The Core Infectious Disease Ontology

Purpose: To make infectious disease-relevant data deriving from different sources comparable

and computable

• Across data types– Sequence data for pathogens, patients– Case report data for patients– Clinical trial data for drugs, vaccines– Epidemiological Data for surveillance, prevention

• Across domains– clinical care and research, basic biomedical research,

and public health domains

• Across diseases– Across pathogens– Across hosts

Benefits of the Template Ontology Approach

• Allows parallel development of multiple interoperable ontologies– Distributed development

• rapid progress• curation by subdomain experts

– Terminological consistency• term names and meanings• Classification

– Single point for checking and testing

• Eliminates duplication of effort• Prevents common mistakes

– Guideline

Purpose of the core IDO

• Provide ontology coverage of entities common to many infectious disease

• Provide a thoroughly tested template

IDO Development Strategy

• Import or refer to terms contained in OBO Foundry reference ontologies

• Define new terms as cross-products from other Foundry ontologies

Independent Continuants in IDO

• Anatomical location: FMA: e.g. lung, kidney

• Protein: PRO: e.g virulence factors such as Eap

• Cell: CL: e.g. macrophages

• Pathological anatomical entity: e.g. granuloma, sputum, pus

Occurrents in IDO

• Imported from GO BP when possible e.g. GO:0044406 : adhesion to host

• Population-level process: e.g. emergence, epidemiological spread of disease

• Clinical process: e.g. injection of PPD• Pathological processes: granuloma

formation• Disease-specific process:

•Adhesion to host•S. aureus adhesion to host

Dependent Continuants in IDO

• Quality: PATO: e.g. attenuated, susceptible, co-infected, immunocompromised, drug resistant, zoonotic

• Role: e.g. host, pathogen, vector, carrier, reservoir, virulence factor, adhesin

Managing the Monster

• Huge scope• Coordination of large number of extensions• Coordination of large number of imported terms

IDO

Tuberculosis

S. aureus

Influenza

Plasmodiumfalciparum

Logistics

• Namespaces and identifiers• Term importing• Versioning of core and extensions• Migration of extensions after changes to

core• Coordination, how will we work together• What kind of services do we need to

offer

Namespaces

• Preserve namespace and identifier of imported terms– benefits

• Namespace for core IDO

• Namespace for extensions– Based on pathogen (e.g. IDO-Br)– Alternatives - disease, pathogen and host

Logistics

• Namespaces and identifiers• Term importing

– Ontology editors– Purl

• Versioning of core and extensions• Migration of extensions after changes to core• Coordination, how will we work together• What kind of services do we need to offer

Logistics

• Namespaces and identifiers• Term importing• Versioning of core and extensions

– CVS– obo.sf.net

• Migration of extensions after changes to core• Coordination, how will we work together• What kind of services do we need to offer

Logistics

• Namespaces and identifiers• Term importing• Versioning of core and extensions• Migration of extensions after changes to

core– Extensions include only subtypes of IDO types– Use Aristotelian definitions– Use of crossproducts

• Coordination, how will we work together• What kind of services do we need to offer

Logistics

• Namespaces and identifiers• Term importing• Versioning of core and extensions• Migration of extensions after changes to core• Coordination, how will we work together

– Wiki– Consistency checker

• What kind of services do we need to offer

Logistics

• Namespaces and identifiers• Term importing• Versioning of core and extensions• Migration of extensions after changes to

core• Coordination, how will we work together• What kind of services do we need to

offer