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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 Influenza Tuberculosis IDO Plasmodium falciparum S. aureus 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