
Sufficient
SCDO:0000446
NCIT:C92803
Genetic Screening
Hemorrhage defined as a blood loss in excess of 500 mL after vaginal delivery or more than 1000 mL after a cesarean delivery.
Sufficient
SCDO:0000916
NCIT:C92853
Postpartum Hemorrhage
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.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C93407
Sufficient
SCDO:0001116
NCIT:C93407
Study Outcome Measure
Study Outcome Measurement
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.
http://purl.obolibrary.org/obo/NCIT_C95437
Sufficient
SCDO:0005115
NCIT:C95437
Acute Pancreatitis
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.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95504
Sufficient
SCDO:0000534
NCIT:C95504
Alpha-Thalassemia Intermedia
Haemoglobin H Disease
Hb H-Disease
Hemoglobin H Disease
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.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95534
Sufficient
SCDO:0000550
NCIT:C95534
Heterozygous Hemoglobinopathy
Hemoglobin Trait
A condition in which a person has reduced protein production from two of the four alpha-globin alleles.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95535
Sufficient
SCDO:0000044
NCIT:C95535
Alpha-Thalassemia Trait
-/- 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.
Alpha Thalassemia Trait
A condition in which a person has reduced protein production from one of the four alpha-globin alleles.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95536
Sufficient
SCDO:0000043
NCIT:C95536
Alpha Thalassemia Silent
Alpha-Thalassemia Silent Carrier
Alpha Thalassemia Silent Carrier
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.
Sufficient
SCDO:0001057
NCIT:C95539
Hb S-Beta Thalassemia
HbS-Beta-Thalassemia Syndrome
HbSBetaThal
S Beta-Thalassemia
S-Beta Thalassemia
Sickle Beta Thalassaemia
Sickle Beta-Thalassaemia
Sickle Cell Beta Thalassemia Disease
Sickle Cell Disease-S Beta Thalassaemia
Sickle Cell-Beta Thalassaemia
Sickle Cell-Beta-Thalassemia
Sickle Cell-Beta-Thalassemia Disease Syndrome
Sickle Beta Thalassemia
A morphologic finding indicating enlargement of the glomeruli in a kidney specimen.
Sufficient
SCDO:0002784
NCIT:C96239
Glomerular Hypertrophy
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.
http://purl.obolibrary.org/obo/NCIT_C96391
Sufficient
SCDO:0006120
NCIT:C96391
MCV4
Menactra
Meningococcal Conjugate Vaccine MCV-4
Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugated Vaccine
Menveo
Meningococcal Conjugate Vaccine MCV4
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.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C97120
Sufficient
SCDO:0000909
NCIT:C97120
PCV 10
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.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C97121
Sufficient
SCDO:0000910
NCIT:C97121
PCV 13
PCV13 Vaccine
Prevnar 13
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.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C97123
Sufficient
SCDO:0000275
NCIT:C97123
Pneumococcal Conjugate Vaccine
Conjugate Pneumococcal Vaccine
Methemoglobinemia that is caused by exposure to certain drugs (xylocaine and benzene) and nitrate-rich foods.
Sufficient
SCDO:0000013
NCIT:C98805
Acquired Methemoglobinemia
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.
Requires further refinement.
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C98835
Sufficient
SCDO:0001058
NCIT:C98835
Hb S Beta 0 Thalassemia
Hemoglobin S Beta 0 Thalassemia
S Beta 0 Thalassemia
S beta-zero
Sickle Beta 0 Thalassemia
Sickle Beta Zero Thalassemia
Sickle Cell-Beta 0 Thalassemia
Sickle Cell-Beta Zero Thalassemia
Sickle Cell Disease-S Beta Zero Thalassemia
The formation of a thrombus in the renal vein.
http://purl.obolibrary.org/obo/NCIT_C99042
Sufficient
SCDO:0005061
NCIT:C99042
Renal Vein Thrombosis
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)
http://purl.obolibrary.org/obo/NCIT_C99063
Sufficient
SCDO:0005226
NCIT:C99063
Spinal Cord Infarction
An assay that produces a picture of an entity.
Perhaps replace this term with "Diagnostic Imaging" from NCIT?
http://purl.obolibrary.org/obo/OBI_0000185
Sufficient
SCDO:0000612
OBI:0000185
Imaging Assay
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.
Sufficient
SCDO:0004249
OBI:0000626
DNA Sequencing
A material entity bearing the disposition to infect an organism
Sufficient
SCDO:0000638
OBI:0000925
Infectious Agent
A microscope that produces an image of an object by targeting it with an electron beam.
Sufficient
SCDO:0000422
OBI:0000990
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.
Electron Microscope
A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs.
Sufficient
SCDO:0001202
OBI:0001098
Ultrasound Machine
A device that is used to generate X-rays.
http://purl.obolibrary.org/obo/OBI_0001138
Sufficient
SCDO:0001251
OBI:0001138
Radiographic Unit
X-Ray Machine
An assay to determine the temperature of an evaluant.
Sufficient
SCDO:1000752
OBI:0002140
Temperature Measurement Assay
An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens.
Sufficient
SCDO:1000195
OBI:0002146
HIV Antibody Assay
The window period for antibody tests in most people is somewhere between 3 to 12 weeks from the time of infection.
HIV Antibody Test
A value specifcation that specifies the youngest age when specifying an age range.
Sufficient
SCDO:1000405
OBI:0002556
Minimum Age Value Specification
A value specifcation that specifies the oldest age when specifying an age range.
Sufficient
SCDO:1000404
OBI:0002557
Maximum Age Value Specification
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).
Sufficient
SCDO:0001138
OBI:0200198
MS/MS
Tandem MS
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.
Tandem Mass Spectrometry
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.
Sufficient
SCDO:0001096
OBI:0400115
Spectrophotometer
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).
Sufficient
SCDO:0000757
OBI:0400169
Microscope
A disease characterized by abnormal and uncontrolled cell division.
http://purl.obolibrary.org/obo/OBI_1110053
Sufficient
SCDO:0000180
OBI:1110053
Malignancy
Malignant Neoplasia
Malignant Neoplasm
Malignant Tumor
Malignant Tumour
Cancer
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
http://bioportal.bioontology.org/ontologies/OGMS?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000023
Sufficient
SCDO:0000893
OGMS:0000023
Phenotype
A clinically abnormal phenotype that is characteristic of a single disease.
Sufficient
SCDO:1000185
OGMS:0000028
Disease Phenotype
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.
http://purl.obolibrary.org/obo/OGMS_0000046
Sufficient
SCDO:0000439
OGMS:0000046
Epigenomic Disorder
Epigenetic Disorder
A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome.
http://purl.obolibrary.org/obo/OGMS_0000047
Sufficient
SCDO:0000445
OGMS:0000047
Genetic Disorder
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?
http://purl.obolibrary.org/obo/OGMS_0000051
Sufficient
SCDO:0000279
OGMS:0000051
Constitutional Genetic Disorder
A communication from a patient about something they perceive as being abnormal about their body or life.
http://purl.obolibrary.org/obo/OGMS_0000088
Sufficient
SCDO:0000872
OGMS:0000088
Patient Symptom Report
An answer to question where the answer is Yes.
Sufficient
SCDO:1000563
OPMI:0000023
yes answer to question
Yes
An answer to question where the answer is No.
Sufficient
SCDO:1000564
OPMI:0000024
no answer to question
No
An answer to question that indicates the response to the specified question is unknown.
Sufficient
SCDO:1000562
OPMI:0000025
Don't know
unknown answer to question
Do Not Know
An answer to question where one declines to answer the specified question.
Sufficient
SCDO:1000561
OPMI:0000027
Refuse to answer
Refused to answer
declined to answer question
declined to answer to question
Refused
An answer to question that is not enumerated in the list and then may be entered with free text in a separate text box
Sufficient
SCDO:1000565
OPMI:0000028
other answer to question
Other
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.
Sufficient
SCDO:1000443
PR:000001318
CD62 Antigen-Like Family Member L
CD62L
Lymph Node Homing Receptor
L-selection is a serum marker for neutrophil activation.
L-Selectin
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).
Sufficient
SCDO:0000756
SBO:0000316
miRNA
MicroRNA
The performance of the basic activities of self care, such as dressing, ambulation, or eating.
http://purl.bioontology.org/ontology/MESH/D000203
Sufficient
SCDO:0000006
MESH:D000203
ADL
Daily Living Activities
Daily Living Activity
Self Care (Rehabilitation)
Self-Care
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.
None
SCDO (Jade Hotchkiss)
Structurally Abnormal Hemoglobin Present in SCD
Abnormal Hemoglobin 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".
http://purl.obolibrary.org/obo/HP_0001877
Sufficient
Abnormality of Red Blood Cell
Abnormality of Red Blood Cells
deprecated Abnormality of Erythrocytes
true
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.
Sufficient
SCDO:0000010
MESH:D000082
Paracetamol
Tylenol
Acetaminophen
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.
None
SCDO
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C14140
http://purl.bioontology.org/ontology/MESH/Q000150
Acute Complications of SCD
Acute Complications of Sickle Cell Disease
An acute onset of wheezing in a person with SCD who has no co-morbid asthma.
Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info.
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.
Normal Chest X-ray
None
Cohen et al 2011 Am J Hematol., Glassberg et al 2014 Curr Opin Pediatr., Knight-Madden et al 2014 Ped Resp Rev
Too specific to SCD to be included in other ontologies?
PFTs may be done to asses for airway hyper-responsiveness.
Acute Non-Specific Wheezing Episode
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)
None
SCDO
Acute Sickle Cell Pain Treatment
Acute Sickle Cell Pain Management
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
SCDO
Acute Upper Respiratory Infection
URI
URTI
Acute Upper Respiratory Tract Infection
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.
Suggest update to description
MESH:D010349
Adherence to Long Term Therapy
Patient Adherence
Patient Compliance
Patient Cooperation
deprecated-Adherence
true
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
Suggest update to label
phenX:130501
Adult Migraine Questionnaire
An adverse event that occurs after a drug administration.
Should this be a sub-class of "Environmental Disease Modifier"?
http://purl.obolibrary.org/obo/OAE_0000005
Sufficient
SCDO:0000028
OAE:0000005
ADE
ADR
Adverse Drug Reaction
Drug Adverse Event
Adverse Drug Event
Electrophoresis in which agar or agarose gel is used as the diffusion medium.
http://purl.bioontology.org/ontology/MESH/D004587
Sufficient
SCDO:0000029
MESH:D004587
Agar Gel Electrophoresis
Agarose Gel Electrophoresis
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.
http://rarediseases.org/rare-diseases/agenesis-of-corpus-callosum/
Suggest update to description
ACC
Absence of Corpus Callosum
Absent Corpus Callosum
Agenesis of the Corpus Callosum
Callosal Agenesis
Corpus Callosum Agenesis
Dysplastic or Absent Corpus Callosum
Agenesis of Corpus Callosum
A quantitative measurement of alanine aminotransferase present in a blood sample.
Suggest update to description in NCIT (from "Alanine Aminotransferase Measurement")
Suggest update to description
NCIT:C64433
ALT Blood Test
Alanine Transaminase Blood Test
Circulating Alanine Transaminase Test
SGPT Test
Serum Glutamic-Pyruvic Transaminase Test
Alanine Aminotransferase Blood Test
The amount of alanine aminotransferase present in a specified volume of blood.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
ALT Level
Alanine Aminotransferase Level
Alanine Transaminase Level
Blood Alanine Transaminase Level
Circulating Alanine Transaminase Level
SGPT Level
Serum Glutamic-Pyruvic Transaminase Level
Alanine Aminotransferase Level
Increased concentration of albumin in the urine; more than 30mg in 24hours or urine albumin creatinine ratio (ACR) >3 mg/mmol.
Suggest update to description in HPO.
http://www.nice.org.uk/guidance/CG182/chapter/introduction
Suggest update to description in HPO.
HP:0012592
Because albuminuria may be affected by non-pathological factors (exercise, menstruation contamination, biological variability, etc.), abnormal values should be confirmed within 1-2 months.
Albuminuria
An indication of whether the respondent has ever consumed any alcoholic beverage during his or her entire life.
Request inclusion into relevant ontology
Not relevant to context of sickle cell
SCDO (Jade Hotchkiss)
Alcohol - Lifetime Use
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/
http://purl.bioontology.org/ontology/MESH/D017085
Sufficient
SCDO:0000042
MESH:D017085
A-Thalassemia
Alpha-Thalassemia
Thalassemia Alpha
Alpha Thalassemia
Drugs that selectively bind to and activate alpha adrenergic receptors.
http://purl.bioontology.org/ontology/MESH/D000316
Sufficient
SCDO:0000045
MESH:D000316
Adrenergic Alpha Agonists
Adrenergic Alpha-Agonists
Alpha Adrenergic Receptor Agonist
Alpha-Adrenergic Agents
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.
None
SCDO (Jade Hotchkiss)
Alpha-Globin Gene Cluster
Alpha-Globin Locus
Methods of pain relief that may be used with or in place of analgesics.
http://purl.bioontology.org/ontology/MESH/D000698
Sufficient
SCDO:0000049
MESH:D000698
Analgesias
Analgesia
A compound capable of relieving pain without the loss of consciousness.
http://purl.bioontology.org/ontology/MESH/D000700
Sufficient
SCDO:0000050
MESH:D000700
Analgesic
Analgesic Agent
Analgesic Drugs
Anodynes
Antinociceptive Agent
Pain Killers
Painkiller
Painkillers
Analgesic
An adverse drug event that results in unexpected and unwanted events due to anesthetic drug treatment.
http://purl.obolibrary.org/obo/OAE_0002348
Sufficient
SCDO:0000053
OAE:0002348
Anesthetic Complication AE
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.
Ballas et al 2010 Am J Hematol
Suggest update to description
DOID:13401
Angioid Streaks
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.
http://purl.bioontology.org/ontology/MESH/D000806
Sufficient
SCDO:0000055
MESH:D000806
ACE
ACE Inhibitors
Angiotensin Converting Enzyme
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
Negligable
phenX:11100
Annual Family Income
Substance that reduces or suppresses inflammation.
http://purl.bioontology.org/ontology/MESH/D000893
Sufficient
SCDO:0000057
MESH:D000893
Anti Inflammatories
Anti Inflammatory Agents
Anti-Inflammatories
Anti-Inflammatory Agents
Anti-Inflammatory Drug
Antiinflammatories
Antiinflammatory Agents
Anti-Inflammatory Agent
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.
http://purl.bioontology.org/ontology/MESH/D006633
Sufficient
SCDO:0000066
MESH:D006633
Antihistamines
Histamine Antagonist
Histamine Antagonists
Antihistamine
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.
http://purl.bioontology.org/ontology/MESH/D000959
Sufficient
SCDO:0000067
MESH:D000959
Agents, Antihypertensive
Anti Hypertensive Agent
Anti-Hypertensives
Antihypertensive Drug
Antihypertensive Drugs
Antihypertensives
Antihypertensive 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.
http://www.ncbi.nlm.nih.gov/gene/8542
Not relevant to context of sickle cell
APO-L
APOL
APOL1 Gene
Apolipoprotein L1 Gene
APOL1
Exercises performed in or underwater for conditioning or rehabilitation (e.g., in injured athletes or patients with joint diseases).
Request inclusion into relevant ontology
http://medical-dictionary.thefreedictionary.com/aquatic+therapy
None
Aqua Therapy
Hydrotherapy
Aquatic Rehabilitation
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.
Sufficient
SCDO:0000071
ERO:0000533
ABG Test
Arterial Blood Gas Test
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.
http://purl.bioontology.org/ontology/MESH/D001165
Sufficient
SCDO:0000072
MESH:D001165
Arteriovenous Malformations
Arteriovenous Malformation
A water-soluble, semi-synthetic derivative of the sesquiterpene lactone artemisinin with anti-malarial, anti-schistosomiasis, antiviral, and potential anti-neoplastic activities.
Sufficient
SCDO:0000073
MESH:D000077332
Artesunic Acid
Dihydroartemisinine 12 Alpha Succinate
Artesunate
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
None
SCDO (Jade Hotchkiss)
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820201
ASCQ-Me - Quality of Life in SCD
Sickle Cell Disease Adult Quality of Life Questionnaire Assessment Score
deprecated ASCQ-Me Score
true
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")
Suggest update to label
phenX:811201
AST Blood Test
Aspartate Transaminase Blood Test
Serum AST Blood Test
Aspartate Aminotransferase Blood Test
The amount of aspartate aminotransferase present in a specified volume of blood.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
AST Level
Aspartate Transaminase Level
Blood Aspartate Transaminase Amount
Aspartate Aminotransferase Level
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")
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820101
PhenX protocol: Quality of Care - Adults #820101
Self
Clinic Patients (Adults with SCD)
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).
18 and older
Suggest update to label
SCDO
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
ASCQ-Me Quality of Care Module
ASCQ-Me - Quality of Care in SCD
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.
None
SCDO (Jade Hotchkiss)
http://purl.obolibrary.org/obo/OBI_0000070
Diagnostic Assay
Diagnostic Method
Diagnostic Technique
Diagnostic Test
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.
http://www.phenxtoolkit.org/toolkit_content/supplemental_info/scd_cardio_pulm_renal/measures/Short_Axis_Function_20May2015.doc
None
MRI of Short-Axis Cardiac Function
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".
http://purl.bioontology.org/ontology/MESH/D001249
Airway hyper-responsiveness
Airway inflammation
Intermittent airway obstruction
It is characterized by spasmodic contraction of airway smooth muscle, wheezing and dyspnea.
Sufficient
SCDO:0000086
MESH:D001249
Asthma
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.
Sufficient
SCDO:0000088
MESH:D003876
Atopic Eczema
Baby Eczema
Infantile Eczema
Atopic Dermatitis
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".
Request inclusion into relevant ontology
http://www.ncbi.nlm.nih.gov/gene/53335
Not relevant to context of sickle cell
B-Cell CLL/Lymphoma 11A Gene
B-cell CLL/lymphoma 11A (zinc finger protein)
B-cell CLL/lymphoma 11A Gene
BAF Chromatin Remodeling Complex Subunit BCL11A Gene
BCL-11A Gene
BCL11A Gene
Fetal Hemoglobin Quantitative Trait Locus 5
HBFQTL5
BCL11A
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.
http://purl.bioontology.org/ontology/MESH/D001419
Sufficient
SCDO:0000098
MESH:D001419
Bacteria
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.
Multiple countries and cultural groups
Self
Clinic Patients
Spanish
17 years and older
yes
Few but definitions not freely available
BAI
Beck Anxiety Inventory
Beck Anxiety Inventory (BAI)
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.
Suggest update to label in PhenX.
PhenX protocol: #131102
Suggest update to label
phenX:131102
BRIEF
Executive Function - Child
Behavior Rating Inventory of Executive Function
The actions or reactions of a person in response to a situation or stimuli.
Few but definitions not specific enough
SCDO
Behaviour
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
http://purl.bioontology.org/ontology/MESH/D015984
Beliefs about Causality
Cultural beliefs, such as re-incarnation and witchcraft, may influence notions on causality of sickle cell disease.
Beliefs About Causes of Illness
Personal or collective understanding of what can remedy or treat illness.
Request inclusion into relevant ontology, perhaps MESH.
none
SCDO
http://www.ncbi.nlm.nih.gov/mesh/68003469
Beliefs About Remedies and Treatment
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
None
Beta - Thalassemia
Beta Minus-Thalassemia
Beta- Thalassemia
Beta-Minus-Thalassemia
Beta Minus Thalassemia
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)
A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed
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/
http://en.wikipedia.org/wiki/Beta_thalassemia
http://purl.obolibrary.org/obo/DOID_12241
Suggest update to description
DOID:12241
Beta Thalassemias
Beta Type Thalassemia
Beta-Thalassemia
Beta-Thalassemias
Hemoglobin F Disease
Mediterranean Anemia
Beta Thalassemia
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.
Sufficient
SCDO:0000112
ORPHA:231222
B+/B+
B0/B+
Beta-Thalassemia Intermedia
Thalassemia Intermedia
Beta Thalassemia Intermedia
A severe early-onset form of beta thalassemia characterized by severe anemia requiring regular red blood cell transfusions.
Sufficient
SCDO:0000113
ORPHA:231214
B0/B0
BT Major
Beta-Thalassemia Major
Cooley Anemia
Cooley's Anemia
Mediterranean Anemia
Thalassemia Major
Beta Thalassemia Major
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".
http://en.wikipedia.org/wiki/Beta_thalassemia
Few but definitions not freely available
B-/B
B0/B
Beta Thalassemia Minor
Beta-Thalassemia Trait
Heterozygosity for Beta-Thalassemia
Heterozygous Beta-Thalassemia
Beta Thalassemia Trait
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).
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
None
Beta 0 Thalassemia
Beta Zero-Thalassemia
Beta-Zero-Thalassemia
Beta0 Thalassemia
Hb Beta Zero-Thalassemia
Hb F only
Beta Zero Thalassemia
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.
Request inclusion into relevant ontology perhaps below "Genetic Locus"/"Globin Locus" (also to be included) in MESH.
None
SCDO (Jade Hotchkiss)
Beta-Globin Cluster
Beta-Globin Gene Cluster
HBB Locus
Beta-Globin Locus
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.
Request inclusion into relevant ontology
Nagel, et. al. NEngl J Med. 1985 Apr 4;312(14):880-4
None
SCDO
Beta-Globin Haplotypes
Beta-Haplotypes
Beta-S Haplotype
Beta-S Haplotypes
Beta-Globin Haplotype
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").
Suggest update to label
phenX:810901
Bilirubin Blood Test
An analytical in vitro procedure used to detect, quantify and/or study the binding or activity of a biological molecule, such as an enzyme.
Request inclusion into relevant ontology.
http://www.nature.com/subjects/biochemical-assays
Negligable
Biochemical Assay
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Biological Disease Modifier
The country in which the respondent was born.
Request inclusion into relevant ontology
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocols&id=010200
Negligable
Place of Birth
Birthplace
The country in which the respondent's biological father was born.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Birthplace of Biological Father
The country in which the respondent's biological mother was born.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Birthplace of Biological Mother
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.
Negligable
SCDO (Jade Hotchkiss)
Birthplace of Grandparents
The country in which the respondent's biological maternal (on the mother's side of the family) grandfather was born.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Birthplace of Maternal Grandfather
The country in which the respondent's biological maternal (on the mother's side of the family) grandmother was born.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Birthplace of Maternal Grandmother
The country or countires in which the respondent's biological parents were born.
Request inclusion into relevant ontology
There is a protocol in PhenX but it is US specific.
Negligable
SCDO (Jade Hotchkiss)
Birthplace of Parents
The country in which the respondent's biological paternal (on the father's side of the family) grandfather was born.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Birthplace of Paternal Grandfather
The country in which the respondent's biological paternal (on the father's side of the family) grandmother was born.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Birthplace of Paternal Grandmother
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.
Request inclusion into relevant ontology.
Ballas et al 2010 Am J Hematol
None
Black Sunburst Lesion
Test used in the analysis of the hemic system.
http://purl.bioontology.org/ontology/MESH/D006403
Sufficient
SCDO:0000133
MESH:D006403
Blood Assay
Blood Tests
Hematologic Test
Hematologic Tests
Hematological Test
HematologyTest
Blood Test
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.
http://purl.bioontology.org/ontology/MESH/D016913
Sufficient
SCDO:0000138
MESH:D016913
Blood Component Transfusion
Test to determine the presence of blood infection (e.g. sepsis; bacteremia).
Sufficient
SCDO:0000139
MESH:D000071997
BC
Culture Blood
Haemoculture
Hemoculture
Blood Culture
The introduction of whole blood or blood component directly into the blood stream. (Dorland, 27th ed)
http://purl.bioontology.org/ontology/MESH/D001803
Sufficient
SCDO:0000147
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
MESH:D001803
Blood Transfusions
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.
Blood Transfusion
The distance from the sole to the crown of the head with body standing on a flat surface and fully extended.
http://www.ebi.ac.uk/efo/EFO_0004339
Sufficient
SCDO:0000149
EFO:0004339
Height
Height/Length
Length/Height
Body Height
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
Sufficient
SCDO:0000152
MESH:D001835
Weight
Body Weight
An abnormal hardening or increased density of bone tissue.
Sufficient
SCDO:0000155
Segen's Medical Dictionary. S.v. "bone sclerosis." Retrieved April 30 2019 from https://medical-dictionary.thefreedictionary.com/bone+sclerosis
MESH:D010026
Bone Scleroses
Osteoscleroses
Osteosclerosis
The bone is more radiopaque than normal on a plain film.
deprecated-Bone Sclerosis
true
A noninvasive method to assess the endothelial dysfunction in the brachial artery.
Request inclusion into relevant ontology.
http://en.wikipedia.org/wiki/Endothelial_dysfunction
None
BAUI
Brachial Artery Ultrasound Imaging
Voltages between parts of the brain that are detectable with an electroencephalograph.
Sufficient
SCDO:0000161
CRISP:0487-1238
Brain Electrophysiological Activity
Brain Oscillography
EEG activity
Brain Electrical Activity
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
Few but definitions not specific enough
Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
NCIT:C9203
There are currently no data that clearly describe or can be used to define breakthrough pain in SCD.
Breakthrough Pain
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.
Multiple countries and cultural groups
Self
Clinic Patients
Many
Good psychometric properties, widely used, has been translated into several languages.
Adults
yes
None
Broadbent E, Petrie KJ, Main J, Weinman, J. (2006). The brief illness perception questionnaire. Journal of Psychosomatic Research, 60, 631-637.
B-IPQ
Brief Illness Perception Questionnaire
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.
Request inclusion into NCIT below "Research or Clinical Assessment Tool".
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.
Self; Proxy (Parent report)
Children with SCD and their parents.
Demonstrated validity in SCD studies.
Children and adults
None
SCDO
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.
Brief RCOPE
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.
Suggest update to description
BDR
Bronchodilator Responsiveness
BDR
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
Suggest update to label
phenX:90301
BDR Test
Bronchodilator Responsiveness Testing
Bronchodilator Responsiveness Test
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)
http://purl.bioontology.org/ontology/MESH/D019075
Sufficient
SCDO:0000182
MESH:D019075
Capillary Electrophoreses
Capillary Zone Electrophoreses
Capillary Zone Electrophoresis
Capillary Electrophoresis
An instrument which, by means of a cathode-ray oscillograph, projects an electrocardiographic record on a luminous screen.
Request inclusion into relevant ontology.
http://encyclopedia2.thefreedictionary.com/cardioscope
None
Cardioscope
'Anatomical system that has as its parts the heart and blood vessels. [Curator team: []]'
http://purl.obolibrary.org/obo/UBERON_0004535
UBERON:0004535
CV system
deprecated Cardiovascular System
true
'Clinical presentations that may be followed by evaluative studies that eventually lead to a diagnosis. [Curator team: []]'
http://purl.bioontology.org/ontology/MESH/D002363
MESH:D002363
Case Histories
Case Studies
Case Study
obsolete Case Reports
true
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.
Suggest update to description in MESH
http://purl.bioontology.org/ontology/MESH/D016022
Suggest update to description
MESH:D016022
Case-Referrent Studies
Case-Control Studies
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".
http://purl.bioontology.org/ontology/MESH/D057785
Sufficient
SCDO:0000190
MESH:D057785
Cannula
Cannulas
Catheters
Catheter
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.
http://purl.obolibrary.org/obo/OAE_0000095
Suggest update to description
OAE:0000095
Causal Adverse Drug Event
A causal adverse drug event that is induced by a drug-drug interaction.
http://purl.obolibrary.org/obo/OAE_0000179
Sufficient
SCDO:0000192
OAE:0000179
Causal Adverse Drug Event Due to Drug-Drug Interaction
A causal adverse drug event that is induced by a food-drug interaction.
http://purl.obolibrary.org/obo/OAE_0000180
Sufficient
SCDO:0000193
OAE:0000180
Causal Adverse Drug Event Due to Food-Drug Interaction
A causal adverse drug event that is induced by genetic predisposition.
Suggest small typo to be fixed in OAE.
http://purl.obolibrary.org/obo/OAE_0000181
Suggest update to description
OAE:0000181
Causal Adverse Drug Event Due to Genetic Predisposition
A causal adverse drug event due to genetic predisposition that is specifically induced by SNP.
http://purl.obolibrary.org/obo/OAE_0000182
Sufficient
SCDO:0000195
OAE:0000182
Causal Adverse Drug Event Due to SNP
The determination of the amount of free hemoglobin present in a sample.
Suggest update to label in NCIT (from "Free Hemoglobin Measurement")
Suggest update to label
NCIT:C127617
Cell Free Hemoglobin Assay
Cell Free Hemoglobin Blood Assay
Cell Free Hemoglobin Test
Free Hemoglobin Blood Test
HGBFR Test
Cell Free Hemoglobin Blood Test
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.
None
SCDO (Jade Hotchkiss)
Cell Free Haemoglobin Level
Cell Free Hemoglobin Concentration
Extracellular Hb Level
Extracellular Hemoglobin Level
HGBFR Level
Cell Free 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
None
Cerebral Collateral Circulation
Cerebral Collateral Flow
A test of how well the cerebrum is functioning.
Request inclusion into relevant ontology.
None
SCDO (Jade Hotchkiss)
Cerebral Function Test
Cerebral Function Assay
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?
None
SCDO (Jade Hotchkiss)
Cerebrovascular Hemodynamics
The analysis of a sample material, called an analyte, using a set of chemical procedures.
Request inclusion into relevant ontology.
http://www.reference.com/science/chemical-assay-80cfe6f498d34be5
None
Chemical Assay
A medical imaging assessment of the chest wall, airways, lungs, pulmonary vessels, heart, mediastinum, and pleura.
Sufficient
SCDO:0000217
phenX:810201
Chest Radiograph
Chest X-Ray
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).
Multiple countries and cultural groups
Self, Proxy
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)
yes
Few but definitions not specific enough
SCDO
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.
CHQ
Child Health Questionnaire
Child Health Questionnaire (CHQ)
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
Negligable
phenX: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.
Request inclusion into relevant ontology. Could be as a child of "Symptom Specific Assessment Tool" in the NCIT.
Multiple countries and cultural groups
Self
Clinic Patients
7 to 17 years
yes
None
Kovacs, M. (1985). The Children's Depression, Inventory (CDI). Psychopharmacology Bulletin, 21, 995-998.
CDI 2
CDI-2
Children's Depression Inventory 2
Children's Depression Inventory-2
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.
Multiple countries and cultural groups
Self
Healthy Children; Children with Medical Conditions
English, Russian, a 9- item shorter Egyptian version
Has adequate reliability, construct validity and internal consistency.
Children and Adolescents
no
Few but definitions not specific enough
CHLC
Children's Health Locus of Control Scale
Children's Health Locus of Control Scale (CHLC)
Surgical removal of the gallbladder.
http://purl.bioontology.org/ontology/MESH/D002763
Sufficient
SCDO:0000222
MESH:D002763
Cholecystectomies
Cholecystectomy
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.
Probably too specific to warrant inclusion into anther ontology.
Used info in "Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014" to link to relevant phenotypes.
None
SCDO
http://purl.bioontology.org/ontology/MESH/Q000150
http://purl.obolibrary.org/obo/HP_0011010
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).
NHLBI SCD New guidelines 2014.
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.
Few but definitions not specific enough
SCDO
NHLBI SCD New guidelines 2014.
DOID:784
CKD
Chronic Kidney Injury
Chronic Renal Failure
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.
Chronic Kidney Disease
Is a long-term condition where the kidneys don't work as well as they should.
There is conflicting positioning of this term in different ontologies. Need an expert to decide descriptions and positioning of this and related terms.
CKD
deprecated-Chronic Kidney Injury
true
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.
Request inclusion into relevant ontology
Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
Few but definitions not freely available
Chronic Neuropathic Pain
This pain occurs in a specific tissue or organ and is usually described as constant and deep, nagging, and achy in nature.
Request inclusion into relevant ontology
Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
None
Chronic Pain in a Specific Tissue or Organ
The only complaint is the patient's self-report of pain that does not go away.
Request inclusion into relevant ontology
Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
http://doi.org/10.1182/blood-2012-04-383430
None
Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
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.
Chronic Pain often Unclear Etiology
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?
None
Chronic Restrictive Ventilatory Defect
Restrictive Lung Disease
Chronic Restrictive Lung Disease
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.
Request inclusion into relevant ontology
SCD Management guidelines - Tanzania
None
SCDO
Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
SCD-Associated Chronic Pain
Chronic Sickle Cell Pain
Sickle cell pain management that aims to restore function and improve the quality of life.
Request inclusion into MESH below "Pain Management" / "Sickle Cell Pain Management" (also to be suggested for inclusion)
None
SCDO
Chronic Sickle Cell Pain Treatment
Chronic Sickle Cell Pain Management
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
None
SCDO (Jade Hotchkiss)
Cigarette Smoking Status Measurement
Cigarette Smoking Status
Meteorological conditions, including temperature, precipitation, and wind, that characteristically prevail in a particular region; includes regions of the earth having particular meteorological conditions.
http://bioportal.bioontology.org/ontologies/CRISP?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCSP%2F1035-6799
Sufficient
SCDO:0000236
CRISP:1035-6799
Climate
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-)
http://purl.bioontology.org/ontology/MESH/D059019
Sufficient
SCDO:0000245
MESH:D059019
Coding
Medical Coding
Clinical Coding
The capability to perform acceptably those duties directly related to patient care.
http://purl.bioontology.org/ontology/MESH/D002983
Sufficient
SCDO:0000246
MESH:D002983
Clinical Competencies
Clinical Competency
Clinical Skill
Competencies, Clinical
Competency, Clinical
Skill, Clinical
Skills, Clinical
Clinical Competence
'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: []]'
http://purl.bioontology.org/ontology/MESH/D016429
MESH:D016429
Clinico-Pathologic Conference
Clinico-Pathological Conference
obsolete Clinical Conference
true
'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
true
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.
Sufficient
SCDO:0000250
phenX:130201
Charcot-Marie-Tooth Neuropathy Score
Neuropathy - Clinical Assessment
Clinical Neuropathy Assessment
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.
Request inclusion into relevant ontology
None
SCDO (Clair Ingram)
Clinical Phenotype of Beta Thalassemia
'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: []]'
http://purl.bioontology.org/ontology/MESH/D000068397
MESH:D000068397
obsolete Clinical Study
true
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
http://purl.bioontology.org/ontology/MESH/D000068456
Sufficient
SCDO:0000253
MESH:D000068456
Clinical Studies as Topic
'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: []]'
http://purl.bioontology.org/ontology/MESH/D016430
MESH:D016430
Intervention Study
obsolete Clinical Trial
true
'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: []]'
http://purl.bioontology.org/ontology/MESH/D017426
MESH:D017426
Clinical Trial, Phase 1
obsolete Clinical Trial, Phase I
true
'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: []]'
http://purl.bioontology.org/ontology/MESH/D017427
MESH:D017427
Clinical Trial, Phase 2
obsolete Clinical Trial, Phase II
true
'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: []]'
http://purl.bioontology.org/ontology/MESH/D017429
MESH:D017429
Clinical Trial, Phase 4
obsolete Clinical Trial, Phase IV
true
'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: []]'
http://purl.bioontology.org/ontology/MESH/D017428
MESH:D017428
Clinical Trial, Phase 3
obsolete Clinical Trial, Phase III
true
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.
http://purl.bioontology.org/ontology/MESH/D002986
Sufficient
SCDO:0000259
MESH:D002986
Clinical Trials as Topic
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.
http://purl.bioontology.org/ontology/MESH/D015928
Sufficient
SCDO:0000262
MESH:D015928
CBT
Cognition Therapies
Cognition Therapy
Cognitive Behavioral Therapies
Cognitive Behavioral Therapy
Cognitive Behaviour Therapy
Cognitive Psychotherapies
Cognitive Psychotherapy
Cognitive Therapies
Cognitive Therapy
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.
http://purl.bioontology.org/ontology/MESH/D015331
Sufficient
SCDO:0000263
MESH:D015331
Cohort Analyses
Cohort Studies
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.
http://purl.bioontology.org/ontology/MESH/D003128
Sufficient
SCDO:0000265
MESH:D003128
Comas
Coma
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
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Additional Disease
Co-Existing Disease
Co-Morbid Condition
Co-Morbid Disease
Comorbid Disease
Comparison of outcomes, results, responses, etc for different techniques, therapeutic approaches or other inputs.
http://purl.bioontology.org/ontology/MESH/D003160
Sufficient
SCDO:0000268
MESH:D003160
Comparative Studies
Comparative Study
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).
http://purl.bioontology.org/ontology/MESH/D000529
Sufficient
SCDO:0000271
MESH:D000529
Complementary Medicine
Complementary Therapy
'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
true
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.
Request inclusion into relevant ontology.
Ballas et al 2010 Am J Hematol
None
Conjunctival Comma Sign
'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: []]'
http://purl.bioontology.org/ontology/MESH/D016446
MESH:D016446
obsolete Consensus Development Conference
true
'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: []]'
http://purl.bioontology.org/ontology/MESH/D016447
MESH:D016447
NIH Consensus Development Conference
obsolete Consensus Development Conference, NIH
true
A tool for collecting standardized information on enrollees' experiences with health plans and their services.
Request inclusion into NCIT below "Research or Clinical Assessment Tool".
PhenX protocol: Quality of Care - Children #820102
Proxy (Primary caregiver)
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
yes
None
PhenX:820102
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.
http://purl.bioontology.org/ontology/MESH/D065187
Sufficient
SCDO:0000282
MESH:D065187
Controlled Before-After Studies
Controlled Pre-Post Studies
'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: []]'
http://purl.bioontology.org/ontology/MESH/D018848
MESH:D018848
obsolete Controlled Clinical Trial
true
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.
http://purl.bioontology.org/ontology/MESH/D018849
Sufficient
SCDO:0000284
MESH:D018849
Controlled Clinical Trials as Topic
A state of harmony between internal needs and external demands and the processes used in achieving this condition.
http://purl.bioontology.org/ontology/MESH/D000223
Sufficient
SCDO:0000286
MESH:D000223
Adaptive Behavior
Adaptive Behaviors
Coping Behavior
Coping Behaviors
Coping Skills
Psychologic Adaptation
Psychological Adaptation
Coping Skill
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.
Request inclusion into NCIT below "Research or Clinical Assessment Tool".
Abrams M.R., Phillips G. and Keefe F.J. (1989). Sickle cell disease pain: Relation of coping strategies
Multiple countries and cultural groups
Self
Adults with SCD
Demonstrated validity with SCD populations USA and UK; several publications.
Adults
None
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.
CSQ-SCD
Coping Strategies Questionnaire revised for Sickle Cell Disease
Coping Strategies Questionnaire revised for Sickle Cell Disease (CSQ-SCD)
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.
Request inclusion into NCIT below "Research or Clinical Assessment Tool".
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.
Multiple countries and cultural groups
Self
Children with SCD
Demonstrated validity with SCD populations USA and UK; several publications.
Children
None
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.
CSQ-SCD Children
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".
None
SCDO (Jade Hotchkiss)
Corticosteroid-Induced Adverse 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).
None
SCDO (Jade Hotchkiss)
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.
http://purl.bioontology.org/ontology/MESH/D017281
Sufficient
SCDO:0000294
MESH:D017281
Burden of Illness
Cost of Disease
Cost of Sickness
Costs of Disease
Disease Cost
Disease Costs
Economic Burden of Disease
Sickness Cost
Cost of Illness
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".
http://www.medicine.ox.ac.uk/bandolier/painres/download/whatis/Cost-effect.pdf
Negligable
Health Care Economics
Health Economics
Cost-Effectiveness of Healthcare
A bioassay to measure the serum concentration of creatinine, a metabolite of muscle creatine that is filtered out of blood by the kidneys.
Sufficient
SCDO:0000296
phenX:141400
Blood Creatinine Assay
Blood Creatinine Test
Serum Creatinine
Serum Creatinine Assay
Creatinine Blood Test
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)
http://purl.bioontology.org/ontology/MESH/D003419
Sufficient
SCDO:0000297
MESH:D003419
Crisis Interventions
Interventions, Crisis
Crisis Intervention
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.
http://purl.bioontology.org/ontology/MESH/D003430
Sufficient
SCDO:0000298
MESH:D003430
Cross-Sectional Analysis
Cross-Sectional Study
Cross-Sectional Studies
A collective expression for all behaviour patterns acquired and socially transmitted through symbols. Culture includes customs, traditions, and language.
http://purl.bioontology.org/ontology/MESH/D003469
Sufficient
SCDO:0000299
MESH:D003469
Cultural Beliefs
Cultural Values
Culture
Therapeutics relating to or used in the cure of diseases.
Request inclusion into relevant ontology
None
SCDO
http://www.merriam-webster.com/dictionary/curative
Curative Therapeutics
The length of time that a person has lived since their birth up until the current day.
Few but available definitions not adequate
SCDO (Jade Hotchkiss)
Current Chronological Age
Current Age
The respondent's highest level of education at the current time.
Request inclusion into MESH below "Socioeconomic Factors".
Few but definitions not freely available
Educational Attainment
Current Educational Attainment
The respondent's current employment status.
PhenX protocol: Current Employment Status #11301
Sufficient
SCDO:0000306
phenX:11301
Employment Status
Current Employment Status
The respondent's current marital status.
Can add sub-classes of "Marital Status" from MESH.
PhenX protocol: Current Marital Status #10902
Sufficient
SCDO:0000307
phenX:10902
Marital Status
Marital or Partnership Status
Current Marital Status
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.
http://purl.bioontology.org/ontology/MESH/D055316
http://www.ebi.ac.uk/efo/EFO_0004617
Suggest update to description in CMO
CMO:0002777
Blood CC Level
Cystatin 3 Level
Gamma Trace Level
Gamma-Trace Level
Neuroendocrine Basic Polypeptide Level
Post Gamma Globulin Level
Post-Gamma-Globulin Level
Blood Cst3 Level
Blood Cystatin C Level
A blood disorder characterized by the appearance of sickle-shaped red blood cells and anemia.
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-
Sufficient
SCDO:0000311
ICD10CM:D57
D57
D57 Sickle-Cell Disorders
Broad term used to describe several different acute conditions occurring with sickle cell disease, including aplastic crisis, hemolytic crisis, and vasoocclusive crisis.
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.0
Sufficient
SCDO:0000312
ICD10CM:D57.0
D57.0
Hb-SS disease with vasoocclusive pain
Sickle cell anemia with crisis
Sickle cell anemia with vasoocclusive pain
D57.0 Hb-SS disease with crisis
-
Few but definitions not available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.01
ICD10CM:D57.01
D57.01
Hb-SS disease with acute chest syndrome
Sickle cell anemia with acute chest syndrome
Sickle cell anemia, acute chest syndrome
D57.01 Hb-SS disease with acute chest syndrome
-
Few but definitions not available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.02
ICD10CM:D57.02
Acute sickle cell splenic sequestration crisis
D57.02
Hb-SS disease with splenic sequestration
Sickle cell anemia acute crisis splenic sequestration
D57.02 Hb-SS disease with splenic sequestration
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.1
ICD10CM:D57.1
D57.1
Sickle cell anemia without crisis
Sickle-cell disease without crisis
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.
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.2
Sufficient
SCDO:0000316
ICD10CM:D57.2
D57.2
D57.2 Sickle-cell/Hb-C disease
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.20
ICD10CM:D57.20
D57.20
Sickle Cell Disease-SC without crisis
Sickle-cell/Hb-C disease without crisis
D57.20 Sickle-cell/Hb-C disease without crisis
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.21
ICD10CM:D57.21
D57.21
Sickle Cell Disease-SC with crisis
Sickle-cell/Hb-C disease with crisis
D57.21 Sickle-cell/Hb-C disease with crisis
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.211
ICD10CM:D57.211
Acute chest syndrome due to sickle cell-hemoglobin c disease crisis
Acute chest syndrome sickle cell hb-c crisis
D57.211
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
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.212
ICD10CM:D57.212
D57.212
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
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.219
ICD10CM:D57.219
D57.219
Sickle Cell Disease-SC with crisis NOS
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.
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.3
Sufficient
SCDO:0000322
ICD10CM:D57.3
D57.3
D57.3 Sickle-cell trait
Hemolytic anemia, in which patients are heterozygous for both the sickle cell gene and a thalassemia gene.
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.4
Sufficient
SCDO:0000323
ICD10CM:D57.4
D57.4
D57.4 Sickle-cell thalassemia
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.40
ICD10CM:D57.40
D57.40
D57.40 Sickle-cell thalassemia without crisis
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.41
ICD10CM:D57.41
D57.41
Sickle-cell thalassemia with (painful) crisis
Sickle-cell thalassemia with crisis
Sickle-cell thalassemia with vasoocclusive pain
D57.41 Sickle-cell thalassemia, unspecified, with crisis
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.411
ICD10CM:D57.411
D57.411
Sickle-cell thalassemia, unspecified, with acute chest syndrome
D57.411 Sickle-cell thalassemia, unspecified, with acute chest syndrome
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.412
ICD10CM:D57.412
D57.412
Sickle cell thalassemia with splenic sequestration
Sickle-cell thalassemia, unspecified, with splenic sequestration
D57.412 Sickle-cell thalassemia, unspecified, with splenic sequestration
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.419
ICD10CM:D57.419
D57.419
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
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.8
ICD10CM:D57.8
D57.8
Other sickle-cell disorders
D57.8 Other sickle-cell disorders
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.80
ICD10CM:D57.80
D57.80
D57.80 Other sickle-cell disorders without crisis
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.81
ICD10CM:D57.81
D57.81
D57.81 Other sickle-cell disorders with crisis
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.811
ICD10CM:D57.811
D57.811
D57.811 Other sickle-cell disorders with acute chest syndrome
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.812
ICD10CM:D57.812
D57.812
D57.812 Other sickle-cell disorders with splenic sequestration
-
Few but definitions not freely available
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.819
ICD10CM:D57.819
D57.819
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: []]'
https://ghr.nlm.nih.gov/primer/howgeneswork/protein
obsolete Protein Molecule
true
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.
Sufficient
SCDO:0000343
ORPHA:231237
Delta Beta Thalassaemia
Delta-Beta-Thalassaemia
Delta-Beta-Thalassemia
F Thalassaemia
Delta Beta Thalassemia
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.
http://purl.bioontology.org/ontology/MESH/D055538
Sufficient
SCDO:0000344
MESH:D055538
Delta Thalassaemia
Delta Thalassaemias
Delta Thalassemias
Delta-Thalassaemia
Delta-Thalassaemias
Delta-Thalassemia
Delta 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.
http://purl.bioontology.org/ontology/MESH/D003715
Sufficient
SCDO:0000346
MESH:D003715
Break Bone Fever
Break-Bone fever
Breakbone Fever
Dengue
Dengue Fever
'The system pertaining to teeth, oral cavity, and associated structures. [Curator team: []]'
http://medical-dictionary.thefreedictionary.com/dentistry
deprecated Dental System
true
Terms that are no longer being used in the ontology.
deprecated terms
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.
http://www.who.int/topics/depression/en/
Sufficient
SCDO:0000360
SIO:000824
Depressive Symptoms
Low Mood
Depression
Skill in performing tasks, especially with the hands.
Request inclusion into relevant ontology
http://en.oxforddictionaries.com/definition/dexterity
Few but definitions not freely available
SCDO
Dexterity
A medical device used to diagnose medical conditions.
http://purl.obolibrary.org/obo/ERO_0001448
Sufficient
SCDO:0000376
ERO:0001448
Diagnostic Device
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.
Request inclusion into relevant ontology.
None
SCDO (Jade Hotchkiss)
Diagnostics
A non-steroidal anti-inflammatory agent (NSAID) with antipyretic and analgesic actions. It is primarily available as the sodium salt.
Sufficient
SCDO:0000380
MESH:D004008
2-((2,6-dichlorophenyl)amino)benzeneacetic acid
Diclofenac Acid
Orthofen
[2-(2,6-dichloroanilino)phenyl]acetic acid
Diclofenac
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?
http://purl.bioontology.org/ontology/MESH/D000066888
Sufficient
SCDO:0000382
MESH:D000066888
Diet, Food, and Nutrition
obsolete Diffusion Capacity by Biochemical Methods
true
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.
http://purl.bioontology.org/ontology/MESH/D011653
Sufficient
SCDO:0000384
MESH:D011653
Alveolar membrane diffusion capacity
DL
Diffusing Capacity
Membrane diffusion capacity
Pulmonary Diffusing Capacity
Diffusion Capacity of Lung
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
Suggest update to label
phenX:810301
Pulmonary Diffusing Capacity Test
Diffusion Capacity Test
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.
Multiple countries and cultural groups
Self; Proxy
All
WHO Global Burden of Disease assessment, also used in SCD studies
Children and adults
no
Few but definitions not specific enough
DALY
Disability-Adjusted Life Year
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.
Disability-Adjusted Life Year (DALY)
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.
http://purl.bioontology.org/ontology/MESH/D004190
Sufficient
SCDO:0000388
MESH:D004190
Disasters
Natural Disaster
Natural Disasters
Disaster
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.
Request inclusion into relevant ontology
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.
None
SCDO (Jade Hotchkiss)
Phenotypic Modifier
Disease Modifier
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.
Request inclusion into relevant ontology
None
SCDO (Clair Ingram)
Doppler Ultrasound Machine - 2 Megahertz
An adverse event that has an outcome of a decreased amount of the drug excreted by the body.
http://purl.obolibrary.org/obo/OAE_0000887
Sufficient
SCDO:0000397
OAE:0000887
Drug Clearance Decreased AE
An adverse drug event that results in the development of a dependence on the drug.
http://purl.obolibrary.org/obo/OAE_0000888
Sufficient
SCDO:0000398
OAE:0000888
Drug Dependence AE
The amount of drug substances taken into the body.
This seemed an obvious addition to the modifier class?
None
SCDO (Jade Hotchkiss)
Drug Intake
A drug AE that has an outcome of lower threshold to the normal pharmacologic action of a drug.
http://purl.obolibrary.org/obo/OAE_0000891
Sufficient
SCDO:0000400
OAE:0000891
Drug Intolerance AE
An adverse event that results in symptoms that occur after the discontinuation of the use of a certain drug.
http://purl.obolibrary.org/obo/OAE_0000893
Sufficient
SCDO:0000401
OAE:0000893
Drug Withdrawal Syndrome AE
A neuropathy AE that is induced by a drug administration.
http://purl.obolibrary.org/obo/OAE_0000165
Sufficient
SCDO:0000402
OAE:0000165
Drug-Induced Neuropathy AE
'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: []]'
http://medical-dictionary.thefreedictionary.com/ear+nose+and+throat
Otolaryngology
deprecated Ear, Nose and Throat
true
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.
Suggest update to description
HP:0031364
Ecchymoses
Ecchymosis
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.
http://purl.obolibrary.org/obo/ERO_0000385
Sufficient
SCDO:0000409
ERO:0000385
Cardiac ECHO
Cardiac US Scan
Diagnostic Ultrasound of Heart
Echocardiographic procedure
Echocardiography
US Scan of Heart
Ultrasonic cardiography
Ultrasonography of Heart
Ultrasound of Heart
Echocardiogram
A machine used for ultrasonic recording of the size, motion, and composition of the heart and surrounding tissues.
Request inclusion into relevant ontology.
http://purl.bioontology.org/ontology/MESH/D004452
None
SCDO (Jade Hotchkiss)
Echocardiography Machine
Acquisition of knowledge as a result of instruction in a formal course of study.
http://purl.bioontology.org/ontology/MESH/D004493
Sufficient
SCDO:0000414
MESH:D004493
Schooling
Education
The visual output that an electrocardiograph produces.
Suggest update to description in ERO?
http://en.wiktionary.org/wiki/electrocardiogram
Suggest update to description
ERO:0000383
ECG
EKG
Electrocardiogram
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.
http://bioportal.bioontology.org/ontologies/CRISP/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCSP%2F1393-7164
Sufficient
SCDO:0000416
CRISP:1393-7164
Ambulatory Electrocardiographic Monitor
Electrocardiocorder
Electrocardiographic Monitor
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.
Sufficient
SCDO:0000417
MESH:D004562
Electrocardiography
A graphic record of the electrical activity of the brain as recorded by an electroencephalograph.
Request inclusion into relevant ontology
http://medical-dictionary.thefreedictionary.com/electroencephalogram
Few but definitions not freely available
Electroencephalogram
An instrument that measures electrical potentials on the scalp and generates a record of the electrical activity of the brain.
Request inclusion into relevant ontology
http://medical-dictionary.thefreedictionary.com/electroencephalograph
Few but definitions not freely available
Encephalograph
Electroencephalograph
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.
http://purl.bioontology.org/ontology/MESH/D004569
Sufficient
SCDO:0000420
MESH:D004569
EEG
Electroencephalography
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.
http://purl.bioontology.org/ontology/MESH/D057286
Sufficient
SCDO:0000423
MESH:D057286
Computerized Health Records
Computerized Medical Records
Electronic Health Record
Electronic Medical Record
Electronic Medical Records
Electronic Health Records
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.
http://purl.bioontology.org/ontology/MESH/D004586
Sufficient
SCDO:0000424
MESH:D004586
Electrophoresis
The system pertaining to the stomach, intestines, and associated organs including liver, gallbladder, and pancreas.
http://medical-dictionary.thefreedictionary.com/gastroenterology
Gastroenterology
deprecated Endocrine and Metabolic
true
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?
None
SCDO (Jade Hotchkiss)
Environmental Disease Modifier
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.
http://purl.bioontology.org/ontology/MESH/D057075
Sufficient
SCDO:0000436
MESH:D057075
Enzyme Assay
Enzymatic Assay
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.
Term to be adapted as necessary to match EDDA Study Designs Taxonomy
http://purl.bioontology.org/ontology/MESH/D016021
Sufficient
SCDO:0000437
MESH:D016021
Epidemiological Studies
Epidemiologic Studies
Types and formulations of studies used in epidemiological and clinical research.
Term to be adapted as necessary to match EDDA Study Designs Taxonomy
http://purl.bioontology.org/ontology/MESH/D016020
MESH:D016020
Epidemiologic Study Characteristics
deprecated Epidemiologic Study Characteristics as Topic
true
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).
Sufficient
SCDO:0000440
phenX:130401
Epilepsy Screener
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.
Request inclusion into NCIT below "Research or Clinical Assessment Tool".
Goldberg, David; Hillier, Valerie (1979). "A scaled version of the General Health Questionnaire". Psychological Medicine. Cambridge University Press. 9 (01): 139–145.
Few but definitions not freely available
SCDO
GHQ
General Health Questionnaire (GHQ)
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.
Few but definitions not specific enough
NCIT:C88893
GAD-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.
http://purl.bioontology.org/ontology/MESH/D005817
Sufficient
SCDO:0000443
MESH:D005817
Prenatal Genetic Counseling
Genetic Counseling
A biological disease modifier that is of a genetic nature.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Genetic Disease Modifier
Organized services to provide diagnosis, treatment, and prevention of genetic disorders.
http://purl.bioontology.org/ontology/MESH/D033142
Sufficiient
MESH:D033142
Genetic Services
Genetic Service
Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.
This and its sub-classes need work!
http://purl.bioontology.org/ontology/MESH/D005821
Sufficient
SCDO:0000448
MESH:D005821
Genetic Technic
Genetic Technics
Genetic Techniques
Genetic Technique
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.
Ballas et al 2010 Am J Hematol
None
Glaucomas
Glaucoma (Secondary to Presence of Blood in the Anterior Chamber of the Eye)
A test to assess the respondent's overall mental capability.
Sufficient
SCDO:0000455
phenX:130700
Global Mental Status Screener
A genetic locus responsible for the encoding of globins.
Request inclusion into relevant ontology, perhaps below "Genetic Locus" in MESH.
None
SCDO (Jade Hotchkiss)
Globin Locus
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.
http://www.ebi.ac.uk/efo/EFO_0005208
Sufficient
SCDO:0000457
EFO:0005208
GFR
Glomerular Filtration Rate
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.
Exists in other ontologies but we have provided a description more relevant to its relationship with SCD.
http://www.ncbi.nlm.nih.gov/gene/2539
Not relevant to context of sickle cell
G-6-PD
G6PD1
Glucose-6-Phosphate 1-Dehydrogenase Gene
Glucose-6-Phosphate Dehydrogenase Gene
G6PD
A deficiency or slowing down of growth pre- and postnatally greater than two standard deviations from the age- and sex-related normal.
Suggest update to description in HPO.
http://purl.obolibrary.org/obo/HP_0001510
Suggest update to description
HP:0001510
Delayed Growth
Growth Deficiency
Growth Failure
Growth Retardation
Poor Growth
Retarded Growth
Growth Delay
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").
Suggest update to label
phenX:10801
Haptoglobin Blood Test
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
Sufficient
SCDO:0000487
APAONTO:Health_Behavior
Health Behavior
Health Behaviour
People's beliefs about health problems, perceived benefits of action and barriers to action, and self-efficacy.
Not relevant to context of sickle cell
Health-Belief Model
The health belief model suggests that health beliefs explain engagement (or lack of engagement) in health-promoting behaviour.
Health Beliefs
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.
Request inclusion into relevant ontology
None
Health Care Resources
Healthcare Resources
Health Financing
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
Negligable
Also applicable to a population not just to an individual.
Health Insurance Coverage
Degree to which individuals have the capacity to obtain, process and understand basic health information and services needed to make appropriate health decisions.
http://purl.bioontology.org/ontology/MESH/D057220
Sufficient
SCDO:0000491
MESH:D057220
Knowledge about Sickle Cell Disease
Genetic Counseling
Health Literacy
Health data accessible to the patient and others.
http://purl.bioontology.org/ontology/MESH/D055991
Sufficient
SCDO:0000492
MESH:D055991
Health Records, Personal
Personal Health Information
Personal Health Record
Personal Health Records
Personal Medical Record
Personal Medical Records
Health Records
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.
Few but definitions not specific enough
Health Care Service Utilization
Health Care Utitlization
Healthcare Utitlization
Health Service Utilization
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
http://www.euro.who.int/en/health-topics/Health-systems/pages/health-systems
Suggest update to description
Health Care Delivery
Health Care System
Health Care Systems
Health System
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.
Request inclusion into relevant ontology
http://www.ncbi.nlm.nih.gov/pubmed/7674256
None
Health Utility Index
Health Utility Measure
Health Utility
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
Negligable
SCDO
Access to Healthcare
Health Care Access
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.
Healthcare Access
Dietary patterns which have been found to be important in reducing disease risk.
http://purl.bioontology.org/ontology/MESH/D000072001
Sufficient
SCDO:0000497
MESH:D000072001
Healthy Eating
Healthy Diet
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.
http://purl.bioontology.org/ontology/MESH/D000070497
Sufficient
SCDO:0000498
MESH:D000070497
Healthy Life Style
Healthy Lifestyle
Examinations used to diagnose and treat heart conditions.
http://purl.bioontology.org/ontology/MESH/D006334
Sufficient
SCDO:0000500
MESH:D006334
Heart Function Tests
Pulmonary Function Test
Heart Function Test
The number of times the heart ventricles contract per unit of time, usually per minute.
http://www.ebi.ac.uk/efo/EFO_0004326
Sufficient
SCDO:0000501
EFO:0004326
Heart Beat
Pulse
Pulse Rate
Heart Rate
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"
None
SCDO (Jade Hotchkiss)
Heart Valve Measurement
A measurement device used to perform complete blood counts, erythrocyte sedimentation rates (ESRs), or coagulation tests.
http://purl.obolibrary.org/obo/ERO_0000494
Sufficient
SCDO:0000504
ERO:0000494
Haematology Analyser
Hematology Analyzer
A test to detect potential blood disorders or diseases in people who do not have any symptoms of disease.
Request inclusion into relevant ontology.
Few but definitions not freely available
Haematology Screening Test
Hematology Screening Test
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.
http://purl.bioontology.org/ontology/MESH/D018380
Sufficient
SCDO:0000506
MESH:D018380
BMT
Bone Marrow Transplant
Hematopoietic SCT
Hematopoietic Stem Cell Transplantation
The blood-making organs and tissues, principally the bone marrow and lymph nodes.
http://purl.bioontology.org/ontology/MESH/D006413
MESH:D006413
deprecated Hematopoietic System
true
Presence of blood in the urine.
http://purl.bioontology.org/ontology/MESH/D006417
Sufficient
SCDO:0000508
MESH:D006417
Blood in Urine
Hematurias
Hematuria
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")
http://www.ncbi.nlm.nih.gov/gene/3162
Suggest update to description
HMOX1 Gene
HO-1
HO1 Gene
Heat Shock Protein, 32-kD Gene
Heme Oxygenase (Decycling) 1 Gene
Heme Oxygenase 1 gene
Hemeoxygenase 1 Gene
Hemoxygenase-1 Gene
HMOX1
Organs involved in the production of BLOOD, including the cellular and the molecular components essential in providing defense against foreign organisms or substances.
obsolete Hemic and Immune Systems
true
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.
http://purl.bioontology.org/ontology/MESH/D006444
Sufficient
SCDO:0000513
MESH:D006444
Hb C
HbC
HbC Hemoglobin
Hemoglobin C
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.
http://purl.bioontology.org/ontology/MESH/D006451
Sufficient
SCDO:0000514
MESH:D006451
Haemoglobin S
Hb S
HbS
HbS Haemoglobin
HbS Hemoglobin
Sickle Haemoglobin
Sickle Hemoglobin
Hemoglobin S
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.
http://purl.bioontology.org/ontology/MESH/D006447
Sufficient
SCDO:0000515
MESH:D006447
Hb H
HbH
HbH Hemoglobin
Hemoglobin H
None
deprecated Hemoglobin A2 Profile
true
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.
http://purl.obolibrary.org/obo/HP_0005507
Suggest update to description
HP:0005507
Haemoglobin Bart's
Haemoglobin Barts
Hb Bart's
Hb Barts
Hemoglobin Bart's
Hemoglobin Barts
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.
http://www.orpha.net/ORDO/Orphanet_163596
Suggest update to description
Orphanet:163596
Alpha-Thalassemia Hydrops Fetalis
Alpha-Thalassemia Major
Haemoglobin Barts Hydrops Fetalis
Hb Barts
Hb Barts Syndrome
Hemoglobin Bart's Hydrops Fetalis
Hemoglobin Barts Hydrops Fetalis Syndrome
Homozygous Alpha 0-Thalassemia
Hemoglobin Barts Hydrops Fetalis
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.
Suggest update to description in NCIT
http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-C
Suggest update to description
NCIT:C34675
Haemoglobin C Disease
Hb C-Disease
Hemoglobin C Disease
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".
http://www.sickle-thal.nwlh.nhs.uk/blood/haemoglobinc.aspx
Few but definitions not freely available
Haemoglobin C-A Disorder
Hb AC
Hemoglobin C-A Disorder
Heterozygous for Hb C
Hemoglobin C 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.'
The description could be more detailed.
http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=GB&Expert=231242
Hb C-Beta Thalassemia Syndrome
Hemoglobin C Beta-Thalassemia
deprecated Hemoglobin C-Beta Thalassemia
true
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.
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C103845
Suggest update to label and description
NCIT:C103845
Haemoglobin Variant Observation
Haemoglobin Variant Test
Haemoglobinopathy Screen
Hemoglobin Variant Measurement
Hemoglobin Variant Observation
Hemoglobinopathy Screen
Hemoglobin Variant Test
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).
Suggest update to description in ORDO
http://www.doh.wa.gov/Portals/1/Documents/5220/HbDFactSheet.pdf
Suggest update to description
DOID:5378
Hb DD
Homozygous Hemoglobin D
Hemoglobin D Disease
The inheritance of the gene for hemoglobin D from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent.
Request inclusion into NCIT below "Hemoglobin Trait".
http://www.doh.wa.gov/Portals/1/Documents/5220/HbDFactSheet.pdf
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Hb AD
Hemoglobin D Trait
'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.'
http://www.doh.wa.gov/Portals/1/Documents/5220/HbDFactSheet.pdf
HbD - BT
Hemoglobin D Beta-Thalassemia
deprecated Hemoglobin D-Beta Thalassemia
true
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".
Few but definitions not freely available
Hemoglobin D (badan)
Hemoglobin D-Ibadan
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".
http://health.utah.gov/nsp/Disorders/HB/Hb_D_Disease_DD/FactSheet_Provider_HbDD_En.pdf
Few but definitions not freely available
Haemoglobin D-Punjab
Hb D-Los Angelese
Hb D-Punjab
Hemoglobin D (Chicago)
Hemoglobin D (Los Angeles)
Hemoglobin D (North Carolina)
Hemoglobin D (Portugal)
Hemoglobin D (Punjab)
Hemoglobin Oak Ridge
Hemoglobin D-Punjab
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
SCDO:0001065
http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-and-other-than-A-C-D-E-F-H-O-Arab-S
deprecated Hemoglobin Disease Other than C,D,E,F,H,O-Arab,S
true
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.
http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-E
Sufficient
SCDO:0000530
ORPHA:2133
Haemoglobin E Disease
Hb E-Disease
Hemoglobin E Disease
The inheritance of the gene for hemoglobin E from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent.
Request inclusion into NCIT below "Hemoglobin Trait".
http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-A-E
Few but definitions not freely available
SCDO
Hb AE
Hb E Trait
Hb E-carriers generally do not have any signs or symptoms related to abnormal hemoglobin.
Hemoglobin E Trait
'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).'
http://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=19177&Disease_Disease_Search_diseaseGroup=Hemoglobin-D-Beta-Thalassemia&Disease_Disease_Search_diseaseType=Pat&Disease(s)/group%20of%20diseases=Hemoglobin-E-beta-thalassemia-syndrome&title=Hemoglobin-E-beta-thalassemia-syndrome&search=Disease_Search_Simple
Haemoglobin E-Beta Thalassemia
Hemoglobin E Beta-Thalassemia
deprecated Hemoglobin E-Beta Thalassemia
true
The score of fetal hemoglobin (Hb F) in the blood of an individual.
Description not clear enough.
None
SCDO (Gaston K Mazandu)
deprecated Hemoglobin F Profile
true
A variant of Hemoglobin Lepore Syndrome.
http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome
Hb Lepore Baltimore
obsolete Hemoglobin Lepore Baltimore
true
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.
Request inclusion into relevant ontology
http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome
None
Hb Lepore Boston Syndrome
Hb Lepore Washington Syndrome
Hb Lepore Washington-Boston Syndrome
Hemoglobin Lepore Boston-Washington
Hemoglobin Lepore Washington Syndrome
Hemoglobin Lepore Washington-Boston Syndrome
Hemoglobin Lepore Boston Disease
A variant of Hemoglobin Lepore Syndrome.
http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome
Hb Hollandia
obsolete Hemoglobin Lepore Hollandia
true
The inheritance of the gene for hemoglobin Lepore from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent.
Request inclusion into relevant ontology
http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Heterozygous Hb Lepore
Hemoglobin Lepore Trait
'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.
Hb Lepore-B-Thalassaemia
Hemoglobin Lepore-B-Thalassaemia
Hemoglobin Lepore-Beta Thalassaemia Syndrome
deprecated Hemoglobin Lepore-Beta Thalassaemia
true
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.
Suggest update to description in MESH
http://medlineplus.gov/ency/article/000562.htm
Few but definitions not available
SCDO (Jade Hotchkiss)
Autosomal Dominant Congenital Methemoglobinemia Type II
Autosomal Dominant Hereditary Methemoglobinemia Type II
Hereditary MetHb Type II
Hereditary Methemoglobinemia Type II
M Hemoglobinopathy
Second Form of Inherited MetHb
Hemoglobin M Disease
Hemoglobin M Disease is autosomal dominant, thus does not seem to have a "trait" condition.
Requires definition and source.
None
obsolete - Hemoglobin M Trait
true
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.
Request inclusion into relevant ontology
http://onlinelibrary.wiley.com/doi/10.1002/pbc.24414/pdf
None
Hb O-Arab Disease
Homozygous Hb O-Arab
Homozygous Hemoglobin O-Arab
Hemoglobin O-Arab Disease
The inheritance of hemoglobin O-Arab from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent.
Request inclusion into NCIT below "Hemoglobin Trait".
http://onlinelibrary.wiley.com/doi/10.1002/pbc.24414/pdf
Few but definitions not freely available
Hb A/O-Arab
Hb AO-Arab
Heterozygous Hb O-Arab
Heterozygous Hemoglobin O-Arab
Hemoglobin O-Arab Trait
The type and relative amounts of various normal and abnormal hemoglobin types.
Request inclusion into relevant ontology.
http://labtestsonline.org/understanding/analytes/sickle/tab/test/
None
SCDO
Hemoglobin Profile
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
Sufficient
SCDO:0000547
phenX:830301
Haemoglobin Characterization
Haemoglobinopathy Screen
Hb Electrophoresis Plus Solubility
Hemoglobin Characterization
Hemoglobin Electrophoresis
Hemoglobin Electrophoresis plus Solubility
Hemoglobin Fractionation
Hemoglobinopathy Evaluation
Hemoglobinopathy Evaluation Profile Blood Test
Hemoglobinopathy Fractionation Profile Blood Test
Hemoglobinopathy Screen
Hemoglobin Profile Assay
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.
http://www.questdiagnostics.com/testcenter/TestDetail.action?ntc=31852
Few but definitions not freely available
SCDO (Clair Ingram)
Hemoglobin S Measurement
Sickle Cell Identification
Hemoglobin S Test
The inheritance of one of the faulty genes that causes thalassemia.
Request inclusion into relevant ontology
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Thalassemia Trait
An inherited disorder of the structure and/or synthesis of hemoglobin, with a variable phenotype expression ranging from benign to severe.
Suggest update to description in NCIT
Suggest update to description
NCIT:C3092
Hemoglobinopathy
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.
Anemia due to Toms River Hemoglobin
Transient Neonatal Cyanosis
obsolete Hemoglobinopathy Toms River
true
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".
http://en.wikipedia.org/wiki/Liver_span
None
Liver Span
Hepatic Span
A test for Hepatitis B Virus.
Which Hepatitis B Test is to be referred to here? (There are various different types below "Immunology Test" in the "Sage Bionetworks Synapse Ontology")
HBV Test
Hepatitis B Virus Test
obsolete Hepatitis B Test
true
A test for Hepatitis C Virus.
Is this test for viral load measurement or or antibody measurement? (See terms below "Immunology Test" in the "Sage Bionetworks Synapse Ontology")
obsolete Hepatitis C Test
true
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).
http://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=3290&disease=Hereditary-methemoglobinemia&search=Disease_Search_Simple
Sufficient
SCDO:0000559
ORPHA:621
Congenital Methemoglobinemia
HM
Hereditary MetHb
Hereditary Methemoglobinemia
Replacement of the hip joint.
http://purl.bioontology.org/ontology/MESH/D019644
Sufficient
SCDO:0000564
MESH:D019644
Hip Prosthesis Implantation
Hip Replacement Arthroplasty
Hip Replacements, Total
Replacement Arthroplasties, Hip
Total Hip Replacement
Hip Replacement Arthroplasty
A study that compares a group of participants receiving an intervention with a similar group from the past who did not.
http://purl.bioontology.org/ontology/MESH/D065386
Sufficient
SCDO:0000565
MESH:D065386
Historically Controlled Study
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
Suggest update to label
phenX:130600
History of Head Trauma Questionnaire
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
Suggest update to label
phenX:140600
History of Kidney Failure Questionnaire
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
Suggest update to label
phenX:130300
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
Suggest update to label
phenX:140500
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.
Also below "Immunochemical Assay"?
Few but definitions not freely available
HIV Assay
Human Immunodeficiency Virus Assay
Human Immunodeficiency Virus Test
HIV Test
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
multiple
Patient Reported Outcome
Clinic Patients
Widely used around the world, also used in SCD
Adults (18 to 91 years)
Few but definitions not specific enough
NCIT:C103520
HADS
HADS Questionnaire
HADS01
Hospital Anxiety and Depression Scale
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?
http://purl.bioontology.org/ontology/MESH/D006760
Sufficient
SCDO:0000573
MESH:D006760
Hospital Admission
Hospitalisation
Hospitalisations
Hospitalizations
Hospitalization
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
Negligable
phenX:11400
Household Roster-Relationships
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)
Suggest update to description
NCIT:C66896
Hydration Therapy
An antineoplastic agent that inhibits DNA synthesis through the inhibition of ribonucleoside diphosphate reductase.
Sufficient
SCDO:0000580
MESH:D006918
Hydrea
Hydroxycarbamide
Oncocarbide
Hydroxyurea
A causal adverse drug event that is induced by hydroxyurea.
Request inclusion into OAE below "Causal Adverse Drug Event".
None
SCDO (Jade Hotchkiss)
Hydroxyurea-Induced Adverse Event
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.
None
SCDO (Jade Hotchkiss)
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.
None
SCDO (Jade Hotchkiss)
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).
http://purl.bioontology.org/ontology/MESH/D006947
Sufficient
SCDO:0000588
MESH:D006947
High Blood Potassium Levels
Hyperkalemias
Hyperpotassemia
Hyperpotassemias
Hyperkalemia
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.
Sufficient
SCDO:0000593
MESH:D017495
Hypermelanoses
Hypermelanosis
Hyperpigmentation of the skin
Skin Hyperpigmentation
Hyperpigmentation
Drugs used to induce drowsiness or sleep or to reduce psychological excitement or anxiety.
http://purl.bioontology.org/ontology/MESH/D006993
Sufficient
SCDO:0000598
MESH:D006993
Hypnotics
Sedatives
Sedatives and Hypnotics
Hypnotics and Sedatives
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.
https://www.cdc.gov/nchs/icd/icd10cm.htm
https://www.findacode.com/icd-10-cm/icd-10-cm-diagnosis-codes-set.html
None
ICD-10-CM Diagnosis Codes
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.
Request inclusion into NCIT below "Research or Clinical Assessment Tool".
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.
multiple
Patient Reported Outcome
Clinic Patients
many
Good psychometric properties, widely used around the world, has been translated into several languages.
Adults
None
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.
IPQ-R
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.
http://purl.bioontology.org/ontology/MESH/D007107
MESH:D007107
deprecated Immune System
true
An assay that identifies a substance (especially a protein) by its action as an antigen.
Request inclusion into relevant ontology
None
Immunochemical Assay
A drug adverse event that has an outcome of decreased levels of immunosuppressant drugs in the patient's body.
http://purl.obolibrary.org/obo/OAE_0001071
Sufficient
SCDO:0000618
OAE:0001071
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"?
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C106536
None
Immunoturbidimetry Test
Immunoturbidimetry Assay
Substances causing insects to turn away from them or reject them as food.
http://purl.bioontology.org/ontology/MESH/D007302
Sufficient
SCDO:0000643
MESH:D007302
Insect Repellents
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).
Life stage: Infant, Toddler, Child
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.
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820504
PhenX protocol: Intelligence Scale - Birth to 3.5 years #820504
Suggest update to description
NCIT:C99150
Bayley Scale of Infant Development III
Bayley Scales of Infant and Toddler Development, Third Edition
Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III)
Bayley-III
Intelligence Scale - Birth to 3.5 years
An adverse drug event that results in the intentional use of a drug in the wrong way (recreationally etc).
http://purl.obolibrary.org/obo/OAE_0001093
Sufficient
SCDO:0000650
OAE:0001093
Intentional Drug Misuse AE
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.
http://purl.bioontology.org/ontology/MESH/D065186
Sufficient
SCDO:0000651
MESH:D065186
ITS Studies
Interrupted Time Series Analysis
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.
Intracerebral Bleeding
deprecated-Intracerebral Haemorrhage
true
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.
Suggest update to description
DOID:4723
Craniospinal Hypotension
Decreased Intracranial Pressure
Intracranial Hypotension
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?
http://medical-dictionary.thefreedictionary.com/intraosseous
http://www.ncbi.nlm.nih.gov/pubmed/6456552
None
IOP
Intraosseous Pressure
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"?
http://purl.bioontology.org/ontology/MESH/D007511
Sufficient
SCDO:0000665
MESH:D007511
Ischemias
Ischemia
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.
http://purl.bioontology.org/ontology/MESH/D007525
Sufficient
SCDO:0000666
MESH:D007525
Electrofocusing
IEF
Isoelectric Focusing
Laboratory tests used to evaluate how well the kidneys are working through examination of blood and urine.
http://purl.bioontology.org/ontology/MESH/D007677
Sufficient
SCDO:0000676
MESH:D007677
Kidney Function Tests
Renal Function Test
Renal Function Tests
Kidney Function Test
A specialized area of medicine in which exercise and movement are used as the primary form of rehabilitation.
Request inclusion into relevant ontology
http://medical-dictionary.thefreedictionary.com/kinesiotherapy
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Kinesiotherapy
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.
https://www.ncbi.nlm.nih.gov/mesh/?term=base%2C+knowledge;
https://www.ncbi.nlm.nih.gov/pubmed/20353928
None
SCDO
Knowledge about Sickle Cell Disease
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"?
Few but definitions not freely available
SCDO (Jade Hotchkiss)
LD Level
LDH Level
Lactate Dehydrogenase Levels
Lactic Acid Dehydrogenase Level
Normal and abnormal ranges given here: https://www.healthline.com/health/lactate-dehydrogenase-test#results
Lactate Dehydrogenase Level
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").
Suggest update to label
phenX:811001
LDH Test
Lactate Dehydrogenase Level Test
Lactic Acid Dehydrogenase Test
Lactate Dehydrogenase Test
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.
http://purl.bioontology.org/ontology/MESH/D007871
Sufficient
SCDO:0000685
MESH:D007871
Leg Ulcers
Leg Ulcer
Typical way of life or manner of living characteristic of an individual or group. (From APA, Thesaurus of Psychological Index Terms, 8th ed).
http://purl.bioontology.org/ontology/MESH/D008019
Sufficient
SCDO:0000689
MESH:D008019
Life Style
Lifestyle
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)
http://purl.bioontology.org/ontology/MESH/D008028
Sufficient
SCDO:0000691
MESH:D008028
Light Coagulations
Photocoagulation
Photocoagulations
Light Coagulation
Any process carried out to determine the condition of a patient's liver.
http://bioportal.bioontology.org/ontologies/IDODEN?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FIDODEN_0003652
Sufficient
SCDO:0000694
IDODEN:0003652
Liver Examination
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.
http://purl.bioontology.org/ontology/MESH/D007389
Sufficient
SCDO:0000698
MESH:D007389
Control Locus
External-Internal Control
Health Locus of Control
Internal-External Control
Sense of Control
Locus of Control
Studies in which variables relating to an individual or group of individuals are assessed over a period of time.
http://purl.bioontology.org/ontology/MESH/D008137
Sufficient
SCDO:0000699
MESH:D008137
Heart Study, Jackson
Longitudinal Studies
A sampling methodology using small sample sizes when conducting surveys in small geographical or population-based areas or lots.
http://purl.bioontology.org/ontology/MESH/D055810
Sufficient
SCDO:0000702
MESH:D055810
LQAS
Lot Quality Assurance Sampling
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.
http://purl.bioontology.org/ontology/MESH/D008176
Sufficient
SCDO:0000704
MESH:D008176
Lung Capacities
Lung Capacity
Lung Volume
Lung Volume Measurements
Lung Volume Measurement
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
Suggest update to label
phenX:810401
Lung Function - Lung Volume
Lung Volume Assay
Pulmonary Volume Assay
Pulmonary Volume Test
Lung Volume Test
'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: []]'
http://purl.obolibrary.org/obo/UBERON_0002465
UBERON:0002465
obsolete Lymphoid System
true
The use of drugs or other agents to prevent malarial infection. Examples: Proguanil, mefloquine, artesunate, insect repellant, insecticide-treated-bednet.
Request inclusion into relevant ontology
http://www.cdc.gov/malaria/travelers/drugs.html
Few but definitions not freely available
Malaria Prevention
Malaria Prophylaxis
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
http://www.dictionary.com/browse/manometer
Negligable
Manometer
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
Negligable
phenX:840101
Marital Status of Primary Caregiver
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
Suggest update to label
phenX:830100
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.
Request inclusion into NCIT below "Research or Clinical Assessment Tool".
J Health Psychol. 2016 May; 21(5): 808–820.
African-Americans
Patient Reported Outcome
Adults with Sickle Cell Disease
Adults 18 years and older
None
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
Measure of Sickle Cell Stigma
MoSCS
Measure of Sickle Cell Stigma (MoSCS)
The weight of the participant in kilograms.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Measured Weight
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.
Request inclusion into relevant ontology.
None
SCDO (Jade Hotchkiss)
Diagnostic Quantitative Measurement
Diagnostic Measurement
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.
Check and show which source was used for the description and whether the description was adapted from the source.
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.
Multiple countries and cultural groups
Self
Clinic patients
Adults 18 years and older
no
Suggest update to description
NCIT:C110969
MOS Social Support Survey
Medical Outcomes Study Social Support Survey
Medical Outcomes Study (MOS) Social Support Survey
Recording of pertinent information concerning patient's illness or illnesses.
http://purl.bioontology.org/ontology/MESH/D008499
Sufficient
SCDO:0000738
MESH:D008499
Medical Records
Voluntary cooperation of the patient in taking drugs or medicine as prescribed. This includes timing, dosage, and frequency.
http://purl.bioontology.org/ontology/MESH/D055118
Sufficient
SCDO:0000739
MESH:D055118
Medication Adherence
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
Negligable
SCDO (Jade Hotchkiss)
Medication Inventory
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)
http://purl.bioontology.org/ontology/MESH/D019122
Sufficient
SCDO:0000741
MESH:D019122
Transcendental Meditation
Meditation
A phospholipid-interacting antimalarial drug (antimalarials). It is very effective against plasmodium falciparum with very few side effects.
Sufficient
SCDO:0000742
MESH:D015767
Lariam
Mephloquine
WR142,490
Mefloquine
A type of glomerulonephropathy characterized by histology with thickening of the basement membrane and deposition of immune complexes in the subepithelial space.
Suggest update to description in HPO
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.
Suggest update to description
HP:0012578
MN
Membranous Glomerulopathy
Membranous Nephropathy
Emotional, psychological, and social well-being of an individual or group.
Sufficient
SCDO:0000746
MESH:D008603
Emotional Health
Mental Hygiene
Mental Health
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.
http://purl.bioontology.org/ontology/MESH/D017418
Sufficient
SCDO:0000747
MESH:D017418
Meta-Analysis
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)
http://purl.bioontology.org/ontology/MESH/D008660
None
MESH:D008660
Metabolic Function
Metabolic State
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)
http://purl.bioontology.org/ontology/MESH/D008708
Sufficient
SCDO:0000753
MESH:D008708
MetHb
Methemoglobinemia
'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?
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C18020
NCIT:C18020
Diagnostic Procedure
deprecated Diagnostic Method
true
A questionnaire to assess migraines and headaches.
Suggest update to label in PhenX (from "Migraine") as we have done.
Suggest update to label
phenX:130500
Headache Disability Questionnaire
Migraine Questionnaire
Transportable radiographic equipment allowing imaging services to be brought to the patient.
Request inclusion into relevant ontology
http://www.who.int/medical_devices/innovation/hospt_equip_26.pdf
https://radiologykey.com/mobile-radiography/
None
SCDO
Mobile Radiographic Unit
Difficulty moving from place to place or from one position to another without assistance.
Suggest update to description in MESH.
http://purl.bioontology.org/ontology/MESH/D051346
Suggest update to description
MESH:D051346
Ambulation Difficulty
Ambulatory Difficulty
Difficulty Ambulation
Difficulty Walking
Mobility Limitations
Mobility Limitation
The biological processes, properties, and objects that are involved in maintaining, expressing, and transmitting from one organism to another, genetically encoded traits.
Sufficient
SCDO:0000765
MESH:D055614
Concepts, Genetic
Genetic Phenomena
http://bioportal.bioontology.org/ontologies/ADO/?p=classes&conceptid=http%3A%2F%2Fscai.fraunhofer.de%2FAlzheimerOntology%23Modifying_the_home_enviornment_and_make_it_safer_for_the_patient
obsolete Modifying the Home Environment and Making it Safer For the Patient
true
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.
Sufficient
SCDO:0000771
MESH:D009020
17-methyl-7,8-didehydro-4,5alpha-epoxymorphinan-17-ium-3,6alpha-diol
Morphia
Morphium
Morphine
'A work that reports on a study executed by several cooperating institutions. [Curator team: []]'
http://purl.bioontology.org/ontology/MESH/D016448
MESH:D016448
obsolete Multicenter Study
true
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.
Sufficient
SCDO:0000775
MESH:D015337
Multicenter Trial
Multicenter Trials
Multicentre Studies as Topic
Multicentre Trial
Multicentre Trials
Multicenter Studies as Topic
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.
Request inclusion into NCIT below "Research or Clinical Assessment Tool".
Multiple countries and cultural groups
Self
Healthy population and patients with specific medical conditions
Spanish; Chinese; Persian
Has adequate construct validity and acceptable metric properties
15 years and above
no
Few but definitions not freely available
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.
MHLC
MHLC Scales
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.
http://purl.obolibrary.org/obo/HP_0003202
Suggest update to description
HP:0003202
Amyotrophy
Muscle Wasting
Muscular Atrophy
Neurogenic Muscle Atrophy
Skeletal Muscle Atrophy
Muscle Atrophy
Anatomical system that consists of the muscular and skeletal systems.
http://purl.obolibrary.org/obo/UBERON_0002204
UBERON:0002204
Musculo-Skeletal System
deprecated Musculoskeletal System
true
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.
Few but definitions not freely available
SCDO (Clair Ingram)
MESH:D006580
Mutation Carrier Detection
This term is very similar to but different (more specific) from the term "Genetic Carrier Screening" in MESH.
Mutation Carrier Screening
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.
Exists in other ontologies but we have provided a description more relevant to its relationship with SCD.
Link to "Hereditary Persistence of fetal hemoglobin".
http://www.ncbi.nlm.nih.gov/gene/4602
Not relevant to context of sickle cell
MYB Gene
MYB Proto-Oncogene, Transcription Factor
MYB-HSP1
MYB
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)"
Suggest update to label
phenX:810501
NT-proBNP Test
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?
Sufficient
SCDO:0000789
MESH:D009270
1-N-Allyl-14-hydroxynordihydromorphinone
17-allyl-3,14-dihydroxy-4,5α-epoxymorphinan-6-one
MRZ-2593
Naloxone
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)
Sufficient
SCDO:0000791
MESH:D014663
Nasal Vasoconstrictor Agents
Nasal Vasoconstrictors
Nasal Decongestants
'A subspecialty of internal medicine concerned with the anatomy, physiology, and pathology of the kidney. [Curator team: []]'
http://purl.bioontology.org/ontology/MESH/D009398
MESH:D009398
obsolete Nephrology
true
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.
Suggest update to description
HP:0000100
Nephrosis
Nephrotic Syndrome
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.
Suggest update to description in HPO.
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).
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.
Suggest update to description
HP:0012593
Nephrotic-Range Proteinuria
Is diagnosed by assessment of proteinuria (see Proteinuria) by 24hr urine collection or by urine protein-creatinine ratio on spot urine sample [KDIGO 2012].
Nephrotic Range Proteinuria
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.
http://purl.obolibrary.org/obo/UBERON_0001016
UBERON:0001016
Neurological System
deprecated Nervous System
true
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.
Request inclusion into relevant ontology
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415156/
None
SCDO
Neurocognitive Impairment
Physician-supervised programs designed to rehabilitate people with diseases, trauma, or disorders of the nervous system.
http://purl.bioontology.org/ontology/MESH/D000066530
Sufficient
SCDO:0000801
MESH:D000066530
Neurologic Rehabilitation
Neurorehabilitation
Rehabilitation, Neurologic
Rehabilitation, Neurological
Neurological Rehabilitation
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
None
Newborn Infant Screening for Sickle Cell
Neonatal 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.
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820801
PhenX protocol: NIH Stroke Scale (NIHSS) #820801
18 years and older
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.
Few but definitions not freely available
phenX:820801
NIH Stroke Scale
NIHSS
NIH Stroke Scale (NIHSS)
Patients who do not turn up for scheduled healthcare appointments.
http://purl.bioontology.org/ontology/MESH/D000067455
Sufficient
SCDO:0000807
MESH:D000067455
No Show Patient
Patient No Show
Patient No-Show
No-Show Patient
Frequent urination at night that interrupts sleep. It is often associated with outflow obstruction, diabetes mellitus, or bladder inflammation (cystitis).
http://purl.bioontology.org/ontology/MESH/D053158
Sufficient
SCDO:0000808
MESH:D053158
Nycturia
Often occuring as a result of heart insufficiency.
Nocturia
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.
http://purl.bioontology.org/ontology/MESH/D018712
Sufficient
SCDO:0000809
MESH:D018712
Non-Narcotic
Nonnarcotic
Nonnarcotic Analgesic
Nonnarcotic Opioid
Nonopioid
Non Opioid
A gene that does not encode a globin family protein.
Perhaps too specific to the SCDO to be included in other ontologies?
None
SCDO (Jade Hotchkiss)
Non-Globin Gene
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".
http://en.wikipedia.org/wiki/Retinopathy
http://eyewiki.aao.org/Sickle_Cell_Retinopathy
None
SCDO (Jade Hotchkiss)
Non-Proliferative 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.
None
SCDO
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: []]'
http://purl.bioontology.org/ontology/MESH/D064888
MESH:D064888
obsolete Observational Study
true
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).
http://purl.bioontology.org/ontology/MESH/D064887
Sufficient
SCDO:0000819
MESH:D064887
Observational Studies as Topic
Skilled treatment that helps individuals achieve independence in all facets of their lives. It assists in the development of skills needed for independent living.
http://purl.bioontology.org/ontology/MESH/D009788
Sufficient
SCDO:0000822
MESH:D009788
Occupational Therapies
Therapies, Occupational
Therapy, Occupational
Occupational Therapy
Low output of urine, defined as an output below 5mL/kg/hr over 6 hours.
Suggest update to description in HPO
Suggest update to description
HP:0100520
Reduced Urine Output
Oliguria
Surgery performed on the eye or any of its parts.
http://purl.bioontology.org/ontology/MESH/D013508
Sufficient
SCDO:0000833
MESH:D013508
Ophthalmologic Surgical Procedures
Ophthalmological Surgical Procedure
Ophthalmologic Surgical Procedure
Device for examining the interior of the eye, permitting the clear visualization of the structures of the eye at any depth.
http://purl.bioontology.org/ontology/MESH/D019721
Sufficient
SCDO:0000834
MESH:D019721
Funduscope
Ophthalmoscopes
Ophthalmoscope
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")
http://purl.bioontology.org/ontology/MESH/D009887
Sufficient
SCDO:0000835
MESH:D009887
Ophthalmoscopy
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.
http://purl.obolibrary.org/obo/HP_0002749
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.
Suggest update to description
HP:0002749
Adult Rickets
Osteomalacia
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.
http://purl.obolibrary.org/obo/HP_0002754
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.
Suggest update to description
HP:0002754
Bone Infection
Osteomyelitis can be acute or chronic and can be caused by a variety of microbial agents.
Osteomyelitis
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"
Few but definitions not freely available
Arterial HbO2
Arterial Oxyhemoglobin Saturation
Arterial SaO2
Arterial Sats
HBOXHGB
Oxygen Saturation of Arterial Blood
Oxyhemoglobin to Total Hemoglobin Ratio Measurement
Oxyhemoglobin/Total Hemoglobin
Arterial Oxygen Saturation
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.
Suggest update to description in HPO.
Provide source for additional info.
http://purl.obolibrary.org/obo/HP_0012531
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.
Suggest update to description
HP:0012531
Pain
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.
Request inclusion into relevant ontology
None
SCDO
Pain Burden
Pain Disability
Pain Impact
Pain Interference
Pain Status
A method of determining the shape and consistency of the liver by feeling with the fingers or hands.
Request inclusion into relevant ontology
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Liver Palpation
Palpation of Liver
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.
http://purl.bioontology.org/ontology/MESH/D010271
Sufficient
SCDO:0000866
MESH:D010271
Parasites
Parasite
Voluntary cooperation of the patient in following a prescribed regimen.
http://purl.bioontology.org/ontology/MESH/D010349
Sufficient
SCDO:0000869
MESH:D010349
Adherence
Patient Adherence
Patient Cooperation
Patient Compliance
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
Suggest update to label
phenX:130502
PedMIDAS
Pediatric Migraine Questionnaire
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.
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820802
PhenX protocol: Pediatric NIH Stroke Scale (PedNIHSS) #820802
2-18 years old
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.
None
phenX:820802
PedNIHSS
Pediatric NIH Stroke Scale
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.
Pediatric NIH Stroke Scale (PedNIHSS)
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.
Suggest update to label
phenX:840200
Pediatric School Performance Measure
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
Self; Proxy (Parent report)
Clinic patients
Validation study in SCD
Children 2 - 18 (child report ages 5 - 18 years; parent proxy report of children ages 2 - 18 years)
None
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.
PedsQL Multidimensional Fatigue Scale
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.
Request inclusion into NCIT below "Pediatric Quality of Life Inventory".
PhenX protocol: PedsQL Sickle Cell Disease Module #820202
Self; Proxy (Parent report)
Clinic Patients (Children with SCD)
Ages 2 to 18
No. The PedsQ Sickle Cell Disease Module is a proprietary instrument and administration requires permission and a license from the MAPI Research Trust.
None
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.
PedsQL Sickle Cell Disease Module
Use of penicillin for the prevention of infections with penicillin-susceptible organisms, e.g. Streptococcus pneumoniae.
Request inclusion into relevant ontology
Few but definitions not freely available
SCDO
Penicillin Prophylaxis
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".
None
SCDO (Jade Hotchkiss)
Percussion of Liver
An estimation of the oxygen saturation level usually measured with a pulse oximeter device.
Request inclusion into CMO below "Oxygen Saturation"
http://en.wikipedia.org/wiki/Oxygen_saturation_(medicine)
Few but definitions not freely available
SNOMEDCT:431314004
Oxygen Saturation of Peripheral Blood
Peripheral SaO2
Peripheral Sats
Peripheral HbO2
Peripheral Oxyhemoglobin Saturation
SpO2
Peripheral Oxygen Saturation
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.
http://bioportal.bioontology.org/ontologies/OGMS?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000023
None
SCDO
OGMS:0000023
Phenotype of Sickle Cell Disease
The physical method (technology) used to measure / readout the effect caused by a perturbagen in the assay environment.
Sufficient
SCDO:0000896
BAO:0000035
Physical Detection Method
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.
Request inclusion into relevant ontology
Physical Environment. Merriam-Webster.com. Merriam-Webster, n.d. Web. 9 Nov. 2016.
Few but definitions not freely available
Physical Environment
Systematic and thorough inspection of the patient for physical signs of disease or abnormality.
http://purl.bioontology.org/ontology/MESH/D010808
Sufficient
SCDO:0000898
MESH:D010808
Physical Assessment
Physical Examination
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?
Few but definitions not specific enough
SCDO
Mobility
Motor Function
Physical Function
Physical Health
Physical Functioning
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.
http://purl.obolibrary.org/obo/ERO_0001292
Sufficient
SCDO:0000902
ERO:0001292
Physiological Assay
A therapeutic intervention that remediates impairments and promotes mobility, function, and quality of life through examination, diagnosis, and physical intervention.
http://purl.obolibrary.org/obo/OAE_0002476
Sufficient
SCDO:0000903
OAE:0002476
Physical Therapy
Physiotherapy
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.
http://purl.bioontology.org/ontology/MESH/D010865
Sufficient
SCDO:0000905
MESH:D010865
Pilot Study
Pilot Projects
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.
Request inclusion into relevant ontology
http://emedicine.medscape.com/article/1844217-overview
Few but definitions not freely available
Pneumatic Retinopexy
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.
Suggest update to description in OBI
http://purl.obolibrary.org/obo/OBI_0000415
Suggest update to description
OBI:0000415
PCR
Polymerase Chain Reaction
'Works about randomized clinical trials that compare interventions in clinical settings and which look at a range of effectiveness outcomes and impacts. [Curator team: []]'
http://purl.bioontology.org/ontology/MESH/D065007
MESH:D065007
Pragmatic Clinical Trial
true
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".
None
SCDO (Clair Ingram)
Prenatal Screening for Sickle Cell
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.")
None
SCDO
Preventive Therapeutics
Prophylactic Therapeutics
Preventative Therapeutics
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.
http://purl.bioontology.org/ontology/MESH/D011317
Sufficient
SCDO:0000923
MESH:D011317
Priapism
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
http://purl.bioontology.org/ontology/MESH/D011320
Sufficient
SCDO:0000924
MESH:D011320
Primary Care
Primary Health Care
Primary Healthcare
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.
Suggest update to description in MESH
Suggest update to description
MESH:D002727
1-(P-Chlorophenyl)-5-isopropylbiguanide
Chlorguanid
Chlorguanide
Chloroguanide
N-(4-Chlorophenyl)-n'-(isopropyl)-imidodicarbonimidic diamide
Proguanil
Sickle retinopathy that involves the upregulation of vascular growth factors due to chronic changes of local hypoxia and ischemia.
Request inclusion into HPO below "Retinopathy/Sickle Retinopathy".
http://eyewiki.aao.org/Sickle_Cell_Retinopathy
None
SCDO (Jade Hotchkiss)
Retinopathy due to SCD Characterized by Neovascularization
Sickle Cell Proliferative Retinopathy
Proliferative Sickle Retinopathy
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.
Suggest update to label in PhenX as we have done.
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=221302
PhenX protocol: Quality of Life - Adult #221302
Suggest update to label
PROMIS 25 Profie v2.0
PROMIS Adult Profile 29
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.
Suggest update to label in PhenX as we have done.
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=221301
PhenX protocol: Quality of Life - Pediatric #221301
Suggest update to label
PROMIS 25
PROMIS 25 Profie
PROMIS Pediatric Profile 25
A planned process that has the objective to reduce the risk of acquiring one or more infections.
Few but definitions not freely available
http://purl.obolibrary.org/obo/OGMS_0000103
Disease Prevention
Infection Prophylaxis
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.
http://purl.bioontology.org/ontology/MESH/D011446
Sufficient
SCDO:0000931
MESH:D011446
Prospective Study
Prospective Studies
Increased amounts of any protein (including albumin) in the urine - typically more than 300mg in a 24hr period.
Suggest update to description in HPO.
http://purl.obolibrary.org/obo/HP_0000093
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.
Suggest update to description
HP:0000093
High Urine Protein Levels
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.
Proteinuria
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.
Request inclusion into NCIT below "Research or Clinical Assessment Tool".
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.
African Americans
Self
Heath care providers
Demonstrated validity with SCD populations in the US
Adults
None
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.
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.
Suggest update to description
HP:0000989
Itchy Skin
Skin Itching
Pruritus
Stress wherein emotional factors predominate.
Sufficient
SCDO:0000937
MESH:D013315
Emotional Stress
Life Stress
Psychological Suffering
Psychological Stress
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.
http://purl.bioontology.org/ontology/MESH/D011610
Sufficient
SCDO:0000938
MESH:D011610
Psychosocial Deprivations
Psychosocial Deprivation
A generic term for the treatment of mental illness or emotional disturbances primarily by verbal or nonverbal communication.
http://purl.bioontology.org/ontology/MESH/D011613
Sufficient
SCDO:0000940
MESH:D011613
Logotherapy
Psycho-Therapy
Psychotherapy
'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: []]'
http://bioportal.bioontology.org/ontologies/EDDA_PT?p=classes&conceptid=http%3A%2F%2Fontologies.dbmi.pitt.edu%2Fedda%2FPublicationType.owl%23publication_type
obsolete Publication Type
true
Measurement of the various processes involved in the act of respiration: inspiration, expiration, oxygen and carbon dioxide exchange, lung volume and compliance, etc.
Sufficient
SCDO:0000942
MESH:D012129
Lung Function Test
PFT
Respiratory Function Test
Pulmonary Function Test
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.
Br J Haematol. 2006 Jul;134(1):109-15.
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.
Few but definitions not specific enough
Increased Blood Pressure in Blood Vessels of Lungs
Pulmonary Arterial Hypertension
Pulmonary hypertension can be secondary to known cardiac, pulmonary, or hepatic disease. If no cause is identifiable, the term primary pulmonary hypertension is used.
Pulmonary Hypertension
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.
http://purl.obolibrary.org/obo/ERO_0000876
Sufficient
SCDO:0000944
ERO:0000876
Blood Oxygen Monitor
Oxygen Monitor
Pulse Oximeter
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
Suggest update to description
phenX:91102
Pulse Oximetry (Rest)
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".
Suggest update to description
EDDA:health_care_quality_assessment
Health Care Quality Assessment
Quality of Health Care Assessment
Quality of Care Measure
The levels of excellence which characterize the health service or health care provided based on accepted standards of quality.
http://purl.bioontology.org/ontology/MESH/D011787
Sufficient
SCDO:0000948
MESH:D011787
Health Care Quality
Healthcare Quality
Quality of Healthcare
Quality of Health Care
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.
None
SCDO
Quality of Life and Care
A measurement tool that is useful in aiding routine clinical practice with regard to quality of life and/or quality of care.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Quality of Life and Care Measurement Scales
Quality of Life and Care Measure
A questionnaire to assess the physical, emotional, and social impact of chronic conditions, such as sickle cell disease (SCD).
Suggest update to label in PhenX.
Suggest update to label
phenX:820200
Quality of Life in 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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Quality of Life Measure
Sickle cell symptoms where there is evidence of some relation with quality of life.
Probably too specific to be included in other ontologies.
None
SCDO
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.
Multiple countries and cultural groups
Self; Proxy
All
Standard global assessment of health interventions, also used in SCD studies
Children and adults
no
Few but definitions not specific enough
QALY
Quality-Adjusted Life Year
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.
Quality-Adjusted Life Year (QALY)
'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: []]'
http://bioportal.bioontology.org/ontologies/MESH?p=classes&conceptid=D011795
MESH:D011795
obsolete Questionnaire
true
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).
http://purl.bioontology.org/ontology/MESH/D011859
Sufficient
SCDO:0000963
MESH:D011859
Imaging by X-Ray
X-Ray
Radiography
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.
http://purl.bioontology.org/ontology/MESH/D011877
Sufficient
SCDO:0000964
MESH:D011877
Imaging by Radionuclide
Scintigraphy
Radionuclide Imaging
'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: []]'
http://purl.bioontology.org/ontology/MESH/D016449
MESH:D016449
obsolete Randomized Controlled Trial
true
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.
Self
Adolescents with SCD
Used in SCD studies
Adolescents
None
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.
REALM-Teen
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.
Suggest update to description in PhenX.
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820702
PhenX protocol: Recovery and Recurrence Questionnaire (RRQ) - Pediatrics #820702
Suggest update to description
phenX:820702
RRQ
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.
Probably too specific to warrant inclusion into anther ontology.
Glassberg et al 2014 Curr Opin Pediatr.
Knight-Madden et al 2014 Ped Resp Rev
Likely related to inflammation of SCD.
Other markers of severity of SCD- eg complications of SCD, high LDH.
None
RWIS
Recurrent Wheeze in Sickle Cell Disease
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?
None
SCDO (Jade Hotchkiss)
Cell-Derived Microparticles
EMP Level
Erythrocyte-Derived Microparticles Level
Level of Red Blood Cell Microparticles
RBC Microparticles Level
Red Blood Cell Derived Microparticles Level
Red Blood Cell 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.
Suggest update to description in HPO.
http://purl.obolibrary.org/obo/HP_0011905
Suggest update to description
HP:0011905
Reduced Hemoglobin A
Restoration of human functions to the maximum degree possible in a person or persons suffering from disease or injury.
http://purl.bioontology.org/ontology/MESH/D012046
Sufficient
SCDO:0000978
MESH:D012046
Habilitation
Rehabilitation
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.
Request inclusion into relevant ontology
http://en.wikipedia.org/wiki/Reincarnation
None
SCDO
Rebirth
Transmigration
Reincarnation
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.
http://purl.bioontology.org/ontology/MESH/D012067
Sufficient
SCDO:0000981
MESH:D012067
Religious Beliefs
Religious Ethics
Religion
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
http://purl.bioontology.org/ontology/MESH/D006435
Sufficient
SCDO:0000983
MESH:D006435
Dialyses, Renal
Extracorporeal Dialyses
Extracorporeal Dialysis
Haemodialysis
Hemodialyses
Renal Dialyses
Renal Dialysis
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.
Suggest update to description
MP:0011758
Kidney Ischaemia
Kidney Ischemia
Nephric Ischaemia
Nephric Ischemia
Renal Ischaemia
Renal Ischemia
The transference of a kidney from one human or animal to another.
http://purl.bioontology.org/ontology/MESH/D016030
Sufficient
SCDO:0000985
MESH:D016030
Kidney Grafting
Kidney Transplant
Kidney Transplantation
Kidney Transplantations
Renal Transplantation
Renal Transplantations
Renal Transplant
Acidosis owing to malfunction of the kidney tubules with accumulation of metabolic acids and hyperchloremia.
Suggest update to description in HPO.
Provide source for additional info.
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.
Suggest update to description
HP:0001947
Accumulation of Acid in Body Due to Kidney Problem
RTA
Renal Tubular Acidosis
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.
Suggest update to label and description
phenX:101300
Reproductive History Diagnostic Instrument
'Anatomical system that has as its parts the organs concerned with reproduction. [Curator team: []]'
http://purl.obolibrary.org/obo/UBERON_0000990
UBERON:0000990
deprecated Reproductive System
true
'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.
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C15429
NCIT:C15429
obsolete Research Activity
true
The number of times an organism breathes with the lungs (respiration) per unit time, usually per minute.
Sufficient
SCDO:0000993
MESH:D056152
Breathing Frequency
Pulmonary Ventilation Rate
Respiration Rate
Respiratory Rate
Lungs and respiratory system of the body.
Pulmonary System
deprecated Respiratory System
true
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.
None
SCDO (Gaston K. Mazandu)
Sickle Cell Disease Ontology
SCDO
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.
Request inclusion into relevant ontology.
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
Few but definitions not freely available
PCR-RFLP
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
Sufficient
SCDO:0001004
MESH:D017701
Reticulocyte Number
Reticulocyte Count
A reticulocyte count that was performed with an electronic haematology analyzer.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Reticulocyte Count by Hematology Analyzer
A reticulocyte count that was performed with microscopy.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Reticulocyte Count by Microsocopy
A procedure that uses intense cold to induce a chorioretinal scar and to destroy retinal or choroidal tissue.
Request inclusion into relevant ontology
http://www.surgeryencyclopedia.com/Pa-St/Retinal-Cryopexy.html
None
Retinal Cryotherapy
Retinal Cryopexy
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.
Ballas et al 2010 Am J Hematol
Not relevant to context of sickle cell
Retinal Detachment
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.
http://purl.bioontology.org/ontology/MESH/D012189
Sufficient
SCDO:0001010
MESH:D012189
Retrospective Study
Retrospective Studies
An open swath of land that has few homes or other buildings, and not very many people.
Request inclusion into relevant ontology
None
Rural
Rural Area
Rural Setting
Rural Location
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.
Request inclusion into relevant ontology.
Ballas et al 2010 Am J Hematol
None
Salmon Patch Hemorrhages
Salmon Patch Hemorrhage
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.
http://purl.bioontology.org/ontology/MESH/D012494
Sufficient
SCDO:0001020
MESH:D012494
Probability Sample
Probability Samples
Sampling Study
Sampling Studies
Pain resulting from the presence of Sickle Cell Disease (SCD). Such pain can be acute, chronic or a mixture of the two.
Request inclusion into relevant ontology
None
SCDO
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
SCD Pain
SCD-Related Pain
SCD Related Pain
An operation for retinal detachment which reduces the size of the globe by indenting the sclera so that it approximates the retina.
http://purl.bioontology.org/ontology/MESH/D012591
Sufficient
SCDO:0001025
MESH:D012591
Scleral Buckle Surgery
Scleral Bucklings
Scleral Buckling
Specialized healthcare delivered as a follow-up or referral from a primary care provider.
http://purl.bioontology.org/ontology/MESH/D063127
Sufficient
SCDO:0001027
MESH:D063127
Secondary Care
Secondary Health Care
Secondary Healthcare
Usual level of physical activity that is less than 30 minutes of moderate-intensity activity on most days of the week.
http://purl.bioontology.org/ontology/MESH/D057185
Sufficient
SCDO:0001029
MESH:D057185
Sedentary Lifestyle
Caring for self when ill or positive actions and adopting behaviors to prevent illness.
http://purl.bioontology.org/ontology/MESH/D012648
Sufficient
SCDO:0001034
MESH:D012648
Self Management
Self-Care
Self-Management
Self Care
Cognitive mechanism based on expectations or beliefs about one's ability to perform actions necessary to produce a given effect.
Sufficient
SCDO:0001035
MESH:D020377
Self-Concept
Self Efficacy
The weight in kilograms or pounds as reported by the participant.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Self-Reported Weight
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.
http://purl.bioontology.org/ontology/MESH/D016036
Sufficient
SCDO:0001041
MESH:D016036
Seroprevalences
Seroepidemiologic Studies
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.
Request inclusion into relevant ontology
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Blood HDL Cholesterol Amount
Blood High Density Lipoprotein Cholesterol Amount
Circulating HDL Cholesterol Amount
Circulating HDL Cholesterol Level
HDL Cholesterol Level
HDL Level
Serum HDL Cholesterol Level
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)")
PhenX protocol: #191201
Self
Healthy people; Clinic patients
Demonstrated validity with SCD populations; multiple publications using the measure in SCD; very widely used with healthy populations and those with chronic conditions
Adults 18 years and older
Suggest update to label
SF-36v2 Health Survey
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.
None
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.
SCD-HRSS
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.
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
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.
None
SCPBI-Y
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.
Request inclusion into relevant ontology
https://labtestsonline.org/tests/sickle-cell-tests
Few but definitions not freely available
Screening for Sickle Cell Disease
Sickle Cell Disease Screening Test
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.
Suggest update to label in PhenX as we have done.
PhenX protocol: Self-efficacy in Sickle Cell Disease #820401
Self
Clinic Patients (Adults with SCD)
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).
18 and older
Suggest update to label
Scale of Self-efficacy in Sickle Cell Disease
Sickle Cell Disease Self-Efficacy Scale
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).
Request inclusion into relevant ontology
http://www.uptodate.com/contents/overview-of-variant-sickle-cell-syndromes
None
SCD Variant
Sickle Cell Disease Variant
Variant Sickle Cell Syndromes
Variant Sickle Cell Syndrome
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".
http://purl.bioontology.org/ontology/MESH/D059408
None
SCDO
Sickle Cell Pain Managements
Sickle Cell 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".
Request inclusion into relevant ontology
None
SCDO
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=830101
Pain Episode
Painful Crisis
Painful Event
Sickle Cell Acute Pain Episode
Sickle Cell Pain Episode
Sickle Cell Painful Event
A cancer that is almost exclusively associated with sickle cell trait and/or sickle cell disease.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Sickle Cell Associated Cancer
Sickle Cell Related Cancer
The condition of being heterozygous for hemoglobin S.
http://purl.bioontology.org/ontology/MESH/D012805
Sufficient
SCDO:0001055
MESH:D012805
AS Genotype
Haemoglobin Genotype AS
Hemoglobin Genotype AS
Sickle Cell Trait
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"
http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C98837
Suggest update to label
NCIT:C98837
S beta-minus
Sickle B- Thalassemia
Sickle Beta Minus Thalassemia
Sickle Cell Disease-S Beta Minus Thalassemia
Sickle Cell-B- Thalassemia
Sickle Cell-Beta Minus Thalassemia
Sickle Cell Disease-S Beta Minus Thalassemia
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.
http://purl.bioontology.org/ontology/MESH/D006450
Sufficient
SCDO:0001059
MESH:D006450
Hb SC-disease
Hemoglobin S / Hemoglobin C Disease
Hemoglobin SC Disease
SC Disease
Sickle Cell Disease SC
Sickle Cell Hemoglobin C Disease
Sickle Cell-Haemoglobin C Disease
Sickle Cell-Hemoglobin C Disease
Sickle-Cell/Hb-C Disease
Sickle Cell Disease-SC
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.
Few but definitions not freely available
Haemoglobin S/D-Punjab
Hemoglobin S/D-Punjab
Sickle Cell-Haemoglobin D-Punjab
Sickle Cell-Hemoglobin D-Punjab Disease
Sickle Cell Disease-S/D-Punjab
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.
http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-S-E
Few but definitions not specific enough
Hb SE-Disease
Hemoglobin SE Disease
Hemoglobin SE-Disease
Sickle Cell Disease SE
Sickle Cell-Haemoglobin E Disease
Sickle Cell-Hemoglobin E Disease
Sickle Cell Disease-SE
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
SCD-S/Lepore Boston
Sickle Cell Disease-S/Lepore
Sickle Cell-Hb Lepore Boston Syndrome
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.
Sickle Cell Disease-S/Lepore Boston
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.
Request inclusion into relevant ontology
http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-S-O-Arab
Few but definitions not freely available
Hb F,S,O-Arab
Hb S O-Arab disease
Hb S,O-Arab
Hemoglobin S O-Arab Disease
SO(Arab) disease
Sickle Cell-Haemoglobin O-Arab Disease
Sickle Cell-Hemoglobin O-Arab Disease
Sickle Cell Disease-S/O-Arab
'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: []]'
http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-S-and-other-than-A-C-D-E-O-Arab
Hb S Other than A,C,D,E,O-Arab
obsolete Sickle Cell-Hemoglobin Other than A,C,D,E,O-Arab
true
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.
Bonanomi et al 2013 Arq Bras Oftalmol
Few but definitions not freely available
Retinopathy due to SCD
Sickle Cell Retinopathy
Sickle Retinopathy
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.
Few but definitions not freely available.
Sickle Cell Identification, Slide Method
Sickling Test
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
http://link.springer.com/referenceworkentry/10.1007%2F978-0-387-79948-3_1833
http://qol.thoracic.org/sections/instruments/pt/pages/sick.html
Few but definitions not specific enough
SCDO
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.
SIP
Sickness Impact Profile
Sickness Impact Profile (SIP)
'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
Dermatologic System
Integumentary System
deprecated Skin
true
An abnormal change in skin color, appearance, or texture.
Suggest update to description in HPO.
Suggest update to description
HP:0000988
Exanthem
Skin Rash
An intrinsic sleep disorder characterized by breathing abnormalities.
http://purl.obolibrary.org/obo/NBO_0000494
Suffcient
NBO:0000494
SBD
Sleep Breathing Disorder
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
Suggest update to label
phenX:121001
National Institute of Mental Health (NIMH) Sleep Patterns and Problems Instrument
Sleep Disorders Screener - Adult
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.
http://purl.bioontology.org/ontology/MESH/D066167
Sufficient
SCDO:0001077
MESH:D066167
Slit Lamp
Inhaling and exhaling the smoke of burning tobacco (Cigar, Cigarette, Hookah, Pipe, Smoking, Waterpipe).
http://purl.bioontology.org/ontology/MESH/D012907
Sufficient
SCDO:0001079
MESH:D012907
Smoking
Discontinuing the habit of smoking.
http://purl.bioontology.org/ontology/MESH/D016540
Sufficient
SCDO:0001080
MESH:D016540
Quit Smoking
Smoking Cessation
The aggregate of social and cultural institutions, forms, patterns, and processes that influence the life of an individual or community.
http://purl.bioontology.org/ontology/MESH/D012931
Sufficient
SCDO:0001082
MESH:D012931
Social Ecology
Social Environment
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.
Few but definitions not freely available
PROMIS Domain Frameworks/Definitions nih.promis.org
Social Functioning
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.
http://purl.bioontology.org/ontology/MESH/D012934
Sufficient
SCDO:0001084
MESH:D012934
Social Isolations
Social Isolation
A role that is ascribed to individuals in a community.
http://semanticscience.org/resource/SIO_000676
Sufficient
SCDO:0001085
SIO:000676
Social Function
Social Role
An extent/ degree to which an individual fulfills the expectations of his/her social role.
Request inclusion into relevant ontology
None
SCDO
Social Role Fulfillment
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.
http://purl.bioontology.org/ontology/MESH/D066107
Sufficient
SCDO:0001087
MESH:D066107
Interpersonal Skill
Social Ability
Social Competence
Social Skills
Social Skill
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.
http://purl.bioontology.org/ontology/MESH/D012944
Sufficient
SCDO:0001088
MESH:D012944
Psychosocial Support System
Social Network
Social Support
Abstract standards or empirical variables in social life which are believed to be important and/or desirable.
http://purl.bioontology.org/ontology/MESH/D012945
Sufficient
SCDO:0001089
MESH:D012945
Value Orientation
Value Orientations
Social Values
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.
http://purl.bioontology.org/ontology/MESH/D012959
Sufficient
SCDO:0001090
MESH:D012959
Socioeconomic Factors
The combination of one's social class and income level. Includes socioeconomic differences between individuals or groups.
http://bioportal.bioontology.org/ontologies/APAONTO/?p=classes&conceptid=http%3A%2F%2Fontology.apa.org%2Fapaonto%2FtermsonlyOUT%2520%285%29.owl%23Socioeconomic_Status
Sufficient
SCDO:0001091
APAONTO:Socioeconomic_Status
Socioeconomic Status
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.
Few but definitions not freely available.
SCDO (Clair Ingram)
Hemoglobin S Solubility Test
Solubility Test
Instruments for measuring arterial blood pressure consisting of an inflatable cuff, inflating bulb, and a gauge showing the blood pressure.
http://purl.bioontology.org/ontology/MESH/D019722
Sufficient
SCDO:0001097
MESH:D019722
Sphygmomanometer
Sensitivity or attachment to religious values, or to things of the spirit as opposed to material or worldly interests.
http://purl.bioontology.org/ontology/MESH/D029181
Sufficient
SCDO:0001098
MESH:D029181
Spiritual Beliefs
Spiritualities
Spirituality
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.
http://purl.obolibrary.org/obo/ERO_0000452
Sufficient
SCDO:0001099
ERO:0000452
Spirometer
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.
Suggest update to description
HP:0012588
Steroid-Resistant Nephrotic Syndrome
A perceived attribute that is deeply discrediting and is considered to be a violation of social norms.
http://purl.bioontology.org/ontology/MESH/D057545
Sufficient
SCDO:0001107
MESH:D057545
Social Stigma
Social Stigmas
Stigmas
Stigma
An oversimplified perception or conception, especially or persons, social groups, etc.
http://purl.bioontology.org/ontology/MESH/D013240
Sufficient
SCDO:0001108
MESH:D013240
Stereotyping
Stigmatization
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.
http://purl.bioontology.org/ontology/MESH/D020521
Sufficient
SCDO:0001111
MESH:D020521
Brain Vascular Accident
CVA
Cerebral Infarction
Cerebral Vascular Event
Cerebrovascular Accident
Cerebrovascular Stroke
Stroke
This measure is a physical assessment to determine neurological deficits due to a stroke.
Suggest update to label in PhenX
This measure is used to describe the consequences of a stroke and to monitor the effects of treatment and recovery.
Suggest update to label
phenX:820800
Stroke Impact/Outcome Measure
Stroke Outcome Measure
Stroke Impact Measure
This questionnaire includes 59 proxy- or self-report items in 8 domains that assess multidimensional stroke outcomes in adults.
Suggest update to description in PhenX.
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820701
PhenX protocol: Stroke Impact Scale (SIS) - Adults #820701
Suggest update to description
phenX:820701
Stroke Impact Scale (SIS) - Adults
Stroke Impact Scale (SIS)
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"?
Sufficient
SCDO:0001114
phenX:821001
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
Few but definitions not freely available
SCDO
Recurrent Priapism
Stuttering Priapism
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.
Few but definitions not specific enough
SCDO
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.
Substance Use History
An indication of whether the respondent has ever used a drug during his or her entire life.
Request inclusion into relevant ontology
Not relevant to context of sickle cell
SCDO (Jade Hotchkiss)
Substances - Lifetime Use
Frequent thinking about or preoccupation with killing oneself.
Suggest update to description in HPO (correct typo in "oneself")
Suggest update to description
HP:0031589
Suicidal Ideation
Suicidal Thoughts
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.
http://purl.bioontology.org/ontology/MESH/D012657
Sufficient
SCDO:0001123
MESH:D012657
Self Help Group
Self-Help Group
Self-Help Groups
Therapeutic Social Club
Support Group
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.
http://purl.bioontology.org/ontology/MESH/D055512
Sufficient
SCDO:0001129
MESH:D055512
Supportive Therapy
Tertiary Prevention
Supportive Therapeutics
A computerized test for the assessment of visual attention problems in individuals ages 8 years old and older.
Suggest update to label in PhenX as we have done.
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=821201
PhenX protocol: Sustained and Selective Attention #821201
Suggest update to label
phenX:821201
Conners CPT 3
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.
Request inclusion into relevant ontology
http://www.medicinenet.com/script/main/art.asp?articlekey=10701
None
SCDO (Jade Hotchkiss)
Symptomatic Treatment
Symptomatic Therapeutics
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.
Request inclusion into relevant ontology
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
SCD Management guidelines - Nigeria
None
SCDO
Acute Sickle Cell Crisis
'Affecting a number of tissues relating to the entire organism as distinguished from and of its individual parts. [Curator team: []]'
http://medical-dictionary.thefreedictionary.com/systemic
deprecated Systemic
true
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.
http://purl.bioontology.org/ontology/MESH/D063128
Sufficient
SCDO:0001140
MESH:D063128
Tertiary Care
Tertiary Health Care
Tertiary Healthcare
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.
Spanish
None
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.
TOFHLA
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.
Self
Adults with SCD
Used in at least one SCD study
Adults
no
None
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.
DUREL
The Duke Religion Index
The Duke Religion Index (DUREL)
A medical device used to prevent and treat medical conditions, or to alleviate pain or injury.
Request inclusion into relevant ontology
Negligable
SCDO
Therapeutic Device
The washing of a body cavity or surface by flowing water or solution for therapy or diagnosis.
http://purl.bioontology.org/ontology/MESH/D007507
Sufficient
SCDO:0001151
MESH:D007507
Lavage
Lavages
Therapeutic Irrigations
Therapeutic Irrigation
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.
Suggest update to description in MESH
Suggest update to description
MESH:D013812
Therapy
Treatment
Therapeutics
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.
http://purl.bioontology.org/ontology/MESH/D054643
Sufficient
SCDO:0001158
MESH:D054643
Insertion-Deletion Mutation
Indel Mutation
Ending the tobacco habits of smoking, chewing, or snuff use.
http://purl.bioontology.org/ontology/MESH/D020340
Sufficient
SCDO:0001159
MESH:D020340
Tobacco Cessation
Tobacco Use Cessation
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.
Request inclusion into relevant ontology, perhaps MESH.
Few but definitions not specific enough
SCDO
Faith Healer
Folk Healer
Healer
Sangoma
Shaman
Traditional Healer
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.
Suggest update to label in PhenX.
PhenX protocol: #131101
Suggest update to label
phenX:131101
Executive Function - Adult
Trail Making Test
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.
http://purl.bioontology.org/ontology/MESH/D017585
Sufficient
SCDO:0001166
MESH:D017585
TCD
Transcranial Doppler
Ultrasonography, Doppler, Transcranial
Transcranial Doppler Ultrasonography
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.
http://purl.bioontology.org/ontology/MESH/D004561
Sufficient
SCDO:0001167
MESH:D004561
Analgesic Cutaneous Electrostimulation
Electroanalgesia
Electroanalgesias
Percutaneous Electrical Nerve Stimulation
Percutaneous Electrical Neuromodulations
Percutaneous Neuromodulation Therapies
Percutaneous Neuromodulation Therapy
TENS
Transcutaneous Electric Stimulation
Transcutaneous Electrical Stimulation
Transcutaneous Nerve Stimulation
Transdermal Electrostimulation
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".
None
SCDO
Amaurosis Fugax
TMB
Temporary Blindness
Transient Monocular 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: []]'
http://purl.bioontology.org/ontology/MESH/D018486
MESH:D018486
obsolete Twin Study
true
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)
http://purl.bioontology.org/ontology/MESH/D018433
Sufficient
SCDO:0001198
MESH:D018433
Twin Studies as Topic
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.
Request inclusion into relevant ontology
Few but definitions not freely available
GNT1
UDP Glucuronosyltransferase Family 1 Member A1
UGT1
UGT1A1 Gene
UGT1A1
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.
Request inclusion into relevant ontology
None
Urban
Urban Area
Urban Environment
Urban Setting
Urban Location
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
Suggest update to label
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.
Urinary Albumin Test
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
Sufficient
SCDO:0001206
phenX:141601
Urinary Creatinine Assay
Urine Creatinine Analysis
Urinary Creatinine Test
Any measurement of protein present in urine.
Suggest update to description in CMO.
Suggest update to description (currently no description provided).
CMO:0000770
Urinary Protein Measurement
The organs and passageways concerned with the production and excretion of urine, including the kidneys, ureters, urinary bladder, and urethra.
http://purl.obolibrary.org/obo/BTO_0003092
BTO:0003092
deprecated Urinary System
true
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.
Suggest update to description
CMO:0000130
Urinary Albumin Concentration
Urinary Albumin Level
Urine Albumin Level
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.
Urine Albumin Concentration
The amount of albumin excreted into the urine within a specified period of time.
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.
http://purl.obolibrary.org/obo/CMO_0000757
Suggest update to description
CMO:0000757
Urinary Albumin Excretion Rate
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).
Urine Albumin Excretion Rate
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.
http://purl.obolibrary.org/obo/CMO_0000384
Suggest update to description
CMO:0000384
ACR
ALBCREAT
Albumin To Creatinine Protein Ratio Measurement
Albumin-Creatinine Ratio
Albumin/Creatinine Ratio
Microalbumin/Creatinine Ratio
UACR
Urinary Albumin-Creatinine Ratio
Urine Albumin Level to Urine Creatinine Level Ratio
Urine Microalbumin-Creatinine Ratio
Urine Albumin-Creatinine Ratio
The concentration of creatinine in a urine specimen.
Request inclusion below "urine creatinine measurement" in the CMO.
None
SCDO (Jade Hotchkiss)
Urinary Creatinine Concentration
Urine Creatinine Amount
Urine Creatinine Concentration Measurement Datum
Urine Creatinine Level
Urine Creatinine Concentration
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.
http://purl.obolibrary.org/obo/MMO_0000504
Sufficient
SCDO:0001215
MMO:0000504
SSA Protein Precipitation Test
Urine SSA Turbidimetry
Urine Sulfosalicylic Acid Turbidimetry
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.
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17243
NCIT:C17243
obsolete Urology
true
Works consisting of research using processes by which the reliability and relevance of a procedure for a specific purpose are established.
http://purl.bioontology.org/ontology/MESH/D023361
Sufficient
SCDO:0001223
MESH:D023361
Validation Studies
Smoking vapors produced from electronic nicotene delivery systems.
http://purl.bioontology.org/ontology/MESH/D000072137
Sufficient
SCDO:0001224
MESH:D000072137
Electronic Cigarrete Use
Vaping
A measure of vascular endothelial cell response to stimulation, for example, by vasoactive substances released by or those that interact with the vascular endothelium.
Request inclusion into relevant ontology
http://circ.ahajournals.org/content/108/17/2054
None
Assessment of Endothelial Cell Function
Endothelium Dysfunction Test
Vascular Endothelial Function Test
Endothelial Function Test
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.
Request inclusion into relevant ontology
Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014
Few but definitions not specific enough
SCDO
Acute Pain Crisis
Sickle Crisis
VOC
Vaso-Occlusive Crisis
Vaso-Occlusive Episodes
Vaso-Occlusive Crisis
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.
http://purl.obolibrary.org/obo/MMO_0000090
Sufficient
SCDO:0001230
MMO:0000090
Venipuncture
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).
Suggest update to label in PhenX as we have done.
http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820601
PhenX protocol: Adaptive Behavior/Adaptive Function #820601
Proxy
This measure can be used to identify individuals with developmental disabilities or delays, perform diagnostic evaluations, monitor progress, and develop programs.
All ages from birth through age 90
Suggest update to label
phenX:820601
VABS
Vineland Adaptive Behavior Scales
Vineland-II
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)
http://purl.bioontology.org/ontology/MESH/D014780
Sufficient
SCDO:0001234
MESH:D014780
Viruses
Virus
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.
http://purl.bioontology.org/ontology/MESH/D014821
Sufficient
SCDO:0001237
MESH:D014821
Vitrectomies
Vitrectomy
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"?
Sufficient
SCDO:0001240
MESH:D015153
Western Immunoblot
Western Blot
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.
Paediatr Respir Rev. 2014 Mar;15(1):13-6. doi: 10.1016/j.prrv.2013.10.005. Epub 2013 Oct 31.
Synergistic inflammatory response due to both SCD and asthma.
Increased severity of episodes.
None
SCDO
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.
Paediatr Respir Rev. 2014 Mar;15(1):13-6. doi: 10.1016/j.prrv.2013.10.005. Epub 2013 Oct 31.
Asthma Attack
Wheezing Episode with Co-Morbid 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).
http://purl.bioontology.org/ontology/MESH/D018599
Sufficient
SCDO:0001246
MESH:D018599
Sorceries
Sorcery
Witchcraft
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
Self
Healthy people; Clinic patients
Demonstrated validity with SCD populations; at least two publications using the measure
None
WHOQOL Group (1993). Measuring quality of life: The development of the World Health Organisation quality of life instrument (WHOQOL). Geneva: WHO.
WHOQOL
World Health Organisation Quality of Life Instrument
World Health Organisation Quality of Life Instrument (WHOQOL)
The visual output that an X-ray machine produces.
Request inclusion into relevant ontology.
Not relevant to context of sickle cell
SCDO (Jade Hotchkiss)
X-Ray Image
The visual output that an X-ray machine produces when imaging the chest.
Request inclusion into relevant ontology.
Negligable
SCDO (Jade Hotchkiss)
Chest X-Ray Image
X-Ray Image of Chest
Medical treatment involving the use of controlled amounts of X-Rays.
http://purl.bioontology.org/ontology/MESH/D014964
Sufficient
SCDO:0001252
MESH:D014964
Roentgenotherapy
X Ray Therapy
X-ray Beam Therapy
Xray Therapy
X-Ray Therapy
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.
This should probably be removed.
http://purl.bioontology.org/ontology/MESH/D014965
Sufficient
SCDO:0001253
MESH:D014965
X-Radiation
X-Ray Electromagnetic Radiation
X-Rays
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.
Multiple countries and cultural groups
Self
Healthy People; Clinic Patients
Widely used around the world, also used in SCD
Adults and Youth (8 to 18 years)
Few but definitions not specific enough
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.
The EuroQol Group. EuroQol-a new facility for the measurement of health-related quality of life. Health Policy. 1990; 16(3):199-208.
EQ-5D
EuroQol Five Dimension Self-Report Questionnaire
EuroQol Five Dimensions Questionnaire
EuroQol Five-Dimensional 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.
Request inclusion into NCIT below "Research or Clinical Assessment Tool".
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.
Self; Proxy (Parent report)
Children with SCD and their parents
Demonstrated validity in SCD studies.
Children and adults
None
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.
FACIT-Sp Scale
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.
http://purl.bioontology.org/ontology/MESH/D001521
Sufficient
SCDO:0001284
MESH:D001521
Behavior Modification
Behavior Modifications
Behavior Therapies
Behavior Therapy
Conditioning Therapies
Conditioning Therapy
Behaviour Therapy
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.
http://purl.bioontology.org/ontology/MESH/D003027
Sufficient
SCDO:0001288
MESH:D003027
Acute Severe Headache
Cluster Headaches
Migraine, Neuralgic
Cluster Headache
Broad term used to describe several different acute conditions occurring with sickle cell disease, including aplastic crisis, hemolytic crisis, and vasoocclusive crisis.
Sufficient
SCDO:0001292
http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.00
ICD10CM:D57.00
D57.00
Hb-SS disease with (painful) crisis NOS
Hb-SS disease with crisis, unspecified
Hb-SS disease with vasoocclusive pain NOS
Hemoglobin S sickling disorder with crisis
Sickle cell anemia, 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.
Request inclusion into relevant ontology
http://en.wiktionary.org/wiki/electrocardiograph
Few but definitions not freely available
Cardiograph
Electrocardiographic Instrument
Electrocardiograph
The transfer of erythrocytes from a donor to a recipient or reinfusion to the donor.
http://purl.bioontology.org/ontology/MESH/D017707
Sufficient
SCDO:0001296
MESH:D017707
Erythrocyte Transfusions
Red Blood Cell Transfusion
Red Blood Cell Transfusions
Transfusion, Erythrocyte
Transfusions, Erythrocyte
Erythrocyte Transfusion
Works consisting of studies determining the effectiveness or utility of processes, personnel, and equipment.
http://purl.bioontology.org/ontology/MESH/D023362
Sufficient
SCDO:0001299
MESH:D023362
Evaluation Studies
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.
Sufficient
SCDO:0001303
MESH:D005078
Exchange Blood Transfusion
Exchange Transfusion, Whole Blood
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.
Sufficient
SCDO:0001304
phenX:131100
Executive Function Measure
The organ of vision that consists of the eyeball and the optic nerve.
http://medical-dictionary.thefreedictionary.com/eye
Oculus
deprecated Eye
true
Facial paralysis is loss of facial movement because of nerve damage.
Is this not the same thing as "Facial Nerve Palsy"?
DOID:13934
obsolete Facial Paralysis
true
Inability to function due to tiredness related to sickle cell disease.
Use the literature cited here to link to other phenotypes.
Not relevant to context of sickle cell
Fatigability
Fatigable
Lassitude
Tiredness
Fatigue
Studies to determine the advantages or disadvantages, practicability, or capability of accomplishing a projected plan, study, or project.
http://purl.bioontology.org/ontology/MESH/D005240
Sufficient
SCDO:0001320
MESH:D005240
Feasibility Studies
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?
Sufficient
SCDO:0001321
MESH:D005283
Duragesic
Durogesic
N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide
Phentanyl
Fentanyl
A bioassay to measure the serum concentration of ferritin (i.e., iron).
Suggest update to label in PhenX (from "Serum or Plasma Ferritin")
Suggest update to label
phenX:811301
Ferritin Blood Test
Ferritin Measurement
Plasma Ferritin Assay
Plasma Ferritin Test
Serum Ferritin Assay
Serum Ferritin Test
The amount of ferritin found in a specified volume of serum.
Suggest update to description and label of "ferritin measurement" in the EFO.
Suggest update to description
SCDO (Jade Hotchkiss)
Blood Serum Ferritin Concentration
Blood Serum Ferritin Concentration Measurement Datum
Serum Ferritin Level
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".
http://purl.bioontology.org/ontology/npo#NPO_1769
Sufficient
SCDO:0001325
NPO:1769
Flow Cytometer
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.
Sufficient
SCDO:0001326
BAO:0000005
Flow Cytometry
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.
http://purl.bioontology.org/ontology/MESH/D005451
Sufficient
SCDO:0001327
MESH:D005451
Fluorescence Angiography
Fluorescein Angiography
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.
Sufficient
SCDO:0001328
ORPHA:1866
Focal Dystonia
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.
Sufficient
SCDO:0001329
MESH:D005492
Folacin
Folate
Folvite
L-Glutamic acid, N-(4-(((2-amino-1,4-dihydro-4-oxo-6-pteridinyl)methyl)amino)benzoyl)-
Pteroylglutamic Acid
Vitamin B9
Vitamin M
Folic Acid
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.
http://purl.bioontology.org/ontology/MESH/D005500
Sufficient
SCDO:0001330
MESH:D005500
Follow Up Studies
Follow-Up Study
Followup Studies
Follow-Up Studies
An observable characteristic of disease that is persistent and long standing.
Request inclusion into relevant ontology
http://purl.obolibrary.org/obo/NCIT_C14141
http://semanticscience.org/resource/SIO_010056
None
SCDO (Clair Ingram)
NCIT:C14141
SIO:010056
Chronic Phenotype
Terms deprecated in the "Phenotype" class.
from phenotype
A questionnaire to measure the health status of individuals who had a stroke.
Sufficient
SCDO:0001339
phenX:820700
Functionality After Stroke Diagnostic Instrument
Functionality After Stroke Measure
'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: []]'
http://medical-dictionary.thefreedictionary.com/gastroenterology
gastrointestinal tract
deprecated Gastrointestinal System
true
Combined effects of genotypes and environmental factors together to affect phenotypic characteristics.
http://purl.bioontology.org/ontology/MESH/D059647
Sufficient
SCDO:0001342
MESH:D059647
Gene-Environment Interaction
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.
Suggest update to description in NCIT
http://purl.obolibrary.org/obo/NCIT_C17248
Suggest update to description
NCIT:C17248
Genetic Variation
'To be defined by an expert [Curator team: []]'
made a synonym of HBB, GLU6LYS
deprecated beta C mutation
true
obsolete heterozygous beta c mutation
true
obsolete homozygous beta c mutation
true
'To be defined by an expert [Curator team: []]'
Made a synonym of "HBB, GLU26LYS"
deprecated beta E mutation
true
'To be defined by an expert [Curator team: []]'
Made a synonym of HBB, GLU6VAL
deprecated beta S mutation
true
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.
Suggest update to description in NCIT.
http://www.ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C75429
Suggest update to description
NCIT:C75429
HBA1 Gene
Hemoglobin Subunit Alpha 1 Gene
Hemoglobin, Alpha 1 Gene
HBA1
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.
Suggest update to description in NCIT.
http://purl.obolibrary.org/obo/NCIT_C75432
Suggest update to description
HBA2 Gene
Hemoglobin Subunit Alpha 2 Gene
Hemoglobin, Alpha 2 Gene
HBA2
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.
Request inclusion into relevant ontology.
https://www.genecards.org/cgi-bin/carddisp.pl?gene=HBG1
None
Gamma-Globin
Haemoglobin Gamma Chain
Haemoglobin Subunit Gamma
Hemoglobin Gamma Chain
Hemoglobin Subunit Gamma
A reduction in the ratio of production of alpha globin to that of gamma globin.
Request inclusion into the HPO below "Imbalanced Hemoglobin Synthesis".
None
SCDO (Nicole Vasilevsky)
Increased Gamma/Alpha Synthesis Ratio
Reduced Alpha/Gamma Synthesis Ratio
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.
None
SCDO (Clair Ingram)
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.
Request inclusion into relevant ontology
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)
None
SCDO (Clair Ingram)
Alpha-Globin Cluster Deletion
Alpha-Globin Gene Cluster Deletion
HBA Locus Deletion
Alpha-Globin Locus Deletion
Deletion of all four alpha-globin genes resulting in the most severe form of alpha thalassemia, Hemoglobin Barts Hydrops Fetalis.
Request inclusion into relevant ontology
None
SCDO (Clair Ingram)
Homozygous Deletion of HBA1 and HBA2
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.
http://purl.bioontology.org/ontology/MESH/D016254
Sufficient
SCDO:0001388
MESH:D016254
Gene Insertion
Insertion Mutation
Insertion
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.
Few but definitions not specific enough
Supplemental Oxygen Therapy
Oxygen Therapy
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.
http://www.orpha.net/ORDO/Orphanet_319319
Sufficient
SCDO:0001511
Shetty A, Matrana MR. Renal medullary carcinoma: a case report and brief review of the literature. Ochsner J. 2014;14(2):270-5.
ORPHA:319319
Kidney Medullary Carcinoma
RMC
Renal Medullary Cancer
Renal Medullary Carcinoma
A part of anthropological linguistics concerned with the interrelation between a language and the cultural behavior of those who speak it.
Sufficient
SCDO:0001551
APAONTO:Ethnolinguistics
Ethnolinguistics
That period when the patient with sickle cell anaemia is free of infection, pain, or other disease processes.
Request inclusion into relevant ontology.
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.
Not relevant to context of sickle cell
SCD Steady State
Steady State
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.
deprecated-Renal Insufficiency
true
Not anemic, i.e. no reduction in erythrocytes volume and/or hemoglobin concentration.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Nonanemic
Non-Anemic
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.
http://purl.bioontology.org/ontology/MESH/D018389
Sufficient
SCDO:0001626
MESH:D018389
Nonsense Codon
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 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.
deprecated-Neuropathic Pain
true
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Trans Deletion of HBA2
Homozygous Deletion of HBA2
A mutation in the beta-globin gene, HBB, that results in reduced beta globin synthesis.
Request inclusion into relevant ontology
None
SCDO
Beta-Minus Thalassemia Mutation
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.
http://purl.obolibrary.org/obo/HP_0001649
Suggest update to description
HP:0001649
Fast Heart Rate
Heart Racing
Racing Heart
Tachycardia
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Crystallisation of Haemoglobin
Crystallization of Haemoglobin
Crystallization of Hemoglobin
Haemoglobin Crystallisation
Haemoglobin Crystallization
Hemoglobin Crystallisation
Hemoglobin Crystallization
Crystallisation of Hemoglobin
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.
Sufficient
SCDO:0002039
EFO:1000003
Zinc Deficiency
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.
http://www.ebi.ac.uk/efo/EFO_1001190
Sufficient
SCDO:0002106
EFO:1001190
Splenic Infarction
This represents the phenotypic feature of mutational effects on a given property of an organism biological system [Gaston K. Mazandu, []].
deprecated-Nature of Mutations
true
The privacy of information and its protection against unauthorized disclosure.
http://purl.bioontology.org/ontology/MESH/D003219
Sufficient
SCDO:0002125
MESH:D003219
Privileged Communications
Confidentiality
The pattern of gene expression at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.
http://purl.bioontology.org/ontology/MESH/D059467
Sufficient
SCDO:0002130
MESH:D059467
Gene Expression Levels
Gene Expression Profile
Gene Expression Profiles
Transcriptome
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.
Negligable
Severity
Disease Severity
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.
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Study Participant Compensation
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.
Research Participant Compensation
A mutation wholly or partly responsible for causing Hemoglobin D Disease.
None
SCDO (Jade Hotchkiss)
Hemoglobin D Disease Causal Mutation
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
Request inclusion into relevant ontology
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.
None
SCDO
Ethical Conduct
A mutation in the beta-globin gene, HBB, that results in absent beta globin synthesis.
Request inclusion into relevant ontology
None
SCDO
Beta Null Mutation
Beta-Zero Thalassemia Mutation
An abnormality of the body's metabolism or homeostasis.
Suggest update to description in HPO. Currenlty the HPO does not have a description.
Suggest update to description
HP:0001939
Homeostasis Abnormality
Metabolism Abnormality
Abnormality of Metabolism/Homeostasis
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).
Sufficient
SCDO:0002798
MESH:D000071184
Pharmacogenomic Variants
'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: []]'
http://www2.nau.edu/~bio372-c/class/evolution/glbgnclst.htm
deprecated Globin Gene
true
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.
Sufficient
SCDO:0002829
SIO:001050
Sample
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.
None
SCDO (Khuthala Mnika)
Hemoglobin Polymer
Polymerised Haemoglobin
Polymerized Hemoglobin
Sickle Hemoglobin Polymer
Sickling Hemoglobin
Polymerised Hemoglobin
A person's ethnic status, whether conserved or mixed ethnicity.
Request inclusion into relevant ontology
None
SCDO (curators)
Tribe
Ethnic Status
Genetic variation in the structure leading to the abnomality of protein structure in non-sickle cell disease hemoglobin.
Curation completed by the SCDO curator team: Clair.
obsolete Non-SCD Structural Variants
true
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.
http://purl.bioontology.org/ontology/MESH/D032962
Sufficient
SCDO:0003572
MESH:D032962
Consent Forms
Consent Form
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
Sufficient
SCDO:0003675
MESH:D020641
Single Nucleotide Polymorphism
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.
Request inclusion into relevant ontology
None
Peripheral Blood Film Examination
Peripheral Blood Smear
Peripheral Blood Film
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.
None
SCDO (Victoria Nembaware)
Third-Party Consent
Proxy Consent
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".
https://www.nature.com/articles/ejhg201471
None
SCDO
Dynamic Consent
Surgical procedure involving either partial or entire removal of the spleen.
Sufficient
SCDO:0003742
MESH:D013156
Splenectomies
Splenectomy
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"?
Suggest update to description
Abnormal Hemoglobin Variant
Abnormal Hemoglobins
Abnormal Variant of Hemoglobin
Abnormal Hemoglobin
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.
Request inclusion into relevant ontology.
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
None
Gap PCR
The genetic constitution of the individual, comprising the alleles present at each genetic locus.
Sufficient
SCDO:0004061
MESH:D005838
Genotype
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.
SCD Management guidelines - Tanzania
None
SCDO
Mesenteric Syndrome
Girdle Syndrome
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.
Few but definitions not specific enough
MESH:D006441
Adult Haemoglobin
Haemoglobin A
Haemoglobin A1
Hb A
HbA
Hemoglobin A
Hemoglobin A1
alpha2beta2
Adult Hemoglobin
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.
Request inclusion into relevant ontology
SCD Management guidelines - South Africa
Few but definitions not freely available
SCDO
Hemolytic Crisis
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.
Suggest update to description
ICO:0000143
Assent
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.
Request inclusion into relevant ontology
None
Crossover between delta and beta globin gene loci
Delta Beta Globin Chain Fusion Product
Delta Beta Globin Fusion Chain
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)
None
SCDO
Chronic Hypersplenism
The sequential set of three nucleotides in transfer RNA that interacts with its complement in messenger RNA, the Codon, during translation in the ribosome.
http://purl.bioontology.org/ontology/MESH/D000926
Sufficient
SCDO:0004598
MESH:D000926
Anticodon
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?
http://purl.bioontology.org/ontology/MESH/D003062
Sufficient
SCDO:0004623
MESH:D003062
Codon
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.
http://purl.bioontology.org/ontology/MESH/D018387
Sufficient
SCDO:0004716
MESH:D018387
Codon, Initiation
Codon, Initiator
Initiation Codon
Initiation Codons
Initiator Codons
Start Codon
Start Codons
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).
http://www.ebi.ac.uk/efo/EFO_0003764
Sufficient
SCDO:0004829
EFO:0003764
Mini Stroke
TIA
Transient Ischemic Attacks
Transient Ischemic Attack
A chest pain that is caused when your heart muscle doesn't get enough oxygen-rich blood.
Sufficient
SCDO:0004836
OAE:0002122
Angina
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.
Request inclusion into relevant ontology
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.
None
SCDO
Acute Hepatic Sequestration
'A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-(4-hydroxyphenyl)acetamido group. [Curator team: []]'
http://purl.obolibrary.org/obo/CHEBI_2676
CHEBI:2676
deprecated-Amoxicillin
true
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.
Few but definitions not freely available
SCDO
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.
FH
Functional Hyposplenism
Deletion of a part of the beta-globin locus.
Request inclusion into relevant ontology
None
SCDO
Beta-Globin Cluster Deletion
Beta-Globin Gene Cluster Deletion
Hemaglobin Beta Gene Deletion
Beta-Globin Locus Deletion
Long lasting form of anemia.
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?
Few but definitions not freely available
SCDO
Chronic 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.'
Request inclusion into relevant ontology
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
None
SCDO
Hyperhemolysis
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.
Sufficient
SCDO:0005243
MESH:D055028
CGH
Comparative Genome Hybridization
Comparative Genomic Analysis
Comparative Genomic Hybridizations
Comparative Genomic Hybridisation
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.
Negligable
SCDO (Jade Hotchkiss)
Reticulocyte Count High
deprecated High Reticulocyte Count
true
The physical characteristics of the globin polypeptides that form hemoglobins.
Request inclusion into relevant ontology.
https://www.ncbi.nlm.nih.gov/pubmed/20339107
None
Globin Chain Phenotype
Globin Phenotype
Work consisting of a structured file of information or a set of logically related data stored and retrieved using computer-based means.
http://purl.bioontology.org/ontology/MESH/D019991
Sufficient
SCDO:0005379
MESH:D019991
Data Base
Database
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.
Sufficient
SCDO:0005446
MESH:D005319
Fetal Haemoglobin
Foetal Haemoglobin
Haemoglobin F
Hb F
HbF
Hemoglobin F
Fetal Hemoglobin
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).
http://www.ebi.ac.uk/efo/EFO_1001375
Sufficient
SCDO:0005464
EFO:1001375
Myocardial Ischemia
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.
http://www.orpha.net/ORDO/Orphanet_86820
Orphanet:86820
ANFH
deprecated-Avascular Necrosis of the Femoral Head
true
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.
http://purl.bioontology.org/ontology/MESH/D005815
Sufficient
SCDO:0005593
MESH:D005815
Genetic Code
Deletion of the HBB and HBD genes that results in delta-beta thalassemia.
Request inclusion into relevant ontology
None
SCDO
HBB and HBD Deletion
A biological object that contains genetic information and that is involved in transmitting genetically encoded traits from one organism to another.
Sufficient
SCDO:0005722
MESH:D040342
Genetic Structures
Genetic Structure
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.
Request inclusion into relevant ontology
https://www.niehs.nih.gov/research/resources/bioethics/glossary/index.cfm#human-subjects-research
Few but definitions not specific enough
SCDO
Justice
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.
Suggest update to description
HP:0001945
NCIT:C3038
Pyrexia
Pyrogenic Reaction
Fever
A person who has not attained the age at which full civil rights are accorded.
http://purl.bioontology.org/ontology/MESH/D033242
Sufficient
SCDO:0006036
MESH:D033242
Minor
An ethnic group that includes persons with significant ethnic contributions from more than one group.
http://purl.obolibrary.org/obo/ERO_0002032
Sufficient
SCDO:0006070
ERO:0002032
Mixed Ethnicity
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.
http://purl.bioontology.org/ontology/MESH/D012106
Sufficient
SCDO:0006339
MESH:D012106
Research
An uncommon complication of cholecystitis and refers to a situation where the gallbladder lumen is filled and distended by purulent material (pus).
Request inclusion into relevant ontology
https://radiopaedia.org/articles/gallbladder-empyema
Few but definitions not freely available
SCDO
Gallbladder Empyema
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.
SCD Management guidelines - Tanzania
None
SCDO
Acutely Severe Anemia
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.
https://www.niehs.nih.gov/research/resources/bioethics/glossary/index.cfm#human-subjects-research
Not relevant to context of sickle cell
Human Subject Research
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.
Suggest update to description in MESH.
Suggest update to description
MESH:D017218
Fetal Blood Sampling
PUBS
Percutaneous Umbilical Cord Blood Sampling
Umbilical Vein Sampling
Cordocentesis
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.
Request inclusion into relevant ontology
Henderson J (2007) Counterpoint: MTAs are a practical necessity. Nat Biotechnol 25: 722–724.
None
MTA
Material Transfer Agreement
A branch of applied ethics that studies the value implications of practices and developments in life sciences, medicine, and health care.
http://purl.bioontology.org/ontology/MESH/D001675
Sufficient
SCDO:0006706
MESH:D001675
Biomedical Ethics
Health Care Ethics
Bioethics
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)
Sufficient
SCDO:0006832
MESH:D001206
Ascorbic Acid Deficiencies
Vitamin C Deficiencies
Vitamin C Deficiency
Ascorbic Acid Deficiency
A rare intracranial arteriopathy involving progressive stenosis of the cerebral vasculature located at the base of the brain causing transient ischemic attacks or strokes.
http://www.orpha.net/ORDO/Orphanet_2573
Sufficient
SCDO:0006833
ORPHA:2573
MMD
Moyamoya Disease
Hemoglobin that presents no inherited health condition phenotype.
Request inclusion into NCIT below "Hemoglobin".
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Hemoglobin Normal
Hemoglobin Normal Variant
Normal 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.
Request inclusion into relevant ontology
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.
SCD Management guidelines - Jamaica
SCD Management guidelines - Nigeria
SCD Management guidelines - South Africa
Few but definitions not freely available
SCDO
Aplastic Crises
Aplastic Crisis
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.
None
SCDO (Jade Hotchkiss)
HBG1 and/or HBG2 Mutations
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.
http://www.ebi.ac.uk/efo/EFO_1000975
Sufficient
SCDO:0006905
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
EFO:1000975
Hypersplenia
Hypersplenism
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.
Request inclusion into relevant ontology
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.
None
SCDO
Hyper-Hemolytic Crisis
An ethnic group that includes persons with ethnic contributions from only one ethnic group.
Request inclusion into relevant ontology
None
SCDO (curators)
Conserved Ethnicity
Hemoglobin with altered structural and biochemical properties.
Request inclusion into NCIT below "Hemoglobin".
https://www.ncbi.nlm.nih.gov/pubmed/23388674
None
SCDO (Clair Ingram)
Hemoglobin Variant
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.
Sufficient
SCDO:0007087
MESH:D007258
Informed Consent
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.
Request inclusion into relevant ontology
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.
Few but definitions not freely available
SCDO
Acute Crisis Splenic Sequestration
Acute Splenic Sequestration Crisis
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.
None
SCDO (Jade Hotchkiss)
Abnormal Hemoglobin Synthesis
Abnormal Synthesis Hemoglobinopathy
Synthesis Hemoglobinopathy
Quantitative Hemoglobinopathy
'Other molecules are complexes which do not contain protein or RNA, including lipids, carbohydrates, etc.'
obsolete Other Molecules
true
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.
Suggest update to description
HP:0000846
Hypoadrenalism
Adrenal Insufficiency
The probability that an event will occur. It encompasses a variety of measures of the probability of a generally unfavorable outcome.
http://purl.bioontology.org/ontology/MESH/D012306
Sufficient
SCDO:0007495
MESH:D012306
Risk
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.
Request inclusion into relevant ontology
Holzer et al 2014 Doi:10.1097/JIM.0000000000000097
Few but definitions not available
Community Engagement
Distinct geographical area.
This term was too general. Was replaced by "Geographic Area".
deprecated Major Area
true
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.
None
SCDO (Jade Hotchkiss)
Descriptor of Consent
In situ death of bone within the humeral head due to disruption of blood supply.
Has synonym: Osteonecrosis of the humeral head
http://www.wheelessonline.com/ortho/Humeral_Head_Osteonecrosis
deprecated-Avascular necrosis of the humeral head
true
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.
http://www.bioassayontology.org/bao#BAO_0170001
Sufficient
SCDO:0007623
BAO:0170001
Molecular Phenotype
HBB genetic variants that result in reduced or absent hemoglobin subunit beta production.
Request inclusion into relevant ontology
PMID: 20301599
None
SCDO
Beta Thalassemia Genotype
Hemolytic anemia, in which patients are compound or double heterozygous for both the sickle cell gene and a thalassemia gene.
Suggest update to description in NCIT
Suggest update to description
NCIT:C61237
Sickle Cell-Thalassemia
Sickle Cell Thalassemia
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.
Request inclusion into relevant ontology
None
SCDO
Ethics Approval
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;
None
Hemoglobin Epsilon
Embryonic Hemoglobin
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.
Suggest update to description in HPO.
SCD Management guidelines - Jamaica
Suggest update to description
HP:0011145
Provoked Seizures
Situation-Related Seizures
Acute Symptomatic Seizure
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Trans Deletion of HBA1
Homozygous Deletion of HBA1
A hemoglobinopathy caused by the presence of structurally abnormal hemoglobins.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Qualitative Hemoglobinopathy
Structural Hemoglobinopathy
Persistence of an inflammatory event in the articulation overtime.
Request inclusion into relevant ontology
None
SCDO
Chronic Arthritis
The obstruction of blood vessels by altered erythrocytes that can result in pain, anemia and tissue ischemia.
Request inclusion into relevant ontology
None
SCDO
Vaso-Occlusion
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.
Request inclusion into relevant ontology
SCD Management guidelines - Jamaica
Few but definitions not freely available
RUQ Pain
Right Upper Quadrant Pain
Right Upper Quadrant Syndrome
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
Suggest update to description
OMIABIS:0000000
Biobank
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.
Request inclusion into relevant ontology
Few but definitions not freely available
SCDO (Clair Ingram)
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.
Request inclusion into relevant ontology
"dental radiograph." Mosby's Medical Dictionary, 8th edition. 2009. Elsevier 7 Nov. 2018 https://medical-dictionary.thefreedictionary.com/dental+radiograph
None
Radiologic Examination, Teeth
Dental Radiograph
The removal of excess iron from the body with special drugs.
Request inclusion into MESH below "Chelation Therapy"
None
Iron Chelation Therapy
The capacity for self-governance, i.e. the ability to make reasonable decisions.
Request inclusion into relevant ontology
Few but definitions not freely available
SCDO
https://www.hhs.gov/ohrp/sites/default/files/the-belmont-report-508c_FINAL.pdf
Autonomy
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.
Suggest update to description in HPO
SCD Management guidelines - Jamaica
Suggest update to description
HP:0025342
Central Retinal Artery Occlusion
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).
Few but definitions not freely available
SCDO
HP:0002953
Compression Fracture
Fractures of Vertebral Bodies
Vertebral Body Compression
Vertebral Compression
Vertebral Compression Fractures
Vertebral Compression or Collapse
Vertebral Collapse
Principle dictating that harm should not come to individuals as a result of their participation in a research project.
Request inclusion into relevant ontology
Shamoo AE and Resnik DB, Responsible Conduct of Research, 3rd ed. (New York: Oxford University Press, 2015).
None
Non-Maleficience
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)
Sufficient
SCDO:0009117
EFO:0001070
Deficiency of Folic Acid
Deficiency of Folic Acid (Disorder)
Folic Acid Deficiencies
Folic Acid Deficiency
Folate Deficiency
A hemoglobinopathy caused by compound heterozygous inheritance of one hemoglobin S allele and one hemoglobin allele that produces structurally abnormal hemoglobin.
obsolete Sickle Plus Structural Variant
true
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".
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Unstable 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."
Suggest update to description
SCDO
Blood Trapped in the Spleen
Can cause severely acute anemia.
Splenic Sequestration
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.
http://www.ebi.ac.uk/efo/EFO_1001004
Sufficient
SCDO:0009445
EFO:1001004
Kidney Papillary Necrosis
Necrotising Renal Papillitis
Necrotizing Renal Papillitis
Papillary Necrosis
Papillary Necrosis (Disorder)
Renal Papillitis Necrotizing
Renal Papillary Necrosis
'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: []]'
http://purl.obolibrary.org/obo/CHEBI_25367
CHEBI:25367
obsolete Molecule
true
Effort made to secure the well-being of persons, maximizing possible benefits and minimizing possible harms.
https://www.hhs.gov/ohrp/sites/default/files/the-belmont-report-508c_FINAL.pdf
Few but definitions not specific enough
SCDO
MESH:D026686
Beneficence
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?
None
SCDO (Jade Hotchkiss)
Protein Phenotype
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?
Negligable
SCDO (Jade Hotchkiss)
deprecated Low Reticulocyte Count
true
'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: []]'
http://www.ihtc.org/medical-professionals/blood-disorders/sickle-cell-disease/aplastic-crisis-intervention/
deprecated Aplastic Crises
true
Pain resulting from tissue ischemia as a result of blockage of mesenteric blood vessels.
Request inclusion into relevant ontology
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.
SCD Management guidelines - Tanzania
Abdominal distension with generalised abdominal tenderness (no rebound tenderness) and reduced bowel sounds. Abdomen moves with respiration. Vomiting/diarrhoea are not common.
None
Abdominal Vaso-Occlusive Crisis
A mutation in the beta-globin gene, HBB, that causes decreased or absent beta-globin synthesis.
Request inclusion into relevant ontology
None
SCDO
Beta Thalassemia Mutation
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.
None
SCDO
Other HBB Variants
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.
Sufficient
SCDO:0009884
BAO:0170003
Biochemical Phenotype
'Genotypes which are not specific to sickle cell trait.'
obsolete Other Genotypes
true
The moral obligations governing the conduct of research. Used for discussions of research ethics as a general topic.
http://purl.bioontology.org/ontology/MESH/D032984
Sufficient
SCDO:0300002
MESH:D032984
Research Ethics
Specific genre of publication.
http://purl.bioontology.org/ontology/MESH/D052180
Sufficient
SCDO:0300003
MESH:D052180
Publication Formats
Types and formulations of studies used in epidemiological and clinical research.
Suggest update to description in MESH
http://purl.bioontology.org/ontology/MESH/D016020
Suggest update to description
MESH:D016020
Epidemiologic Study Characteristics
Elements, types, descriptions and formulations of a research study.
Request inclusion into relevant ontology
None
SCDO (Gaston K. Mazandu)
Research Characteristics
Revealing of information, by oral or written communication.
http://purl.bioontology.org/ontology/MESH/D030881
Sufficient
SCDO:0300006
MESH:D030881
Information Disclosure
Reporting to parents or guardians about care to be provided to a minor (minors).
http://purl.bioontology.org/ontology/MESH/D035622
Sufficient
SCDO:0300007
MESH:D035622
Parental Notification
A legal requirement that designated types of information acquired by professionals or institutions in the course of their work be reported to appropriate authorities.
http://purl.bioontology.org/ontology/MESH/D019221
Sufficient
SCDO:0300008
MESH:D019221
Mandatory Reporting
Making information permanently non-identifiable that is associated with the identity of specific entities via encryption or other methods.
Suggest update to description in MESH
http://purl.bioontology.org/ontology/MESH/D000068240
Suggest update to description
MESH:D000068240
Data De-Identification
Data Masking
De-Identification
Data Anonymization
An observable characteristic of disease that has a severe and rapid onset of symptoms with short duration.
Request inclusion into relevant ontology
http://purl.obolibrary.org/obo/NCIT_C14140
http://semanticscience.org/resource/SIO_010056
None
SCDO (Clair Ingram)
Acute Phenotype
A unique identifier generated either manually or electronically when adding a subject to a study.
deprecated Research Subject ID
true
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?
http://purl.bioontology.org/ontology/MESH/D017582
Sufficient
SCDO:1000004
MESH:D017582
Renal Replacement Therapy
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.
Request inclusion in the HPO, below "Abnormal Hemoglobin".
Few but definitions not freely available
Haemoglobin D
Hb D
HbD
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.
http://purl.bioontology.org/ontology/MESH/D006449
Suggest update to description
MESH:D006449
Hb M
HbM Hemoglobin
Hemoglobin M
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.
http://purl.bioontology.org/ontology/MESH/D006446
Sufficient
SCDO:1000009
MESH:D006446
Hb E
Hemoglobin E
A group of disorders caused by large deletions of the beta-globin gene complex; typically 30% fetal haemoglobin.
Request inclusion into relevant ontology
http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf?_tid=691c25c0-5826-11e7-b704-00000aacb35e&acdnat=1498230953_4d1264c47385275daf8fc2a1e1de62e3
None
HPFH-Sickle Cell Disease Syndrome
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
Sickle Cell Disease-S/HPFH
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.
Sufficient
SCDO:1000012
MESH:D055544
Beta-Globins
Beta-Globin Family Members
This gene encodes the hemoglobin subunit beta and is located on chromosome 11 mapped at 11p15.5.
Request inclusion into relevant ontology
Negligable
NCBIGene:3043
Beta-Globin Gene
HBB Gene
HBB1
Hemoglobin Beta Gene
Hemoglobin Beta Locus
Hemoglobin Subunit Beta Gene
HBB
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).
Suggest update to description in NCIT
http://purl.obolibrary.org/obo/NCIT_C84961
Suggest update to description
NCIT:C84961
HBD Gene
Hemoglobin Delta Gene
Hemoglobin Subunit Delta Gene
HBD
An abnormal hemoglobin that results from the substitution of glutamic acid with lysine at position 121 of the beta chain.
Request inclusion in the HPO, below "Abnormal Hemoglobin".
MESH and Zimmerman SA. Am J Hematol. 1999 Apr; 60(4) 279-84
Few but definitions not freely available
Hb O-Arab
Hb-Arab
Hemoglobin-Arab
Hemoglobin O-Arab
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.
http://purl.obolibrary.org/obo/ERO_0000378
Sufficient
SCDO:1000017
ERO:0000378
Surgery
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.
Request inclusion into relevant ontology
http://purl.bioontology.org/ontology/MESH/D015985
None
SCDO
Management of Precipitating Factors
Management of Underlying Cause
Treatment of Underlying Cause
Treatment of Precipitating Factors
'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.
http://www.geneontology.org/faq/what-evidence-code
obsolete Evidence Code
true
'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 []]'
http://geneontology.org/page/automatically-assigned-evidence-codes
obsolete IEA (inferred from electronic annotation)
true
'This should be used for information extracted from articles in the medical literature. [Curator team: []]'
obsolete PCS (published clinical study)
true
'Can be used for annotations based on individual clinical experience. [Curator team: []]'
obsolete ICE (individual clinical experience)
true
'Not described [Curator team: []]'
obsolete ITM (inferred by text-mining)
true
'Usually reviews or disease entries (e.g. OMIM) that only refers to the original publication. [Curator team: []]'
obsolete TAS (traceable author statement)
true
'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: []]'
http://www.geneontology.org/page/nas-non-traceable-author-statement
obsolete NAS (non-traceable author statement)
true
'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: []]'
http://www.geneontology.org/page/ic-inferred-curator
obsolete IC (inferred by curator)
true
Terms deprecated in the "Personal Attribute" class.
from personal attribute
A diagnostic instrument, technique, laboratory assay or test, or method of patient examination used for differential diagnosis.
Request inclusion into relevant ontology.
None
SCDO (Jade Hotchkiss)
Diagnostic Tool
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.
Request inclusion into relevant ontology
http://en.wikipedia.org/wiki/Questionnaire
Few but definitions not freely available
Diagnostic Questionnaire
Diagnostic Instrument
Terms deprecated in the "Diagnostics" class.
from diagnostics
Terms deprecated in the "Therapeutics" class.
from therapeutics
When the abnormal hemoglobin, hemoglobin C (HbC), has been detected in a blood sample.
Few but definitions not available
SCDO (Jade Hotchkiss)
Haemoglobin C Present
Haemoglobin C in Blood
HbC Present
HbC in Blood
Hemoglobin C in Blood
Hemoglobin C Present
An abnormality of the cerebral vasculature.
Few but definitions not available
HP:0100659
Abnormality of the Cerebral Blood Vessels
Cerebrovascular Disorder
Abnormality of the Cerebral Vasculature
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
None
SCDO (Jade Hotchkiss)
SCD Causal Mutation
The glutamic acid in position 6 in the primary sequence of a beta-chain produced by the HBB gene is replaced by valine.
Request inclusion into relevant ontology
http://www.bloodjournal.org/content/bloodjournal/46/3/363.full.pdf?sso-checked=true
Negligable
Beta S Mutation
E6V
Glu6Val
Sickle Cell Mutation
HBB, GLU6VAL
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.
Request inclusion into relevant ontology
Negligable
SCDO (Jade Hotchkiss)
Beta O-Arab Mutation
Contributing Beta S-Oman Mutation
Glu121Lys
HBB, GLU121LYS
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.
Request inclusion into relevant ontology
Negligable
SCDO (Jade Hotchkiss)
Beta C mutation
HbC Mutation
HBB, GLU6LYS
A mutation in the HBB gene causing substitution of glutamic acid for lysine at the 26th position of the beta-globin chain.
Request inclusion into relevant ontology
Negligable
SCDO (Jade Hotchkiss)
Beta E Mutation
HbE Mutation
HBB, GLU26LYS
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.
Sufficient
SCDO:1000043
MESH:D005783
Gender Identity
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.
Request inclusion into relevant ontology
http://www.bloodjournal.org/content/bloodjournal/46/3/363.full.pdf?sso-checked=true
Negligable
SCDO (Jade Hotchkiss)
Asp73Asn
D73N
HBB, ASP73ASN
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.
Request inclusion into relevant ontology
Negligable
SCDO (Jade Hotchkiss)
Contributing Beta S-Antilles Mutation
Contributing Hb S-Antilles Mutation
HBB, VAL23ILE
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.
Request inclusion into relevant ontology
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.
Negligable
SCDO (Jade Hotchkiss)
Hb Quebec-Chori Mutation
HBB, THR87ILE
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.
Request inclusion into relevant ontology
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.
Negligable
SCDO (Jade Hotchkiss)
Contributing Hb Jamaica Plain Mutation
HBB, LEU68PHE
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?
http://www.nature.com/scitable/definition/genotype-234
None
SCDO (Jade Hotchkiss)
Sickle Cell Disease Genotype
Sickle Genotype
SCD Genotype
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Haemoglobin Genotype SC
SC Genotype
beta6Glu>Val/beta6Glu>Lys
Hemoglobin Genotype SC
Compound heterozygosity for the hemoglobin S (HBB Glu6Val) and hemoglobin D-Punjab (HBB Glu121Gln) variants.
Hemoglobin Genotype S/D-Punjab
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
None
Haemoglobin Genotype S/D-Punjab
S/D-Punjab Genotype
beta6Glu>Val/beta121Glu>Gln
Hemoglobin Genotype S/D-Punjab
Compound heterozygosity for the hemoglobin S (HBB Glu6Val) and hemoglobin O-Arab (HBB GluU121Lys) variants.
Request inclusion into relevant ontology
Lancet. 2010 Dec 11;376(9757):2018-31. doi: 10.1016/S0140-6736(10)61029-X. Epub 2010 Dec 3.
None
Haemoglobin Genotype S/OArab
S/O-Arab Genotype
beta6Glu>Val/beta121Glu>Lys
Hemoglobin Genotype S/O-Arab
Compound heterozygosity for the hemoglobin S (HBB Glu6Val) and hemoglobin E (HBB Glu26Lys) variants.
Request inclusion into relevant ontology
Lancet. 2010 Dec 11;376(9757):2018-31. doi: 10.1016/S0140-6736(10)61029-X. Epub 2010 Dec 3.
None
Haemoglobin Genotype SE
SE Genotype
SE Hemoglobin Genotype
beta6Glu>Val/beta26Glu>Lys
Hemoglobin Genotype SE
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.
Request inclusion into relevant ontology
Few but definitions not specific enough
SCDO (Jade Hotchkiss)
Haemoglobin Genotype SS
Hemoglobin S Genotype
SS Genotype
beta6Glu>Val/beta6Glu>Val
Hemoglobin Genotype SS
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).
Request inclusion into relevant ontology
None
SCDO
Haemoglobin Genotype SD
SD Genotype
Hemoglobin Genotype SD
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).
Request inclusion into relevant ontology
PMID: 1148394
None
SCDO
Haemoglobin Genotype S/C-Harlem
S/C-Harlem Genotype
beta6Glu>Val/beta6Glu>Val, beta73Asp>Asn
Hemoglobin Genotype S/C-Harlem
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".
https://www.omim.org/entry/141900#0243
Few but definitions not freely available
SCDO (Jade Hotchkiss)
HbS-HBC-Harlem
Hemoglobin C-Georgetown
Hemoglobin S-Hemoglobin C-Harlem
Hemoglobin C-Harlem
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.
Request inclusion into NCIT below "Hemoglobin Trait".
None
SCDO (Jade Hotchkiss)
Hb AD-Punjab
Hemoglobin D-Punjab Trait causes no clinical or hematological alterations
Hemoglobin D-Punjab Trait
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?
None
SCDO (Clair Ingram)
SCD Molecular Phenotype
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).
Probably too specific to SCD be included in other ontologies.
None
SCDO (Jade Hotchkiss)
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.
Request inclusion into relevant ontology
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.
None
SCDO (Clair Ingram)
SC(Harlem) Disease
Sickle Cell-Hemoglobin C-Harlem Disease
Sickle Cell Disease-S/C-Harlem
A 106-kb deletion of the beta globin gene cluster.
Request inclusion into relevant ontology
Negligable
SCDO (Jade Hotchkiss)
HPFH1
HBB, 106-KB DEL
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.
https://www.genome.gov/27559022/informed-consent-glossary/
None
Tiered Consent
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".
https://www.alrc.gov.au/publications/15-human-genetic-research-and-consent/specific-consent
None
SCDO
Specific 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?
Suggest update to label
NCIT:C92262
Fetal Hemoglobin Test
HGBF Test
Hemoglobin F Test
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.
Request inclusion into relevant ontology
None
S/Beta-Zero-Thal Genotype
S/Beta-Zero-Thalassaemia Genotype
S/Beta-Zero-Thalassemia
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-Thal
Severe S/Beta-Plus-Thal Genotype
Severe S/Beta-Plus-Thalassaemia Genotype
deprecated Severe S/Beta-Plus-Thal
true
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.
Request inclusion into relevant ontology
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
None
SCDO (Clair Ingram)
Haemoglobin Genotype S/HPFH
S/HPFH Genotype
Hemoglobin Genotype S/HPFH
A compound heterozygous genotype, involving the mutations for Hemoglobin S (beta6Glu>Val) and Hemoglobin Lepore Boston.
Request inclusion into relevant ontology
PMID: 7055103
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.
None
Haemoglobin Genotype S/Lepore
S/Lepore
S/Lepore Boston Genotype
S/Lepore Genotype
Hemoglobin Genotype S/Lepore Boston
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.
Request inclusion into relevant ontology
http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf?_tid=691c25c0-5826-11e7-b704-00000aacb35e&acdnat=1498230953_4d1264c47385275daf8fc2a1e1de62e3
None
A/Jamaica Plain Genotype
A/Jamaica Plain Haemoglobin Genotype
A/Jamaica Plain Hemoglobin Genotype
Haemoglobin Genotype A/Jamaica Plain
Hemoglobin Genotype A/Jamaica Plain
A sickling hemoglobin with reduced oxygen affinity that causes severe hemolytic anemia and sickling of erythrocytes.
Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions".
http://www.nejm.org/doi/full/10.1056/NEJMoa040771#t=article
None
SCDO (Jade Hotchkiss)
Hb JP
Hb Jamaica Plain
Hemoglobin JP
Hemoglobin Jamaica Plain
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.
Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions".
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Hemoglobin S-Antilles
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.
Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions".
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.
Negligable
SCDO (Jade Hotchkiss)
Hb S-Oman
Hemoglobin S (Oman)
Hemoglobin S-Oman
Dominant heterozygosity for the double HBB Glu6Val and Glu121Lys mutation.
Request inclusion into relevant ontology
PMID: 9834244
None
A/S-Oman Genotype
A/S-Oman Haemoglobin Genotype
A/S-Oman Hemoglobin Genotype
Haemoglobin Genotype A/S-Oman
Hemoglobin Genotype A/S-Oman
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.
Request inclusion into relevant ontology
Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031.
None
SCDO (Clair Ingram)
Mild Sickle Cell Disease-S Beta Minus Thalassaemia
Mild Sickle Cell-Beta Minus Thalassaemia
Mild Sickle Cell-Beta Minus Thalassemia
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.
Request inclusion into relevant ontology
Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031.
None
SCDO (Clair Ingram)
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.
Request inclusion into relevant ontology
Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031.
None
SCDO (Clair Ingram)
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: []]'
Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031.
Moderate S/Beta-Plus-Thalassaemia
deprecated Moderate S/Beta-Plus-Thal
true
'Not described [Curator team: []]'
Mild S/Beta-Plus-Thalassaemia
deprecated Mild S/Beta-Plus-Thal
true
Compound heterozygosity for the hemoglobin C (HBB Glu6Lys) mutation and the double HBB Glu6Val, Val23Ile mutation of hemoglobin S-Antilles.
Request inclusion into relevant ontology
DOI: 10.1016/S0140-6736(10)61029-X
PMID: 21131035
None
C/S Antilles Genotype
C/S Antilles Haemoglobin Genotype
C/S Antilles Hemoglobin Genotype
Haemoglobin Genotype C/S Antilles
beta6Glu>Lys/beta6Glu>Val, beta23Val>Ile
Hemoglobin Genotype C/S Antilles
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".
None
Doubly Substituted Sickling 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.
Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions".
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.
Negligable
SCDO (Jade Hotchkiss)
Hemoglobin S-South End
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.
Request inclusion into relevant ontology
Pediatr Blood Cancer. 2007 Aug;49(2):207-10.
None
SCDO
Haemoglobin Genotype S/Quebec-Chori
S/Quebec-Chori Genotype
beta6Glu>Val/beta87Thr>Ile
Hemoglobin Genotype S/Quebec-Chori
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
Suggest update to description
http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf?_tid=691c25c0-5826-11e7-b704-00000aacb35e&acdnat=1498230953_4d1264c47385275daf8fc2a1e1de62e3
MESH:C070823
Hb Quebec-Chori
Hemoglobin Quebec Chori
A severe compound heterozygous sickling disorder characterized by the presence of both hemoglobin S and hemoglobin Quebec Chori.
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None
SCDO (Jade Hotchkiss)
Sickle Cell-Hemoglobin Quebec Chori Disease
Sickle Cell Disease-S/Quebec Chori
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.
Request inclusion into relevant ontology
Negligable
SCDO (Jade Hotchkiss)
Contributing Beta S-South End Mutation
Contributing Hb S-South End Mutation
Hb Yamagata Mutation
LYS132ASN
HBB, LYS132ASN
A compound heterozygous genotype, involving the mutations for hemoglobin S and hemoglobin S-South End.
Request inclusion into relevant ontology
None
Haemoglobin Genotype S/S-South End
S/S-South End Genotype
beta Glu6Val, GAG>GTG/beta Glu6Val, GAG>GTG; beta Lys132Asn, AAA>AAC
beta6Glu>Val/beta132Lys>Asn
Hemoglobin Genotype S/S-South End
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
http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome#Homozygous_Hb_Lepore
http://globin.cse.psu.edu/html/huisman/variants/hybrid/Lepore-Boston-Washington.html
Few but definitions not freely available
Hb Lepore Boston-Washington
Hb Lepore-B-W
Hb Lepore-Boston-Washington
Hb Lepore-WB
Hb Lepore-Washington-Boston
Hemoglobin Lepore Boston-Washington
Hemoglobin Lepore-Boston-Washington
Hemoglobin Lepore Boston
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.
Request inclusion into relevant ontology
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.
None
SCDO (Clair Ingram)
Sickle Cell-Hemoglobin S-South End Disease
Sickle Cell Disease-S/S-South End
'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: []]'
deprecated Sickle beta plus thalassemia
true
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.
Ask a clinician if this is different to a cluster headache?
https://meshb.nlm.nih.gov/record/ui?ui=D003027
MESH:D003027
deprecated-Acute Severe Headache
true
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.
Sufficient
SCDO:1000093
OAE:0000001
Adverse Reaction
Adverse Event (AE)
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.
Request inclusion into relevant ontology
Shamoo AE and Resnik DB, Responsible Conduct of Research, 3rd ed. (New York: Oxford University Press, 2015).
None
SCDO
Research 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.
http://purl.bioontology.org/ontology/MESH/D016265
Few but definitions not specific enough
MESH:D016265
Interest Conflict
Conflict of Interest
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).
Sufficient
SCDO:1000097
ERO:0001964
Human Subject
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
None
SCDO
Case Report Form (CRF)
Genes with alleles that affect the phenotype associated with a nonallelic gene.
Sufficient
SCDO:1000099
MESH:D060045
Gene, Modifier
Modifier Gene
The type of ICD-10-CM code, in terms of a code's usability for reimbursement purposes.
None
SCDO (Jade Hotchkiss)
ICD-10-CM Code Type
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.
Sufficient
SCDO:1000103
MESH:D056426
Genetic Loci
Loci, Genetic
Locus, Genetic
Genetic Locus
The protein subunits that comprise multimeric hemoglobins.
Sufficient
SCDO:1000104
MESH:D055554
Hemoglobin Subunits
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.
Sufficient
SCDO:1000105
MESH:D055542
Alpha-Globins
Alpha-Globin Family Members
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.
Few but definitions not specific enough
Banana Cell Disease
Drepanocytosis
SCD
Sickle Cell Disorder
Sickle Cell Hemoglobinopathy
Sickle Hemoglobinopathy
Sickle-Cell Disorder
Sickle Cell Disease
The combination of the hemoglobin S mutation (beta6Glu>Val) and a beta-thalassemia mutation.
Request inclusion into relevant ontology
None
Hemoglobin Genotype S/Beta Thalassaemia
S/Beta -Thal Genotype
S/Beta -Thalassaemia Genotype
Hemoglobin Genotype S/Beta Thalassemia
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.
Request inclusion into relevant ontology
Negligable
SCDO (Jade Hotchkiss)
Beta D-Agri Mutation
HBB, SER9TYR
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.
Request inclusion into relevant ontology
Negligable
SCDO (Jade Hotchkiss)
Beta 121Glu>Gln
Beta D-Punjab Mutation
Derived from a point mutation in the beta-globin gene (HBB: c.364G>C; rs33946267).
HBB, GLU121GLN
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.
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Negligable
SCDO (Jade Hotchkiss)
Beta D-Bushman Mutation
HBB, GLY16ARG
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.
Request inclusion into relevant ontology
Negligable
SCDO (Jade Hotchkiss)
Beta D-Ouled Rabah Mutation
HBB, ASN19LYS
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.
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Negligable
SCDO (Jade Hotchkiss)
Beta D-Iran Mutation
HBB, GLU22GLN
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.
Request inclusion into relevant ontology
Negligable
SCDO (Jade Hotchkiss)
Beta D-Granada Mutation
HBB, GLU22VAL
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.
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Negligable
SCDO (Jade Hotchkiss)
Beta D-Ibadan Mutation
HBB, THR87LYS
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.
Request inclusion into relevant ontology
Negligable
SCDO (Jade Hotchkiss)
Beta D-Neath Mutation
HBB, GLU121ALA
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?
Negigable
Demographic and Health Surveys Program (2011-2012)
Adja Ethnic Group
Adja
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
Negligable
Demographic and Health Surveys Program (2011-2012)
Bariba Ethnic Group
Bariba
Negligable
Dendi Ethnic Group
Dendi
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
None
Demographic and Health Surveys Program (2011-2012)
Fon Ethnic Group
Fon
None
Yoa Ethnic Group
Yoa
None
Betamaribe Ethnic Group
Betamaribe
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
Negligable
Demographic and Health Surveys Program (2015)
Embu Ethnic Group
Embu
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
None
Demographic and Health Surveys Program (2015)
Kalenjin Ethnic Group
Kalenjin
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
None
Demographic and Health Surveys Program (2015)
Kamba Ethnic Group
Kamba
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
Few but definitions not freely available
Demographic and Health Surveys Program (2015)
Kikuyu Ethnic Group
Kikuyu
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
Few but definitions not specific enough
Demographic and Health Surveys Program (2015)
Gusii
Kisii Ethnic Group
Kisii
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).
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
None
Demographic and Health Surveys Program (2015)
Luhya Ethnic Group
Luhya
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
Few but definitions not freely available
Demographic and Health Surveys Program (2015)
Luo Ethnic Group
Luo
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
None
Demographic and Health Surveys Program (2015)
Maasai Ethnic Group
Maasai
None
Peulh Ethnic Group
Peulh
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
Few but definitions not specific enough
Demographic and Health Surveys Program (2011-2012)
Yoruba Ethnic Group
Yoruba
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
Not relevant to context of sickle cell
Demographic and Health Surveys Program (2015)
Meru Ethnic Group
Meru
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
Negligable
Demographic and Health Surveys Program (2015)
Mijikenda
Mijikenda Ethnic Group
Mijikenda/Swahili
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
Few but definitions not freely available
Demographic and Health Surveys Program (2015)
Somali Ethnic Group
Somali
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?
Negligable
Demographic Health and Surveys Program (2015)
Taita/Taveta Ethnic Group
Taveta Ethnic Group
Taita/Taveta
The Borana are a branch of the populous Oromo people found in southern Ethiopia and northern Kenya.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
Negligable
Demographic and Health Surveys Program (2015)
Borana Ethnic Group
Borana
It is the second largest sub-tribe of the Luhya ethnic group in Kenya.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
None
Demographic and Health Surveys Program (2015)
Maragoli Ethnic Group
Maragoli
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
None
Demographic Health and Surveys Program (2015)
Pokot Ethnic Group
Pokot
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.
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
None
Demographic and Health Surveys Program (2015)
Turkana Ethnic Group
Turkana
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).
Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT?
Negligable
Demographic and Health Surveys Program (2013)
Bassa Ethnic Group
Bassa
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.
Sufficient
SCDO:1000142
BAO:0000049
Spectrophotometry Method
Spectrophotometry
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.
Sufficient
SCDO:1000143
SCDO (Jade Hotchkiss)
FaBiO:d4e2515
Clinical Guideline
Disease Management Guideline
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.
None
South African Management Guidelines
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.
Probably not necessary to include in other ontologies.
National guideline for the control and management of sickle cell disease. 2014.
None
A Nigerian document.
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.
Probably not necessary to include in other ontologies.
Management of Sickle Cell Disease - The United Republic of Tanzania
None
SCDO (Jade Hotchkiss)
Tanzania Management Guidelines
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.
Probably not necessary to include in other ontologies.
A parent's guide to managing sickle cell disease. Brent Sickle Cell and Thalassaemia Centre. 3rd Edition 2012.
None
A UK document.(for parents)
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.
Probably not necessary to include in other ontologies.
Standards for Clinical Care of Adults with Sickle Cell Disease in the UK, 2nd Edition. 2018, Sickle Cell Society.
None
A UK document (for adults with SCD)
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.
Probably not necessary to include in other ontologies.
Sickle Cell Disease: The Clinical Care Guidelines of the Sickle Cell Unit, 2015
None
SCDO (Jade Hotchkiss)
Jamaican Management Guidelines
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.
Probably not necessary to include in other ontologies.
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.
None
A Canadian document.
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.
Probably not necessary to include in other ontologies.
Sickle cell disease in children, standards and guidelines for clinic care. 2nd edition. October 2010
None
A UK document (for children with SCD)
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.
Probably not necessary to include in other ontologies.
Evidence-Based Management of Sickle Cell Disease: Expert Panel Report, 2014
None
USA Management Guidelines Children
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.
Probably not necessary to include in other ontologies.
None
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.
European document (Colombatti)
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.
Probably not necessary to include in other ontologies.
None
Am J Hematol. 2011 Jan;86(1):72-5. doi: 10.1002/ajh.21865.
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.
Sufficient
SCDO:1000155
EDDA:familial_study
Familial Studies
Familial Study
Family Based Study
Family Study
Family Study
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?
None
SCDO (Jade Hotchkiss)
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.
Request inclusion into the HPO, below "Abnormal Hemoglobin".
None
SCDO (Jade Hotchkiss)
Crystallised Haemoglobin
Crystallized Haemoglobin
Crystallized Hemoglobin
Haemoglobin Crystals
Hemoglobin Crystals
Crystallised Hemoglobin
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
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"?
Sufficient
SCDO:1000160
MESH:D016431
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.
Request inclusion into relevant ontology
None
SCDO
Haemoglobin Genotype AS
Sickle Cell Trait Genotype
Hemoglobin Genotype AS
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
Dominant Sickle Cell Disease
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
true
A hemoglobinopathy in which the sickle mutation (HBB, Glu6Val) is inherited in combination with another beta-globin gene mutation, other thanHBB, Glu6Val.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Compound Heterozygous Sickling Disorder
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Sickle Cell Disease A/Jamaica Plain
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Sickle Cell Disease A/S-Oman
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Sickle Cell Disease C/S Antilles
A directive information entity that specifies how to establish a diagnosis based on clinical findings.
Sufficient
SCDO:1000170
AERO:0000001
Diagnosis Guideline
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.
None
SCDO (Jade Hotchkiss)
Specific ICD-10-CM Code
Billable ICD-10-CM 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.
None
SCDO (Jade Hotchkiss)
Non-specific ICD-10-CM Code
Non-Billable ICD-10-CM Code
-
Few but definitions not freely available
ICD10CM:N48.32
N48.32
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.
None
SCDO (Jade Hotchkiss)
SickleInAfrica Extended Demographics DE
SickleInAfrica Extended Demographics Data Element
A lack of production of hemoglobin E.
Few but definitions not available
SCDO (Jade Hotchkiss)
Absent Haemoglobin E
Haemoglobin E Absent
Hemoglobin E Absent
Normal Haemoglobin E Level
Normal Hemoglobin E Level
Absent Hemoglobin E
When the abnormal hemoglobin, hemoglobin E (HbE), has been detected in a blood sample.
Few but definitions not available
SCDO (Jade Hotchkiss)
Haemoglobin E Present
Haemoglobin E in Blood
HbE Present
HbE in Blood
Hemoglobin E in Blood
Hemoglobin E Present
When the level of hemoglobin A2 detected in a sample of blood falls in the normal range for HbA2.
None
SCDO (Jade Hotchkiss)
Normal Haemoglobin A2 Level
Normal HbA2 Level
Normal Hemoglobin A2 Concentration
Normal Hemoglobin A2 Level
A test to detect both HIV antibodies and HIV antigens (a part of the virus) in blood.
Request inclusion into relevant ontology.
None
SCDO (Khuthala Mnika)
Antibody/Antigen Tests
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.
HIV Combination Test
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.
None
SCDO (Khuthala Mnika)
NAT
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.
HIV Nucleic Acid Test
NAT
An abnormal albumin excretion rate of more than 300 mg/g urine creatinine.
Request inclusion into relevant ontology
Few but definitions not freely available
Macro-albuminuria
Macroalbuminuria
High Level Albuminuria
A clinically severe form of sickle cell disease resulting when a person is homozygous for Hemoglobin C-Harlem.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Hemoglobin C-Harlem Disease
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.
Sufficient
SCDO:1000206
MESH:D011995
Recombination
Recombination, Genetic
Genetic Recombination
An exchange of DNA between matching or similar sequences.
Sufficient
SCDO:1000207
MESH:D059765
Homologous Recombinations
Homologous Recombination
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.
link this term to
Sufficient
SCDO:1000208
MESH:D003434
Crossing Over, Genetic
Genetic Crossing Over
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
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.
None
SCDO (Jade Hotchkiss)
Dominant Sickle Cell Syndrome
Dominant Sickle Syndrome
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.
Dominant Sickle Cell Disease
deprecated Disease Caused by A/Jamaica Plain Genotype
true
deprecated Disease Caused by A/S-Oman Genotype
true
deprecated Disease Caused by C/S Antilles Genotype
true
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.
None
SCDO (Jade Hotchkiss)
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
-/alpha alpha/alpha
Alpha Thalassemia Silent Genotype
Increased susceptibility to bruising.
Suggest update to label of HPO's "Bruising Susceptibility".
"Bruising Susceptibility" and "Easy Bruisability" are not actually the same thing.
Suggest update to label
SCDO (Jade Hotchkiss)
Bruisability, Bruising susceptibility, Easy bruising
Bruise Easily
Bruising Susceptibility
Easy Bruising
Easy Bruisability
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.
None
SCDO (Clair Ingram)
AC Genotype
AC Hemoglobin Genotype
Haemoglobin Genotype AC
Hemoglobin C Trait Genotype
beta / beta6Glu>Lys
Hemoglobin Genotype AC
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.
None
SCDO (Clair Ingram)
AD Genotype
AD Hemoglobin Genotype
Haemoglobin Genotype AD
Hemoglobin D Trait Genotype
Hemoglobin Genotype AD
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.
Request inclusion into relevant ontology
None
SCDO (Clair Ingram)
AE Genotype
AE Hemoglobin Genotype
Haemoglobin Genotype AE
Hemoglobin E Trait Genotype
beta / beta26Glu>Lys
Hemoglobin Genotype AE
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
AO-Arab Genotype
AO-Arab Hemoglobin Genotype
Haemoglobin Genotype AO-Arab
beta / beta121Glu>Lys
Hemoglobin Genotype AO-Arab
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
EE Genotype
EE Hemoglobin Genotype
Haemoglobin Genotype EE
Hemoglobin E Genotype
beta6Glu>Lys / beta26Glu>Lys
Hemoglobin Genotype EE
The homozygous genotype that involves a hemoglobin D mutation in both beta-globin gene (HBB) alleles.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
DD Genotype
DD Hemoglobin Genotype
Haemoglobin Genotype DD
Hemoglobin C Genotype
Hemoglobin Genotype DD
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.
Probably not necessary to include in other ontologies.
None
SCDO (Jade Hotchkiss)
Haemoglobin Genotype O-Arab
O-Arab Genotype
O-Arab Hemoglobin Genotype
beta121Glu>Lys / beta121Glu>Lys
Hemoglobin Genotype O-Arab
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
CC Genotype
CC Hemoglobin Genotype
Haemoglobin Genotype CC
Hemoglobin C Genotype
beta6Glu>Lys / beta6Glu>Lys
Hemoglobin Genotype CC
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Haemoglobin Genotype M
Hemoglobin M Genotype
Hemoglobin Genotype M
Hemoglobin M Disease is autosomal dominant, thus does not seem to have a "trait" condition.
obsolete - Hemoglobin M trait Genotype
true
Either homozygosity or heterozygosity for the HPFH1 mutation, a 106-KB deletion in the beta globin gene cluster.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Hemoglobin Lepore Boston Genotype
The inheritance of one normal HBB gene along with an abnormal HBB gene that contains two amino acid substitutions, namely Glu6Val (HbS) and Asp73Asn.
Request inclusion into NCIT below "Hemoglobin Trait".
None
SCDO (Jade Hotchkiss)
Hb CH-Trait
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.
Hemoglobin C-Harlem Trait
A mutation in the NADH-Cytochrome b5 Reductase 3 gene, CYB5R3, that contributes to the presence of methemoglobinemia (type I or II).
Request inclusion into relevant ontology
None
DIA 1 Mutation
Diaphorase Mutation
Methemoglobinemia Mutation
NADH-Cytochrome b5 Reductase 3 Mutation
CYB5R3 Mutation
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).
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Heterozygous Deletion of HBA1 or HBA2
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?
None
SCDO (Jade Hotchkiss)
Reduced or Absent Hemoglobin A
A lack of production of normal adult hemoglobin.
Request inclusion into HPO below "Abnormal Hemoglobin Concentration".
Negligable
SCDO (Jade Hotchkiss)
Hemoglobin A Absent
Absent Hemoglobin A
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).
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Autosomal Homozygous Recessive Inheritance
Autosomal Recessive Homozygous
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).
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
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).
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Glutamine Oral Powder
Glutamine Oral Powder Product
Glutamine Powder
L-Glutamine Powder
Oral Glutamine
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.
L-Glutamine Oral Powder
A phenotype in which a specific molecular function is abnormal.
Sufficient
SCDO:1000250
FYPO:0000707
deprecated Abnormal Molecular Function
true
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.
Suggest update to description.
SCDO (Jade Hotchkiss)
HP:0005502
Increased Erythrocyte Osmotic Fragility
Increased Red Cell Fragility
Increased Red Cell Osmotic Fragility
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.
Few but definitions not freely available
HP:0005546
Increased Red Cell Osmotic Resistance
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.
Sufficient
SCDO:1000253
FYPO:0005447
Abnormal Biological Process
When deoxygenated, malfunctioning or mutated hemoglobins clump together and form a long polymer.
None
SCDO (Jade Hotchkiss)
Hemoglobin Polymerisation
Polymerisation of Hemoglobin
Guidelines that examine current available evidence on indications for transfusion in sickle cell disease.
Probably not necessary to include in other ontologies.
Br J Haematol. 2017 Jan;176(2):192-209. doi: 10.1111/bjh.14383. Epub 2016 Nov 18.
None
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.
Probably not necessary to include in other ontologies.
None
SCDO
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.
Probably not necessary to include in other ontologies.
None
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.
Probably not necessary to include in other ontologies.
Am Fam Physician. 2000 Mar 1;61(5):1544-1550.
None
SCDO
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".
None
SCDO (Jade Hotchkiss)
Unusual Hemoglobin Variant
Unusual Hemoglobin
Any feeling of illness or physical or mental change that results from strenuous exercise.
Suggest update to description in OMIM (currently no description provided).
Few but definitions not freely available
OMIM:MTHU024836
Symptom Induced by Strenuous Exercise
A condition due to a deficiency of one or more essential vitamins. (Dorland, 27th ed)
Sufficient
SCDO:1000261
MESH:D001361
Vitamin Deficiencies
Vitamin Deficiency
Avitaminosis
Abnormality originating in one or more muscles of the set of muscles in the body.
Suggest update to description
HP:0003011
Abnormality of the Musculature
An abnormal level of hemoglobin that occurs in one or more forms of Sickle Cell Disease (SCD).
Probably too specific to SCD be included in other ontologies.
None
SCDO (Jade Hotchkiss)
Abnormal Hemoglobin Level in SCD
Hemochromatosis that results from repeated blood transfusions.
Request inclusion into relevant ontology
None
SCDO
Transfusion Haemochromatosis
Transfusion-Induced Iron Overload
Transfusion Hemochromatosis
An acquired metabolic disorder characterized by iron accumulation in the tissues.
Suggest inclusion into existing ontology.
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Secondary Hemochromatosis
When the abnormal hemoglobin, hemoglobin D-Punjab (Hb D-Punjab), has been detected in a blood sample.
None
SCDO (Jade Hotchkiss)
Haemoglobin D-Punjab Present
Haemoglobin D-Punjab in Blood
Hb D-Punjab Present
Hb D-Punjab in Blood
Hemoglobin D-Punjab in Blood
Hemoglobin D-Punjab Present
When the abnormal hemoglobin, hemoglobin G-Philadelphia (Hb G-Philadelphia), has been detected in a blood sample.
None
SCDO (Jade Hotchkiss)
Haemoglobin G-Philadelphia Present
Haemoglobin G-Philadelphia in Blood
Hb G-Philadelphia Present
Hb G-Philadelphia in Blood
Hemoglobin G-Philadelphia in Blood
Hemoglobin G-Philadelphia Present
When the abnormal hemoglobin, hemoglobin O-Arab (Hb O-Arab), has been detected in a blood sample.
None
SCDO (Jade Hotchkiss)
Haemoglobin O-Arab Present
Haemoglobin O-Arab in Blood
Hb O-Arab Present
Hb O-Arab in Blood
Hemoglobin O-Arab in Blood
Hemoglobin O-Arab Present
When the level of hemoglobin F detected in a sample of blood falls in the normal range for HbF.
None
SCDO (Jade Hotchkiss)
Normal Haemoglobin F Level
Normal HbF Level
Normal Hemoglobin F Concentration
Normal Hemoglobin F Level
The score obtained from a quality of life-related diagnostic instrument.
Request inclusion into relevant ontology
Negligable
SCDO (Jade Hotchkiss)
Quality of Life Score
Quality of Life Assessment Score
The score obtained from the Adult Sickle Cell Quality-of-Life Measurement Information System (ASCQ-Me) diagnostic instrument.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
ASCQ-Me - Quality of Life in SCD Score
Sickle Cell Disease Adult Quality of Life Questionnaire Assessment Score
ASCQ-Me Score
A diagnostic instrument that involves an assessment of quality of life- and/or quality of care-related elements.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
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")
Suggest update to label
NCIT:C64850
HBSAG Test
HBsAg Test
Hepatitis B Surface Antigen Test
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.
Hepatitis B Virus Surface Antigen Test
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")
Suggest update to label
NCIT:C74711
HBSAB Test
HBsAb Test
Hepatitis B Virus Surface Antibody Test
anti-HBs Test
Hepatitis B Surface Antibody Test
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")
Suggest update to label
NCIT:C96660
Anti-HBc Test
HBCAB Test
HBcAB Test
Hepatitis B Virus Core Antibody Test
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.
Hepatitis B Core Antibody Test
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Hepatitis B Panel
Hepatitis B Panel of Blood Tests
Hepatitis B Blood Panel
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")
Suggest update to label
NCIT:C125944
HBAB Test
Hepatitis B Antibody Test
Hepatitis B Virus Antibody Test
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")
Suggest update to label
NCIT:C119280
HBCIGGAB Test
Hepatitis B Virus Core IgG Antibody Test
Hepatitis B 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")
Suggest update to label
NCIT:C96661
HBCIGMAB Test
Hepatitis B Virus Core IgM Antibody Test
Hepatitis B 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
Sufficient
SCDO:1000305
phenX:91001
Pulse Oximetry (Exercise)
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"
Suggest update to label
NCIT:C116196
HCAG Test
Hepatitis C Virus Antigen Measurement
Hepatitis C Virus Antigen Test
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")
Suggest update to label and description
NCIT:C92535
HCAB Test
Hepatitis C Antibody Measurement
Hepatitis C Virus Antibody Test
Hepatitis C Antibody Test
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")
Suggest update to label
NCIT:C135424
HCCAG Test
HCV Core Antigen Measurement
HCV Core Antigen Test
Hepatitis C Core Antigen Test
Hepatitis C Virus Core Antigen Measurement
Hepatitis C Virus Core Antigen Test
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")
Suggest update to label
NCIT:C74712
Hepatitis C Surface Antibody Measurement
Hepatitis C Surface Antibody Test
The determination of the amount of cystatin C present in a sample.
Suggest update to label in NCIT (from "Cystatin C Measurement")
Suggest update to label
NCIT:C92290
CYSTATC Blood Test
Cystatin C Blood Test
The visual output that a specific diagnostic device produces.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Visual Output of a Diagnostic Device
Diagnostic Device Visual Output
A bioassay to measure levels of red blood cell microparticles.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Red Blood Cell Microparticles Assay
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")
Suggest update to label
NCIT:C61041
Serum HDL Cholesterol Measurement
Serum HDL Cholesterol Test
A technique used to measure velocity and amount of blood flow and circulation in the living system.
None
SCDO (Jade Hotchkiss)
Blood Flow Test
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).
Suggest update to description
CMO:0000670
Heart Measurement
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
None
SCDO (Jade Hotchkiss)
Diagnostic Instrument Outcome
Diagnostic Instrument Measurement
Questions asking the respondent about smoking status in his or her entire life.
Request inclusion into relevant ontology
None
Cigarette Smoking Status Diagnostic Instrument
Questions asking an adult respondent about smoking status in his or her entire life.
Request inclusion into relevant ontology
PhenX protocol: Cigarette Smoking Status - Adult #30604
None
SCDO (Jade hotchkiss)
Cigarette Smoking Status Diagnostic Instrument - Adult
Questions asking an adolescentt respondent about smoking status in his or her entire life.
Request inclusion into relevant ontology
PhenX protocol: Cigarette Smoking Status - Adolescent #30603
None
SCDO (Jade hotchkiss)
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."
Not relevant to context of sickle cell
SCDO (Jade Hotchkiss)
Never Smoker
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."
Not relevant to context of sickle cell
SCDO (Jade Hotchkiss)
Current Every-Day Smoker
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."
Not relevant to context of sickle cell
SCDO (Jade Hotchkiss)
Current Some-Day Smoker
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."
Not relevant to context of sickle cell
SCDO (Jade Hotchkiss)
Former Smoker
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.
None
SCDO (Jade Hotchkiss)
Ever-Smoker
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.
None
SCDO (Jade Hotchkiss)
Past 30-Day Smoker
A person who had smoked every day of the past 30 days at the time of the interview.
None
SCDO (Jade Hotchkiss)
Past 30-Day Every-Day Smoker
Question asking the respondent if s/he has ever consumed any alcoholic beverage during his or her entire life.
Suggest update to label in PhenX
PhenX protocol: #30101
Suggest update to label
phenX:030100
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.
None
SCDO (Jade Hotchkiss)
phenX:130401
Epilepsy Screener for Adults
Epilepsy Screener - Adult
A nine-item, interviewer-administered questionnaire to screen for the presence of epilepsy in family members, including children and those who are deceased.
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.
None
SCDO (Jade Hotchkiss)
phenX:130402
Family History of Epilepsy Screening Interview
Ottman Brief Epilepsy Screener - Proxy-reported Version
Epilepsy Screener - Child/Proxy
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.
Few but definitions not freely available
Defects in Executive Function
Executive Function Deficit
Executive Dysfunction
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
Few but definitions not freely available
The Ages & Stages Questionnaires, Third Edition (ASQ-3)
Global Mental Status Screener - Child
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.
Frequency of Sickle Cell Pain Episodes
Questions from the National Epidemiologic Survey on Alcohol and Related Conditions-III (NESARC-III) related to their lifetime use of illicit and prescribed substances.
Suggest update to label in PhenX
PhenX protocol: Substances - Lifetime Use #31102
Suggest update to label
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
None
SCDO (Jade Hotchkiss)
phenX:121002
Sleep Disturbances Scale for Children
Sleep Disorders Screener - Children
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.
Not relevant to context of sickle cell
SCDO (Jade Hotchkiss)
History of Head Trauma
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.
Few but definitions not freely available
SCDO (Jade Hotchkiss)
History of Stroke
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.
Not relevant to context of sickle cell
SCDO (Jade Hotchkiss)
History of Kidney Failure
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
Suggest update to label
phenX:830200
History of Transfusion Diagnostic Instrument
A record of an individual's history of type 1 and type 2 diabetes.
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.
Not relevant to context of sickle cell
SCDO (Jade Hotchkiss)
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.
SCDO (Jade Hotchkiss)
Reproductive History Diagnostic Instrument - Male
A questionnaire to assess females' 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 - Female #101301
Suggest update to label and description.
SCDO (Jade Hotchkiss)
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).
Sufficient
SCDO:1000348
phenX:121000
Sleep Disorders Screener
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
Suggest update to label
phenX:40501
Heart Valve Function Test
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
Suggest update to description
SCDO (Jade Hotchkiss)
Spirometry - Adult
Measurement of the breathing capacity of a child'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 - Child #91602
Suggest update to description
SCDO (Jade Hotchkiss)
Spirometry - Child
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.
Sufficient
SCDO:1000354
MESH:D000073599
Health Risk Behaviors
Risky Health Behavior
Risky Health Behaviors
Health Risk Behavior
Physical surroundings or conditions of a hospital or other health facility and influence of these factors on patients and staff.
Sufficient
SCDO:1000355
MESH:D006272
Health Facility Environment
Height above sea level or above the earth's surface.
Sufficient
SCDO:1000356
CSP:1035-6505
Altitude
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
Sufficient
SCDO:1000357
EFO:0004784
Self Reported Educational Attainment
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.
Suggest update to description in NCIT.
Suggest update to description
NCIT:C142196
Globin Gene Family
Globin Genes
Globin Gene
A gene that provides instructions for making a protein called alpha-globin.
Request inclusion into relevant ontology
Negligable
SCDO (Jade Hotchkiss)
Alpha-Globin Gene
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.
Negligable
SCDO (Jade Hotchkiss)
Beta-Globin Gene
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.
Sufficient
SCDO:1000363
MESH:D055543
HBAZ
Haemoglobin Subunit Zeta
Haemoglobin Zeta Chain
Hemoglobin Zeta Chain
Zeta Globin
Zeta-Globin
Hemoglobin Subunit Zeta
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".
Sufficient
SCDO:1000364
MESH:D006443
A2, Hemoglobin
HbA2
Normal Variant of Hemoglobin A
alpha2delta2
Hemoglobin A2
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.
Request inclusion into relevant ontology
None
SCDO (Jade Hotchkiss)
Delta Beta Thalassaemia Mutation
Delta Beta Thalassemia Mutation
A health abnormality in a woman during pregnancy.
Suggest update to description in HP. Currently no description.
Suggest update to description
SCDO (Jade Hotchkiss)
HP:0002686
Maternal Health Problem
Prenatal Maternal Abnormality
In situ death of bone within the humeral head due to disruption of blood supply.
Request inclusion into NCIT as sub-class of "Avascular Necrosis of Humerus".
None
SCDO (Jade Hotchkiss)
Aseptic Necrosis of the Humeral Head
Avascular Necrosis of the Humeral Head
Osteonecrosis of the Humeral Head
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.
Sufficient
SCDO:1000379
MESH:D065246
Care, Culturally Congruent
Culturally Congruent Care
Culturally Competent Care
Any kidney disorder occurring as a consequence of injury to the kidney.
Few but definitions not available
SCDO (Jade Hotchkiss)
Kidney Complication
Renal Complication
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.
Sufficient
SCDO:1000392
MESH:D016329
Transcription Factor, Sp1
Sp1 Transcription Factor
A gene component is a component of a gene.
Sufficient
SCDO:1000394
SIO:010444
Gene Component
A gene regulatory component is a gene component that exerts a regulatory function.
Sufficient
SCDO:1000395
SIO:010085
Gene Regulatory Component
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.
Sufficient
SCDO:1000396
SIO:010086
Gene Enhancer
A gene promoter is a region of DNA that initiates transcription of a particular gene.
Sufficient
SCDO:1000397
SIO:010446
Gene Promoter
None
Erythroid Specific Enhancer of Bcl11A
BCL11A Erythroid Enhancer
A characteristic that further describes the nature of data.
None
SCDO (Jade Hotchkiss)
Data Descriptor
The predominant publication type for articles and other items indexed for NLM databases.
Sufficient
SCDO:1000402
MESH:D016428
Journal Article
A characteristic or directive that further describes the nature of data sharing.
None
SCDO (Jade Hotchkiss)
Data Sharing Descriptor
Requirements indicate additional conditions set for use of data.
Suggest update to description in DUO
Suggest update to description
DUO:0000017
Data Use Requirements
The standard method of providing feedback to study participants regarding their information (data, biological samples, genetic material) that has been shared.
None
SCDO (Jade Hotchkiss)
Policy for Feedback to Participant
Policy for Returning Results
Policy for Returning Results to Participant
Participant Feedback Policy
An element or information entity that is required to be provided in consent forms.
None
SCDO (Jade Hotchkiss)
Basic Element of a Consent Form
The policy regarding participants' right to withdraw their participation in a study.
None
SCDO (Jade Hotchkiss)
Participant Withdrawal Policy
A course or principle of action adopted or proposed by a study.
None
SCDO (Jade Hotchkiss)
Study Policy
A statement of what the key investigational purpose of the study is.
None
SCDO (Jade Hotchkiss)
Study Focus Statement
A statement about how the researcher is obligated by law to report if the participant is found to have a communicable disease.
None
SCDO (Jade Hotchkiss)
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.
Sufficient
SCDO:1000429
MESH:D004992
Medical Ethics
Concepts related to ethics, excluding types of ethics.
None
SCDO (Jade Hotchkiss)
Ethics Related Concept
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.
Suggest update to description in NCIT
Few but definitions not specific enough
NCIT:C29616
FABPI
Fatty Acid-Binding Protein, Intestinal
I-FABP
Intestinal-Type Fatty Acid-Binding Protein
iFABP
Intestinal 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.
None
SCDO (Jade Hotchkiss)
Serum Intestinal Fatty-Acid Binding Protein Level
Measured in ng/ml
Serum iFABP Level
Damage inflicted on the intestine.
Few but definitions not available
SCDO (Jade Hotchkiss)
Intestinal Damage
Intestinal Injury
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.
Sufficient
SCDO:1000436
EFO:0002687
Hypoxia-Reoxygenation Injury
Hypoxia/Reperfusion Injury
IRI
Ischaemia Reperfusion Injury
Ischemia Reperfusion Injury
Reoxygenation Injury
Hypoxia-Reperfusion Injury
An increased circulating blood concentration of the intestinal fatty-acid binding protein.
None
SCDO (Jade Hotchkiss)
Significantly high serum iFABP levels is evidence of intestinal injury.
Elevated Serum iFABP Level
The level of L-selectin in the systemic circulation (serum).
None
SCDO (Jade Hotchkiss)
Serum CD62L Level
Soluble CD62L
Serum L-Selectin Level
The number of aged neutrophils in a specified volume of blood, usually 1 cubic millimeter.
None
SCDO (Jade Hotchkiss)
Activated Neutrophil Count
Aged Neutrophil Count
A medication that is typically used for indications other than pain control but provides control of pain in some painful diseases.
None
Adjuvant Analgesic Agent
Adjunct Analgesic Agent
An infusion of ketamine at a low dose (up to 5 µg/kg/min).
None
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.
Low-Dose Ketamine Infusion
Pain that may be caused by or related to cellular, tissue, and systemic changes that occur during neoplasm growth, tissue invasion, and metastasis.
Sufficient
SCDO:1000452
MESH:D000072716
Cancer-Related Pain
Pains, Neoplasm-Related
Cancer Pain
The current age of a patient, calculated using the current date and the patient's date of birth and provided in years.
None
SCDO (Jade Hotchkiss)
Calculated Current Age in Years
Calculated Current Age (Years)
A type of consent that includes an aspect of timing (i.e. an indication of when consent was acquired).
Request inclusion into ICO below "Informed Consent".
None
SCDO (Jade Hotchkiss)
Temporal Consent Concept
Consent given prior to enrollment.
Request inclusion into the Informed Consent Ontology.
None
SCDO (Jade Hotchkiss)
Prospective Consent
Consent that is taken later after enrollment into study especially in emergency situations.
Request inclusion into the Informed Consent Ontology.
None
SCDO (Victoria Nembaware)
Deferred Consent
Informed consent given prior to enrollment.
Request inclusion into ICO below "Informed Consent".
None
SCDO (Victoria Nembaware)
Prospective Informed Consent
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.
Request inclusion into the Informed Consent Ontology.
None
SCDO (Victoria Nembaware)
Waived Consent
A decision made by a research ethics committee.
Request inclusion into the Informed Consent Ontology.
None
SCDO (Jade Hotchkiss)
Research Ethics Committee Decision
When a research ethics committee approves a study's application for approval of their proposed research.
Request inclusion into the Informed Consent Ontology.
None
SCDO (Jade Hotchkiss)
Approval of Ethics
When a research ethics committee declines a study's application for approval of their proposed research.
Request inclusion into the Informed Consent Ontology.
None
SCDO (Jade Hotchkiss)
Disapproval of Ethics
A method in which a patient or their legal representative provides consent.
Request inclusion into the Informed Consent Ontology.
None
SCDO (Jade Hotchkiss)
Mode of Providing Consent
When the participant or a legal representative or family member provides consent by filling out and/or signing a written form.
Request inclusion into the Informed Consent Ontology.
None
SCDO (Jade Hotchkiss)
Written Consent
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.
Request inclusion into the Informed Consent Ontology.
None
SCDO
Verbal Consent
A unique identifier assigned to a study participant's data when it is registered in the SickleInAfrica data registry.
None
SCDO (Jade Hotchkiss)
SickleInAfrica Participant Number
The name of the country where the sample or data was collected.
Few but definitions not specific enough
FLU:0000831
Country of Data Collection
The rules by which data are described and recorded.
Not relevant to context of sickle cell
SCDO (Jade Hotchkiss)
Data Standards
A data element used to capture or facilitate the capture of data in a clinical or research assessment.
None
SCDO (Jade Hotchkiss)
Clinical or Research Assessment Data Element
A type of question pertaining to a clinical or research assessment data element.
None
SCDO (Jade Hotchkiss)
Clinical or Research Assessment Question Type
deprecated Field Type
true
deprecated Calculation Field Type
true
deprecated Checkbox Field Type
true
deprecated Descriptive Field Type
true
deprecated Dropdown Field Type
true
deprecated Dropdown Multiple Choice Field Type
true
deprecated Dropdown Single Choice Field Type
true
deprecated File Upload Field Type
true
deprecated Radio Field Type
true
deprecated Text Box Field Type
true
deprecated Notes Box Field Type
true
deprecated Slider - Visual Analog Scale
true
The situation, with regard to obtaining consent from a respondent, at a particular stage during a process.
None
SCDO (Jade Hotchkiss)
Consent Status
A question that provides the respondent with specific answer options to choose from.
None
SCDO (Jade Hotchkiss)
Close-Ended Question
A question that allows the respondent to give their own answer instead of selecting an answer from answer options.
None
SCDO (Jade Hotchkiss)
Open-Ended Question
A close-ended question that provides two possible answers.
None
SCDO (Jade Hotchkiss)
Dichotomous Question
A close-ended question that provides multiple answers for respondents to select from and allows for the selection of multiple options.
None
SCDO (Jade Hotchkiss)
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.
None
SCDO (Jade Hotchkiss)
Multiple Choice Single Selection Question
A dichotomous question that has answer options "true" and "false".
None
SCDO (Jade Hotchkiss)
True-False Question
A dichotomous question that has answer options "yes" and "no".
None
SCDO (Jade Hotchkiss)
Yes-No Question
A open ended question that restricts the nature of the text answer that can be provided by the respondent.
None
SCDO (Jade Hotchkiss)
Open-Ended Question - Restricted
A open ended question that allows the respondent to respond in free text, without any restrictions on the nature of the text answer provided.
None
SCDO (Jade Hotchkiss)
Open-Ended Question - Free Text
A data element in a SickleInAfrica data capture instrument.
None
SCDO (Jade Hotchkiss)
SickleInAfrica DE
SickleInAfrica Data Element
A data element in the SickleInAfrica core data capture instrument.
None
SCDO (Jade Hotchkiss)
SickleInAfrica Core DE
SickleInAfrica Core Data Element
The Sickle in Africa core data element that collects the concentration of albumin in the respondent's urine.
Urinary albumin concentration
urinary_microalbumin_conc
Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise)
µg/mL; PX141501
3
Number
text
SickleInAfrica CDE - Urinary Albumin Concentration Question
The Sickle in Africa core data element that records whether the respondent has consented as necessary.
1, Yes
2, No
-7, Refused
-9, Don't Know
Has the patient consented?
consent_obtained
Consent
1
radio
SickleInAfrica CDE - Informed Consent Obtained Question
An indication of whether informed consent was obtained from the respondent and/or their proxy.
Few but definitions not available
SCDO (Jade Hotchkiss)
Informed Consent Obtained
Voluntary authorization given by a respondent and/or their proxy to be enrolled into a study as a research subject.
Request inclusion into relevant ontology, perhaps the ICO.
None
SCDO (Jade Hotchkiss)
Study Enrollment Consent
Voluntary authorization given by a study respondent and/or their proxy to have their specimen(s) stored.
Request inclusion into relevant ontology, perhaps the ICO.
None
SCDO (Jade Hotchkiss)
Specimen Storage Consent
Voluntary authorization given by a study paticipant to have their genetic material stored.
Request inclusion into relevant ontology, perhaps the ICO.
None
SCDO (Jade Hotchkiss)
Genetic Material Storage Consent
0
4
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
Type(s) of informed consent obtained
consent_type
Consent
2
checkbox
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.
None
SCDO (Jade Hotchkiss)
Type of Informed Consent Obtained
Time-related information that can be observed and is related to consent.
None
SCDO (Jade Hotchkiss)
Temporal Observable of Consent
The current age of a patient, calculated using the current date and the patient's date of birth.
None
SCDO (Jade Hotchkiss)
Calculated Current Age
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)
consent_date
Consent
3
date_dmy
text
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.
Consented by:
consented_by
Consent
4
text
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.
None
SCDO (Jade Hotchkiss)
Blood Transfusion Since Last Visit
An indication of whether the consent form used for obtaining informed consent from the respondent has been uploaded to the relevant electronic system.
None
SCDO (Jade Hotchkiss)
Consent Form Uploaded
The name of the person who conducted consenting of the respondent.
None
SCDO (Jade Hotchkiss)
Consented By
Time-related information that can be observed.
Few but definitions not freely available
SCDO (Jade Hotchkiss)
Temporal Observable
Time-related information that can be observed and is related to a diagnosis.
None
SCDO (Jade Hotchkiss)
Diagnosis Temporal Observable
The Sickle in Africa core data element that records the visit date, in the format dd/mm/yyyy.
Visit date (dd/mm/yyyy)
date_today
Demographics
1
date_dmy
text
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 participant number
participant_number
Demographics
Site-specific ID eg. GH20181234 for Ghana, NG20184321 for Nigeria or TZ20180001 for Tanzania
3
text
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.
Date of birth (dd/mm/yyyy)
date_of_birth
Demographics
9
date_dmy
text
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.
None
SCDO (Jade Hotchkiss)
Calculated Current Age in Months
Calculated Current Age (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.
None
SCDO (Jade Hotchkiss)
Self-Reported Age in Years
Self-Reported Current Age in Years
Self-Reported Current Age (Years)
The Sickle in Africa core data element that records the respondent's age, as reported by the respondent in years.
Self-reported age (in years)
age_on_day_of_visit
Demographics
Age on day of visit
11
Number
0
125
RH
text
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
Current marital status
marital_status
Demographics
15
radio
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.
Date of blood transfusion
transfusion_date
Management Details
8
date_dmy
[blood_transfusion] = "Yes"
text
SCDO (Jade Hotchkiss)
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.
If other test, please specify:
other_test
SCD Diagnosis Details
6
[type_of_test] = '6'
text
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
Respondent's sex
respondent_sex
Demographics
14
radio
SickleInAfrica CDE - Sex Question
The Sickle in Africa core data element that records whether the respondent knows the date of their SCD diagnosis.
1, Yes
0, No
Is date of SCD diagnosis known?
diagnosis_date_known
SCD Diagnosis Details
1
yesno
SickleInAfrica CDE - Date of Diagnosis Known Question
Information or a description that further describes a diagnosis.
None
SCDO (Jade Hotchkiss)
Diagnosis Descriptor
An indication of whether the date of the respondent's diagnosis of a disease is known by the respondent or the respondent's guardian.
None
SCDO (Jade Hotchkiss)
Date of Diagnosis Known
An indication of whether the date of the respondent's SCD diagnosis is known by the respondent or the respondent's guardian.
None
SCDO (Jade Hotchkiss)
Date of SCD Diagnosis Known
The Sickle in Africa core data element that records the respondent's date of diagnosis in the format dd/mm/yyyy.
Date of SCD diagnosis (dd/mm/yyyy)
exact_diagnosis_date
SCD Diagnosis Details
2
date_dmy
[diagnosis_date_known] = '1'
text
SickleInAfrica CDE - Date of Diagnosis Question
The date on which a diagnosis of sickle cell disease was made.
None
SCDO (Jade Hotchkiss)
Date of SCD Diagnosis
The date on which a patient received a blood transfusion.
None
SCDO (Jade Hotchkiss)
Date of Blood Transfusion
The year in which a sickle cell disease diagnosis was made.
None
SCDO (Jade Hotchkiss)
Year of SCD Diagnosis
The month when a diagnosis was assigned to an individual's condition.
None
SCDO (Jade Hotchkiss)
Month of Diagnosis
The month when a sickle cell disease diagnosis was made.
None
SCDO (Jade Hotchkiss)
Month of SCD Diagnosis
The Sickle in Africa core data element that records the month of the year in which the respondent was diagnosed with SCD.
-9, Don't know
1, 1
2, 2
3, 3
4, 4
5, 5
6, 6
7, 7
8, 8
9, 9
10, 10
11, 11
12, 12
Month of SCD diagnosis
month_of_diagnosis
SCD Diagnosis Details
4
[diagnosis_date_known] = '0'
dropdown
SickleInAfrica CDE - Month of Diagnosis Question
A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.
Sufficient
SCDO:1000572
SIO:001331
Diagnosis
The Sickle in Africa core data element that records the respondent's SCD test result.
1, SS
2, SBThal
3, SC
4, AS
5, Other
SCD test result
scd_test_result
SCD Diagnosis Details
SS = Sickle Cell Disease-SS | SBThal = Sickle Beta Thalassemia | SC = Sickle Cell Disease-SC | AS = Sickle Cell Trait
3
RH
dropdown
SickleInAfrica CDE - SCD Test Result Question
The result of a medical investigation to identify the type of sickle cell disease that a person has.
None
SCDO (Jade Hotchkiss)
SCD Test Result
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
Type of test?
type_of_test
SCD Diagnosis Details
HPLC = High-Performance Liquid Chromatography| HBE = Hemoglobin Electrophoresis | IEF = Isoelectric Focusing| Basique = Basique SCD Test | Acide = Acide SCD Test
5
dropdown
SickleInAfrica CDE - Type of SCD Test Question
A piece of information that further describes a diagnostic measurement.
None
SCDO (Jade Hotchkiss)
Diagnostic Measurement Descriptor
The type of test that was used to obtain a sickle cell disease diagnosis.
None
SCDO (Jade Hotchkiss)
Type of SCD Test
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:
other_scd_test_result
SCD Diagnosis Details
4
text
SickleInAfrica CDE - SCD Test Other Result Question
The Sickle in Africa core data element that records the respondent's ABO Blood Group.
1, A+
2, A-
3, B+
4, B-
5, O+
6, O-
7, AB+
8, AB-
ABO blood group
abo_blood_group
SCD Diagnosis Details
7
dropdown
SCDO (Jade Hotchkiss)
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
Few but definitions not available
Electrophoresis - hemoglobin
HBE
Haemoglobin Electrophoresis
Hb electrophoresis
Hemoglobinopathy - electrophoresis
Hgb electrophoresis
Sickle cell - electrophoresis
Thalassemia Screening
Thallasemia - electrophoresis
Hemoglobin Electrophoresis
A blood type containing type A red blood cell surface markers, with the presence of a protein called rhesus (Rh) factor.
Few but definitions not available
SCDO (Kambe Banda)
A+
Blood group A Rh(D) positive
Type A blood, Rh positive
Blood Type A Positive
A blood type containing type A red blood cell surface markers, with the absence of a protein called rhesus (Rh) factor.
SCDO (Kambe Banda)
Few but definitions not available
A-
Blood group A Rh(D) negative
Type A blood, Rh negative
Blood Type A Negative
A blood type containing type B red blood cell surface markers, with the presence of a protein called rhesus (Rh) factor.
Few but definitions not available
SCDO (Kambe Banda)
B+
Blood group B Rh(D) positive
Type B blood, Rh positive
Blood Type B Positive
A blood type containing type B red blood cell surface markers, with the absence of a protein called rhesus (Rh) factor.
Few but definitions not available
SCDO (Kambe Banda)
B-
Blood group B Rh(D) negative
Type B blood, Rh negative
Blood Type B Negative
A blood type containing no surface markers on red blood cells, with the presence of a protein called rhesus (Rh) factor.
Few but definitions not available
SCDO (Kambe Banda)
Blood group O Rh(D) positive
O+
Type O blood, Rh positive
Blood Type O Positive
A blood type containing no surface markers on red blood cells, with the absence of a protein called rhesus (Rh) factor.
Few but definitions not available
SCDO (Kambe Banda)
Blood group O Rh(D) negative
O-
Type O blood, Rh negative
Blood Type O Negative
A blood type containing both type A and B red blood cell surface markers, with the presence of a protein called rhesus (Rh) factor.
Few but definitions not available
SCDO (Kambe Banda)
AB+
Blood group AB Rh(D) positive
Type AB blood, Rh positive
Blood Type AB Positive
A blood type containing both type A and B red blood cell surface markers, with the absence of a protein called rhesus (Rh) factor
Few but definitions not available
SCDO (Kambe Banda)
AB-
Blood group AB Rh(D) negative
Type AB blood, Rh negative
Blood Type AB Negative
Information about how a patient's SCD is being managed.
None
SCDO (Jade Hotchkiss)
SCD Management Details
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).
1, Yes
0, No
Using hydroxyurea
using_hydroxyurea
Management Details
1
RH
yesno
SickleInAfrica CDE - Hydroxyurea Use Question
An indication of whether the respondent is using hydroxyurea.
None
SCDO (Jade Hotchkiss)
Hydroxyurea Use Status
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)
date_of_initiation_of_hydr
Management Details
2
date_dmy
text
SickleInAfrica CDE - Hydroxyurea Initiation Date Question
The date on which hydroxyurea therapy was initiated.
None
SCDO (Jade Hotchkiss)
Date of Hydroxyurea Therapy Initiation
The Sickle in Africa core data element that records whether the respondent is using penicillin V as a prophylaxis against bacterial infections.
1, Yes
2, No
-6, NA
Using penicillin V (prophylaxis)
penicillin_v_prophylaxis
Management Details
3
RH
radio
SickleInAfrica CDE - Penicillin V Use Question
An indication of whether the respondent is using penicillin V prophylaxis.
None
SCDO (Jade Hotchkiss)
Penicillin V Prophylaxis Use Status
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).
1, Yes
0, No
Using folic acid
folic_acid
Management Details
5
RH
yesno
SickleInAfrica CDE - Folic Acid Use Question
An indication of whether the respondent is using folic acid.
None
SCDO (Jade Hotchkiss)
Folic Acid Use Status
An indication of whether the respondent is using malaria prophylaxis.
None
SCDO (Jade Hotchkiss)
Malaria Prophylaxis Status
The Sickle in Africa core data element that records whether the respondent is using malaria chemoprophylaxis (drugs that prevent malaria).
1, Yes
2, No
-6, NA
Using malaria chemoprophylaxis
antimalaria_prophylaxis
Management Details
4
radio
SickleInAfrica CDE - Malaria Prophylaxis Question
The Sickle in Africa core data element that records whether the respondent's pneumococcal vaccination is up to date.
1, Yes
0, No
Pneumococcal vaccination up to date
pneumococcal_vacc_uptodate
Management Details
6
RH
yesno
SickleInAfrica CDE - Pneumococcal Vaccination Question
An indication of whether the respondent is up to date with their pneumococcal vaccinations.
None
SCDO (Jade Hotchkiss)
Pneumococcal Vaccination Status
The person who recorded the information about how a patient's condition is being managed.
None
SCDO (Jade Hotchkiss)
Management Details Added By
Any assay which measures the amount, level or concentration of urea in whole blood.
Sufficient
SCDO:1000605
MMO:0000272
Blood Urea Analysis
The date on which the respondent's management details were added/recorded.
None
SCDO (Jade Hotchkiss)
Management Details Add Date
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.
Red blood cell count (RBC)
cbc_redbloodcount
Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise)
million cells/µL
1
text
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.
White blood cell count (WBC)
cbc_whitebloodcount
Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise)
1000 cells/µL
2
text
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."
Suggest update to description
HP:0001881
Abnormal Leukocyte Morphology
The Sickle in Africa core data element that collects the platelet count in the respondent's blood, as measured by a complete blood count.
Platelet count
cbc_platelet_count
Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise)
1000 cells/µL
3
text
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.
Hemoglobin
cbc_hemoglobin
Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise)
g/dL
4
text
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.
Mean cell volume (MCV)
cbc_mean_cell_volume
Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise)
fL
5
text
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.
Mean cell hemoglobin (MCH)
cbc_mean_cell_hemoglobin
Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise)
pg
6
text
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)
cbc_mchc
Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise)
g/dL
7
text
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.
Red cell distribution width (RDW)
cbc_redcelldistributionwidth
Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise)
%
8
text
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.
Sufficient
SCDO:1000638
EFO:0009188
RCDW
RDW
Red Cell Distribution Width
Red Blood Cell Distribution Width
The Sickle in Africa core data element that collects the level of serum creatinine in the respondent's blood.
Serum creatinine concentration
serum_creatinine_conc
Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise)
mg/dL; PX141401
1
Number
text
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")
Suggest update to description
HP:0003259
Elevated Creatinine
High Blood Creatinine Level
Increased Creatinine
Increased Serum Creatinine
Elevated Serum Creatinine
The Sickle in Africa core data element that collects the concentration of creatinine in the respondent's urine.
Urinary creatinine concentration
urinary_creatinine_conc
Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise)
mg/dL; PX141601
4
Number
text
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.
Alanine aminotransferase level
results_of_alanine_at_assay
Liver Function Assay (PhenX protocol PX190801 unless stated otherwise)
IU/L
1
Number
text
SCDO (Jade Hotchkiss)
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.
Aspartate aminotransferase level
results_of_aspartate_at_assay
Liver Function Assay (PhenX protocol PX190801 unless stated otherwise)
IU/L
2
Number
text
SCDO (Jade Hotchkiss)
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.
Alkaline phosphatase level
results_of_alkaline_phosphatase_assay
Liver Function Assay (PhenX protocol PX190801 unless stated otherwise)
IU/L
3
Number
text
SCDO (Jade Hotchkiss)
SickleInAfrica CDE - Alkaline Phosphatase Level Question
A quantitative measurement of alkaline phosphatase present in a blood sample.
Few but definitions not available
SCDO (Jade Hotchkiss)
Alkaline Phosphatase Test
Alkaline Phosphatase Blood Test
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.
None
SCDO (Jade Hotchkiss)
Sickle SCAN Rapid Test
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).
None
SCDO (Jade Hotchkiss)
Current Partner Status
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).
None
SCDO (Jade Hotchkiss)
Past Partner Status
The Sickle in Africa core data element that collects the level of billirubin in the respondent's blood.
Total billirubin concentration
billirubin_total_billirubin_conc
Laboratory Results: Bilirubin Level (PhenX protocol PX0810901 unless stated otherwise)
mg/dL
1
Number
text
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.
Lactate dehydrogenase level
lactate_dehydrogenase_conc
Laboratory Results: Lactate Dehydrogenase Level (PhenX protocol PX0811001 unless stated otherwise)
IU/L
1
Number
text
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.
Suggest update to label
HP:0045041
Decreased Lactate Dehydrogenase Level
Reduced Lactate Dehydrogenase Level
The Sickle in Africa core data element that collects the reticulocyte count in the respondent's blood, as measured by a complete blood count.
Number of reticulocytes
reticulocyte_amount
Laboratory Results: Reticulocyte Count (PhenX protocol PX0810601 unless stated otherwise)
1000 cells/µL
1
Number
text
SickleInAfrica CDE - Reticulocyte Count Question
A test used to measure the reticulocyte count (number of reticulocytes in a given volume of blood).
Few but definitions not available
SCDO (Jade Hotchkiss)
Retic Count
Reticulocyte Count Test
Reticulocyte Count Assay
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?
scd_hemoglobin_assay_results
Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise)
Select all relevant options
1
LH
checkbox
SickleInAfrica CDE - Hb Assay Results Recorded Question
The hemoglobins for which assay results were recorded.
None
SCDO (Jade Hotchkiss)
Hemoglobin Assay Results 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.
Sufficient
SCDO:1000689
LNC:LP16433-2
Hb G-Phil
Hb G-Philadelphia
HbG Phil
Hemoglobin G Philadelphia
Hemoglobin G-Philadelphia
The amount of hemoglobin A present in a specified volume of blood.
Negligible
SCDO (Jade Hotchkiss)
Haemoglobin A Level
Hemoglobin A Level
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin A.
Record the levels of Hb A if measured.
hba2
Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise)
%
2
Number
[scd_hemoglobin_assay_results(1)] = '1'
text
SickleInAfrica CDE - Hemoglobin A Level Question
The amount of hemoglobin S present in a specified volume of blood.
Few but definitions not available
SCDO (Jade Hotchkiss)
Haemoglobin S Level
Hemoglobin S Level
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin S.
Record the levels of Hb S if measured.
hbs
Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise)
%
4
Number
[scd_hemoglobin_assay_results(3)] = '1'
text
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.
Record the levels of Hb C if measured.
hbc
Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise)
%
5
Number
[scd_hemoglobin_assay_results(4)] = '1'
text
SickleInAfrica CDE - Hemoglobin C Level Question
The amount of hemoglobin C present in a specified volume of blood.
Few but definitions not available
SCDO (Jade Hotchkiss)
Haemoglobin C Level
Hemoglobin C Level
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin E.
Record the levels of Hb E if measured.
hbe
Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise)
%
6
Number
[scd_hemoglobin_assay_results(5)] = '1'
text
SickleInAfrica CDE - Hemoglobin E Level Question
The amount of hemoglobin E present in a specified volume of blood.
Few but definitions not available
SCDO (Jade Hotchkiss)
Haemoglobin E Level
Hemoglobin E Level
The amount of hemoglobin A2 present in a specified volume of blood.
Few but definitions not available
SCDO (Jade Hotchkiss)
Haemoglobin A2 Level
Hemoglobin A2 Level
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin A2.
Record the levels of Hb A2 if measured.
hb_a2
Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise)
%
7
Number
[scd_hemoglobin_assay_results(6)] = '1'
text
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.
hb_dpunjab
Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise)
%
8
Number
[scd_hemoglobin_assay_results(7)] = '1'
text
SickleInAfrica CDE - Hemoglobin D-Punjab Level Question
The amount of hemoglobin D-Punjab present in a specified volume of blood.
Few but definitions not available
SCDO (Jade Hotchkiss)
Haemoglobin D-Punjab Level
Hemoglobin D-Punjab Level
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.
hb_gphilidelphia
Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise)
%
9
Number
[scd_hemoglobin_assay_results(8)] = '1'
text
SickleInAfrica CDE - Hemoglobin G-Philadelphia Level Question
The amount of hemoglobin G-Philadelphia present in a specified volume of blood.
None
SCDO (Jade Hotchkiss)
Haemoglobin G-Philadelphia Level
Hemoglobin G-Philadelphia Level
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.
hb_o_arab
Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise)
%
10
Number
[scd_hemoglobin_assay_results(9)] = '1'
text
SickleInAfrica CDE - Hemoglobin O-Arab Level Question
The amount of hemoglobin O-Arab present in a specified volume of blood.
None
SCDO (Jade Hotchkiss)
Haemoglobin O-Arab Level
Hemoglobin O-Arab Level
The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin F.
Record the levels of Hb F if measured.
hbf_percent
Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise)
%
3
Number
[scd_hemoglobin_assay_results(2)] = '1'
text
SickleInAfrica CDE - Hemoglobin F Level Question
The amount of hemoglobin F present in a specified volume of blood.
Few but definitions not available
SCDO (Jade Hotchkiss)
Haemoglobin F Level
Hemoglobin F Level
The sex of the respondent's spouse, as provided by the respondent.
None
SCDO (Jade Hotchkiss)
Sex of Spouse
The sex of the respondent's partner (where the partner is not a spouse), as provided by the respondent.
None
SCDO (Jade Hotchkiss)
Sex of Partner
The Sickle in Africa core data element that collects the respondent's body temperature.
Patient's body temperature
body_temperature
Vital Signs
degrees Celsius
1
Number
13
46
text
SCDO (Jade Hotchkiss)
SickleInAfrica CDE - Body Temperature Question
The Sickle in Africa core data element that collects the respondent's respiratory rate.
Patient's respiratory rate
respiratory_rate
Vital Signs
breaths per minute
3
Number
text
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.
Partial pressure of carbon dioxide (PaCO2)
partial_pressure_co2
Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise)
mmHg
1
Number
text
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.
Partial pressure of oxygen (PaO2)
partial_pressure_of_oxygen
Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise)
mmHg
2
Number
text
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.
Few but available definitions not adequate
CMO:0000381
Oxygen Tension
PaO2
Partial Pressure of Blood Oxygen
Partial Pressure of Blood Oxygen (Po2)
Partial Pressure of Oxygen (PaO2)
Po2
Partial Pressure of Oxygen
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.
Oxyhemoglobin saturation (HbO2)
oxyhemoglobin_saturation
Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise)
%
3
Number
text
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.
Carboxyhemoglobin (COHb)
carboxyhemoglobin
Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise)
%
4
Number
text
SCDO (Jade Hotchkiss)
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.
Methemoglobin (MetHb)
methemoglobin
Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise)
%
5
Number
text
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.
EFO:0009226
HGBMHGB
MetHb Saturation
Methemoglobin Saturation
Methemoglobin to Total Hemoglobin Ratio Measurement
Methemoglobin/Total Hemoglobin
Methemoglobin to Total Hemoglobin Ratio
The ratio of carboxyhemoglobin 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.
EFO:0009203
COHb Saturation
Carboxyhemoglobin Saturation
Carboxyhemoglobin/Total Hemoglobin
Carboxyhemoglobin to Total Hemoglobin Ratio
An elevated concentration in the blood of methemoglobin, which is the ferric (Fe(3+)) form of hemoglobin.
Few but definitions not available
SCDO (Jade Hotchkiss)
Methemoglobin Increased
Raised Methemoglobin
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.
Increased Methemoglobin
A site-specific unique identifier assigned to a study participant by the data collectors at the data collection site.
None
SCDO (Jade Hotchkiss)
Site Participant Number
A unique identifier provided on SCD passports.
None
SCDO (Jade Hotchkiss)
SCD Passport Number
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 Participant Number
record_id
text
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.
Calculated age (in months)
calc_age_on_day_of_visit
Demographics
datediff([date_today],[date_of_birth], "M","dmy")
Age on day of visit
10
RH
calc
SCDO (Jade Hotchkiss)
SickleInAfrica CDE - Age In Months Calculation
A data capture instrument designed and applied by the Sickle In Africa Consortium.
None
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)
SCDO (Jade Hotchkiss)
SickleInAfrica Core Data Element Instrument
The Sickle in Africa core data element that collects the total concentration of hemoglobin in the respondent's blood.
Total hemoglobin (Hbtotal)
total_hemoglobin
Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise)
g/dL
11
Number
text
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
None
SCDO (Jade Hotchkiss)
Oral Temperature Taking
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
None
SCDO (Jade Hotchkiss)
Tympanic Temperature Taking
Body Temperature - Tympanic Measurement Assay
The temperature of the oral cavity.
Sufficient
SCDO:1000755
VSO:0000025
Oral Body Temperature
Oral Temperature
The temperature of the external acoustic tube.
Sufficient
SCDO:1000756
VSO:0000045
Tympanic (ear) Temperature
Tympanic Body Temperature
Tympanic Temperature
The temperature of the lumen of the rectum.
Sufficient
SCDO:1000757
VSO:0000033
Rectal Body Temperature
Rectal Temperature
The temperature of the axillary fossa.
Sufficient
SCDO:1000758
VSO:0000003
Armpit Temperature
Axillary (armpit) Temperature
Axillary Temperature
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
Type of body temperature taken
type_of_temp
Vital Signs
2
dropdown
SickleInAfrica CDE - Type of Temperature Question
Type of Body Temperature
An answer to a question where the answer is a year between 1900 and the current year, selected from a provided list of years.
None
SCDO (Jade Hotchkiss)
Year 1900 - Current
An answer to a question where the answer is a month between 1 - 12, selected form a list of months.
None
SCDO (Jade Hotchkiss)
Month 1 - 12
Waiting for description for this.
Acide
Waiting for description for this.
Basique
-
Few but definitions not available
ICD10CM:D57.03
D57.03
Hb-SS disease with cerebral vascular involvement
Sickle cell anemia with cerebral vascular involvement
D57.03 Hb-SS disease with cerebral vascular involvement
-
yes
Few but definitions not available
ICD10CM:D57.09
D57.09
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.
None
SCDO (Jade Hotchkiss)
Normal Hemoglobin Concentration
A lack of production of hemoglobin S.
Few but definitions not available
SCDO (Jade Hotchkiss)
MEDDRA:10055604
Absent Haemoglobin S
Haemoglobin S Absent
Hemoglobin S Absent
Normal Haemoglobin S Level
Normal Hemoglobin S Level
Absent Hemoglobin S
-
Few but definitions not freely available
ICD10CM:D57.213
D57.213
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
-
Few but definitions not freely available
ICD10CM:D57.218
D57.218
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
-
Few but definitions not freely available
ICD10CM:D57.413
D57.413
D57.413 Sickle-cell thalassemia, unspecified, with cerebral vascular involvement
-
Few but definitions not freely available
ICD10CM:D57.418
D57.418
Sickle-cell thalassemia, unspecified, with crisis with other specified complication
D57.418 Sickle-cell thalassemia, unspecified, with crisis with other specified complication
-
Few but definitions not freely available
ICD10CM:D57.42
D57.42
Sickle-cell thalassemia beta zero without crisis
D57.42 Sickle-cell thalassemia beta zero without crisis
-
Few but definitions not freely available
ICD10CM:D57.43
D57.43
Sickle-cell thalassemia beta zero with crisis
D57.43 Sickle-cell thalassemia beta zero with crisis
-
Few but definitions not freely available
ICD10CM:D57.431
D57.431
Sickle-cell thalassemia beta zero with acute chest syndrome
D57.431 Sickle-cell thalassemia beta zero with acute chest syndrome
-
Few but definitions not freely available
ICD10CM:D57.432
D57.432
Sickle-cell thalassemia beta zero with splenic sequestration
D57.432 Sickle-cell thalassemia beta zero with splenic sequestration
-
Few but definitions not freely available
ICD10CM:D57.433
D57.433
Sickle-cell thalassemia beta zero with cerebral vascular involvement
D57.433 Sickle-cell thalassemia beta zero with cerebral vascular involvement
-
Few but definitions not freely available
ICD10CM:D57.438
D57.438
Sickle-cell thalassemia beta zero with crisis with other specified complication
D57.438 Sickle-cell thalassemia beta zero with crisis with other specified complication
-
Few but definitions not freely available
ICD10CM:D57.439
D57.439
Sickle-cell thalassemia beta zero with crisis, unspecified
D57.439 Sickle-cell thalassemia beta zero with crisis, unspecified
-
Few but definitions not freely available
ICD10CM:D57.44
D57.44
Sickle-cell thalassemia beta minus without crisis
Sickle-cell thalassemia beta plus without crisis
D57.44 Sickle-cell thalassemia beta plus without crisis
-
Few but definitions not freely available
ICD10CM:D57.45
D57.45
Sickle-cell thalassemia beta minus with crisis
Sickle-cell thalassemia beta plus with crisis
D57.45 Sickle-cell thalassemia beta plus with crisis
-
Few but definitions not freely available
ICD10CM:D57.451
D57.451
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
-
Few but definitions not freely available
ICD10CM:D57.452
D57.452
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
-
Few but definitions not freely available
ICD10CM:D57.453
D57.453
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
-
Few but definitions not freely available
ICD10CM:D57.458
D57.458
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
-
Few but definitions not freely available
ICD10CM:D57.459
D57.459
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
-
Few but definitions not freely available
ICD10CM:D57.818
D57.818
D57.818 Other sickle-cell disorders with crisis with other specified complication
-
Few but definitions not freely available
ICD10CM:D57.813
D57.813
D57.813 Other sickle-cell disorders with cerebral vascular involvement
A lack of production of hemoglobin C.
None
SCDO (Jade Hotchkiss)
Absent Haemoglobin C
Haemoglobin C Absent
Hemoglobin C Absent
Normal Haemoglobin C Level
Normal Hemoglobin C Level
Absent Hemoglobin C
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).
Few but definitions not available
SCDO (Jade Hotchkiss)
Carboxyhemoglobin Increased
Raised Carboxyhemoglobin
Increased Carboxyhemoglobin
An abnormal reduction in the amount of oxygen bound to hemoglobin in arterial blood expressed as a percentage of the maximal binding capacity.
Few but definitions not available
SCDO (Jade Hotchkiss)
Arterial Oxygen Saturation Decreased
Decreased Arterial HbO2
Decreased Arterial Oxyhemoglobin Saturation
Decreased Arterial SaO2
Decreased Arterial Sats
Decreased Oxygen Saturation of Arterial Blood
Decreased Oxyhemoglobin/Total Hemoglobin
Low Arterial Oxygen Saturation
Decreased Arterial Oxygen Saturation
A phenotype of the body's metabolism or homeostasis that is not clinically abnormal.
None
SCDO (Jade Hotchkiss)
Normal Metabolism/Homeostasis Phenotype
When the degree to which oxygen is bound to hemoglobin in arterial blood is in the normal range.
Few but definitions not available
SCDO (Jade Hotchkiss)
Normal Arterial Blood Oxygen Saturation
Normal Arterial Oxygen Saturation
When the level of carboxyhemoglobin detected in a sample of blood falls in the normal range for carboxyhemoglobin.
Few but definitions not available
SCDO (Jade Hotchkiss)
Carboxyhemoglobin Normal
Normal Carboxyhemoglobin Concentration
Normal Carboxyhemoglobin Level
When the level of methemoglobin detected in a sample of blood falls in the normal range for methemoglobin.
None
SCDO (Jade Hotchkiss)
MetHb Normal
Normal MetHb Level
Normal Methemoglobin Concentration
Normal Methemoglobin Level
A lack of production of hemoglobin D-Punjab.
None
SCDO (Jade Hotchkiss)
Absent Haemoglobin D-Punjab
Haemoglobin D-Punjab Absent
Hemoglobin D-Punjab Absent
Normal Haemoglobin D-Punjab Level
Normal Hemoglobin D-Punjab Level
Absent Hemoglobin D-Punjab
A lack of production of hemoglobin G-Philadelphia.
None
SCDO (Jade Hotchkiss)
Absent Haemoglobin G-Philadelphia
Haemoglobin G-Philadelphia Absent
Hemoglobin G-Philadelphia Absent
Normal Haemoglobin G-Philadelphia Level
Normal Hemoglobin G-Philadelphia Level
Absent Hemoglobin G-Philadelphia
A lack of production of hemoglobin O-Arab.
None
SCDO (Jade Hotchkiss)
Absent Haemoglobin O-Arab
Haemoglobin O-Arab Absent
Hemoglobin O-Arab Absent
Normal Haemoglobin O-Arab Level
Normal Hemoglobin O-Arab Level
Absent Hemoglobin O-Arab
An abnormal reduction in the pressure exerted by oxygen dissolved in the blood.
Few but definitions not available
SCDO (Jade Hotchkiss)
Arterial Oxygen Partial Pressure Decreased
Decreased Oxygen Tension
Decreased PO2
Decreased PaO2
Decreased Partial Pressure of Blood Oxygen
PO2 Decreased
Decreased Partial Pressure of 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.
Few but definitions not specific enough
Haematopoietic System Phenotype
Haemopoietic System Phenotype
Hemopoietic System Phenotype
Hematopoietic System Phenotype
A phenotype of the body's hematopoietic system that is not clinically abnormal.
None
SCDO (Jade Hotchkiss)
Normal Hematopoietic System Phenotype
When the number of red blood cells in a specified volume of blood falls in the normal range.
Few but definitions not available
SCDO (Jade Hotchkiss)
Normal RBC Count
RBC Count Normal
Red Blood Cell Count Normal
Normal Red Blood Cell Count
When the number of white blood cells in a specified volume of blood falls in the normal range.
Few but definitions not available
SCDO (Jade Hotchkiss)
Normal WBC Count
WBC Count Normal
White Blood Cell Count Normal
Normal White Blood Cell Count
When the number of platelets in a specified volume of blood falls in the normal range.
Few but definitions not available
SCDO (Jade Hotchkiss)
Platelet Count Normal
Normal Platelet Count
When the average volume or size of a single red blood cell falls in the normal range.
Few but definitions not available
SCDO (Jade Hotchkiss)
MCV Normal
Mean Cell Volume Normal
Mean Corpuscular Volume Normal
Normal MCV
Normal Mean Cell Volume
Normal Mean Corpuscular Volume
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.
Few but definitions not available
SCDO (Jade Hotchkiss)
MCH Normal
Mean Cell Hemoglobin Normal
Mean Corpuscular Hemoglobin Level Normal
Mean Corpuscular Hemoglobin Normal
Normal MCH
Normal Mean Cell Hemoglobin
Normal Mean Corpuscular Hemoglobin
Normal Mean Corpuscular Hemoglobin Level
Normal Mean Corpuscular Hemoglobin
When the amount of hemoglobin in a given volume of packed red blood cells falls in the normal range.
None
SCDO (Jade Hotchkiss)
MCHC Normal
Mean Corpuscular Hemoglobin Concentration Normal
Normal MCHC
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.
Few but definitions not available
SCDO (Jade Hotchkiss)
Normal RBC Distribution Width
Normal RCDW
RBC Distribution Width Normal
RCDW Normal
Red Blood Cell Distribution Width Normal
Normal Red Blood Cell Distribution Width
When the level of serum creatinine is in the normal range.
Few but definitions not available
SCDO (Jade Hotchkiss)
Normal Serum Creatinine Level
Serum Creatinine Level Normal
Serum Creatinine Normal
Normal Serum Creatinine
When the level of serum alanine aminotransferase is in the normal range.
Few but definitions not available
SCDO (Jade Hotchkiss)
ALT Level Normal
ALT Normal
Normal ALT
Normal ALT Level
Normal Alanine Aminotransferase Level
Normal Alanine Transaminase
Normal Serum Alanine Aminotransferase Level
Serum Alanine Aminotransferase Level Normal
Serum Alanine Aminotransferase Normal
Normal Serum Alanine Aminotransferase
When the level of serum aspartate aminotransferase is in the normal range.
Few but definitions not available
SCDO (Jade Hotchkiss)
AST Level Normal
AST Normal
Normal AST
Normal AST Level
Normal Aspartate Aminotransferase
Normal Serum AST
Normal Serum Aspartate Aminotransferase Level
Serum AST Normal
Serum Aspartate Aminotransferase Normal
Normal Serum Aspartate Aminotransferase
When the level of serum alkaline aminotransferase is in the normal range.
Few but definitions not available
SCDO (Jade Hotchkiss)
AP Level Normal
AP Normal
Alkaline Phosphatase Level Normal
Alkaline Phosphatase Normal
Normal AP
Normal AP Level
Normal Serum AP Level
Normal Serum Alkaline Phosphatase Level
Normal Serum Alkaline Phosphatase
When the level of the enzyme lactate dehydrogenase in the serum is in the normal range.
Few but definitions not available
SCDO (Jade Hotchkiss)
LD Level Normal
LD Normal
LDH Level Normal
LDH Normal
Lactate Dehydrogenase Level Normal
Lactate Dehydrogenase Normal
Normal LD
Normal LD Level
Normal LDH
Normal LDH Level
Normal Lactate Dehydrogenase Level
When the number of reticulocytes in a specified volume of blood falls in the normal range.
Few but definitions not available
SCDO (Jade Hotchkiss)
Reticulocyte Count Normal
Normal Reticulocyte Count
When the total bilirubin level in the serum is in the normal range.
Few but definitions not available
SCDO (Jade Hotchkiss)
Serum Bilirubin Total Normal
Total Serum Bilirubin Level Normal
Total Serum Bilirubin Normal
Normal Total Serum Bilirubin
When the concentration of urinary albumin falls in the normal range.
None
SCDO (Jade Hotchkiss)
Normal Urinary Albumin Concentration
Urinary Albumin Concentration Normal
Urine Albumin Concentration Normal
Normal Urine Albumin Concentration
When the concentration of urine creatinine falls in the normal range.
Few but definitions not available
SCDO (Jade Hotchkiss)
Creatinine Urine Normal
Normal Urinary Creatinine
Normal Urinary Creatinine Level
Normal Urine Creatinine
Urinary Creatinine Level Normal
Urine Creatinine Level Normal
Normal Urine Creatinine Level
When the pressure exerted by oxygen dissolved in the blood falls in the normal range.
None
SCDO (Jade Hotchkiss)
Normal Oxygen Tension
Normal PO2
Normal PaO2
Normal Partial Pressure of Blood Oxygen
PO2 Normal
PaO2 Normal
Partial Pressure of Blood Oxygen Normal
Partial Pressure of Oxygen Normal
Normal Partial Pressure of Oxygen
When the pressure exerted by carbon dioxide dissolved in the blood falls in the normal range.
None
SCDO (Jade Hotchkiss)
Normal Carbon Dioxide Tension
Normal PaCO2
Normal Partial Pressure of Blood Carbon Dioxide
PaCO2 Normal
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.
None
SCDO (Jade Hotchkiss)
Decreased PCO2
Decreased PaCO2
Decreased Partial Pressure of Blood Carbon Dioxide
PCO2 Decreased
PaCO2 Decreased
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.
None
SCDO (Jade Hotchkiss)
Elevated Partial Pressure of Carbon Dioxide
Increased PCO2
Increased PaCO2
Increased Partial Pressure of Blood Carbon Dioxide
PCO2 Increased
PaCO2 Increased
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.
Sufficient
SCDO:1000842
MESH:D016857
Hypocarbia
Hypocapnia
A clinical manifestation of abnormal increase in the amount of carbon dioxide in arterial blood.
Sufficient
SCDO:1000843
MESH:D006935
Hypercarbia
Hypercapnia
When the abnormal hemoglobin, hemoglobin S (HbS), has been detected in a blood sample.
None
SCDO (Jade Hotchkiss)
Haemoglobin S Present
Haemoglobin S in Blood
HbS Present
HbS in Blood
Hemoglobin S in Blood
Hemoglobin S Present
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
Type of visit
visit_type
Demographics
2
dropdown
SickleInAfrica CDE - Type of Visit Question
A clinical visit occuring because of an acute (severe with sudden onset) health condition.
Few but definitions not specific enough
SCDO (Jade Hotchkiss)
Acute Clinical Visit
The Sickle in Africa core data element that records the patient's medical record number.
Medical record number (MRN)
medical_record_number
Demographics
4
text
MRN
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.
Hospital name
hospital_name
Demographics
5
text
SickleInAfrica CDE - Hospital Name Question
The name of the hospital visited by a patient.
None
SCDO (Jade Hotchkiss)
Hospital Name
The Sickle in Africa core data element that records a respondent's first name.
First name
first_name
Demographics
6
text
SickleInAfrica CDE - First Name Question
The Sickle in Africa core data element that records a respondent's middle name.
Middle name
middle_name
Demographics
7
text
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.
Sufficient
SCDO:1000858
sio:FirstName
Forename
Given Name
First Name
A middle name is a name assigned to an individual that is not the first or last name.
Sufficient
SCDO:1000860
sio:MiddleName
Middle 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.
Sufficient
SCDO:1000861
sio:LastName
Last Name
The Sickle in Africa core data element that records a respondent's last name.
Last name
last_name
Demographics
8
text
SickleInAfrica CDE - Last Name Question
The Sickle in Africa core data element that records a respondent's height.
Height/Length
height_length
Demographics
cm
12
Number
text
SickleInAfrica CDE - Height Question
The Sickle in Africa core data element that records a respondent's measured weight.
Weight
weight
Demographics
kg
13
Number
text
SickleInAfrica CDE - Weight Question
The Sickle in Africa core data element that records the ethnic group to which a respondent belongs.
Ethnic Group
tribe
Demographics
16
text
SickleInAfrica CDE - Ethnic Group Question
The Sickle in Africa core data element that records the religion of a respondent.
Religion
religion
Demographics
17
text
SickleInAfrica CDE - Religion Question
The Sickle in Africa core data element that records the region in which the respondent lives.
Region
region
Demographics
18
text
SickleInAfrica CDE - Region Question
A street name is the token given to identify a particular street.
Sufficient
SCDO:1000871
SIO:000766
Street Name
The Sickle in Africa core data element that records the name of the street in which the respondent lives.
Street
street
Demographics
19
text
SickleInAfrica CDE - Street Question
The Sickle in Africa core data element that records the landmark that is nearest to where the participant lives.
Nearest landmark
nearest_landmark
Demographics
20
text
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.
None
SCDO (Jade Hotchkiss)
Nearest Geographical Landmark
The name of a respondent's next of kin.
None
SCDO (Jade Hotchkiss)
Next of Kin Name
The Sickle in Africa core data element that records the participant's primary telephone number.
Telephone 1
telephone_1
Demographics
21
text
SickleInAfrica CDE - Telephone 1 Question
The Sickle in Africa core data element that records the participant's secondary telephone number.
Telephone 2
telephone_2
Demographics
22
text
SickleInAfrica CDE - Telephone 2 Question
The Sickle in Africa core data element that records the name of the participant's next of kin.
Next of kin name
next_of_kin_name
Demographics
23
text
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.
Next of kin telephone number
next_of_kin_telephone_numb
Demographics
24
text
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.
Relationship to participant
next_of_kin_relationship
Demographics
25
text
SickleInAfrica CDE - Relationship to Participant Question
A respondent's primary telephone number.
None
SCDO (Jade Hotchkiss)
Telephone Number 1
A respondent's secondary telephone number.
None
SCDO (Jade Hotchkiss)
Telephone Number 2
The telephone number of a respondent's next of kin.
None
SCDO (Jade Hotchkiss)
Next of Kin Telephone Number
The relationship that the participant's next of kin has with the participant.
None
SCDO (Jade Hotchkiss)
Next of Kin Relationship to Patient
Next of Kin Relationship to Participant
The Sickle in Africa core data element that records whether the participant was given a blood transfusion.
1, Yes
0, No
Blood transfusion
blood_transfusion
Management Details
7
yesno
SCDO (Jade Hotchkiss)
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.
Units transfused
units_transfused
Management Details
9
Number
[blood_transfusion] = "Yes"
text
SickleInAfrica CDE - Units Transfused Question
The number of units of blood that a patient received during a blood transfusion.
None
SCDO (Jade Hotchkiss)
Number of Units Transfused
The Sickle in Africa core data element that records whether a participant has difficulty in breathing.
1, Yes
0, No
Difficulty in breathing
difficulty_in_breathing
Vital Signs
4
yesno
SickleInAfrica CDE - Difficulty in Breathing Question
The Sickle in Africa core data element that records a participant's systolic blood pressure.
Systolic blood pressure
systolic_blood_press
Vital Signs
mmHg
5
text
SickleInAfrica CDE - Systolic Blood Pressure Question
The Sickle in Africa core data element that records a participant's diastolic blood pressure.
Diastolic blood pressure
diastol_blood_press
Vital Signs
mmHg
6
text
SickleInAfrica CDE - Diastolic Blood Pressure Question
The Sickle in Africa core data element that records whether a participant has priapism.
1, Yes
0, No
Priapism
priapism
Vital Signs
7
yesno
SickleInAfrica CDE - Priapism Question
The Sickle in Africa core data element that records whether a participant has chest pain.
1, Yes
0, No
Chest Pain
chest_pain
Vital Signs
8
yesno
SCDO (Jade Hotchkiss)
SickleInAfrica CDE - Chest Pain Question
The Sickle in Africa core data element that records whether a participant has anaemia.
1, Yes
0, No
Anaemia
anaemia
Vital Signs
9
yesno
SCDO (Jade Hotchkiss)
SickleInAfrica CDE - Anaemia Question
The Sickle in Africa core data element that records whether a participant has jaundice.
1, Yes
0, No
Jaundice
jaundice
Vital Signs
10
yesno
SickleInAfrica CDE - Jaundice Question
The Sickle in Africa core data element that collects the concentration of urea in the respondent's blood.
Urea
urea
Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise)
mmol/L
2
Number
text
SickleInAfrica CDE - Urea Question
A clinical visit that is the patient's first clinical visit.
None
SCDO (Jade Hotchkiss)
First Visit
A clinical visit that is a follow-up for a previous visit.
Not relevant to context of sickle cell
SCDO (Jade Hotchkiss)
Review Visit
Follow-Up 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.
http://purl.obolibrary.org/obo/STATO_0000091
Sufficient
SCDO:0000450
STATO:0000091
GWAS
Genome Wide Association Study
A neurological and physiological symptom characterized by a painful or apprehensive uneasiness of mind usually over an impending or anticipated ill.
http://purl.obolibrary.org/obo/SYMP_0000412
Sufficient
SCDO:0000068
http://www.apa.org/topics/anxiety/
SYMP:0000412
Anxiety Symptoms
Panic
Worry
Physical symptoms include increased blood pressure (rapid heartbeat), trembling or dizziness.
Anxiety
Muscle pain is a pain characterized by pain in one or more muscles.
Provide source for additional info
http://purl.obolibrary.org/obo/SYMP_0019161
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).
Pain of a muscle or a group of muscles.
Sufficient
SCDO:0000779
SYMP:0019161
Myalgia
Muscle Pain
A standardized quantity of a physical quality.
Sufficient
SCDO:1000478
UO:0000000
Unit
Unit of Measure
Units
Unit of Measurement
A unit which is a standard measure of the distance between two points.
Sufficient
SCDO:1000864
UO:0000001
Length Unit
A unit which is a standard measure of the amount of matter/energy of a physical object.
Sufficient
SCDO:1000628
UO:0000002
Mass Unit
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
Sufficient
SCDO:1000712
UO:0000005
Temperature Unit
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
Sufficient
SCDO:1000867
UO:0000009
Kilogram
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
Sufficient
SCDO:1000865
UO:0000015
Centimeter
A mass unit which is equal to 10^[-12] g.
Sufficient
SCDO:1000629
UO:0000025
picogram
pg
A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
Sufficient
SCDO:1000491
UO:0000051
Concentration Unit
A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
Sufficient
SCDO:1000622
UO:0000095
Volume Unit
A volume unit which is equal to 10^[-15] L.
Sufficient
SCDO:1000623
UO:0000104
cubic micrometre
femtoliter
femtolitre
μm^3
fL
A unit which is a standard measure of the force applied to a given area.
Sufficient
SCDO:1000720
UO:0000109
Pressure Unit
A concentration unit which is a standard measure of the mass of a substance in a given volume (density).
Sufficient
SCDO:1000506
UO:0000180
Unit of Density
Definition from BioAssay Ontology
Mass Per Unit Volume
A unit which is a standard measure of physical quantity consisting of only a numerical number without any units.
Sufficient
SCDO:1000642
UO:0000186
Dimensionless Unit
A dimensionless ratio unit which denotes numbers as fractions of 100.
Sufficient
SCDO:1000644
UO:0000187
%
Percent
A dimensionless unit which denotes an amount or magnitude of one quantity relative to another.
Sufficient
SCDO:1000643
UO:0000190
Ratio
A concentration unit which denotes the average cell number in a given volume.
Sufficient
SCDO:1000503
UO:0000200
Cell Concentration Unit
A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth.
Sufficient
SCDO:1000721
UO:0000272
millimetres of mercury
mmHg
A unit which represents a standard measurement occurrence of a process per unit time.
Sufficient
SCDO:1000715
UO:0000280
Rate Unit
A unit of cell concentration which is equal to one cell in a volume of 1 microliter.
Sufficient
SCDO:1000507
UO:0000316
cells per microliter
cells/µL
cells per 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.
http://purl.obolibrary.org/obo/VO_0000001
Sufficient
SCDO:0001221
VO:0000001
Vaccine
A viral vaccine that protects against infection with influenza virus.
http://purl.obolibrary.org/obo/VO_0000642
Sufficient
SCDO:0000642
VO:0000642
Influenza Virus Vaccine
A Streptococcal vaccine that is used against S. pneumoniae infection, which causes pneumococcal diseases.
http://purl.obolibrary.org/obo/VO_0000675
Sufficient
SCDO:0001109
VO:0000675
Pneumococcal Vaccine
Streptococcus Pneumoniae Vaccine
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.
Sufficient
SCDO:1000499
VT:0000202
AP Level
Blood Alkaline Phosphatase Amount
Circulating ALP Level
Circulating Alkaline Phosphatase Level
Alkaline Phosphatase Level
ERO:0001964
NCIT:C84981
NCIT:C84982
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.
Surgery
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.
Severely Increased Albuminuria
Pulse Oximeter
Scintigraphy
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.
no
D011877
May be Acute (acute kidney injury) or chronic (see chronic kidney disease).
Hair-pulling
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
main treatments are:
lifestyle changes to ensure you remain as healthy as possible
medication to control associated problems such as high blood pressure and high cholesterol
dialysis – treatment to replicate some of the kidney's functions; this may be necessary in advanced CKD
kidney transplant – this may also be necessary in advanced CKD
Hemoglobin M Disease
Pain Management
Biologic therapy, Antibody therapy, Stem-cell transplantation, Splenectomy, Steroid treatment, Radioimmunotherapy, Surgery, chemotherapy, and radiation therapy,
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.
essential measures (annotations)
example to be eventually removed
Anti-inflammatory medications for joint pain and stiffness. Steroid creams for rashes. Corticosteroids to minimize the immune response. Antimalarial drugs for skin and joint problems.
Test for Stroke Risk in Children with Sickle Cell Disease - TCD
Assessment for Hepatomegaly
uncurated
yes
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.
Neurological disorders
Neurology
no
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.
PMID:22655528
PMID:6690472