The Core Infectious Disease Ontology

1. The Core Infectious Disease Ontology

2. 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

3. 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

4. Purpose of the core IDO Provide ontology coverage of entities common to many infectious disease Provide a thoroughly tested template

5. IDO Development Strategy Import or refer to terms contained in OBO Foundry reference ontologies Define new terms as cross-products from other Foundry ontologies

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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