Vol.:(0123456789)1 3

Mammalian Genome (2023) 34:389–407 
https://doi.org/10.1007/s00335-023-10005-4

Bridging mouse and human anatomies; a knowledge‑based approach 
to comparative anatomy for disease model phenotyping

Jesús Ruberte1,2 · Paul N. Schofield3,4 · John P. Sundberg3,5 · Alfonso Rodriguez‑Baeza6 · Ana Carretero1,2 · 
Colin McKerlie7,8

Received: 16 April 2023 / Accepted: 13 June 2023 / Published online: 8 July 2023 
© The Author(s) 2023

Abstract
The laboratory mouse is the foremost mammalian model used for studying human diseases and is closely anatomically 
related to humans. Whilst knowledge about human anatomy has been collected throughout the history of mankind, the first 
comprehensive study of the mouse anatomy was published less than 60 years ago. This has been followed by the more recent 
publication of several books and resources on mouse anatomy. Nevertheless, to date, our understanding and knowledge of 
mouse anatomy is far from being at the same level as that of humans. In addition, the alignment between current mouse and 
human anatomy nomenclatures is far from being as developed as those existing between other species, such as domestic 
animals and humans. To close this gap, more in depth mouse anatomical research is needed and it will be necessary to extent 
and refine the current vocabulary of mouse anatomical terms.

Introduction

The mouse remains the key animal model for exploring 
human disease and, despite its small comparative size, the 
laboratory mouse is anatomically similar to humans, pro-
viding even unexpected anatomical analogies in structures 
with high interspecies variation such as the presence of the 
clavicle. Knowledge of human anatomy has been collected 
and recorded throughout human history, however, the first 

comprehensive study of mouse anatomy was published by 
Margaret J. Cook in 1965 (Cook 1965). Since the release of 
Cook’s atlas, several books and resources of mouse anat-
omy and have been published (Table 1). Nevertheless, the 
understanding and published descriptions of mouse anatomy 
(Mus musculus) is far from the body of knowledge available 
for humans (Homo sapiens). The most recently discovered 
anatomical structure in humans, the cisterna chyli, was first 
described four hundred years ago (Natale et al. 2017). In 
contrast, there still remain examples of anatomical structures 
of the mouse such as the bulbourethral glands with only 
poorly described structural detail. Other examples of the gap 
in complete description between human and mouse anatomy 
are: (1) the extant knowledge of normal human anatomical 
variation is well documented and quantified, but is poorly 
characterized in the mouse. As an example, a previously 
accepted anatomical difference between mouse and human, 
the presence of a supratrochlear foramen in the humerus, is 
now known to be incorrect because a percentage of humans 
present with this foramen; (2) the disparity between the 
number of anatomical entities in “gold-standard” ontolo-
gies: 3257 in the Mouse Anatomy (MA) ontology (version 
2017-02-07) (Hayamizu et al. 2005b) versus 7800 in the Ter-
minologia Anatomica (TA) (version 2021-16-08) (F.I.P.A.T 
2019); and (3) existing mouse and human anatomic ontolo-
gies (Rosse and Mejino 2008) have only ~ 50% of terms have 
a conceptual or lexical match.

 * Jesús Ruberte 
 jesus.ruberte@uab.es

1 Center for Animal Biotechnology and Gene Therapy, 
Universitat Autònoma de Barcelona, Barcelona, Spain

2 Department of Animal Health and Anatomy, Universitat 
Autònoma de Barcelona, Barcelona, Spain

3 The Jackson Laboratory, Bar Harbor, ME, USA
4 Department of Physiology, Development and Neuroscience, 

University of Cambridge, Cambridge, UK
5 Department of Dermatology, Vanderbilt University Medical 

Center, Nashville, TN, USA
6 Department of Morphological Sciences, Universitat 

Autònoma de Barcelona, Barcelona, Spain
7 The Hospital for Sick Children, Toronto, Canada
8 Department of Lab Medicine and Pathobiology, Faculty 

of Medicine, University of Toronto, Toronto, Canada

http://crossmark.crossref.org/dialog/?doi=10.1007/s00335-023-10005-4&domain=pdf


390 J. Ruberte et al.

1 3

Ta
bl

e 
1 

 P
ub

lic
at

io
ns

 o
n 

m
ou

se
 a

na
to

m
y

Ti
tle

Ye
ar

A
ut

ho
rs

Pu
bl

is
he

r
C

ha
ra

ct
er

ist
ic

s

B
io

lo
gy

 o
f t

he
 L

ab
or

at
or

y 
M

ou
se

19
41

Sn
el

l G
D

D
ov

er
 P

ub
lic

at
io

ns
O

ne
 c

ha
pt

er
 o

n 
m

ou
se

 a
na

to
m

y 
by

 F
ek

et
e 

E.
 D

ra
w

-
in

gs
 a

nd
 p

ho
to

gr
ap

hs
 fr

om
 h

ist
ol

og
ic

al
 se

ct
io

ns
Th

e 
A

na
to

m
y 

of
 th

e 
La

bo
ra

to
ry

 M
ou

se
19

65
C

oo
k 

M
J

A
ca

de
m

ic
 P

re
ss

A
tla

s o
f d

ra
w

in
gs

. F
re

el
y 

av
ai

la
bl

e 
at

: h
ttp

://
 w

w
w.

 
in

fo
r m

at
ic

s. j
ax

. o
rg

/ c
oo

kb
 oo

k
A

tla
s o

f t
he

 M
ou

se
 B

ra
in

 a
nd

 S
pi

na
l C

or
d

19
71

Si
dm

an
 R

L,
 A

ng
ev

in
e 

JB
, P

ie
rc

e 
ET

H
ar

va
rd

 U
ni

ve
rs

ity
 P

re
ss

A
tla

s w
ith

 c
or

on
al

, s
ag

itt
al

, a
nd

 h
or

iz
on

ta
l b

ra
in

 
an

d 
sp

in
al

 se
ct

io
ns

 a
nd

 d
ia

gr
am

s. 
N

om
en

cl
at

ur
e 

in
 L

at
in

Th
e 

M
ou

se
 in

 B
io

m
ed

ic
al

 R
es

ea
rc

h
19

83
Fo

ste
r H

L,
 S

m
al

l J
D

, F
ox

 JG
A

ca
de

m
ic

 P
re

ss
O

ne
 c

ha
pt

er
 o

n 
m

ou
se

 a
na

to
m

y 
by

 M
J C

oo
k

N
ec

ro
ps

y 
G

ui
de

: R
od

en
ts

 a
nd

 th
e 

R
ab

bi
t

19
88

Fe
ld

m
an

 D
B

, S
ee

ly
 JC

C
RC

 P
re

ss
A

na
to

m
ic

al
 b

as
is

 fo
r t

he
 m

ou
se

 n
ec

ro
ps

y.
 P

ho
to

-
gr

ap
hs

 a
nd

 te
xt

A
 G

ui
de

d 
To

ur
 o

f V
et

er
in

ar
y 

A
na

to
m

y.
 D

om
es

tic
 

U
ng

ul
at

es
 a

nd
 L

ab
or

at
or

y 
M

am
m

al
s

19
92

Sm
al

lw
oo

d 
JE

W
B

 S
au

nd
er

s C
om

pa
ny

O
ne

 c
ha

pt
er

 d
ed

ic
at

ed
 to

 la
bo

ra
to

ry
 m

am
m

al
 

an
at

om
y.

 T
ex

t a
nd

 d
ia

gr
am

s
C

ol
ou

r A
tla

s o
f A

na
to

m
y 

of
 S

m
al

l L
ab

or
at

or
y 

A
ni

m
al

s. 
Vo

lu
m

e 
tw

o:
 R

at
, M

ou
se

, a
nd

 H
am

ste
r

19
92

Po
pe

sk
o 

P,
 R

aj
to

vá
 V

, H
or

ák
 J

Sa
un

de
rs

 C
om

pa
ny

A
tla

s o
f c

ol
ou

r d
ra

w
in

gs
. U

se
s N

om
in

a 
A

na
to

m
ic

a 
Ve

te
rin

ar
ia

 in
 L

at
in

 a
nd

 E
ng

lis
h

Pa
th

ol
og

y 
of

 th
e 

M
ou

se
19

99
M

ar
on

po
t R

R
C

ac
he

 R
iv

er
 P

re
ss

A
na

to
m

ic
al

 a
nd

 h
ist

ol
og

ic
al

 in
tro

du
ct

io
n 

in
 e

ac
h 

of
 

th
e 

ch
ap

te
rs

Sy
ste

m
at

ic
 E

va
lu

at
io

n 
of

 th
e 

M
ou

se
 E

ye
. 

A
na

to
m

y,
 P

at
ho

lo
gy

, a
nd

 B
io

m
et

ho
ds

20
00

Sm
ith

 R
S,

 Jo
hn

 S
W

M
, N

is
hi

na
 P

M
, S

un
db

er
g 

JP
C

RC
 P

re
ss

O
ne

 se
ct

io
n 

(3
 c

ha
pt

er
s)

 d
ed

ic
at

ed
 to

 th
e 

ey
e 

an
at

om
y 

an
d 

de
ve

lo
pm

en
t. 

Te
xt

 a
nd

 p
ho

to
gr

ap
hs

A
tla

s o
f M

ou
se

 H
em

at
op

at
ho

lo
gy

20
00

Fr
ed

ric
ks

on
 T

N
 a

nd
 H

ar
ris

 A
W

H
ar

w
oo

d 
A

ca
de

m
ic

Th
re

e 
ch

ap
te

rs
 a

bo
ut

 th
e 

an
at

om
y,

 h
ist

ol
og

y,
 a

nd
 

cy
to

lo
gy

 o
f l

ym
ph

at
ic

 a
nd

 h
em

at
op

oi
et

ic
 sy

ste
m

s
Pa

th
ol

og
y 

of
 G

en
et

ic
al

ly
 E

ng
in

ee
re

d 
M

ic
e

20
00

W
ar

d 
JM

, M
ah

le
r J

F,
 M

ar
on

po
t R

R
, S

un
db

er
g 

J, 
Fr

ed
er

ic
ks

on
 R

M
Io

w
a 

St
at

e 
Pr

es
s

Se
ve

ra
l c

ha
pt

er
s w

ith
 a

na
to

m
ic

al
 in

tro
du

ct
io

ns

A
 c

ol
or

 A
tla

s o
f S

ec
tio

na
l A

na
to

m
y 

of
 th

e 
M

ou
se

20
01

Iw
ak

i T
, Y

am
as

hi
ta

 H
, H

ay
ak

aw
a 

T
B

ra
in

tre
e 

Sc
ie

nt
ifi

c 
In

c
C

ol
or

 a
tla

s w
ith

 p
ho

to
gr

ap
hs

 o
f s

ke
le

to
n,

 d
is

se
c-

tio
ns

, a
nd

 tr
an

sv
er

se
, s

ag
itt

al
, a

nd
 d

or
sa

l s
ec

tio
ns

La
bo

ra
to

ry
 A

ni
m

al
 M

ed
ic

in
e.

 S
ec

on
d 

Ed
iti

on
20

02
Fo

x 
JG

, A
nd

er
so

n 
LC

, L
oe

w
 F

M
, Q

ui
m

by
, F

W
A

ca
de

m
ic

 P
re

ss
Sh

or
t i

nt
ro

du
ct

io
n 

to
 th

e 
m

ou
se

 a
na

to
m

y 
ta

ke
n 

fro
m

 
C

oo
k’

s b
oo

k
A

tla
s o

f L
ab

or
at

or
y 

M
ou

se
 H

ist
ol

og
y

20
04

C
on

ti 
C

J, 
G

im
en

ez
-C

on
ti 

IB
, B

en
av

id
es

 F
, F

ri-
jh

off
 A

FW
, C

on
ti 

M
A

Te
xa

s H
ist

op
ag

es
 In

c
A

tla
s w

ith
 p

ho
to

gr
ap

hs
 a

nd
 d

ia
gr

am
s. 

C
D

 fo
rm

at

A
na

to
m

ia
 d

eg
li 

A
ni

m
al

i d
a 

La
bo

ra
to

rio
20

06
C

oz
zi

 B
, B

al
la

rin
 C

, P
er

uff
o 

A
, C

ar
ù 

F
C

as
a 

Ed
itr

ic
e 

A
m

br
os

ia
na

A
tla

s w
ith

 p
ho

to
gr

ap
hs

 fr
om

 d
is

se
ct

io
ns

 a
nd

 h
ist

o-
lo

gi
ca

l s
ec

tio
ns

Th
e 

M
ou

se
 B

ra
in

 in
 S

te
re

ot
ax

ic
 C

oo
rd

in
at

es
. 

C
om

pa
ct

 T
hi

rd
 E

di
tio

n
20

08
Pa

xi
no

s G
 a

nd
 F

ra
nk

lin
 K

B
J

A
ca

de
m

ic
 P

re
ss

A
tla

s w
ith

 1
00

 c
or

on
al

 h
ist

ol
og

ic
al

 b
ra

in
 se

ct
io

ns
 

(p
ho

to
gr

ap
hs

 a
nd

 d
ia

gr
am

s)
A

lle
n 

Re
fe

re
nc

e 
A

tla
s. 

A
 D

ig
ita

l C
ol

or
 B

ra
in

 
A

tla
s o

f t
he

 C
57

B
L/

6J
 M

al
e 

M
ou

se
20

08
D

on
g 

H
W

W
ile

y
A

tla
s w

ith
 1

51
 h

ist
ol

og
ic

al
 b

ra
in

 se
ct

io
ns

 (c
or

on
al

 
an

d 
sa

gi
tta

l) 
ac

co
m

pa
ni

ed
 b

y 
di

ag
ra

m
s a

nd
 a

 sy
s-

te
m

at
ic

 h
ie

ra
rc

hi
ca

lly
 o

rg
an

iz
ed

 ta
xo

no
m

y.
 h

ttp
s:

// 
m

ou
se

. b
ra

in
- m

ap
. o

rg
H

ist
ol

og
ic

 B
as

is
 o

f M
ou

se
 E

nd
oc

rin
e 

Sy
ste

m
 

D
ev

el
op

m
en

t: 
A

 C
om

pa
ra

tiv
e 

A
na

ly
si

s
20

10
K

au
fm

an
 M

, N
ik

iti
n 

A
Y,

 S
un

db
er

g 
JP

C
RC

 P
re

ss
A

na
to

m
y,

 h
ist

ol
og

y 
an

d 
de

ve
lo

pm
en

t o
f o

va
ry

, 
te

sti
s, 

pa
nc

re
as

, h
yp

op
hy

si
s, 

th
yr

oi
d,

 p
ar

at
hy

ro
id

, 
an

d 
pi

ne
al

 g
la

nd
s

C
om

pa
ra

tiv
e 

A
na

to
m

y 
of

 th
e 

M
ou

se
 a

nd
 th

e 
R

at
20

11
C

on
st

an
tin

es
cu

 G
M

C
RC

 P
re

ss
C

ol
or

 a
tla

s w
ith

 il
lu

str
at

io
ns

 d
ra

w
n 

fro
m

 d
is

se
c-

tio
ns

. U
se

s t
he

 N
om

in
a 

A
na

to
m

ic
a 

Ve
te

rin
ar

ia

http://www.informatics.jax.org/cookbook
http://www.informatics.jax.org/cookbook
https://mouse.brain-map.org
https://mouse.brain-map.org


391Bridging mouse and human anatomies; a knowledge‑based approach to comparative anatomy for…

1 3

Ta
bl

e 
1 

 (c
on

tin
ue

d)

Ti
tle

Ye
ar

A
ut

ho
rs

Pu
bl

is
he

r
C

ha
ra

ct
er

ist
ic

s

Th
e 

M
ou

se
 N

er
vo

us
 S

ys
te

m
20

11
W

at
so

n 
C

, P
ax

in
os

 G
, P

ue
lle

s L
A

ca
de

m
ic

 P
re

ss
Te

xt
 w

ith
 p

ho
to

gr
ap

hs
 p

ro
vi

di
ng

 a
 c

om
pr

eh
en

si
ve

 
an

at
om

y 
of

 th
e 

ce
nt

ra
l n

er
vo

us
 sy

ste
m

 o
f t

he
 

m
ou

se
C

om
pa

ra
tiv

e 
A

na
to

m
y 

an
d 

H
ist

ol
og

y.
 A

 M
ou

se
 

an
d 

H
um

an
 A

tla
s

20
12

Tr
eu

tin
g 

PM
, D

in
tz

is
 S

M
, F

re
ve

rt 
C

W
, L

ig
gi

tt 
D

A
ca

de
m

ic
 P

re
ss

Te
xt

 a
nd

 A
tla

s. 
Fo

r c
om

pa
ris

on
 w

ith
 h

um
an

 
an

at
om

y 
us

es
 N

et
te

r i
m

ag
es

 a
nd

 M
A

 o
nt

ol
og

y
Th

e 
La

bo
ra

to
ry

 M
ou

se
. S

ec
on

d 
ed

iti
on

20
12

H
ed

ric
h 

H
J

A
ca

de
m

ic
 P

re
ss

O
ne

 c
ha

pt
er

 o
n 

m
ou

se
 a

na
to

m
y 

by
 K

om
ár

ek
 V

. 
D

ra
w

in
gs

 ta
ke

n 
fro

m
 P

op
es

ko
 e

t a
l. 

(2
00

2)
A

 P
ra

ct
ic

al
 G

ui
de

 to
 th

e 
H

ist
ol

og
y 

of
 th

e 
M

ou
se

20
14

Sc
ud

am
or

e 
C

L
W

ill
ey

 B
la

ck
w

el
l

H
ist

ol
og

ic
al

 te
xt

 a
nd

 a
tla

s w
ith

 th
e 

ba
si

s o
f m

ou
se

 
an

at
om

y
M

or
ph

ol
og

ic
al

 M
ou

se
 P

he
no

ty
pi

ng
. A

na
to

m
y,

 
H

ist
ol

og
y 

an
d 

Im
ag

in
g

20
16

20
17

Ru
be

rte
 J,

 C
ar

re
te

ro
 A

, N
av

ar
ro

 M
Ed

ito
ria

l M
ed

ic
a 

Pa
n-

am
er

ic
a 

A
ca

de
m

ic
 P

re
ss

Te
xt

 a
nd

 a
tla

s. 
22

00
 o

rig
in

al
 p

ho
to

gr
ap

hs
 fr

om
 d

is
-

se
ct

io
ns

, h
ist

ol
og

ic
al

 se
ct

io
ns

, a
nd

 im
ag

in
g.

 U
se

s 
th

e 
N

om
in

a 
A

na
to

m
ic

a 
Ve

te
rin

ar
ia

C
om

pa
ra

tiv
e 

A
na

to
m

y 
an

d 
H

ist
ol

og
y.

 A
 M

ou
se

, 
R

at
, a

nd
 H

um
an

 A
tla

s
20

18
Tr

eu
tin

g 
PM

, D
in

tz
is

 S
M

, M
on

tin
e 

K
S

A
ca

de
m

ic
 P

re
ss

Te
xt

 a
nd

 A
tla

s. 
Th

is
 se

co
nd

 e
di

tio
n 

ad
ds

 th
e 

ra
t a

s 
co

m
pa

ra
to

r s
pe

ci
es

Th
e 

La
bo

ra
to

ry
 M

ou
se

. A
 g

ui
de

 to
 th

e 
Lo

ca
tio

n 
of

 
Ti

ss
ue

s f
or

 O
pt

im
al

 H
ist

ol
og

ic
al

 E
va

lu
at

io
n

20
19

Jo
hn

so
n 

J, 
D

el
G

ui
di

ce
 B

, B
an

ga
ri 

D
S,

 P
et

er
so

n 
E,

 
U

lin
sk

i G
, R

ya
n 

S,
 T

hu
rb

er
g 

B
L,

 C
al

lis
 G

C
RC

 P
re

ss
A

na
to

m
ic

al
 b

as
is

 fo
r t

he
 lo

ca
tio

n 
of

 p
rin

ci
pa

l a
na

-
to

m
ic

al
 st

ru
ct

ur
es

 in
 m

ou
se

X
-R

ay
 A

nn
ot

at
io

n 
M

ou
se

 A
tla

s
20

21
Ru

be
rte

 J,
 C

ar
re

te
ro

 A
, C

at
er

 H
, G

ra
ci

a 
G

, L
al

ly
 

C
D

oc
to

r H
er

rio
t S

L
A

tla
s. 

15
2 

X
-r

ay
s a

nd
 5

90
 a

na
to

m
ic

al
 re

fe
re

nc
es

. 
U

se
s t

he
 N

om
in

a 
A

na
to

m
ic

a 
Ve

te
rin

ar
ia

Es
se

nt
ia

ls
 o

f L
ab

or
at

or
y 

A
ni

m
al

 S
ci

en
ce

: P
rin

ci
-

pl
es

 a
nd

 P
ra

ct
ic

es
20

21
N

ag
ar

an
 P

, R
am

ac
ha

nd
ra

 G
, S

rin
iv

as
an

 R
Sp

rin
ge

r
O

ne
 c

ha
pt

er
 d

ev
ot

ed
 to

 m
ou

se
 a

na
to

m
y 

an
d 

ph
ys

io
l-

og
y

Pa
th

ol
og

y 
of

 G
en

et
ic

al
ly

 E
ng

in
ee

re
d 

an
d 

ot
he

r 
M

ut
an

t M
ic

e
20

22
Su

nd
be

rg
 JP

, V
og

el
 P

, W
ar

d 
JM

W
ile

y 
B

la
ck

w
el

l
Se

ve
ra

l c
ha

pt
er

s w
ith

 a
na

to
m

ic
al

 in
tro

du
ct

io
ns



392 J. Ruberte et al.

1 3

Advances in imaging and high resolution phenotyping 
in recent years have generated a need for a granular and 
complete anatomical terminology for the mouse which is 
cognate to that available for humans. To answer this need we 
conclude this commentary by discussing the development of 
a standard anatomical nomenclature for the mouse following 
the principles of the TA terminology. Because the mouse 
and human should have similar complexity, this mouse Ter-
minologia Anatomica (mTA) should have a number of nor-
malised anatomical concepts similar to that of the TA, and 
would greatly assist in the further development of the adult 
mouse anatomy ontology and related resources.

Mice are a small animal model 
but anatomically similar to humans

Recognition of the anatomical and physiological similarities 
and commonalities between different species can be traced 
in the literature to Aristotle who probably reflected estab-
lished opinions when he wrote in the 4th C BCE:

“Ought we, for instance, to begin by discussing each 
separate species-man, lion, ox, and the like—taking each 
kind in hand independently of the rest, or ought we rather to 
deal first with the attributes which they have in common in 
virtue of some common element of their nature, and proceed 
from this as a basis for the consideration of them separately” 
(Περὶ ζῴων μορίων; On the parts of animals. Aristotle. 
Trans. William Ogle, 1882).

The common anatomy, physiology and ontogeny of spe-
cies closely related to humans has made mammals the obvi-
ous model organisms for increasing our understanding of 
human biology and disease since the Greco-Roman period, 
and arguably earlier. Galen (129–216 CE) compared the sur-
gical anatomy of wounded gladiators from the arena of Per-
gamum and of his patients in Rome, with that of primates, 
goats and pigs. Using the opportunities presented by dead 
and living individuals of all species, including occasion-
ally living humans, he attempted to establish the function 
of anatomical structures and their involvement in disease, 
and initiated a long tradition of developing surgical practice 
using animal models (Matter 2013).

Since Galen and his Greek precedents, animal models 
have historically played a critical role in the exploration and 
characterization of disease and in the development of novel 
therapeutic agents and treatments, now being called the One 
medicine, One pathology, One health concept (Sundberg 
and Schofield 2009). The mouse has now become the most 
widely used, and arguably the most important, mammalian 
model for studying human disease. Mice are biologically 
very similar to humans and manifest many of the same or 
closely-related diseases (McGonigle and Ruggeri 2014). 
Most significantly, work since the beginning of the twentieth 

century, on generating genetically inbred strains of mice, 
has established the mouse as the most powerful organism 
for discovery of the genetic basis of disease. Mapping of 
spontaneous genetic variation between mouse strains, the 
experimental modification of the genome, and the ability to 
manipulate processes of development has greatly contrib-
uted to our understanding of the molecular mechanisms of 
human disease, and allowed the creation of models of human 
diseases that can be used for the development of therapeutics 
and further our understanding of pathobiology (Vandamme 
2014). Furthermore, mice are a cost-effective research tool. 
They have a short inter-generational lifespan, relatively short 
longevity, and they are easy to house and transport at scale.

Mice are biologically very comparable to humans, have 
~ 15,000 genes with human orthologues, and are therefore 
susceptible to the majority of mono- and polygenic inher-
ited disorders affecting the human population. Mice can be 
genetically manipulated to mimic the causative or contribut-
ing genetic mutation or mutations underlying many human 
disease conditions (Brown 2021). Furthermore, mice are 
a cost-efficient research tool (Leader and Padgett 1980) 
with an accelerated lifespan (one mouse year equaling ~ 30 
human years), small footprint animal holding, and are rela-
tively easy to handle and transport; particularly as frozen 
germ plasm.

Although in comparison with humans, mice are small 
(Fig. 1A), they display a relatively similar anatomy. As an 
example of this, Fig. 1B shows a comparison between the 
human and mouse femur; the latter enlarged using scanning 
electron microscopy. The same gross anatomical details: 
head of the femur, the lesser and great trochanter, as well 
as, the trochanteric fossa, can be observed both in the proxi-
mal epiphysis of human and mouse femur. These anatomical 
similarities not only represent a morphological homology 
between these two mammalian species, but they also reflect 
similarities in the biomechanics and function of the bone. 
The comparatively larger size of the head of the femur in 
humans reflects the different body positions of both species 
(Fig. 1B). Humans are bipedal and the entire body weight 
is transmitted through the femoral heads to the ground. By 
contrast, in the mouse, a quadrupedal species, the body 
weight is transmitted to the ground through all four limbs.

Sometimes, anatomical similarities between humans 
and mice are unexpected (Fig. 2). In bipedal primates and 
humans, the clavicle, a bone belonging to the pectoral girdle, 
is well-developed because there is an adaptation to tasks 
that depend on using hands distant from the central trunk 
axis, such as climbing and reaching distant objects (Rock-
wood et al. 2009). By contrast, in many quadrupedal mam-
mals, such as ungulates, carnivores and several rodents, the 
clavicle has disappeared or has been dramatically reduced 
(De Souza et al. 2020). This reduction or loss is common to 
mammals that use the thoracic limb for cursorial locomotion 



393Bridging mouse and human anatomies; a knowledge‑based approach to comparative anatomy for…

1 3

(Rockwood et al. 2009). However, the quadrupedal mouse 
has a well-developed clavicle that, as happens in man, joins 
the sternum and the acromion of the scapula (Fig. 2). A pos-
sible reason for this unexpected anatomical similarity may 
be the consequence of the thoracic limb freedom that mice 
have. Mice are often seen standing on their hind limbs trying 
to climb their cage walls and this rearing action is associ-
ated with exploration and manipulation of the environment. 
Recordings using high-speed close-up video of mice eating 
seeds (Barrett et al. 2020) show well developed manual dex-
terity for manipulating small objects.

Despite these similarities, mice and humans do pre-
sent clear anatomical differences. These manifest at the 
macroscopic, microscopic and system levels. For exam-
ple, the sexual dimorphism of the mouse kidney is well 
known (Butterfield 1972). One of the most notable macro-
scopic differences lies in the mouse brain, which in human 

anatomical terms is lissencephalic, since its cerebral cortex 
does not have folds (gyri), and its telencephalon does not 
completely cover the mesencephalon and the cerebellum, 
as happens in humans (Fig. 3). Despite these overt ana-
tomic differences, the mouse has nevertheless contributed 
enormously to our understanding of human lissencephaly 
and its underlying genetics, reflecting fundamental simi-
larities in the development of the CNS between the species 
(Del-Valle-Anton and Borrell 2022; Mota and Herculano-
Houzel 2015). There are other very well-established ana-
tomical differences, such as the presence of a characteristic 
supratrochlear foramen in the mouse humerus (Fig. 4A), 
however, on close consideration this turns out not to be 
a real difference to humans. Proximal to the trochlea of 
the human humerus there is a thin region of bone that is 
sometimes perforated forming a supratrochlear foramen 
like the mouse (Fig. 4B). The prevalence of this foramen 
varies from 6.5% in Europeans (Mays 2008) to 26.7% of 
people from India (Shivaleela et al. 2016). Functionally, 
a supratrochlear foramen in human allows hyperextension 
of the elbow (de Wilde et al. 2004). Women who are more 
flexible than men and people that generally practice dis-
ciplines that need improved flexibility, such as yoga, have 
higher prevalence of a supratrochlear foramen (Akabori 
1934; Shivaleela et al. 2016). Similarly, it is reasonable 
to suppose that the supratrochlear foramen in mice pro-
vides the elbow with the capacity to hyperextend. It is just 
as likely that careful examination of this structure in the 
new, highly genetically variable, collaborative cross strains 
(Collaborative Cross 2012) and Diversity Outbred mice 
(Churchill et al. 2012) will identify a wide variety features 
that do or do not resemble human anatomy.

As discussed below, the rate of discovery of new ana-
tomical structures and entities in humans is now quite 
slow, but several recent discoveries were paradoxically 
made first in the mouse. For example, the recent discov-
ery of functional lymphatic vessels lining the dural sinuses 
originated in detailed functional and molecular studies in 
the mouse CNS (Aspelund et al. 2015; Eide et al. 2018; 
Louveau et al. 2017, 2015). Understanding the functions 
and relationships of the glymphatic system and meningeal 
lymphatics (Eide et al. 2018). Similarly, with the discovery 
of the network of transcortical capillaries in long bones 
that now helps to explain previous puzzles in the migration 
of neutrophils and the closed circulation system of bone 
(Grüneboom et al. 2019). It is noteworthy that in both of 
these cases the development of imaging techniques and the 
unique ability to use molecular markers, tissue prepara-
tions and experimental procedures in the mouse facilitated 
these discoveries. Are we moving into an era of discovery 
of new human anatomical features from the mouse or as a 
result of better analytical tools?

Fig. 1  HYPERLINK "sps:id::fig1||locator::gr1||mediaobject::0" A 
Skeleton of a mouse relative to the human hand. B Comparison of the 
human and mouse proximal epiphyses of the femur. Similarity of the 
anatomical structures of the head of the femur (1), great trochanter 
(2), lesser trochanter (3), and trochanteric fossa (4) using scanning 
microscopy and image size correction for the mouse. Mouse images 
modified from Ruberte et al. (2016) with permission



394 J. Ruberte et al.

1 3

Mice and humans: a similar anatomical 
complexity but different level of knowledge 
and resources

Knowledge about human anatomy has been collected 
throughout history. Since Galen's anatomical descriptions, 
and even before, up to the present, the level of detail found in 
human anatomical books, and other resources has continu-
ously increased. This is especially true for anatomic varia-
tions. The classic, Bergman’s Comprehensive Encyclopedia 
of Human Anatomic Variation (Tubs et al. 2016), gives some 
an idea of the current level of knowledge; 1456 pages and 
more than 12,500 references.

An anatomic variation can be defined as difference in 
morphology that is outside of the canonical. It is impor-
tant to remember, however, that the canonical is often an 
accepted abstract standard, as the dominant morph may well 

be different for genetically different populations. For exam-
ple, the supratrochlear foramen in human humerus was first 
described two centuries ago (Meckel 1825). By contrast, the 
first comprehensive study of mouse anatomy was published 
by Margaret J. Cook in 1965. Cook worked at the MRC 
Laboratory Animal Centre in Carshalton (UK) and carried 
out intracardiac latex injections describing for the first time 
the mouse arterial and venous system. In Cook’s atlas fore-
word (Cook 1965), W. Lane-Petter stated that at that time no 
complete study of the anatomy of the mouse had so far been 
made and that gap in the knowledge was even more surpris-
ing as the mouse was at that time the most commonly used 
vertebrate in the laboratory.

Subsequent to the publication of Cook’s atlas, several 
comprehensive textbooks and other resources in mouse 
anatomy and histology, singly or as part of larger com-
pendia, have been published. Table 1 lists the title, year of 

Fig. 2  The quadrupedal mouse 
has unexpected anatomical 
similarities to the bipedal 
human, such as the presence of 
the clavicle (1). The clavicle 
in both attaches the sternum 
(2) and the acromion of the 
scapula (3). Acromial end (4), 
body of clavicle (5), esternal 
end (6). Mouse images modified 
from Ruberte et al. (2016) with 
permission



395Bridging mouse and human anatomies; a knowledge‑based approach to comparative anatomy for…

1 3

publication, authors, publisher, and characteristics of the 
extant resource. However, despite the steady release of text-
book or on-line resources since Cook’s seminal publication, 
the depth of detailed description and understanding of vari-
ation in mouse anatomy is far from comparable to human 
anatomy thereby presenting a challenge for using the mouse 

as a comparable and informative model of human biology 
and disease.

Of originals and copies: the case 
of bulbourethral glands

Anatomy is perceived as an objective scientific discipline, 
because it involves the observation and description of defin-
able material entities. However, dissection, the most preemi-
nent technique to physically dissociate and isolate individual 
structures for examination is, like other analytical scientific 
methods, susceptible to artifact. The discovery of bulboure-
thral glands in the mouse and the historical way to under-
stand its morphology and topography is a good example of 
how dissection can be misleading, and that anatomy is not 
always as obvious as the “nose on your face”.

The bulbourethral glands are part of the male accessory 
genital glands, which are located along the pelvic portion of 
the urethra producing secretions for the nutrition, transporta-
tion and protection of spermatozoa. Not all mammals have 
bulbourethral glands. The dog lacks bulbourethral glands, 
which might explain why they were missed in Cook's book. 
In her atlas, six drawings were devoted to the male genital 
system, however, bulbourethral glands were not noted. In 
fact, it would be necessary to wait until 1983, when Cook, in 
a book about the use of mouse in biomedical research (Cook 
1983) showed and drew the location of two paired bulboure-
thral glands emptying into the urethra and associated with a 
urethral diverticulum (Fig. 5A). From that time, several clas-
sic and modern mouse books used the same figure to locate 
and describe these glands (Maronpot et al. 1999; Treuting 
et al. 2018). However, this anatomical description for the 
mouse bulbourethral glands is not the only one that appears 
in textbooks. Several years before the publication of Cook´s 
atlas, The Jackson Laboratory published its celebrated book: 
Biology of Laboratory Mouse (Snell 1941) in which, E. 
Fekete, who at that time was responsible of the histology 
laboratory, carried out a different anatomical description 
for the mouse bulbourethral glands. Fekete’s representation 
showed the bulbourethral glands related with two urethral 
diverticula, each of them covered by the bulbospongiosus 
muscle. As happened with Cook's description, Fekete's ana-
tomical interpretation was later followed by Popesko et al. 
(1992) in its beautiful anatomy atlas of laboratory animals, 
and subsequently Popesko’s drawings were copied by V. 
Komàrek in the first and second editions of the Laboratory 
Mouse book (Hedrich 2012; Hedrich and Bullock 2004). 
Furthermore in 2011, G.M. Constantinescu, Professor of 
Veterinary Anatomy and Medical Illustrator at the Univer-
sity of Missouri-Columbia, carrying out new original ana-
tomical preparations for its book “Comparative Anatomy of 

Fig. 3  Mouse and human have anatomical differences in the brain. A 
The human cerebral cortex is gyrencephalic with characteristic gyri 
(ridges) and sulci (depressions or furrows). B The mouse cerebral 
cortex is lissencephalic with a smooth surface and the telencephalon 
(1) does not cover the mesencephalon (2) and cerebellum (3). Mouse 
image modified from Ruberte et al. (2016) with permission

Fig. 4  A A previously purported anatomical difference between 
mouse and human humeri is the presence of a supratrochlear foramen 
(1) in the humerus of the mouse but not in the human humerus. B 
Variable presence of the supratrochlear foramen in humans. Trochlea 
of humerus (2). Mouse image modified from Ruberte et  al. (2016) 
with permission



396 J. Ruberte et al.

1 3

the Mouse and the Rat” (Constantinescu 2011) described 
mouse bulbourethral glands as did E. Fekete in 1941.

The last macroscopic organ discovered in humans was the 
cisterna chyli, that was first described in 1651 by the French 
physician Jean Pecquet, as a lymph reservoir at the origin 
of the thoracic duct (Natale et al. 2017). In other words, 
for almost four hundred years we have had a very complete 
description of human macroscopic anatomy. By contrast, 
in the mouse we have severe discrepancies in anatomical 
descriptions for important organs, such as the bulbourethral 
gland (Fig. 5). One reason for these discordances could be 
that the classic technique used to collect the accessory geni-
tal glands in male mouse, a ventral approach after opening 
the abdominal cavity, is not optimal to identify and dissect 
the bulbourethral glands, which are located laterally at the 
base of the tail between the crus and the bulb of the penis 
(Fig. 6A). This difficulty was brought to light in several 
mouse histology books, such as the one published in 2014 by 

C.L. Scudamore (Scudamore 2014), which comments that 
in standard necropsy sampling protocols, the bulbourethral 
glands are usually missing. The difficulty of dissecting the 
bulbourethral glands is also obvious, when in a recent pub-
lished guide for the location and orientation of mouse tissues 
for optimal histological evaluation (Johnson et al. 2019), no 
specific instruction is provided to dissect and sample the bul-
bourethral glands. However, the abnormal swelling of these 
glands, that presents with male mice seeming to have “4 
testicles”, enables easy identification of these structures such 
that they can be dissected and studied (Kiupel et al. 2000).

To understand the anatomical relations of bulbourethral 
glands in the mouse and to clarify which of the two mor-
phological representations is more accurate, injection of a 
polymerizable resin  (Mercox®) in the urethra of C57/BL6J 
male mice was done via the urinary bladder. The four casts 
obtained were immersed in 60 °C soapy water for 24 h, cor-
roded in 3% KOH and washed in distilled water. Casts were 
mounted on stubs, sputtered with gold and observed in a 
Hitachi S-570 scanning electron microscope at an acceler-
ating voltage of 10–15 kV. Analysis of the urethral casts 
(Figs. 6B and 7B) and correlative dissections and histologi-
cal sections (Figs. 6A, C and 7A) showed that the pelvic 
part of the urethra in mice, as happens in humans, presented 
a large membranous portion. There is a narrowing of the 
urethra when it turns around the ischial arch, the urethral 
isthmus, which is well documented in domestic mammals 
(Fig. 6B). At the penile urethra, inside the bulb of the penis, 
only a single urethral recess was noticed (Figs. 6B and 7B). 
The histological sections showed that this diverticulum is 
covered by the bulbospongiosus muscle and surrounded by 
a narrow band of erectile tissue corresponding to the cor-
pus spongiosum (Fig. 6C). The two corpora cavernosa, that 
complete the penile erectile system, are inside the crura 
penis covered by the ischiocavernosus muscles (Fig. 6C). 
The ducts of the two bulbourethral glands join the penile 
urethra distal to the urethral recess (Fig. 7). The urethral 
recess of the mouse has a homonymous dilation of the ure-
thra in male humans. Our study suggests that the anatomical 
description of Cook (1983), although incomplete, is more 
accurate (Fig. 5). Only one diverticulum is present in the 
mouse urethra and not two as Fekete (1941) and her follow-
ers point out.

Mouse vs human anatomical terminology 
and nomenclature

Terminology is understood as a set of terms used in a 
specific scientific field, whereas nomenclature is a nor-
malized system of exactly defined terms arranged accord-
ing to certain classification principles. A nomenclature 

Fig. 5  Comparison between Cook’s and Fekete’s representations of 
mouse bulbourethral glands. A Cook described paired glands (1) with 
only one urethral recess (2). B Fekete described two paired glands (1) 
and two paired urethral diverticula (2) (adapted from Cook 1965 and 
Snell 1941)



397Bridging mouse and human anatomies; a knowledge‑based approach to comparative anatomy for…

1 3

is approved and refined by a scientific commission and is 
widely accepted by the professional community (Kachlik 
et al. 2008).

The origins of anatomical terminology date back to the 
ancient period, more than 2500 years ago, however, the 
first effort to compile a unified anatomical terminology, the 
Basle Nomina Anatomica, was made in 1885 (His 1885). At 
that time, the number of human anatomical terms reached 
50,000, many of them synonyms. Structures and organs were 
given eponyms from the person first credited with the first 
description, and in many cases the same organ was asso-
ciated with the names of different anatomists in different 
countries (O’Rahilly 1989). This first Nomina Anatomica 
was followed by seven revisions. The last revision was pub-
lished with the title of Terminologia Anatomica (TA) and 
consists of a list of terms in Latin including their corre-
sponding translation in English (F.I.P.A.T 2019). The TA 
is not applicable to domestic animals because the terms 
of direction were based on the erect position of the human 
body and not in the quadrupedal position of animals, like the 
mouse. Therefore, a Nomina Anatomica Veterinaria (NAV) 
was established and today it is in its sixth revised edition 
(I.C.V.G.A.N. 2017).

There are 7635 terms in the TA and 6500 in the NAV, 
that are equivalent and have the same principles: (1) each 
structure should be designated by a single term; (2) each 
term in the official list is in Latin, but with liberty to trans-
late; (3) each term is, so far as possible, short and simple; 
(4) the terms are primarily memory signs, but do have some 
informative or descriptive value, and (5) terms derived from 
proper names (eponyms) should not be used.

Largely driven by the advent of high throughput gene 
expression analysis it became important to capture knowl-
edge about anatomy that might be used computationally 
across very large datasets. This need was further reinforced 
by the development of large phenotype databases for the 
mouse which needed a formally computable structure in 
order to search it. Very rapidly it became apparent that 
these needs would be answered by the development of for-
mal ontologies to describe anatomy, at all levels, and pheno-
type—the latter necessarily needing to incorporate anatomy 
into its concepts, and pathology where the location of a 
lesion needed to be captured.

For these needs to be met, the “anatome”, the complete 
set of anatomical structures associated with an organism, 
needed to be organized in a computer-comprehensible way 

Fig. 6  Analysis of the urethra in 
C57BL/6J male mice identified 
only one urethral recess within 
the bulbospongiosus muscle. A 
Gross dissection of the pelvis 
(lateral aspect). B Scanning 
microscopy of corrosion cast 
of the urethra (lateral aspect). 
Hematoxylin and eosin stained 
histological section of the root 
of the penis. Urethral recess (1); 
bulbospongiosus muscle (2); 
bulbourethral gland (3); corpus 
cavernosum (4); ischiocaverno-
sus muscle (5); urethra mem-
branosa (6); urethral isthmus 
(7), penile urethra (8); penis 
(9); rectum (10). Mouse images 
modified from Ruberte et al. 
(2016) with permission



398 J. Ruberte et al.

1 3

in order to support inference, reasoning, and estimates of 
semantic similarity. Lists of anatomical terms alone, like TA 
and the NAV, are inadequate for this formalization because 
anatomical nomenclatures cannot easily put in the format 
appropriate for the structure of relational databases (Bard 
2005).

The solution adopted was to organize the anatomy of each 
organism in a hierarchy of anatomical structures and linking 
relationships (e.g., the bulbourethral gland is_a male repro-
ductive gland and is part_of male urethra). The adoption of 
a formal ontology to describe the domain of anatomy has 
very important advantages over other approaches and allows 
the use for formal semantic methods to make inference, sub-
sume related concepts under higher concepts (parents) and 
to use automated reasoning. The advent of the Ontology 
Web Language (OWL) for most bio-ontologies allows for 
much more precise and expressive modelling of the concept 
domain, with restrictions, properties, instances and complex 
relationships that allow the capture of a great deal of knowl-
edge. While an ontology is not intrinsically a graph, it may 
be expressed as such, especially as humans are familiar with 

navigating hierarchies of concepts—a knowledge structure 
that goes back to the Etymologiae of Isidore of Seville in 
the sixth century CE (Barney et al. 2006). A formal ontol-
ogy allows for modelling of the knowledge within it and it 
is interesting that here several anatomical ontologies, nota-
ble the Foundational Model of Anatomy (FMA) ontology 
(Rosse and Mejino 2008), the time-dependent embryological 
anatomy ontology of the mouse (EMAPA) (Hayamizu et al. 
2013) and the Mouse Anatomy (MA) ontology, differ. As 
we will see below these differences in modelling decisions 
make it complicated to map and align these ontologies, spe-
cifically the FMA, which is important for integrating human 
and mouse data. The development of the Uberon metazoan 
ontology (Mungall et al. 2012) (https:// obofo undry. org/ ontol 
ogy/ uberon) was designed to bridge the anatomical ‘silos” 
particularly between vertebrates.

The first attempt to develop a mouse anatomy ontology 
was an internet-accessible database of names and synonyms 
of the tissues in the first 22 Theiler stages of development 
(Bard et al. 1998). A few years later, an adult Mouse Anat-
omy (MA) ontology was developed in The Jackson Labora-
tory (Hayamizu et al. 2005a). MA ontology contains 3300 
unique terms to provide standardized nomenclature for ana-
tomical structures in the mouse. The MA ontology can be 
accessed at the Mouse Genome Informatics website:

(MGI, https:// www. infor matics. jax. org/ vocab/ gxd/ ma_ 
ontol ogy).

MA is a polyhierarchy with several different axes of 
organization. These include anatomic region organ system, 
organ, substance, and tissue. The grouping of individual 
organs and structures by function or physiology, for example 
the duodenal glands (formally called Brunner’s glands) is_a 
exocrine gland and is part_of the small intestine.

The MA Browser enables one to navigate through the 
ontology in two ways. Progressively, scrolling through the 
various hierarchies and in the Term tab obtaining informa-
tion about individual terms, including ID and relationship 
to other terms. Alternatively, an anatomy search could be 
done introducing any text sequence in the query field. Then, 
all terms in the MA vocabulary, including any synonyms, 
contained in text will be displayed (Hayamizu et al. 2005a, 
2015). The MA ontology can also be downloaded from the 
Open Biomedical Ontologies website (OBO; https:// sourc 
eforge. net/ proje cts/ obo). The MA ontology is currently 
used to annotate: (1) developmental expression data in the 
Gene Expression Database (GXD; http:// www. infor matics. 
jax. org/ expre ssion. html) (Smith et al. 2015); (2) phenotype 
data obtained in the International Mouse Phenotyping Con-
sortium (IMPC; https:// www. mouse pheno type. org) (Elmore 
et al. 2018); and (3) pathology data in Pathbase (http:// www. 
pathb ase. net) (Schofield et al. 2004). Post-natal mouse anat-
omy terms are also available as Theiler stages 27 and 28 
in the EMAPA ontology where developmental anatomy is 

Fig. 7  A Gross dissection of the root of the penis (caudal aspect). 
B Scanning microscopy of corrosion cast of the urethra (caudal 
aspect). Urethral recess (1); bulbourethral gland (2); penile urethra 
(3); bulbospongiosus muscle (4); ischiocavernosus muscles (5); ure-
thra membranosa (6); bulbourethral gland ducts to the penile urethra 
(arrows). Mouse image modified from Ruberte et al. (2016) with per-
mission

https://obofoundry.org/ontology/uberon
https://obofoundry.org/ontology/uberon
https://www.informatics.jax.org/vocab/gxd/ma_ontology
https://www.informatics.jax.org/vocab/gxd/ma_ontology
https://sourceforge.net/projects/obo
https://sourceforge.net/projects/obo
http://www.informatics.jax.org/expression.html
http://www.informatics.jax.org/expression.html
https://www.mousephenotype.org
http://www.pathbase.net
http://www.pathbase.net


399Bridging mouse and human anatomies; a knowledge‑based approach to comparative anatomy for…

1 3

available in the same hierarchy as adult/postnatal (Hayamizu 
et al. 2013).

No scientific terminology can be considered complete and 
permanent as long as research in the field continues, and the 
MA ontology like others in the OBO Foundry continues to 
be developed by its curators in response to new applications 
and the discovery of new knowledge. MA ontology devel-
opers have continued to refine terminology, adding syno-
nyms, and revising anatomical concepts. However, due to the 
increasing number of publications and books dealing with 
mouse anatomy published in recent years (Table 1) there is 
a need to continuously develop the ontology and to align 
mouse and human anatomy.

We propose the development of a mouse version of the 
Terminologica Anatomica with high resolution detail, struc-
tured and consistent with the principles established in the TA 
and the NAV, the mTA. One example of how such a termi-
nology might deal with anatomical complexity and existing 
standards is for the carpal bones.

Carpal bones in mice are arranged in two rows (Fig. 8). 
There are several aspects that could be considered regarding 
this hierarchy and terminology. First, the falciform carpal 
bone is not a true carpal bone, in fact is a sesamoid bone 
embedded in the flexor retinaculum (Wirtschafter and Tsu-
jimura 1961), therefore, it should not be considered to be a 
carpal bone. Furthermore, carpal bones in mouse present 
many anatomic variations (Ruberte et al. 2021). In 15% of 
28 C57BL/6J carpals analyzed a supernumerary bone, the 
central carpal bone, was observed between the proximal and 
distal row. Additionally, this bone was fused to the scapholu-
nate (in 45% of cases) and to the trapezoid (40%), thus the 
central carpal bone should be considered, as happens in the 
TA, as an actual carpal bone in mouse. It is a common prac-
tice to number the carpal bones from medial to lateral, first 
in the proximal row and then in the distal row. This proce-
dure was first adopted by Vesalius (Vesalius 1543) and after 
that all anatomy resources have followed this rule, including 
TA and NAV.

Fig. 8  Dorsal ventral radio-
graphs of human hand (A) and 
mouse forepaw (B). Diagram 
showing the topography and 
organization of mouse carpal 
bones (C). Alizarin stained 
mouse carpus (palmar aspect) 
(D). Carpal bones (1); metacar-
pal bones (2); phalanges (3); 
scapholunate (4); triquetral 
(5); pisiform (6); trapezium 
(7); trapezoid (8); capitate (9); 
hamate (10); falciform carpal 
bone (11), which is a sesamoid 
bone embedded in the flexor 
retinaculum and not a true car-
pal bone; ulnar sesamoid bone 
(12). Roman numerals indicate 
the medial to lateral order of 
digits



400 J. Ruberte et al.

1 3

As a corollary to the previous comments, it seems clear 
that it would be useful to integrate or map terms in an mTA 
to mouse anatomical terms in the MA and EMAPA ontolo-
gies, using community effort. Table 2 shows the comparison 
of the current terminologies with the proposed mTA. The 
great advantage of the Open Biomedical Ontology principles 
is that they encourage community input to the development 
and continuous refinement of ontologies by the user com-
munity. Because the mouse, domestic animals, and humans 
have a similar anatomical complexity, mTA probably should 
have a number of terms similar to those of the TA and NAV, 
around 6000, considerably increasing granularity, although 
attention needs to be paid to structuring classes in both ter-
minologies when considering these absolute numbers. More 
importantly formal mapping or axiomatization of MA to 
FMA could also be considered along with cross references 
to classes in the human Terminologica Anatomica. We are 
confident that this development would greatly support mor-
phological phenotyping of mouse models as modern imag-
ing methods increasingly need a higher degree of anatomical 
granularity for annotation than is currently available.

Alignment of mouse and human anatomy 
ontologies and its application

Alignment of mouse and human anatomy ontologies facili-
tates the integration of mouse and human phenotype/gen-
otype data and promotes the translation of basic research 
discoveries into clinical settings (Bodenreider et al. 2005). 
Such alignment is critical when integrating phenotype data 
from humans and mice in search of disease-causing genes 
(Boudellioua et al. 2017; Hoehndorf et al. 2011, 2013, 2015, 
2011; Mungall et al. 2010; Robinson and Webber 2014; 
Schofield et al. 2010). However, the modelling decisions for 
the FMA were radically different from those in MA (Hay-
amizu et al. 2005a), reflecting that it was designed for differ-
ent purposes, and the FMA contains a particularly rich set of 
relations, multiple axes of classification and concepts such 
as boundaries, landmarks, lines, voids and spatial relations, 
particularly relevant for human clinical imaging and surgical 
applications, for example. Both are excellent at what they do, 
but they were designed for different purposes. Some work 
has been done with anatomy ontology matching with terms 
from UMLS (https:// www. nlm. nih. gov/ resea rch/ umls), a 
widely used terminology that is not strictly an ontology, with 
a degree of success allowing for cross-species searching for 
example but not complex computation.

Under the Mouse–Human Anatomy Project (MHAP), the 
MA ontology and the human anatomical terms included in 
the National Cancer Institute (NCI) Thesaurus (Coronado 
et al. 2004) were compared. In the preliminary identification 
of equivalent terms using a combination of automated and 

manual curation approaches approximately 830 matching 
pairs were identified (Hayamizu et al. 2012). Afterwards, 
the harmonization of both ontologies by addition of terms 
represented only in one ontology, changes in the hierarchy, 
and augmented synonymy, reached 1634 matching terms, 
meaning that approximately half of the terms do not match 
and are specific to one of the two ontologies (Hayamizu 
et al. 2012). An overall comparison of automatically map-
pable terms (Bioportal; accessed 29.5.23) shows that while 
74,000 of 105,000 FMA classes can be mapped lexically 
and organisationally to MA, this includes a very large num-
ber of one-to-many mappings (FMA to MA), contrasting 
with the 1634 manually matched terms above. This is due 
to the inclusion of concepts such as clustered anatomical 
structures, relations and subregions and the high degree of 
granularity of the FMA. For example there are 15 terms in 
FMA mapped onto one term, soleus, in the mouse. Only a 
very limited number of the species-specific terms identified 
represented real anatomical differences between the two spe-
cies, and there were consequences of decisions made regard-
ing the views and resources used to build each ontology. The 
MA ontology was based on major sources and expertise, 
including mouse atlases as well as anatomy and histology 
text resources. Once the list of terms was generated, each 
term was confirmed to represent a real mouse anatomical 
structure. However, MA ontology developers found that 
this confirmation was sometimes ambiguous, since numer-
ous structures described in anatomy and histology textbooks 
do not have unambiguous evidence of their existence in the 
mouse, and then consequently were not included in the 
ontology (Hayamizu et al. 2005a).

There are additional complications in mappings from 
human to mouse, sometimes in the “views” of the topology, 
such as where concepts have been created to reflect clusters 
or features of more specific structures. In other cases, there 
are real debates about the way to describe structures and 
others where the topology is quite distinct across species. 
For example, in the mouse the prostate has identifiable ante-
rior, dorsal, lateral, and ventral lobes (Ruberte et al. 2017); 
the dorsal and lateral being viewed in combination as the 
dorsolateral prostate. The human gland is much less easily 
differentiated into lobes but in the NCI thesaurus anatomy 
the lateral, medial, and posterior lobes are defined, and an 
additional term used; “overlapping zones”. Originally the 
human prostate was believed to contain five lobes, but these 
are only recognizable during development where it origi-
nates from five pairs of epithelial buds. The human prostate 
is unilobular but contains three identifiable zones: central, 
transitional and peripheral. The central zone surrounds the 
ejaculatory duct, the transitional zone surrounds the urethra, 
and the peripheral zone makes up most of the prostate, lying 
against the rectal wall on the dorsal surface of the gland 
(Ittmann 2018). Given the profound structural differences 

https://www.nlm.nih.gov/research/umls


401Bridging mouse and human anatomies; a knowledge‑based approach to comparative anatomy for…

1 3

Ta
bl

e 
2 

 C
om

pa
ris

on
 b

et
w

ee
n 

cu
rr

en
t a

na
to

m
ic

al
 te

rm
in

ol
og

ie
s/

on
to

lo
gi

es
 a

n 
th

e 
pr

op
os

ed
 m

TA

Te
rm

in
ol

-
og

y/
O

nt
ol

-
og

y

Sc
op

e 
an

d 
Fo

cu
s

St
ru

ct
ur

e 
an

d 
or

ga
ni

za
tio

n
A

nn
ot

at
io

n 
an

d 
de

ta
il

A
pp

lic
at

io
ns

N
o 

of
 c

la
ss

es
O

nt
ol

og
y 

de
pt

h
A

xe
s o

f c
la

s-
si

fic
at

io
n

Fo
rm

al
 o

nt
ol

-
og

y 
(O

W
L)

K
no

w
le

dg
e 

ba
se

/te
rm

in
ol

-
og

y

A
ss

er
te

d 
re

fe
r-

en
ce

s/
im

po
rte

d 
cl

as
se

s

A
ut

ho
rit

y

U
B

ER
O

N
M

ul
ti-

sp
ec

ie
s 

an
at

om
y 

on
to

l-
og

y 
th

at
 a

im
s 

to
 p

ro
vi

de
 

a 
co

m
m

on
 

fr
am

ew
or

k 
fo

r 
re

pr
es

en
tin

g 
an

at
om

ic
al

 
str

uc
tu

re
s, 

bo
th

 a
du

lt 
an

d 
de

ve
lo

pm
en

-
ta

l, 
ac

ro
ss

 
di

ve
rs

e 
or

ga
n-

is
m

s, 
in

cl
ud

-
in

g 
hu

m
an

s, 
m

ic
e,

 a
nd

 
ot

he
r m

od
el

 
or

ga
ni

sm
s

B
ui

lt 
on

 th
e 

pr
in

ci
pl

es
 o

f 
th

e 
O

pe
n 

B
io

-
m

ed
ic

al
 O

nt
ol

-
og

ie
s (

O
BO

) 
Fo

un
dr

y,
 u

si
ng

 
a 

hi
er

ar
ch

ic
al

 
str

uc
tu

re
 o

f 
cl

as
se

s a
nd

 
re

la
tio

ns
hi

ps
 

to
 re

pr
es

en
t 

an
at

om
ic

al
 

en
tit

ie
s, 

ce
lls

 
tis

su
es

 a
nd

 
fe

at
ur

es
 a

cr
os

s 
di

ffe
re

nt
 sp

e-
ci

es
. I

nc
lu

de
s 

m
an

y 
re

la
tio

n-
sh

ip
 ty

pe
s 

su
ch

 a
s '

in
ne

r-
va

te
d_

by
", 

"p
ar

t_
of

" e
tc

A
im

s t
o 

pr
ov

id
e 

a 
br

oa
d 

co
ve

ra
ge

 o
f 

an
at

om
ic

al
 

en
tit

ie
s a

cr
os

s 
sp

ec
ie

s b
ut

 
m

ay
 n

ot
 h

av
e 

ex
te

ns
iv

e 
de

ta
il 

at
 th

e 
le

ve
l o

f i
nd

i-
vi

du
al

 sp
ec

ie
s 

or
 d

ev
el

op
-

m
en

ta
l s

ta
ge

s

W
id

el
y 

us
ed

 in
 

bi
oi

nf
or

m
at

ic
s 

an
d 

co
m

pa
ra

-
tiv

e 
an

at
om

y 
stu

di
es

 to
 

in
te

gr
at

e 
an

d 
an

al
yz

e 
an

a-
to

m
ic

al
 d

at
a 

ac
ro

ss
 sp

ec
ie

s 
an

d 
to

 su
pp

or
t 

cr
os

s-
sp

ec
ie

s 
re

se
ar

ch

25
,9

30
34

C
om

pl
ex

 h
ie

ra
r-

ch
y 

co
nt

ai
ni

ng
 

m
ix

ed
 b

io
lo

gi
-

ca
l c

on
ce

pt
s 

an
d 

se
m

an
tic

 
ty

pe
s;

 n
ot

 
al

l a
na

to
m

i-
ca

l S
pa

tia
l, 

ta
xo

no
m

ic
, 

de
ve

lo
pm

en
ta

l 
an

d 
sy

ste
m

at
ic

 
re

la
tio

ns

Ye
s

N
o

Re
fe

rs
 to

 o
r 

im
po

rts
 

m
or

e 
th

an
 3

0 
an

at
om

y,
 sp

e-
ci

es
 sp

ec
ifi

c,
 

m
ol

ec
ul

ar
 a

nd
 

fu
nc

tio
na

l 
on

to
lo

gi
es

, 
e.

g.
 G

O
, 

C
hE

B
I, 

M
A

, 
FM

A
 e

tc
. 

Sp
ec

ifi
es

 
pr

es
en

ce
 o

f 
cl

as
se

s i
n 

ta
xo

n

U
be

ro
n 

cu
ra

tio
n 

te
am

M
A

Sp
ec

ifi
ca

lly
 

fo
cu

se
s o

n 
th

e 
an

at
om

i-
ca

l s
tru

ct
ur

es
 

of
 th

e 
ad

ul
t 

m
ou

se
, p

ro
vi

d-
in

g 
de

ta
ile

d 
in

fo
rm

a-
tio

n 
ab

ou
t 

th
e 

m
ou

se
 

an
at

om
y 

at
 th

e 
m

ac
ro

sc
op

ic
 

an
d 

m
ic

ro
-

sc
op

ic
 le

ve
ls

U
se

s a
 h

ie
ra

rc
hi

-
ca

l s
tru

ct
ur

e 
to

 o
rg

an
iz

e 
an

at
om

ic
al

 
str

uc
tu

re
s 

w
ith

in
 th

e 
ad

ul
t m

ou
se

, 
in

cl
ud

in
g 

re
gi

on
s, 

or
ga

ns
, a

nd
 

tis
su

es
. I

t p
ro

-
vi

de
s s

pe
ci

fic
 

in
fo

rm
at

io
n 

re
le

va
nt

 to
 

th
e 

m
ou

se
 

an
at

om
y.

 
"i

s_
a"

 a
nd

 
"p

ar
t_

of
"

Pr
ov

id
es

 d
et

ai
le

d 
an

no
ta

tio
ns

 
sp

ec
ifi

c 
to

 th
e 

an
at

om
y 

of
 th

e 
ad

ul
t m

ou
se

, 
in

cl
ud

in
g 

in
fo

rm
at

io
n 

on
 

or
ga

n 
sy

ste
m

s, 
str

uc
tu

re
s, 

an
d 

th
ei

r s
pa

tia
l 

re
la

tio
ns

hi
ps

Pr
im

ar
ily

 u
se

d 
in

 m
ou

se
 

re
se

ar
ch

, s
uc

h 
as

 st
ud

ie
s 

in
vo

lv
in

g 
m

ou
se

 m
od

el
s 

of
 h

um
an

 
di

se
as

es
 o

r 
in

ve
sti

ga
tio

ns
 

in
to

 th
e 

m
ou

se
 

an
at

om
y 

fo
r 

ex
pe

rim
en

ta
l 

de
si

gn
 a

nd
 

in
te

rp
re

ta
tio

n

32
57

9
A

na
to

m
ic

al
ly

 
sy

ste
m

at
ic

. 
Re

gi
on

, o
rg

an
 

sy
ste

m
, b

od
y 

flu
id

, s
ub

-
st

an
ce

, o
rg

an

Ye
s

N
o

M
A

 lo
ca

l c
ur

at
io

n 
te

am
, T

he
 Ja

ck
-

so
n 

La
bo

ra
to

ry



402 J. Ruberte et al.

1 3

Ta
bl

e 
2 

 (c
on

tin
ue

d)

Te
rm

in
ol

-
og

y/
O

nt
ol

-
og

y

Sc
op

e 
an

d 
Fo

cu
s

St
ru

ct
ur

e 
an

d 
or

ga
ni

za
tio

n
A

nn
ot

at
io

n 
an

d 
de

ta
il

A
pp

lic
at

io
ns

N
o 

of
 c

la
ss

es
O

nt
ol

og
y 

de
pt

h
A

xe
s o

f c
la

s-
si

fic
at

io
n

Fo
rm

al
 o

nt
ol

-
og

y 
(O

W
L)

K
no

w
le

dg
e 

ba
se

/te
rm

in
ol

-
og

y

A
ss

er
te

d 
re

fe
r-

en
ce

s/
im

po
rte

d 
cl

as
se

s

A
ut

ho
rit

y

FM
A

Fo
cu

s o
n 

hu
m

an
 

an
at

om
y,

 
pr

ov
id

in
g 

a 
co

m
pr

eh
en

si
ve

 
re

pr
es

en
ta

-
tio

n 
of

 h
um

an
 

an
at

om
ic

al
 

str
uc

tu
re

s a
nd

 
th

ei
r r

el
at

io
n-

sh
ip

s

Em
pl

oy
s a

 c
om

-
pl

ex
 st

ru
ct

ur
e 

ba
se

d 
on

 a
 

fo
un

da
tio

na
l 

m
od

el
, u

til
iz

-
in

g 
a 

m
ix

 o
f 

hi
er

ar
ch

ic
al

 
re

la
tio

ns
hi

ps
, 

pa
rto

no
m

ic
 

re
la

tio
ns

hi
ps

, 
an

d 
ot

he
r 

ax
io

m
s t

o 
re

p-
re

se
nt

 h
um

an
 

an
at

om
ic

al
 

en
tit

ie
s a

nd
 

th
ei

r a
ttr

ib
ut

es

Pr
ov

id
e 

co
m

-
pr

eh
en

si
ve

 
an

d 
de

ta
ile

d 
in

fo
rm

at
io

n 
ab

ou
t h

um
an

 
an

at
om

ic
al

 
str

uc
tu

re
s, 

in
cl

ud
-

in
g 

sp
at

ia
l 

re
la

tio
ns

hi
ps

, 
hi

er
ar

ch
ic

al
 

or
ga

ni
za

tio
n,

 
an

d 
fu

nc
tio

na
l 

at
tri

bu
te

s

Ex
te

ns
iv

el
y 

us
ed

 
in

 v
ar

io
us

 
hu

m
an

 c
lin

ic
al

 
fie

ld
s, 

in
cl

ud
-

in
g 

m
ed

ic
al

 
ed

uc
at

io
n,

 
cl

in
ic

al
 

in
fo

rm
at

ic
s, 

im
ag

in
g 

an
d 

an
at

om
ic

al
 

re
se

ar
ch

, t
o 

pr
ov

id
e 

a 
de

ta
ile

d 
an

d 
st

an
da

rd
iz

ed
 

re
pr

es
en

ta
-

tio
n 

of
 h

um
an

 
an

at
om

y

10
4,

72
1

23
A

na
to

m
ic

al
ly

 
sy

ste
m

at
ic

. 
Ph

ys
ic

al
 a

nd
 

no
n 

ph
ys

ic
al

 
an

at
om

i-
ca

l e
nt

iti
es

, 
in

cl
ud

in
g 

re
la

tio
ns

 a
nd

 
tra

ns
fo

rm
at

io
n 

en
tit

ie
s

Ye
s

N
o

FM
A

 lo
ca

l c
ur

a-
tio

n 
te

am

N
AV

N
AV

 a
im

s t
o 

es
ta

bl
is

h 
a 

st
an

da
rd

iz
ed

 
no

m
en

cl
at

ur
e 

fo
r a

na
to

m
i-

ca
l s

tru
ct

ur
es

 
in

 v
et

er
in

ar
y 

m
ed

ic
in

e 
co

v-
er

in
g 

th
e 

m
ai

n 
ve

te
rin

ar
y 

sp
e-

ci
es

. C
ov

er
s 

a 
w

id
e 

ra
ng

e 
of

 a
ni

m
al

 sp
e-

ci
es

, i
nc

lu
di

ng
 

ca
t, 

do
g,

 p
ig

, 
ca

ttl
e,

 sh
ee

p,
 

go
at

, h
or

se
, 

an
d 

ra
bb

it

N
AV

 is
 

or
ga

ni
ze

d 
sy

ste
m

at
ic

al
ly

, 
pr

ov
id

in
g 

hi
er

ar
ch

ic
al

 
re

la
tio

ns
hi

ps
 

be
tw

ee
n 

an
a-

to
m

ic
al

 st
ru

c-
tu

re
s. 

Te
rm

s 
ar

e 
cl

as
si

fie
d 

ba
se

d 
on

 
th

ei
r p

os
iti

on
, 

fu
nc

tio
n,

 a
nd

 
re

la
tio

ns
hi

p 
w

ith
 o

th
er

 
str

uc
tu

re
s. 

Th
is

 h
ie

ra
rc

hi
-

ca
l o

rg
an

iz
a-

tio
n 

al
lo

w
s f

or
 

cl
ea

r i
de

nt
i-

fic
at

io
n 

an
d 

cl
as

si
fic

at
io

n 
of

 a
na

to
m

ic
al

 
en

tit
ie

s

N
AV

 in
cl

ud
es

 
sp

ec
ie

s-
sp

ec
ifi

c 
te

rm
s 

to
 a

dd
re

ss
 

an
at

om
ic

al
 

va
ria

tio
ns

 a
nd

 
di

ffe
re

nc
es

 
am

on
g 

di
f-

fe
re

nt
 a

ni
m

al
 

sp
ec

ie
s. 

It 
re

co
gn

iz
es

 th
at

 
an

im
al

s m
ay

 
ha

ve
 u

ni
qu

e 
an

at
om

ic
al

 
fe

at
ur

es
, a

nd
 

th
e 

te
rm

in
ol

-
og

y 
pr

ov
id

es
 

sp
ec

ie
s-

sp
ec

ifi
c 

te
rm

s 
to

 a
cc

ur
at

el
y 

de
sc

rib
e 

th
os

e 
str

uc
tu

re
s

It 
pr

ov
id

es
 a

 
co

m
m

on
 la

n-
gu

ag
e 

an
d 

se
t 

of
 te

rm
s f

or
 

ac
cu

ra
te

ly
 a

nd
 

co
ns

ist
en

tly
 

de
sc

rib
in

g 
an

at
om

ic
al

 
str

uc
tu

re
s 

in
 a

ni
m

al
s. 

U
se

d 
by

 
ve

te
rin

ar
ia

ns
, 

re
se

ar
ch

er
s, 

an
d 

an
at

om
ist

s 
m

ai
nl

y 
in

 
th

e 
cl

in
ic

al
 

do
m

ai
n.

 
G

lo
ba

l r
ea

ch
 

an
d 

av
ai

la
bl

e 
in

 L
at

in
 a

nd
 

En
gl

is
h

>
 65

00
N

/A
H

ie
ra

rc
hi

ca
l 

str
uc

tu
re

. 
G

en
er

al
 d

iv
i-

si
on

s o
n 

m
aj

or
 

an
at

om
ic

al
 

sy
ste

m
s o

r 
re

gi
on

s o
f t

he
 

bo
dy

, s
pe

ci
fc

 
re

gi
on

s o
r 

str
uc

tu
re

s 
w

ith
in

 e
ac

h 
ge

ne
ra

l 
sy

ste
m

. 
H

ie
ra

rc
hi

ca
l 

re
la

tio
ns

hi
ps

 
ca

pt
ur

ed
 

an
d 

sp
ec

ie
s 

sp
ec

ifi
c 

te
rm

i-
no

lo
gy

N
o

Ye
s

M
ai

nt
ai

ne
d 

an
d 

up
da

te
d 

by
 th

e 
In

te
rn

at
io

na
l 

C
om

m
itt

ee
 o

n 
Ve

te
rin

ar
y 

G
ro

ss
 

A
na

to
m

ic
al

 
N

om
en

cl
at

ur
e 

(I
C

V
G

A
N

)



403Bridging mouse and human anatomies; a knowledge‑based approach to comparative anatomy for…

1 3

Ta
bl

e 
2 

 (c
on

tin
ue

d)

Te
rm

in
ol

-
og

y/
O

nt
ol

-
og

y

Sc
op

e 
an

d 
Fo

cu
s

St
ru

ct
ur

e 
an

d 
or

ga
ni

za
tio

n
A

nn
ot

at
io

n 
an

d 
de

ta
il

A
pp

lic
at

io
ns

N
o 

of
 c

la
ss

es
O

nt
ol

og
y 

de
pt

h
A

xe
s o

f c
la

s-
si

fic
at

io
n

Fo
rm

al
 o

nt
ol

-
og

y 
(O

W
L)

K
no

w
le

dg
e 

ba
se

/te
rm

in
ol

-
og

y

A
ss

er
te

d 
re

fe
r-

en
ce

s/
im

po
rte

d 
cl

as
se

s

A
ut

ho
rit

y

m
TA

m
TA

 a
im

s t
o 

es
ta

bl
is

h 
a 

st
an

da
rd

iz
ed

 
no

m
en

cl
at

ur
e 

fo
r c

on
fir

m
ed

 
an

at
om

ic
al

 
str

uc
tu

re
s i

n 
la

bo
ra

to
ry

 
m

ic
e 

(M
us

 
m

us
cu

lu
s)

m
Ta

 w
ill

 b
e 

or
ga

ni
se

d 
sy

ste
m

at
ic

al
ly

 
in

 se
ve

ra
l s

ec
-

tio
ns

: g
en

er
al

 
te

rm
s, 

re
gi

on
s 

of
 th

e 
bo

dy
, 

os
te

ol
og

y,
 

ar
th

ro
lo

gy
, 

m
yo

lo
gy

, 
di

ge
sti

ve
 a

pp
a-

ra
tu

s, 
re

sp
ira

-
to

ry
 a

pp
ar

at
us

, 
th

or
ac

ic
 c

av
-

ity
, u

ro
ge

ni
ta

l 
ap

pa
ra

tu
s, 

ur
i-

na
ry

 o
rg

an
s, 

m
al

e 
an

d 
fe

m
al

e 
ge

ni
ta

l o
rg

an
s, 

pe
rin

eu
m

, 
pe

rit
on

eu
m

, 
en

do
cr

in
e 

gl
an

ds
, a

ng
io

l-
og

y,
 n

er
vo

us
 

sy
ste

m
, a

nd
 

co
m

m
on

 
in

te
gu

m
en

t. 
A

na
to

m
ic

al
 

te
rm

s a
re

 c
la

s-
si

fie
d 

ba
se

d 
on

 th
ei

r p
os

i-
tio

n,
 sh

ap
e,

 
fu

nc
tio

n 
an

d 
re

la
tio

ns
hi

p 
w

ith
 o

th
er

 
str

uc
tu

re
s

m
TA

 w
ill

 
pr

ov
id

e 
de

fin
i-

tio
ns

 o
f m

ou
se

 
an

at
om

ic
al

 
te

rm
s a

nd
 

its
 re

la
tio

n 
to

 h
um

an
 

an
at

om
ic

al
 

co
nc

ep
ts

 a
nd

 
str

uc
tu

re
s

It 
w

ill
 p

ro
vi

de
 

a 
se

t o
f 

co
nfi

rm
ed

 
an

at
om

ic
al

 
str

uc
tu

re
s f

or
 

ac
cu

ra
te

ly
 a

nd
 

co
ns

ist
en

tly
 

de
sc

rib
-

in
g 

m
ou

se
 

m
or

ph
ol

og
y.

 
D

efi
ni

tio
ns

 
of

 a
na

to
m

ic
al

 
te

rm
s w

ill
 b

e 
ac

co
m

pa
ni

ed
 

by
 a

nn
ot

at
ed

 
dr

aw
in

g 
im

ag
es

. I
t w

ill
 

be
 av

ai
la

bl
e 

in
 L

at
in

 a
nd

 
En

gl
is

h 
an

d 
La

tin

~ 
65

00
N

/A
It 

w
ill

 b
e 

a 
hi

er
ar

ch
ic

al
 

str
uc

tu
re

. 
G

en
er

al
 d

iv
i-

si
on

s o
n 

m
aj

or
 

an
at

om
ic

al
 

sy
ste

m
s o

r 
re

gi
on

s o
f t

he
 

bo
dy

, s
pe

ci
fic

 
re

gi
on

s o
r 

str
uc

tu
re

s 
w

ith
in

 e
ac

h 
or

ga
n

N
o

Ye
s

It 
w

ill
 b

e 
de

ve
l-

op
ed

 a
nd

 c
ur

at
ed

 
by

 a
 e

xp
er

t 
pa

ne
l o

f m
ou

se
 

m
or

ph
ol

og
ist

s



404 J. Ruberte et al.

1 3

between the human and mouse prostates the question must 
also be raised as to whether a lobe-specific mapping between 
the species, as is often attempted, is biologically justified. It 
is, however, possible to map mouse and human at a broader 
concept level and simply map the human to mouse prostate, 
and that complete collection of lobes/zones from each spe-
cies. This is a useful mapping approach but only reflects a 
ground truth when made at this higher organizational level. 
The MA ontology and NCI thesaurus both contain broader 
concepts prostate gland and prostate gland lobe, and these 
allow accurate mappings at a biologically meaningful level 
of granularity.

Breaking down the anatomical barriers between human 
and mouse anatomy, indeed between these and other meta-
zoan anatomies, is an important part of data integration, par-
ticularly for functional genomics and, as mentioned above, 
discovery of human disease genes using model organism 
phenotypes. Given the problems of anatomy ontology map-
ping a cross-species anatomy ontology was developed—
Uberon. The problems with data integration across species 
become more difficult with evolutionary distance and where 
the matching of human to model organism anatomies is 
desired to “de-silo” data, particularly phenotype data, map-
pings can only be done at a low level of granularity. Such a 
mapping of evolutionarily homologous structures and ana-
tomical concepts was achieved with the Uberon ontology 
(Mungall et al. 2012; Haendel et al. 2014). While not as 
granular as MA, Uberon has become a de facto standard 
for expressing anatomical location in gene expression stud-
ies, and also through equivalence axioms facilitating cross-
species phenotype similarity assessments using the major 
metazoan phenotype ontologies, for example MP (https:// 
www. ebi. ac. uk/ ols/ ontol ogies/ mp) and HPO (https:// hpo. 
jax. org) (Robinson and Webber 2014; Gkoutos et al. 2017). 
As well as the incompleteness issues, Uberon has complex 
axes of classification and contains mixed semantic types. 
Detailed anatomical annotation of images, and high reso-
lution phenotype capture were not applications for which 
Uberon was designed.

The use of anatomy ontologies, and specifically the MA 
ontology goes further than axiomatization and they have 
proved extremely useful in collecting and coding data for 
subsequent computational analysis. The collection of his-
topathology data at scale is complicated by the inability to 
compute on existing terminologies and the limited scope of 
existing terminologies when attempting to cover the entire 
domain of pathology in the mouse. Such terminologies 
would been many hundreds of thousands of concepts were 
they to pre-compose all the possible locations and types of 
lesions. This problem is solved by using an anatomy ontol-
ogy, in this case MA, in combination with a foundational 
pathology ontology (MPATH) (Schofield et al. 2013) to 
post-compositionally create specific terms as required 

(Alghamdi et al. 2019). This approach has been applied for 
the high throughput pathology studies by the International 
IMPC (Elmore et al. 2018) and a large-scale study on the 
pathology of aging laboratory mice (Sundberg et al. 2011) 
using a dedicated data capture system, MODIS (Sundberg 
et al. 2008).

Conclusions

The ability to relate and map anatomical structures between 
mice and humans is a critical part of using laboratory mice 
for the discovery of disease genes and pathological mecha-
nisms. An accurate and granular formal terminology or 
ontology is essential for these activities, and permits not only 
accurate data capture, but also computational approaches 
to cross-species phenotyping. Such terminologies need to 
be grounded in biological truth and mappings made using 
knowledge-driven criteria. The problems mapping high 
resolution anatomical data from humans to mice and vice 
versa are, however, impacted by a major difference in the 
completeness of the two species’ anatomical descriptions. 
It is currently not possible to represent mouse anatomy with 
the precision available to FMA using the MA, and indeed 
the MA was not designed for the detailed representation 
required to annotate and interpret high resolution imaging 
and modern anatomical techniques, or the small variations 
seen between species and genetic backgrounds.

While it is not the aim of this commentary to propose a 
new anatomy ontology for the adult mouse, we have dis-
cussed how advances in imaging particularly have generated 
a requirement for more granular terminologies, the model 
for which is the TA or the NAV. Such knowledgebase level 
terminologies themselves have limited use computationally 
and we would strongly support establishment of a close rela-
tionship with MA curation to include new recommendations 
in the existing, gold-standard ontology as appropriate.

The study of human anatomy has a long history, mainly 
motivated by surgery and therapeutics. As we discuss above, 
it is currently more detailed and complete than mouse 
anatomy, so work to increase the accuracy and coverage 
of mouse anatomy will greatly assist in making accurate 
and meaningful mappings between the two species. The 
development of new imaging technologies, such as MRI, 
CT, SPECT, PET, two photon tomography (STP) (Ragan 
et al. 2012), light sheet microscopy (Stelzer et al. 2021) 
and experimental procedures such as CLARITY, 3DISCO 
and CUBIC (Ueda et al. 2020) have not only improved our 
knowledge of mouse anatomy but, in a sense, have turned 
anatomical investigations inside out. Traditionally human 
anatomy proceeded from the outside-in. Contemporary 
investigations can increasingly proceed from the inside-out 
(Standring 2016) and we are entering a new phase in the 

https://www.ebi.ac.uk/ols/ontologies/mp
https://www.ebi.ac.uk/ols/ontologies/mp
https://hpo.jax.org
https://hpo.jax.org


405Bridging mouse and human anatomies; a knowledge‑based approach to comparative anatomy for…

1 3

description and understanding of anatomy, where mouse 
anatomical studies may inform those in humans rather than 
vice versa.

Added to this is the increasing awareness of anatomi-
cally definable functional units which do not have morpho-
logically explicit physical boundaries and structures at a 
macro-scale, yet can be demonstrated through high reso-
lution molecular, imaging and functional techniques, has 
changed some of our concepts of what anatomy actually is, 
for example the brain connectome and the identification of 
the angiome (D'Angelo and Jirsa 2022; Taylor and Palmer 
1987).

Integration of cellular and tissue anatomy is a topic we 
have not addressed in this commentary, but multiscale inte-
gration of anatomy is crucial to the generation of the virtual 
physiome (Hoekstra et al. 2018; Kokash and de Bono 2021) 
and much work is proceeding to make this computationally 
coherent in support of modelling physiological processes, 
which in turn allows for comparison of abnormal processes 
between species.

Finally, the need for training in these rapidly develop-
ing fields will be important in implementing the advantages 
gained from improved comparative anatomy between mice 
and humans, and training courses aimed at a new generation 
of investigators are under development in the community 
(Ruberte et al. 2020).

Acknowledgements This work was supported by a grant from the 
Erasmus Mundus of the Education, Audiovisual and Culture Execu-
tive Agency (EACEA) of the European Union (Reference Number: 
101082155). The name of the project is the Erasmus Mundus Joint 
Master degree in “Human Diseases Models Morphological Phenotyp-
ing” (MorphoPHEN). The authors thank Prof. Martin Ringwald and Dr. 
Jerrold M. Ward for helpful comments on the manuscript.

Author contributions J Ruberte, P Schofield, J Sundberg, and C MacK-
erlie wrote the main manuscript text. A Carretero and A Rodriguez 
prepared anatomical preparations and figures. All authors reviewed 
the manuscript.

Funding Open Access Funding provided by Universitat Autonoma de 
Barcelona.

Declarations 

Competing interests The authors declare no competing interests.

Open Access  This article is licensed under a Creative Commons Attri-
bution 4.0 International License, which permits use, sharing, adapta-
tion, distribution and reproduction in any medium or format, as long 
as you give appropriate credit to the original author(s) and the source, 
provide a link to the Creative Commons licence, and indicate if changes 
were made. The images or other third party material in this article are 
included in the article's Creative Commons licence, unless indicated 
otherwise in a credit line to the material. If material is not included in 
the article's Creative Commons licence and your intended use is not 
permitted by statutory regulation or exceeds the permitted use, you will 
need to obtain permission directly from the copyright holder. To view a 
copy of this licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/.

References

Akabori E (1934) Septal apertures in the humerus on Japanese, Ainu 
and Koreans. Am J Phys Anthropol 18:395–400

Alghamdi SM, Sundberg BA, Sundberg JP, Schofield PN, Hoehndorf 
R (2019) Quantitative evaluation of ontology design patterns for 
combining pathology and anatomy ontologies. Sci Rep 9:4025

Aspelund A, Antila S, Proulx ST (2015) A dural lymphatic vascular 
system that drains brain interstitial fluid and macromolecules. J 
Exp Med 212:991–999

Bard JB (2005) Anatomics: the intersection of anatomy and bioinfor-
matics. J Anat 206:1–16

Bard JBL, Kaufman MH, Dubreuil C, Brune RM, Burger A, Baldock 
RA, Davidson DR (1998) An internet-accessible database of 
mouse developmental anatomy based on a systematic nomencla-
ture. Mech Dev 74:111–120

Barney S, Lewis W, Beach J, Berghof O (eds) (2006) The etymologies 
of Isidore of Seville. Cambridge University Press, Cambridge

Barrett JM, RaineriTapies MG, Shepherd GMG (2020) Manual dexter-
ity of mice during food-handling involves the thumb and a set of 
fast basic movements. PLoS One 15:e0226774

Bodenreider O, Hayamizu TF, Ringwald M, De Coronado S, Zhang S 
(2005) Of mice and men: aligning mouse and human anatomies. 
AMIA Annu Symp Proc, pp 61–65

Boudellioua I, Mahamad Razali RB, Kulmanov M, Hashish Y, Bajic 
VB, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield 
PN, Hoehndorf R (2017) Semantic prioritization of novel causa-
tive genomic variants. PLoS Comput Biol 13:e1005500

Brown SDM (2021) Advances in mouse genetics for the study of 
human disease. Hum Mol Genet 30:R274–R284

Butterfield LB (1972) The fine structure of Bowman’s capsule in male 
C3H/HeJ mice. Lab Anim Sci 5:652–657

Churchill GA, Gatti DM, Munger SC, Svenson KL (2012) The Diver-
sity Outbred mouse population. Mamm Genome 23:713–718

Collaborative Cross C (2012) The genome architecture of the col-
laborative cross mouse genetic reference population. Genetics 
190:389–401

Constantinescu GM (2011) Comparative anatomy of the mouse and the 
rat: a color atlas and text. American Association for Laboratory 
Animal Science, Memphis

Cook MJ (1965) The anatomy of the laboratory mouse. Academic 
Press, New York

Cook MJ (1983) Anatomy, chapter 7. In: Foster HL, Small JD, Fox JG 
(eds) The mouse in biomedical research. Academic Press, New 
York, pp 101–120

Coronado S, Haber MW, Sioutos N, Tuttle M, Wright LW (2004) NCI 
Thesaurus: using science based terminology to integrate cancer 
research results. Medinfo 2004:33–37

D’Angelo E, Jirsa V (2022) The quest for multiscale brain modeling. 
Trends Neurosci 45:777–790

De Souza P, Viotto-Souza W, Pereira V, Coelho F, Leite B, Abidu-
Figueiredo M, Quagliatto A (2020) Clavicle in carnivorans: a 
forgotten bone. Anat Rec 303:1831–1841

de Wilde V, Maeseneer M, Lenchik L, Roy P, Beeckman P, Osteaux 
M (2004) Normal osseous variants presenting as cystic or lucent 
areas on radiography and CT imaging: a pictorial overview. Eur 
J Radiol 51:77–84

Del-Valle-Anton L, Borrell V (2022) Folding brains: from development 
to disease modelling. Physiol Rev 2:511–550

Eide PK, Vatnehol SAS, Ke E (2018) Magnetic resonance imaging 
provides evidence of glymphatic drainage from human brain to 
cervical lymph nodes. Sci Rep 8:7194

Elmore SA, Cardiff R, Cesta MF, Gkoutos GV, Hoehndorf R, Keenan 
CM, McKerlie C, Schofield PN, Sundberg JP, Ward JM (2018) A 

http://creativecommons.org/licenses/by/4.0/


406 J. Ruberte et al.

1 3

review of current standards and the evolution of histopathology 
nomenclature for laboratory animals. ILAR J 59:29–39

F.I.P.A.T (2019) Federative International Programme for Anatomi-
cal Nomenclature (2019) Terminologia Anatomica, 2nd edn; 
approved by the Federation of Association of Anatomist in 2020

Gkoutos GV, Schofield PN, Hoehndorf R (2017) The anatomy of phe-
notype ontologies: principles properties and applications. Brief 
Bioinform 19(5):1008–1021. https:// doi. org/ 10. 1093/ bib/ bbx035

Grüneboom A, Hawwari I, Weidner D (2019) A network of trans-cor-
tical capillaries as mainstay for blood circulation in long bones. 
Nat Metab 1:236–250

Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Brad-
ford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, 
Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, 
Robinson-Rechavi M, Sereno PC, Mungall CJ (2014) Unification 
of multi-species vertebrate anatomy ontologies for comparative 
biology in Uberon. J Biomed Semantics 5:21

Hayamizu TF, Mangan M, Corradi JP, Kadin JA, Ringwald M (2005a) 
The Adult Mouse Anatomical Dictionary: a tool for annotating 
and integrating data. Genome Biol 6:R29

Hayamizu TF, Mangan M, Jp C (2005b) The adult mouse anatomical 
dictionary: a tool for annotating and integrate data. Genom Biol 
6:R29

Hayamizu TF, Coronado S, Fragoso G (2012) The mouse–human 
anatomy ontology mapping project. Database article ID bar066

Hayamizu TF, Wicks MN, Davidson DR, Burger A, Ringwald M, Bal-
dock RA (2013) EMAP/EMAPA ontology of mouse developmen-
tal anatomy: 2013 update. J Biomed Semant 4:15

Hayamizu TF, Baldock RA, Ringwald M (2015) Mouse anatomy 
ontologies: enhancements and tools for exploring and integrating 
biomedical data. Mamm Genome 26:422–430

Hedrich HJ (ed) (2012) The Laboratory Mouse. Academic Press, 
Boston

Hedrich HJ, Bullock G (2004) The laboratory mouse. Elsevier, 
Amsterdam

His W (1885) Die anatomische Nomenclatur. Nomina anatomica, 
Verzeichniss der von der anatomischen Gesellschaft auf ihrer IX. 
Versammlung in Basel angenommenen Namen. Metzger, Leipzig

Hoehndorf R, Schofield PN, Gkoutos GV (2011) PhenomeNET: a 
whole-phenome approach to disease gene discovery. Nucleic 
Acids Res 39:e119

Hoehndorf R, Schofield PN, Gkoutos GV (2013) An integrative, trans-
lational approach to understanding rare and orphan genetically 
based diseases. Interface Focus 3:20120055

Hoehndorf R, Schofield PN, Gkoutos GV (2015) The role of ontologies 
in biological and biomedical research: a functional perspective. 
Brief Bioinform 16:1069–1080

Hoekstra AG, van Bavel ET, Siebes M, Gijsen FJH, Geris L (2018) 
Virtual physiological human 2016: translating the virtual physi-
ological human to the clinic. Interface Focus 8

I.C.V.G.A.N. (2017) Nomina Anatomica Veterinaria (2017) World 
Association of Veterinary Anatomists (WAVA. I.C.o.V.G.A. 
Nomenclature)

Ittmann M (2018) Anatomy and histology of the human and murine 
prostate. Cold Spring Harb Perspect Med 8:a030346

Johnson J, DelGiudice B, Bangari D, Peterson E, Ulinski G, Ryan S, 
Thurberg B (2019) The laboratory mouse: a guide to the location 
and orientation of tissues for optimal histological evaluation. CRC 
Press, Boca Raton

Kachlik D, Baca V, Bozdechova I (2008) Anatomical terminology 
and nomenclature: past, present and highlights. Surg Radiol Anat 
30:459–466

Kiupel M, Brown KS, Sundberg JP (2000) Bulbourethral (Cowper’s) 
gland abnormalities in inbred laboratory mice. J Exp Anim Sci 
40:178–188

Kokash N, de Bono B (2021) Knowledge representation for multi-scale 
physiology route modeling. Front Neuroinform 15:560050

Leader RW, Padgett GA (1980) The genesis and validation of animal 
models. Am J Pathol 101:S11-16

Louveau A, Smirnov I, Keyes T (2015) Structural and functional 
features of central nervous system lymphatic vessels. Nature 
523:337–341

Louveau A, Plog BA, Antila S, Alitalo K, Nedergaard M, Kipnis J 
(2017) Understanding the functions and relationships of the 
glymphatic system and meningeal lymphatics. J Clin Investig 
127:3210–3219

Maronpot RR, Boorman GA, Gaul BW (1999) Pathology of the mouse. 
Reference and atlas. Cache River Press, Vienna

Matter SP (2013) The prince of medicine; Galen in the Roman Empire. 
Oxford University Press, Oxford

Mays S (2008) Septal aperture of the humerus in a mediaeval human 
skeletal population. Am J Phys Anthropol 136:432–440

McGonigle P, Ruggeri B (2014) Animal models of human dis-
ease: challenges in enabling translation. Biochem Pharmacol 
87:162–171

Meckel JH (1825) A note on the septal apertures in the humerus of 
Central Indians. Eastern Anthropol 33:270–284

Mota B, Herculano-Houzel S (2015) Cortical folding scales universally 
with surface area and thickness, not number of neurons. Science 
349:74–77

Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ash-
burner M (2010) Integrating phenotype ontologies across multiple 
species. Genome Biol 11:R2

Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA (2012) 
Uberon, an integrative multi-species anatomy ontology. Genome 
Biol 13:R5

Natale G, Bocci G, Ribatti D (2017) Scholars and scientists in the his-
tory of the lymphatic system. J Anat 231:417–429

O’Rahilly R (1989) Anatomical terminology, then and now. Acta Anat 
134:291–300

Popesko P, Rajtova V, Horak J (1992) A Color Atlas of Anatomy of 
Small Laboratory Animals. Wolfe Publishing Ltd, London

Ragan T, Kadiri LR, Venkataraju KU, Bahlmann K, Sutin J, Taranda 
J, Arganda-Carreras I, Kim Y, Seung HS, Osten P (2012) Serial 
two-photon tomography for automated ex vivo mouse brain imag-
ing. Nat Methods 9:255–258

Robinson PN, Webber C (2014) Phenotype ontologies and cross-spe-
cies analysis for translational research. PLoS Genet 10:e1004268

Rockwood C, Matsen F, Wirth M, Lippit S (2009) The shoulder. Saun-
ders/Elsevier, Philadelphia

Rosse C, Mejino JLV (2008) The foundational model of anatomy ontol-
ogy. Comput Biol 6

Ruberte J, Carretero A, Navarro M (2016 and 2017) Morphological 
mouse phenotyping. Editorial Medica Panamericana, Buenos 
Aires and Academic Press, Cambridge

Ruberte J, Schofield PN, Brakebusch C, Vogel P, Herault Y, Gracia G, 
McKerlie C, Hrabe de Angelis M, Hagn M, Sundberg JP (2020) 
PATHBIO: an international training program for precision mouse 
phenotyping. Mamm Genome 31:49–53

Ruberte J, Carretero A, Cater H, Gracia G, Lally C (2021) X ray anno-
tation mouse atlas. Doctor Herriot S.L., Zaragoza

Schofield PN, Bard JB, Booth C, Boniver J, Covelli V, Delvenne P, 
Ellender M, Engstrom W, Goessner W, Gruenberger M, Hoefler 
H, Hopewell J, Mancuso M, Mothersill C, Potten CS, Quintanilla-
Fend L, Rozell B, Sariola H, Sundberg JP, Ward A (2004) Path-
base: a database of mutant mouse pathology. Nucleic Acids Res 
32:D512–D515

Schofield PN, Gkoutos GV, Gruenberger M, Sundberg JP, Hancock 
JM (2010) Phenotype ontologies for mouse and man: bridging 
the semantic gap. Dis Model Mech 3:281–289

https://doi.org/10.1093/bib/bbx035


407Bridging mouse and human anatomies; a knowledge‑based approach to comparative anatomy for…

1 3

Schofield PN, Sundberg JP, Hoehndorf R, Gkoutos GV (2011) New 
approaches to the representation and analysis of phenotype knowl-
edge in human diseases and their animal models. Brief Funct 
Genom 10:258–265

Schofield PN, Sundberg JP, Sundberg BA, McKerlie C, Gkoutos GV 
(2013) The mouse pathology ontology, MPATH; structure and 
applications. J Biomed Semant 4:18

Scudamore CL (2014) A practical guide to the histology of the mouse. 
Wiley, London

Shivaleela C, Afroze KH, Lakshmiprabha S (2016) An osteological 
study of supratrochlear foramen of humerus of south Indian popu-
lation with reference to anatomical and clinical implications. Anat 
Cell Biol 49:249–253

Smith CM, Finger JH, Tf H (2015) GXD—a community resource of 
mouse Gene Expression Data. Mamm Genome 26:314–324

Snell GD (1941) Biology of the laboratory mouse, 1st edn. McGraw-
Hill, New York

Standring S (2016) A brief history of topographical anatomy. J Anat 
229:32–62

Stelzer EHK, Strobl F, Chang B-J, Preusser F, Preibisch S, McDole 
K, Fiolka R (2021) Light sheet fluorescence microscopy. Nat Rev 
Methods Primers 1:73

Sundberg JP, Schofield PN (2009) One medicine, one pathology, and 
the one health concept. J Am Vet Med Assoc 234:1530–1531

Sundberg JP, Sundberg BA, Schofield PN (2008) Integrating mouse 
anatomy and pathology ontologies into a diagnostic/phenotyping 
database: tools for record keeping and teaching. Mamm Genome 
19:413–419

Sundberg J, Berndt A, Sundberg B, Silva KA, Kennedy V, Bronson R, 
Yuan R, Paigen B, Harrison D, Schofield PN (2011) The mouse 
as a model for understanding chronic diseases of aging: the his-
topathologic basis of aging in inbred mice. Pathobiol Aging Age-
Relat Dis 1:71719

Taylor GI, Palmer JH (1987) The vascular territories (angiosomes) of 
the body: experimental study and clinical applications. Br J Plast 
Surg 40:113–141

Treuting P, Dintzis S, Montine KS (2018) Comparative anatomy and 
histology. A mouse, rat, and human atlas. Academic Press, San 
Diego

Tubs R, Shoja MM, M L, (2016) Bergman’s comprehensive encyclo-
pedia of human anatomic variation. Wiley Blackwell, Hoboken

Ueda HR, Ertürk A, Chung K, Gradinaru V, Chédotal A, Tomancak P, 
Keller PJ (2020) Tissue clearing and its applications in neurosci-
ence. Nat Rev Neurosci 21:61–79

Vandamme TF (2014) Use of rodents as models of human diseases. J 
Pharm Bioallied Sci 1:2–9

Vesalius A (1543) De humani corporis fabrica libri septem. Joannis 
Oporini, Basle

Wirtschafter ZT, Tsujimura JK (1961) The sesamoid bones in the C3H 
mouse. Anat Rec 139:399–408

Publisher's Note Springer Nature remains neutral with regard to 
jurisdictional claims in published maps and institutional affiliations.


	Bridging mouse and human anatomies; a knowledge-based approach to comparative anatomy for disease model phenotyping
	Abstract
	Introduction
	Mice are a small animal model but anatomically similar to humans
	Mice and humans: a similar anatomical complexity but different level of knowledge and resources
	Of originals and copies: the case of bulbourethral glands
	Mouse vs human anatomical terminology and nomenclature
	Alignment of mouse and human anatomy ontologies and its application
	Conclusions
	Acknowledgements 
	References