BFO-aligned Ontologies for Clinical and Translational Research: OGMS, IDO, and VO (Orlando Presentation, 2/8/2013) http:// ncorwiki.buffalo.edu/index.php/CTSA_Ontology_Workshop Yongqun “Oliver” He University of Michigan Medical School Ann Arbor, MI 48109
18
Embed
BFO-aligned Ontologies for Clinical and Translational Research: OGMS, IDO, and VO (Orlando Presentation, 2/8/2013) .
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
BFO-aligned Ontologies for Clinical and Translational Research:
• BFO has been used a top level ontology for many ontologies associated with clinical and translational research
• Examples: OGMS, IDO, VO, OBI, OAE
• All OBO foundry library ontologies follow OBO Foundry principles, e.g., openness, collaboration, and use of a common shared syntax
OGMS: Ontology of General
Medical Science • An ontology of the major
types of entities involved in a clinical encounter.– An upper ontology for
clinical medicine– A mid-level ontology with
respect to BFO
• Includes ~100 general terms
• By: – Albert Goldfain – Richard Scheuermann– Barry Smith, …
https://code.google.com/p/ogms/
Wide OGMS Applications
Ontologies using OGMS:
• IDO• DO• SDO• AERO • OAE• VSO• OMRSE• VO• ...
Courtesy: figure kindly provided by Albert Goldfain
OGMS application example:Development of OAE
• OAE: Ontology of Adverse Events• OAE ‘adverse event’:
– = def. a OGMS: ‘pathological bodily process’ that occurs after a medical intervention.
– Does not assume causality – ‘causal adverse event’ assumes causality
• >1,000 specific AE terms in OAE now, mapped to MedDRA terms
OAE for AE data analysisRef: Sarntivijai et al., 2012PLoS ONE
IDO: Infectious Disease Ontology
• IDO: represent the entire infectious disease domain
• Interoperability with other disease and health domains
• IDO-core: by Lindsay Cowell, Barry Smith, and others
Courtesy: figure kindly provided by Lindsay Cowell
IDO-core Central Terms:
IDO Core-Extension Development Strategy
• IDO extensions are developed by extending IDO-core
OGMS
OBIGO BP
CL
I IDO-Core
IDO-Bac
IDO-Virus
IDO-Sa
IDO-Flu IDO-Mal
IDO-Par
IDO-Fun
IDO-Flav
IDO-TB
IDO-Sch
IDO-Asp
IDO-Cry
Courtesy: figure kindly provided by Lindsay Cowell
• We developed an IDO extension: Brucellosis Ontology
IDOBRU: Brucellosis Ontology as an IDO Extension
• Focuses on the domain of zoonotic brucellosis, caused by Gram-negative bacterium Brucella.
• Incorporates all IDO-core terms, has over 880 Brucella-specific terms, and imports terms from other ontologies.
Citation: “Asiyah” Yu Lin, Zuoshuang Xiang, Yongqun He. Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. Journal of Biomedical Semantics. 2011 Oct 31;2(1):9. PMID: 22041276.
IDO-core is the top ontology of IDOBRU
Vaccine Ontology (VO)
• VO: A biomedical ontology in the domain of vaccine and vaccination
• Support data integration, literature mining, and reasoning
• Integrated with VIOLIN• VIOLIN: a vaccine database and analysis
system, including many programs, e.g.:o ~3000 vaccineso Protegen: protective antigens. ~600o Vaxjo: vaccine adjuvants: > 100o Vaxign: vaccine designo Widely used by vaccine community
• OntoFox to import external terms and axioms from other 16 ontologies
• Ontorat to generate a large number of terms and axioms automatically
• VO includes >1000 vaccines for >20 host spp. against various diseases
VO imports OBI terms for vaccine investigation
OBI/VO modeling of “vaccine protection
assay”
Reference: Brinkman et al. (2007). Modeling biomedical experimental processes with OBI. Journal of Biomedical Semantics. 2010, 1(Suppl 1):S7. PMID: 20626927.
OBI: Ontology for Biomedical Investigations
~20 communities involved
Example: Afluria Influenza Vaccine
Afluria-1Flu vaccine
is_a
CSL Limited
intramuscular vaccination
adaptive immune response
is_manufactured
_byinactivated
chicken egg protein allergen
has_quality has_part
bearer_of
vaccine allergen
disposition
bearer_of
dose specification
viral vaccine-induced
immunization
has_specified_output_ofis_specified_
input_of
has_part bearer_of some ‘acquired immunity to Influenza virus’
age
viral pathogen target role
Influenza virus
has_participant
is_about
Bob (a human)
realizes
vaccine host role
has_quality
age measurement datum (value: 6
unit: month)
quality_is_measured_as
has_participant
realizes
bearer_of
measurementdata
is_a has_participant
plan specification
is_realized
-byhas_part
U of Michigan Ontology Research
• UM Ontology Working Group:o Members: Marcy Harris, Alla Karnovsky, Frank Manion,
Oliver He, Asiyah Yu Lin, Jeff Cowall, … o Activities: Biweekly meetings, …o Developing a Clinical and Translational Research Ontology.
• UM MCubed pilot award:o Title: Ontology Development and Applications for Clinical
and Translational Scienceo To: Alla, Marcy, and Oliver; Period: 1.5 years
• UM CTSA: Michigan Institute for Clinical & Health Research (MICHR)o Ontology research needed to integrate huge datasets o Committed to collaborative community efforto One project: Informed Consent Ontology (ICO) (next slide)
• Case study: Head and neck cancer biorepository
Informed Consent Ontology (ICO)• ICO: A prototype, aligned with BFO.• Currently focused on research permissions• UM CTSA Project Team:
Alla Karnovsky, Frank Manion, Marcy Harris, Oliver He, Nick Steneck, Blake Roessler
Reference: Development of an Informed Consent Ontology to Support Biobanking. Alla Karnovsky, Frank J. Manion, Oliver He, Terry Weymouth, V. Glenn Tarcea; Lisa Powell, Blake J. Roessler, Nicholas H. Steneck. AMIA 2012 Annual Symposium.
Protocol
Patient Record
Institutional Records
IRB/eResearch
Informed Consent Form
Subject matter expert view
Courtesy: figures kindly provided by Alla Karnovsky and Nickolas Steneck
Clinical Data Integration Required• Records of millions of patients in UM Health System (UMHS)• Ontology is needed for true clinical data integration