88
Ontology Alignment state of the art and an application in literature search Patrick Lambrix Linköpings universitet
Ont
olog
yA
lignm
ent
stat
eof
the
art
and
an a
pplic
atio
nin
lite
ratu
rese
arch
Patr
ick
Lam
brix
Lin
köpi
ngs
univ
ersi
tet
Ont
olog
ies
“Ont
olog
ies
defi
ne th
e ba
sic
term
s an
d re
lati
ons
com
pris
ing
the
voca
bula
ry o
f a
topi
c ar
ea, a
s w
ell a
s th
e ru
les
for
com
bini
ng te
rms
and
rela
tion
s to
def
ine
exte
nsio
ns to
the
voca
bula
ry.”
(Nec
hes,
Fik
es, F
inin
, Gru
ber,
Sen
ator
, Sw
arto
ut, 1
991)
Exa
mpl
eG
EN
E O
NT
OL
OG
Y (
GO
)
imm
une
resp
onse
i-
acut
e-ph
ase
resp
onse
i-
anap
hyla
xis
i-an
tige
n pr
esen
tatio
n i-
anti
gen
proc
essi
ngi-
cell
ular
def
ense
res
pons
ei-
cyto
kine
met
abol
ism
i-
cyto
kine
bio
synt
hesi
s sy
nony
mcy
toki
ne p
rodu
ctio
n…
p-re
gula
tion
of c
ytok
ine
bios
ynth
esis
…… i-
B-c
ell a
ctiv
atio
n
i-B
-cel
l dif
fere
ntia
tion
i-
B-c
ell p
roli
fera
tion
i-
cellu
lar
defe
nse
resp
onse
… i-
T-c
ell a
ctiv
atio
n
i-ac
tiva
tion
of
natu
ral k
ille
r ce
ll a
ctiv
ity
…
Ont
olog
ies
used
…
nfo
r co
mm
unic
atio
n be
twee
n pe
ople
and
or
gani
zatio
nsn
for
enab
ling
know
ledg
e re
use
and
shar
ing
nas
bas
is f
or in
tero
pera
bilit
y be
twee
n sy
stem
sn
as r
epos
itory
of
info
rmat
ion
nas
que
ry m
odel
for
info
rmat
ion
sour
ces
Key
tech
nolo
gy f
or th
e Se
man
tic W
eb
Bio
med
ical
Ont
olog
ies
-ef
fort
s
OB
O –
Ope
n B
iom
edic
al O
ntol
ogie
sht
tp://
ww
w.o
bofo
undr
y.or
g/(o
ver
50 o
ntol
ogie
s)
”T
he m
issi
on o
f O
BO
is to
sup
port
com
mun
ity
mem
bers
who
are
de
velo
ping
and
publ
ishi
ngon
tolo
gies
in th
e bi
omed
ical
dom
ain.
It i
s ou
rvi
sion
that
a c
ore
of th
ese
onto
logi
esw
illbe
fu
llyin
tero
pera
ble,
by
virt
ueof
a c
omm
onde
sign
phi
loso
phy
and
impl
emen
tatio
n, th
ereb
yen
ablin
gsc
ient
ists
and
thei
rin
stru
men
ts to
com
mun
icat
ew
ith
min
imum
am
bigu
ity.
In
this
way
the
data
gen
erat
edin
the
cour
seof
bio
med
ical
rese
arch
will
form
a s
ingl
e, c
onsi
sten
t, cu
mul
ativ
ely
expa
ndin
g, a
nd a
lgor
ithm
ical
lytr
acta
ble
who
le. T
his
core
will
be k
now
nas
the
"OB
O F
ound
ry".
.”
OB
O F
ound
ry
1.op
enan
d av
aila
ble
2.co
mm
onsh
ared
synt
ax
3.un
ique
iden
tifie
rsp
ace
4.pr
oced
ures
for
iden
tifyi
ngdi
stin
ctsu
cces
sive
ver
sion
s5.
clea
rly
spec
ifie
dan
d cl
earl
yde
linea
ted
cont
ent
6.te
xtua
ldef
initi
ons
for
all t
erm
s7.
use
rela
tions
fro
m O
BO
Rel
atio
n O
ntol
ogy
8.w
elld
ocum
ente
d9.
plur
ality
of in
depe
nden
t use
rs10
.de
velo
ped
colla
bora
tivel
yw
ith o
ther
OB
O F
ound
rym
embe
rs
Bio
med
ical
Ont
olog
ies
-ef
fort
s
Nat
iona
l Cen
ter
for
Bio
med
ical
Ont
olog
y ht
tp://
bioo
ntol
ogy.
org/
inde
x.ht
ml
Fund
edby
Nat
iona
l Ins
titut
esof
Hea
lth
”The
goa
lof
the
Cen
ter
is to
sup
port
bio
med
ical
rese
arch
ers
in
thei
rkn
owle
dge-
inte
nsiv
ew
ork,
by
prov
idin
gon
line
tool
san
d a
Web
por
tal e
nabl
ing
them
to a
cces
s, r
evie
w, a
nd in
tegr
ate
disp
arat
e on
tolo
gica
lres
ourc
esin
all
aspe
cts
of b
iom
edic
alin
vest
igat
ion
and
clin
ical
prac
tice.
A m
ajor
foc
usof
our
wor
kin
volv
esth
e us
eof
bio
med
ical
onto
logi
esto
aid
in th
e m
anag
emen
t and
ana
lysi
sof
dat
a de
rive
dfr
om c
ompl
exex
peri
men
ts.”
Syst
ems
Bio
logy
Ont
olog
ies
-ef
fort
s
nSy
stem
s B
iolo
gy O
ntol
ogy
nPr
oteo
mic
sSt
anda
rd I
nitia
tive
for
Mol
ecul
arIn
tera
ctio
n
nB
ioPA
X
Ont
olog
yA
lignm
ent
nnO
ntol
ogy
alig
nmen
tO
ntol
ogy
alig
nmen
t
nO
ntol
ogy
alig
nmen
t str
ateg
ies
nE
valu
atio
n of
ont
olog
y al
ignm
ent s
trat
egie
s
nC
urre
ntis
sues
nO
ntol
ogy-
base
dlit
erat
ure
sear
ch
Ont
olog
ies
in b
iom
edic
al r
esea
rch
nm
any
biom
edic
al o
ntol
ogie
s
npr
actic
al u
se o
f bi
omed
ical
onto
logi
ese.
g. d
atab
ases
ann
otat
ed w
ith
GO
GE
NE
ON
TO
LO
GY
(G
O)
imm
une
resp
onse
i-
acut
e-ph
ase
resp
onse
i-
anap
hyla
xis
i-an
tigen
pre
sent
atio
n i-
antig
en p
roce
ssin
gi-
cellu
lar
defe
nse
resp
onse
i-cy
toki
ne m
etab
olis
m
i-cy
toki
ne b
iosy
nthe
sis
syno
nym
cyto
kine
pro
duct
ion
…p-
regu
latio
n of
cyt
okin
e bi
osyn
thes
is…
… i-B
-cel
l act
ivat
ion
i-
B-c
ell d
iffe
rent
iatio
n i-
B-c
ell p
rolif
erat
ion
i-
cellu
lar
defe
nse
resp
onse
… i-
T-c
ell a
ctiv
atio
n
i-ac
tivat
ion
of n
atur
al k
iller
ce
ll ac
tivit
y …
Ont
olog
ies
with
ove
rlap
ping
in
form
atio
n
SIG
NA
L-O
NT
OL
OG
Y (
SigO
)
Imm
une
Res
pons
ei-
Alle
rgic
Res
pons
ei-
Ant
igen
Pro
cess
ing
and
Pre
sent
atio
ni-
B C
ell A
ctiv
atio
ni-
B C
ell D
evel
opm
ent
i-C
ompl
emen
t Sig
nalin
g sy
nony
m c
ompl
emen
t act
ivat
ion
i-C
ytok
ine
Res
pons
e i-
Imm
une
Supp
ress
ion
i-In
flam
mat
ion
i-In
test
inal
Im
mun
ity
i-L
euko
trie
ne R
espo
nse
i-L
euko
trie
ne M
etab
olis
m
i-N
atur
al K
iller
Cel
l Res
pons
ei-
T C
ell A
ctiv
atio
ni-
T C
ell D
evel
opm
ent
i-T
Cel
l Sel
ectio
n in
Thy
mus
GE
NE
ON
TO
LO
GY
(G
O)
imm
une
resp
onse
i-ac
ute-
phas
e re
spon
se
i-an
aphy
laxi
s i-
antig
en p
rese
ntat
ion
i-an
tigen
pro
cess
ing
i-ce
llula
r de
fens
e re
spon
sei-
cyto
kine
met
abol
ism
i-
cyto
kine
bio
synt
hesi
ssy
nony
m c
ytok
ine
prod
uctio
n…
p-re
gula
tion
of c
ytok
ine
bios
ynth
esis
…… i-
B-c
ell a
ctiv
atio
ni-
B-c
ell d
iffe
rent
iatio
n i-
B-c
ell p
rolif
erat
ion
i-
cellu
lar
defe
nse
resp
onse
… i-
T-c
ell a
ctiv
atio
ni-
activ
atio
n of
nat
ural
kill
er
cell
activ
ity
…
Ont
olog
ies
with
ove
rlap
ping
in
form
atio
nn
Use
of
mul
tiple
ont
olog
ies
e.g.
cus
tom
-spe
cifi
c on
tolo
gy +
sta
ndar
d on
tolo
gydi
ffer
ent v
iew
s on
sam
e do
mai
nco
nnec
ting
rela
ted
area
s
nB
otto
m-u
p cr
eatio
n of
ont
olog
ies
expe
rts
can
focu
s on
thei
r do
mai
n of
exp
ertis
e
impo
rtan
t to
know
the
inte
rim
port
ant t
o kn
ow th
e in
ter --
onto
logy
on
tolo
gy
rela
tion
ship
sre
lati
onsh
ips
SIG
NA
L-O
NT
OL
OG
Y (
SigO
)
Imm
une
Res
pons
ei-
Alle
rgic
Res
pons
ei-
Ant
igen
Pro
cess
ing
and
Pre
sent
atio
ni-
B C
ell A
ctiv
atio
n i-
B C
ell D
evel
opm
ent
i-C
ompl
emen
t Sig
nalin
g sy
nony
m c
ompl
emen
t act
ivat
ion
i-C
ytok
ine
Res
pons
e i-
Imm
une
Supp
ress
ion
i-In
flam
mat
ion
i-In
test
inal
Im
mun
ity
i-L
euko
trie
ne R
espo
nse
i-L
euko
trie
ne M
etab
olis
m
i-N
atur
al K
iller
Cel
l Res
pons
e i-
T C
ell A
ctiv
atio
n i-
T C
ell D
evel
opm
ent
i-T
Cel
l Sel
ectio
n in
Thy
mus
GE
NE
ON
TO
LO
GY
(G
O)
imm
une
resp
onse
i-
acut
e-ph
ase
resp
onse
i-
anap
hyla
xis
i-an
tigen
pre
sent
atio
n i-
antig
en p
roce
ssin
gi-
cellu
lar
defe
nse
resp
onse
i-cy
toki
ne m
etab
olis
m
i-cy
toki
ne b
iosy
nthe
sis
syno
nym
cyt
okin
e pr
oduc
tion
…p-
regu
latio
n of
cyt
okin
e bi
osyn
thes
is…
… i-B
-cel
l act
ivat
ion
i-
B-c
ell d
iffe
rent
iatio
n i-
B-c
ell p
rolif
erat
ion
i-
cellu
lar
defe
nse
resp
onse
… i-
T-c
ell a
ctiv
atio
n
i-ac
tivat
ion
of n
atur
al k
iller
ce
ll ac
tivit
y…
Ont
olog
y A
lignm
ent
equi
vale
nt c
once
pts
equi
vale
nt r
elat
ions
is-a
rel
atio
n
SIG
NA
L-O
NT
OL
OG
Y (
SigO
)
Imm
une
Res
pons
ei-
Alle
rgic
Res
pons
ei-
Ant
igen
Pro
cess
ing
and
Pre
sent
atio
ni-
B C
ell A
ctiv
atio
ni-
B C
ell D
evel
opm
ent
i-C
ompl
emen
t Sig
nalin
g sy
nony
m c
ompl
emen
t act
ivat
ion
i-C
ytok
ine
Res
pons
e i-
Imm
une
Supp
ress
ion
i-In
flam
mat
ion
i-In
test
inal
Im
mun
ity
i-L
euko
trie
ne R
espo
nse
i-L
euko
trie
ne M
etab
olis
m
i-N
atur
al K
iller
Cel
l Res
pons
ei-
T C
ell A
ctiv
atio
ni-
T C
ell D
evel
opm
ent
i-T
Cel
l Sel
ectio
n in
Thy
mus
GE
NE
ON
TO
LO
GY
(G
O)
imm
une
resp
onse
i-ac
ute-
phas
e re
spon
se
i-an
aphy
laxi
s i-
antig
en p
rese
ntat
ion
i-an
tigen
pro
cess
ing
i-ce
llula
r de
fens
e re
spon
sei-
cyto
kine
met
abol
ism
i-
cyto
kine
bio
synt
hesi
ssy
nony
m c
ytok
ine
prod
uctio
n…
p-re
gula
tion
of c
ytok
ine
bios
ynth
esis
…… i-
B-c
ell a
ctiv
atio
ni-
B-c
ell d
iffe
rent
iatio
n i-
B-c
ell p
rolif
erat
ion
i-
cellu
lar
defe
nse
resp
onse
… i-
T-c
ell a
ctiv
atio
ni-
activ
atio
n of
nat
ural
kill
er
cell
activ
ity
…
Def
inin
g th
e re
latio
ns b
etw
een
the
term
s in
dif
fere
nt o
ntol
ogie
s
Ont
olog
yA
lignm
ent
nO
ntol
ogy
alig
nmen
t
nnO
ntol
ogy
alig
nmen
t str
ateg
ies
Ont
olog
y al
ignm
ent s
trat
egie
s
nE
valu
atio
n of
ont
olog
y al
ignm
ent s
trat
egie
s
nC
urre
ntis
sues
nO
ntol
ogy-
base
dlit
erat
ure
sear
ch
An
Ali
gnm
entF
ram
ewor
k
Pre
proc
essi
ng
Prep
roce
ssin
g
For
exam
ple,
nSe
lect
ion
of f
eatu
res
nSe
lect
ion
of s
earc
h sp
ace
Mat
cher
s
nSt
rate
gies
bas
ed o
n lin
guis
tic m
atch
ing
nSt
ruct
ure-
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d st
rate
gies
nC
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rain
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sed
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stan
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ased
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seof
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form
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n
Mat
cher
Str
ateg
ies
nnSt
rate
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bas
ed o
n lin
guis
tic m
atch
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Stra
tegi
es b
ased
on
lingu
istic
mat
chin
g
SigO
: c
ompl
emen
t si
gnal
ing
syno
nym
com
plem
ent
acti
vati
on
GO
:C
ompl
emen
t A
ctiv
atio
n
Exa
mpl
em
atch
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nE
dit d
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nce
¤N
umbe
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ns, i
nser
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nest
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nce
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nN
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m¤
N-g
ram
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con
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tive
char
acte
rsin
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trin
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¤Si
mila
rity
base
don
set
com
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son
of n
-gra
ms
¤aa
aa: {
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a, a
a};
baa
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ba, a
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b}
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cher
Str
ateg
ies
nSt
rate
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n lin
guis
tic m
atch
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ased
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y
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erat
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ces
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g m
atch
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ased
st
rate
gies
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asic
intu
ition
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ilari
tym
easu
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mpu
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ic N
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esm
atch
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ora
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seco
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yte
rm in
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etri
eve
mos
trec
ent P
ubM
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cts
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ate
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ers
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aive
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escl
assi
fier
s, o
nepe
r on
tolo
gy
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ific
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n¤
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trac
ts r
elat
edto
one
onto
logy
are
clas
sifi
edto
the
conc
ept
in th
e ot
her
onto
logy
with
hig
hest
post
erio
rpr
obab
ility
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|d)
nC
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late
sim
ilar
itie
s
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cher
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ateg
ies
nSt
rate
gies
bas
ed li
ngui
stic
mat
chin
g
nSt
ruct
ure-
base
d st
rate
gies
nC
onst
rain
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sed
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oach
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stan
ce-b
ased
stra
tegi
es
nnU
seU
seof
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form
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rmed
iate
onto
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mpl
em
atch
ers
nU
seof
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dNet
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seW
ordN
etto
fin
dsy
nony
ms
¤U
seW
ordN
etto
fin
dan
cest
ors
and
desc
enda
nts
in th
e is
-a
hier
arch
y
nU
seof
Uni
fied
Med
ical
Lan
guag
e Sy
stem
(U
ML
S)¤
Incl
udes
man
yon
tolo
gies
¤In
clud
esm
any
map
ping
s(n
ot c
ompl
ete)
¤U
seU
ML
S m
appi
ngs
in th
e co
mpu
tatio
nof
the
sim
ilar
ity
valu
es
Ontology Alignment and Mergning Systems
Com
bina
tion
s
Com
bina
tion
Stra
tegi
es
nU
sual
ly w
eigh
ted
sum
of
sim
ilari
ty v
alue
s of
di
ffer
ent m
atch
ers
nM
axim
um o
f si
mila
rity
val
ues
of d
iffe
rent
m
atch
ers
Filt
erin
g
nT
hres
hold
filte
ring
Pair
s of
con
cept
s w
ith s
imila
rity
hig
her
or e
qual
th
an th
resh
old
are
map
ping
sug
gest
ions
Filte
ring
tech
niqu
es
th
( 2,
B )
( 3,
F )
( 6,
D )
( 4,
C )
( 5,
C )
( 5,
E )
……
sugg
est
disc
ard
sim
Filte
ring
tech
niqu
es
low
er-t
h
( 2,
B )
( 3,
F )
( 6,
D )
( 4,
C )
( 5,
C )
( 5,
E )
……
uppe
r-th
nD
oubl
eth
resh
old
filte
ring
(1)
Pair
s of
con
cept
s w
ith s
imila
rity
hig
her
than
or
equa
l to
uppe
rth
resh
old
are
map
ping
sug
gest
ions
(2)
Pair
s of
con
cept
s w
ith s
imila
rity
bet
wee
n lo
wer
and
uppe
rth
resh
olds
are
m
appi
ng s
ugge
stio
ns if
they
mak
e se
nse
with
res
pect
to th
e st
ruct
ure
of th
e on
tolo
gies
and
the
sugg
esti
ons
acco
rdin
g to
(1)
Exa
mpl
e al
ignm
ent s
yste
m S
AM
BO
–pr
epro
cess
ing,
mat
cher
s, c
ombi
nati
on, f
ilter
Exa
mpl
e al
ignm
ent s
yste
m S
AM
BO
–su
gges
tion
mod
e
Exa
mpl
e al
ignm
ent s
yste
m
SAM
BO
–m
anua
l mod
e
Ont
olog
yA
lignm
ent
nO
ntol
ogy
alig
nmen
t
nO
ntol
ogy
alig
nmen
t str
ateg
ies
nnE
valu
atio
n of
ont
olog
y al
ignm
ent s
trat
egie
s E
valu
atio
n of
ont
olog
y al
ignm
ent s
trat
egie
s
nC
urre
ntis
sues
nO
ntol
ogy-
base
dlit
erat
ure
sear
ch
Eva
luat
ion
mea
sure
s
nPr
ecis
ion:
#
corr
ect s
ugge
sted
map
ping
s #
sugg
este
d m
appi
ngs
nR
ecal
l: #
corr
ect s
ugge
sted
map
ping
s #
corr
ect m
appi
ngs
nF-
mea
sure
: com
bina
tion
of p
reci
sion
and
re
call
Ont
olog
yA
lignm
ent
Eva
luat
ion
Init
iati
ve
OA
EI
nSi
nce
2004
nE
valu
atio
n of
sys
tem
s
nD
iffe
rent
trac
ks¤
com
pari
son:
ben
chm
ark
(ope
n)
¤ex
pres
sive
: ana
tom
y (b
lind)
, fis
heri
es (
expe
rt)
¤di
rect
orie
s an
d th
esau
ri: d
irec
tory
, lib
rary
, cr
ossl
ingu
alre
sour
ces
(blin
d)
¤co
nsen
sus:
con
fere
nce
OA
EI
2007
n17
sys
tem
s pa
rtic
ipat
ed¤
benc
hmar
k (1
3)n
ASM
OV
: p =
0.9
5, r
= 0
.90
¤an
atom
y (1
1)
nA
OA
S: f
= 0
.86,
r+
= 0
.50
nSA
MB
O: f
=0.
81, r
+ =
0.5
8
¤lib
rary
(3)
nT
hesa
urus
mer
ging
: FA
LC
ON
: p =
0.9
7, r
= 0
.87
nA
nnot
atio
n sc
enar
io:
¤FA
LC
ON
: pb
=0.
65, r
b=
0.49
, pa
= 0
.52,
ra
= 0.
36, J
a=
0.30
¤Si
las:
pb
= 0
.66,
rb=
0.4
7, p
a =
0.53
, ra
= 0
.35,
Ja
= 0
.29
¤di
rect
ory
(9),
foo
d (6
), e
nvir
onm
ent (
2), c
onfe
renc
e (6
)
OA
EI
2008
–an
atom
y tr
ack
nA
lign
¤M
ouse
ana
tom
y: 2
744
term
s¤
NC
I-an
atom
y: 3
304
term
s¤
Map
ping
s: 1
544
(of
whi
ch 9
34 ‘
triv
ial’
)
nT
asks
¤
1. A
lign
and
optim
ize
f¤
2-3.
Alig
n an
d op
timiz
e p
/ r¤
4. A
lign
whe
n pa
rtia
l ref
eren
ce a
lignm
ent i
s gi
ven
and
optim
ize
f
OA
EI
2008
–an
atom
y tr
ack#
1
n9
syst
ems
part
icip
ated
nSA
MB
O¤
p=0.
869,
r=
0.83
6, r
+=
0.58
6, f
=0.
852
nSA
MB
Odt
f¤
p=0.
831,
r=
0.83
3, r
+=
0.57
9, f
=0.
832
nU
se o
f T
erm
WN
and
UM
LS
OA
EI
2008
–an
atom
y tr
ack#
1
Is b
ackg
roun
d kn
owle
dge
(BK
) ne
eded
?
Of
the
non-
triv
ial m
appi
ngs:
¤C
a 50
% f
ound
by
syst
ems
usin
g B
K a
nd s
yste
ms
not
usin
g B
K¤
Ca
13%
fou
nd o
nly
by s
yste
ms
usin
g B
K¤
Ca
13%
fou
nd o
nly
by s
yste
ms
not u
sing
BK
¤C
a 25
% n
ot f
ound
Proc
essi
ng ti
me:
ho
urs
with
BK
, min
utes
with
out B
K
OA
EI
2008
–an
atom
y tr
ack#
4
Can
we
use
give
n m
appi
ngs
whe
n co
mpu
ting
sugg
estio
ns?
part
ial r
efer
ence
alig
nmen
t giv
en w
ith a
ll tr
ivia
l and
50
non-
triv
ial m
appi
ngs
nSA
MB
O¤
p=0.
636
0.66
0, r
=0.
626
0.62
4, f
=0.
631
0.64
2
nSA
MB
Odt
f¤
p=0.
563
0.60
3, r
=0.
622
0.63
0, f
=0.
591
0.61
6
(mea
sure
s co
mpu
ted
on n
on-g
iven
par
t of
the
refe
renc
e al
ignm
ent)
OA
EI
2007
-200
8
nSy
stem
s ca
n us
e on
ly o
ne c
ombi
natio
n of
st
rate
gies
per
task
syst
ems
use
sim
ilar
stra
tegi
es¤
text
: str
ing
mat
chin
g, tf
-idf
¤st
ruct
ure:
pro
paga
tion
of s
imil
arity
to a
nces
tors
an
d/or
des
cend
ants
¤th
esau
rus
(Wor
dNet
)
¤do
mai
n kn
owle
dge
impo
rtan
t for
ana
tom
y ta
sk?
Ont
olog
yA
lignm
ent
nO
ntol
ogy
alig
nmen
t
nO
ntol
ogy
alig
nmen
t str
ateg
ies
nE
valu
atio
n of
ont
olog
y al
ignm
ent s
trat
egie
s
nnC
urre
nt I
ssue
sC
urre
nt I
ssue
s
nO
ntol
ogy-
base
dlit
erat
ure
sear
ch
Cur
rent
issu
es
nSy
stem
s an
d al
gori
thm
s¤
Com
plex
onto
logi
es
¤U
seof
inst
ance
-bas
edte
chni
ques
¤A
lignm
entt
ypes
(equ
ival
ence
, is-
a, …
)
¤C
ompl
exm
appi
ngs
(1-n
, m-n
)
¤C
onne
ctio
n on
tolo
gyty
pes
–al
ignm
ents
trat
egie
s
nE
valu
atio
n¤
SEA
LS
–S
eman
ticE
valu
atio
nA
t Lar
geSc
ale
Cur
rent
issu
es
nR
ecom
men
ding
’bes
t’al
ignm
ents
trat
egie
s
nU
seof
Par
tialR
efer
ence
Alig
nmen
t
----
----
----
----
----
----
----
----
----
----
----
----
----
----
-
nIn
tegr
atio
n of
ont
olog
yal
ignm
enta
nd r
epai
rof
th
e st
ruct
ure
of o
ntol
ogie
s
Ont
olog
yA
lignm
ent
nO
ntol
ogy
alig
nmen
t
nO
ntol
ogy
alig
nmen
t str
ateg
ies
nE
valu
atio
n of
ont
olog
y al
ignm
ent s
trat
egie
s
nC
urre
nt is
sues
nnO
ntol
ogy
Ont
olog
y --ba
sed
liter
atur
e se
arch
base
d lit
erat
ure
sear
ch
Lit
erat
ure
sear
ch
nH
uge
amou
nt o
f sc
ient
ific
lite
ratu
re.
nN
eed
to in
tegr
ate
a sp
ectr
um o
f in
form
atio
n to
pe
rfor
m a
task
.
Lit
erat
ure
sear
ch
nH
ow to
kno
w w
hat i
s in
the
repo
sito
ry¤
Lac
k of
kno
wle
dge
of th
e do
mai
n
nH
ow to
com
pose
an
expr
essi
ve q
uery
¤L
ack
of k
now
ledg
e of
sea
rch
tech
nolo
gy
Exa
mpl
e sc
enar
io“L
ipid
”
nK
eyw
ord
sear
ch r
etur
ns a
ll do
cum
ents
co
ntai
ning
lipi
d.¤
No
know
ledg
e; te
rmin
olog
y pr
oble
m
nR
elat
ions
hips
: use
of
mul
tiple
key
wor
ds
with
/with
out b
oole
anop
erat
ors,
e.g.
lipi
d an
d di
seas
e
Exa
mpl
e sc
enar
io“L
ipid
”
nK
eyw
ord
sear
ch r
etur
ns a
list
of
rele
vant
qu
esti
ons
conc
erni
ng li
pid.
Use
r se
lect
s qu
esti
on
and
retr
ieve
s kn
owle
dge
and
prov
enan
ce
docu
men
ts.
nM
ultip
le s
earc
h te
rms:
req
uire
men
t tha
t the
re a
re
rele
vant
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nect
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bet
wee
n th
e ke
ywor
ds.
lipid
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evan
t qu
erie
s
nR
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udin
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num
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tions
fro
m a
n on
tolo
gy
conn
ecte
dsu
b-gr
aph
of th
e on
tolo
gyth
at in
clud
esth
e co
ncep
tsan
d re
latio
ns.
(que
rygr
aph
base
don
the
conc
epts
and
rela
tion
s;
slic
e is
set
of a
ll q
uery
grap
hsba
sed
on th
e co
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om a
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498
PubM
edab
stra
cts
rele
vant
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rian
Can
cer.
683
pap
ers
incl
uded
lipid
nam
esfr
om w
hich
241
full
pape
rsw
ere
dow
nloa
dabl
e.
nO
ntol
ogy
and
onto
logy
alig
nmen
trep
osito
ry¤
Lip
id o
ntol
ogy
¤Si
gnal
ont
olog
y¤
Alig
men
t usi
ngSA
MB
O
2) S
ente
nce
Ext
ract
ion
1) D
ocum
ent C
onte
nt
3) S
ente
nce
Det
ectio
n: li
pid
inte
ract
ion
prot
ein
4) E
ntity
Rec
ogni
tion:
te
rm id
entif
icat
ion
/ ass
ign
lipid
clas
s
5) N
orm
aliz
atio
n: c
olla
pse
lipid
syno
nym
s
6) R
elat
ion
Ext
ract
ion:
Lip
id-P
rote
in o
r Li
pid
Dis
ease
8) P
opul
ate
OW
L on
tolo
gy (
JEN
A -
AP
I)
Com
plet
e In
stan
tiate
d O
WL-
DL
Ont
olog
y
Ter
m L
ist D
B’s
:Li
pid
nam
es,
LIP
IDM
AP
S, L
ipid
Ban
k,
KE
GG
cla
ssifi
catio
ns,
Dis
ease
nam
es,
Pro
tein
nam
esS
tem
med
Inte
ract
ions
Doc
umen
t and
se
nten
ce m
eta
data
"T
LR4
bind
s to
PO
PC
", ta
gged
as
"TLR
4 bi
nds
to P
OP
C",
tagg
ed a
s "<
term
cat
egor
y="
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rm c
ateg
ory=
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tein
prot
ein
"> T
LR4<
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>
"> T
LR4<
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>
bind
s to
bi
nds
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rm c
ateg
ory=
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term
cat
egor
y=" l
ipid
lipid
">P
OP
C<
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>"
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OP
C<
/term
>"
7) C
lass
ifica
tion:
Iden
tify
onto
logy
cla
sses
and
spe
cify
rela
tions
for
all s
ente
nces
, pro
tein
s,lip
idsu
bcla
sses
.
Kno
wle
dge
base
inst
anti
atio
n
Lipid Instance
Lipid Instance
Lipid Class
Protein
Instance
Kno
wle
dge
base
inst
anti
atio
n
Slic
e ge
nera
tion
nC
urre
ntim
plem
enta
tion
focu
ses
on s
lices
ba
sed
on c
once
pts.
nD
epth
-fir
sttr
aver
salo
f on
tolo
gyto
fin
dpa
ths
betw
een
give
n co
ncep
ts; p
aths
can
be p
utto
geth
erto
fin
dsl
ices
/que
rygr
aphs
.
Slic
e al
ignm
ent
nA
lgor
ithm
com
pute
ssu
bset
of a
ligne
dsl
ice.
nA
ssum
ptio
n: s
hort
erpa
ths
repr
esen
tclo
ser
rela
tion
ship
s.
nA
lgor
ithm
conn
ects
slic
es u
sing
shor
test
path
sfr
om g
iven
con
cept
sin
one
onto
logy
to g
iven
co
ncep
tsin
oth
eron
tolo
gy.
Slic
ing
thro
ugh
the
liter
atur
e
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ein
lipid
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ase
Sig
nal-p
athw
ay Invo
lved
-inIn
tera
cts-
with
Impl
icat
ed-in
Nat
ural
lang
uage
quer
yge
nera
tion
nT
ripl
ere
pres
enta
tion:
<li
pid,
inte
ract
s-w
ith,
pro
tein
>
nR
ule
base
to g
ener
ate
NL
sta
tem
ents
.
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tlip
id in
tera
cts
wit
h pr
otei
ns?
¤L
earn
edfr
om e
xam
ples
.
nA
ggre
gatio
n of
sta
tem
ents
from
dif
fere
nt
trip
les,
gra
mm
arch
ecki
ng.
Que
ry
nSe
ndnR
QL
quer
yto
RA
CE
R.
Fut
ure
Wor
k
nT
rade
off
in q
uery
gen
erat
ion
betw
een
com
plet
enes
s an
d in
form
atio
n ov
erlo
ad.
nR
elev
ance
mea
sure
and
que
ry r
anki
ng.
nIn
tegr
ated
impl
emen
tatio
n.
nSc
alab
ility
test
ing.
Furt
her
read
ing
Ont
olog
y al
ignm
ent
-ge
nera
l
nht
tp://
ww
w.o
ntol
ogym
atch
ing.
org
(ple
nty
of r
efer
ence
sto
art
icle
san
d sy
stem
s)
nO
ntol
ogy
alig
nmen
t eva
luat
ion
initi
ativ
e: h
ttp://
oaei
.ont
olog
ymat
chin
g.or
g(h
ome
page
of
the
initi
ativ
e)
nE
uzen
at, S
hvai
ko, O
ntol
ogy
Mat
chin
g, S
prin
ger,
200
7.
nL
ambr
ix, S
tröm
bäck
, Tan
, Inf
orm
atio
n in
tegr
atio
n in
bio
info
rmat
ics
with
on
tolo
gies
and
stan
dard
s, in
Bry
, Mal
uszy
nski
(eds
), S
eman
tic
Tec
hniq
ues
for
the
Web
: T
he R
EW
ER
SE p
ersp
ecti
ve, c
hapt
er 8
, 343
-376
, 200
9.(c
onta
ins
curr
ently
larg
esto
verv
iew
of o
ntol
ogy
alig
nmen
tsys
tem
s)
Furt
her
read
ing
Ont
olog
y al
ignm
ent
-sy
stem
sn
Lam
brix
, Tan
, SA
MB
O –
a sy
stem
for
alig
ning
and
mer
ging
bio
med
ical
on
tolo
gies
, Jou
rnal
of W
eb S
eman
tics
, 4(3
):19
6-20
6, 2
006.
(des
crip
tion
of th
e SA
MB
O to
olan
d ov
ervi
ewof
eva
luat
ions
of d
iffe
rent
m
atch
ers)
nL
ambr
ix, T
an, A
tool
for
eva
luat
ing
onto
logy
alig
nmen
t str
ateg
ies,
Jou
rnal
on
Dat
a Se
man
tics
, VII
I:18
2-20
2, 2
007.
(des
crip
tion
of th
e K
itAM
Oto
olfo
r ev
alua
ting
mat
cher
s)
Furt
her
read
ing
Ont
olog
yal
ignm
ent
-re
com
men
dati
onof
alig
nmen
tst
rate
gies
nT
an, L
ambr
ix, A
met
hod
for
reco
mm
endi
ng o
ntol
ogy
alig
nmen
t str
ateg
ies,
In
tern
atio
nal S
eman
tic
Web
Con
fere
nce,
494
-507
, 200
7.
nE
hrig
, Sta
ab, S
ure,
Boo
tstr
appi
ng o
ntol
ogy
alig
nmen
t met
hods
with
A
PFE
L, I
nter
nati
onal
Sem
anti
c W
eb C
onfe
renc
e, 1
86-2
00, 2
005.
nM
ocho
l, Je
ntzs
ch, E
uzen
at, A
pply
ing
an a
naly
ticm
etho
dfo
r m
atch
ing
appr
oach
sel
ecti
on, I
nter
nati
onal
Wor
ksho
p on
Ont
olog
yM
atch
ing,
200
6.
Ont
olog
yal
ignm
ent
-P
RA
in o
ntol
ogy
alig
nmen
tn
Lam
brix
, Liu
, Usi
ngpa
rtia
lref
eren
ceal
ignm
ents
to a
lign
onto
logi
es,
Eur
opea
n Se
man
tic
Web
Con
fere
nce,
188
-202
, 200
9.
Lit
erat
ure
sear
chn
Bak
er, L
ambr
ix, L
auri
la B
ergm
an, K
anag
asab
ai, A
ng, S
licin
gth
roug
hth
e sc
ient
ific
liter
atur
e, D
ata
Inte
grat
ion
in th
e Li
fe S
cien
ces,
127
-140
, 200
9.
DIL
S 20
107t
h In
tern
atio
nal C
onfe
renc
e on
D
ata
Inte
grat
ion
in t
he L
ife
Scie
nces
Aug
ust
25-2
7, G
othe
nbur
g, S
wed
en
pape
rsu
bmis
sion
dead
line
in A
pril
