The FAIRVASC Ontology
type: Ontology
imports: bvas
license: http://creativecommons.org/licenses/by/4.0/
creator: ADAPT
date: 2021-05-06
publisher: www.adapt-centre.ie
rights: The FAIRVASC Ontology is available under the CC 4.0 BY License; see http://creativecommons.org/licenses/by/4.0/. This license lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. For proper attribution, simply include the statement: "This work is based on the analysis of Rare Kidney Disease Registries in seven European countries; Ireland, Sweden, Germany, Czechoslovakia, Poland, UK and France and has been developed in collaboration with the ADAPT Centre, Trinity College Dublin.
comment: The labels for concepts introduced for this ontology are still pending approval.
version info: 2.00.000

has Anti-neutrophil cytoplasm antibodies (ANCA)
type: ObjectProperty
domain: Patient Overview
range: Anti-neutrophil cytoplasm antibodies (ANCA)
comment: Relates a patient overview/summary to their overall ANCA results.

has Birmingham Vasculitis Activity Score (BVAS)
type: ObjectProperty
domain: Encounter
range: BVAS
comment: Relates an encounter to a birmingham vasculitis score

has Clinical Outcome
type: ObjectProperty
domain: Patient
range: Clinical Outcomes
comment: Relates a patient to the clinical outcome of their disease.

has Clinical Test
type: ObjectProperty
domain: Encounter
range: Clinical Test
comment: Relates an encounter to a clinical test.

has Comorbidities
type: ObjectProperty
domain: Patient Overview
range: Comorbidities
comment: Relates a patient overview to their comorbidities.

has Complication
type: ObjectProperty
domain: Clinical Outcomes
domain: Encounter
range: This class represents any complications that a patient of a vasculitis registry experienced due to vasculitis.
comment: Relates a patients outcomes to complications.

has Diagnosis
type: ObjectProperty
domain: Patient Overview
range: Diagnosis
comment: Relates a patient overview/summary to their overall diagnosis.

has Encounter
type: ObjectProperty
domain: Patient
range: Encounter
comment: Relates a patient to an encounter related to their vasculitis.

has Organ Pattern
type: ObjectProperty
domain: Patient Overview
range: Organ Pattern
comment: Relates a patients overivew/summary to their overall organ pattern organ pattern.

has Patient Overview
type: ObjectProperty
domain: Patient
range: Patient Overview
comment: Relates a Patient to their Patient Overview/Summary

has received treatments
type: ObjectProperty
domain: Patient Overview
range: Treatment
comment: Relates a patients overview to a treatments

has received induction treatments
type: ObjectProperty
sub property of: has received treatments
domain: Patient Overview
range: An induction treatment
comment: Relates a patients overview to their induction treatments

body mass index
type: DatatypeProperty
domain: Patient Overview
range: double
comment: body mass index

approximated end stage kidney disease
type: DatatypeProperty
domain: Clinical Outcomes
range: boolean
comment: An approximate defition for ESKD defined by the registry

dialysis indicating end stage kidney disease
type: DatatypeProperty
domain: Clinical Outcomes
range: boolean
comment: Dialysis indicating end stage kidney disease occured

standard defintion of end stage kidney disease
type: DatatypeProperty
domain: Clinical Outcomes
range: boolean
comment: The standard defintion for ESKD in FAIRVASC is defined as any of: a) dialysis for >90 days; b) sustained CKD 5 (eGFR < 15 ml/min/1.73m2) for >90 days; and/or c) kidney transplantation

organ affected
type: DatatypeProperty
domain: Organ Pattern
range: anyURI
comment: a string value which represents the organ affected

has ANCA Immunofluorescence (IF) result
type: DatatypeProperty
domain: Anti-neutrophil cytoplasm antibodies (ANCA)
range: string
comment: Value for ANCA Immunofluorescence (IF). Possible values are: <cANCA positive, pANCA positive, Atypical, Negative, Not tested>

has ANCA Specificity (ELISA) results
type: DatatypeProperty
domain: Anti-neutrophil cytoplasm antibodies (ANCA)
range: string
comment: The ELISA (enzyme-linked immunosorbent assay) is a widely used application for detecting and quantifying proteins and antigens from various samples. Possible values include: <MPO positive, ELISA negative, PR3 positive, other, No Elisa performed, MPO and PR3 positive>

cause of death
type: DatatypeProperty
domain: Clinical Outcomes
range: string
comment: the main cause of a patients death

complication severity
type: DatatypeProperty
domain: This class represents any complications that a patient of a vasculitis registry experienced due to vasculitis.
range: anyURI
comment: the severity of a complication

type of complication
type: DatatypeProperty
domain: This class represents any complications that a patient of a vasculitis registry experienced due to vasculitis.
range: anyURI
comment: the type of complication

date of complications
type: DatatypeProperty
domain: This class represents any complications that a patient of a vasculitis registry experienced due to vasculitis.
range: dateTime
comment: the date when complications took place

date of death
type: Property
type: DatatypeProperty
domain: Clinical Outcomes
range: dateTime
comment: the date a patient died

date of diagnosis
type: DatatypeProperty
domain: Diagnosis
range: dateTime
comment: the date this patients diagnosis took place

date of end stage kidney disease
type: DatatypeProperty
domain: Clinical Outcomes
range: dateTime
comment: date when end stage kidney disease took place

date of encounter
type: DatatypeProperty
domain: Encounter
range: dateTime
comment: the date when an encounter took place

death
type: DatatypeProperty
domain: Clinical Outcomes
range: boolean
comment: Did death occur?

gender
type: DatatypeProperty
domain: Patient
range: string
comment: The gender of the patient. Possble values are <Male, Female, other>

is generic
type: DatatypeProperty
domain: This class represents any complications that a patient of a vasculitis registry experienced due to vasculitis.
domain: Organ Pattern
range: boolean
comment: this indicates whether the term returned is a generic term, or a more specific term

height
type: DatatypeProperty
domain: Patient Overview
range: double
comment: patients height at diagnosis

last recorded contact
type: DatatypeProperty
domain: Clinical Outcomes
range: dateTime
comment: the date of the last recorded contact of the patient with the registry

main diagnosis
type: DatatypeProperty
domain: Diagnosis
range: anyURI
comment: The main diagnosis for the patient

MPO Titre
type: DatatypeProperty
domain: Clinical Test
range: string
comment: mpo Titre has a value of either negative, not available, or high low positive. The threshold for Low / High positive is derived based on a local analysis, using geometric mean as a cut off.

MPO Titre Default
type: DatatypeProperty
domain: Clinical Test
range: string
comment: MPO Titre default give either a negative, positive or not available value

organ disease pattern lungs
type: DatatypeProperty
domain: Organ Pattern
range: anyURI
comment: a string value which represents a disease pattern for lungs

patient identifier
type: DatatypeProperty
domain: Patient
range: string
comment: an identifier for a patient, generally taken from the identifier in the associated registry

PR3 Titre
type: DatatypeProperty
domain: Clinical Test
range: string
comment: PR3 Titre has a value of either negative, not available, or high low positive. The threshold for Low / High positive is derived based on a local analysis, using geometric mean as a cut off.

PR3 Titre Default
type: DatatypeProperty
domain: Clinical Test
range: string
comment: PR3 Titre default give either a negative, positive or not available value

severe
type: DatatypeProperty
domain: This class represents any complications that a patient of a vasculitis registry experienced due to vasculitis.
range: boolean
comment: was a complication severe

date test took place
type: DatatypeProperty
domain: Clinical Test
range: dateTime
comment: the date a clinical test took place (which could be after a specific patient encounter)

type of test
type: DatatypeProperty
domain: Clinical Test
range: string
comment: the type of test

unit of test
type: DatatypeProperty
domain: Clinical Test
range: string
comment: the unit used in a test

value of test
type: DatatypeProperty
domain: Clinical Test
range: double
comment: the value of a test

treatment type
type: DatatypeProperty
domain: Treatment
range: anyURI
comment: relates a patients overview with a specific type of treatment

weight
type: DatatypeProperty
domain: Patient Overview
range: double
comment: patients weight at diagnosis

year of birth
type: DatatypeProperty
domain: Patient
range: gYear
comment: the year a patient was born

Anti-neutrophil cytoplasm antibodies (ANCA)
type: Class
comment: These are autoantibodies that target a type of human white blood cell called neutrophils, which are important in health for fighting infection partly through the release of toxic substances that destroy bacteria. In ANCA-associated vasculitis, ANCA specifically bind to two proteins called proteinase 3 (PR3) and myeloperoxidase (MPO). Patients with ANCA-associated vasculitis usually have autoantibodies against PR3 (PR3-ANCA) or MPO (MPO-ANCA) but not both. ANCA also contributes to blood vessel damage.

Clinical Outcomes
type: Class
comment: Clinical outcomes represent the class of measurable changes in health, function or quality of life that result from a treatment of care , for vasculitis. Important outcomes are related to date recorded of end stage kidney disease, death (and cause) of death, and the last recorded contact of the patient with the registry. Clinical Outcomes are also related to complications

Clinical Test
type: Class
comment: This class represents a test conducted at an encounter, for example, a blood test. A typical blood test in vasculitis would be to determine creatinine levels. Creatinine is a waste product produced by muscles and is excreted from the body by the kidneys. Blood levels of creatinine are used as a measure of kidney function.

Comorbidities
type: Class
comment: This classes representesnt comorbidities a patient had when they enlisted as a patient to the registry.

This class represents any complications that a patient of a vasculitis registry experienced due to vasculitis.
type: Class
label: Complication

Complication Cardiovascular
type: Class
subclass of: This class represents any complications that a patient of a vasculitis registry experienced due to vasculitis.
comment: This class represents cardiovascular complications that are the related to vasculitis.

Complication Infection
type: Class
subclass of: This class represents any complications that a patient of a vasculitis registry experienced due to vasculitis.
comment: This class represents infections that are the result of complications related to vasculitis.

Complication Malignancy
type: Class
subclass of: This class represents any complications that a patient of a vasculitis registry experienced due to vasculitis.
comment: This class represents malignancies that are the result of complications related to vasculitis.

Complication Thromboembolism
type: Class
subclass of: This class represents any complications that a patient of a vasculitis registry experienced due to vasculitis.
comment: This class represents thromboembolism complications that are the related to vasculitis.

Diagnosis
type: Class
comment: This class represents a person's diagnosis of vasculitis and (possibly a small number of) other diseases.

Encounter
type: Class
comment: This class covers all “encounters” the patient has with their medical professionals. Types of encounters include; BVAS, Tests (e.g. blood tests which include all recorded creatinine levels), and a record of each recorded complications over the course of their disease etc.

Organ Pattern
type: Class
comment: This class represents the different organs which have been affected by vasculitis. It is important to note that not every organ system will be affected in every patient. The pattern of organ involvement (and symptoms) is unique to the individual, as well as the type of vasculitis. It is derived either from direct observations, or through the use of BVAS. Organ patterns are mapped to SNOMED-CT codes.

Patient
type: Class
comment: A patient of a vasculitis registry.

Patient Overview
type: Class
comment: This class represents an overview of the patient health in relation to vasculitis. The overview consists of the patient’s current diagnosis, their ANCA and also how their organs have been affected over the course of their disease.

Provenenace Activity Query
type: Class
subclass of: Activity
comment: This class represents provenance data related to activity og querying of an RDF graph, for example when a query was made, who made a query and the type of query made.

Provenenace Activity Uplift
type: Class
subclass of: Activity
comment: This class represents provenance data related to the activity of uplifting of tabular data into RDF. It records data such as the name of the file being uplidfted (e.g. a CSV file name), the name of the mapping file (e.g. an R2RML mapping file), the name of the resulting graph generated by this uplift, and the responsible party for conducting the uplift activity.

Treatment
type: Class
comment: This class describes the treatments for AAV. The most important component of treatment is strong medication which suppresses the immune system, which is inappropriately activated in AAV. This immunosuppressive treatment is typically considered as either 'induction' or 'maintenance' therapy.

An induction treatment
type: Class
subclass of: Treatment
comment: Induction therapy is very strong immunosuppression given with the intent of controlling active, potentially life-threatening, AAV. Once disease control is achieved, a transition to maintenance therapy can take place, which typically consists of moderate strength immunosuppressive treatments. Typical induction treatment includes a combination of IV or oral cyclophosphamide, IV rituximab, high-dose IV or oral glucocorticoids and plasma exchange.

A maintenance treatment
type: Class
subclass of: Treatment
comment: Typical maintenance therapy might include azathioprine, low-dose glucocorticoids or intermittent IV rituximab. If a patient suffers a serious relapse, induction treatment may be used again. Overall, treatment usually continues for at least two years.

date of care pathway start
type: DatatypeProperty
domain: Patient
range: dateTime
comment: the date of starting care pathway for patients

date at onset
type: DatatypeProperty
domain: Diagnosis
range: dateTime
comment: the date of onset for patients

Consent
type: Class
comment: Consent

the identifier for the biobank
type: DatatypeProperty
domain: Consent
range: dateTime
comment: the date of onset for patients
label: date at onset

Future Contact Consent Information
type: DatatypeProperty
domain: Consent
range: boolean
comment: Future Contact Consent Information

Data Use In Registry Consent Information
type: DatatypeProperty
domain: Consent
range: boolean
comment: Data Use In Registry Consent Information

Biobank Consent Information
type: DatatypeProperty
domain: Consent
range: boolean
comment: Biobank Consent Information