Transcript Cowell IDO - Buffalo Ontology Site

The Core Infectious Disease
Ontology
Purpose: To make infectious disease-relevant
data deriving from different sources comparable
and computable
• Across data types
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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
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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
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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
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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
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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
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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