The Hereditary Ontology for Genomic Data
type: Ontology
version IRI: https://w3id.org/hereditary/ontology/genomics/1.0/
imports: core
creator: Laura Menotti
creator: Gianmaria Silvello
description: The Hereditary ontology for Genomic Data models models genetic data following GA4GH standards like the Beacon v2 data model.
license: Copyright 2024-2027 University of Padua, Italy Licensed under the Creative Commons Attribution 4.0 International License https://creativecommons.org/licenses/by/4.0/ You may obtain a copy of the License at https://creativecommons.org/licenses/by/4.0/legalcode This work has been supported by the HEREDITARY project https://hereditary-project.eu/ funded by the European Union’s Horizon Europe research and innovation programme under the grant agreement No GA101137074
version info: 1.0

ageRangeEnd
type: ObjectProperty
domain: Age Range
range: Age
comment: The end age range.

ageRangeStart
type: ObjectProperty
domain: Age Range
range: Age
comment: The start age range.

alleleOrigin
type: ObjectProperty
domain: Case Level Variant
range: Allele Origin
comment: Links the case level variant to the allele origin.

analysis
type: ObjectProperty
domain: Case Level Variant
range: Analysis
comment: Links the case level variant to the bioinformatics analysis.

annotatedWith
type: ObjectProperty
domain: PhenoClinic Effect
range: Software Tool
comment: Links the pehnoclinic effect to the software tool used to annotate it.

assay
type: ObjectProperty
domain: Measurement
range: Assay
comment: Links the measurement to the assay used to produce the measurement.

biosample
type: ObjectProperty
domain: Class
  union of: Analysis
  union of: Case Level Variant
  union of: Run
range: Biosample
comment: Links the case level variant to its biosample.

biosampleStatus
type: ObjectProperty
domain: Biosample
range: Biosample Status
comment: Links the biosample to its status.

caseLevelData
type: ObjectProperty
domain: Genomic Variation
range: Case Level Variant
comment: Links the considered genomic variation to variation instances observed in individual analyses.

category
type: ObjectProperty
domain: PhenoClinic Effect
range: PhenoClinic Category
comment: Links the phenoclinic effect to the type of disease, condition, phenotypics measurement, etc.

chromosomeSpecies
type: ObjectProperty
domain: Chromosome Location
range: Species
comment: Links a chromosome location to the species.

clinicalInterpretation
type: ObjectProperty
domain: Class
  union of: Case Level Variant
  union of: Variant Level Data
range: PhenoClinic Effect
comment: Links the variant level data and case level variant to its phenoclinic effects.

cohortAgeRange
type: ObjectProperty
domain: Cohort Criteria
range: Age Range
comment: Individual age range in cohort inclusion criteria. [Definition Source: Beacon v2 Data Model]

cohortDataType
type: ObjectProperty
domain: Cohort
range: Cohort Data Type
comment: Links a cohort to the types of information.

cohortDesign
type: ObjectProperty
domain: Cohort
range: Cohort Design
comment: Links a cohort to the cohort type by its design.

cohortDisease
type: ObjectProperty
domain: Cohort Criteria
range: Cohort Disease
comment: Diseases in cohort inclusion criteria. [Definition Source: Beacon v2 Data Model]

cohortEthnicity
type: ObjectProperty
domain: Cohort Criteria
comment: Ethnicities in cohort inclusion criteria. [Definition Source: BEacon v2 Data Model]

cohortLocation
type: ObjectProperty
domain: Cohort Criteria
range: Geographic Location
comment: Geographic location(s) in cohort inclusion criteria. [Definition Source: Beacon v2 Data Model]

cohortSex
type: ObjectProperty
domain: Cohort Criteria
range: Cohort Sex
comment: Sex(es) in cohort inclusion criteria. [Definition Source: Beacon v2 Data Model]

collectionEvent
type: ObjectProperty
domain: Cohort
range: Collection Event
comment: Links a cohort to the collection event.

cytobandInterval
type: ObjectProperty
domain: Chromosome Location
range: Cytoband Interval
comment: Links a chromosome location to the cytoband interval.

diagnosticMarker
type: ObjectProperty
domain: Biosample
range: Diagnostic Marker
comment: Links a biosample to clinically relevant biomarkers.

diseaseAgeOnset
type: ObjectProperty
domain: Cohort Disease
range: Time Element
comment: Links the disease to the the age at which an individual first experiences the disease.

diseaseCode
type: ObjectProperty
domain: Cohort Disease
comment: Links the disease to the disease identifier.

diseaseStage
type: ObjectProperty
domain: Cohort Disease
range: Disease Stage
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1707790
comment: Links the disease to the stage.

distribution
type: ObjectProperty
domain: Data Availability and Distribution
range: Element Distribution
comment: Links the aggregated information to the results or counts for each category.

effect
type: ObjectProperty
domain: PhenoClinic Effect
comment: Links the phenoclinic effect class to the annotated phenotypic or clinical effect

elementType
type: ObjectProperty
domain: Element Distribution
comment: Links the element distribution to the category.

eventDistribution
type: ObjectProperty
domain: Collection Event
range: Data Availability and Distribution
comment: Links a collection event to aggregated information obtained from individual level info of the cohort members.

eventTimeline
type: ObjectProperty
domain: Collection Event
range: Event Timeline
comment: Links a Collection Event to the Event Timeline.

evidence
type: ObjectProperty
domain: PhenoClinic Effect
range: PhenoClinic Evidence
comment: Links the phenoclinic effect to the type of evidence supporting variant-disease association.

exclusionCriteria
type: ObjectProperty
domain: Cohort
range: Cohort Criteria
comment: Exclusion criteria used for defining the cohort. It is assumed that NONE of the cohort participants will match such criteria. [Definition Source: Beacon v2 Data Model]

featureModifier
type: ObjectProperty
domain: Phenotypic Feature
range: Phenotypic Feature Modifier
comment: Links the phenotypic feature to specific characteristics.

featureOnset
type: ObjectProperty
domain: Phenotypic Feature
range: Time Element
comment: Age or time at which the feature was first observed. [Definition Source: Beacon v2 Data Model]

featureResolution
type: ObjectProperty
domain: Phenotypic Feature
range: Time Element
comment: Age or time at which the feature resolved or abated. [Definition Source: Beacon v2 Data Model]

featureType
type: ObjectProperty
domain: Phenotypic Feature
range: Phenotypic Feature Type
comment: Links a phenotypic feature to its type.

frequency
type: ObjectProperty
domain: Frequency In Population
range: Population Frequency
comment: Links the Frequency In Population class to allele frequency information of each population.

frequencyInPopulation
type: ObjectProperty
domain: Genomic Variation
range: Frequency In Population
comment: Links the considered genomic variation to frequency information of different populations.

genomicFeature
type: ObjectProperty
domain: Molecular Attribute
range: Genomic Feature
comment: Links a genomic variation to the genomic feature(s) affected by it.

genomicFeatureClass
type: ObjectProperty
domain: Genomic Feature
range: Genomic Feature Class
comment: Links the genomic feature to the class of genomic feature affected by the variant.

genotypeMember
type: ObjectProperty
domain: Genotype
range: Genotype Member
comment: Links the genotype varoation to the members describes a Molecular Variation and the count of that variation at the locus.

genotypeVariation
type: ObjectProperty
domain: Genotype Member
range: Molecular Variation
comment: Links a genotype locus to the molecular variation.

haplotypeMember
type: ObjectProperty
domain: Haplotype
range: Allele
comment: Links the haplotype to the co-occurring allele.

histologicalDiagnosis
type: ObjectProperty
domain: Biosample
comment: Links the biosample to the disease diagnosis that was inferred from the histological examination. [Definition Source: GA4GH Beacon v2 Data Model]

inCohort
type: ObjectProperty
domain: Patient
range: Cohort
comment: Links a patient to the belonging cohort.

inVcfFile
type: ObjectProperty
domain: VCF Record
range: VCF File
comment: Links the VCF record to the corresponding VCF file.

inclusionCriteria
type: ObjectProperty
domain: Cohort
range: Cohort Criteria
comment: Inclusion criteria used for defining the cohort. It is assumed that all cohort participants will match such criteria. [Definition Source: Beacon v2 Data Model]

individual
type: ObjectProperty
domain: Class
  union of: Analysis
  union of: Biosample
  union of: Case Level Variant
  union of: Run
range: Person
comment: Links the case level variant to the considered individual.

librarySource
type: ObjectProperty
domain: Run
range: Library Source
comment: Links an experimental run to the the source of the sequencing or hybridization library.

location
type: ObjectProperty
domain: Class
  union of: Allele
  union of: Copy Number Change
  union of: Copy Number Count
  union of: Legacy Variation
range: Location
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1706949
comment: Links a class to the genomic location.

measurement
type: ObjectProperty
domain: Biosample
range: Measurement
comment: Links a biosample to the measurement.

measurementMoment
type: ObjectProperty
domain: Measurement
range: Time Element
comment: Moment in time at which measurement was performed. [Definition Source: GA4GH Beacon v2 Data Model]

measurementUOM
type: ObjectProperty
domain: Measurement
range: Unit Of Measure
comment: Links a measurement to the employed Unit Of Measure.

molecularAttribute
type: ObjectProperty
domain: Genomic Variation
range: Molecular Attribute
comment: Links the considered genomic variation to its molecular attributes.

molecularEffect
type: ObjectProperty
domain: Molecular Attribute
range: Molecular Effect
comment: Links a molecular attribute to its molecular effect.

molecularVariationType
type: ObjectProperty
type: FunctionalProperty
domain: Molecular Variation
range: Class
  union of: Allele
  union of: Haplotype
comment: Links a molecular variation to the variation type.

obtentionProcedure
type: ObjectProperty
domain: Class
  union of: Biosample
  union of: Measurement
range: Obtention Procedure
comment: The procedure for sample or measurement obtention.

pathologicalStage
type: ObjectProperty
domain: Biosample
range: Pathological Stage
comment: Links the biosample to the detected pathological stage.

pathologicalTNMFinding
type: ObjectProperty
domain: Biosample
range: Pathological TNM Finding
comment: Links the biosample to the detected pathological TNM finding.

phenotypicCondition
type: ObjectProperty
domain: Cohort Criteria
range: Phenotypic Feature
comment: Links the cohort criteria to the phenotypic condition(s) in cohort inculsion criteria.

phenotypicEffect
type: ObjectProperty
domain: Class
  union of: Case Level Variant
  union of: Variant Level Data
range: PhenoClinic Effect
comment: Links the variant level data and case level variant to its phenoclinic effects.

phenotypicFeature
type: ObjectProperty
domain: Biosample
range: Phenotypic Feature
comment: Link the biosample to the phenotypic abnormalities of the sample.

platformModel
type: ObjectProperty
domain: Run
range: Platform Model
comment: Links the experimental run to the experimental platform or methodology used.

refersToCohort
type: ObjectProperty
domain: VCF File
range: Cohort
comment: Links the VCF file tot the corresponding cohort

run
type: ObjectProperty
domain: Class
  union of: Analysis
  union of: Case Level Variant
range: Run
comment: Links the case level variant to the experimental run.

sampleOriginDetail
type: ObjectProperty
domain: Biosample
range: Sample Origin Detail
comment: Links the biosample to the sample origin detail.

sampleOriginType
type: ObjectProperty
domain: Biosample
range: Sample Origin Type
comment: Links the biosample to the sample origin type.

sampleProcessing
type: ObjectProperty
domain: Biosample
range: Sample Processing
comment: Links the biosample to how the specimen was processed.

sequenceComponent
type: ObjectProperty
domain: Composed Sequence Expression
range: Class
  union of: Derived Sequence Expression
  union of: Literal Sequence Expression
  union of: Repeated Sequence Expression
comment: Sequence Expression components comprising the expression.

sequenceExpression
type: ObjectProperty
domain: Repeated Sequence Expression
range: Class
  union of: Derived Sequence Expression
  union of: Literal Sequence Expression
comment: Links the repeated sequence expression to the expression of the repeating subsequence.

sequenceInterval
type: ObjectProperty
domain: Sequence Location
range: Sequence Interval
comment: Links the sequence location to the sequence interval.

sequenceLocation
type: ObjectProperty
domain: Derived Sequence Expression
range: Sequence Location
comment: Links a sequence expression to the sequence location.

sequenceState
type: ObjectProperty
domain: Allele
range: Sequence Expression
comment: Links the allele to an expression of the sequence state.

severity
type: ObjectProperty
domain: Class
  union of: Cohort Disease
  union of: Phenotypic Feature
range: Severity
comment: Links a disease or phenotypic feature to its severity.

systemicVariationType
type: ObjectProperty
type: FunctionalProperty
domain: Systemic Variation
range: Class
  union of: Copy Number Change
  union of: Copy Number Count
  union of: Genotype
comment: Links a systemic variation to the variation type.

timeIntervalEnd
type: ObjectProperty
domain: Time Interval
range: Timestamp
comment: The timestamp in which a time interval has ended.

timeIntervalStart
type: ObjectProperty
domain: Time Interval
range: Timestamp
comment: The timestamp in which a time interval has started.

tumorGrade
type: ObjectProperty
domain: Biosample
range: Tumor Grade
comment: Links the biosample to the detected tumor grade.

tumorProgression
type: ObjectProperty
domain: Biosample
range: Tumor Progression
comment: Links the biosample to the observed tumor progression.

variantAlternativeID
type: ObjectProperty
domain: Genomic Variation
range: Variant Alternative ID
comment: Links a genomic variation to the variant alternative ID.

variantLevelData
type: ObjectProperty
domain: Genomic Variation
range: Variant Level Data
comment: Links the considered genomic variation to its variant level data.

variantQuality
type: ObjectProperty
domain: Genomic Variation
range: Variant Quality
comment: Links the considered genomic variation to the quality score of the variation.

variationCopyChange
type: ObjectProperty
domain: Copy Number Change
range: Copy Number Assessment
comment: Links the Copy Number Change to the type of variation change.

vcfRecord
type: ObjectProperty
domain: Genomic Variation
range: VCF Record
comment: Links the considered genomic variation to the VCF record mentioning it.

zygosity
type: ObjectProperty
domain: Case Level Variant
range: Zygosity
comment: Links the case level variant to the observed zigosity.

alleleFrequency
type: DatatypeProperty
domain: Population Frequency
range: float
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0017270
comment: Allele frequency between 0 and 1. Example: 0.00003186. [Definition Source: GA4GH Beacon v2 Data Model]

alternateBases
type: DatatypeProperty
domain: Legacy Variation
range: PlainLiteral
comment: Alternate bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used as\n a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of deletions with the maximally\n trimmed, deleted sequence being indicated in `ReferenceBases`. Pattern: "^([ACGTUNRYSWKMBDHV\\-\\.]*)$" [Definition Source: GA4Gh Beacon v2 Data Model]

alternativeIDReference
type: DatatypeProperty
domain: Variant Alternative ID
range: PlainLiteral
comment: External reference of the variant alternative ID.

aminoacidChange
type: DatatypeProperty
domain: Molecular Attribute
range: PlainLiteral
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1953353
comment: Change at aminoacid level for protein affecting variants. Example: "V304*". [Definition Source: GA4GH Beacon v2 Data Model]

analysisAligner
type: DatatypeProperty
domain: Analysis
range: PlainLiteral
comment: Reference to mapping/alignment software. [Definition Source: GA4GH Beacon v2 Data Model]

analysisDate
type: DatatypeProperty
domain: Analysis
range: dateTime
comment: Date at which analysis was performed. [Definition Source: GA4GH Beacon v2 Data Model]

analysisPipelineName
type: DatatypeProperty
domain: Analysis
range: PlainLiteral
comment: Analysis pipeline and version if a standardized pipeline was used. [Definition Source: GA4GH Beacon v2 Data Model]

analysisPipelineRef
type: DatatypeProperty
domain: Analysis
range: PlainLiteral
comment: Link to Analysis pipeline resource. [Definition Source: GA4GH Beacon v2 Data Model]

availability
type: DatatypeProperty
domain: Data Availability and Distribution
range: boolean
comment: Data availability. [Definition Source: GA4GH Beacon v2 Data Model]

availabilityCount
type: DatatypeProperty
domain: Data Availability and Distribution
range: integer
comment: Count of individuals with data available. [Definition Source: GA4GH Beacon v2 Data Model]

biosampleCollectionDate
type: DatatypeProperty
domain: Biosample
range: dateTime
comment: Date of biosample collection in ISO8601 format. [Definition Source: GA4GH Beacon v2 Data Model]

biosampleCollectionMoment
type: DatatypeProperty
domain: Biosample
range: PlainLiteral
comment: Individual's or cell cullture age at the time of sample collection in the ISO8601 duration format `P[n]Y[n]M[n]DT[n]H[n]M[n]S`. [Definition Source: GA4GH Beacon v2 Data Model]

clinicalRelevance
type: DatatypeProperty
domain: PhenoClinic Effect
range: Datatype
  one of: Benign
  one of: Likely Benign
  one of: Likely Pathogenic
  one of: Pathogenic
  one of: Uncertain Significance
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C5239127
comment: Indication of the clinical relevance of the variant Recommended: A value from the five-tiered classification from the American College of Medical Genetics (ACMG) designed to describe the likelihood that a genomic sequence variant is causative of an inherited disease. (ACMG Classification of Genomic Variant Pathogenicity: NCIT:C168798). [Definition Source: GA4GH Beacon v2 Data Model]

clinvarVariantID
type: DatatypeProperty
domain: Genomic Variation
range: PlainLiteral
comment: ClinVar variant id. Other id values used by ClinVar can be added to `variantAlternativeIds`. pattern: "^(clinvar:)?\\d+$". [Definition Source: GA4GH Beacon v2 Data Model]

cohortName
type: DatatypeProperty
domain: Cohort
range: PlainLiteral
comment: Name of the cohort. For `user-defined` this field could be generated upon the query, e.g. a value that is a concatenationor some representation of the user query. [Definition Source: Beacon v2 Data Model]

cohortSize
type: DatatypeProperty
domain: Cohort
range: integer
comment: Count of unique Individuals in cohort (individuals meeting criteria for `user-defined` cohorts). If not previously known, it could be calculated by counting the individuals in the cohort. [Definition Source: Beacon v2 Data Model]

cohortType
type: DatatypeProperty
domain: Cohort
range: PlainLiteral
comment: Cohort type by its definition. If a cohort is declared `study-defined` or `beacon-defined` criteria are to be entered `in cohort_inclusion_criteria`; if a cohort is declared `user-defined` `cohort_inclusion_criteria` could be automatically populated from the parameters used to perform the query. [DEfinition Source: Beacon v2 Data Model]

cytobandEnd
type: DatatypeProperty
domain: Cytoband Interval
range: PlainLiteral
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C5236541
comment: The end cytoband region. MUST specify a region nearer the terminal end (telomere) of the chromosome q-arm than start. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

cytobandStart
type: DatatypeProperty
domain: Cytoband Interval
range: PlainLiteral
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C5236543
comment: The start cytoband region. MUST specify a region nearer the terminal end (telomere) of the chromosome p-arm than end. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

earliestEvent
type: DatatypeProperty
domain: Event Timeline
range: dateTime
comment: Earliest date of visit or collection timeline. [Definition Source: GA4GH Beacon v2 Data Model]

elementDistribution
type: DatatypeProperty
domain: Element Distribution
range: integer
comment: Results or counts for each category.

eventCases
type: DatatypeProperty
domain: Collection Event
range: integer
comment: Number of cases. [Definition Source: GA4GH Beacon v2 Data Model]

eventControls
type: DatatypeProperty
domain: Collection Event
range: integer
comment: Number of controls. [Definition SOurce: GA4GH Beacon v2 Data Model]

eventDate
type: DatatypeProperty
domain: Collection Event
range: dateTime
comment: Date of collection event/data point. [Definition Source: GA4GH Beacon v2 Data Model]

eventSize
type: DatatypeProperty
domain: Collection Event
range: integer
comment: Count of individuals in cohort at data point (for "user-defined" cohorts, this is individuals meeting criteria) obtained from individual level info in database. [Definition Source: GA4GH Beacon v2 Data Model]

familyHistory
type: DatatypeProperty
domain: Cohort Disease
range: boolean
comment: Boolean indicating determined or self-reported presence of family history of the disease. [Definition Source: Beacon v2 Data Model]

featureExcluded
type: DatatypeProperty
domain: Phenotypic Feature
range: boolean
comment: Flag to indicate whether the phenotypic feature was observed or not. Default is "FALSE", in other words the phenotype was observed. Therefore it is only used in cases where the phenotype was looked for but found to be absent. More formally, this modifier indicates the logical negation of the OntologyClass used in the `featureType` field. CAUTION: It is imperative to check this field for correct interpretation of the phenotype! Source: Phenopackets v2 [Definition Source: Beacon v2 Data Model]

filename
type: DatatypeProperty
domain: VCF File
range: PlainLiteral
comment: The name of the file.

filepath
type: DatatypeProperty
domain: VCF File
range: PlainLiteral
comment: The path to the file.

geneID
type: DatatypeProperty
domain: Molecular Attribute
range: PlainLiteral
comment: Symbolic name or identifier used for a gene. [Definition Source: GA4GH Beacon v2 Data Model]

genomeAssembly
type: DatatypeProperty
domain: VCF Record
range: PlainLiteral
comment: Identifier for the genome assembly used to call the allele. [Definition Source: Phenopacket v2 Data Model]

genomicHGVSID
type: DatatypeProperty
domain: Genomic Variation
range: PlainLiteral
comment: The Human Genome Variation Society (HGVS) ID descriptor. [Definition Source: GA4GH Beacon v2 Data Model]

genotypeCount
type: DatatypeProperty
domain: Genotype Member
range: integer
comment: The number of copies of the variation at a Genotype locus. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

gestationalDays
type: DatatypeProperty
domain: Gestational Age
range: integer
comment: Days beyond the completed weeks, if available. [Definition Source: GA4GH Beacon v2 Data Model]

gestationalWeeks
type: DatatypeProperty
domain: Gestational Age
range: integer
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C5203192
comment: Completed weeks of gestation. [Definition Source: GA4GH Beacon v2 Data Model]

iso8601duration
type: DatatypeProperty
domain: Age
range: PlainLiteral
comment: Represents age as a ISO8601 duration (e.g., 'P40Y10M05D'). [Definition Source: GA4GH Beacon v2 Data Model]

latestEvent
type: DatatypeProperty
domain: Event Timeline
range: dateTime
comment: Latest date of visit or collection timeline. [Definition Source: GA4GH Beacon v2 Data Model]

libraryLayout
type: DatatypeProperty
domain: Run
range: Datatype
  one of: PAIRED
  one of: SINGLE
comment: Ontology value for the library layout e.g "PAIRED", "SINGLE" [Definition Source: GA4GH Beacon v2 Data Model]

librarySelection
type: DatatypeProperty
domain: Run
range: PlainLiteral
comment: Selection method for library preparation, e.g "RANDOM", "RT-PCR". [Definition Source: GA4GH Beacon v2 Data Model]

libraryStrategy
type: DatatypeProperty
domain: Run
range: PlainLiteral
comment: Library strategy, e.g. "WGS". [Definition SOurce: GA4GH Beacon v2 Data Model]

locationChr
type: DatatypeProperty
domain: Chromosome Location
range: PlainLiteral
comment: The symbolic chromosome name. For humans, chromosome names MUST be one of 1..22, X, Y (case-sensitive) [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

measurementDate
type: DatatypeProperty
domain: Measurement
range: dateTime
comment: Date of measurement. [Definition Source: GA4GH Beacon v2 Data Model]

measurementRefRangeHigh
type: DatatypeProperty
domain: Measurement
range: float
comment: The reference range to determine the measurement to be high.

measurementRefRangeLow
type: DatatypeProperty
domain: Measurement
range: float
comment: The reference range to determine the measurement to be low.

measurementValue
type: DatatypeProperty
domain: Measurement
range: float
comment: The value of the measurement in the units,

molecularVariationCount
type: DatatypeProperty
domain: Genotype
range: integer
comment: The total number of copies of all Molecular Variation at this locus, MUST be greater than or equal to the sum of GenotypeMember copy counts and MUST be greater than or equal to 1. If greater than the total of GenotypeMember counts, this field describes additional Molecular Variation that exist but are not explicitly described. [Definition Source: Ga4GH Variation Representation Specification (VRS) v1.2]

notes
type: DatatypeProperty
domain: Class
  union of: Cohort Disease
  union of: Measurement
  union of: Phenotypic Feature
  union of: Variant Alternative ID
range: PlainLiteral
comment: Unstructured text to provide additional information.

population
type: DatatypeProperty
domain: Population Frequency
range: PlainLiteral
comment: A name for the population. A population could an ethnic, geographical one or just the members of a study. Examples: "East Asian", "Men", "ICGC Chronic Lymphocytic Leukemia-ES". [Definition Source: GA4GH Beacon v2 Data Model]

proteinHGVSID
type: DatatypeProperty
domain: Genomic Variation
range: PlainLiteral
comment: The Human Genome Variation Society (HGVS) ID descriptor(s) at protein level (for protein-altering variants). [Definition Source: GA4GH Beacon v2 Data Model]

referenceBases
type: DatatypeProperty
domain: Legacy Variation
range: PlainLiteral
comment: Reference bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used\n as a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of insertions with the maximally\n trimmed, inserted sequence being indicated in `AlternateBases`. Pattern: "^([ACGTUNRYSWKMBDHV\\-\\.]*)$" [Definition Source: Ga4GH Beacon v2 Data Model]

referenceSequence
type: DatatypeProperty
domain: Sequence Location
range: PlainLiteral
comment: A VRS Computed Identifier for the reference Sequence. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

repeatedSequenceCount
type: DatatypeProperty
domain: Repeated Sequence Expression
range: integer
comment: The count of repeated units, as an integer or inclusive range. [Defintion Source: GA4GH VAriation Representation Specification (VRS) v1.2]

reverseComplement
type: DatatypeProperty
domain: Derived Sequence Expression
range: boolean
comment: A flag indicating if the expressed sequence is the reverse complement of the sequence referred to by location. [definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

runDate
type: DatatypeProperty
domain: Run
range: dateTime
comment: Date at which the experiment was performed. [Definition Source: Ga4GH Beacon v2 Data Model]

runPlatform
type: DatatypeProperty
domain: Run
range: PlainLiteral
comment: General platform technology label. It SHOULD be a subset of the platformModel and used only for query convenience, e.g. "return everything sequenced with Illimuna", where the specific model is not relevant. [Definition Source: GA4GH Beacon v2 Data Model]

sampleStorage
type: DatatypeProperty
domain: Biosample
range: PlainLiteral
comment: Status of how the specimen was stored. [Definition Source: GA4GH Beacon v2 Data Model]

sequence
type: DatatypeProperty
domain: Literal Sequence Expression
range: PlainLiteral
comment: A character string representation of a contiguous, linear polymer of nucleic acid or amino acid Residues. Sequences are the prevalent representation of these polymers, particularly in the domain of variant representation. [Definition Source: Ga4GH Variation Representation Specification (VRS) v1.2]

sequenceIntervalEnd
type: DatatypeProperty
domain: Sequence Interval
range: PlainLiteral
comment: The end coordinate or range of the interval. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range greater than the value of start. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

sequenceIntervalStart
type: DatatypeProperty
domain: Sequence Interval
range: PlainLiteral
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C4525827
comment: The start coordinate or range of the interval. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range less than the value of end. [Definition Source: Ga4GH variation Representation Specification (VRS) v1.2]

source
type: DatatypeProperty
domain: Frequency In Population
range: PlainLiteral
comment: The study reporting the frequency information. Examples: "The Genome Aggregation Database (gnomAD)", "The European Genome-phenome Archive (EGA)". [Definition Source: GA4GH Beacon v2 Data Model]

sourceReference
type: DatatypeProperty
domain: Frequency In Population
range: PlainLiteral
comment: A reference to further documentation or details. Examples: "https://gnomad.broadinstitute.org/", "https://ega-archive.org/". [Definition Source: GA4GH Beacon v2 Data Model]

sourceVersion
type: DatatypeProperty
domain: Frequency In Population
range: PlainLiteral
comment: Version of the source data. Example: "gnomAD v3.1.1". [Definition Source: GA4GH Beacon v2 Data Model]

timestamp
type: DatatypeProperty
domain: Timestamp
range: dateTimeStamp
comment: The datetime of the timestamp.

toolName
type: DatatypeProperty
domain: Software Tool
range: PlainLiteral
comment: Name of the software tool. [Definition Source: GA4GH Beacon v2 Data Model]

toolReference
type: DatatypeProperty
domain: Software Tool
range: PlainLiteral
comment: References to the software tool. [Definition Source: GA4GH Beacon v2 Data Model]

toolVersion
type: DatatypeProperty
domain: Software Tool
range: PlainLiteral
comment: Software Tool version used. [Definition Source: GA4GH Beacon v2 Data Model]

transcriptHGVSID
type: DatatypeProperty
domain: Genomic Variation
range: PlainLiteral
comment: The Human Genome Variation Society (HGVS) ID descriptor(s) at transcript level.

valueID
type: DatatypeProperty
domain: Variant Alternative ID
range: PlainLiteral
comment: The variant alternative ID.

variantCaller
type: DatatypeProperty
domain: Analysis
range: PlainLiteral
comment: Reference to variant calling software / pipeline. [Definition Source: GA4GH Beacon v2 Data Model]

variantFilter
type: DatatypeProperty
domain: Variant Quality
range: PlainLiteral
comment: FILTER — filter status: PASS if this position has passed all filters, i.e., a call is made at this position. Otherwise, if the site has not passed all filters, a semicolon-separated list of codes for filters that fail. e.g. “q10;s50” might indicate that at this site the quality is below 10 and the number of samples with data is below 50% of the total number of samples. ‘0’ is reserved and must not be used as a filter String. If filters have not been applied, then this field must be set to the MISSING value. (String, no whitespace or semicolons permitted, duplicate values not allowed.) [Definition Source: VCF Specification v4.4]

variantInternalID
type: DatatypeProperty
domain: Genomic Variation
range: PlainLiteral
comment: Reference to the **internal** variant ID. This represents the primary key/identifier of that variant **inside** a given Beacon instance. Different Beacon instances may use identical id values, referring to unrelated variants. Public identifiers such as the GA4GH Variant Representation Id (VRSid) MUST be returned in the `identifiers` section. A Beacon instance can, of course, use the VRSid as their own internal id but still MUST represent this then in the `identifiers` section. [Definition Source: GA4GH Beacon v2 Data Model]

variantQual
type: DatatypeProperty
domain: Variant Quality
range: float
comment: QUAL — quality: Phred-scaled quality score for the assertion made in ALT. i.e. −10log10 prob(call in ALT is wrong). If ALT is ‘.’ (no variant) then this is −10log10 prob(variant), and if ALT is not ‘.’ this is −10log10 prob(no variant). If unknown, the MISSING value must be specified. (Float) [Definition Source: VCF Specification v4.4]

variantType
type: DatatypeProperty
domain: Legacy Variation
range: PlainLiteral
comment: The `variantType` declares the nature of the variation in relation to a reference. In a response, it is used to describe the variation. Examples here are e.g. structural variants such as `DUP` (increased allelic count of material from the genomic region between `start` and `end` positions without assumption about the placement of the additional sequence) or `DEL` (deletion of sequence following `start`). Either `alternateBases` or `variantType` is required in representing a `LegacyVariation`. Deafult value is "SNP". [Definition Source: Ga4GH Beacon v2 Data Model]

variationCopies
type: DatatypeProperty
domain: Copy Number Count
range: integer
comment: The integral number of copies of the subject in a system. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

vcfAlt
type: DatatypeProperty
domain: VCF Record
range: PlainLiteral
comment: Alternate base. [Definition Source: Phenopacket v2 Data Model]

vcfChrom
type: DatatypeProperty
domain: VCF Record
range: PlainLiteral
comment: Chromosome or contig identifier. [Definition Source: Phenopacket v2 Data Model]

vcfFilter
type: DatatypeProperty
domain: VCF Record
range: PlainLiteral
comment: Filter status: PASS if this position has passed all filters. [Definition Source: Phenopacket v2 Data Model]

vcfInfo
type: DatatypeProperty
domain: VCF Record
range: PlainLiteral
comment: Additional information: Semicolon-separated series of additional information fields. [Definition Source: Phenopacket v2 Data Model]

vcfPos
type: DatatypeProperty
domain: VCF Record
range: PlainLiteral
comment: The reference position, with the 1st base having position 1. [Definition Source: Phenopacket v2 Data Model]

vcfQual
type: DatatypeProperty
domain: VCF Record
range: PlainLiteral
comment: Quality: Phred-scaled quality score for the assertion made in ALT. [Definition Source: Phenopacket v2 Data Model]

vcfRef
type: DatatypeProperty
domain: VCF Record
range: PlainLiteral
comment: Reference base. [Definition Source: Phenopacket v2 Data Model]

Person
type: Class
comment: A human being. [Definition Source: NCI]

Disease, Disorder or Finding
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1511989
comment: A condition that is relevant to human neoplasms and non-neoplastic disorders. This includes observations, test results, history and other concepts relevant to the characterization of human pathologic conditions. [Definition Source: NCI]

Group (social concept)
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1257890
comment: A group of individuals united by a common factor (e.g., geographic location, ethnicity, disease, age, gender) [Definition Source: NCI]

Patient
type: Class
subclass of: Person
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0030705
comment: A person who receives medical attention, care, or treatment, or who is registered with medical professional or institution with the purpose to receive medical care when necessary. [Definition Source: NCI]

Age
type: Class
equivalent class: Restriction
  on property: iso8601duration
  min qualified cardinality: 1
  on data range: PlainLiteral
subclass of: Time Element
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0001779
comment: Age value definition. [Definition Source: GA4GH Beacon v2 Data Model]

Age Range
type: Class
equivalent class: Restriction
  on property: ageRangeEnd
  min qualified cardinality: 1
  on class: Age
equivalent class: Restriction
  on property: ageRangeStart
  min qualified cardinality: 1
  on class: Age
subclass of: Time Element
comment: Age range definition. [Definition Source: Ga4GH Beacon v2 Data Model]

Age Range Data Availability and Distribution
type: Class
equivalent class: Restriction
  on property: distribution
  some values from: Age Range Element Distribution
subclass of: Data Availability and Distribution
comment: Individual age range, obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]

Age Range Element Distribution
type: Class
equivalent class: Restriction
  on property: elementType
  some values from: Age Range
subclass of: Element Distribution
comment: Results or counts for each category. [Definition Source: GA4GH Beacon v2 Data Model]

Allele
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0002085
comment: The state of a molecule at a Location. [Definition Source: Ga4GH Variation Representation Specification (VRS) v1.2]

Allele Origin
type: Class
comment: SKOS Concept hierarchy comprising allele origin of variant in sample from the Variant Origin (SO:0001762). Categories are `somatic variant`, `germline variant`, `maternal variant`, `paternal variant`, `de novo variant`, `pedigree specific variant`, `population specific variant`. Corresponds to Variant Inheritance in FHIR. [Definition Source: GA4GH Beacon v2 Data Model]

Analysis
type: Class
equivalent class: Restriction
  on property: analysisDate
  min qualified cardinality: 1
  on data range: dateTime
equivalent class: Restriction
  on property: analysisPipelineName
  min qualified cardinality: 1
  on data range: PlainLiteral
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0936012
comment: A sequencing bioinformatics analysis. [Definition Source: GA4GH Beacon v2 Data Model]

Assay
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1510438
comment: The assay used to produce the measurement. [Definition Source: Phenopacket v2]

Biosample
type: Class
equivalent class: Restriction
  on property: biosampleStatus
  min qualified cardinality: 1
  on class: Biosample Status
equivalent class: Restriction
  on property: sampleOriginType
  min qualified cardinality: 1
  on class: Sample Origin Type
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1706958
comment: BioSamples are products of treatments that are of interest. BioSamples are often used as the sources for other biosamples. The Type attribute describes the role the BioSample holds in the treatment hierarchy. This type can be an extract. (caMAGE) [Definition Source: NCI]

Biosample Status
type: Class
comment: SKOS Concept hierarchy from Experimental Factor Ontology (EFO) Material Entity term (BFO:0000040). Classification of the sample in abnormal sample (EFO:0009655) or reference sample (EFO:0009654).

Case Level Variant
type: Class
equivalent class: Restriction
  on property: biosample
  min qualified cardinality: 1
  on class: Biosample
comment: Reports about the variation instances observed in individual analyses. [Definition Source: GA4GH Beacon v2 Data Model]

Chromosome Location
type: Class
equivalent class: Restriction
  on property: chromosomeSpecies
  qualified cardinality: 1
  on class: Species
equivalent class: Restriction
  on property: cytobandInterval
  qualified cardinality: 1
  on class: Cytoband Interval
equivalent class: Restriction
  on property: locationChr
  qualified cardinality: 1
  on data range: PlainLiteral
subclass of: Location
comment: A Location on a chromosome defined by a species and chromosome name. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

Cohort
type: Class
equivalent class: Restriction
  on property: cohortName
  qualified cardinality: 1
  on data range: PlainLiteral
equivalent class: Restriction
  on property: cohortType
  qualified cardinality: 1
  on data range: PlainLiteral
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0599755
comment: A cohort is a collection of material entities grouped together based on some common property of interest, such as age or disease stage. [Definition Source: The Experimental Factor Ontology (EFO)]

Cohort Criteria
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C5237785
comment: Criteria used for defining the cohort. It is assumed that all cohort participants will match or NOT match such criteria. [Definition Source: Beacon v2 Data Model]

Cohort Data Type
type: Class
comment: SKOS Concept hierarchy describing the type of information. Preferably values from Genomics Cohorts Knowledge Ontology (GeCKO) or others when GeCKO is not applicable. [Definition Source: Beacon v2 Data Model]

Cohort Design
type: Class
comment: SKOS Concept hierarchy describing the cohort type by its design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Value from Ontologized MIABIS (OMIABIS) Study design ontology term tree (OBI:0500000). [Definition Source: Beacon v2 Data Model]

Cohort Disease
type: Class
comment: Diseases in cohort inclusion criteria. [Definition Source: Beacon v2 Data Model]

Cohort Sex
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1522384
comment: Sex of the individual. Recommended values from NCIT General Qualifier (NCIT:C27993). Sex refers to the biological characteristics that define humans as female or male. While these sets of biological characteristics are not mutually exclusive, as there are individuals who possess both, they tend to differentiate humans as males and females. [Definition Source: World Health Organization]

Collection Event
type: Class
comment: Aggregated information of cohort data collection obtained from individual level info of the cohort members.

Composed Sequence Expression
type: Class
subclass of: Seq
subclass of: Sequence Expression
comment: An expression of a sequence composed from multiple other Sequence Expressions objects. MUST have at least one component that is not a ref:LiteralSequenceExpression. CANNOT be composed from nested composed sequence expressions. [Definition Source: GA4GH Variation Representation SPecification (VRS) v1.2]

Copy Number Assessment
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C5552747
comment: SKOS Concept hierarchy describing the type of copy number change allowed.

Copy Number Change
type: Class
equivalent class: Restriction
  on property: location
  qualified cardinality: 1
  on class: Location
equivalent class: Restriction
  on property: variationCopyChange
  qualified cardinality: 1
  on class: Copy Number Assessment
comment: An assessment of the copy number of a Location or a Feature within a system (e.g. genome, cell, etc.) relative to a baseline ploidy. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

Copy Number Count
type: Class
equivalent class: Restriction
  on property: location
  qualified cardinality: 1
  on class: Location
equivalent class: Restriction
  on property: variationCopies
  qualified cardinality: 1
  on data range: integer
comment: The absolute count of discrete copies of a Location or Feature, within a system (e.g. genome, cell, etc.). [Defintion Source: GA4GH Variation Representation Specification (VRS) v1.2]

Cytoband Interval
type: Class
equivalent class: Restriction
  on property: cytobandEnd
  qualified cardinality: 1
  on data range: PlainLiteral
equivalent class: Restriction
  on property: cytobandStart
  qualified cardinality: 1
  on data range: PlainLiteral
conforms to: NCIT C164377
comment: A contiguous span on a chromosome defined by cytoband features. The span includes the constituent regions described by the start and end cytobands, as well as any intervening regions. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

Data Availability and Distribution
type: Class
equivalent class: Restriction
  on property: availability
  qualified cardinality: 1
  on data range: boolean
comment: Aggregated information obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]

Data Type Data Availability and Distribution
type: Class
equivalent class: Restriction
  on property: distribution
  some values from: Data Type Element Distribution
subclass of: Data Availability and Distribution
comment: Aggregated data type information available for each cohort data type as declared in `cohortDataTypes`, and obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]

Data Type Element Distribution
type: Class
equivalent class: Restriction
  on property: elementType
  some values from: Cohort Data Type
subclass of: Element Distribution
comment: Results or counts for each data type category. [Definition Source: GA4GH Beacon v2 Data Model]

Derived Sequence Expression
type: Class
equivalent class: Restriction
  on property: sequenceLocation
  qualified cardinality: 1
  on class: Sequence Location
equivalent class: Restriction
  on property: reverseComplement
  qualified cardinality: 1
  on data range: boolean
subclass of: Sequence Expression
comment: An approximate expression of a sequence that is derived from a referenced sequence location. Use of this class indicates that the derived sequence is approximately equivalent to the reference indicated, and is typically used for describing large regions in contexts where the use of an approximate sequence is inconsequential. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

Diagnostic Marker
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1511876
comment: Clinically relevant biomarkers. RECOMMENDED. [Definition Source: GA4GH Beacon v2 Data Model]

Disease Data Availability and Distribution
type: Class
equivalent class: Restriction
  on property: distribution
  some values from: Disease Element Distribution
subclass of: Data Availability and Distribution
comment: Aggregated information of disease/condition(s) obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]

Disease Element Distribution
type: Class
equivalent class: Restriction
  on property: elementType
  some values from: Cohort Disease
subclass of: Element Distribution
comment: Results or counts for each disease category. [Definition Source: GA4GH Beacon v2 Data Model]

Disease Stage
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0699749
comment: SKOS Concept hierarchy descrbinig the disease stage. Value from Ontology for General Medical Science (OGMS), e.g. acute onset (OGMS:0000119). [Defintion Source: Beacon v2 Data Model]

Element Distribution
type: Class
comment: Results or counts for each category. [Definition Source: GA4GH Beacon v2 Data Model]

Ethnicity Data Availability and Distribution
type: Class
equivalent class: Restriction
  on property: distribution
  some values from: Ethnicity Element Distribution
subclass of: Data Availability and Distribution
comment: Aggregated information of ethnicity obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]

Ethnicity Element Distribution
type: Class
subclass of: Element Distribution
comment: Results or counts for each ethnicity category. [Definition Source: GA4GH Beacon v2 Data Model]

Event Timeline
type: Class
comment: Aggregated information of dates of visit | diagnostic | inclusion in study obtained from individual level info of the cohort members. [Definition Source: GA4GH Beacon v2 Data Model]

Frequency In Population
type: Class
equivalent class: Restriction
  on property: frequency
  min qualified cardinality: 1
  on class: Population Frequency
equivalent class: Restriction
  on property: source
  min qualified cardinality: 1
  on data range: PlainLiteral
equivalent class: Restriction
  on property: sourceReference
  min qualified cardinality: 1
  on data range: PlainLiteral
comment: Reports frequency information of the considered genomic variation.

Genomic Feature
type: Class
comment: Genomic feature(s) related to the variant. NOTE: Although genes could also be referenced using these attributes, they have an independent section to allow direct queries. [Definition Source: GA4GH Beacon v2 Data Model]

Genomic Feature Class
type: Class
equivalent class: Restriction
  on property: genomicFeatureClass
  min qualified cardinality: 1
  on class: Genomic Feature Class
comment: SKOS Concept hierarchy describing the class of genomic feature affected by the variant. Values from SO (Sequence ontology) are recommended, e.g. `SO:0001623: 5 prime UTR variant`

Genomic Variation
type: Class
equivalent class: Restriction
  on property: variantInternalID
  min qualified cardinality: 1
  on data range: PlainLiteral
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C5555770
comment: A genomic variant entry. [Definition Source: GA4GH Beacon v2 Data Model]

Genotype
type: Class
equivalent class: Restriction
  on property: genotypeMember
  min qualified cardinality: 1
  on class: Genotype Member
equivalent class: Restriction
  on property: molecularVariationCount
  qualified cardinality: 1
  on data range: integer
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0017431
comment: A quantified set of Molecular Variation associated with a genomic locus. [Defintion Source: GA4GH Variation Representation Specification (VRS) v1.2]

Genotype Member
type: Class
equivalent class: Restriction
  on property: genotypeVariation
  qualified cardinality: 1
  on class: Molecular Variation
equivalent class: Restriction
  on property: genotypeCount
  qualified cardinality: 1
  on data range: integer
comment: A class for expressing the count of a specific Molecular Variation present in-trans at a genomic locus represented by a Genotype. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

Geographic Location
type: Class
comment: Country or region of origin of the individual (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448). [Definition Source: Beacon v2 Data Model]

Gestational Age
type: Class
equivalent class: Restriction
  on property: gestationalWeeks
  min qualified cardinality: 1
  on data range: integer
subclass of: Time Element
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0017504
comment: Gestational age (or menstrual age) is the time elapsed between the first day of the last normal menstrual period and the day of delivery. The first day of the last menstrual period occurs approximately 2 weeks before ovulation and approximately 3 weeks before implantation of the blastocyst. Because most women know when their last period began but not when ovulation occurred, this definition traditionally has been used when estimating the expected date of delivery. In contrast, chronological age (or postnatal age) is the time elapsed after birth. [Definition Source: Phenopackets v2]

Haplotype
type: Class
equivalent class: Restriction
  on property: haplotypeMember
  min qualified cardinality: 2
  on class: Allele
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0018591
comment: A set of non-overlapping Allele members that co-occur on the same molecule. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

Legacy Variation
type: Class
equivalent class: Restriction
  on property: location
  min qualified cardinality: 1
  on class: Location
equivalent class: Restriction
  on property: alternateBases
  min qualified cardinality: 1
  on data range: PlainLiteral
equivalent class: Restriction
  on property: variantType
  min qualified cardinality: 1
  on data range: PlainLiteral
subclass of: Genomic Variation
comment: Other genomic variations.

Library Source
type: Class
comment: SKOS Concept hierarchy describing the source of the sequencing or hybridization library. [Definition Source: GA4GH Beacon v2 Data Model]. The library source specifies the type of source material that is being sequenced. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]

Literal Sequence Expression
type: Class
equivalent class: Restriction
  on property: sequence
  qualified cardinality: 1
  on data range: PlainLiteral
subclass of: Sequence Expression
comment: An explicit expression of a Sequence. [Defintion Source: GA4GH Variation Representation Specification (VRS) v1.2]

Location
type: Class
comment: A contiguous segment of a biological sequence. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

Location Data Availability and Distribution
type: Class
equivalent class: Restriction
  on property: distribution
  some values from: Location Element Distribution
subclass of: Data Availability and Distribution
comment: Aggregated information of geographic location obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]

Location Element Distribution
type: Class
equivalent class: Restriction
  on property: elementType
  some values from: Geographic Location
subclass of: Element Distribution
comment: Results or counts for each location category. [Definition Source: GA4GH Beacon v2 Data Model]

Measurement
type: Class
equivalent class: Restriction
  on property: assay
  min qualified cardinality: 1
  on class: Assay
equivalent class: Restriction
  on property: measurementValue
  min qualified cardinality: 1
  on data range: float
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0242485
comment: Definition of a measurement class. Provenance: GA4GH Phenopackets v2 `Measurement`. [Definition Source: GA4GH Beacon v2 Data Model]

Molecular Attribute
type: Class
comment: Chemical properties, physical properties, and structural properties of molecules, including drugs. Molecular properties typically do not include pharmacological or biological properties of a chemical compound.

Molecular Effect
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C5909625
comment: SKOS Concept hiearchy describing the class of molecular consequence generated by the variant. Values from SO (Sequence Ontology) are recommended, e.g. `SO:0001583: missense variant`.

Molecular Variation
type: Class
subclass of: Genomic Variation
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C3273703
comment: A Variation on a contiguous molecule. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

Obtention Procedure
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0184661
comment: An activity that produces an effect, or that is intended to alter the course of a disease in a patient or population. This is a general term that encompasses the medical, social, behavioral, and environmental acts that can have preventive, therapeutic, or palliative effects. [Definition Source: NCI]

Pathological Stage
type: Class
comment: Pathological stage, if applicable, preferably as subclass of NCIT:C28108 - Disease Stage Qualifier. [Definition Source: GA4GH Beacon v2 Data Model]

Pathological TNM Finding
type: Class
comment: Pathological TNM findings, if applicable, preferably as subclass of Cancer TNM Finding Category (NCIT:C48698). [Definition Source: GA4GH Beacon v2 Data Model]

PhenoClinic Category
type: Class
comment: SKOS Concept Hierarchy comprising the type of disease, condition, phenotypic measurement, etc.

PhenoClinic Effect
type: Class
comment: Annotated effects on disease or phenotypes. [Definition Source: GA4GH Beacon v2 Data Model]

PhenoClinic Evidence
type: Class
comment: Ontology term for the type of evidence supporting variant-disease association Recommended: values from the Evidence & Conclusion Ontology (ECO) [Definition Source: GA4GH Beacon v2 Data Model]

Phenotype Data Availability and Distribution
type: Class
equivalent class: Restriction
  on property: distribution
  some values from: Phenotype Element Distribution
subclass of: Data Availability and Distribution
comment: Aggregated information of phenotype(s) obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]

Phenotype Element Distribution
type: Class
equivalent class: Restriction
  on property: elementType
  some values from: Phenotypic Feature
subclass of: Element Distribution
comment: Results or counts for each phenotype category. [Definition Source: GA4GH Beacon v2 Data Model]

Phenotypic Feature
type: Class
equivalent class: Restriction
  on property: featureType
  qualified cardinality: 1
  on class: Phenotypic Feature Type
comment: Describes a phenotype that characterizes the subject or biosample. [Definition Source: GA4GH Beaocn v2 Data Model]

Phenotypic Feature Modifier
type: Class
comment: SKOS Concept hierarchy to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. Example use here would be one or more terms from HPO Clinical Modifier (HP:0012823). Source: Phenopackets v2 [Definition Source: Beacon v2 Data Model]

Phenotypic Feature Type
type: Class
comment: SKOS Concept hierarchy denoting the phenotypic feature, preferably using a value from Human Phenotype Ontology (HPO). [Definition Source: Beacon v2 Data Model]

Platform Model
type: Class
comment: SKOS Concept hierarchy describing the experimental platform or methodology used. For sequencing platforms the use of "OBI:0400103 - DNA sequencer" is suggested.

Population Frequency
type: Class
equivalent class: Restriction
  on property: alleleFrequency
  min qualified cardinality: 1
  on data range: PlainLiteral
equivalent class: Restriction
  on property: population
  min qualified cardinality: 1
  on data range: PlainLiteral
comment: Reports frequency information of the considered poplutation.

Repeated Sequence Expression
type: Class
subclass of: Sequence Expression
comment: An expression of a sequence comprised of a tandem repeating subsequence. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

Run
type: Class
equivalent class: Restriction
  on property: biosample
  min qualified cardinality: 1
  on class: Biosample
equivalent class: Restriction
  on property: runDate
  min qualified cardinality: 1
  on data range: dateTime
comment: An experimental run (e.g. sequencing run, array processing...) leading to the raw data for the (computational) analysis. [Definition Source: Ga4GH Beacon v2 Data Model]

Sample Origin Detail
type: Class
comment: Tissue from which the sample was taken or sample origin matching the category set in 'sampleOriginType'. Value from Uber-anatomy ontology (UBERON) or BRENDA tissue / enzyme source (BTO), Ontology for Biomedical Investigations (OBI) or Cell Line Ontology (CLO). [Definition source: GA4GH Beacon v2 Data Model]

Sample Origin Type
type: Class
comment: Category of sample origin. Value from Ontology for Biomedical Investigations (OBI) material entity (BFO:0000040) ontology. [Definition Source: GA4GH Beacon v2 Data Model]

Sample Processing
type: Class
comment: Status of how the specimen was processed. Example: a child term of EFO:0009091. [Definition Source: GA4GH Beacon v2 Data Model]

Sequence Expression
type: Class
comment: An expression describing a Sequence. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

Sequence Interval
type: Class
equivalent class: Restriction
  on property: sequenceIntervalEnd
  qualified cardinality: 1
  on data range: PlainLiteral
equivalent class: Restriction
  on property: sequenceIntervalStart
  qualified cardinality: 1
  on data range: PlainLiteral
comment: A Sequence Interval represents a span on a Sequence. Positions are always represented by contiguous spans using interbase coordinates or coordinate ranges. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]

Sequence Location
type: Class
equivalent class: Restriction
  on property: sequenceInterval
  qualified cardinality: 1
  on class: Sequence Interval
equivalent class: Restriction
  on property: referenceSequence
  qualified cardinality: 1
  on data range: PlainLiteral
subclass of: Location
comment: A Location defined by an interval on a referenced Sequence. The reference is typically a chromosome, transcript, or protein sequence. [Definition Source: Variation Representation Specification (VRS) v1.2]

Severity
type: Class
comment: SKOS Concept Hierarchy describing the severity level.

Sex Data Availability and Distribution
type: Class
equivalent class: Restriction
  on property: distribution
  some values from: Sex Element Distribution
subclass of: Data Availability and Distribution
comment: Aggregated information of sex(es) obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]

Sex Element Distribution
type: Class
equivalent class: Restriction
  on property: elementType
  some values from: Cohort Sex
subclass of: Element Distribution
comment: Results or counts for each sex category. [Definition Source: GA4GH Beacon v2 Data Model]

Software Tool
type: Class
equivalent class: Restriction
  on property: toolName
  min qualified cardinality: 1
  on data range: PlainLiteral
equivalent class: Restriction
  on property: toolReference
  min qualified cardinality: 1
  on data range: PlainLiteral
equivalent class: Restriction
  on property: toolVersion
  min qualified cardinality: 1
  on data range: PlainLiteral
comment: Software used to evaluate phenoclinic effects.

Species
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1705920
comment: SKOS Concept hierarchy representing a species from the NCBI species taxonomy.

Systemic Variation
type: Class
subclass of: Genomic Variation
comment: A Variation of multiple molecules in the context of a system, e.g. a genome, sample, or homologous chromosomes. [Definition Source: Ga4GH Variation Representation Specification (VRS) v1.2]

Time Element
type: Class
comment: This class identifies time elements, e.g. age, time interval, and timestamp.

Time Interval
type: Class
equivalent class: Restriction
  on property: timeIntervalEnd
  min qualified cardinality: 1
  on class: Timestamp
equivalent class: Restriction
  on property: timeIntervalStart
  min qualified cardinality: 1
  on class: Timestamp
subclass of: Time Element
comment: Time interval with start and end defined as ISO8601 time stamps. [Definition Source: GA4GH Beacon v2 Data Model]

Timestamp
type: Class
equivalent class: Restriction
  on property: timestamp
  min qualified cardinality: 1
  on data range: dateTimeStamp
subclass of: Time Element
comment: A timestamp is a sequence of characters or encoded information identifying when a certain event occurred, usually giving date and time of day, sometimes accurate to a small fraction of a second. [Defintion Source:Wikipedia]

Tumor Grade
type: Class
comment: SKOS Concept hierarchy representing the tumor grade. Child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent. [Definition Source: GA4GH Beacon v2 Data model]

Tumor Progression
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0178874
comment: Tumor progression category indicating primary, metastatic or recurrent progression. Ontology value from Neoplasm by Special Category ontology (NCIT:C7062). [Definition Source: GA4GH Beacon v2 Data Model]

Unit Of Measure
type: Class
comment: The kind of unit. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants. [Definition Source: GA4GH Beacon v2 Data Model]

VCF File
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C4284335
comment: A Variant Call Format (VCF) file.

VCF Record
type: Class
comment: Describes variants using the Variant Call Format, which is in near universal use for exome, genome, and other Next-Generation-Sequencing-based variant calling. It is an appropriate option to use for variants reported according to their chromosomal location as derived from a VCF file. [Definition Source: Phenopacket v2 Data Model]

Variant Alternative ID
type: Class
comment: Cross-referencing ID(s), for the variant in other databases (e.g. dbSNP, ClinVar, ClinGen, COSMIC), as `externalReferences` with CURIE(s). [Definition Source: GA4GH Beacon v2 Data Model]

Variant Level Data
type: Class
comment: Reports about the variation instances observed in the genomic variation.

Variant Quality
type: Class
comment: Quality information about the genomic variation.

Zygosity
type: Class
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1710709
comment: SKOS concept hierarchy comprising zygosity in which variant is present in the sample from the Zygosity Ontology (GENO:0000391) , e.g `heterozygous` (GENO:0000135) [Definition Source: GA4GH Beacon v2 Data Model]

Amenorrhea due to Pituitary Dysfunction
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Amenorrhea
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C5546135
comment: The absence of menses in a woman who has achieved reproductive age due to disorder of pituitary gland. [Partial Defintion Source: NCI

Caucasian
type: NamedIndividual
type: Concept
type: Group (social concept)
broader transitive: Ethnic Group
in scheme: Group Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0043157
comment: A person having origins in any of the original peoples of Europe, the Middle East, or North Africa. (OMB) [Definition Source: NCI]

Autoimmune Pancytopenia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Pancytopenia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0271893
comment: The autoimmune inability of the bone marrow to produce hematopoietic elements. [Definition Source: NCI]

Bell's Palsy
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Cranial Nerve VII Palsy
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0376175
comment: A syndrome characterized by the acute onset of unilateral FACIAL PARALYSIS which progresses over a 2-5 day period. Weakness of the orbicularis oculi muscle and resulting incomplete eye closure may be associated with corneal injury. Pain behind the ear often precedes the onset of paralysis. This condition may be associated with HERPESVIRUS 1, HUMAN infection of the facial nerve. (Adams et al., Principles of Neurology, 6th ed, p1376) [Defintion Source: MSH]

Lumbar Hernia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Hernia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0401119
comment: Lumbar Hernia [Definition Source: SNOMEDCT]

Pulmonary Thromboembolism
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Thromboembolism
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0524702
comment: Pulmonary embolism is caused by emboli, which have originated from venous thrombi, travelling to and occluding the arteries of the lung. [PMID:29770793]

Atopic Dermatitis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Eczema
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0011615
comment: 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. [Definition Source: MSH]

Neutropenic Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0027947
comment: A decrease in the number of NEUTROPHILS found in the blood. [Definition Source: MSH]

Black (ethnic group)
type: NamedIndividual
type: Concept
type: Group (social concept)
broader transitive: Ethnic Group
in scheme: Group Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0005680
comment: A person having origins in the original peoples of sub-Saharan Africa or the Caribbean.

Asian (ethnic group)
type: NamedIndividual
type: Concept
type: Group (social concept)
broader transitive: Ethnic Group
in scheme: Group Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1282531
comment: A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, including for example, Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and Vietnam. (OMB) [Definition Source: NCI]

Ethnic Group
type: NamedIndividual
type: Concept
type: Group (social concept)
in scheme: Group Taxonomy
comment: A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. [Definition Source: CSP]

Motor Neuron Disease
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Central Nervous System Degenerative Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0085084
comment: Diseases characterized by a selective degeneration of the motor neurons of the spinal cord, brainstem, or motor cortex. Clinical subtypes are distinguished by the major site of degeneration. In AMYOTROPHIC LATERAL SCLEROSIS there is involvement of upper, lower, and brainstem motor neurons. In progressive muscular atrophy and related syndromes (see MUSCULAR ATROPHY, SPINAL) the motor neurons in the spinal cord are primarily affected. With progressive bulbar palsy (BULBAR PALSY, PROGRESSIVE), the initial degeneration occurs in the brainstem. In primary lateral sclerosis, the cortical neurons are affected in isolation. (Adams et al., Principles of Neurology, 6th ed, p1089) [Definition Source: MSH]

Allergic Asthma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Asthma
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0155877
comment: Allergic Asthma

Hispanic
type: NamedIndividual
type: Concept
type: Group (social concept)
broader transitive: Ethnic Group
in scheme: Group Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0086409
comment: A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. The term, "Spanish origin" can be used in addition to "Hispanic or Latino". (OMB) [Definition Source: NCI]

Closed Fracture of Tibia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Tibia Fracture
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0159870
comment: A closed fracture of the tibia.

Pneumonia Caused By SARS-CoV-2
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Pneumonia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C5244027
comment: Pneumonia caused by severe acute respiratory syndrome coronavirus 2 [Definition Source: SNOMEDCT]

Neck Trauma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Head and Neck Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0027531
comment: General or unspecified injuries to the neck. It includes injuries to the skin, muscles, and other soft tissues of the neck. [Defintion Source: MSH]

Herpes Simplex Keratitis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Herpes Simplex Virus Infection
broader transitive: Keratitis
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0019357
comment: A superficial, epithelial Herpesvirus hominis infection of the cornea, characterized by the presence of small vesicles which may break down and coalesce to form dendritic ulcers (KERATITIS, DENDRITIC). (Dictionary of Visual Science, 3d ed) [Defintion Source: MSH]

Material Entity
type: NamedIndividual
type: Concept
type: Sample Origin Type
in scheme: Sample Origin Type Taxonomy
comment: A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray. [Definition Source: BFO]

Experimental Evidence
type: NamedIndividual
type: Concept
type: PhenoClinic Evidence
in scheme: Phenoclinic Evidence Taxonomy
comment: A type of evidence that is the output of a scientific procedure performed to make a discovery, test a hypothesis, or demonstrate a known fact. [Definition Source: Evidence and Conclusion Ontology]

Inferential Evidence
type: NamedIndividual
type: Concept
type: PhenoClinic Evidence
in scheme: Phenoclinic Evidence Taxonomy
comment: A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means. [Definition Source: Evidence and Conclusion Ontology]

Library Source
type: NamedIndividual
type: Concept
in scheme: Library Source Taxonomy
comment: The library source specifies the type of source material that is being sequenced. [Definition Source: GENEPIO]

Genomic Source
type: NamedIndividual
type: Concept
type: Library Source
broader transitive: Library Source
in scheme: Library Source Taxonomy
comment: Genomic DNA (includes PCR products from genomic DNA). [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]

Metagenomic Source
type: NamedIndividual
type: Concept
type: Library Source
broader transitive: Library Source
in scheme: Library Source Taxonomy
comment: Mixed material from metagenome. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]

Metatranscriptomic Source
type: NamedIndividual
type: Concept
type: Library Source
broader transitive: Library Source
in scheme: Library Source Taxonomy
comment: Transcription products from community targets. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]

Other Library Source
type: NamedIndividual
type: Concept
type: Library Source
broader transitive: Library Source
in scheme: Library Source Taxonomy
comment: Other, unspecified, or unknown library source material. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]

Synthetic Source
type: NamedIndividual
type: Concept
type: Library Source
broader transitive: Library Source
in scheme: Library Source Taxonomy
comment: Synthetic DNA. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]

Transcriptomic Source
type: NamedIndividual
type: Concept
type: Library Source
broader transitive: Library Source
in scheme: Library Source Taxonomy
comment: Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries). [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]

Viral RNA Source
type: NamedIndividual
type: Concept
type: Library Source
broader transitive: Library Source
in scheme: Library Source Taxonomy
comment: Viral RNA. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]

Zygosity
type: NamedIndividual
type: Concept
in scheme: Zygosity Taxonomy
comment: An allelic state that describes the degree of similarity between features in a 'single locus complement', within the genome of a cell or organism (i.e., whether the alleles or haplotypes that reside at the same location on paired chromosomes are the same or different). [Definition Source: GENO]

Hemizygous
type: NamedIndividual
type: Concept
type: Zygosity
broader transitive: Zygosity
in scheme: Zygosity Taxonomy
comment: A zygosity quality inhering in a 'single locus complement' with half the number of alleles than normal (e.g. a single allele in a diploid genome, for example, a locus on the Y chromosome in a eukaryotic male genome, or a transgene that is present only in one of the two parental chromosome sets) [Definition Source: GENO Ontology]

Homozygous
type: NamedIndividual
type: Concept
type: Zygosity
broader transitive: Zygosity
in scheme: Zygosity Taxonomy
comment: A zygosity quality inhering in a 'single locus complement' where all copies of the feature at this location have the same sequence (in a eukaryotic diploid genome, this means having identical alleles on each of the two homologous chromosomes, one inherited from each parent). [Definition Source: GENO Ontology]

Heterozygous
type: NamedIndividual
type: Concept
type: Zygosity
broader transitive: Zygosity
in scheme: Zygosity Taxonomy
comment: A zygosity quality inhering in 'single locus complement'; where the copies of the feature at this location have at least one difference in sequence (in a eukaryotic diploid genome, this means having two distinct alleles on each of the two homologous chromosomes, one inherited from each parent). [Definition Source: GENO Ontology]

Compouns Heterozygous
type: NamedIndividual
type: Concept
type: Zygosity
broader transitive: Heterozygous
in scheme: Zygosity Taxonomy
comment: A heterozygous quality inhering in a single locus complement comprised of two different varaint alleles and no wild type locus. (e.g.fgf8a<ti282a>/fgf8a<x15>) [Definition Source: GENO Ontology]

Simple Heterozygous
type: NamedIndividual
type: Concept
type: Zygosity
broader transitive: Heterozygous
in scheme: Zygosity Taxonomy
comment: a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a<ti282a/+>) [Definition Source: GENO Ontology]

Hemizygous X-Linked
type: NamedIndividual
type: Concept
type: Zygosity
broader transitive: Hemizygous
in scheme: Zygosity Taxonomy

Hemizygous Y-Linked
type: NamedIndividual
type: Concept
type: Zygosity
broader transitive: Hemizygous
in scheme: Zygosity Taxonomy

Hemizygous Insertion-Linked
type: NamedIndividual
type: Concept
type: Zygosity
broader transitive: Hemizygous
in scheme: Zygosity Taxonomy

Nullizygous
type: NamedIndividual
type: Concept
type: Zygosity
broader transitive: Zygosity
in scheme: Zygosity Taxonomy
comment: A disomic zygosity quality inhering in a 'single locus complement' that is comprised of two non-functional copies of a gene. Loss of function may result from the gene being entirely missing via a deletion, or mutated in a way that eliminates its function. [Definition Source: GENO Ontology]

Disease or Disorder (MONDO)
type: NamedIndividual
type: Concept
type: PhenoClinic Category
in scheme: Phenoclinic Category Taxonomy
comment: A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. [Definition Source: MONDO Ontology]

Two Vessel Coronary Disease
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Cardiovascular Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0581375
comment: There was greater than or equal to 50% stenosis (reduction in cross-sectional area) in two coronary arteries (or greater than or equal to 50% stenosis in the left main coronary artery). (ACC) [Definition Source: NCI]

Sign or Symptom
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0037088
comment: Objective evidence of disease perceptible to the examining practitioner (sign) and subjective evidence of disease perceived by the patient (symptom). [Definition Source: NCI]

Spina Bifida
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Non-Neoplastic Central Nervous System Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0080178
comment: A congenital neural tube defect in which vertebrae are not fully formed. It results in the protrusion of the spinal cord through the opening of the vertebrae. [Definition Source: NCI]

Angioedema
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0002994
comment: Rapid swelling of the deep layers of the skin due to transient vascular leakage of serous fluid. [Definition Source: NCI][attribution: NICHD]

Blepharitits
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0005741
comment: Inflammation of the eyelids near the eyelashes. [Definition Source: NCI][attribution: NICHD]

Drug Hypersensitivity Syndrome
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C3541994
comment: A potentially life-threatening hypersensitivity reaction to a pharmacologic substance that is characterized by rash, lymphadenopathy, fever, hematologic abnormalities and involvement of one or more internal organs. [Definition Source: NCI][attribution: NICHD]

Molluscum Contagiosum Virus
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0026394
comment: A species of enveloped and brick-shaped viruses in the Poxviridae family and Molluscipoxvirus genus. The genome is composed of non-segmented, linear double-stranded DNA. Molluscum contagiosum viruses are found in humans and can cause the disease Molluscum contagiosum. Molluscum contagiosum viruses are transmitted via direct person-to-person contact and contact with infected fomites. [Definition Source: NCI]

Tinea Versicolor
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0040262
comment: A skin condition characterized by hypopigmented, pink or tan, confetti-like, discrete and confluent scaly macules distributed on the chest, shoulders and upper back. [Definition Source: NCI]

Ureteral Stenosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0521618
comment: Narrowing of the luminal diameter of one or both ureters due to intrinsic factors. [Definition Source: NCI]

Anosmia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0003126
comment: Inability to smell. [Definition Source: NCI]

Subdural Hematoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0018946
comment: A collection of blood between the dura mater and the brain. [Definition Source: NCI]

Cognitive Impariment
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0338656
comment: Diminished mental function. [Definition Source: NCI]

Migraine With Aura
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Migraine
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0154723
comment: A migraine disorder characterized by episodes that are preceded by focal neurological symptoms. [Definition Source: NCI]

Post-Herpetic Neuralgia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Symptom
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0032768
comment: Pain that occurs after the disappearance of herpes zoster infection lesions. [Definition Source: NCI]

Blepharospasm
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Head and Neck Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0005747
comment: Involuntary twitching of the eyelid. [Definition Source: NCI]

Dog Bite
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Injury
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0259797
comment: A wound received from the teeth of a dog. [Definition Source: NCI]

Acute Pyelonephritis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0520575
comment: Sudden onset pyelonephritis. [Definition Source: NCI][attribution: NICHD]

Viral Pericarditis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0276139
comment: Pericarditis that is caused by an infection with a viral agent. [Definition Source: NCI]

Acquired Hypothyroidism
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Hypothyroidism
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0700502
comment: Hypothyroidism, the cause of which is not present at birth. [Definition Source: NCI]

Herpes Simplex Virus Infection
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0019348
comment: An infection that is caused by herpes simplex virus. [Definition Source: NCI]

Basal Cell Carcinoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Carcinoma
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0007117
comment: A carcinoma involving the basal cells. [Definition Source: NCI]

Opioid Use Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C4324621
comment: The use of opioids that results in the development of a dependency that adversely affects an individual's life. [Definition Source: NCI]

Pneumococcal Pneumonia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Pneumonia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0155862
comment: Pneumonia that is attributed to the bacteria Streptococcus pneumonia. [Definition Source: NCI]

Female
type: NamedIndividual
type: Concept
type: Cohort Sex
in scheme: Cohort Sex Taxonomy
comment: 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. [Definition Source: NCI]

COVID-19 Infection
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C5203670
comment: An acute infection of the respiratory tract that is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Based on currently available information, SARS-CoV-2 is thought to mainly spread from person to person through respiratory droplets. Typically, there is a two- to 14-day incubation period and infected persons can present with no symptoms or mild to severe fever, dry cough, fatigue, and difficulty breathing. Dysgeusia, anosmia, and gastrointestinal and flu-like symptoms have also been reported. Older adults and persons of any age who have serious underlying medical conditions may be of higher risk for severe illness, including secondary infections, respiratory failure, and multi-organ dysfunction. [Definition Source: NCI]

Thoracic Trauma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Injury
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0039980
comment: Trauma to the chest. [Definition Source: NCI]

Unknown
type: NamedIndividual
type: Concept
type: Cohort Sex
in scheme: Cohort Sex Taxonomy
comment: Not known, observed, recorded; or reported as unknown by the data contributor. [Defintion Source: NCI]

Hepatic Toxicity
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Injury
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0235378
comment: Toxicity that impairs or damages the liver. [Definition Source: NCI]

Male
type: NamedIndividual
type: Concept
type: Cohort Sex
in scheme: Cohort Sex Taxonomy
comment: 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. [Definition Source: NCI]

Abdominal Pain
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Symptom
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0000737
comment: Painful sensation in the abdominal region. [Definition Source: NCI]

Bacterial Pneumonia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Pneumonia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0004626
comment: Acute infection of the lung parenchyma caused by bacteria (e.g., Streptococcus pneumoniae, Haemophilus influenzae, Chlamydia pneumoniae, Mycoplasma pneumoniae, and Legionella pneumophila). Signs and symptoms include productive cough, fever, chills, shortness of breath, and chest pain. [Definition Source: NCI]

Celiac Disease
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0007570
comment: An autoimmune genetic disorder with an unknown pattern of inheritance that primarily affects the digestive tract. It is caused by intolerance to dietary gluten. Consumption of gluten protein triggers an immune response which damages small intestinal villi and prevents adequate absorption of nutrients. Clinical signs include abdominal cramping, diarrhea or constipation and weight loss. If untreated, the clinical course may progress to malnutrition, anemia, osteoporosis and an increased risk of intestinal malignancies. However, the prognosis is favorable with successful avoidance of gluten in the diet. [Definition Source: NCI]

Type 2 Diabetes Mellitus
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Diabetes Mellitus
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0011860
comment: A type of diabetes mellitus that is characterized by insulin resistance or desensitization and increased blood glucose levels. This is a chronic disease that can develop gradually over the life of a patient and can be linked to both environmental factors and heredity. [Definition Source: NCI]

Cranial Nerve VII Palsy
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0015469
comment: Partial or complete paralysis of the facial muscles of one side of a person's face. It is caused by damage to the seventh cranial nerve. It is usually temporary but it may recur. [Definition Source: NCI]

Femur Fracture
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Injury
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0015802
comment: A traumatic or pathologic injury to the femur in which the continuity of the femur is broken. [Definition Source: NCI]

Gastritis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0017152
comment: Inflammation of the stomach. [Definition Source: NCI]

Glaucoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0017601
comment: Increased pressure in the eyeball due to obstruction of the outflow of aqueous humor. [Definition Source: NCI]

Hypothyroidism
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Thyroid Gland Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0020676
comment: Abnormally low levels of thyroid hormone. [Definition Source: NCI][attribution: NICHD]

Keratitis
type: NamedIndividual
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0022568
comment: Inflammation of the cornea. [Definition Source: NCI]

Keratoconus
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0022578
comment: A degenerative, structural disorder of the eye, characterized by a cone-shaped protrusion of the cornea. It may lead to visual disturbances. [Definition Source: NCI]

Leukopenia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0750394
comment: A laboratory test result indicating a decreased number of white blood cells in the peripheral blood. [Definition Source: NCI]

Lymphopenia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Leukopenia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0853986
comment: An abnormally small number of lymphocytes in the circulating blood. [Definition Source: NCI]

Parkinson's Disease
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Extrapyramidal Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0030567
comment: A progressive degenerative disorder of the central nervous system characterized by loss of dopamine producing neurons in the substantia nigra and the presence of Lewy bodies in the substantia nigra and locus coeruleus. Signs and symptoms include tremor which is most pronounced during rest, muscle rigidity, slowing of the voluntary movements, a tendency to fall back, and a mask-like facial expression. [Definition Source: NCI]

Retinal Detachment
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0035305
comment: An eye emergency condition which may lead to blindness if left untreated. It is characterized by the separation of the inner retina layers from the underlying pigment epithelium. Causes include trauma, advanced diabetes mellitus, high myopia, and choroid tumors. Symptoms include sudden appearance of floaters, sudden light flushes, and blurred vision. [Definition Source: NCI]

Thyroid Gland Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0040128
comment: A non-neoplastic or neoplastic disorder that affects the thyroid gland. Representative examples include hyperthyroidism, hypothyroidism, thyroiditis, follicular adenoma, and carcinoma. [Definition Source: NCI]

Thyroiditis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Thyroid Gland Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0040147
comment: Inflammation of the thyroid gland. This category includes Hashimoto thyroiditis, Riedel thyroiditis, acute thyroiditis, subacute thyroiditis, and radiation-induced thyroiditis. [Definition Source: NCI]

Vitiligo
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0042900
comment: Generalized well circumscribed patches of leukoderma that are generally distributed over symmetric body locations and is due to autoimmune destruction of melanocytes. [Definition Source: NCI][attribution: NICHD]

Fever Chills
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Symptom
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0085594
comment: Shivering secondary to a febrile process. [Definition Source: NCI]

Acute Cystitis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0149523
comment: An acute infection of the bladder. It is usually caused by bacteria. Signs and symptoms include increased frequency of urination, pain or burning during urination, fever, cloudy or bloody urine, and suprapubic pain. [Definition Source: NCI]

Alanine Aminotransferase Increased
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0151905
comment: An increase in the level of alanine aminotransferase in the blood. [Definition Source: NCI]

Trigeminal Nerve Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0152177
comment: A non-neoplastic or neoplastic disorder affecting the trigeminal nerve (fifth cranial nerve). [Definition Source: NCI]

Ankle Fracture
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Injury
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0159877
comment: Traumatic or pathological injury to the ankle joint in which the continuity of an ankle bone is broken. Symptoms include pain, swelling, and difficulty moving the affected leg and foot. [Definition Source: NCI]

Interstitial Pneumonia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Pneumonia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0206061
comment: Inflammation of interstitial lung tissue, usually associated with infection. [Definition Source: NCI]

Acute Respiratory Failure
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0264490
comment: Life-threatening respiratory failure that develops rapidly. Causes include injury, sepsis, drug overdose, and pancreatitis. It manifests with dyspnea and cyanosis and may lead to cardiovascular shock. [Definition Source: NCI]

Obstructive Sleep Apnea Syndrome
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0520679
comment: A disorder characterized by recurrent episodic disruptions of breathing during sleep. It is caused by the intermittent relaxation of pharyngeal muscles leading to the narrowing or complete blockage of the upper airway. This results in compensatory arousal from sleep to breathe again. An anatomically narrow airway from body habitus or enlarged pharyngeal structures may also predispose to obstruction. Clinical presentation usually includes snoring, daytime sleepiness, difficulty concentrating and fatigue. Clinical course may progress to chronic hypoxemia with cardiovascular and cerebrovascular sequelae. [Definition Source: NCI]

Hashimoto Thyroiditis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Thyroiditis
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0677607
comment: An autoimmune disorder caused by the production of autoantibodies against thyroid tissue. There is progressive destruction of the thyroid follicles leading to hypothyroidism. [Definition Source: NCI]

Non-Neoplastic Central Nervous System Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1335000
comment: Any disorder other than abnormal tissue growth resulting from uncontrolled cell proliferation affecting the nervous system.

Disease Grade Qualifier
type: NamedIndividual
type: Concept
type: Tumor Grade
in scheme: Tumor Grade Taxonomy
comment: A term that refers to the cellular differentiation of a malignant cellular infiltrate. A cancer is defined through grades I-IV (or 1-4), or as well, moderately, poorly differentiated or undifferentiated. [Definition Source: NCI]

Disease Stage Qualifier
type: NamedIndividual
type: Concept
type: Pathological Stage
in scheme: Pathological Stage Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1511987
comment: An adjectival term that can specify or describe a disease stage. [Definition Source: NCIT]

Thromboembolism
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Cardiovascular Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0040038
comment: Occlusion of the lumen of a vessel by a thrombus that has migrated from a distal site via the blood stream. [Definition Source: NCI]

Asthma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Chronic Lung Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0004096
comment: A chronic respiratory disease manifested as difficulty breathing due to the narrowing of bronchial passageways. [Definition Source: NCI]

Adenocarcinoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Carcinoma
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0001418
comment: A common cancer characterized by the presence of malignant glandular cells. Morphologically, adenocarcinomas are classified according to the growth pattern (e.g., papillary, alveolar) or according to the secreting product (e.g., mucinous, serous). Representative examples of adenocarcinoma are ductal and lobular breast carcinoma, lung adenocarcinoma, renal cell carcinoma, hepatocellular carcinoma (hepatoma), colon adenocarcinoma, and prostate adenocarcinoma. [Definition Source: NCI]

Alzheimer's Disease
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Dementia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0002395
comment: A progressive, neurodegenerative disease characterized by loss of function and death of nerve cells in several areas of the brain leading to loss of cognitive function such as memory and language. [Definition Source: NCI]

Anemia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0002871
comment: A reduction in the number of red blood cells, the amount of hemoglobin, and/or the volume of packed red blood cells. Clinically, anemia represents a reduction in the oxygen-transporting capacity of a designated volume of blood, resulting from an imbalance between blood loss (through hemorrhage or hemolysis) and blood production. Signs and symptoms of anemia may include pallor of the skin and mucous membranes, shortness of breath, palpitations of the heart, soft systolic murmurs, lethargy, and fatigability. [Definition Source: NCI]

Anorexia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
comment: Loss of appetite. [Definition Source: NCI]
comment: https://uts.nlm.nih.gov/uts/umls/concept/C1971624

Anxiety Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Psychiatric Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0003469
comment: A category of psychiatric disorders which are characterized by anxious feelings or fear often accompanied by physical symptoms associated with anxiety. [Definition Source: NCI]

Arrhythmia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Cardiovascular Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0003811
comment: Any variation from the normal rate or rhythm (which may include the origin of the impulse and/or its subsequent propagation) in the heart. [Definition Source: NCI]

Arthritis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0003864
comment: An inflammatory process affecting a joint. Causes include infection, autoimmune processes, degenerative processes, and trauma. Signs and symptoms may include swelling around the affected joint and pain. [Definition Source: NCI]

Rheumatoid Arthritis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Arthritis
broader transitive: Autoimmune Disease
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0003873
comment: A chronic, systemic autoimmune disorder characterized by inflammation in the synovial membranes and articular surfaces. It manifests primarily as a symmetric, erosive polyarthritis that spares the axial skeleton and is typically associated with the presence in the serum of rheumatoid factor. [Definition Source: NCI]

Autoimmune Disease
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0004364
comment: A disorder resulting from loss of function or tissue destruction of an organ or multiple organs, arising from humoral or cellular immune responses of the individual to his own tissue constituents. It may be systemic (e.g., systemic lupus erythematosus), or organ specific, (e.g., thyroiditis). [Definition Source: NCI]

Psychiatric Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0004936
comment: A disorder characterized by behavioral and/or psychological abnormalities, often accompanied by physical symptoms. The symptoms may cause clinically significant distress or impairment in social and occupational areas of functioning. Representative examples include anxiety disorders, cognitive disorders, mood disorders and schizophrenia. [Definition Source: NCI]

Vulvovaginal Candidiasis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0006852
comment: Infection of the vulva and vagina with a fungus of the genus CANDIDA. It is a disease associated with HIV infection. [Definition Source: NCI]

Carcinoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Malignant Neoplasm
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0007097
comment: A malignant tumor arising from epithelial cells. Carcinomas that arise from glandular epithelium are called adenocarcinomas, those that arise from squamous epithelium are called squamous cell carcinomas, and those that arise from transitional epithelium are called transitional cell carcinomas. Morphologically, the malignant epithelial cells may display abnormal mitotic figures, anaplasia, and necrosis. Carcinomas are graded by the degree of cellular differentiation as well, moderately, or poorly differentiated. Carcinomas invade the surrounding tissues and tend to metastasize to other anatomic sites. Lung carcinoma, skin carcinoma, breast carcinoma, colon carcinoma, and prostate carcinoma are the most frequently seen carcinomas. [Definition Source: NCI]

Malignant Skin Neoplasm
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Malignant Neoplasm
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0007114
comment: A primary or metastatic malignant neoplasm involving the skin. Primary malignant skin neoplasms most often are carcinomas (either basal cell or squamous cell carcinomas) or melanomas. Metastatic malignant neoplasms to the skin include carcinomas and lymphomas. [Definition Source: NCI]

Skin Basal Cell Carcinoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Basal Cell Carcinoma
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0007117
comment: The most frequently seen skin cancer. It arises from basal cells of the epidermis and pilosebaceous units. Clinically it is divided into the following types: nodular, ulcerative, superficial, multicentric, erythematous, and sclerosing or morphea-like. More than 95% of these carcinomas occur in patients over 40. They develop on hair-bearing skin, most commonly on sun-exposed areas. Approximately 85% are found on the head and neck and the remaining 15% on the trunk and extremities. Basal cell carcinoma usually grows in a slow and indolent fashion. However, if untreated, the tumor may invade the subcutaneous fat, skeletal muscle and bone. Distant metastases are rare. Excision, curettage and irradiation cure most basal cell carcinomas. [Definition Source: NCI]

Skin Basosquamous Cell Carcinoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Skin Basal Cell Carcinoma
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0007118
comment: A basal cell carcinoma which displays squamous differentiation. The neoplastic cells have more abundant cytoplasm with more marked keratinization than typical basal cell carcinomas. It usually has a more aggressive clinical course compared to typical basal cell carcinoma, and it may produce regional or widespread metastases. [Definition Source: NCI]

Cardiovascular Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0007222
comment: A non-neoplastic or neoplastic disorder affecting the heart or the vessels (arteries, veins and lymph vessels). Representative examples of non-neoplastic cardiovascular disorders are endocarditis and hypertension. Representative examples of neoplastic cardiovascular disorders are endocardial myxoma and angiosarcoma. [Definition Source: NCI]

Cyst
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0010709
comment: A sac-like closed membranous structure that may be empty or contain fluid or amorphous material. [Definition Source: NCI]

Depression
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Mood Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0011570
comment: A melancholy feeling of sadness and despair. [Definition Source: NCI]

Diabetes Mellitus
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0011849
comment: A metabolic disorder characterized by abnormally high blood sugar levels due to diminished production of insulin or insulin resistance/desensitization. [Definition Source: NCI]

Type 1 Diabtes Mellitus
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Autoimmune Disease
broader transitive: Diabetes Mellitus
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0011854
comment: A chronic condition characterized by minimal or absent production of insulin by the pancreas. [Definition Source: NCI][attribution: NICHD]

Mumps
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0026780
comment: A contagious viral infection caused by the mumps virus. Symptoms include swollen and tender parotid glands, fever, muscle aches and fatigue. Due to vaccination programs, mumps has become a rare disease. [Definition Source: NCI]

Disease or Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0012634
comment: Any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. The term is often used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function. [Definition Source: NCI]

Eczema
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0013595
comment: A form of dermatitis characterized by red, itchy, scaly, or crusty patches that can be chronic or intermittent. [Definition Source: NCI][attribution: NICHD]

Endometriosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0014175
comment: The growth of functional endometrial tissue in anatomic sites outside the uterine body. It most often occurs in the pelvic organs. [Definition Source: NCI]

Seizure Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0014544
comment: A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions. [Definition Source: NCI]

Generalized Epilepsy
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Seizure Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0014548
comment: A chronic condition characterised by recurrent generalised seizures. [Definition Source: NCI]

Fibroma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0016045
comment: A non-metastasizing neoplasm arising from the fibrous tissue. It is characterized by the presence of spindle-shaped fibroblasts. [Definition Source: NCI]

Cavernous Hemangioma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Cardiovascular Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0018920
comment: A hemangioma characterized by the presence of cavernous vascular spaces. [Definition Source: NCI]

Hepatitis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0019158
comment: Inflammation of the liver; usually from a viral infection, but sometimes from toxic agents. [Definition Source: NCI]

Hepatitis A Infection
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0019159
comment: Acute inflammation of the liver caused by the hepatitis A virus. It is highly contagious and usually contracted through close contact with an infected individual or their feces, contaminated food or water. [Definition Source: NCI]

Langerhans Cell Histiocytosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0019621
comment: A neoplastic proliferation of Langerhans cells which contain Birbeck granules by ultrastructural examination. Three major overlapping syndromes are recognized: eosinophilic granuloma, Letterer-Siwe disease, and Hand-Schuller-Christian disease. The clinical course is generally related to the number of organs affected at presentation. (WHO, 2001) [Definition Source: NCI]

Hypersensitivity
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0020517
comment: An immune response that occurs following exposure to an innocuous antigen, but that does not require the presence of preformed antibodies to the antigen. [Definition Source: NCI]

Hypertension
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0020538
comment: Blood pressure that is abnormally high. [Definition Source: NCI]

Hypertensive Crisis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Cardiovascular Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0020546
comment: A severe, acute increase in blood pressure that may result in stroke or myocardial ischemia. [Definition Source: NCI]

Hyperthyroidism
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Thyroid Gland Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0020550
comment: Overactivity of the thyroid gland resulting in overproduction of thyroid hormone and increased metabolic rate. Causes include diffuse hyperplasia of the thyroid gland (Graves' disease), single nodule in the thyroid gland, and thyroiditis. The symptoms are related to the increased metabolic rate and include weight loss, fatigue, heat intolerance, excessive sweating, diarrhea, tachycardia, insomnia, muscle weakness, and tremor. [Definition Source: NCI]

Epidermal Inclusion Cyst
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Cyst
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0014511
comment: The most common type of cutaneous cyst. It results from the proliferation of epidermal cells in a circumscribed space within the dermis. It is usually asymptomatic and presents as a firm, round nodule. [Definition Source: NCI]

Multiple Sclerosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Non-Neoplastic Central Nervous System Disorder
broader transitive: Autoimmune Nervous System Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0026769
comment: A progressive autoimmune disorder affecting the central nervous system resulting in demyelination. Patients develop physical and cognitive impairments that correspond with the affected nerve fibers. [Definition Source: NCI]

Fungal Infection
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0026946
comment: An infection caused by a fungus. [Definition Source: NCI]

Neoplasm
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0375111
comment: A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias. [Definition Source: NCI]

Obesity
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0028754
comment: Having a high amount of body fat (body mass index [BMI] of 30 or more). [Definition Source: NCI]

Osteoporosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0029456
comment: A condition of reduced bone mass, with decreased cortical thickness and a decrease in the number and size of the trabeculae of cancellous bone (but normal chemical composition), resulting in increased fracture incidence. Osteoporosis is classified as primary (Type 1, postmenopausal osteoporosis; Type 2, age-associated osteoporosis; and idiopathic, which can affect juveniles, premenopausal women, and middle-aged men) and secondary osteoporosis (which results from an identifiable cause of bone mass loss). [Definition Source: NCI]

Pituitary Neuroendocrine Tumor
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0032000
comment: A well-differentiated neuroendocrine neoplasm that arises from the adenohypophysial cells of the anterior lobe of the pituitary gland. The tumor can be hormonally functioning or not. It has a low frequency of metastatic spread. When metastatic, the term metastatic pituitary neuroendocrine tumor is endorsed instead of pituitary carcinoma. (WHO) [Definition Source: NCI] It has exact synonim: Pituitary Gland Adenoma.

Pleural Effusion
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0032227
comment: Increased amounts of fluid within the pleural cavity. Symptoms include shortness of breath, cough, and chest pain. It is usually caused by lung infections, congestive heart failure, pleural and lung tumors, connective tissue disorders, and trauma. [Definition Source: NCI]

Pneumonia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0032285
comment: An acute, acute and chronic, or chronic inflammation focally or diffusely affecting the lung parenchyma, due to infections (viruses, fungi, mycoplasma, or bacteria), treatment (e.g. radiation), or exposure (inhalation) to chemicals. Symptoms include cough, shortness of breath, fevers, chills, chest pain, headache, sweating, and weakness. [Definition Source: NCI]

Psoriasis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0033860
comment: An autoimmune condition characterized by red, well-delineated plaques with silvery scales that are usually on the extensor surfaces and scalp. They can occasionally present with these manifestations: pustules; erythema and scaling in intertriginous areas, and erythroderma, that are often distributed on extensor surfaces and scalp. [Definition Source: NCI][attribution: NICHD]

Finding
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1285578
comment: Clinical, laboratory or molecular evidence, or absence of evidence of disease. [Definition Source: NCI]

Stroke
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Non-Neoplastic Central Nervous System Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0038454
comment: A sudden loss of neurological function secondary to hemorrhage or ischemia in the brain parenchyma due to a vascular event. [Definition Source: NCI]

Toxoplasmosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0040558
comment: A parasitic disease contracted by the ingestion or fetal transmission of toxoplasma gondii. [Definition Source: NCI]

Uterine Corpus Leiomyoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0042133
comment: A benign smooth muscle neoplasm arising from the body of the uterus. It is characterized by the presence of spindle cells with cigar-shaped nuclei, interlacing fascicles, and a whorled pattern. [Definition Source: NCI]

Congenital Adrenal Hyperplasia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0001627
comment: A genetic disorder characterized by defects in the synthesis of cortisol and/or aldosterone, resulting in hyperplasia of the adrenal cortical cells. [Definition Source: NCI]

Amyotrophic Lateral Sclerosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Motor Neuron Disease
broader transitive: Central Nervous System Degenerative Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0002736
comment: A neurodegenerative disorder characterized by progressive degeneration of the motor neurons of the central nervous system. It results in weakness and atrophy of the muscles which leads to an inability to initiate and control voluntary movements. [Definition Source: NCI]

Hereditary Hemolytic Anemia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Anemia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0002881
comment: A congenital hemolytic anemia caused by defects of the erythrocyte membrane, enzyme deficiencies, or hemoglobinopathies. [Definition Source: NCI]

Bipolar Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Mood Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0005586
comment: A disorder of the brain that causes unusual shifts in mood, energy, activity levels and the ability to carry out day-to-day tasks. Often these moods range and shift from periods of elation and energized behavior to those of hopelessness and depression. [Definition Source: NCI]

Closed Dislocation of Shoulder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Shoulder Dislocation
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0434579
comment: A closed dislocation of the shoulder [Definition Source: NCI]

Common Bile Duct Stone
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0009438
comment: The presence of one or more stones in the common bile duct. They are composed either of cholesterol or, less commonly, calcium salts and bilirubin. [Definition Source: NCI]

Favism
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Anemia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0015702
comment: A condition associated with glucose-6-phosphate dehydrogenase deficiency, which is characterized by hemolysis. [Definition Source: NCI]

Gastroenteritits
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0017160
comment: An inflammatory disorder that affects the upper and lower gastrointestinal tract. Most commonly, this is attributed to viruses; however bacteria, parasites or adverse reactions can also be the culprit. Symptoms include acute diarrhea and vomiting. [Definition Source: NCI]

Head Trauma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Head and Neck Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0018674
comment: A traumatic injury to the head. [Definition Source: NCI]

Headache
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0018681
comment: Pain in various parts of the head, not confined to the area of distribution of any nerve. [Definition Source: NCI]

Hernia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0019270
comment: The protrusion of part of an organ or fibroadipose tissue through an abnormal opening. [Definition Source: NCI]

Palmar Fibromatosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0013312
comment: A superficial fibromatosis arising from the soft tissue of the palm. It is characterized by the presence of spindle-shaped fibroblasts, and an infiltrative growth pattern. It predominantly affects adult males. [Definition Source: NCI] It has exact synonim: Dupuytren Contracture; Palmar Fibromatosis; Dupuytren's Contracture.

Inguinal Hernia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Hernia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0019294
comment: The protrusion of a sac-like structure containing fibroadipose tissue through an abnormal opening in the inguinal region. [Definition Source: NCI]

Cold Sore
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Herpes Simplex Virus Infection
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0019345
comment: A lesion caused by type 1 or type 2 herpes simplex virus, involving the oralfacial region. [Definition Source: NCI]

Infectious Mononucleosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0021345
comment: A clinical syndrome of fever, sore throat, fatigue, and lymphadenopathy caused by infection with the Epstein-Barr virus. Subsequent physical findings may include hepatomegaly, palatal petechiae, jaundice, uvular edema, and splenomegaly. [Definition Source: NCI]

Intestinal Pseudo-Obstruction
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0021847
comment: Ileus of the intestine in which there is no mechanical obstruction. [Definition Source: NCI]

Iridocyclitis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0022073
comment: Inflammation of the iris and the ciliary body. [Definition Source: NCI]

Essential Hypertension
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Hypertension
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0085580
comment: Hypertension that presents without an identifiable cause. [Definition Source: NCI]

Long QT Syndrome
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0023976
comment: A ventricular arrhythmia characterized by a long QT interval, and accompanied by syncopal episodes sometimes leading to sudden death due to paroxysmal ventricular arrhythmia. This arrhythmia is associated with a prolongation of repolarization following depolarization of the cardiac ventricles. The prolongation of the Q-T interval combined with torsades de pointes manifests as several different forms; some may be acquired or congenital; some may lead to serious arrhythmia and sudden cardiac death. [Definition Source: NCI]

Pancytopenia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0030312
comment: A finding of low numbers of red and white blood cells and platelets in the peripheral blood. [Definition Source: NCI]

Penicillin Allergy
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Drug Hypersensitivity Syndrome
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0030824
comment: An allergy to Penicillin. [Definition Source: NCI]

Personality Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Psychiatric Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0031212
comment: A diverse category of psychiatric disorders characterized by behavior that deviates markedly from the expectations of the individual's culture; this pattern of deviation is pervasive and inflexible and is stable over time. The behavioral pattern negatively interferes with relationships and work. [Definition Source: NCI]

Aspiration Pneumonitis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1761609
comment: Inflammation of the lungs due to the inhalation of solid or liquid material. [Definition Source: NCI]

Baker Cyst
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Cyst
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0032650
comment: Swelling and protrusion of the gastrocnemius-semimembranosus bursa due to an accumulation of synovial fluid. [Definition Source: NCI]

Sarcoidosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0036202
comment: An idiopathic inflammatory disorder characterized by the formation of non-necrotizing epithelioid granulomas which contain giant cells. It usually affects the lungs, lymph nodes, liver, and skin. Cardiac involvement is also possible. [Definition Source: NCI]

Pulmonary Sarcoidosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Sarcoidosis
broader transitive: Chronic Lung Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0036205
comment: Sarcoidosis affecting the lung parenchyma. It is characterized by the presence of non-necrotizing granulomas in the lung tissues. It is manifested with dyspnea, cough, fever, night sweats, fatigue, and weight loss. [Definition Source: NCI]

Shoulder Dislocation
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Injury
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0037005
comment: A dislocation of the shoulder joint. [Definition Source: NCI]

Sinusitis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0037199
comment: An acute or chronic inflammatory process affecting the mucous membranes of any sinus cavity. [Definition Source: NCI]

Staphylococcal Infection
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0038160
comment: Infection by Staphylococcus. [Definition Source: NCI]

Syncope
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0039070
comment: A spontaneous loss of consciousness caused by insufficient blood supply to the brain. [Definition Source: NCI]

Thalassemia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0039730
comment: 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. [Definition Source: NCI]

Cutaneous Melanoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Malignant Skin Neoplasm
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0151779
comment: A primary melanoma arising from atypical melanocytes in the skin. Precursor lesions include acquired and congenital melanocytic nevi, and dysplastic nevi. Several histologic variants have been recognized, including superficial spreading melanoma, acral lentiginous melanoma, nodular melanoma, and lentigo maligna melanoma. [Definition Source: NCI]

Vulvovaginitis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0042998
comment: An inflammatory pathologic process that affects the vulva and the vagina. [Definition Source: NCI]

Acute Myocardial Infarction
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0155626
comment: Necrosis of the myocardium, as a result of interruption of the blood supply to the area. It is characterized by a severe and rapid onset of symptoms that may include chest pain, often radiating to the left arm and left side of the neck, dyspnea, sweating, and palpitations. [Definition Source: NCI]

Closed Fracture of Rib
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Injury
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0435750
comment: A traumatic break in one of the bones in the rib cage that does not involve a break in the adjacent skin. [Definition Source: NCI]

Tooth Abscess
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0518988
comment: An infectious process that affects a tooth. It is characterized by localized periapical or periodontal collection of pus. It presents with pain and swelling of the gums and/or cheek. [Definition Source: NCI]

Monoclonal Gammopathy
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1136085
comment: An abnormal laboratory test result indicating the presence of monoclonal immunoglobulins in the blood or urine. [Definition Source: NCI]

Head and Neck Finding
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0575141
comment: Symptoms, physical examination results, and/or laboratory test results related to the head and neck. [Definition Source: NCI]

Injury
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C3263723
comment: Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. [Definition Source: NCI]

Bradycardia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Arrhythmia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0428977
comment: An abnormally slow heart rate. Thresholds for different age, gender, and patient populations exist. [Definition Source: NCI]

Vertigo
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0042571
comment: A feeling of movement, a sensation as if the external world were revolving around the patient (objective vertigo) or as if he himself were revolving in space (subjective vertigo). Vertigo is medically distinct from dizziness, lightheadedness, and unsteadiness. [Definition Source: NCI]

Skin Cyst
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Cyst
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0241060
comment: A cystic lesion located in the skin. [Definition Source: NCI]

High Grade Cervical Squamous Intraepithelial Neoplasia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1512433
comment: A precancerous neoplastic process that affects the cervical squamous epithelium. It is usually associated with human papillomavirus infection. It is classified as cervical squamous intraepithelial neoplasia 2 when there is nuclear atypia in both the upper and lower epithelial layers, mitotic figures are confined to the basal two-thirds of the epithelium, and maturation is present in the upper half of the epithelium. It is classified as cervical squamous intraepithelial neoplasia 3 when there is nuclear atypia and mitotic figures throughout the entire thickness of the epithelium, and maturation is absent or confined to the upper third of the epithelium. [Definition Source: NCI]

Unit by Category
type: NamedIndividual
type: Concept
type: Unit Of Measure
in scheme: Unit of Measure Taxonomy

Myeloproliferative Neoplasm
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Neoplasm
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1292778
comment: A clonal hematopoietic stem cell disorder, characterized by proliferation in the bone marrow of one or more of the myeloid (i.e., granulocytic, erythroid, megakaryocytic, and mast cell) lineages. It is primarily a neoplasm of adults. (WHO 2008) [Definition Source: NCI]

Colon Adenocarcinoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Adenocarcinoma
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0338106
comment: An adenocarcinoma arising from the colon. It is more frequently seen in populations with a Western type diet and in patients with a history of chronic inflammatory bowel disease. Signs and symptoms include intestinal bleeding, anemia, and change in bowel habits. According to the degree of cellular differentiation, colonic adenocarcinomas are divided into well, moderately, and poorly differentiated. Histologic variants include mucinous adenocarcinoma, signet ring cell carcinoma, medullary carcinoma, serrated adenocarcinoma, cribriform comedo-type adenocarcinoma, and micropapillary adenocarcinoma. [Definition Source: NCI]

Dementia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Central Nervous System Degenerative Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0497327
comment: Loss of intellectual abilities interfering with an individual's social and occupational functions. Causes include Alzheimer's disease, brain injuries, brain tumors, and vascular disorders. [Definition Source: NCI]

Central Nervous System Degenerative Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Non-Neoplastic Central Nervous System Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0270715
comment: A disorder of the central nervous system characterized by gradual and progressive loss of neural tissue and neurologic function. [Definition Source: NCI]

Cancer TNM Finding Category
type: NamedIndividual
type: Concept
type: Pathological TNM Finding
in scheme: Pathological TNM Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1707255

Breast Carcinoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Carcinoma
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0678222
comment: A carcinoma arising from the breast, most commonly the terminal ductal-lobular unit. It is the most common malignant tumor in females. Risk factors include country of birth, family history, menstrual and reproductive history, fibrocystic disease and epithelial hyperplasia, exogenous estrogens, contraceptive agents, and ionizing radiation. The vast majority of breast carcinomas are adenocarcinomas (ductal or lobular). Breast carcinoma spreads by direct invasion, by the lymphatic route, and by the blood vessel route. The most common site of lymph node involvement is the axilla. [Definition Source: NCI]

Symptom
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Sign or Symptom
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1457887
comment: Subjective evidence of disease perceived by the patient. [Definition Source: NCI]

Skin Carcinoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Carcinoma
broader transitive: Malignant Skin Neoplasm
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0699893
comment: A carcinoma that arises from the skin. Representative examples are basal cell carcinoma and squamous cell carcinoma. [Definition Source: NCI]

Deep Vein Thrombosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Cardiovascular Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0149871
comment: A blood clot in a deep vein, predominantly in the lower extremity, but may include the pelvis or upper extremity. [Definition Source: NCI][attribution: NICHD]

Atrial Fibrillation
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Arrhythmia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0004238
comment: A disorder characterized by an electrocardiographic finding of a supraventricular arrhythmia characterized by the replacement of consistent P waves by rapid oscillations or fibrillatory waves that vary in size, shape and timing and are accompanied by an irregular ventricular response. (CDISC) [Definition Source: NCI]

Diabetic Ketoacidosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0011880
comment: The metabolic condition resulted from uncontrolled diabetes mellitus, in which the shift of acid-base status of the body toward the acid side because of loss of base or retention of acids other than carbonic acid is accompanied by the accumulation of ketone bodies in body tissues and fluids. [Definition Source: NCI]

Heart Failure
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0018801
comment: Inability of the heart to pump blood at an adequate rate to meet tissue metabolic requirements. Clinical symptoms of heart failure include: unusual dyspnea on light exertion, recurrent dyspnea occurring in the supine position, fluid retention or rales, jugular venous distension, pulmonary edema on physical exam, or pulmonary edema on chest x-ray presumed to be cardiac dysfunction. [Definition Source: NCI]

Lumbar Puncture Headache
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Headache
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0270697
comment: Headache in erect position, after lumbar puncture; due to lowering of intracranial pressure by leakage of cerebrospinal fluid through the needle tract. [Definition Source: NCI]

Neonatal Hearing Impairment
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1709158
comment: An abnormality that affects hearing within the first month after birth. It may or may not result in hearing loss. [Definition Source: NCI]

Pulmonary Embolism
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Cardiovascular Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0034065
comment: The obstruction of the pulmonary artery or one of its branches by an embolus, sometimes associated with infarction of the lung. [Definition Source: NCI]

Transient Ischemic Attack
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Non-Neoplastic Central Nervous System Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0007787
comment: A brief attack (from a few minutes to an hour) of cerebral dysfunction of vascular origin, with no persistent neurological deficit. [Definition Source: NCI]

Atrial Flutter
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Arrhythmia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0004239
comment: A disorder characterized by an electrocardiographic finding of an organized, regular atrial rhythm with atrial rate of 240-340 beats per minute. Multiple P waves typically appear in the inferior leads in a saw tooth-like pattern between the QRS complexes. (CDISC) [Definition Source: NCI]

Sign
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Sign or Symptom
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0311392
comment: Objective evidence of disease perceptible to the examining healthcare provider. [Definition Source: NCI]

Anorectal Fistula
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0149889
comment: A pathologic tract that connects an opening in the anal canal to the perianal skin. In the vast majority of cases there is a history of perianal abscess. [Definition Source: NCI]

Myasthenia Gravis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Autoimmune Nervous System Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0026896
comment: A chronic autoimmune neuromuscular disorder characterized by skeletal muscle weakness. It is caused by the blockage of the acetylcholine receptors at the neuromuscular junction. [Definition Source: NCI]

Psoriatic Arthritis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Arthritis
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0003872
comment: Joint inflammation associated with psoriasis. [Definition Source: NCI]

Amenorrhea
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0002453
comment: The absence of menses in a woman who has achieved reproductive age. [Definition Source: NCI]

Neurofibromatosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0162678
comment: An autosomal dominant hereditary neoplastic syndrome. Two distinct clinicopathological entities are recognized: neurofibromatosis type 1 and neurofibromatosis type 2. Neurofibromatosis type 1 is associated with the presence of cafe-au-lait cutaneous lesions, multiple neurofibromas, malignant peripheral nerve sheath tumors, optic nerve gliomas, and bone lesions. Neurofibromatosis type 2 is associated with the presence of schwannomas, meningiomas, and gliomas. [Definition Source: NCI]

Serositis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0036749
comment: Inflammation of a serous membrane. [Definition Source: NCI]

Neoplasm by Special Category
type: NamedIndividual
type: Concept
type: Tumor Progression
in scheme: Tumor Progression Taxonomy
comment: A neoplasm defined by its unique characteristic as they apply to clinical presentation and course, morphologic patterns, frequency, and/or age distribution. [Definition Source: NCI]

Herpes Zoster
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0019360
comment: A common dermal and neurologic disorder caused by reactivation of the varicella-zoster virus that has remained dormant within dorsal root ganglia, often for decades, after the patient's initial exposure to the virus in the form of varicella (chickenpox). It is characterized by severe neuralgic pain along the distribution of the affected nerve and crops of clustered vesicles over the area. [Definition Source: NCI]

Malignant Thyroid Gland Neoplasm
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Thyroid Gland Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0007115
comment: A primary or metastatic malignant neoplasm affecting the thyroid gland. [Definition Source: NCI]

Melanocytic Nevus
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Neoplasm
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0027962
comment: A neoplasm composed of melanocytes that usually appears as a dark spot on the skin. [Definition Source: NCI]

Flu-Like Symptoms
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Symptom
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0392171
comment: Complaints describing a pattern similar to influenza, which may include one or more of the following symptoms: fever, chills, muscle or body aches, cough, sore throat, rhinitis, or fatigue. [Definition Source: NCI]

Renal Colic
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0152169
comment: Paroxysmal and severe flank pain radiating to the inguinal area. It is caused by the passage of a kidney stone through the ureter. [Definition Source: NCI]

Allergic Rhinitis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C2607914
comment: Inflammation of the nasal mucous membranes caused by an IgE-mediated response to external allergens. The inflammation may also involve the mucous membranes of the sinuses, eyes, middle ear, and pharynx. Symptoms include sneezing, nasal congestion, rhinorrhea, and itching. It may lead to fatigue, drowsiness, and malaise thus causing impairment of the quality of life. [Definition Source: NCI]

Extrapyramidal Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Central Nervous System Degenerative Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0015371
comment: A movement disorder caused by defects in the basal ganglia. The clinical manifestations include changes in the muscle tone, dyskinesia, and akinesia. Causes include vascular disorders, degenerative disorders, and antipsychotic drugs. [Definition Source: NCI]

Monoclonal B_Cell Lymphocytosis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C2698259
comment: A monoclonal expansion of B-lymphocytes with or without the characteristic immunophenotype of chronic lymphocytic leukemia. It precedes virtually all cases of chronic lymphocytic leukemia/small lymphocytic lymphoma. [Definition Source: NCI]

Dyslipidemia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0242339
comment: A lipoprotein metabolism disorder characterized by decreased levels of high-density lipoproteins, or elevated levels of plasma cholesterol, low-density lipoproteins and/or triglycerides. [Definition Source: NCI]

Iron-Deficiency Anemia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Anemia
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0162316
comment: Anemia caused by low iron intake, inefficient iron absorption in the gastrointestinal tract, or chronic blood loss. [Definition Source: NCI]

Brown-Sequard Syndrome
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0242644
comment: A disorder caused by a spinal injury leading to an incomplete spinal lesion. Patients develop paralysis, ataxia and loss of sensation. Causes include spinal cord tumors, spinal traumas, ischemia, and inflammatory processes affecting the spine. [Definition Source: NCI]

Hereditary Factor XI Deficiency
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0015523
comment: A rare inherited bleeding disorder caused by deficiency of coagulation factor XI. It may be asymptomatic or manifest with bleeding. [Definition Source: NCI]

Ann Arbor Stage IV Mantle Cell Lymphoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0677721
comment: Ann Arbor Classification: Stage IV: Diffuse or disseminated involvement of one or more extralymphatic organs, with or without associated lymph node involvement; or isolated extralymphatic organ involvement in the absence of adjacent regional lymph node involvement, but in conjunction with disease in distant site(s); or any involvement of the liver or bone marrow, lungs (other than by direct extension from another site), or cerebrospinal fluid. [Definition Source: NCI]

Optic Neuritis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0029134
comment: A disorder characterized by inflammation of the optic nerve. Causes include autoimmune disorders, infections, toxins, drugs, and multiple sclerosis. It may manifest with acute loss of vision and pain. [Definition Source: NCI]

Primary Progressive Aphasia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0282513
comment: A rare neurologic progressive disorder characterized by impairment of the language and speech abilities. [Definition Source: NCI]

Primary Neoplasm
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Neoplasm
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0677930
comment: A tumor at the original site of origin. [Definition Source: NCI]

Spinal and Bulbar Muscular Atrophy, X-linked 1
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C1839259
comment: A rare, slowly progressive degenerative disorder affecting males. It is caused by mutations in the androgen receptor (AR) gene. It is characterized by bulbar and limb muscle weakness and atrophy, and gynecomastia. [Definition Source: NCI]

Ann Arbor Stage IV T-Cell Non-Hodgkin Lymphoma
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0854831
comment: Ann Arbor Classification: Stage IV: Diffuse or disseminated involvement of one or more extralymphatic organs, with or without associated lymph node involvement; or isolated extralymphatic organ involvement in the absence of adjacent regional lymph node involvement, but in conjunction with disease in distant site(s); or any involvement of the liver or bone marrow, lungs (other than by direct extension from another site), or cerebrospinal fluid. [Definition Source: NCI]

Fibromyalgia
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0016053
comment: A chronic disorder of unknown etiology characterized by pain, stiffness, and tenderness in the muscles of neck, shoulders, back, hips, arms, and legs. Other signs and symptoms include headaches, fatigue, sleep disturbances, and painful menstruation. [Definition Source: NCI]

Migraine
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0149931
comment: A common, severe type of vascular headache often associated with increased sympathetic activity, resulting in nausea, vomiting, and light sensitivity. [Definition Source: NCI]

Bowel Obstruction
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0021843
comment: Blockage of the normal flow of the intestinal contents within the bowel. [Definition Source: NCI]

Mood Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Psychiatric Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0525045
comment: A category of psychiatric disorders which have as their most predominant feature a disturbance in mood. [Definition Source: NCI]

Malignant Colon Neoplasm
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0007102
comment: A primary or metastatic malignant neoplasm that affects the colon. Representative examples include carcinoma, lymphoma, and sarcoma. [Definition Source: NCI]

Gastroesophageal Reflux
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C4317146
comment: The backward flow of stomach acid contents into the esophagus (the tube that connects the mouth to the stomach). [Definition Source: NCI]

Alcohol Dependance
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0001973
comment: Physical and psychological dependence on alcohol. [Definition Source: NCI]

Malignant Neoplasm
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Neoplasm
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0006826
comment: A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas, Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas. [Definition Source: NCI]

Scarlet Fever
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0036285
comment: A streptococcal infection, mainly occurring among children, that is characterized by a red skin rash, sore throat, and fever. [Definition Source: NCI]

Chicken Pox
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0008049
comment: A contagious childhood disorder caused by the varicella zoster virus. It is transmitted via respiratory secretions and contact with chickenpox blister contents. It presents with a vesicular skin rash, usually associated with fever, headache, and myalgias. The pruritic fluid-filled vesicles occur 10-21 days after exposure and last for 3-4 days. An additional 3-4 days of malaise follows before the affected individual feels better. An individual is contagious 1-2 days prior to the appearance of the blisters until all blisters are crusted over. Generally, healthy individuals recover without complications. [Definition Source: NCI]

Acute Tonsillitis
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0001361
comment: An acute inflammation of the tonsils caused by viruses or bacteria. Signs and symptoms include fever, enlargement of the tonsils, difficulty swallowing, and enlargement of the regional lymph nodes. [Definition Source: NCI]

Chronic Lung Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0746102
comment: A persistent non-neoplastic disorder of the lungs. Representative examples include: chronic obstructive pulmonary disease, chronic bronchitis, emphysema, pulmonary fibrosis, pneumoconiosis, asbestosis, atelectasis, radiation induced pneumonitis, and radiation fibrosis. [Definition Source: NCI]

Klippel-Feil Syndrome
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Disease or Disorder
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0022738
comment: A rare congenital syndrome characterized by the fusion of the vertebrae in the cervical spine. Patients present with a short neck and restricted mobility of the upper spine. Other signs and symptoms include scoliosis, spina bifida, cleft palate, and rib malformations. [Definition Source: NCI]

Radius Fracture
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Injury
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0034628
comment: Traumatic or pathological injury to the radius bone in which the continuity of the bone is broken. [Definition Source: NCI]

Tibia Fracture
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Injury
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0040185
comment: Traumatic or pathological injury to the tibia in which the continuity of the bone is broken. [Definition Source: NCI]

Autoimmune Nervous System Disorder
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Autoimmune Disease
in scheme: Disease, Disorder or Finding Taxonomy
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C0751871
comment: A disorder characterized by the degeneration of the nervous system due to autoimmunity. Representative examples include multiple sclerosis, Guillain-Barre syndrome, and myasthenia gravis. [Definition Source: NCI]

DNA Sequencer
type: NamedIndividual
type: Concept
type: Platform Model
comment: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. [Definition Source: Ontology for Biomedical Investigations (OBI)]

Study Design
type: NamedIndividual
type: Concept
type: Cohort Design
in scheme: Cohort Design Taxonomy
comment: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. [Definition Source: OBI]

Variant Origin
type: NamedIndividual
type: Concept
type: Allele Origin
in scheme: Allele Origin Taxonomy
comment: A quality inhering in a variant by virtue of its origin. [Definition Source: SO]

Maternal Variant
type: NamedIndividual
type: Concept
type: Allele Origin
broader transitive: Variant Origin
in scheme: Allele Origin Taxonomy
comment: A variant in the genetic material inherited from the mother. [Definition Source: Sequence Types and Features Ontology]

Paternal Variant
type: NamedIndividual
type: Concept
type: Allele Origin
broader transitive: Variant Origin
in scheme: Allele Origin Taxonomy
comment: A variant in the genetic material inherited from the father. [Definition Source: Sequence Types and Features Ontology]

Somatic Variant
type: NamedIndividual
type: Concept
type: Allele Origin
broader transitive: Variant Origin
in scheme: Allele Origin Taxonomy
comment: A variant that has arisen after splitting of the embryo, resulting in the variant being found in only some of the tissues or cells of the body. [Definition Source: Sequence Types and Features Ontology]

Germline Variant
type: NamedIndividual
type: Concept
type: Allele Origin
broader transitive: Variant Origin
in scheme: Allele Origin Taxonomy
comment: A variant present in the embryo that is carried by every cell in the body. [Definition Source: Sequence Types and Features Ontology]

Pedigree Specific Variant
type: NamedIndividual
type: Concept
type: Allele Origin
broader transitive: Variant Origin
in scheme: Allele Origin Taxonomy
comment: A variant that is found only by individuals that belong to the same pedigree. [Definition Source: Sequence Types and Features Ontology]

Population Specific Variant
type: NamedIndividual
type: Concept
type: Allele Origin
broader transitive: Variant Origin
in scheme: Allele Origin Taxonomy
comment: A variant found within only speficic populations. [Definition Source: Sequence Types and Features Ontology]

De-Novo Variant
type: NamedIndividual
type: Concept
type: Allele Origin
broader transitive: Variant Origin
in scheme: Allele Origin Taxonomy
comment: A variant arising in the offspring that is not found in either of the parents. [Definition Source: Sequence Types and Features Ontology]

Case Control Design
type: NamedIndividual
type: Concept
type: Biosample Status
in scheme: Biosample Status Taxonomy
comment: A case-control study design compares two groups of subjects: those with the disease or condition under study (cases) and a very similar group of subjects who do not have the disease or condition (controls). [Definition Source: EFO]

Sample Dissociation
type: NamedIndividual
type: Concept
type: Sample Processing
in scheme: Sample Processing Taxonomy
comment: Process which results in the separation of a biological specimen into individual cells or a cell suspension. [Definition Source: EFO]

Reference Sample
type: NamedIndividual
type: Concept
type: Biosample Status
broader transitive: Case Control Design
in scheme: Biosample Status Taxonomy
comment: A material sample derived from cells or tissue representing a physiologically or phenotypically normal state. [Definition Source: The Experimental Factor Ontology]

Abnormal Sample
type: NamedIndividual
type: Concept
type: Biosample Status
broader transitive: Case Control Design
in scheme: Biosample Status Taxonomy
comment: A material sample derived from cells or tissue representing an observed or suspected physiologically, genomically or phenotypically abnormal state. [Definition Source: The Experimental Factor Ontology]

Neoplastic Sample
type: NamedIndividual
type: Concept
type: Biosample Status
broader transitive: Abnormal Sample
in scheme: Biosample Status Taxonomy
comment: A material sample derived from neoplastic cells or tissue. [Definition Source: The Experimental Factor Ontology]

Metastasis Sample
type: NamedIndividual
type: Concept
type: Biosample Status
broader transitive: Neoplastic Sample
in scheme: Biosample Status Taxonomy
comment: A neoplastic sample derived from a cancer metastasis (not from a primary tumor). [Definition Source: The Experimental Factor Ontology]

Primary Tumor Sample
type: NamedIndividual
type: Concept
type: Biosample Status
broader transitive: Neoplastic Sample
in scheme: Biosample Status Taxonomy
comment: A neoplastic sample derived from a primary tumor (not from a cancer metastasis). [Definition Source: The Experimental Factor Ontology]

Recurrent Tumor Sample
type: NamedIndividual
type: Concept
type: Biosample Status
broader transitive: Neoplastic Sample
in scheme: Biosample Status Taxonomy
comment: A neoplastic sample derived from a recurrent tumor (not from a primary occurrence of a neoplasm). [Definition Source: The Experimental Factor Ontology]

High-Level Copy Number Loss
type: NamedIndividual
type: Concept
type: Copy Number Assessment
broader transitive: Copy Number Loss
in scheme: Copy Number Assessment Taxonomy
comment: Assessment of high-level copy loss. High-level loss is associated with a large negative log ratio between the ploidy at an indicated position and regional base ploidy. High-level loss is typically indicative of focal deletions. This term should be preferred in contrast to complete genomic deletion when a complete loss of all alleles at an indicated position cannot be reasonably assessed. [Definition Source: The Experimental Factor Ontology (EFO)]

Cancer Cell Line Sample
type: NamedIndividual
type: Concept
type: Biosample Status
broader transitive: Neoplastic Sample
in scheme: Biosample Status Taxonomy
comment: A neoplastic sample derived from a cancer cell line. [Definition Source: The Experimental Factor Ontology]

Copy Number Assessment
type: NamedIndividual
type: Concept
in scheme: Copy Number Assessment Taxonomy
comment: Result of genomic copy number assessment of a genomic element or region. Assessment of the copy number of a genomic feature or region, referenced to the expected allele count in a given sample. Examples of an expected count would be: a) autosomal chromosome in human germline: 2; b) X-chromosome in human male: 1; c) triploid cancer cell line: 3, i.e. a region with 2 alleles in a triploid cell line would correspond to a low-level copy number loss. [Definition Source: EFO]

Regional Base Ploidy
type: NamedIndividual
type: Concept
type: Copy Number Assessment
broader transitive: Copy Number Assessment
in scheme: Copy Number Assessment Taxonomy
comment: Copy number assessment of regional base ploidy. [Definition Source: The Experimental Factor Ontology (EFO)]

Copy Number Loss
type: NamedIndividual
type: Concept
type: Copy Number Assessment
broader transitive: Copy Number Assessment
in scheme: Copy Number Assessment Taxonomy
comment: Assessment of genomic copy number loss.

Low-Level Copy Number Loss
type: NamedIndividual
type: Concept
type: Copy Number Assessment
broader transitive: Copy Number Loss
in scheme: Copy Number Assessment Taxonomy
comment: Assessment of low-level genomic copy number loss. [Definition Source: The Experimental Factor ontology (EFO)]

Complete Genomic Deletion
type: NamedIndividual
type: Concept
type: Copy Number Assessment
broader transitive: High-Level Copy Number Loss
in scheme: Copy Number Assessment Taxonomy
comment: Assessment of complete genomic deletion. [Definition Source: The Experimental Factor Ontology (EFO)]

Copy Number Gain
type: NamedIndividual
type: Concept
type: Copy Number Assessment
broader transitive: Copy Number Assessment
in scheme: Copy Number Assessment Taxonomy
comment: Assessment of genomic copy number gain. [Definition Source: The Experimental Factor ontology (EFO)]

Low-Level Copy Number Gain
type: NamedIndividual
type: Concept
type: Copy Number Assessment
broader transitive: Copy Number Gain
in scheme: Copy Number Assessment Taxonomy
comment: Assessment of low-level genomic copy number gain. [Definition Source: The Experimental Factor Ontology (EFO)]

High-Level Copy Number Gain
type: NamedIndividual
type: Concept
type: Copy Number Assessment
broader transitive: Copy Number Gain
in scheme: Copy Number Assessment Taxonomy
comment: Assessment of high-level genomic copy number gain. [Definition Source: The Experimental Factor Ontology (EFO)]

Missense Variant
type: NamedIndividual
type: Concept
type: Molecular Effect
in scheme: Molecular Effect Taxonomy
comment: A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved. [Definition Source: The Sequence Ontology]

5 Prime UTR Variant
type: NamedIndividual
type: Concept
type: Genomic Feature Class
in scheme: Genomic Feature Class Taxonomy
comment: A UTR variant of the 5' UTR. [Definition Source: The Sequence Ontology]

Stop Gained NMD Escaping
type: NamedIndividual
type: Concept
type: Molecular Effect
in scheme: Molecular Effect Taxonomy
comment: A stop_gained (SO:0001587) variant that allows the transcript to escape nonsense-mediated decay (NMD). [Definition Source: The Sequence Ontology]

Phenotypic Abnormality
type: NamedIndividual
type: Concept
type: PhenoClinic Category
in scheme: Phenoclinic Category Taxonomy
comment: A deviation from normal morphology, physiology, or behavior, and good phenotyping is a cornerstone of a doctor's daily work. [PMID: 25109851]

Clinical Modifier
type: NamedIndividual
type: Concept
type: Phenotypic Feature Modifier
in scheme: Phenotypic Feature Modifier Taxonomy
comment: Characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. [Definition Source: HP]

Severity
type: NamedIndividual
type: Concept
comment: The intensity or degree of a manifestation. [Definition Source: HP]

Mild
type: NamedIndividual
type: Concept
type: Severity
broader transitive: Severity
in scheme: Severity Taxonomy
comment: Having a relatively minor degree of severity. For quantitative traits, a deviation of between two and three standard deviations from the appropriate population mean. [Definition Source: The Human Phenotype Ontology (HP)]

Moderate
type: NamedIndividual
type: Concept
type: Severity
broader transitive: Severity
in scheme: Severity Taxonomy
comment: Having a medium degree of severity. For quantitative traits, a deviation of between three and four standard deviations from the appropriate population mean. [Definition Source: The Human Phenotype Ontology (HP)]

Borderline
type: NamedIndividual
type: Concept
type: Severity
broader transitive: Severity
in scheme: Severity Taxonomy
comment: Having a minor degree of severity that is considered to be on the boundary between the normal and the abnormal ranges. For quantitative traits, a deviation of that is less than two standard deviations from the appropriate population mean. [Definition Source: The Human Phenotype Ontology (HP)]

Severe
type: NamedIndividual
type: Concept
type: Severity
broader transitive: Severity
in scheme: Severity Taxonomy
comment: Having a high degree of severity. For quantitative traits, a deviation of between four and five standard deviations from the appropriate population mean. [Definition Source: The Human Phenotype Ontology (HP)]

Profound
type: NamedIndividual
type: Concept
type: Severity
broader transitive: Severity
in scheme: Severity Taxonomy
comment: Having an extremely high degree of severity. For quantitative traits, a deviation of more than five standard deviations from the appropriate population mean. [Definition Source: The Human Phenotype Ontology (HP)]

Laura Menotti
type: NamedIndividual
type: Person

Gianmaria Silvello
type: NamedIndividual
type: Person

Behavioral Impairment
type: NamedIndividual
type: Concept
type: Disease, Disorder or Finding
broader transitive: Finding
in scheme: Disease, Disorder or Finding Taxonomy
comment: Diminished psychological function.

Allele Origin Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Variant Origin
comment: This taxonomy describes allele origin of variant in sample from the Variant Origin (SO:0001762). Categories are `somatic variant`, `germline variant`, `maternal variant`, `paternal variant`, `de novo variant`, `pedigree specific variant`, `population specific variant`. Corresponds to Variant Inheritance in FHIR. [Definition Source: GA4GH Beacon v2 Data Model]

Assay Taxonomy
type: NamedIndividual
type: ConceptScheme
comment: This taxonomy describes the assay used to produce the measurement. [Definition Source: Phenopacket v2]

Biosample Status Taxonomy
type: NamedIndividual
type: ConceptScheme
comment: Concept hierarchy from Experimental Factor Ontology (EFO) Material Entity term (BFO:0000040). Classification of the sample in abnormal sample (EFO:0009655) or reference sample (EFO:0009654).

Cohort Data Type Taxonomy
type: NamedIndividual
type: ConceptScheme
comment: SKOS Concept hierarchy describing the type of information. Preferably values from Genomics Cohorts Knowledge Ontology (GeCKO) or others when GeCKO is not applicable. [Definition Source: Beacon v2 Data Model]

Cohort Design Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Study Design
comment: SKOS Concept hierarchy describing the cohort type by its design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Value from Ontologized MIABIS (OMIABIS) Study design ontology term tree (OBI:0500000). [Definition Source: Beacon v2 Data Model]

Cohort Sex Taxonomy
type: NamedIndividual
type: ConceptScheme
comment: Sex of the individual. Recommended values from NCIT General Qualifier (NCIT:C27993). Sex refers to the biological characteristics that define humans as female or male. While these sets of biological characteristics are not mutually exclusive, as there are individuals who possess both, they tend to differentiate humans as males and females. [Definition Source: World Health Organization]

Copy Number Assessment Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Copy Number Assessment
comment: SKOS Concept hierarchy describing the type of copy number change allowed.

Diagnostic Marker Taxonomy
type: NamedIndividual
type: ConceptScheme
comment: This taxonomy describes clinically relevant biomarkers.

Disease Stage Taxonomy
type: NamedIndividual
type: ConceptScheme
label: SKOS Concept hierarchy descrbinig the disease stage. Value from Ontology for General Medical Science (OGMS), e.g. acute onset (OGMS:0000119). [Defintion Source: Beacon v2 Data Model]

Genomic Feature Class Taxonomy
type: NamedIndividual
type: ConceptScheme
comment: SKOS Concept hierarchy describing the class of genomic feature affected by the variant. Values from SO (Sequence ontology) are recommended, e.g. `SO:0001623: 5 prime UTR variant`

Geographic Location Taxonomy
type: NamedIndividual
type: ConceptScheme
comment: Country or region of origin of the individual (birthplace or residence place regardless of ethnic origin). Value from GAZ Geographic Location ontology (GAZ:00000448). [Definition Source: Beacon v2 Data Model]

Library Source Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Library Source
comment: This taxonomy describes the source of the sequencing or hybridization library. [Definition Source: GA4GH Beacon v2 Data Model]. The taxonomy is based on GENEPIO.

Molecular Effect Taxonomy
type: NamedIndividual
type: ConceptScheme
comment: SKOS Concept hiearchy describing the class of molecular consequence generated by the variant. Values from SO (Sequence Ontology) are recommended, e.g. `SO:0001583: missense variant`.

Obtention Procedure Taxonomy
type: NamedIndividual
type: ConceptScheme
comment: This taxonomy describes the obtention procedures to retrieve a biosample or a measurement.

Pathological Stage Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Disease Stage Qualifier
comment: Pathological stage, if applicable, preferably as subclass of NCIT:C28108 - Disease Stage Qualifier. [Definition Source: GA4GH Beacon v2 Data Model]

Pathological TNM Finding Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Cancer TNM Finding Category
comment: Pathological TNM findings, if applicable, preferably as subclass of Cancer TNM Finding Category (NCIT:C48698). [Definition Source: GA4GH Beacon v2 Data Model]

Phenoclinic Category Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Disease or Disorder (MONDO)
comment: This taxonomy comprises the type of disease, condition, phenotypic measurement, etc. The taxonomy is mainly based on MONDO on Human Phenotype Ontology (HP)

Phenoclinic Evidence Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Experimental Evidence
has top concept: Inferential Evidence
comment: This taxonomy describes the type of evidence supporting variant-disease association. Recommended: values from the Evidence & Conclusion Ontology (ECO) [Definition Source: GA4GH Beacon v2 Data Model]

Phenotypic Feature Modifier Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Clinical Modifier
comment: SKOS Concept hierarchy to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. Example use here would be one or more terms from HPO Clinical Modifier (HP:0012823). Source: Phenopackets v2 [Definition Source: Beacon v2 Data Model]

Phenotypic Feature Type Taxonomy
type: NamedIndividual
type: ConceptScheme
comment: SKOS Concept hierarchy denoting the phenotypic feature, preferably using a value from Human Phenotype Ontology (HPO). [Definition Source: Beacon v2 Data Model]

Platform Model Taxonomy
type: NamedIndividual
type: ConceptScheme
comment: This taxonomy describes the experimental platform or methodology used. For sequencing platforms the use of "OBI:0400103 - DNA sequencer" is suggested.

Sample Origin Taxonomy
type: NamedIndividual
type: ConceptScheme
comment: Tissue from which the sample was taken or sample origin matching the category set in 'sampleOriginType'. Value from Uber-anatomy ontology (UBERON) or BRENDA tissue / enzyme source (BTO), Ontology for Biomedical Investigations (OBI) or Cell Line Ontology (CLO). [Definition source: GA4GH Beacon v2 Data Model]

Sample Origin Type Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Material Entity
comment: Category of sample origin. Value from Ontology for Biomedical Investigations (OBI) material entity (BFO:0000040) ontology. [Definition Source: GA4GH Beacon v2 Data Model]

Sample Processing Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Sample Dissociation

Severity Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Severity
comment: SKOS Concept Hierarchy describing the severity level. Values from HP Ontology.

Species Taxonomy
type: NamedIndividual
type: ConceptScheme
comment: SKOS Concept hierarchy representing a species from the NCBI species taxonomy.

Tumor Grade Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Disease Grade Qualifier
comment: SKOS Concept hierarchy representing the tumor grade. Child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent. [Definition Source: GA4GH Beacon v2 Data model]

Tumor Progression Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Neoplasm by Special Category
comment: Tumor progression category indicating primary, metastatic or recurrent progression. Ontology value from Neoplasm by Special Category ontology (NCIT:C7062). [Definition Source: GA4GH Beacon v2 Data Model]

Unit of Measure Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Unit by Category
comment: This taxonomy describes the kind of unit. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants. [Definition Source: GA4GH Beacon v2 Data Model]

Zygosity Taxonomy
type: NamedIndividual
type: ConceptScheme
broader transitive: Zygosity
has top concept: Zygosity
comment: This taxonomy describes the zygosity in which variant is present in the sample from the Zygosity Ontology (GENO:0000391) , e.g `heterozygous` (GENO:0000135) [Definition Source: GA4GH Beacon v2 Data Model]

Disease, Disorder or Finding Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Disease or Disorder
has top concept: Finding
comment: This taxonomy comprises disease, disorder or findings. The taxonomy is mainly based on NCIT.

Group Taxonomy
type: NamedIndividual
type: ConceptScheme
has top concept: Ethnic Group
comment: This taxonomy describes the different ethinic groups. The taxonomy is based on SNOMED-CT.

Human
type: NamedIndividual
type: Concept
type: Species
in scheme: Species Taxonomy
comment: NCBI Taxonomy ID: 9606