Towards an Autoimmune Disease Ontology Alexander D. Diehl 6/13/12

Neurological Disease Ontology (ND) – Based on the Ontology for General Medical Sciences – Incorporates parts of NIF-Dysfunction – Three initial areas of focus Dementia, in particular Alzheimer’s Disease Multiple Sclerosis Stroke, Cerebrovascular events

Goals To provide a comprehensive representation of neurological diseases to support clinicians and researchers in the diagnosis, treatment, and study of these diseases. To facilitate querying of medical databases for such purposes as performing quality analysis checks on diagnostic criteria at various stages of a disease’s progression. To allow physicians and researchers to provide a comprehensive clinical picture of a patient using a standardized language, and to connect and leverage structured descriptions in clinical and translational medicine, in EHRs and published research. To develop best practices for the development of other clinically oriented ontologies by identifying a robust set of relations for use with diseases and by providing an applied template for representing temporal entities within a domain.

BFO-OGMS-ND

Diseases

Alzheimer’s Disease

Referenced Ontologies Ontology Name:Use in ND: Basic Formal Ontology (BFO)Top-level parent ontology Ontology for General Medical Science (OGMS) Mid-level parent ontology Neuroscience Information Framework (NIF)-Dysfunction Externally referenced many disease terms Relations Ontology (RO)Imported core relations Protein Ontology (PR)MIREOTed protein terms Foundational Model of Anatomy (FMA) MIREOTed anatomical terms PATO, ChEBI, GO, CL, and OBIMIREOTed select terms

Status  ND currently contains 335 classes  199 classes have textual definitions  52 classes have logical definitions  157 classes have external references  There are 190 children of disease First Public release planned by September 2012.

What is Autoimmunity? In immunology, the condition in which one's own tissues are subject to deleterious effects of actions of the immune system, as in autoallergy and in autoimmune disease; specific humoral or cell-mediated immune response against the body's own tissues.

What is Autoimmunity? Autoimmunity: A misdirected immune response that occurs when the immune system goes awry and attacks the body itself. Autoimmunity is present to some extent in everyone and is usually harmless. However, autoimmunity can cause a broad range of human illnesses, known collectively as autoimmune diseases. Autoimmune diseases occur when there is progression from benign autoimmunity to pathogenic autoimmunity. This progression is determined by genetic influences as well as environmental triggers. Autoimmunity is evidenced by the presence of autoantibodies (antibodies directed against the person who produced them) and T cells that are reactive with host antigens.

GO Definition of Immune Response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. Source: GO_REF: , GOC:add, GOC:mtg_15nov05

Autoimmune Response An immune response directed against an antigen, such as protein, carbohydrate, or nucleic acid, which has been produced by the same organism that is mounting the immune response. Antigen (GO) Any substance which is capable of inducing a specific immune response and of reacting with the products of that response.

Antigen A material entity that has the antigen role. (OBI) Antigen Role Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response. (OBI) (would seem to exclude auto-antigens)

Antigen A material entity bearing the antigen role. Antigen Role A role played by material entity in virtue of its being a substrate for binding by an adaptive immune receptor.

Epitope A material entity bearing the epitope role. (OBI) Epitope Role (not defined by OBI) A role played by a portion of a material entity in virtue of its being a substrate for binding by an adaptive immune receptor.

antigenepitope Has_part

Immunogen A material entity bearing the immunogen role. (OBI) Immunogen Role Any entity capable of eliciting an immune response when introduced to components of the immune system. (OBI) (suggestive of immunization)

antigenepitope has_part immunogen is_a

Adaptive Immune Response An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory). Source: GO_REF: , GOC:add, GOC:mtg_15nov05, ISBN:

Are there autoimmune disease which are solely driven by the innate immune response?

Innate Immune Response Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. Source: GO_REF: , GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu “potential pathogen” = mistaken recognition of self component.

Terms needed adaptive autoimmune response innate autoimmune response autoimmune disorder A disorder resulting from a clinically abnormal autoimmune response. autoimmune disease A disease that has as its material basis an autoimmune disorder.

Acknowledgments University at Buffalo Alexander Cox Mark Jensen William Duncan Kinga Szigeti Bianca Weinstock-Guttman Alan Ruttenberg Barry Smith