The Hereditary Ontology for Genomic Data
The Hereditary ontology for Genomic Data models models genetic data following GA4GH standards like the Beacon v2 data model.
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
The end age range.
ageRangeEnd
The start age range.
ageRangeStart
Links the case level variant to the allele origin.
alleleOrigin
Links the case level variant to the bioinformatics analysis.
analysis
Links the pehnoclinic effect to the software tool used to annotate it.
annotatedWith
Links the measurement to the assay used to produce the measurement.
assay
Links the case level variant to its biosample.
biosample
Links the biosample to its status.
biosampleStatus
Links the considered genomic variation to variation instances observed in individual analyses.
caseLevelData
Links the phenoclinic effect to the type of disease, condition, phenotypics measurement, etc.
category
Links a chromosome location to the species.
chromosomeSpecies
Links the variant level data and case level variant to its phenoclinic effects.
clinicalInterpretation
Individual age range in cohort inclusion criteria. [Definition Source: Beacon v2 Data Model]
cohortAgeRange
Links a cohort to the types of information.
cohortDataType
Links a cohort to the cohort type by its design.
cohortDesign
Diseases in cohort inclusion criteria. [Definition Source: Beacon v2 Data Model]
cohortDisease
Ethnicities in cohort inclusion criteria. [Definition Source: BEacon v2 Data Model]
cohortEthnicity
Geographic location(s) in cohort inclusion criteria. [Definition Source: Beacon v2 Data Model]
cohortLocation
Sex(es) in cohort inclusion criteria. [Definition Source: Beacon v2 Data Model]
cohortSex
Links a cohort to the collection event.
collectionEvent
Links a chromosome location to the cytoband interval.
cytobandInterval
Links a biosample to clinically relevant biomarkers.
diagnosticMarker
Links the disease to the the age at which an individual first experiences the disease.
diseaseAgeOnset
Links the disease to the disease identifier.
diseaseCode
Links the disease to the stage.
diseaseStage
Links the aggregated information to the results or counts for each category.
distribution
Links the phenoclinic effect class to the annotated phenotypic or clinical effect
effect
Links the element distribution to the category.
elementType
Links a collection event to aggregated information obtained from individual level info of the cohort members.
eventDistribution
Links a Collection Event to the Event Timeline.
eventTimeline
Links the phenoclinic effect to the type of evidence supporting variant-disease association.
evidence
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]
exclusionCriteria
Links the phenotypic feature to specific characteristics.
featureModifier
Age or time at which the feature was first observed. [Definition Source: Beacon v2 Data Model]
featureOnset
Age or time at which the feature resolved or abated. [Definition Source: Beacon v2 Data Model]
featureResolution
Links a phenotypic feature to its type.
featureType
Links the Frequency In Population class to allele frequency information of each population.
frequency
Links the considered genomic variation to frequency information of different populations.
frequencyInPopulation
Links a genomic variation to the genomic feature(s) affected by it.
genomicFeature
Links the genomic feature to the class of genomic feature affected by the variant.
genomicFeatureClass
Links the genotype varoation to the members describes a Molecular Variation and the count of that variation at the locus.
genotypeMember
Links a genotype locus to the molecular variation.
genotypeVariation
Links the haplotype to the co-occurring allele.
haplotypeMember
Links the biosample to the disease diagnosis that was inferred from the histological examination. [Definition Source: GA4GH Beacon v2 Data Model]
histologicalDiagnosis
Links a patient to the belonging cohort.
inCohort
Links the VCF record to the corresponding VCF file.
inVcfFile
Inclusion criteria used for defining the cohort. It is assumed that all cohort participants will match such criteria. [Definition Source: Beacon v2 Data Model]
inclusionCriteria
Links the case level variant to the considered individual.
individual
Links an experimental run to the the source of the sequencing or hybridization library.
librarySource
Links a class to the genomic location.
location
Links a biosample to the measurement.
measurement
Moment in time at which measurement was performed. [Definition Source: GA4GH Beacon v2 Data Model]
measurementMoment
Links a measurement to the employed Unit Of Measure.
measurementUOM
Links the considered genomic variation to its molecular attributes.
molecularAttribute
Links a molecular attribute to its molecular effect.
molecularEffect
Links a molecular variation to the variation type.
molecularVariationType
The procedure for sample or measurement obtention.
obtentionProcedure
Links the biosample to the detected pathological stage.
pathologicalStage
Links the biosample to the detected pathological TNM finding.
pathologicalTNMFinding
Links the cohort criteria to the phenotypic condition(s) in cohort inculsion criteria.
phenotypicCondition
phenotypicEffect
Link the biosample to the phenotypic abnormalities of the sample.
phenotypicFeature
Links the experimental run to the experimental platform or methodology used.
platformModel
Links the VCF file tot the corresponding cohort
refersToCohort
Links the case level variant to the experimental run.
run
Links the biosample to the sample origin detail.
sampleOriginDetail
Links the biosample to the sample origin type.
sampleOriginType
Links the biosample to how the specimen was processed.
sampleProcessing
Sequence Expression components comprising the expression.
sequenceComponent
Links the repeated sequence expression to the expression of the repeating subsequence.
sequenceExpression
Links the sequence location to the sequence interval.
sequenceInterval
Links a sequence expression to the sequence location.
sequenceLocation
Links the allele to an expression of the sequence state.
sequenceState
Links a disease or phenotypic feature to its severity.
severity
Links a systemic variation to the variation type.
systemicVariationType
The timestamp in which a time interval has ended.
timeIntervalEnd
The timestamp in which a time interval has started.
timeIntervalStart
Links the biosample to the detected tumor grade.
tumorGrade
Links the biosample to the observed tumor progression.
tumorProgression
Links a genomic variation to the variant alternative ID.
variantAlternativeID
Links the considered genomic variation to its variant level data.
variantLevelData
Links the considered genomic variation to the quality score of the variation.
variantQuality
Links the Copy Number Change to the type of variation change.
variationCopyChange
Links the considered genomic variation to the VCF record mentioning it.
vcfRecord
Links the case level variant to the observed zigosity.
zygosity
Allele frequency between 0 and 1. Example: 0.00003186. [Definition Source: GA4GH Beacon v2 Data Model]
alleleFrequency
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\\-\\.]*)$" [Definition Source: GA4Gh Beacon v2 Data Model]
alternateBases
External reference of the variant alternative ID.
alternativeIDReference
Change at aminoacid level for protein affecting variants. Example: "V304*". [Definition Source: GA4GH Beacon v2 Data Model]
aminoacidChange
Reference to mapping/alignment software. [Definition Source: GA4GH Beacon v2 Data Model]
analysisAligner
Date at which analysis was performed. [Definition Source: GA4GH Beacon v2 Data Model]
analysisDate
Analysis pipeline and version if a standardized pipeline was used. [Definition Source: GA4GH Beacon v2 Data Model]
analysisPipelineName
Link to Analysis pipeline resource. [Definition Source: GA4GH Beacon v2 Data Model]
analysisPipelineRef
Data availability. [Definition Source: GA4GH Beacon v2 Data Model]
availability
Count of individuals with data available. [Definition Source: GA4GH Beacon v2 Data Model]
availabilityCount
Date of biosample collection in ISO8601 format. [Definition Source: GA4GH Beacon v2 Data Model]
biosampleCollectionDate
Individual's or cell cullture age at the time of sample collection in the ISO8601 duration format `P[n]Y[n]M[n]DT[n]H[n]M[n]S`. [Definition Source: GA4GH Beacon v2 Data Model]
biosampleCollectionMoment
Benign
Likely Benign
Likely Pathogenic
Pathogenic
Uncertain Significance
Indication of the clinical relevance of the variant Recommended: A value from the five-tiered classification from the American College of Medical Genetics (ACMG) designed to describe the likelihood that a genomic sequence variant is causative of an inherited disease. (ACMG Classification of Genomic Variant Pathogenicity: NCIT:C168798). [Definition Source: GA4GH Beacon v2 Data Model]
clinicalRelevance
ClinVar variant id. Other id values used by ClinVar can be added to `variantAlternativeIds`. pattern: "^(clinvar:)?\\d+$". [Definition Source: GA4GH Beacon v2 Data Model]
clinvarVariantID
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]
cohortName
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]
cohortSize
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]
cohortType
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]
cytobandEnd
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]
cytobandStart
Earliest date of visit or collection timeline. [Definition Source: GA4GH Beacon v2 Data Model]
earliestEvent
Results or counts for each category.
elementDistribution
Number of cases. [Definition Source: GA4GH Beacon v2 Data Model]
eventCases
Number of controls. [Definition SOurce: GA4GH Beacon v2 Data Model]
eventControls
Date of collection event/data point. [Definition Source: GA4GH Beacon v2 Data Model]
eventDate
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]
eventSize
Boolean indicating determined or self-reported presence of family history of the disease. [Definition Source: Beacon v2 Data Model]
familyHistory
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]
featureExcluded
The name of the file.
filename
The path to the file.
filepath
Symbolic name or identifier used for a gene. [Definition Source: GA4GH Beacon v2 Data Model]
geneID
Identifier for the genome assembly used to call the allele. [Definition Source: Phenopacket v2 Data Model]
genomeAssembly
The Human Genome Variation Society (HGVS) ID descriptor. [Definition Source: GA4GH Beacon v2 Data Model]
genomicHGVSID
The number of copies of the variation at a Genotype locus. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
genotypeCount
Days beyond the completed weeks, if available. [Definition Source: GA4GH Beacon v2 Data Model]
gestationalDays
Completed weeks of gestation. [Definition Source: GA4GH Beacon v2 Data Model]
gestationalWeeks
Represents age as a ISO8601 duration (e.g., 'P40Y10M05D'). [Definition Source: GA4GH Beacon v2 Data Model]
iso8601duration
Latest date of visit or collection timeline. [Definition Source: GA4GH Beacon v2 Data Model]
latestEvent
PAIRED
SINGLE
Ontology value for the library layout e.g "PAIRED", "SINGLE" [Definition Source: GA4GH Beacon v2 Data Model]
libraryLayout
Selection method for library preparation, e.g "RANDOM", "RT-PCR". [Definition Source: GA4GH Beacon v2 Data Model]
librarySelection
Library strategy, e.g. "WGS". [Definition SOurce: GA4GH Beacon v2 Data Model]
libraryStrategy
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]
locationChr
Date of measurement. [Definition Source: GA4GH Beacon v2 Data Model]
measurementDate
The reference range to determine the measurement to be high.
measurementRefRangeHigh
The reference range to determine the measurement to be low.
measurementRefRangeLow
The value of the measurement in the units,
measurementValue
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]
molecularVariationCount
Unstructured text to provide additional information.
notes
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]
population
The Human Genome Variation Society (HGVS) ID descriptor(s) at protein level (for protein-altering variants). [Definition Source: GA4GH Beacon v2 Data Model]
proteinHGVSID
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]
referenceBases
A VRS Computed Identifier for the reference Sequence. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
referenceSequence
The count of repeated units, as an integer or inclusive range. [Defintion Source: GA4GH VAriation Representation Specification (VRS) v1.2]
repeatedSequenceCount
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]
reverseComplement
Date at which the experiment was performed. [Definition Source: Ga4GH Beacon v2 Data Model]
runDate
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]
runPlatform
Status of how the specimen was stored. [Definition Source: GA4GH Beacon v2 Data Model]
sampleStorage
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]
sequence
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]
sequenceIntervalEnd
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]
sequenceIntervalStart
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]
source
A reference to further documentation or details. Examples: "https://gnomad.broadinstitute.org/", "https://ega-archive.org/". [Definition Source: GA4GH Beacon v2 Data Model]
sourceReference
Version of the source data. Example: "gnomAD v3.1.1". [Definition Source: GA4GH Beacon v2 Data Model]
sourceVersion
The datetime of the timestamp.
timestamp
Name of the software tool. [Definition Source: GA4GH Beacon v2 Data Model]
toolName
References to the software tool. [Definition Source: GA4GH Beacon v2 Data Model]
toolReference
Software Tool version used. [Definition Source: GA4GH Beacon v2 Data Model]
toolVersion
The Human Genome Variation Society (HGVS) ID descriptor(s) at transcript level.
transcriptHGVSID
The variant alternative ID.
valueID
Reference to variant calling software / pipeline. [Definition Source: GA4GH Beacon v2 Data Model]
variantCaller
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]
variantFilter
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]
variantInternalID
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]
variantQual
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]
variantType
The integral number of copies of the subject in a system. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
variationCopies
Alternate base. [Definition Source: Phenopacket v2 Data Model]
vcfAlt
Chromosome or contig identifier. [Definition Source: Phenopacket v2 Data Model]
vcfChrom
Filter status: PASS if this position has passed all filters. [Definition Source: Phenopacket v2 Data Model]
vcfFilter
Additional information: Semicolon-separated series of additional information fields. [Definition Source: Phenopacket v2 Data Model]
vcfInfo
The reference position, with the 1st base having position 1. [Definition Source: Phenopacket v2 Data Model]
vcfPos
Quality: Phred-scaled quality score for the assertion made in ALT. [Definition Source: Phenopacket v2 Data Model]
vcfQual
Reference base. [Definition Source: Phenopacket v2 Data Model]
vcfRef
A human being. [Definition Source: NCI]
Person
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]
Disease, Disorder or Finding
A group of individuals united by a common factor (e.g., geographic location, ethnicity, disease, age, gender) [Definition Source: NCI]
Group (social concept)
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]
Patient
Age value definition. [Definition Source: GA4GH Beacon v2 Data Model]
Age
Age range definition. [Definition Source: Ga4GH Beacon v2 Data Model]
Age Range
Individual age range, obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
Age Range Data Availability and Distribution
Results or counts for each category. [Definition Source: GA4GH Beacon v2 Data Model]
Age Range Element Distribution
The state of a molecule at a Location. [Definition Source: Ga4GH Variation Representation Specification (VRS) v1.2]
Allele
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]
Allele Origin
A sequencing bioinformatics analysis. [Definition Source: GA4GH Beacon v2 Data Model]
Analysis
The assay used to produce the measurement. [Definition Source: Phenopacket v2]
Assay
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
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).
Biosample Status
Reports about the variation instances observed in individual analyses. [Definition Source: GA4GH Beacon v2 Data Model]
Case Level Variant
A Location on a chromosome defined by a species and chromosome name. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
Chromosome Location
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 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 Criteria
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 Data Type
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 Design
Cohort Disease
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]
Cohort Sex
Aggregated information of cohort data collection obtained from individual level info of the cohort members.
Collection Event
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]
Composed Sequence Expression
SKOS Concept hierarchy describing the type of copy number change allowed.
Copy Number Assessment
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 Change
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]
Copy Number Count
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]
Cytoband Interval
Aggregated information obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
Data Availability and Distribution
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 Data Availability and Distribution
Results or counts for each data type category. [Definition Source: GA4GH Beacon v2 Data Model]
Data Type Element Distribution
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]
Derived Sequence Expression
Clinically relevant biomarkers. RECOMMENDED. [Definition Source: GA4GH Beacon v2 Data Model]
Diagnostic Marker
Aggregated information of disease/condition(s) obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
Disease Data Availability and Distribution
Results or counts for each disease category. [Definition Source: GA4GH Beacon v2 Data Model]
Disease Element Distribution
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]
Disease Stage
Element Distribution
Aggregated information of ethnicity obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
Ethnicity Data Availability and Distribution
Results or counts for each ethnicity category. [Definition Source: GA4GH Beacon v2 Data Model]
Ethnicity Element Distribution
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]
Event Timeline
Reports frequency information of the considered genomic variation.
Frequency In Population
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
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 Feature Class
A genomic variant entry. [Definition Source: GA4GH Beacon v2 Data Model]
Genomic Variation
A quantified set of Molecular Variation associated with a genomic locus. [Defintion Source: GA4GH Variation Representation Specification (VRS) v1.2]
Genotype
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]
Genotype Member
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]
Geographic Location
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]
Gestational Age
A set of non-overlapping Allele members that co-occur on the same molecule. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
Haplotype
Other genomic variations.
Legacy Variation
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)]
Library Source
An explicit expression of a Sequence. [Defintion Source: GA4GH Variation Representation Specification (VRS) v1.2]
Literal Sequence Expression
A contiguous segment of a biological sequence. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
Location
Aggregated information of geographic location obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
Location Data Availability and Distribution
Results or counts for each location category. [Definition Source: GA4GH Beacon v2 Data Model]
Location Element Distribution
Definition of a measurement class. Provenance: GA4GH Phenopackets v2 `Measurement`. [Definition Source: GA4GH Beacon v2 Data Model]
Measurement
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 Attribute
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 Effect
A Variation on a contiguous molecule. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
Molecular Variation
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]
Obtention Procedure
Pathological stage, if applicable, preferably as subclass of NCIT:C28108 - Disease Stage Qualifier. [Definition Source: GA4GH Beacon v2 Data Model]
Pathological Stage
Pathological TNM findings, if applicable, preferably as subclass of Cancer TNM Finding Category (NCIT:C48698). [Definition Source: GA4GH Beacon v2 Data Model]
Pathological TNM Finding
SKOS Concept Hierarchy comprising the type of disease, condition, phenotypic measurement, etc.
PhenoClinic Category
Annotated effects on disease or phenotypes. [Definition Source: GA4GH Beacon v2 Data Model]
PhenoClinic Effect
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]
PhenoClinic Evidence
Aggregated information of phenotype(s) obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
Phenotype Data Availability and Distribution
Results or counts for each phenotype category. [Definition Source: GA4GH Beacon v2 Data Model]
Phenotype Element Distribution
Describes a phenotype that characterizes the subject or biosample. [Definition Source: GA4GH Beaocn v2 Data Model]
Phenotypic Feature
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 Modifier
SKOS Concept hierarchy denoting the phenotypic feature, preferably using a value from Human Phenotype Ontology (HPO). [Definition Source: Beacon v2 Data Model]
Phenotypic Feature Type
SKOS Concept hierarchy describing the experimental platform or methodology used. For sequencing platforms the use of "OBI:0400103 - DNA sequencer" is suggested.
Platform Model
Reports frequency information of the considered poplutation.
Population Frequency
An expression of a sequence comprised of a tandem repeating subsequence. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
Repeated Sequence Expression
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]
Run
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 Detail
Category of sample origin. Value from Ontology for Biomedical Investigations (OBI) material entity (BFO:0000040) ontology. [Definition Source: GA4GH Beacon v2 Data Model]
Sample Origin Type
Status of how the specimen was processed. Example: a child term of EFO:0009091. [Definition Source: GA4GH Beacon v2 Data Model]
Sample Processing
An expression describing a Sequence. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
Sequence Expression
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 Interval
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]
Sequence Location
SKOS Concept Hierarchy describing the severity level.
Severity
Aggregated information of sex(es) obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
Sex Data Availability and Distribution
Results or counts for each sex category. [Definition Source: GA4GH Beacon v2 Data Model]
Sex Element Distribution
Software used to evaluate phenoclinic effects.
Software Tool
SKOS Concept hierarchy representing a species from the NCBI species taxonomy.
Species
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]
Systemic Variation
This class identifies time elements, e.g. age, time interval, and timestamp.
Time Element
Time interval with start and end defined as ISO8601 time stamps. [Definition Source: GA4GH Beacon v2 Data Model]
Time Interval
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]
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 Grade
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]
Tumor Progression
The kind of unit. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants. [Definition Source: GA4GH Beacon v2 Data Model]
Unit Of Measure
A Variant Call Format (VCF) file.
VCF File
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]
VCF Record
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 Alternative ID
Reports about the variation instances observed in the genomic variation.
Variant Level Data
Quality information about the genomic variation.
Variant Quality
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]
Zygosity
The absence of menses in a woman who has achieved reproductive age due to disorder of pituitary gland. [Partial Defintion Source: NCI
Amenorrhea due to Pituitary Dysfunction
A person having origins in any of the original peoples of Europe, the Middle East, or North Africa. (OMB) [Definition Source: NCI]
Caucasian
The autoimmune inability of the bone marrow to produce hematopoietic elements. [Definition Source: NCI]
Autoimmune Pancytopenia
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]
Bell's Palsy
Lumbar Hernia [Definition Source: SNOMEDCT]
Lumbar Hernia
Pulmonary embolism is caused by emboli, which have originated from venous thrombi, travelling to and occluding the arteries of the lung. [PMID:29770793]
Pulmonary Thromboembolism
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]
Atopic Dermatitis
A decrease in the number of NEUTROPHILS found in the blood. [Definition Source: MSH]
Neutropenic Disorder
A person having origins in the original peoples of sub-Saharan Africa or the Caribbean.
Black (ethnic group)
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]
Asian (ethnic group)
A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. [Definition Source: CSP]
Ethnic Group
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]
Motor Neuron Disease
Allergic Asthma
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]
Hispanic
A closed fracture of the tibia.
Closed Fracture of Tibia
Pneumonia caused by severe acute respiratory syndrome coronavirus 2 [Definition Source: SNOMEDCT]
Pneumonia Caused By SARS-CoV-2
General or unspecified injuries to the neck. It includes injuries to the skin, muscles, and other soft tissues of the neck. [Defintion Source: MSH]
Neck Trauma
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]
Herpes Simplex Keratitis
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]
Material Entity
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]
Experimental Evidence
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]
Inferential Evidence
The library source specifies the type of source material that is being sequenced. [Definition Source: GENEPIO]
Genomic DNA (includes PCR products from genomic DNA). [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
Genomic Source
Mixed material from metagenome. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
Metagenomic Source
Transcription products from community targets. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
Metatranscriptomic Source
Other, unspecified, or unknown library source material. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
Other Library Source
Synthetic DNA. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
Synthetic Source
Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries). [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
Transcriptomic Source
Viral RNA. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
Viral RNA Source
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]
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]
Hemizygous
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]
Homozygous
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]
Heterozygous
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]
Compouns Heterozygous
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]
Simple Heterozygous
Hemizygous X-Linked
Hemizygous Y-Linked
Hemizygous Insertion-Linked
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]
Nullizygous
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]
Disease or Disorder (MONDO)
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]
Two Vessel Coronary Disease
Objective evidence of disease perceptible to the examining practitioner (sign) and subjective evidence of disease perceived by the patient (symptom). [Definition Source: NCI]
Sign or Symptom
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]
Spina Bifida
Rapid swelling of the deep layers of the skin due to transient vascular leakage of serous fluid. [Definition Source: NCI][attribution: NICHD]
Angioedema
Inflammation of the eyelids near the eyelashes. [Definition Source: NCI][attribution: NICHD]
Blepharitits
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]
Drug Hypersensitivity Syndrome
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]
Molluscum Contagiosum Virus
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]
Tinea Versicolor
Narrowing of the luminal diameter of one or both ureters due to intrinsic factors. [Definition Source: NCI]
Ureteral Stenosis
Inability to smell. [Definition Source: NCI]
Anosmia
A collection of blood between the dura mater and the brain. [Definition Source: NCI]
Subdural Hematoma
Diminished mental function. [Definition Source: NCI]
Cognitive Impariment
A migraine disorder characterized by episodes that are preceded by focal neurological symptoms. [Definition Source: NCI]
Migraine With Aura
Pain that occurs after the disappearance of herpes zoster infection lesions. [Definition Source: NCI]
Post-Herpetic Neuralgia
Involuntary twitching of the eyelid. [Definition Source: NCI]
Blepharospasm
A wound received from the teeth of a dog. [Definition Source: NCI]
Dog Bite
Sudden onset pyelonephritis. [Definition Source: NCI][attribution: NICHD]
Acute Pyelonephritis
Pericarditis that is caused by an infection with a viral agent. [Definition Source: NCI]
Viral Pericarditis
Hypothyroidism, the cause of which is not present at birth. [Definition Source: NCI]
Acquired Hypothyroidism
An infection that is caused by herpes simplex virus. [Definition Source: NCI]
Herpes Simplex Virus Infection
A carcinoma involving the basal cells. [Definition Source: NCI]
Basal Cell Carcinoma
The use of opioids that results in the development of a dependency that adversely affects an individual's life. [Definition Source: NCI]
Opioid Use Disorder
Pneumonia that is attributed to the bacteria Streptococcus pneumonia. [Definition Source: NCI]
Pneumococcal Pneumonia
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]
Female
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]
COVID-19 Infection
Trauma to the chest. [Definition Source: NCI]
Thoracic Trauma
Not known, observed, recorded; or reported as unknown by the data contributor. [Defintion Source: NCI]
Unknown
Toxicity that impairs or damages the liver. [Definition Source: NCI]
Hepatic Toxicity
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]
Male
Painful sensation in the abdominal region. [Definition Source: NCI]
Abdominal Pain
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]
Bacterial Pneumonia
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]
Celiac Disease
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]
Type 2 Diabetes Mellitus
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]
Cranial Nerve VII Palsy
A traumatic or pathologic injury to the femur in which the continuity of the femur is broken. [Definition Source: NCI]
Femur Fracture
Inflammation of the stomach. [Definition Source: NCI]
Gastritis
Increased pressure in the eyeball due to obstruction of the outflow of aqueous humor. [Definition Source: NCI]
Glaucoma
Abnormally low levels of thyroid hormone. [Definition Source: NCI][attribution: NICHD]
Hypothyroidism
Inflammation of the cornea. [Definition Source: NCI]
Keratitis
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]
Keratoconus
A laboratory test result indicating a decreased number of white blood cells in the peripheral blood. [Definition Source: NCI]
Leukopenia
An abnormally small number of lymphocytes in the circulating blood. [Definition Source: NCI]
Lymphopenia
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]
Parkinson's Disease
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]
Retinal Detachment
A non-neoplastic or neoplastic disorder that affects the thyroid gland. Representative examples include hyperthyroidism, hypothyroidism, thyroiditis, follicular adenoma, and carcinoma. [Definition Source: NCI]
Thyroid Gland Disorder
Inflammation of the thyroid gland. This category includes Hashimoto thyroiditis, Riedel thyroiditis, acute thyroiditis, subacute thyroiditis, and radiation-induced thyroiditis. [Definition Source: NCI]
Thyroiditis
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]
Vitiligo
Shivering secondary to a febrile process. [Definition Source: NCI]
Fever Chills
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]
Acute Cystitis
An increase in the level of alanine aminotransferase in the blood. [Definition Source: NCI]
Alanine Aminotransferase Increased
A non-neoplastic or neoplastic disorder affecting the trigeminal nerve (fifth cranial nerve). [Definition Source: NCI]
Trigeminal Nerve Disorder
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]
Ankle Fracture
Inflammation of interstitial lung tissue, usually associated with infection. [Definition Source: NCI]
Interstitial Pneumonia
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]
Acute Respiratory Failure
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]
Obstructive Sleep Apnea Syndrome
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]
Hashimoto Thyroiditis
Any disorder other than abnormal tissue growth resulting from uncontrolled cell proliferation affecting the nervous system.
Non-Neoplastic Central Nervous System Disorder
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 Grade Qualifier
An adjectival term that can specify or describe a disease stage. [Definition Source: NCIT]
Disease Stage Qualifier
Occlusion of the lumen of a vessel by a thrombus that has migrated from a distal site via the blood stream. [Definition Source: NCI]
Thromboembolism
A chronic respiratory disease manifested as difficulty breathing due to the narrowing of bronchial passageways. [Definition Source: NCI]
Asthma
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]
Adenocarcinoma
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]
Alzheimer's Disease
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]
Anemia
Loss of appetite. [Definition Source: NCI]
Anorexia
A category of psychiatric disorders which are characterized by anxious feelings or fear often accompanied by physical symptoms associated with anxiety. [Definition Source: NCI]
Anxiety Disorder
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]
Arrhythmia
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]
Arthritis
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]
Rheumatoid Arthritis
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]
Autoimmune Disease
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]
Psychiatric Disorder
Infection of the vulva and vagina with a fungus of the genus CANDIDA. It is a disease associated with HIV infection. [Definition Source: NCI]
Vulvovaginal Candidiasis
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]
Carcinoma
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]
Malignant Skin Neoplasm
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 Basal Cell Carcinoma
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]
Skin Basosquamous Cell Carcinoma
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]
Cardiovascular Disorder
A sac-like closed membranous structure that may be empty or contain fluid or amorphous material. [Definition Source: NCI]
Cyst
A melancholy feeling of sadness and despair. [Definition Source: NCI]
Depression
A metabolic disorder characterized by abnormally high blood sugar levels due to diminished production of insulin or insulin resistance/desensitization. [Definition Source: NCI]
Diabetes Mellitus
A chronic condition characterized by minimal or absent production of insulin by the pancreas. [Definition Source: NCI][attribution: NICHD]
Type 1 Diabtes Mellitus
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]
Mumps
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]
Disease or Disorder
A form of dermatitis characterized by red, itchy, scaly, or crusty patches that can be chronic or intermittent. [Definition Source: NCI][attribution: NICHD]
Eczema
The growth of functional endometrial tissue in anatomic sites outside the uterine body. It most often occurs in the pelvic organs. [Definition Source: NCI]
Endometriosis
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]
Seizure Disorder
A chronic condition characterised by recurrent generalised seizures. [Definition Source: NCI]
Generalized Epilepsy
A non-metastasizing neoplasm arising from the fibrous tissue. It is characterized by the presence of spindle-shaped fibroblasts. [Definition Source: NCI]
Fibroma
A hemangioma characterized by the presence of cavernous vascular spaces. [Definition Source: NCI]
Cavernous Hemangioma
Inflammation of the liver; usually from a viral infection, but sometimes from toxic agents. [Definition Source: NCI]
Hepatitis
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]
Hepatitis A Infection
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]
Langerhans Cell Histiocytosis
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]
Hypersensitivity
Blood pressure that is abnormally high. [Definition Source: NCI]
Hypertension
A severe, acute increase in blood pressure that may result in stroke or myocardial ischemia. [Definition Source: NCI]
Hypertensive Crisis
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]
Hyperthyroidism
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]
Epidermal Inclusion Cyst
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]
Multiple Sclerosis
An infection caused by a fungus. [Definition Source: NCI]
Fungal Infection
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]
Neoplasm
Having a high amount of body fat (body mass index [BMI] of 30 or more). [Definition Source: NCI]
Obesity
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]
Osteoporosis
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.
Pituitary Neuroendocrine Tumor
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]
Pleural Effusion
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]
Pneumonia
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]
Psoriasis
Clinical, laboratory or molecular evidence, or absence of evidence of disease. [Definition Source: NCI]
Finding
A sudden loss of neurological function secondary to hemorrhage or ischemia in the brain parenchyma due to a vascular event. [Definition Source: NCI]
Stroke
A parasitic disease contracted by the ingestion or fetal transmission of toxoplasma gondii. [Definition Source: NCI]
Toxoplasmosis
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]
Uterine Corpus Leiomyoma
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]
Congenital Adrenal Hyperplasia
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]
Amyotrophic Lateral Sclerosis
A congenital hemolytic anemia caused by defects of the erythrocyte membrane, enzyme deficiencies, or hemoglobinopathies. [Definition Source: NCI]
Hereditary Hemolytic Anemia
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]
Bipolar Disorder
A closed dislocation of the shoulder [Definition Source: NCI]
Closed Dislocation of Shoulder
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]
Common Bile Duct Stone
A condition associated with glucose-6-phosphate dehydrogenase deficiency, which is characterized by hemolysis. [Definition Source: NCI]
Favism
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]
Gastroenteritits
A traumatic injury to the head. [Definition Source: NCI]
Head Trauma
Pain in various parts of the head, not confined to the area of distribution of any nerve. [Definition Source: NCI]
Headache
The protrusion of part of an organ or fibroadipose tissue through an abnormal opening. [Definition Source: NCI]
Hernia
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.
Palmar Fibromatosis
The protrusion of a sac-like structure containing fibroadipose tissue through an abnormal opening in the inguinal region. [Definition Source: NCI]
Inguinal Hernia
A lesion caused by type 1 or type 2 herpes simplex virus, involving the oralfacial region. [Definition Source: NCI]
Cold Sore
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]
Infectious Mononucleosis
Ileus of the intestine in which there is no mechanical obstruction. [Definition Source: NCI]
Intestinal Pseudo-Obstruction
Inflammation of the iris and the ciliary body. [Definition Source: NCI]
Iridocyclitis
Hypertension that presents without an identifiable cause. [Definition Source: NCI]
Essential Hypertension
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]
Long QT Syndrome
A finding of low numbers of red and white blood cells and platelets in the peripheral blood. [Definition Source: NCI]
Pancytopenia
An allergy to Penicillin. [Definition Source: NCI]
Penicillin Allergy
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]
Personality Disorder
Inflammation of the lungs due to the inhalation of solid or liquid material. [Definition Source: NCI]
Aspiration Pneumonitis
Swelling and protrusion of the gastrocnemius-semimembranosus bursa due to an accumulation of synovial fluid. [Definition Source: NCI]
Baker Cyst
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]
Sarcoidosis
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]
Pulmonary Sarcoidosis
A dislocation of the shoulder joint. [Definition Source: NCI]
Shoulder Dislocation
An acute or chronic inflammatory process affecting the mucous membranes of any sinus cavity. [Definition Source: NCI]
Sinusitis
Infection by Staphylococcus. [Definition Source: NCI]
Staphylococcal Infection
A spontaneous loss of consciousness caused by insufficient blood supply to the brain. [Definition Source: NCI]
Syncope
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]
Thalassemia
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]
Cutaneous Melanoma
An inflammatory pathologic process that affects the vulva and the vagina. [Definition Source: NCI]
Vulvovaginitis
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]
Acute Myocardial Infarction
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]
Closed Fracture of Rib
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]
Tooth Abscess
An abnormal laboratory test result indicating the presence of monoclonal immunoglobulins in the blood or urine. [Definition Source: NCI]
Monoclonal Gammopathy
Symptoms, physical examination results, and/or laboratory test results related to the head and neck. [Definition Source: NCI]
Head and Neck Finding
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]
Injury
An abnormally slow heart rate. Thresholds for different age, gender, and patient populations exist. [Definition Source: NCI]
Bradycardia
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]
Vertigo
A cystic lesion located in the skin. [Definition Source: NCI]
Skin Cyst
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]
High Grade Cervical Squamous Intraepithelial Neoplasia
Unit by Category
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]
Myeloproliferative Neoplasm
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]
Colon Adenocarcinoma
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]
Dementia
A disorder of the central nervous system characterized by gradual and progressive loss of neural tissue and neurologic function. [Definition Source: NCI]
Central Nervous System Degenerative Disorder
Cancer TNM Finding Category
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]
Breast Carcinoma
Subjective evidence of disease perceived by the patient. [Definition Source: NCI]
Symptom
A carcinoma that arises from the skin. Representative examples are basal cell carcinoma and squamous cell carcinoma. [Definition Source: NCI]
Skin Carcinoma
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]
Deep Vein Thrombosis
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]
Atrial Fibrillation
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]
Diabetic Ketoacidosis
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]
Heart Failure
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]
Lumbar Puncture Headache
An abnormality that affects hearing within the first month after birth. It may or may not result in hearing loss. [Definition Source: NCI]
Neonatal Hearing Impairment
The obstruction of the pulmonary artery or one of its branches by an embolus, sometimes associated with infarction of the lung. [Definition Source: NCI]
Pulmonary Embolism
A brief attack (from a few minutes to an hour) of cerebral dysfunction of vascular origin, with no persistent neurological deficit. [Definition Source: NCI]
Transient Ischemic Attack
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]
Atrial Flutter
Objective evidence of disease perceptible to the examining healthcare provider. [Definition Source: NCI]
Sign
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]
Anorectal Fistula
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]
Myasthenia Gravis
Joint inflammation associated with psoriasis. [Definition Source: NCI]
Psoriatic Arthritis
The absence of menses in a woman who has achieved reproductive age. [Definition Source: NCI]
Amenorrhea
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]
Neurofibromatosis
Inflammation of a serous membrane. [Definition Source: NCI]
Serositis
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]
Neoplasm by Special Category
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]
Herpes Zoster
A primary or metastatic malignant neoplasm affecting the thyroid gland. [Definition Source: NCI]
Malignant Thyroid Gland Neoplasm
A neoplasm composed of melanocytes that usually appears as a dark spot on the skin. [Definition Source: NCI]
Melanocytic Nevus
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]
Flu-Like Symptoms
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]
Renal Colic
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]
Allergic Rhinitis
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]
Extrapyramidal Disorder
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]
Monoclonal B_Cell Lymphocytosis
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]
Dyslipidemia
Anemia caused by low iron intake, inefficient iron absorption in the gastrointestinal tract, or chronic blood loss. [Definition Source: NCI]
Iron-Deficiency Anemia
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]
Brown-Sequard Syndrome
A rare inherited bleeding disorder caused by deficiency of coagulation factor XI. It may be asymptomatic or manifest with bleeding. [Definition Source: NCI]
Hereditary Factor XI Deficiency
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]
Ann Arbor Stage IV Mantle Cell Lymphoma
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]
Optic Neuritis
A rare neurologic progressive disorder characterized by impairment of the language and speech abilities. [Definition Source: NCI]
Primary Progressive Aphasia
A tumor at the original site of origin. [Definition Source: NCI]
Primary Neoplasm
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]
Spinal and Bulbar Muscular Atrophy, X-linked 1
Ann Arbor Stage IV T-Cell Non-Hodgkin Lymphoma
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]
Fibromyalgia
A common, severe type of vascular headache often associated with increased sympathetic activity, resulting in nausea, vomiting, and light sensitivity. [Definition Source: NCI]
Migraine
Blockage of the normal flow of the intestinal contents within the bowel. [Definition Source: NCI]
Bowel Obstruction
A category of psychiatric disorders which have as their most predominant feature a disturbance in mood. [Definition Source: NCI]
Mood Disorder
A primary or metastatic malignant neoplasm that affects the colon. Representative examples include carcinoma, lymphoma, and sarcoma. [Definition Source: NCI]
Malignant Colon Neoplasm
The backward flow of stomach acid contents into the esophagus (the tube that connects the mouth to the stomach). [Definition Source: NCI]
Gastroesophageal Reflux
Physical and psychological dependence on alcohol. [Definition Source: NCI]
Alcohol Dependance
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]
Malignant Neoplasm
A streptococcal infection, mainly occurring among children, that is characterized by a red skin rash, sore throat, and fever. [Definition Source: NCI]
Scarlet Fever
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]
Chicken Pox
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]
Acute Tonsillitis
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]
Chronic Lung Disorder
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]
Klippel-Feil Syndrome
Traumatic or pathological injury to the radius bone in which the continuity of the bone is broken. [Definition Source: NCI]
Radius Fracture
Traumatic or pathological injury to the tibia in which the continuity of the bone is broken. [Definition Source: NCI]
Tibia Fracture
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]
Autoimmune Nervous System Disorder
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. [Definition Source: Ontology for Biomedical Investigations (OBI)]
DNA Sequencer
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]
Study Design
A quality inhering in a variant by virtue of its origin. [Definition Source: SO]
Variant Origin
A variant in the genetic material inherited from the mother. [Definition Source: Sequence Types and Features Ontology]
Maternal Variant
A variant in the genetic material inherited from the father. [Definition Source: Sequence Types and Features Ontology]
Paternal Variant
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]
Somatic Variant
A variant present in the embryo that is carried by every cell in the body. [Definition Source: Sequence Types and Features Ontology]
Germline Variant
A variant that is found only by individuals that belong to the same pedigree. [Definition Source: Sequence Types and Features Ontology]
Pedigree Specific Variant
A variant found within only speficic populations. [Definition Source: Sequence Types and Features Ontology]
Population Specific Variant
A variant arising in the offspring that is not found in either of the parents. [Definition Source: Sequence Types and Features Ontology]
De-Novo Variant
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]
Case Control Design
Process which results in the separation of a biological specimen into individual cells or a cell suspension. [Definition Source: EFO]
Sample Dissociation
A material sample derived from cells or tissue representing a physiologically or phenotypically normal state. [Definition Source: The Experimental Factor Ontology]
Reference Sample
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]
Abnormal Sample
A material sample derived from neoplastic cells or tissue. [Definition Source: The Experimental Factor Ontology]
Neoplastic Sample
A neoplastic sample derived from a cancer metastasis (not from a primary tumor). [Definition Source: The Experimental Factor Ontology]
Metastasis Sample
A neoplastic sample derived from a primary tumor (not from a cancer metastasis). [Definition Source: The Experimental Factor Ontology]
Primary Tumor Sample
A neoplastic sample derived from a recurrent tumor (not from a primary occurrence of a neoplasm). [Definition Source: The Experimental Factor Ontology]
Recurrent Tumor Sample
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)]
High-Level Copy Number Loss
A neoplastic sample derived from a cancer cell line. [Definition Source: The Experimental Factor Ontology]
Cancer Cell Line Sample
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]
Copy number assessment of regional base ploidy. [Definition Source: The Experimental Factor Ontology (EFO)]
Regional Base Ploidy
Assessment of genomic copy number loss.
Copy Number Loss
Assessment of low-level genomic copy number loss. [Definition Source: The Experimental Factor ontology (EFO)]
Low-Level Copy Number Loss
Assessment of complete genomic deletion. [Definition Source: The Experimental Factor Ontology (EFO)]
Complete Genomic Deletion
Assessment of genomic copy number gain. [Definition Source: The Experimental Factor ontology (EFO)]
Copy Number Gain
Assessment of low-level genomic copy number gain. [Definition Source: The Experimental Factor Ontology (EFO)]
Low-Level Copy Number Gain
Assessment of high-level genomic copy number gain. [Definition Source: The Experimental Factor Ontology (EFO)]
High-Level Copy Number Gain
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]
Missense Variant
A UTR variant of the 5' UTR. [Definition Source: The Sequence Ontology]
5 Prime UTR Variant
A stop_gained (SO:0001587) variant that allows the transcript to escape nonsense-mediated decay (NMD). [Definition Source: The Sequence Ontology]
Stop Gained NMD Escaping
A deviation from normal morphology, physiology, or behavior, and good phenotyping is a cornerstone of a doctor's daily work. [PMID: 25109851]
Phenotypic Abnormality
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]
Clinical Modifier
The intensity or degree of a manifestation. [Definition Source: HP]
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)]
Mild
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)]
Moderate
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)]
Borderline
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)]
Severe
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)]
Profound
Laura Menotti
Gianmaria Silvello
Diminished psychological function.
Behavioral Impairment
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]
Allele Origin Taxonomy
This taxonomy describes the assay used to produce the measurement. [Definition Source: Phenopacket v2]
Assay Taxonomy
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).
Biosample Status Taxonomy
Cohort Data Type Taxonomy
Cohort Design Taxonomy
Cohort Sex Taxonomy
Copy Number Assessment Taxonomy
This taxonomy describes clinically relevant biomarkers.
Diagnostic Marker Taxonomy
Disease Stage Taxonomy
Genomic Feature Class Taxonomy
Geographic Location Taxonomy
This taxonomy describes the source of the sequencing or hybridization library. [Definition Source: GA4GH Beacon v2 Data Model]. The taxonomy is based on GENEPIO.
Library Source Taxonomy
Molecular Effect Taxonomy
This taxonomy describes the obtention procedures to retrieve a biosample or a measurement.
Obtention Procedure Taxonomy
Pathological Stage Taxonomy
Pathological TNM Finding Taxonomy
This taxonomy comprises the type of disease, condition, phenotypic measurement, etc. The taxonomy is mainly based on MONDO on Human Phenotype Ontology (HP)
Phenoclinic Category Taxonomy
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]
Phenoclinic Evidence Taxonomy
Phenotypic Feature Modifier Taxonomy
Phenotypic Feature Type Taxonomy
This taxonomy describes the experimental platform or methodology used. For sequencing platforms the use of "OBI:0400103 - DNA sequencer" is suggested.
Platform Model Taxonomy
Sample Origin Taxonomy
Sample Origin Type Taxonomy
Sample Processing Taxonomy
SKOS Concept Hierarchy describing the severity level. Values from HP Ontology.
Severity Taxonomy
Species Taxonomy
Tumor Grade Taxonomy
Tumor Progression Taxonomy
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]
Unit of Measure Taxonomy
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]
Zygosity Taxonomy
This taxonomy comprises disease, disorder or findings. The taxonomy is mainly based on NCIT.
Disease, Disorder or Finding Taxonomy
This taxonomy describes the different ethinic groups. The taxonomy is based on SNOMED-CT.
Group Taxonomy
NCBI Taxonomy ID: 9606
Human