bfo-aligned ontologies for clinical and translational research: ogms, ido, and vo (orlando...
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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 SchoolAnn Arbor, MI 48109
BFO and OBO Foundry Principles
• BFO: Basic Formal Ontology
• 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
• Funded by a NIAID R01 grant
http://www.violinet.org/vaccineontology
http://www.violinet.org
Many Ontology Tools developed during VO development
is_aontology
development tool
Hegroup RDF triple
store
Ontorat: generate new ontology
terms
OntoFox: reuse existing ontology
terms
is_a
Ontodog: generate ontology community
view
Ontobee: linked ontology
data server
uses
is_a
ontology application
tool
uses
uses
uses is_a
is_a
uses is_a
OntoCOG: COG enrichment
analysis tool
Ontobat: biodata analysis tool
(In development)
Ontology fetching tool Linked ontology data server
Mass generation of new terms
Ontology community view generator
Ontology data analysis
VO Statistics and Development
# Class ObjectProperty Subtotal
VO 4800 7 4807BFO 2 22 38 60
RO 0 4 4CARO 9 0 9CHEBI 20 0 20DOID 57 0 57
GO 19 0 19OBI 36 11 47
OGMS 1 0 1PATO 17 0 17FMA 2 0 2IAO 18 2 20IDO 2 0 2
NCBITaxon 397 0 397PRO 2 0 2
UBERON 8 0 8UO 1 0 1
Subtotal 5411 62 5473
• 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
Courtesy: figure kindly provided by Jeff Cowall
Acknowledgements
Funding: NIH grants R01AI081062 & U54-DA-021519UM MCubed pilot project, MICHR (UM CTSA)
Oliver He Group:
• Zuoshuang “Allen” Xiang• “Asiyah” Yu Lin• Sirarat Sarntivijai
UM Literature Mining Collaborators:
• Arzucan Özgür • Junguk Hur
VO Collaborators:
Barry, Lindsay, Alan, Bjoern, ….
Barry Smith (BFO, OGMS, IDO, VO, ...)
OBI Consortium:
• Bjoern Peters• Jie Zheng• Chris Stoeckert• Alan Rutternberg• Melanie Courtot, …
UM Ontology Working Group Listed in a previous slide
Lindsay Cowell (IDO)
OGMS Development Team
• Albert Goldfain • Richard Scheuermann, …
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