1. Toward a Brucellosis ontology
“Asiyah” Yu Lin, Zuoshuang Xiang, Yongqun “Olive” He
University of Michigan Medical School
Ann Arbor, MI 48109, USA

2. Classification of Brucella
Bacteria, Proteobacteria, a-Proteobacteria, Rhizobiales, Brucellaceae
Brucella listed as CDC and NIH priority category B pathogen
Species
Host
B. abortus
cattle, human
B. canis
dogs, foxes, coyotes, human
B. melitensis
sheep, goats, human
B. neotomae
desert wood rats
B. ovis
rams
B. suis
pigs, human
Brucella is a Gram-negative bacteria. They are non-encapsulated cocbacillus; and their function as facultative intracellular parasite. There are a few different species of Brucella, each with slightly different host specificity.
Gram negative, cocco-bacillus;
facultative intracellular bacterium

3. Symptoms of Brucellosis
Animals:
Chronic infection leading to abortion and
infertility
Clinical signs & symptoms vary with species
- metritis, spondylitis, lameness, paralysis
- testicular swelling, lympadenitis, splenitis
Humans:
Clinical signs & symptoms: fever (Undulant Fever)
anorexia, back pain, fatigue, malaise, myalgia,
sweats, weight loss.
Mortality rate is low; abortions NOT common
Clinical manifestations - a lot, including reactive
arthritis (a type of spondylitis)
Brucella is the cause of brucellosis, which is a zoonosis. In animals, the chronic infection usually leading to abortion and infertility. And in humans, the clinical signs and symptoms are not specific, the most common symptom is undulant fever, sometimes it can be a substitute term for brucellosis. Because Brucella is an intracellular bacteria, it causes a multi-organs’ damage, and the clinical manifestations is quite various. It is not easy to make a correct diagnosis.

4. Brucellosis Ontology (BO)
An extension of IDO-core
Uniqueness of BO:
The first zoonosis disease ontology to be developed.
The first Gram-negative bacteria to be carefully modeled under the scope of IDO.
The first “select agent” to be modeled.
Goal: data integration and text mining

5. Statistics of BO BO Classes in total : 452 Clinical Entities
Biological Entities
Investigational Entities
IDO (full)
OGMS
SYMP
FLU
TRANS VO GO
PRO
CHEBI
NCBI taxonomy
OBI
IAO

6. Developing methodology
Top-down & Bottom-up (scenarios)
Design patterns
Host-pathogen transmission
Brucella virulence factors (pathogenesis)
Intentional release and epidemiology
Diagnosis and treatment
Protective antigen

7. Host-pathogen interaction/transmission
Infects
Regional
Systemic
Entry
Lymph
Spread
phagocytic
cells
Nodes
Liver, spleen,
other lymph
nodes; uterus
in ungulates
Abortion
Infection
Unpasteurized milk,
Cheese or dairy products
Dead fetus, placentas
& secretions
Transmission to other vertebrates = Zoonosis

8. Host-pathogen & transmission modeling
human brucellosis pathogen role
bearer_of
B.abortus
human brucellosis
bearer_of
has_part
is_realized_by
is_realized_by
cattle brucellosis pathogen role
cattle brucellosis disease course
abortion process
human brucellosis disease course
has_function
is_realized_by
is_realized_by
Brucella-contaminated milk producing function
Brucella-infected cow
is_a
brucellosis patient role
cattle brucellosis
cattle brucellosis
brucellosis
is_a
bearer_of
is_realized_by
is_a
brucellosis patient
bearer_of
disposition
Brucella-contaminated milk　producing process
has_specified_ output
Brucella-contaminated milk drinking process
Scenario:
A brucellosis patient got
infected by drinking the unpasteurized Brucella-contaminated milk, which was produced by a Brucella-infected cow.
Brucella-contaminated milk
is_realized_by
is_specified
_ input_of
is_a
is_a
drinking function
drinking function
unpasteurized milk
inheres_in
human
Brucelloa host role
cow
cow
bearer_of
bearer_of
is_realized_by
is_a
B. abortus infectious course
is_a
brucella infectious course

9. Brucella Virulence factors
Brucella virulence factors are aerobic facultative intracellular pathogen; and it is unusual in:
It doesn’t have classical virulence factors.
It maintain an intracellular existence within its host cells, such as macrophages, dendritic cells, placental trophoblasts, epithelial cells
The interactions with those host cells dictate the outcomes of infection.
Candidate GO terms:
intracellular viral protein transport (GO: biological process)
establishment of localization in cell (GO: biological process)
entry into host cell (GO: biological process)
Other terms:
cellular host? …

10. Brucella virulence factor modeling
Senario:
Brucella
invading into macrophages,
the Brucella virb1
is the virulence factor
participant_in
participant_in
Brucella
Process of Brucella’s
replication in macrophages
Process of Brucella’s
survival in macrophages
has_part
Brucella entry into macrophages
establishment of Brucella
intracellular infection
is_a
has_part
Entry into host cell (GO: )
is_realized_by
bearer_of
bearer_of
Brucella virb1
Brucella virulence factor disposition
virulence factor
is_a
bearer_of
is_a
is_a
is_a
Brucella protein
Brucella protein virulence factor
Brucella virulence factor
After reasoning, ‘Brucella virb1’ is_a Brucella protein virulence factor
Statistics: >200 Brucella virulence factors, collected by He Lab, stored in BO already.

11. Epidemiology and Intentional release
Brucella can be intentionally released for bioterrorism
Scenario:
Brucella organisms could be released in aerosol form, by accidental spills of culture suspensions or live vaccines, or in liquids such as dairy products or water. Brucellosis has fairly low fatality rate, but could be used as an incapacitating agent, as the disease tends to be chronic, requiring prolonged treatment

12. Brucella intentional release modeling
bioterrorism agent role
bearer_of
disinfectant role
is_specified_input_of
is_a
bearer_of
Brucella
aerosolized Brucella
Brucella intentional release
bleach (a disinfectant)
is_specified_output_of
has_part
is_specified_input_of
is_a
is_specified_input_of
is_a
is_a
bleach disinfection of aerosolized Brucella
Brucella aerosolization
planned process
is_a
Brucella containment

13. Diagnosis of brucellosis
Brucellosis infects many species, especially cattle, sheep, goats, pigs.
Different Brucella types infect different species preferentially.
Brucellosis presents typically as abortion in cattle.
Diagnosis can only be confirmed by laboratory tests, such as PCR !

14. PCR diagnosis based on Brucella OMP-2 Detection
has_specified_input
OMP-2 forward primer
PCR test for detection of Brucella OMP-2
has_specified_output
has_specified_input
PCR product of PCR test for detection of Brucella OMP-2
OMP-2reverse primer
Is_specified_output_of
hasSize:169
is_specified_input_of
Brucella-contaminated
body fluids
amplifies
amplifies
part_of
169bp’s region located in OMP-2 gene
B. abortus
part_of
is_denoted_by
part_of
is_
denoted_by
B. abortus genome
part_of
part_of
B. melitensis genome
OMP-2 gene
is_denoted_by
codes_for
codes_for
is_denoted_by
OBI’s modeling: PCR is_a enzymatic amplification and realizes the synthesizing function of the DNA polymerase complex, or that it achieves a material transformation objective
data item
B. abortus genome sequence data
OMP-2 protein
B. meltitensis genome sequence data
is_a
letter string
letter string
Is_subset_of (transitive property)
OMP-2 reverse primer sequence data
is_a
end_with
PCR product sequence data
is_a
sequence data
Is_subset_of (transitive property)
OMP-2 forward primer sequence data
start_with
* sequence data
OBI_

15. Continue with PCR diagnosis…
is_a
is_about
diagnosis
Brucellosis diagnosis
clinical manifestation of brucellosis
is_a
inheres_in
data item
???
brucellosis patient
is_a
has_role
laboratory finding of OMP2-detection
has_specified_output
brucellosis patient role
is_a
PCR test for detection
of brucella OMP-2
laboratory test
is_realized_by
has_part
brucellosis disease course
fever process
is_realized_by
Brucellosis pathogen role
specimen
patient
bearer_of
is_a
is_a
part_of
contains
Brucella-contaminated
body fluids
is_a
brucellosis patient
derived specimen
brucellosis
patient
is_a
Brucella
Homo sapiens
is_a
is_a
pathogen
is_a
infected host
host infected with Brucella

16. Protective antigen
Protective antigens are those antigens that are specifically targeted by the acquired immune response of the host, and when introduced into the host body, are able to stimulate the production of antibodies and/or cell-mediated immunity against certain pathogens or the causes of other diseases.

17. Protective antigen modeling
immune response (GO_ )
is_a
adaptive immune response
is_a
is_a
Brucella protective antigen
stimulated acquired immune response
Brucella-specific protective T cell
mediated immune response
is_realized_by
antigen role (OBI_ )
is_a
Brucella protective antigen role
bearer_of
is_a
antigen (OBI_ )
MaterialEntity(OBI)
Brucella protective antigen
is_a

18. Treatment A scenario from WHO recommend treatment is as following :
Treatment of uncomplicated cases in adults and children eight years of age and older: doxycycline 100 mg twice a day for six weeks + streptomycin 1 g daily for two to three weeks.

19. Treatment Modeling brucellosis treatment objective is_a
objective specification
has_part
Is_concritization_of (WHO standard treatment specification for human brucellosis)
is_a
plan specification
realizes
part_of
Doxycycline specification in WHO standard treatment for human brucellosis
100 mg twice a day for six weeks
WHO standard treatment for human brucellosis
is_concretized_as
is_realized_by
WHO standard doxycycline treatment for human brucellosis
patient role
is_specified_input_of
>=8
has_role
doxycycline
is_a
inheres_in
brucellosis patient
is_a
quality
age
human
* Green box shows the difficulties

20. A proposal modeling for age
Specifically, adults and children eight years of age and older
8 year
has_quality specified
is_a
inheres_in
quality
age
brucellosis patient eight years of age and older
has_function
viable function
* Black and blue arrows differ two kinds of modeling
is_realized_by
living process
has_temporal_region
connected temporal region of living till now
start_with
end_with
starting temporal boundary
the 8th year
is_a
ending temporal boundary
is_a
is_a
temporal boundary

21. Open for discussion Interactions between upper and lower ontologies
When upper ontology changes…
Downstream ontologies should provide new terms to upper ontologies
The granularity for modeling
For example, shall we model the molecular level of virulence factor?
Symptoms and signs:
The established vocabulary is not sufficient, neither OGMS nor Symptom Ontology
How to model: (IAO’s scope)
100 mg twice a day for six weeks

22. Acknowledgments
OBI and IDO developers
Funding: NIH-NIAID R01AI081062