Download VO - Buffalo Ontology Site

Vaccine Ontology (VO)
Yongqun “Oliver” He
Unit for Laboratory Animal Medicine
Department of Microbiology and Immunology
Center for Computational Medicine and Biology
& Comprehensive Cancer Center
University of Michigan Medical School
Ann Arbor, MI 48109
Vaccine Research & Development
(R & D)
• Vaccine: improve immunity to a particular
disease
• 1796: Edward Jenner’s cowpox-based
vaccine against smallpox
• Louis Pasteur: developed several vaccines
– Anthrax vaccine (1881),
– Rabies Vaccine (1885)
• Ever increasing Vaccine R&D:
– Cost effectiveness
– Post-genomic technologies
Vaccine Publications in PubMed
200000
No. of Vaccine Publications
180000
160000
140000
120000
100000
80000
60000
40000
20000
0
18901950
1960
1970
1980
1990
2000
2008
Time (Year)
Vaccine publications have increased exponentially
Vaccine Databases
• Government, e.g.
– CDC ( http://www.cdc.gov/vaccines/ )
– NIH ( http://www3.niaid.nih.gov/Biodefense/Research/funding.htm )
– FDA ( http://www.fda.gov/cber/vaccines.htm )
• Organizations, e.g.
– WHO ( http://www.who.int/immunization_safety/en/ )
– The Vaccines Page ( http://www.vaccines.org/ )
– National Network for Immunization Information:
( http://www.immunizationinfo.org/VaccineInfo/index.cfm )
• Academia, e.g.,
– HIV Vaccine Trials Network: ( http://chi.ucsf.edu/vaccines/ )
• Commercial vaccine companies
• Focus: knowledge and administration of licensed
vaccines or vaccines in clinical trial
VIOLIN: Vaccine Investigation
and Online Information Network
• Overall goal: A vaccine research database and
vaccine data analysis system
• Aims:
– Curate from publications: vaccines and vaccine
candidates in use, clinical trials, and research
– Vaccine data mining and comparison
– Help vaccine design
– Community-based vaccine information network
• Publically available: http://www.violinet.org/
VIOLIN Database Contents
Host
Response
Host
protect
cause
disease
Host Gene
Response
induce
Vaccine
Gene/
Protein
against
made by
Pathogen
Gene
Engineer
Focus: gene/protein engineering/response
VIOLIN Statistics
275 vaccines
20 pathogens
129 pathogen
genes
530 papers
Data Analysis:
** Vaccine query
** Vaccine genes and antigens
** BLAST
** Vaccine target predication
** Data exchange: VIOLINML
Literature tools:
Literature:
>24,000 abstracts
>10,000 full text articles
-- Litesearch
-- Vaxpresso: NLP
-- Vaxmesh: MeSH
-- Vaxlert: Paper alert
Query Example:
New! Q: How to predict vaccine targets?
Vaxign: Vaccine Design Program
Predict vaccine protein and epitope targets
 Reverse vaccinology
http://www.violinet.org/vaxign
What’s Missing in VIOLIN?
• Lacks efficient ways to let computers answer
literature mining question from >160,000
papers.
• Difficult to establish vaccine-induced host
immune response networks.
• How to deal with it?
Solution: Vaccine Ontology!
Collaborative VO Development
• VO is developed as a collaborative effort:
– VIOLIN and Vaccine Researchers at U of Michigan (UM)
• Yongqun “Oliver” He (Interest: Brucella vaccine R&D)
• Harry Mobley (Interest: E. coli vaccine R&D)
• UM vaccine informatics and resource advisory committee
– Infectious Disease Ontology
(IDO, http://www.infectiousdiseaseontology.org/ )
• Lindsay Cowell (Duke)
• Barry Smith (Buffalo)
• Yongqun “Oliver” He (Michigan)
– National Center for Biomedical Ontology
(NCBO, http://bioontology.org/ )
• Barry Smith (Buffalo)
• Mark Musen (Stanford)
• Web site: http://www.violinet.org/vaccineontology/
Vaccine Ontology (VO)
• Two forms of VO:
– Core VO: general terms for all diseases
– Disease-specific extensions: e.g., diseases caused by E.
coli & Brucella spp.
• Utilize the Basic Formal Ontology (BFO), the toplevel ontology, developed by Dr. Barry Smith and his
associates.
• Follow OBO Foundry principles, e.g.,
– Developed in a collaborative effort
– Use common relations that are unambiguously defined
– Provide procedures for user feedback
Reference: Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K,
Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA,
Scheuermann RH, Shah N, Whetzel PL, Lewis S. (2007). The OBO Foundry: coordinated evolution
of ontologies to support biomedical data integration. Nat Biotechnol 25 (11): 1251-5.
Core Vaccine Ontology
*
*
> 500 vaccine-related terms included
A Typical User Case Study
Question: what are live
attenuated Brucella
vaccines?
Should be both
“Brucella vaccine” AND
“live attenuated vaccine”
This VO contains two:
B. abortus vaccine RB51
and
B. abortus vaccine strain 19
VO allows automated reasoning
What are immune responses induced
by live attenuated Brucella vaccines?
The question becomes:
What are the immune
responses induced by
B. abortus vaccines
RB51 and strain 19?
Do they induce any
immune responses
defined by VO?
Immune Response Terms in VO
If reported
 retrieve & analyze
Not yet studied
 predict & analyze
VO-based NLP Literature Mining
• A VO-natural language processing (NLP)
program is being developed
– Retrieve VO-specified vaccine data from literature
– Expand existing VO by finding more vaccinerelated terms and relationships
– Study vaccine-induced host immune response
networks
• Collaboration with NCIBI:
– NCIBI: National Center for Integrative Biomedical
Informatics (http://www.ncibi.org)
• Drs. David States, Brian Athey, and Gil Omenn
– NCIBI processes all PubMed papers by NLP
More Tasks & Questions
• Assign gene names to VO terms.
• Relationships with Ontologies: IDO,
GO, OBI
• Collaborate with OBI (Bjoern Peters,
Richard Scheuermann) -- vaccine
investigation, experiment …
• VO application in VIOLIN DB: add
instances to VO  Knowledgebase
• Vaccine Semantic Web?
Acknowledgements
Oliver He Lab at UM:
• Zuoshuang Xiang
• Thom Todd
• Fang Chen
• Andrew Hodges
• G. Bill Jourdian
• Charlie Larson
• Kimberly Ku
• Bethany Kovacic
• Elizabeth Olenzek
• Boyang Zhao
University of Michigan (UM):
• NCIBI:
• David States
• Brian Athey
• Gil Omenn
• Harry Mobley
• Steve Qin
• Howard Rush
• Lesley Colby
• Yuying Tian
• Janet Gilsdorf
Infectious Disease Ontology (IDO):
• Barry Smith (NCBO, Buffalo)
• Lindsay Cowell (Duke)
http://www.violinet.org/vaccineontology
Brucellosis Ontology
• Basic Idea: Extend IDO to brucellosis:
Brucellosis Ontology