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The Hereditary Ontology for Genomics Data

This version:
https://w3id.org/hereditary/ontology/genomics/
Latest version:
https://w3id.org/hereditary/ontology/genomics/
Ontology Version IRI:
https://w3id.org/hereditary/ontology/genomics/1.0/
Revision:
1.0
Authors:
Laura Menotti
Gianmaria Silvello
Download serialization:
RDF/XML TTL
License:
https://creativecommons.org/licenses/by-sa/4.0/
Cite as:
Laura Menotti, Gianmaria Silvello. The Hereditary Ontology for Genomics Data. Revision: 1.0. Retrieved from: https://w3id.org/hereditary/ontology/genomics/schema/1.0/
Ontology Specification Draft

Introduction back to ToC

The Genomic Data Modeling of the Hereditary Ontology (HERO) represents genomics data for ALS and MS patients. HERO-Clinical allows to store whether a patient’s genome presents specific gene mutations linked to ALS or MS, however, there is no representation for genetic testing and storing gene sequencing variations, e.g. Single Nucleotide Polymorphisms (SNPs).

Figure 1 reports the complete schema of the Genomic Data Modeling. The Genomic Data Modeling in the HEREDITARY ontology follows the Beacon Data Model, employing the “Genomic Variation" component as the core class of the ontology. HERO-Genomics allows the storage of genetic variations, e.g. SNVs, insertions, deletions, and structural variants, alongside with their annotations, modeled with the “Case Level Variant" class. HERO-Genomics provides a direct mapping from VCFs files, or Beacon, to Resource Description Framework (RDF) format, thanks to classes “VCF Record", “VCF File", and “Variant Quality". It is possible to link HERO-Clinical to HERO-Genomics thanks to the shared “Patient" class. In addition, HERO-Genomics comprises the class “Disease, Disorder or Finding" defined in HERO-Clinical.

HEREDIATRY Ontology for Genomic Data
Figure 1. The Genomic Data Modeling in HERO-Genomic. The ontology rely on Beacon v2 Data Model, with the addition of a few classes (highlighted in green).

Namespace declarations

Table 1: Namespaces used in the document
[Ontology NS Prefix]<https://w3id.org/hereditary/ontology/genomics/schema/>
bto<https://w3id.org/brainteaser/ontology/schema/>
contact<http://www.w3.org/2000/10/swap/pim/contact#>
dc<http://purl.org/dc/elements/1.1/>
efo<http://www.ebi.ac.uk/efo/>
foaf<http://xmlns.com/foaf/0.1/>
obo<http://purl.obolibrary.org/obo/>
orcid<https://orcid.org/0000-0002-0676-682>
owl<http://www.w3.org/2002/07/owl#>
rdf<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
rdfs<http://www.w3.org/2000/01/rdf-schema#>
skos<http://www.w3.org/2004/02/skos/core#>
terms<http://purl.org/dc/terms/>
xml<http://www.w3.org/XML/1998/namespace>
xsd<http://www.w3.org/2001/XMLSchema#>

Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

Named Individuals

The Hereditary Ontology for Genomic Data: Description back to ToC

Domain requirements

In the context of the HEREDITARY project, genetic information is collected in VCF files comprising SNPs. A SNP is a one-letter place where an individual’s genome varies with respect to another sequence, usually called “Reference Genome". SNPs are SNVs present in a sufficiently large fraction, e.g. at least 1%, of a specific population.VCF is a text format widely used for storing genetic variations, such as Single Nucleotide Variants (SNVs), insertions, deletions, and structural variants, together with rich annotations [Danecek et al., 2011]. The format was developed for the 1000 Genome Project 7 and has been adopted in several other projects, e.g. dbSNP 8. Each VCF file comprises a header and a body. The former provides metadata describing the body of the file and keywords that optionally describe the fields used in the body. The latter is tap-separated and comprises 8 mandatory columns and an unlimited number of optional columns that may record additional information about the sample. When optional columns are used, the first of these columns describes the format of the additional columns. The mandatory columns are:

  • CHROM, the name of the sequence, typically a chromosome, on which the variation is being called;
  • POS, the one-based position of the variation;
  • ID, the identifier of the variation, e.g. dbSNP rs identifier;
  • REF, the reference base;
  • ALT, the alternative allele;
  • QUAL, the quality score associated with the inference of the given allele;
  • FILTER, the flag indicating which filters have failed or PASS if all filters were successfully passed;
  • INFO, the description of the variation. This column is highly variable and its content can vary across VCFs;
  • FORMAT, an optional list of fields for describing the samples;
  • SAMPLEs, optional values describing the samples.

The HEREDITARY ontology will answer the Beacon genomic queries provided and other queries of inter- est to the genomics community. The Beacon queries comprise:

  • Sequence Queries for the existence of a specified sequence at a given genomic position;
  • Range Queries for matching variants at least overlapping with a specified region;
  • GeneId Queries for returning variants affecting a gene’s coding region;
  • Bracket Queries for matching variants falling in a start range and end range;
  • Genomic Allele Queries for matching variants with the specified allele;
  • Amino Acid Change Queries for matching variants with the specified amino acid change.

Ontology Schema

Figure 2 reports the schema of genomic variations and VCF files. HERO- Genomics records systemic variations, e.g. Copy Number Change, molecular variations, and legacy varia- tions, e.g. SNPs. For each variation, one can store the VCF row with class “VCF Record" and link it to the corresponding file with class “VCF File". VCF annotations such as molecular effects and amino acid changes are represented by the class “Molecular Attribute". Class “Case Level Data" stores information about the ob- served zygosity, a SKOS taxonomy from the Gene Ontology, phenotypic effects, and clinical interpretations. In addition, the class links the genomic variation to the corresponding biosample (“Biosample"), run (“Run"), analysis (“Analysis"), and patient (“Patient" from HERO-Clinical). The location of the variation can stored by means of the class “Location", which provides a representation both for sequence location, to specify the sequence interval and reference genome, and chromosome location, to specify the cytoband interval of the chromosome where the variation occurs.
Genomic Variation
Figure 2.. Genomic Variation Modeling in HERO-Genomics. HERO-Genomics records systemic variations, e.g. Copy Number Change, molecular variations, and legacy variations, e.g. SNPs. For each variation, one can store the corresponding VCF row and store additional annotations with classes “Molecular Attribute", “Case Level Variant", and “Variant Level Data". Classes in blue represent components from the Beacon Data Model, those in green were added to satisfy HEREDITARY’s data requirements, and those in purple are classes that represent a SKOS taxonomy.

Cross-reference for classes, object properties and data properties back to ToC

This section provides details for each class and property defined by The Hereditary Ontology for Genomic Data.

Classes

Agec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Age

Age value definition. [Definition Source: GA4GH Beacon v2 Data Model]
is equivalent to
iso8601duration dp min 1
has super-classes
Time Element c
is in domain of
iso8601duration dp
is in range of
ageRangeEnd op, ageRangeStart op

Age Rangec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/AgeRange

Age range definition. [Definition Source: Ga4GH Beacon v2 Data Model]
is equivalent to
ageRangeEnd op min 1 Age c
ageRangeStart op min 1 Age c
has super-classes
Time Element c
is in domain of
ageRangeEnd op, ageRangeStart op
is in range of
cohortAgeRange op

Age Range Data Availability and Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/AgeRangeDAD

Individual age range, obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
is equivalent to
distribution op some Age Range Element Distribution c
has super-classes
Data Availability and Distribution c

Age Range Element Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/AgeRangeElementDistribution

Results or counts for each category. [Definition Source: GA4GH Beacon v2 Data Model]
is equivalent to
elementType op some Age Range c
has super-classes
Element Distribution c

Allelec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Allele

The state of a molecule at a Location. [Definition Source: Ga4GH Variation Representation Specification (VRS) v1.2]
is in domain of
sequenceState op
is in range of
haplotypeMember op

Allele Originc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/AlleleOrigin

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]
is in range of
alleleOrigin op
has members
De-Novo Variant ni, Germline Variant ni, Maternal Variant ni, Paternal Variant ni, Pedigree Specific Variant ni, Population Specific Variant ni, Somatic Variant ni, Variant Origin ni

Analysisc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Analysis

A sequencing bioinformatics analysis. [Definition Source: GA4GH Beacon v2 Data Model]
is equivalent to
analysisDate dp min 1
analysisPipelineName dp min 1
is in domain of
analysisAligner dp, analysisDate dp, analysisPipelineName dp, analysisPipelineRef dp, variantCaller dp
is in range of
analysis op

Assayc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Assay

The assay used to produce the measurement. [Definition Source: Phenopacket v2]
is in range of
assay op

Biosamplec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Biosample

A biosample entry. [Definition Source: GA4GH Beacon v2 Data Model]
is equivalent to
biosampleStatus op min 1 Biosample Status c
sampleOriginType op min 1 Sample Origin Type c
is in domain of
biosampleCollectionDate dp, biosampleCollectionMoment dp, biosampleStatus op, diagnosticMarker op, histologicalDiagnosis op, measurement op, pathologicalStage op, pathologicalTNMFinding op, phenotypicFeature op, sampleOriginDetail op, sampleOriginType op, sampleProcessing op, sampleStorage dp, tumorGrade op, tumorProgression op
is in range of
biosample op

Biosample Statusc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/BiosampleStatus

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).
is in range of
biosampleStatus op
has members
Abnormal Sample ni, Cancer Cell Line Sample ni, Case Control Design ni, Metastasis Sample ni, Neoplastic Sample ni, Primary Tumor Sample ni, Recurrent Tumor Sample ni, Reference Sample ni

Case Level Variantc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/CaseLevelVariant

Reports about the variation instances observed in individual analyses. [Definition Source: GA4GH Beacon v2 Data Model]
is equivalent to
biosample op min 1 Biosample c
is in domain of
alleleOrigin op, analysis op, zygosity op
is in range of
caseLevelData op

Chromosome Locationc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/ChromosomeLocation

A Location on a chromosome defined by a species and chromosome name. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
is equivalent to
chromosomeSpecies op exactly 1 Species c
cytobandInterval op exactly 1 Cytoband Interval c
locationChr dp exactly 1
has super-classes
Location c
is in domain of
chromosomeSpecies op, cytobandInterval op, locationChr dp

Cohortc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Cohort

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)]
is equivalent to
cohortName dp exactly 1
cohortType dp exactly 1
is in domain of
cohortDataType op, cohortDesign op, cohortName dp, cohortSize dp, cohortType dp, collectionEvent op, exclusionCriteria op, inclusionCriteria op
is in range of
inCohort op, refersToCohort op

Cohort Criteriac back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/CohortCriteria

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]
is in domain of
cohortAgeRange op, cohortDisease op, cohortEthnicity op, cohortLocation op, cohortSex op, phenotypicCondition op
is in range of
exclusionCriteria op, inclusionCriteria op

Cohort Data Typec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/CohortDataType

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]
is in range of
cohortDataType op

Cohort Designc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/CohortDesign

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]
is in range of
cohortDesign op
has members
Study Design ni

Cohort Diseasec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/CohortDisease

Diseases in cohort inclusion criteria. [Definition Source: Beacon v2 Data Model]
is in domain of
diseaseAgeOnset op, diseaseCode op, diseaseStage op, familyHistory dp
is in range of
cohortDisease op

Cohort Sexc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/CohortSex

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]
is in range of
cohortSex op
has members
Female ni, Male ni, Unknown ni

Collection Eventc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/CollectionEvent

Aggregated information of cohort data collection obtained from individual level info of the cohort members.
is in domain of
eventCases dp, eventControls dp, eventDate dp, eventDistribution op, eventSize dp, eventTimeline op
is in range of
collectionEvent op

Composed Sequence Expressionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/ComposedSequenceExpression

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]
has super-classes
Sequence Expression c, seq c
is in domain of
sequenceComponent op

Copy Number Assessmentc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/CopyNumberAssessment

SKOS Concept hierarchy describing the type of copy number change allowed.
Is defined by
http://www.ebi.ac.uk/efo/EFO_0030063
is in range of
variationCopyChange op
has members
Complete Genomic Deletion ni, Copy Number Assessment ni, Copy Number Gain ni, Copy Number Loss ni, High-Level Copy Number Gain ni, High-Level Copy Number Loss ni, Low-Level Copy Number Gain ni, Low-Level Copy Number Loss ni, Regional Base Ploidy ni

Copy Number Changec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/CopyNumberChange

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]
is equivalent to
location op exactly 1 Location c
variationCopyChange op exactly 1 Copy Number Assessment c
is in domain of
variationCopyChange op

Copy Number Countc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/CopyNumberCount

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]
is equivalent to
location op exactly 1 Location c
variationCopies dp exactly 1
is in domain of
variationCopies dp

Cytoband Intervalc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/CytobandInterval

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]
is equivalent to
cytobandEnd dp exactly 1
cytobandStart dp exactly 1
is in domain of
cytobandEnd dp, cytobandStart dp
is in range of
cytobandInterval op

Data Availability and Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/DataAvailabilityAndDistribution

Aggregated information obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
is equivalent to
availability dp exactly 1
has sub-classes
Age Range Data Availability and Distribution c, Data Type Data Availability and Distribution c, Disease Data Availability and Distribution c, Ethnicity Data Availability and Distribution c, Location Data Availability and Distribution c, Phenotype Data Availability and Distribution c, Sex Data Availability and Distribution c
is in domain of
availability dp, availabilityCount dp, distribution op
is in range of
eventDistribution op

Data Type Data Availability and Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/DataTypeDAD

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]
is equivalent to
distribution op some Data Type Element Distribution c
has super-classes
Data Availability and Distribution c

Data Type Element Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/DataTypeElementDistribution

Results or counts for each data type category. [Definition Source: GA4GH Beacon v2 Data Model]
is equivalent to
elementType op some Cohort Data Type c
has super-classes
Element Distribution c

Derived Sequence Expressionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/DerivedSequenceExpression

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]
is equivalent to
sequenceLocation op exactly 1 Sequence Location c
reverseComplement dp exactly 1
has super-classes
Sequence Expression c
is in domain of
reverseComplement dp, sequenceLocation op

Diagnostic Markerc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/DiagnosticMarker

Clinically relevant biomarkers. RECOMMENDED. [Definition Source: GA4GH Beacon v2 Data Model]
is in range of
diagnosticMarker op

Disease Data Availability and Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/DiseaseDAD

Aggregated information of disease/condition(s) obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
is equivalent to
distribution op some Disease Element Distribution c
has super-classes
Data Availability and Distribution c

Disease Element Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/DiseaseElementDistribution

Results or counts for each disease category. [Definition Source: GA4GH Beacon v2 Data Model]
is equivalent to
elementType op some Cohort Disease c
has super-classes
Element Distribution c

Disease Stagec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/DiseaseStage

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]
is in range of
diseaseStage op

Disease, Disorder or Findingc back to ToC or Class ToC

IRI: https://w3id.org/brainteaser/ontology/schema/DiseaseDisorderOrFinding

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]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C7057
has members
Abdominal Pain ni, Acquired Hypothyroidism ni, Acute Cystitis ni, Acute Myocardial Infarction ni, Acute Pyelonephritis ni, Acute Respiratory Failure ni, Acute Tonsillitis ni, Adenocarcinoma ni, Alanine Aminotransferase Increased ni, Alcohol Dependance ni, Allergic Asthma ni, Allergic Rhinitis ni, Alzheimer's Disease ni, Amenorrhea ni, Amenorrhea due to Pituitary Dysfunction ni, Amyotrophic Lateral Sclerosis ni, Anemia ni, Angioedema ni, Ankle Fracture ni, Ann Arbor Stage IV Mantle Cell Lymphoma ni, Ann Arbor Stage IV T-Cell Non-Hodgkin Lymphoma ni, Anorectal Fistula ni, Anorexia ni, Anosmia ni, Anxiety Disorder ni, Arrhythmia ni, Arthritis ni, Aspiration Pneumonitis ni, Asthma ni, Atopic Dermatitis ni, Atrial Fibrillation ni, Atrial Flutter ni, Autoimmune Disease ni, Autoimmune Nervous System Disorder ni, Autoimmune Pancytopenia ni, Bacterial Pneumonia ni, Baker Cyst ni, Basal Cell Carcinoma ni, Behavioral Impairment ni, Bell's Palsy ni, Bipolar Disorder ni, Blepharitits ni, Blepharospasm ni, Bowel Obstruction ni, Bradycardia ni, Breast Carcinoma ni, Brown-Sequard Syndrome ni, COVID-19 Infection ni, Carcinoma ni, Cardiovascular Disorder ni, Cavernous Hemangioma ni, Celiac Disease ni, Central Nervous System Degenerative Disorder ni, Chicken Pox ni, Chronic Lung Disorder ni, Closed Dislocation of Shoulder ni, Closed Fracture of Rib ni, Closed Fracture of Tibia ni, Cognitive Impariment ni, Cold Sore ni, Colon Adenocarcinoma ni, Common Bile Duct Stone ni, Congenital Adrenal Hyperplasia ni, Cranial Nerve VII Palsy ni, Cutaneous Melanoma ni, Cyst ni, Deep Vein Thrombosis ni, Dementia ni, Depression ni, Diabetes Mellitus ni, Diabetic Ketoacidosis ni, Disease or Disorder ni, Dog Bite ni, Drug Hypersensitivity Syndrome ni, Dyslipidemia ni, Eczema ni, Endometriosis ni, Epidermal Inclusion Cyst ni, Essential Hypertension ni, Extrapyramidal Disorder ni, Favism ni, Femur Fracture ni, Fever Chills ni, Fibroma ni, Fibromyalgia ni, Finding ni, Flu-Like Symptoms ni, Fungal Infection ni, Gastritis ni, Gastroenteritits ni, Gastroesophageal Reflux ni, Generalized Epilepsy ni, Glaucoma ni, Hashimoto Thyroiditis ni, Head Trauma ni, Head and Neck Finding ni, Headache ni, Heart Failure ni, Hepatic Toxicity ni, Hepatitis ni, Hepatitis A Infection ni, Hereditary Factor XI Deficiency ni, Hereditary Hemolytic Anemia ni, Hernia ni, Herpes Simplex Keratitis ni, Herpes Simplex Virus Infection ni, Herpes Zoster ni, High Grade Cervical Squamous Intraepithelial Neoplasia ni, Hypersensitivity ni, Hypertension ni, Hypertensive Crisis ni, Hyperthyroidism ni, Hypothyroidism ni, Infectious Mononucleosis ni, Inguinal Hernia ni, Injury ni, Interstitial Pneumonia ni, Intestinal Pseudo-Obstruction ni, Iridocyclitis ni, Iron-Deficiency Anemia ni, Keratitis ni, Keratoconus ni, Klippel-Feil Syndrome ni, Langerhans Cell Histiocytosis ni, Leukopenia ni, Long QT Syndrome ni, Lumbar Hernia ni, Lumbar Puncture Headache ni, Lymphopenia ni, Malignant Colon Neoplasm ni, Malignant Neoplasm ni, Malignant Skin Neoplasm ni, Malignant Thyroid Gland Neoplasm ni, Melanocytic Nevus ni, Migraine ni, Migraine With Aura ni, Molluscum Contagiosum Virus ni, Monoclonal B_Cell Lymphocytosis ni, Monoclonal Gammopathy ni, Mood Disorder ni, Motor Neuron Disease ni, Multiple Sclerosis ni, Mumps ni, Myasthenia Gravis ni, Myeloproliferative Neoplasm ni, Neck Trauma ni, Neonatal Hearing Impairment ni, Neoplasm ni, Neurofibromatosis ni, Neutropenic Disorder ni, Non-Neoplastic Central Nervous System Disorder ni, Obesity ni, Obstructive Sleep Apnea Syndrome ni, Opioid Use Disorder ni, Optic Neuritis ni, Osteoporosis ni, Palmar Fibromatosis ni, Pancytopenia ni, Parkinson's Disease ni, Penicillin Allergy ni, Personality Disorder ni, Pituitary Neuroendocrine Tumor ni, Pleural Effusion ni, Pneumococcal Pneumonia ni, Pneumonia ni, Pneumonia Caused By SARS-CoV-2 ni, Post-Herpetic Neuralgia ni, Primary Neoplasm ni, Primary Progressive Aphasia ni, Psoriasis ni, Psoriatic Arthritis ni, Psychiatric Disorder ni, Pulmonary Embolism ni, Pulmonary Sarcoidosis ni, Pulmonary Thromboembolism ni, Radius Fracture ni, Renal Colic ni, Retinal Detachment ni, Rheumatoid Arthritis ni, Sarcoidosis ni, Scarlet Fever ni, Seizure Disorder ni, Serositis ni, Shoulder Dislocation ni, Sign ni, Sign or Symptom ni, Sinusitis ni, Skin Basal Cell Carcinoma ni, Skin Basosquamous Cell Carcinoma ni, Skin Carcinoma ni, Skin Cyst ni, Spina Bifida ni, Spinal and Bulbar Muscular Atrophy, X-linked 1 ni, Staphylococcal Infection ni, Stroke ni, Subdural Hematoma ni, Symptom ni, Syncope ni, Thalassemia ni, Thoracic Trauma ni, Thromboembolism ni, Thyroid Gland Disorder ni, Thyroiditis ni, Tibia Fracture ni, Tinea Versicolor ni, Tooth Abscess ni, Toxoplasmosis ni, Transient Ischemic Attack ni, Trigeminal Nerve Disorder ni, Two Vessel Coronary Disease ni, Type 1 Diabtes Mellitus ni, Type 2 Diabetes Mellitus ni, Ureteral Stenosis ni, Uterine Corpus Leiomyoma ni, Vertigo ni, Viral Pericarditis ni, Vitiligo ni, Vulvovaginal Candidiasis ni, Vulvovaginitis ni

Element Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/ElementDistribution

Results or counts for each category. [Definition Source: GA4GH Beacon v2 Data Model]
has sub-classes
Age Range Element Distribution c, Data Type Element Distribution c, Disease Element Distribution c, Ethnicity Element Distribution c, Location Element Distribution c, Phenotype Element Distribution c, Sex Element Distribution c
is in domain of
elementDistribution dp, elementType op
is in range of
distribution op

Ethnicity Data Availability and Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/EthnicityDAD

Aggregated information of ethnicity obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
is equivalent to
distribution op some Ethnicity Element Distribution c
has super-classes
Data Availability and Distribution c

Ethnicity Element Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/EthnicityElementDistribution

Results or counts for each ethnicity category. [Definition Source: GA4GH Beacon v2 Data Model]
has super-classes
Element Distribution c

Event Timelinec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/EventTimeline

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]
is in domain of
earliestEvent dp, latestEvent dp
is in range of
eventTimeline op

Frequency In Populationc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/FrequencyInPopulation

Reports frequency information of the considered genomic variation.
is equivalent to
frequency op min 1 Population Frequency c
source dp min 1
sourceReference dp min 1
is in domain of
frequency op, source dp, sourceReference dp, sourceVersion dp
is in range of
frequencyInPopulation op

Genomic Featurec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/GenomicFeature

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]
is in domain of
genomicFeatureClass op
is in range of
genomicFeature op

Genomic Feature Classc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/GenomicFeatureClass

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`
is equivalent to
genomicFeatureClass op min 1 Genomic Feature Class c
is in range of
genomicFeatureClass op
has members
5 Prime UTR Variant ni

Genomic Variationc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/GenomicVariation

A genomic variant entry. [Definition Source: GA4GH Beacon v2 Data Model]
is equivalent to
variantInternalID dp min 1
has sub-classes
Legacy Variation c, Molecular Variation c, Systemic Variation c
is in domain of
caseLevelData op, clinvarVariantID dp, frequencyInPopulation op, genomicHGVSID dp, molecularAttribute op, proteinHGVSID dp, transcriptHGVSID dp, variantAlternativeID op, variantInternalID dp, variantLevelData op, variantQuality op, vcfRecord op

Genotypec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Genotype

A quantified set of Molecular Variation associated with a genomic locus. [Defintion Source: GA4GH Variation Representation Specification (VRS) v1.2]
is equivalent to
genotypeMember op min 1 Genotype Member c
molecularVariationCount dp exactly 1
is in domain of
genotypeMember op, molecularVariationCount dp

Genotype Memberc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/GenotypeMember

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]
is equivalent to
genotypeVariation op exactly 1 Molecular Variation c
genotypeCount dp exactly 1
is in domain of
genotypeCount dp, genotypeVariation op
is in range of
genotypeMember op

Geographic Locationc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/GeographicLocation

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]
Is defined by
http://purl.obolibrary.org/obo/GAZ_00000448
is in range of
cohortLocation op

Gestational Agec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/GestationalAge

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]
is equivalent to
gestationalWeeks dp min 1
has super-classes
Time Element c
is in domain of
gestationalDays dp, gestationalWeeks dp

Group (social concept)c back to ToC or Class ToC

IRI: https://w3id.org/brainteaser/ontology/schema/Group

A group of individuals united by a common factor (e.g., geographic location, ethnicity, disease, age, gender) [Definition Source: NCI]
Is defined by
http://purl.bioontology.org/ontology/SNOMEDCT/389109008
has members
Asian (ethnic group) ni, Black (ethnic group) ni, Caucasian ni, Ethnic Group ni, Hispanic ni

Haplotypec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Haplotype

A set of non-overlapping Allele members that co-occur on the same molecule. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
is equivalent to
haplotypeMember op min 2 Allele c
is in domain of
haplotypeMember op

Legacy Variationc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/LegacyVariation

Other genomic variations.
is equivalent to
location op min 1 Location c
alternateBases dp min 1
variantType dp min 1
has super-classes
Genomic Variation c
is in domain of
alternateBases dp, referenceBases dp, variantType dp

Library Sourcec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/LibrarySource

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)]
Is defined by
http://purl.obolibrary.org/obo/GENEPIO_0001965
is in range of
librarySource op
has members
Genomic Source ni, Library Source ni, Metagenomic Source ni, Metatranscriptomic Source ni, Other Library Source ni, Synthetic Source ni, Transcriptomic Source ni, Viral RNA Source ni

Literal Sequence Expressionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/LiteralSequenceExpression

An explicit expression of a Sequence. [Defintion Source: GA4GH Variation Representation Specification (VRS) v1.2]
is equivalent to
sequence dp exactly 1
has super-classes
Sequence Expression c
is in domain of
sequence dp

Locationc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Location

A contiguous segment of a biological sequence. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
has sub-classes
Chromosome Location c, Sequence Location c
is in range of
location op

Location Data Availability and Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/LocationDAD

Aggregated information of geographic location obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
is equivalent to
distribution op some Location Element Distribution c
has super-classes
Data Availability and Distribution c

Location Element Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/LocationElementDistribution

Results or counts for each location category. [Definition Source: GA4GH Beacon v2 Data Model]
is equivalent to
elementType op some Geographic Location c
has super-classes
Element Distribution c

Measurementc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Measurement

Definition of a measurement class. Provenance: GA4GH Phenopackets v2 `Measurement`. [Definition Source: GA4GH Beacon v2 Data Model]
is equivalent to
assay op min 1 Assay c
measurementValue dp min 1
is in domain of
assay op, measurementDate dp, measurementMoment op, measurementRefRangeHigh dp, measurementRefRangeLow dp, measurementUOM op, measurementValue dp
is in range of
measurement op

Molecular Attributec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/MolecularAttribute

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.
is in domain of
aminoacidChange dp, geneID dp, genomicFeature op, molecularEffect op
is in range of
molecularAttribute op

Molecular Effectc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/MolecularEffect

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`.
is in range of
molecularEffect op
has members
Missense Variant ni, Stop Gained NMD Escaping ni

Molecular Variationc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/MolecularVariation

A Variation on a contiguous molecule. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
has super-classes
Genomic Variation c
is in domain of
molecularVariationType op
is in range of
genotypeVariation op

Obtention Procedurec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/ObtentionProcedure

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]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C25218
is in range of
obtentionProcedure op

Pathological Stagec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/PathologicalStage

Pathological stage, if applicable, preferably as subclass of NCIT:C28108 - Disease Stage Qualifier. [Definition Source: GA4GH Beacon v2 Data Model]
is in range of
pathologicalStage op
has members
Disease Stage Qualifier ni

Pathological TNM Findingc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/PathologicalTNMFinding

Pathological TNM findings, if applicable, preferably as subclass of Cancer TNM Finding Category (NCIT:C48698). [Definition Source: GA4GH Beacon v2 Data Model]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C48698
is in range of
pathologicalTNMFinding op
has members
Cancer TNM Finding Category ni

Patientc back to ToC or Class ToC

IRI: https://w3id.org/brainteaser/ontology/schema/Patient

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]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C16960
has super-classes
Person c
is in domain of
inCohort op

Personc back to ToC or Class ToC

IRI: http://www.w3.org/2000/10/swap/pim/contact#Person

A human being. [Definition Source: NCI]
has sub-classes
Patient c
is in range of
individual op
has members
Gianmaria Silvello ni, Laura Menotti ni

PhenoClinic Categoryc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/PhenoClinicCategory

SKOS Concept Hierarchy comprising the type of disease, condition, phenotypic measurement, etc.
is in range of
category op
has members
Disease or Disorder (MONDO) ni, Phenotypic Abnormality ni

PhenoClinic Effectc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/PhenoClinicEffect

Annotated effects on disease or phenotypes. [Definition Source: GA4GH Beacon v2 Data Model]
is in domain of
annotatedWith op, category op, clinicalRelevance dp, effect op, evidence op
is in range of
clinicalInterpretation op, phenotypicEffect op

PhenoClinic Evidencec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/PhenoClinicEvidence

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]
is in range of
evidence op
has members
Experimental Evidence ni, Inferential Evidence ni

Phenotype Data Availability and Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/PhenotypeDAD

Aggregated information of phenotype(s) obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
is equivalent to
distribution op some Phenotype Element Distribution c
has super-classes
Data Availability and Distribution c

Phenotype Element Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/PhenotypeElementDistribution

Results or counts for each phenotype category. [Definition Source: GA4GH Beacon v2 Data Model]
is equivalent to
elementType op some Phenotypic Feature c
has super-classes
Element Distribution c

Phenotypic Featurec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/PhenotypicFeature

Describes a phenotype that characterizes the subject or biosample. [Definition Source: GA4GH Beaocn v2 Data Model]
is equivalent to
featureType op exactly 1 Phenotypic Feature Type c
is in domain of
featureExcluded dp, featureModifier op, featureOnset op, featureResolution op, featureType op
is in range of
phenotypicCondition op, phenotypicFeature op

Phenotypic Feature Modifierc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/PhenotypicFeatureModifier

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]
is in range of
featureModifier op
has members
Clinical Modifier ni

Phenotypic Feature Typec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/PhenotypicFeatureType

SKOS Concept hierarchy denoting the phenotypic feature, preferably using a value from Human Phenotype Ontology (HPO). [Definition Source: Beacon v2 Data Model]
is in range of
featureType op

Platform Modelc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/PlatformModel

SKOS Concept hierarchy describing the experimental platform or methodology used. For sequencing platforms the use of "OBI:0400103 - DNA sequencer" is suggested.
is in range of
platformModel op
has members
DNA Sequencer ni

Population Frequencyc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/PopulationFrequency

Reports frequency information of the considered poplutation.
is equivalent to
alleleFrequency dp min 1
population dp min 1
is in domain of
alleleFrequency dp, population dp
is in range of
frequency op

Repeated Sequence Expressionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/RepeatedSequenceExpression

An expression of a sequence comprised of a tandem repeating subsequence. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
has super-classes
Sequence Expression c
is in domain of
repeatedSequenceCount dp, sequenceExpression op

Runc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Run

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]
is equivalent to
biosample op min 1 Biosample c
runDate dp min 1
is in domain of
libraryLayout dp, librarySelection dp, librarySource op, libraryStrategy dp, platformModel op, runDate dp, runPlatform dp
is in range of
run op

Sample Origin Detailc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/SampleOriginDetail

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]
is in range of
sampleOriginDetail op

Sample Origin Typec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/SampleOriginType

Category of sample origin. Value from Ontology for Biomedical Investigations (OBI) material entity (BFO:0000040) ontology. [Definition Source: GA4GH Beacon v2 Data Model]
is in range of
sampleOriginType op
has members
Material Entity ni

Sample Processingc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/SampleProcessing

Status of how the specimen was processed. Example: a child term of EFO:0009091. [Definition Source: GA4GH Beacon v2 Data Model]
is in range of
sampleProcessing op
has members
Sample Dissociation ni

Sequence Expressionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/SequenceExpression

An expression describing a Sequence. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
has sub-classes
Composed Sequence Expression c, Derived Sequence Expression c, Literal Sequence Expression c, Repeated Sequence Expression c
is in range of
sequenceState op

Sequence Intervalc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/SequenceInterval

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]
is equivalent to
sequenceIntervalEnd dp exactly 1
sequenceIntervalStart dp exactly 1
is in domain of
sequenceIntervalEnd dp, sequenceIntervalStart dp
is in range of
sequenceInterval op

Sequence Locationc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/SequenceLocation

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]
is equivalent to
sequenceInterval op exactly 1 Sequence Interval c
referenceSequence dp exactly 1
has super-classes
Location c
is in domain of
referenceSequence dp, sequenceInterval op
is in range of
sequenceLocation op

Severityc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Severity

SKOS Concept Hierarchy describing the severity level.
Is defined by
https://hpo.jax.org/browse/term/HP:0012824
is in range of
severity op
has members
Borderline ni, Mild ni, Moderate ni, Profound ni, Severe ni, Severity ni

Sex Data Availability and Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/SexDAD

Aggregated information of sex(es) obtained from individual level info of the cohort members. [Definition Source: GAGH Beacon v2 Data Model]
is equivalent to
distribution op some Sex Element Distribution c
has super-classes
Data Availability and Distribution c

Sex Element Distributionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/SexElementDistribution

Results or counts for each sex category. [Definition Source: GA4GH Beacon v2 Data Model]
is equivalent to
elementType op some Cohort Sex c
has super-classes
Element Distribution c

Software Toolc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/SoftwareTool

Software used to evaluate phenoclinic effects.
is equivalent to
toolName dp min 1
toolReference dp min 1
toolVersion dp min 1
is in domain of
toolName dp, toolReference dp, toolVersion dp
is in range of
annotatedWith op

Speciesc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Species

SKOS Concept hierarchy representing a species from the NCBI species taxonomy.
is in range of
chromosomeSpecies op
has members
Human ni

Systemic Variationc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/SystemicVariation

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]
has super-classes
Genomic Variation c
is in domain of
systemicVariationType op

Time Elementc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/TimeElement

This class identifies time elements, e.g. age, time interval, and timestamp.
has sub-classes
Age c, Age Range c, Gestational Age c, Time Interval c, Timestamp c
is in range of
diseaseAgeOnset op, featureOnset op, featureResolution op, measurementMoment op

Time Intervalc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/TimeInterval

Time interval with start and end defined as ISO8601 time stamps. [Definition Source: GA4GH Beacon v2 Data Model]
is equivalent to
timeIntervalEnd op min 1 Timestamp c
timeIntervalStart op min 1 Timestamp c
has super-classes
Time Element c
is in domain of
timeIntervalEnd op, timeIntervalStart op

Timestampc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Timestamp

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]
is equivalent to
timestamp dp min 1
has super-classes
Time Element c
is in domain of
timestamp dp
is in range of
timeIntervalEnd op, timeIntervalStart op

Tumor Gradec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/TumorGrade

SKOS Concept hierarchy representing the tumor grade. Child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent. [Definition Source: GA4GH Beacon v2 Data model]
is in range of
tumorGrade op
has members
Disease Grade Qualifier ni

Tumor Progressionc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/TumorProgression

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]
is in range of
tumorProgression op
has members
Neoplasm by Special Category ni

Unit Of Measurec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/UnitOfMeasure

The kind of unit. Recommended from NCIT Unit of Category ontology term (NCIT:C42568) descendants. [Definition Source: GA4GH Beacon v2 Data Model]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C42568
is in range of
measurementUOM op
has members
Unit by Category ni

Variant Alternative IDc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/VariantAlternativeID

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]
is in domain of
alternativeIDReference dp, valueID dp
is in range of
variantAlternativeID op

Variant Level Datac back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/VariantLevelData

Reports about the variation instances observed in the genomic variation.
is in range of
variantLevelData op

Variant Qualityc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/VariantQuality

Quality information about the genomic variation.
is in domain of
variantFilter dp, variantQual dp
is in range of
variantQuality op

VCF Filec back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/VCFFile

A Variant Call Format (VCF) file.
is in domain of
filename dp, filepath dp, refersToCohort op
is in range of
inVcfFile op

VCF Recordc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/VCFRecord

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]
is in domain of
genomeAssembly dp, inVcfFile op, vcfAlt dp, vcfChrom dp, vcfFilter dp, vcfInfo dp, vcfPos dp, vcfQual dp, vcfRef dp
is in range of
vcfRecord op

Zygosityc back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Zygosity

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]
is in range of
zygosity op
has members
Compouns Heterozygous ni, Hemizygous ni, Hemizygous Insertion-Linked ni, Hemizygous X-Linked ni, Hemizygous Y-Linked ni, Heterozygous ni, Homozygous ni, Nullizygous ni, Simple Heterozygous ni, Zygosity ni

Object Properties

ageRangeEndop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/ageRangeEnd

The end age range.
has domain
Age Range c
has range
Age c

ageRangeStartop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/ageRangeStart

The start age range.
has domain
Age Range c
has range
Age c

alleleOriginop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/alleleOrigin

Links the case level variant to the allele origin.
has domain
Case Level Variant c
has range
Allele Origin c

analysisop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/analysis

Links the case level variant to the bioinformatics analysis.
has domain
Case Level Variant c
has range
Analysis c

annotatedWithop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/annotatedWith

Links the pehnoclinic effect to the software tool used to annotate it.
has domain
PhenoClinic Effect c
has range
Software Tool c

assayop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/assay

Links the measurement to the assay used to produce the measurement.
has domain
Measurement c
has range
Assay c

biosampleop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/biosample

Links the case level variant to its biosample.
has domain
Analysis c or Case Level Variant c or Run c
has range
Biosample c

biosampleStatusop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/biosampleStatus

Links the biosample to its status.
has domain
Biosample c
has range
Biosample Status c

caseLevelDataop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/caseLevelData

Links the considered genomic variation to variation instances observed in individual analyses.
has domain
Genomic Variation c
has range
Case Level Variant c

categoryop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/category

Links the phenoclinic effect to the type of disease, condition, phenotypics measurement, etc.
has domain
PhenoClinic Effect c
has range
PhenoClinic Category c

chromosomeSpeciesop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/chromosomeSpecies

Links a chromosome location to the species.
has domain
Chromosome Location c
has range
Species c

clinicalInterpretationop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/clinicalInterpretation

Links the variant level data and case level variant to its phenoclinic effects.
has domain
Case Level Variant c or Variant Level Data c
has range
PhenoClinic Effect c

cohortAgeRangeop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cohortAgeRange

Individual age range in cohort inclusion criteria. [Definition Source: Beacon v2 Data Model]
has domain
Cohort Criteria c
has range
Age Range c

cohortDataTypeop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cohortDataType

Links a cohort to the types of information.
has domain
Cohort c
has range
Cohort Data Type c

cohortDesignop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cohortDesign

Links a cohort to the cohort type by its design.
has domain
Cohort c
has range
Cohort Design c

cohortDiseaseop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cohortDisease

Diseases in cohort inclusion criteria. [Definition Source: Beacon v2 Data Model]
has domain
Cohort Criteria c
has range
Cohort Disease c

cohortEthnicityop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cohortEthnicity

Ethnicities in cohort inclusion criteria. [Definition Source: BEacon v2 Data Model]
has domain
Cohort Criteria c

cohortLocationop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cohortLocation

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

cohortSexop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cohortSex

Sex(es) in cohort inclusion criteria. [Definition Source: Beacon v2 Data Model]
has domain
Cohort Criteria c
has range
Cohort Sex c

collectionEventop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/collectionEvent

Links a cohort to the collection event.
has domain
Cohort c
has range
Collection Event c

cytobandIntervalop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cytobandInterval

Links a chromosome location to the cytoband interval.
has domain
Chromosome Location c
has range
Cytoband Interval c

diagnosticMarkerop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/diagnosticMarker

Links a biosample to clinically relevant biomarkers.
has domain
Biosample c
has range
Diagnostic Marker c

diseaseAgeOnsetop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/diseaseAgeOnset

Links the disease to the the age at which an individual first experiences the disease.
has domain
Cohort Disease c
has range
Time Element c

diseaseCodeop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/diseaseCode

Links the disease to the disease identifier.
has domain
Cohort Disease c

diseaseStageop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/diseaseStage

Links the disease to the stage.
has domain
Cohort Disease c
has range
Disease Stage c

distributionop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/distribution

Links the aggregated information to the results or counts for each category.
has domain
Data Availability and Distribution c
has range
Element Distribution c

effectop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/effect

Links the phenoclinic effect class to the annotated phenotypic or clinical effect
has domain
PhenoClinic Effect c

elementTypeop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/elementType

Links the element distribution to the category.
has domain
Element Distribution c

eventDistributionop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/eventDistribution

Links a collection event to aggregated information obtained from individual level info of the cohort members.
has domain
Collection Event c
has range
Data Availability and Distribution c

eventTimelineop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/eventTimeline

Links a Collection Event to the Event Timeline.
has domain
Collection Event c
has range
Event Timeline c

evidenceop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/evidence

Links the phenoclinic effect to the type of evidence supporting variant-disease association.
has domain
PhenoClinic Effect c
has range
PhenoClinic Evidence c

exclusionCriteriaop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/exclusionCriteria

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]
has domain
Cohort c
has range
Cohort Criteria c

featureModifierop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/featureModifier

Links the phenotypic feature to specific characteristics.
has domain
Phenotypic Feature c
has range
Phenotypic Feature Modifier c

featureOnsetop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/featureOnset

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

featureResolutionop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/featureResolution

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

featureTypeop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/featureType

Links a phenotypic feature to its type.
has domain
Phenotypic Feature c
has range
Phenotypic Feature Type c

frequencyop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/frequency

Links the Frequency In Population class to allele frequency information of each population.
has domain
Frequency In Population c
has range
Population Frequency c

frequencyInPopulationop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/frequencyInPopulation

Links the considered genomic variation to frequency information of different populations.
has domain
Genomic Variation c
has range
Frequency In Population c

genomicFeatureop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/genomicFeature

Links a genomic variation to the genomic feature(s) affected by it.
has domain
Molecular Attribute c
has range
Genomic Feature c

genomicFeatureClassop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/genomicFeatureClass

Links the genomic feature to the class of genomic feature affected by the variant.
has domain
Genomic Feature c
has range
Genomic Feature Class c

genotypeMemberop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/genotypeMember

Links the genotype varoation to the members describes a Molecular Variation and the count of that variation at the locus.
has domain
Genotype c
has range
Genotype Member c

genotypeVariationop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/genotypeVariation

Links a genotype locus to the molecular variation.
has domain
Genotype Member c
has range
Molecular Variation c

haplotypeMemberop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/haplotypeMember

Links the haplotype to the co-occurring allele.
has domain
Haplotype c
has range
Allele c

histologicalDiagnosisop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/histologicalDiagnosis

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

inclusionCriteriaop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/inclusionCriteria

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

inCohortop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/inCohort

Links a patient to the belonging cohort.
has domain
Patient c
has range
Cohort c

individualop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/individual

Links the case level variant to the considered individual.
has domain
Analysis c or Biosample c or Case Level Variant c or Run c
has range
Person c

inVcfFileop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/inVcfFile

Links the VCF record to the corresponding VCF file.
has domain
VCF Record c
has range
VCF File c

librarySourceop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/librarySource

Links an experimental run to the the source of the sequencing or hybridization library.
has domain
Run c
has range
Library Source c

locationop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/location

Links a class to the genomic location.
has domain
Allele c or Copy Number Change c or Copy Number Count c or Legacy Variation c
has range
Location c

measurementop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/measurement

Links a biosample to the measurement.
has domain
Biosample c
has range
Measurement c

measurementMomentop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/measurementMoment

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

measurementUOMop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/measurementUOM

Links a measurement to the employed Unit Of Measure.
has domain
Measurement c
has range
Unit Of Measure c

molecularAttributeop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/molecularAttributes

Links the considered genomic variation to its molecular attributes.
has domain
Genomic Variation c
has range
Molecular Attribute c

molecularEffectop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/molecularEffect

Links a molecular attribute to its molecular effect.
has domain
Molecular Attribute c
has range
Molecular Effect c

molecularVariationTypeop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/molecularVariationType

Links a molecular variation to the variation type.

has characteristics: functional

has domain
Molecular Variation c
has range
Allele c or Haplotype c

obtentionProcedureop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/obtentionProcedure

The procedure for sample or measurement obtention.
has domain
Biosample c or Measurement c
has range
Obtention Procedure c

pathologicalStageop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/pathologicalStage

Links the biosample to the detected pathological stage.
has domain
Biosample c
has range
Pathological Stage c

pathologicalTNMFindingop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/pathologicalTNMFinding

Links the biosample to the detected pathological TNM finding.
has domain
Biosample c
has range
Pathological TNM Finding c

phenotypicConditionop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/phenotypicConditions

Links the cohort criteria to the phenotypic condition(s) in cohort inculsion criteria.
has domain
Cohort Criteria c
has range
Phenotypic Feature c

phenotypicEffectop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/phenotypicEffect

Links the variant level data and case level variant to its phenoclinic effects.
has domain
Case Level Variant c or Variant Level Data c
has range
PhenoClinic Effect c

phenotypicFeatureop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/phenotypicFeature

Link the biosample to the phenotypic abnormalities of the sample.
has domain
Biosample c
has range
Phenotypic Feature c

platformModelop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/platformModel

Links the experimental run to the experimental platform or methodology used.
has domain
Run c
has range
Platform Model c

refersToCohortop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/refersToCohort

Links the VCF file tot the corresponding cohort
has domain
VCF File c
has range
Cohort c

runop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/run

Links the case level variant to the experimental run.
has domain
Analysis c or Case Level Variant c
has range
Run c

sampleOriginDetailop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sampleOriginDetail

Links the biosample to the sample origin detail.
has domain
Biosample c
has range
Sample Origin Detail c

sampleOriginTypeop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sampleOriginType

Links the biosample to the sample origin type.
has domain
Biosample c
has range
Sample Origin Type c

sampleProcessingop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sampleProcessing

Links the biosample to how the specimen was processed.
has domain
Biosample c
has range
Sample Processing c

sequenceComponentop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sequenceComponent

Sequence Expression components comprising the expression.
has domain
Composed Sequence Expression c
has range
Derived Sequence Expression c or Literal Sequence Expression c or Repeated Sequence Expression c

sequenceExpressionop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sequenceExpression

Links the repeated sequence expression to the expression of the repeating subsequence.
has domain
Repeated Sequence Expression c
has range
Derived Sequence Expression c or Literal Sequence Expression c

sequenceIntervalop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sequenceInterval

Links the sequence location to the sequence interval.
has domain
Sequence Location c
has range
Sequence Interval c

sequenceLocationop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sequenceLocation

Links a sequence expression to the sequence location.
has domain
Derived Sequence Expression c
has range
Sequence Location c

sequenceStateop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sequenceState

Links the allele to an expression of the sequence state.
has domain
Allele c
has range
Sequence Expression c

severityop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/severity

Links a disease or phenotypic feature to its severity.
has domain
Cohort Disease c or Phenotypic Feature c
has range
Severity c

systemicVariationTypeop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/systemicVariationType

Links a systemic variation to the variation type.

has characteristics: functional

has domain
Systemic Variation c
has range
Copy Number Change c or Copy Number Count c or Genotype c

timeIntervalEndop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/timeIntervalEnd

The timestamp in which a time interval has ended.
has domain
Time Interval c
has range
Timestamp c

timeIntervalStartop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/timeIntervalStart

The timestamp in which a time interval has started.
has domain
Time Interval c
has range
Timestamp c

tumorGradeop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/tumorGrade

Links the biosample to the detected tumor grade.
has domain
Biosample c
has range
Tumor Grade c

tumorProgressionop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/tumorProgression

Links the biosample to the observed tumor progression.
has domain
Biosample c
has range
Tumor Progression c

variantAlternativeIDop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/variantAlternativeID

Links a genomic variation to the variant alternative ID.
has domain
Genomic Variation c
has range
Variant Alternative ID c

variantLevelDataop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/variantLevelData

Links the considered genomic variation to its variant level data.
has domain
Genomic Variation c
has range
Variant Level Data c

variantQualityop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/variantQuality

Links the considered genomic variation to the quality score of the variation.
has domain
Genomic Variation c
has range
Variant Quality c

variationCopyChangeop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/variationCopyChange

Links the Copy Number Change to the type of variation change.
has domain
Copy Number Change c
has range
Copy Number Assessment c

vcfRecordop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/vcfRecord

Links the considered genomic variation to the VCF record mentioning it.
has domain
Genomic Variation c
has range
VCF Record c

zygosityop back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/zygosity

Links the case level variant to the observed zigosity.
has domain
Case Level Variant c
has range
Zygosity c

Data Properties

alleleFrequencydp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/alleleFrequency

Allele frequency between 0 and 1. Example: 0.00003186. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Population Frequency c
has range
float

alternateBasesdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/alternateBases

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]
has domain
Legacy Variation c
has range
plain literal

alternativeIDReferencedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/alternativeIDReference

External reference of the variant alternative ID.
has domain
Variant Alternative ID c
has range
plain literal

aminoacidChangedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/aminoacidChange

Change at aminoacid level for protein affecting variants. Example: "V304*". [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Molecular Attribute c
has range
plain literal

analysisAlignerdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/analysisAligner

Reference to mapping/alignment software. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Analysis c
has range
plain literal

analysisDatedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/analysisDate

Date at which analysis was performed. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Analysis c
has range
date time

analysisPipelineNamedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/analysisPipelineName

Analysis pipeline and version if a standardized pipeline was used. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Analysis c
has range
plain literal

analysisPipelineRefdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/analysisPipelineRef

Link to Analysis pipeline resource. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Analysis c
has range
plain literal

availabilitydp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/availability

Data availability. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Data Availability and Distribution c
has range
boolean

availabilityCountdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/availabilityCount

Count of individuals with data available. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Data Availability and Distribution c
has range
integer

biosampleCollectionDatedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/biosampleCollectionDate

Date of biosample collection in ISO8601 format. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Biosample c
has range
date time

biosampleCollectionMomentdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/biosampleCollectionMoment

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]
has domain
Biosample c
has range
plain literal

clinicalRelevancedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/clinicalRelevance

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]
has domain
PhenoClinic Effect c
has range
{ "Benign" , "Likely Benign" , "Likely Pathogenic" , "Pathogenic" , "Uncertain Significance" }

clinvarVariantIDdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/clinvarVariantID

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

cohortNamedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cohortName

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]
has domain
Cohort c
has range
plain literal

cohortSizedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cohortSize

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]
has domain
Cohort c
has range
integer

cohortTypedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cohortType

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]
has domain
Cohort c
has range
plain literal

cytobandEnddp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cytobandEnd

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]
has domain
Cytoband Interval c
has range
plain literal

cytobandStartdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cytobandStart

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]
has domain
Cytoband Interval c
has range
plain literal

earliestEventdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/earliestEvent

Earliest date of visit or collection timeline. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Event Timeline c
has range
date time

elementDistributiondp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/elementDistribution

Results or counts for each category.
has domain
Element Distribution c
has range
integer

eventCasesdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/eventCases

Number of cases. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Collection Event c
has range
integer

eventControlsdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/eventControls

Number of controls. [Definition SOurce: GA4GH Beacon v2 Data Model]
has domain
Collection Event c
has range
integer

eventDatedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/eventDate

Date of collection event/data point. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Collection Event c
has range
date time

eventSizedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/eventSize

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]
has domain
Collection Event c
has range
integer

familyHistorydp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/familyHistory

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

featureExcludeddp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/featureExcluded

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]
has domain
Phenotypic Feature c
has range
boolean

filenamedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/filename

The name of the file.
has domain
VCF File c
has range
plain literal

filepathdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/filepath

The path to the file.
has domain
VCF File c
has range
plain literal

geneIDdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/geneID

Symbolic name or identifier used for a gene. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Molecular Attribute c
has range
plain literal

genomeAssemblydp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/genomeAssembly

Identifier for the genome assembly used to call the allele. [Definition Source: Phenopacket v2 Data Model]
has domain
VCF Record c
has range
plain literal

genomicHGVSIDdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/genomicHGVSID

The Human Genome Variation Society (HGVS) ID descriptor. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Genomic Variation c
has range
plain literal

genotypeCountdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/genotypeCount

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

gestationalDaysdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/gestationalDays

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

gestationalWeeksdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/gestationalWeeks

Completed weeks of gestation. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Gestational Age c
has range
integer

iso8601durationdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/iso8601duration

Represents age as a ISO8601 duration (e.g., 'P40Y10M05D'). [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Age c
has range
plain literal

latestEventdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/latestEvent

Latest date of visit or collection timeline. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Event Timeline c
has range
date time

libraryLayoutdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/libraryLayout

Ontology value for the library layout e.g "PAIRED", "SINGLE" [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Run c
has range
{ "PAIRED" , "SINGLE" }

librarySelectiondp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/librarySelection

Selection method for library preparation, e.g "RANDOM", "RT-PCR". [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Run c
has range
plain literal

libraryStrategydp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/libraryStrategy

Library strategy, e.g. "WGS". [Definition SOurce: GA4GH Beacon v2 Data Model]
has domain
Run c
has range
plain literal

locationChrdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/locationChr

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]
has domain
Chromosome Location c
has range
plain literal

measurementDatedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/measurementDate

Date of measurement. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Measurement c
has range
date time

measurementRefRangeHighdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/measurementRefRangeHigh

The reference range to determine the measurement to be high.
has domain
Measurement c
has range
float

measurementRefRangeLowdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/measurementRefRangeLow

The reference range to determine the measurement to be low.
has domain
Measurement c
has range
float

measurementValuedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/measurementValue

The value of the measurement in the units,
has domain
Measurement c
has range
float

molecularVariationCountdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/molecularVariationCount

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]
has domain
Genotype c
has range
integer

notesdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/notes

Unstructured text to provide additional information.
has domain
Cohort Disease c or Measurement c or Phenotypic Feature c or Variant Alternative ID c
has range
plain literal

populationdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/population

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]
has domain
Population Frequency c
has range
plain literal

proteinHGVSIDdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/proteinHGVSID

The Human Genome Variation Society (HGVS) ID descriptor(s) at protein level (for protein-altering variants). [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Genomic Variation c
has range
plain literal

referenceBasesdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/referenceBases

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]
has domain
Legacy Variation c
has range
plain literal

referenceSequencedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/referenceSequence

A VRS Computed Identifier for the reference Sequence. [Definition Source: GA4GH Variation Representation Specification (VRS) v1.2]
has domain
Sequence Location c
has range
plain literal

repeatedSequenceCountdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/repeatedSequenceCount

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

reverseComplementdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/reverseComplement

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]
has domain
Derived Sequence Expression c
has range
boolean

runDatedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/runDate

Date at which the experiment was performed. [Definition Source: Ga4GH Beacon v2 Data Model]
has domain
Run c
has range
date time

runPlatformdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/runPlatform

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]
has domain
Run c
has range
plain literal

sampleStoragedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sampleStorage

Status of how the specimen was stored. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Biosample c
has range
plain literal

sequencedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sequence

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]
has domain
Literal Sequence Expression c
has range
plain literal

sequenceIntervalEnddp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sequenceIntervalEnd

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]
has domain
Sequence Interval c
has range
plain literal

sequenceIntervalStartdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sequenceIntervalStart

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]
has domain
Sequence Interval c
has range
plain literal

sourcedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/source

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]
has domain
Frequency In Population c
has range
plain literal

sourceReferencedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sourceReference

A reference to further documentation or details. Examples: "https://gnomad.broadinstitute.org/", "https://ega-archive.org/". [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Frequency In Population c
has range
plain literal

sourceVersiondp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sourceVersion

Version of the source data. Example: "gnomAD v3.1.1". [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Frequency In Population c
has range
plain literal

timestampdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/timestamp

The datetime of the timestamp.
has domain
Timestamp c
has range
date time stamp

toolNamedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/toolName

Name of the software tool. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Software Tool c
has range
plain literal

toolReferencedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/toolReference

References to the software tool. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Software Tool c
has range
plain literal

toolVersiondp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/toolVersion

Software Tool version used. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Software Tool c
has range
plain literal

transcriptHGVSIDdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/transcriptHGVSID

The Human Genome Variation Society (HGVS) ID descriptor(s) at transcript level.
has domain
Genomic Variation c
has range
plain literal

valueIDdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/valueID

The variant alternative ID.
has domain
Variant Alternative ID c
has range
plain literal

variantCallerdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/variantCaller

Reference to variant calling software / pipeline. [Definition Source: GA4GH Beacon v2 Data Model]
has domain
Analysis c
has range
plain literal

variantFilterdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/variantFilter

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]
has domain
Variant Quality c
has range
plain literal

variantInternalIDdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/variantInternalID

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]
has domain
Genomic Variation c
has range
plain literal

variantQualdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/variantQual

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]
has domain
Variant Quality c
has range
float

variantTypedp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/variantType

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]
has domain
Legacy Variation c
has range
plain literal

variationCopiesdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/variationCopies

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

vcfAltdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/vcfAlt

Alternate base. [Definition Source: Phenopacket v2 Data Model]
has domain
VCF Record c
has range
plain literal

vcfChromdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/vcfChrom

Chromosome or contig identifier. [Definition Source: Phenopacket v2 Data Model]
has domain
VCF Record c
has range
plain literal

vcfFilterdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/vcfFilter

Filter status: PASS if this position has passed all filters. [Definition Source: Phenopacket v2 Data Model]
has domain
VCF Record c
has range
plain literal

vcfInfodp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/vcfInfo

Additional information: Semicolon-separated series of additional information fields. [Definition Source: Phenopacket v2 Data Model]
has domain
VCF Record c
has range
plain literal

vcfPosdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/vcfPos

The reference position, with the 1st base having position 1. [Definition Source: Phenopacket v2 Data Model]
has domain
VCF Record c
has range
plain literal

vcfQualdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/vcfQual

Quality: Phred-scaled quality score for the assertion made in ALT. [Definition Source: Phenopacket v2 Data Model]
has domain
VCF Record c
has range
plain literal

vcfRefdp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/vcfRef

Reference base. [Definition Source: Phenopacket v2 Data Model]
has domain
VCF Record c
has range
plain literal

Named Individuals

5 Prime UTR Variantni back to ToC or Named Individual ToC

IRI: http://www.sequenceontology.org/browser/current_release/term/SO:0001623

A UTR variant of the 5' UTR. [Definition Source: The Sequence Ontology]
belongs to
concept
Genomic Feature Class c

Abdominal Painni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26682

Painful sensation in the abdominal region. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Abnormal Sampleni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0009655

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]
belongs to
concept
Biosample Status c

Acquired Hypothyroidismni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C129644

Hypothyroidism, the cause of which is not present at birth. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Acute Cystitisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26934

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]
belongs to
concept
Disease, Disorder or Finding c

Acute Myocardial Infarctionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C35204

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]
belongs to
concept
Disease, Disorder or Finding c

Acute Pyelonephritisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C123215

Sudden onset pyelonephritis. [Definition Source: NCI][attribution: NICHD]
belongs to
concept
Disease, Disorder or Finding c

Acute Respiratory Failureni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C27043

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]
belongs to
concept
Disease, Disorder or Finding c

Acute Tonsillitisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C97142

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]
belongs to
concept
Disease, Disorder or Finding c

Adenocarcinomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2852

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]
belongs to
concept
Disease, Disorder or Finding c

Alanine Aminotransferase Increasedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26948

An increase in the level of alanine aminotransferase in the blood. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Alcohol Dependanceni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C93040

Physical and psychological dependence on alcohol. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Allele Origin Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/alleleOriginTaxonomy

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]
belongs to
concept scheme

Allergic Asthmani back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/389145006

Allergic Asthma
belongs to
concept
Disease, Disorder or Finding c

Allergic Rhinitisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C79532

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]
belongs to
concept
Disease, Disorder or Finding c

Alzheimer's Diseaseni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2866

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]
belongs to
concept
Disease, Disorder or Finding c

Amenorrheani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C61443

The absence of menses in a woman who has achieved reproductive age. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Amenorrhea due to Pituitary Dysfunctionni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/1144987003

The absence of menses in a woman who has achieved reproductive age due to disorder of pituitary gland. [Partial Defintion Source: NCI
belongs to
concept
Disease, Disorder or Finding c

Amyotrophic Lateral Sclerosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34373

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]
belongs to
concept
Disease, Disorder or Finding c

Anemiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2869

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]
belongs to
concept
Disease, Disorder or Finding c

Angioedemani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C112175

Rapid swelling of the deep layers of the skin due to transient vascular leakage of serous fluid. [Definition Source: NCI][attribution: NICHD]
belongs to
concept
Disease, Disorder or Finding c

Ankle Fractureni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26989

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]
belongs to
concept
Disease, Disorder or Finding c

Ann Arbor Stage IV Mantle Cell Lymphomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C8486

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]
belongs to
concept
Disease, Disorder or Finding c

Ann Arbor Stage IV T-Cell Non-Hodgkin Lymphomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C8668

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]
belongs to
concept
Disease, Disorder or Finding c

Anorectal Fistulani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C60785

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]
belongs to
concept
Disease, Disorder or Finding c

Anorexiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2875

Loss of appetite. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Anosmiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C116369

Inability to smell. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Anxiety Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2878

A category of psychiatric disorders which are characterized by anxious feelings or fear often accompanied by physical symptoms associated with anxiety. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Arrhythmiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2881

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]
belongs to
concept
Disease, Disorder or Finding c

Arthritisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2883

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]
belongs to
concept
Disease, Disorder or Finding c

Asian (ethnic group)ni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/315280000

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]
belongs to
concept
Group (social concept) c

Aspiration Pneumonitisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34932

Inflammation of the lungs due to the inhalation of solid or liquid material. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Assay Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/assayTaxonomy

This taxonomy describes the assay used to produce the measurement. [Definition Source: Phenopacket v2]
belongs to
concept scheme

Asthmani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C28397

A chronic respiratory disease manifested as difficulty breathing due to the narrowing of bronchial passageways. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Atopic Dermatitisni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/24079001

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]
belongs to
concept
Disease, Disorder or Finding c

Atrial Fibrillationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C50466

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]
belongs to
concept
Disease, Disorder or Finding c

Atrial Flutterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51224

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]
belongs to
concept
Disease, Disorder or Finding c

Autoimmune Diseaseni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2889

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]
belongs to
concept
Disease, Disorder or Finding c

Autoimmune Nervous System Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C99383

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]
belongs to
concept
Disease, Disorder or Finding c

Autoimmune Pancytopeniani back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/183005

The autoimmune inability of the bone marrow to produce hematopoietic elements. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Bacterial Pneumoniani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26704

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]
belongs to
concept
Disease, Disorder or Finding c

Baker Cystni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34935

Swelling and protrusion of the gastrocnemius-semimembranosus bursa due to an accumulation of synovial fluid. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Basal Cell Carcinomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C156767

A carcinoma involving the basal cells. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Behavioral Impairmentni back to ToC or Named Individual ToC

IRI: https://w3id.org/brainteaser/ontology/schema/BehavioralImpairment

Diminished psychological function.
belongs to
concept
Disease, Disorder or Finding c

Bell's Palsyni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/193093009

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]
belongs to
concept
Disease, Disorder or Finding c

Biosample Status Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/biosampleStatusTaxonomy

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).
belongs to
concept scheme

Bipolar Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34423

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]
belongs to
concept
Disease, Disorder or Finding c

Black (ethnic group)ni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/315240009

A person having origins in the original peoples of sub-Saharan Africa or the Caribbean.
belongs to
concept
Group (social concept) c

Blepharititsni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C112183

Inflammation of the eyelids near the eyelashes. [Definition Source: NCI][attribution: NICHD]
belongs to
concept
Disease, Disorder or Finding c

Blepharospasmni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C118723

Involuntary twitching of the eyelid. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Borderlineni back to ToC or Named Individual ToC

IRI: https://hpo.jax.org/browse/term/HP:0012827

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)]
belongs to
concept
Severity c

Bowel Obstructionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C9175

Blockage of the normal flow of the intestinal contents within the bowel. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Bradycardiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C37920

An abnormally slow heart rate. Thresholds for different age, gender, and patient populations exist. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Breast Carcinomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4872

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]
belongs to
concept
Disease, Disorder or Finding c

Brown-Sequard Syndromeni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C84601

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]
belongs to
concept
Disease, Disorder or Finding c

Cancer Cell Line Sampleni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0030035

A neoplastic sample derived from a cancer cell line. [Definition Source: The Experimental Factor Ontology]
belongs to
concept
Biosample Status c

Cancer TNM Finding Categoryni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C48698

belongs to
concept
Pathological TNM Finding c

Carcinomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2916

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]
belongs to
concept
Disease, Disorder or Finding c

Cardiovascular Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2931

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]
belongs to
concept
Disease, Disorder or Finding c

Cardiovascular Systemni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/UATC/C

belongs to
concept
pharmacologic substance c

Case Control Designni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0001427

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]
belongs to
concept
Biosample Status c

Caucasianni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/14045001

A person having origins in any of the original peoples of Europe, the Middle East, or North Africa. (OMB) [Definition Source: NCI]
belongs to
concept
Group (social concept) c

Cavernous Hemangiomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3086

A hemangioma characterized by the presence of cavernous vascular spaces. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Celiac Diseaseni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26714

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]
belongs to
concept
Disease, Disorder or Finding c

Central Nervous System Degenerative Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4802

A disorder of the central nervous system characterized by gradual and progressive loss of neural tissue and neurologic function. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Chicken Poxni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C97132

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]
belongs to
concept
Disease, Disorder or Finding c

Chronic Lung Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C98541

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]
belongs to
concept
Disease, Disorder or Finding c

Clinical Modifierni back to ToC or Named Individual ToC

IRI: https://hpo.jax.org/browse/term/HP:0012823

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]
belongs to
concept
Phenotypic Feature Modifier c

Closed Dislocation of Shoulderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34486

A closed dislocation of the shoulder [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Closed Fracture of Ribni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C35350

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]
belongs to
concept
Disease, Disorder or Finding c

Closed Fracture of Tibiani back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/447139008

A closed fracture of the tibia.
belongs to
concept
Disease, Disorder or Finding c

Cognitive Imparimentni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C116921

Diminished mental function. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Cohort Data Type Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cohortDataTypeTaxonomy

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]
belongs to
concept scheme

Cohort Design Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cohortDesignTaxonomy

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]
belongs to
concept scheme

Cohort Sex Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/cohortSexTaxonomy

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]
belongs to
concept scheme

Cold Soreni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34695

A lesion caused by type 1 or type 2 herpes simplex virus, involving the oralfacial region. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Colon Adenocarcinomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4349

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]
belongs to
concept
Disease, Disorder or Finding c

Common Bile Duct Stoneni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34499

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]
belongs to
concept
Disease, Disorder or Finding c

Complete Genomic Deletionni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0030069

Assessment of complete genomic deletion. [Definition Source: The Experimental Factor Ontology (EFO)]
belongs to
concept
Copy Number Assessment c

Compouns Heterozygousni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000402

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]
belongs to
concept
Zygosity c

Congenital Adrenal Hyperplasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34360

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]
belongs to
concept
Disease, Disorder or Finding c

Copy Number Assessmentni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0030063

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]
belongs to
concept
Copy Number Assessment c

Copy Number Assessment Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/copyNumberAssessmentTaxonomy

SKOS Concept hierarchy describing the type of copy number change allowed.
belongs to
concept scheme

Copy Number Gainni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0030070

Assessment of genomic copy number gain. [Definition Source: The Experimental Factor ontology (EFO)]
belongs to
concept
Copy Number Assessment c

Copy Number Lossni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0030067

Assessment of genomic copy number loss.
belongs to
concept
Copy Number Assessment c

Coronary Artery Bypass Graftni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/232717009

Surgery performed to bypass partially or completely occluded coronary arteries, thereby increasing the blood supply of the heart. [Definition Source: NCI]
belongs to
concept
surgical type c

COVID-19 Infectionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C171133

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]
belongs to
concept
Disease, Disorder or Finding c

Cranial Nerve VII Palsyni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26769

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]
belongs to
concept
Disease, Disorder or Finding c

Cutaneous Melanomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3510

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]
belongs to
concept
Disease, Disorder or Finding c

Cystni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2978

A sac-like closed membranous structure that may be empty or contain fluid or amorphous material. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

De-Novo Variantni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/SO_0001781

A variant arising in the offspring that is not found in either of the parents. [Definition Source: Sequence Types and Features Ontology]
belongs to
concept
Allele Origin c

Deep Vein Thrombosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C49343

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]
belongs to
concept
Disease, Disorder or Finding c

Dementiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4786

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]
belongs to
concept
Disease, Disorder or Finding c

Depressionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2982

A melancholy feeling of sadness and despair. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Diabetes Mellitusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2985

A metabolic disorder characterized by abnormally high blood sugar levels due to diminished production of insulin or insulin resistance/desensitization. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Diabetic Ketoacidosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C50530

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]
belongs to
concept
Disease, Disorder or Finding c

Diagnostic Marker Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/diagnosticMarkerTaxonomy

This taxonomy describes clinically relevant biomarkers.
belongs to
concept scheme

Disease Grade Qualifierni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C28076

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]
belongs to
concept
Tumor Grade c

Disease or Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2991

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]
belongs to
concept
Disease, Disorder or Finding c

Disease or Disorder (MONDO)ni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0000001

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]
belongs to
concept
PhenoClinic Category c

Disease Stage Qualifierni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C28108

An adjectival term that can specify or describe a disease stage. [Definition Source: NCIT]
belongs to
concept
Pathological Stage c

Disease Stage Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/diseaseStageTaxonomy

belongs to
concept scheme

Disease, Disorder or Finding Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/phenoclinical/schema/diseaseDisorderFindingTaxonomy

This taxonomy comprises disease, disorder or findings. The taxonomy is mainly based on NCIT.
belongs to
concept scheme

DNA Sequencerni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0400103

A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. [Definition Source: Ontology for Biomedical Investigations (OBI)]
belongs to
concept
Platform Model c

Dog Biteni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C122419

A wound received from the teeth of a dog. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Drug Hypersensitivity Syndromeni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C112208

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]
belongs to
concept
Disease, Disorder or Finding c

Dyslipidemiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C80385

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]
belongs to
concept
Disease, Disorder or Finding c

Eczemani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3001

A form of dermatitis characterized by red, itchy, scaly, or crusty patches that can be chronic or intermittent. [Definition Source: NCI][attribution: NICHD]
belongs to
concept
Disease, Disorder or Finding c

Endometriosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3014

The growth of functional endometrial tissue in anatomic sites outside the uterine body. It most often occurs in the pelvic organs. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Epidermal Inclusion Cystni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3134

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]
belongs to
concept
Disease, Disorder or Finding c

Essential Hypertensionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3478

Hypertension that presents without an identifiable cause. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Ethnic Groupni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/372148003

A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. [Definition Source: CSP]
belongs to
concept
Group (social concept) c

Experimental Evidenceni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ECO_0000006

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]
belongs to
concept
PhenoClinic Evidence c

Extrapyramidal Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C79593

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]
belongs to
concept
Disease, Disorder or Finding c

Favismni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34607

A condition associated with glucose-6-phosphate dehydrogenase deficiency, which is characterized by hemolysis. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Femaleni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C16576

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]
belongs to
concept
Cohort Sex c

Femur Fractureni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26774

A traumatic or pathologic injury to the femur in which the continuity of the femur is broken. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Fever Chillsni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26921

Shivering secondary to a febrile process. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Fibromani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3041

A non-metastasizing neoplasm arising from the fibrous tissue. It is characterized by the presence of spindle-shaped fibroblasts. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Fibromyalgiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C87497

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]
belongs to
concept
Disease, Disorder or Finding c

Findingni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3367

Clinical, laboratory or molecular evidence, or absence of evidence of disease. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Flu-Like Symptomsni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C78302

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]
belongs to
concept
Disease, Disorder or Finding c

Fungal Infectionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3245

An infection caused by a fungus. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Gastritisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26780

Inflammation of the stomach. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Gastroenterititsni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34632

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]
belongs to
concept
Disease, Disorder or Finding c

Gastroesophageal Refluxni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C92560

The backward flow of stomach acid contents into the esophagus (the tube that connects the mouth to the stomach). [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Gastroplastyni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/9429009

Surgical procedures involving the STOMACH and sometimes the lower ESOPHAGUS to correct anatomical defects, or to treat MORBID OBESITY by reducing the size of the stomach. There are several subtypes of bariatric gastroplasty, such as vertical banded gastroplasty, silicone ring vertical gastroplasty, and horizontal banded gastroplasty. [Definition Source: MSH]
belongs to
concept
surgical type c

Generalized Epilepsyni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3021

A chronic condition characterised by recurrent generalised seizures. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Genomic Feature Class Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/genomicFeatureClassTaxonomy

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`
belongs to
concept scheme

Genomic Sourceni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENEPIO_0001966

Genomic DNA (includes PCR products from genomic DNA). [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
belongs to
concept
Library Source c

Geographic Location Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/geographicLocationTaxonomy

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]
belongs to
concept scheme

Germline Variantni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/SO_0001778

A variant present in the embryo that is carried by every cell in the body. [Definition Source: Sequence Types and Features Ontology]
belongs to
concept
Allele Origin c

Gianmaria Silvelloni back to ToC or Named Individual ToC

IRI: https://orcid.org/0000-0003-4970-4554

belongs to
Person c

Glaucomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26782

Increased pressure in the eyeball due to obstruction of the outflow of aqueous humor. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Group Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/phenoclinical/schema/groupTaxonomy

This taxonomy describes the different ethinic groups. The taxonomy is based on SNOMED-CT.
belongs to
concept scheme

Hashimoto Thyroiditisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C27191

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]
belongs to
concept
Disease, Disorder or Finding c

Head and Neck Findingni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C36282

Symptoms, physical examination results, and/or laboratory test results related to the head and neck. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Head Traumani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34660

A traumatic injury to the head. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Headacheni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34661

Pain in various parts of the head, not confined to the area of distribution of any nerve. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Heart Failureni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C50577

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]
belongs to
concept
Disease, Disorder or Finding c

Hemizygousni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000134

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]
belongs to
concept
Zygosity c

Hemizygous Insertion-Linkedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000606

belongs to
concept
Zygosity c

Hemizygous X-Linkedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000604

belongs to
concept
Zygosity c

Hemizygous Y-Linkedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000605

belongs to
concept
Zygosity c

Hepatic Toxicityni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C185645

Toxicity that impairs or damages the liver. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Hepatitisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3095

Inflammation of the liver; usually from a viral infection, but sometimes from toxic agents. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Hepatitis A Infectionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3096

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]
belongs to
concept
Disease, Disorder or Finding c

Hepatitis B, Purified Antigenni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/UATC/J07BC01

belongs to
concept
pharmacologic substance c

Hereditary Factor XI Deficiencyni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C84705

A rare inherited bleeding disorder caused by deficiency of coagulation factor XI. It may be asymptomatic or manifest with bleeding. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Hereditary Hemolytic Anemiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34379

A congenital hemolytic anemia caused by defects of the erythrocyte membrane, enzyme deficiencies, or hemoglobinopathies. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Herniani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34685

The protrusion of part of an organ or fibroadipose tissue through an abnormal opening. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Herpes Simplex Keratitisni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/9389005

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]
belongs to
concept
Disease, Disorder or Finding c

Herpes Simplex Virus Infectionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C155871

An infection that is caused by herpes simplex virus. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Herpes Zosterni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C71079

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]
belongs to
concept
Disease, Disorder or Finding c

Heterozygousni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000391

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]
belongs to
concept
Zygosity c

High Grade Cervical Squamous Intraepithelial Neoplasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C40197

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]
belongs to
concept
Disease, Disorder or Finding c

High-Level Copy Number Gainni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0030072

Assessment of high-level genomic copy number gain. [Definition Source: The Experimental Factor Ontology (EFO)]
belongs to
concept
Copy Number Assessment c

High-Level Copy Number Lossni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0020073

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)]
belongs to
concept
Copy Number Assessment c

Hispanicni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/414408004

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]
belongs to
concept
Group (social concept) c

Homozygousni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000136

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]
belongs to
concept
Zygosity c

Humanni back to ToC or Named Individual ToC

IRI: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606

NCBI Taxonomy ID: 9606
belongs to
concept
Species c

Hypersensitivityni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3114

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]
belongs to
concept
Disease, Disorder or Finding c

Hypertensionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3117

Blood pressure that is abnormally high. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Hypertensive Crisisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3122

A severe, acute increase in blood pressure that may result in stroke or myocardial ischemia. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Hyperthyroidismni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3123

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]
belongs to
concept
Disease, Disorder or Finding c

Hypothyroidismni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26800

Abnormally low levels of thyroid hormone. [Definition Source: NCI][attribution: NICHD]
belongs to
concept
Disease, Disorder or Finding c

Infectious Mononucleosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34726

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]
belongs to
concept
Disease, Disorder or Finding c

Inferential Evidenceni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ECO_0000361

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]
belongs to
concept
PhenoClinic Evidence c

Inguinal Herniani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34690

The protrusion of a sac-like structure containing fibroadipose tissue through an abnormal opening in the inguinal region. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Injuryni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3671

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]
belongs to
concept
Disease, Disorder or Finding c

Interstitial Pneumoniani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C27006

Inflammation of interstitial lung tissue, usually associated with infection. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Intestinal Pseudo-Obstructionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34733

Ileus of the intestine in which there is no mechanical obstruction. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Iridocyclitisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34736

Inflammation of the iris and the ciliary body. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Iron-Deficiency Anemiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C84484

Anemia caused by low iron intake, inefficient iron absorption in the gastrointestinal tract, or chronic blood loss. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Keratitisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26805

Inflammation of the cornea. [Definition Source: NCI]
belongs to
Disease, Disorder or Finding c

Keratoconusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26806

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]
belongs to
concept
Disease, Disorder or Finding c

Klippel-Feil Syndromeni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C98967

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]
belongs to
concept
Disease, Disorder or Finding c

Langerhans Cell Histiocytosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3107

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]
belongs to
concept
Disease, Disorder or Finding c

Laura Menottini back to ToC or Named Individual ToC

IRI: https://orcid.org/0000-0002-0676-682X

belongs to
Person c

Leukopeniani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26816

A laboratory test result indicating a decreased number of white blood cells in the peripheral blood. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Library Sourceni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENEPIO_0001965

The library source specifies the type of source material that is being sequenced. [Definition Source: GENEPIO]
belongs to
concept
Library Source c

Library Source Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/librarySourceTaxonomy

This taxonomy describes the source of the sequencing or hybridization library. [Definition Source: GA4GH Beacon v2 Data Model]. The taxonomy is based on GENEPIO.
belongs to
concept scheme

Long QT Syndromeni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34786

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]
belongs to
concept
Disease, Disorder or Finding c

Low-Level Copy Number Gainni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0030071

Assessment of low-level genomic copy number gain. [Definition Source: The Experimental Factor Ontology (EFO)]
belongs to
concept
Copy Number Assessment c

Low-Level Copy Number Lossni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0030068

Assessment of low-level genomic copy number loss. [Definition Source: The Experimental Factor ontology (EFO)]
belongs to
concept
Copy Number Assessment c

Lumbar Herniani back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/23344004

Lumbar Hernia [Definition Source: SNOMEDCT]
belongs to
concept
Disease, Disorder or Finding c

Lumbar Puncture Headacheni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C50643

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]
belongs to
concept
Disease, Disorder or Finding c

Lymphopeniani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26823

An abnormally small number of lymphocytes in the circulating blood. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Maleni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C20197

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]
belongs to
concept
Cohort Sex c

Malignant Colon Neoplasmni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C9242

A primary or metastatic malignant neoplasm that affects the colon. Representative examples include carcinoma, lymphoma, and sarcoma. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Malignant Neoplasmni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C9305

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]
belongs to
concept
Disease, Disorder or Finding c

Malignant Skin Neoplasmni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2920

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]
belongs to
concept
Disease, Disorder or Finding c

Malignant Thyroid Gland Neoplasmni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C7510

A primary or metastatic malignant neoplasm affecting the thyroid gland. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Material Entityni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000040

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]
belongs to
concept
Sample Origin Type c

Maternal Variantni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/SO_0001775

A variant in the genetic material inherited from the mother. [Definition Source: Sequence Types and Features Ontology]
belongs to
concept
Allele Origin c

Melanocytic Nevusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C7570

A neoplasm composed of melanocytes that usually appears as a dark spot on the skin. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Metagenomic Sourceni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENEPIO_0001967

Mixed material from metagenome. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
belongs to
concept
Library Source c

Metastasis Sampleni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0010941

A neoplastic sample derived from a cancer metastasis (not from a primary tumor). [Definition Source: The Experimental Factor Ontology]
belongs to
concept
Biosample Status c

Metatranscriptomic Sourceni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENEPIO_0001968

Transcription products from community targets. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
belongs to
concept
Library Source c

Migraineni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C89715

A common, severe type of vascular headache often associated with increased sympathetic activity, resulting in nausea, vomiting, and light sensitivity. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Migraine With Aurani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C117005

A migraine disorder characterized by episodes that are preceded by focal neurological symptoms. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Mildni back to ToC or Named Individual ToC

IRI: https://hpo.jax.org/browse/term/HP:0012825

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)]
belongs to
concept
Severity c

Missense Variantni back to ToC or Named Individual ToC

IRI: http://www.sequenceontology.org/browser/current_release/term/SO:0001583

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]
belongs to
concept
Molecular Effect c

Moderateni back to ToC or Named Individual ToC

IRI: https://hpo.jax.org/browse/term/HP:0012826

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)]
belongs to
concept
Severity c

Molecular Effect Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/molecularEffectTaxonomy

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`.
belongs to
concept scheme

Molluscum Contagiosum Virusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C112357

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]
belongs to
concept
Disease, Disorder or Finding c

Monoclonal B_Cell Lymphocytosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C80310

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]
belongs to
concept
Disease, Disorder or Finding c

Monoclonal Gammopathyni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C35548

An abnormal laboratory test result indicating the presence of monoclonal immunoglobulins in the blood or urine. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Mood Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C92200

A category of psychiatric disorders which have as their most predominant feature a disturbance in mood. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Motor Neuron Diseaseni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/37340000

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]
belongs to
concept
Disease, Disorder or Finding c

Multiple Sclerosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3243

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]
belongs to
concept
Disease, Disorder or Finding c

Mumpsni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C29888

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]
belongs to
concept
Disease, Disorder or Finding c

Myasthenia Gravisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C60989

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]
belongs to
concept
Disease, Disorder or Finding c

Myeloproliferative Neoplasmni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4345

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]
belongs to
concept
Disease, Disorder or Finding c

Neck Traumani back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/90460009

General or unspecified injuries to the neck. It includes injuries to the skin, muscles, and other soft tissues of the neck. [Defintion Source: MSH]
belongs to
concept
Disease, Disorder or Finding c

Neonatal Hearing Impairmentni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C50667

An abnormality that affects hearing within the first month after birth. It may or may not result in hearing loss. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Neoplasmni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3262

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]
belongs to
concept
Disease, Disorder or Finding c

Neoplasm by Special Categoryni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C7062

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]
belongs to
concept
Tumor Progression c

Neoplastic Sampleni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0009656

A material sample derived from neoplastic cells or tissue. [Definition Source: The Experimental Factor Ontology]
belongs to
concept
Biosample Status c

Neurofibromatosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C6727

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]
belongs to
concept
Disease, Disorder or Finding c

Neutropenic Disorderni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/303011007

A decrease in the number of NEUTROPHILS found in the blood. [Definition Source: MSH]
belongs to
concept
Disease, Disorder or Finding c

Non-Neoplastic Central Nervous System Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C27586

Any disorder other than abnormal tissue growth resulting from uncontrolled cell proliferation affecting the nervous system.
belongs to
concept
Disease, Disorder or Finding c

Nullizygousni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000978

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]
belongs to
concept
Zygosity c

Obesityni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3283

Having a high amount of body fat (body mass index [BMI] of 30 or more). [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Obstructive Sleep Apnea Syndromeni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C27168

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]
belongs to
concept
Disease, Disorder or Finding c

Obtention Procedure Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/obtentionProcedureTaxonomy

This taxonomy describes the obtention procedures to retrieve a biosample or a measurement.
belongs to
concept scheme

Opioid Use Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C157942

The use of opioids that results in the development of a dependency that adversely affects an individual's life. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Optic Neuritisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C84950

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]
belongs to
concept
Disease, Disorder or Finding c

Osteoporosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3298

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]
belongs to
concept
Disease, Disorder or Finding c

Other Library Sourceni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENEPIO_0001969

Other, unspecified, or unknown library source material. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
belongs to
concept
Library Source c

Palmar Fibromatosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3469

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.
belongs to
concept
Disease, Disorder or Finding c

Pancytopeniani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34889

A finding of low numbers of red and white blood cells and platelets in the peripheral blood. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Parkinson's Diseaseni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26845

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]
belongs to
concept
Disease, Disorder or Finding c

Paternal Variantni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/SO_0001776

A variant in the genetic material inherited from the father. [Definition Source: Sequence Types and Features Ontology]
belongs to
concept
Allele Origin c

Pathological Stage Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/pathologicalStageTaxonomy

Pathological stage, if applicable, preferably as subclass of NCIT:C28108 - Disease Stage Qualifier. [Definition Source: GA4GH Beacon v2 Data Model]
belongs to
concept scheme

Pathological TNM Finding Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/pathologicalTNMFindingTaxonomy

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

Pedigree Specific Variantni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/SO_0001779

A variant that is found only by individuals that belong to the same pedigree. [Definition Source: Sequence Types and Features Ontology]
belongs to
concept
Allele Origin c

Penicillin Allergyni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34911

An allergy to Penicillin. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Personality Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34922

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]
belongs to
concept
Disease, Disorder or Finding c

Phenoclinic Category Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/phenoClinicCategoryTaxonomy

This taxonomy comprises the type of disease, condition, phenotypic measurement, etc. The taxonomy is mainly based on MONDO on Human Phenotype Ontology (HP)
belongs to
concept scheme

Phenoclinic Evidence Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/phenoclinicEvidenceTaxonomy

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]
belongs to
concept scheme

Phenotypic Abnormalityni back to ToC or Named Individual ToC

IRI: https://hpo.jax.org/browse/term/HP:0000118

A deviation from normal morphology, physiology, or behavior, and good phenotyping is a cornerstone of a doctor's daily work. [PMID: 25109851]
belongs to
concept
PhenoClinic Category c

Phenotypic Feature Modifier Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/phenotypicFeatureModifierTaxonomy

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]
belongs to
concept scheme

Phenotypic Feature Type Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/phenotypicFeatureTypeTaxonomy

SKOS Concept hierarchy denoting the phenotypic feature, preferably using a value from Human Phenotype Ontology (HPO). [Definition Source: Beacon v2 Data Model]
belongs to
concept scheme

Pituitary Neuroendocrine Tumorni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3329

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.
belongs to
concept
Disease, Disorder or Finding c

Platform Model Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/platformModelTaxonomy

This taxonomy describes the experimental platform or methodology used. For sequencing platforms the use of "OBI:0400103 - DNA sequencer" is suggested.
belongs to
concept scheme

Pleural Effusionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3331

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]
belongs to
concept
Disease, Disorder or Finding c

Pneumococcal Pneumoniani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C157959

Pneumonia that is attributed to the bacteria Streptococcus pneumonia. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Pneumoniani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3333

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]
belongs to
concept
Disease, Disorder or Finding c

Pneumonia Caused By SARS-CoV-2ni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/882784691000119100

Pneumonia caused by severe acute respiratory syndrome coronavirus 2 [Definition Source: SNOMEDCT]
belongs to
concept
Disease, Disorder or Finding c

Population Specific Variantni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/SO_0001780

A variant found within only speficic populations. [Definition Source: Sequence Types and Features Ontology]
belongs to
concept
Allele Origin c

Post-Herpetic Neuralgiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C117084

Pain that occurs after the disappearance of herpes zoster infection lesions. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Primary Neoplasmni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C8509

A tumor at the original site of origin. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Primary Progressive Aphasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C85024

A rare neurologic progressive disorder characterized by impairment of the language and speech abilities. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Primary Tumor Sampleni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0010942

A neoplastic sample derived from a primary tumor (not from a cancer metastasis). [Definition Source: The Experimental Factor Ontology]
belongs to
concept
Biosample Status c

Profoundni back to ToC or Named Individual ToC

IRI: https://hpo.jax.org/browse/term/HP:0012829

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)]
belongs to
concept
Severity c

Psoriasisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3346

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]
belongs to
concept
Disease, Disorder or Finding c

Psoriatic Arthritisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C61277

Joint inflammation associated with psoriasis. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Psychiatric Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2893

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]
belongs to
concept
Disease, Disorder or Finding c

Pulmonary Embolismni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C50713

The obstruction of the pulmonary artery or one of its branches by an embolus, sometimes associated with infarction of the lung. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Pulmonary Sarcoidosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34997

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]
belongs to
concept
Disease, Disorder or Finding c

Pulmonary Thromboembolismni back to ToC or Named Individual ToC

IRI: http://purl.bioontology.org/ontology/SNOMEDCT/233935004

Pulmonary embolism is caused by emboli, which have originated from venous thrombi, travelling to and occluding the arteries of the lung. [PMID:29770793]
belongs to
concept
Disease, Disorder or Finding c

Radius Fractureni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C99039

Traumatic or pathological injury to the radius bone in which the continuity of the bone is broken. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Recurrent Tumor Sampleni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0010943

A neoplastic sample derived from a recurrent tumor (not from a primary occurrence of a neoplasm). [Definition Source: The Experimental Factor Ontology]
belongs to
concept
Biosample Status c

Reference Sampleni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0009654

A material sample derived from cells or tissue representing a physiologically or phenotypically normal state. [Definition Source: The Experimental Factor Ontology]
belongs to
concept
Biosample Status c

Regional Base Ploidyni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0030064

Copy number assessment of regional base ploidy. [Definition Source: The Experimental Factor Ontology (EFO)]
belongs to
concept
Copy Number Assessment c

Renal Colicni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C78593

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]
belongs to
concept
Disease, Disorder or Finding c

Retinal Detachmentni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26874

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]
belongs to
concept
Disease, Disorder or Finding c

Rheumatoid Arthritisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2884

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]
belongs to
concept
Disease, Disorder or Finding c

Sample Dissociationni back to ToC or Named Individual ToC

IRI: http://www.ebi.ac.uk/efo/EFO_0009091

Process which results in the separation of a biological specimen into individual cells or a cell suspension. [Definition Source: EFO]
belongs to
concept
Sample Processing c

Sample Origin Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sampleOriginDetailTaxonomy

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]
belongs to
concept scheme

Sample Origin Type Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sampleOriginTypeTaxonomy

Category of sample origin. Value from Ontology for Biomedical Investigations (OBI) material entity (BFO:0000040) ontology. [Definition Source: GA4GH Beacon v2 Data Model]
belongs to
concept scheme

Sample Processing Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/sampleProcessingTaxonomy

belongs to
concept scheme

Sarcoidosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C34995

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]
belongs to
concept
Disease, Disorder or Finding c

Scarlet Feverni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C94575

A streptococcal infection, mainly occurring among children, that is characterized by a red skin rash, sore throat, and fever. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Seizure Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3020

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]
belongs to
concept
Disease, Disorder or Finding c

Serositisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C70428

Inflammation of a serous membrane. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Severeni back to ToC or Named Individual ToC

IRI: https://hpo.jax.org/browse/term/HP:0012828

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)]
belongs to
concept
Severity c

Severityni back to ToC or Named Individual ToC

IRI: https://hpo.jax.org/browse/term/HP:0012824

The intensity or degree of a manifestation. [Definition Source: HP]
belongs to
concept
Severity c

Severity Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/severityTaxonomy

SKOS Concept Hierarchy describing the severity level. Values from HP Ontology.
belongs to
concept scheme

Shoulder Dislocationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C35020

A dislocation of the shoulder joint. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Signni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C53458

Objective evidence of disease perceptible to the examining healthcare provider. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Sign or Symptomni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C100104

Objective evidence of disease perceptible to the examining practitioner (sign) and subjective evidence of disease perceived by the patient (symptom). [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Simple Heterozygousni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000458

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]
belongs to
concept
Zygosity c

Sinusitisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C35024

An acute or chronic inflammatory process affecting the mucous membranes of any sinus cavity. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Skin Basal Cell Carcinomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2921

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]
belongs to
concept
Disease, Disorder or Finding c

Skin Basosquamous Cell Carcinomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2922

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]
belongs to
concept
Disease, Disorder or Finding c

Skin Carcinomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4914

A carcinoma that arises from the skin. Representative examples are basal cell carcinoma and squamous cell carcinoma. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Skin Cystni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3884

A cystic lesion located in the skin. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Somatic Variantni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/SO_0001777

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]
belongs to
concept
Allele Origin c

Species Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/speciesTaxonomy

SKOS Concept hierarchy representing a species from the NCBI species taxonomy.
belongs to
concept scheme

Spina Bifidani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C101214

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]
belongs to
concept
Disease, Disorder or Finding c

Spinal and Bulbar Muscular Atrophy, X-linked 1ni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C85233

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]
belongs to
concept
Disease, Disorder or Finding c

Staphylococcal Infectionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C35038

Infection by Staphylococcus. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Stop Gained NMD Escapingni back to ToC or Named Individual ToC

IRI: http://www.sequenceontology.org/browser/current_release/term/SO:0002322

A stop_gained (SO:0001587) variant that allows the transcript to escape nonsense-mediated decay (NMD). [Definition Source: The Sequence Ontology]
belongs to
concept
Molecular Effect c

Strokeni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3390

A sudden loss of neurological function secondary to hemorrhage or ischemia in the brain parenchyma due to a vascular event. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Study Designni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500000

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]
belongs to
concept
Cohort Design c

Subdural Hematomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C116585

A collection of blood between the dura mater and the brain. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Symptomni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4876

Subjective evidence of disease perceived by the patient. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Syncopeni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C35053

A spontaneous loss of consciousness caused by insufficient blood supply to the brain. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Synthetic Sourceni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENEPIO_0001970

Synthetic DNA. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
belongs to
concept
Library Source c

Thalassemiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C35069

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]
belongs to
concept
Disease, Disorder or Finding c

Thoracic Traumani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C171204

Trauma to the chest. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Thromboembolismni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C28195

Occlusion of the lumen of a vessel by a thrombus that has migrated from a distal site via the blood stream. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Thyroid Gland Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26893

A non-neoplastic or neoplastic disorder that affects the thyroid gland. Representative examples include hyperthyroidism, hypothyroidism, thyroiditis, follicular adenoma, and carcinoma. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Thyroiditisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26894

Inflammation of the thyroid gland. This category includes Hashimoto thyroiditis, Riedel thyroiditis, acute thyroiditis, subacute thyroiditis, and radiation-induced thyroiditis. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Tibia Fractureni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C99083

Traumatic or pathological injury to the tibia in which the continuity of the bone is broken. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Tinea Versicolorni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C112833

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]
belongs to
concept
Disease, Disorder or Finding c

Tooth Abscessni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C35475

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]
belongs to
concept
Disease, Disorder or Finding c

Toxoplasmosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3418

A parasitic disease contracted by the ingestion or fetal transmission of toxoplasma gondii. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Transcriptomic Sourceni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENEPIO_0001971

Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries). [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
belongs to
concept
Library Source c

Transient Ischemic Attackni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C50781

A brief attack (from a few minutes to an hour) of cerebral dysfunction of vascular origin, with no persistent neurological deficit. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Trigeminal Nerve Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26952

A non-neoplastic or neoplastic disorder affecting the trigeminal nerve (fifth cranial nerve). [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Tumor Grade Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/tumorGradeTaxonomy

SKOS Concept hierarchy representing the tumor grade. Child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent. [Definition Source: GA4GH Beacon v2 Data model]
belongs to
concept scheme

Tumor Progression Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/tumorProgressionTaxonomy

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]
belongs to
concept scheme

Two Vessel Coronary Diseaseni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C100023

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]
belongs to
concept
Disease, Disorder or Finding c

Type 1 Diabtes Mellitusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2986

A chronic condition characterized by minimal or absent production of insulin by the pancreas. [Definition Source: NCI][attribution: NICHD]
belongs to
concept
Disease, Disorder or Finding c

Type 2 Diabetes Mellitusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26747

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]
belongs to
concept
Disease, Disorder or Finding c

Unit by Categoryni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C42568

belongs to
concept
Unit Of Measure c

Unit of Measure Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/uomTaxonomy

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]
belongs to
concept scheme

Unknownni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C17998

Not known, observed, recorded; or reported as unknown by the data contributor. [Defintion Source: NCI]
belongs to
concept
Cohort Sex c

Ureteral Stenosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C115958

Narrowing of the luminal diameter of one or both ureters due to intrinsic factors. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Uterine Corpus Leiomyomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3434

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]
belongs to
concept
Disease, Disorder or Finding c

Variant Originni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/SO_0001762

A quality inhering in a variant by virtue of its origin. [Definition Source: SO]
belongs to
concept
Allele Origin c

Vertigoni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C38057

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]
belongs to
concept
Disease, Disorder or Finding c

Viral Pericarditisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C128405

Pericarditis that is caused by an infection with a viral agent. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Viral RNA Sourceni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENEPIO_0001972

Viral RNA. [Definition Source: Genomic Epidemiology Ontology (GenEpiO)]
belongs to
concept
Library Source c

Vitiligoni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26915

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]
belongs to
concept
Disease, Disorder or Finding c

Vulvovaginal Candidiasisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2914

Infection of the vulva and vagina with a fungus of the genus CANDIDA. It is a disease associated with HIV infection. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Vulvovaginitisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C35131

An inflammatory pathologic process that affects the vulva and the vagina. [Definition Source: NCI]
belongs to
concept
Disease, Disorder or Finding c

Zygosityni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000133

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]
belongs to
concept
Zygosity c

Zygosity Taxonomyni back to ToC or Named Individual ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/zigosityTaxonomy

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]
belongs to
concept scheme

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals

References back to ToC

Acknowledgments back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.