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.
The FAIRVASC Ontology
The labels for concepts introduced for this ontology are still pending approval.
Relates a patient overview/summary to their overall ANCA results.
has Anti-neutrophil cytoplasm antibodies (ANCA)
Relates an encounter to a birmingham vasculitis score
has Birmingham Vasculitis Activity Score (BVAS)
Relates a patient to the clinical outcome of their disease.
has Clinical Outcome
Relates an encounter to a clinical test.
has Clinical Test
Relates a patient overview to their comorbidities.
has Comorbidities
Relates a patients outcomes to complications.
has Complication
Relates a patient overview/summary to their overall diagnosis.
has Diagnosis
Relates a patient to an encounter related to their vasculitis.
has Encounter
Relates a patients overivew/summary to their overall organ pattern organ pattern.
has Organ Pattern
Relates a Patient to their Patient Overview/Summary
has Patient Overview
Relates a patients overview to a treatments
has received treatments
Relates a patients overview to their induction treatments
has received induction treatments
body mass index
An approximate defition for ESKD defined by the registry
approximated end stage kidney disease
Dialysis indicating end stage kidney disease occured
dialysis indicating end stage kidney disease
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
standard defintion of end stage kidney disease
a string value which represents the organ affected
organ affected
Value for ANCA Immunofluorescence (IF). Possible values are: <cANCA positive, pANCA positive, Atypical, Negative, Not tested>
has ANCA Immunofluorescence (IF) result
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>
has ANCA Specificity (ELISA) results
cause of death
complication severity
type of complication
date of complications
date of death
the date this patients diagnosis took place
date of diagnosis
date when end stage kidney disease took place
date of end stage kidney disease
date of encounter
death
The gender of the patient. Possble values are <Male, Female, other>
gender
this indicates whether the term returned is a generic term, or a more specific term
is generic
patients height at diagnosis
height
the date of the last recorded contact of the patient with the registry
last recorded contact
main diagnosis
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
MPO Titre default give either a negative, positive or not available value
MPO Titre Default
a string value which represents a disease pattern for lungs
organ disease pattern lungs
an identifier for a patient, generally taken from the identifier in the associated registry
patient identifier
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
PR3 Titre default give either a negative, positive or not available value
PR3 Titre Default
severe
the date a clinical test took place (which could be after a specific patient encounter)
date test took place
type of test
unit of test
value of test
relates a patients overview with a specific type of treatment
treatment type
weight
year of birth
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.
Anti-neutrophil cytoplasm antibodies (ANCA)
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 Outcomes
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.
Clinical Test
This classes representesnt comorbidities a patient had when they enlisted as a patient to the registry.
Complication
This class represents any complications that a patient of a vasculitis registry experienced due to vasculitis.
This class represents cardiovascular complications that are the related to vasculitis.
Complication Cardiovascular
This class represents infections that are the result of complications related to vasculitis.
Complication Infection
This class represents malignancies that are the result of complications related to vasculitis.
Complication Malignancy
This class represents thromboembolism complications that are the related to vasculitis.
Complication Thromboembolism
This class represents a person's diagnosis of vasculitis and (possibly a small number of) other diseases.
Diagnosis
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.
Encounter
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.
Organ Pattern
Patient
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.
Patient Overview
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 Query
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.
Provenenace Activity Uplift
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.
Treatment
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.
An induction treatment
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.
A maintenance treatment