Special Issue on ICIT 2009 Conference - Bioinformatics and Image

INTEGRATING BIOMEDICAL ONTOLOGIES OBR-SCOLIO

ONTOLOGY

Vanja Lukovi
Information technology

Danijela Miloevi
Information technology

Goran Devedi
Information technology

ABSTRACT
This paper analyses a broad scope of research papers dealing with the process of integrating biomedical
ontology with the FMA reference ontology. Namely, we want to investigate the capability of this process
appliance in development of the OBR-Scolio application ontology for the pathology domain of spine, rather
the scoliosis domen. Such ontology is one of the many objectives in the realization of the project named:
Ontological modeling in bioengineering in the domain of orthopedics and physical medicine.

Keywords: Biomedical ontology, Formal ontology, Reference ontology, Application ontology

1 INTRODUCTION ontology, forming this way FMA-RadLex

application radiology ontology. This described
Biomedical ontologies are being developed in process is then utilized for forming the OBR-Scolio
ever growing numbers, but there is too little application ontology for the pathology domain of
attention paid for ontology alignment and spine (scoliosis domen) from the OBR reference
integration, in other that results already obtained by ontology.
the one terminology based application ontology can
be utilized in other similar application ontologies. 2 BFO ONTOLOGY
No scientific advance can be obtained with the
horizontally integration between two application BFO [3] is a formal, top-level ontology which is
ontologies, although vertical integration between based on tested principles for ontology
ontologies in all categories is needed [1]. In this construction. BFO consists of the SPAN and SNAP
way formal, top level ontologies should provide the ontologies. The SPAN ontology relates to
validated framework for reference ontologies, occurrents, processing entities (events, actions,
which represent the domains of reality studied by procedures, happenings) which unfold over an
the basic biomedical sciences. The latter should interval of time. The complementary SNAP
then in turn provide the scientifically tested ontology relates to continuants, the participants in
framework for a variety of terminology-based such processes, which are entities that endure over
ontologies developed for specific application the time, during the period of their existence.
purposes. Anatomy is a science that studies biological
In this paper according to [1], we denote how continuants, while physiology studies biological
the process of vertical integration of the FMA occurrents. Pathology, on the other hand, is
(Foundational Model of Anatomy) reference concerned with structural alterations of biological
ontology [5] with the BFO (Basic Formal continuants and with perturbations of biological
Ontology) top-level ontology [3] can support the occurrents which together are manifested as
process of horizontal integration of the two diseases. Moreover, BFO draws distinctions also
reference ontologies: PRO (Physiology Reference between instances and universals and specifies
Ontology) [8] and PathRO (Pathology Reference relations which link them.
Ontology), forming accordingly the new reference
ontology OBR (Ontology of Biomedical Reality), 3. FMA ONTOLOGY
which is therefore federation of the three
independent reference ontologies which range over The FMA [5] is reference ontology for anatomy,
the domains of anatomy, physiology and pathology. which according independent evaluations satisfies
Moreover according to [9], we denote the fundamental requirements for ontological
process of vertical integration of the RadLex representation of human anatomy [6, 7].
radiology terminology with the FMA reference

UbiCC Journal - Volume 4 No. 3 664

Special Issue on ICIT 2009 Conference - Bioinformatics and Image

Hence, the domain of the FMA is anatomy of pathological entity. The class Material anatomical
the idealized human body. FMA uses the hierarchy entity is subdivided into classes: Anatomical
of classes of anatomical entities (anatomical structure and Portion of canonical body substance,
universals) which exist in reality through their on the basis of the possession or non-possession of
instances. The root of the FMAs anatomy inherent 3D shape. Within the class anatomical
taxonomy (AT) is Anatomical entity and its structure OBR ontology make a distinction between
dominant class is Anatomical structure. Anatomical canonical anatomical structures, which exist in the
structure is defined as a material entity which has idealized organism, and variant anatomical
its own inherent 3D shape and which has been structures, which result from an altered expression
generated by the coordinated expression of the pattern of normal structural genes, without health
organisms own structural genes. This class related consequences for the organism. The class
includes material objects that range in size and Material pathological entity is subdivided into
complexity from biological macromolecules to classes: Pathological structure and Portion of
whole organisms. The dominant role of Anatomical pathological body substance, on the basis of the
structure is reflected by the fact that non-material possession or non-possession of inherent 3D shape,
physical anatomical entities (spaces, surfaces, lines too. Pathological structures are result from an
and points) and body are conceptualized in the altered expression pattern of normal structural
FMA, in terms of their relationship to anatomical genes, with negative health consequences for the
structures. organism.
The class Dependent organismal continuant is
4. OBR ONTOLOGY subdivided into classes: Immaterial anatomical
continuant, Immaterial pathological continuant and
Physiological continuant. Although the existence of
immaterial anatomical and pathological spaces and
surfaces and anatomical lines and points depends
on corresponding independent continuant entities,
they are dependent continuants. Besides them
classes: Function, Physiological state and
Physiological role and classes: Malfunction,
Pathological state and Pathological role also
belongs to Dependent organismal continuant,
because their entities do not exist without
corresponding independent continuant entities.
Functions are certain sorts of potentials of
Figure 1. Ontology of Biomedical Reality OBR independent anatomical continuants for
engagement and participation in one or more
The root of OBR is the universal Biological processes through which the potential becomes
entity (Fig. 1). A distinction is then drawn between realized. he function is a continuant, since it
the classes: Biological continuant and Biological endures through time and exists even during those
occurrent, the definitions of which are inherited times when it is not being realized.
from BFO [3]. The class Biological continuant is Whether or not a function becomes realized
subdivided into classes: rganismal continuant, depends on the physiological or pathological state
which includes entities that range over single of the associated independent anatomical
organisms and their parts and Extra-organismal continuant. Thereat, physiological and pathological
continuant, which includes entities that range over state is a certain enduring constellation of values of
aggregates of organisms. Accordingly, the class an independent continuants aggregate physical
Biological occurrent is subdivided into classes: properties. These physical properties are
rganismal occurent and Extra-organismal represented in the Ontology of Physical Attributes
occurent, which include processes associated with (OPA), which provides the values for the physical
single organisms and their parts i.e. processes properties of organismal continuants. Namely, the
associated with aggregates of organisms. states of these continuants can be specified in terms
The class Organismal continuant is subdivided of specific ranges of attribute values.
into classes: Independent organismal continuant The independent continuants that participate in
and Dependent organismal continuant. a physiological or pathological process may play
Extrapolating from the FMAs principles, different roles in the process (e.g. as agent, co-
Independent organismal continuants have mass and factor, catalyst, etc.). Such a process may transform
are material, whereas Dependent organismal one state into another (for example a physiological
continuant are immaterial and do not have mass. into another physiological, or into a pathological
OBR ontology distinguishes anatomical state).
(normal) from pathological (abnormal) material The class Organismal occurent is subdivided
entities. Accordingly, the class Independent into classes: Physiological process and
organismal continuant is subdivided into classes: Pathological process. Physiological process
Material anatomical entity and Material courses transformations of one physiological state

UbiCC Journal - Volume 4 No. 3 665

Special Issue on ICIT 2009 Conference - Bioinformatics and Image

into another physiological state, whereas 6. DERIVATION THE FMA-RADLEX

pathological process courses transformation of a APPLICATION ONTOLOGY
physiological state into a pathological state or one
pathological state into another pathological state.
The relative balance of these processes results
either in the maintenance of health or in the
pathogenesis of material pathological entities, and
thus in the establishment and progression of
diseases. Transformation of a pathological state into
a physiological, manifest as healing or recovery
from a disease, comes about through physiological
processes that successfully compete with and
ultimately replace pathological processes, namely
function is restored. Processes are extended not
only in time but also in space by virtue of the nature
of their participants.

5. RADLEX TERMINOLOGY

The Radiological Society of North America

Figure 3: FMA-RadLex (right) derived from the
(RSNA) developed a publicly available
FMA (left)
terminology, RadLex [12], to provide a uniform
standard for all radiology-related information.
Terms relating to anatomy are represented in the
RadLex terminology is organized into a hierarchy
RadLex terminology category Anatomic location,
(Fig. 2) and subsumes over 7400 terms organized in
which corresponds to the category Anatomical
9 main categories or types with RadLex term as the
entity, used by other disciplines of biomedicine.
root. However RadLex terminology does not yet
This is not radiology image entity, yet the entity
have a principled ontological framework [14] for
that exists in the reality. Anatomic location is
these three reasons:
therefore renamed as the FMA root term
Anatomical entity (Fig. 3). For the image findings
1) being term-oriented, RadLex currently
representing radiology images entities the separate
ignores the entities to which its terms
ontology should be created.
project;
Application ontology from the FMA can be
2) the lack of a taxonomy grounded in
derived either by:
biomedical reality;
1. Obtaining an entire copy of the FMA and
3) the ambiguity and mixing of relations
pruning the ontology down to the required
(such as is_a, part_of, contained_in)
specifications - de novo construction.
represented by the links between the nodes
2. Mapping the existing terminology project to
of the term hierarchy (Fig. 2).
the FMA, carving out the ontology around
the mappings and finally incorporating the
In the next section, according [9] is described
derivatives into the existing terminology
how a portion of reference ontology, such as the
project.
FMA, can be adopted to lend application ontology
The latter method was applied in constructing
in which all challenges mentioned above are
the anatomy application ontology for RadLex [9].
resolved.
Hence, high level RadLex terms are first mapped to
the corresponding FMA terms, and then their
corresponding FMA super-types are imported into
the RadLex taxonomy. After that, other terms at
different levels of the RadLex tree are mapped to
the corresponding FMA terms, and then their
corresponding FMA super-types are imported into
the RadLex taxonomy super-types. In RadLex
anatomy taxonomy the highest level parents of the
imported super-types of the FMA are incorporating,
as well: Anatomical structure which subsumes 3-D
objects that have inherent shape, e.g. body, organ
system, and organ, and Immaterial anatomical
entity which encompasses types that have no mass
property, such as: anatomical space, anatomical
Figure 2. RadLex hierarchy in Protg surface, anatomical line and anatomical point.
Hence, this conclusion can be divided: the
operation of construction the same ontology via the

UbiCC Journal - Volume 4 No. 3 666

Special Issue on ICIT 2009 Conference - Bioinformatics and Image

de novo approach, would involve a series of The hierarchical tree of the OBR ontology
deletion and addition of links (Figure 3, left) from class Pathological structure and also its subclasses:
the FMA reference ontology. For example, the is_a Subdivision of pathological organ system,
link of the class Anatomical structure is deleted Subdivision of pathological skeletal system and
from Material anatomical entity and then added Subdivision of pathological axial skeletal system,
directly to Anatomical entity. Both Physical from which all subclasses which are not relevant
anatomical entity and Material anatomical entity for the pathological domen of spine are deleted, are
are then deleted from the FMA taxonomy. Beside illustrated in Fig. 5, Fig. 6, Fig. 7 and Fig. 8.
that, FMA types representing microscopic entities
which are not relevant to radiology such as Cell,
Cardinal cell part, Biological macromolecule,
Cardinal tissue part, are also deleted from
Anatomical structure. These operations can be
carried out in all levels of the hierarchical tree.

7. DERIVATION OF THE OBR-SCOLIO

APPLICATION ONTOLOGY

In constructing the OBR-Scolio application

ontology for the pathology domain of spine
(scoliosis domen) from the OBR reference ontology
the de novo method was applied (Figure 4). All the
classes which are not relevant to the pathology
domain of spine, such as: Matherial anatomical
entity, Immaterial anatomical continuant,
Physiological continuant, ExtraOrganismal
continuant, Biological occurent and also theirs
relevant subclasses are deleted from the Figure 5: Subclasses of the Pathological
hierarchical tree of the OBR reference ontology. structure class

Figure 6: Subclasses of the Subdivision of

pathological organ system class

Figure 4: OBR-Scolio application ontology

derived from the OBR reference ontology

UbiCC Journal - Volume 4 No. 3 667

Special Issue on ICIT 2009 Conference - Bioinformatics and Image

OBR-Scolio application ontology in the pathology

domain of spine (scoliosis), which is one of the
many objectives in the realization of the project
named: Ontological modeling in bioengineering 1
in the domain of orthopedics and physical
medicine.

8. REFERENCES

[1] Cornelius Rosse, MD, DSc, Anand Kumar,

MD,PhD, Jose LV Mejino Jr, MD, Daniel L Cook,
MD, PhD, Landon T Detwiler, Barry Smith, PhD:
A Strategy for Improving and Integrating
Biomedical Ontologies, AMIA Annu Symp Proc.
(2005), pp. 639-643.

[2] http://www.loucnr.it/DOLCE.html

[3] Grenon P, Smith B, Goldberg L: Biodynamic

ontology: applying BFO in the biomedical domain,
In DM Pisanelli (ed.), Ontologies in Medicine,
Amsterdam: IOS Press, 2004,20-38.

[4] Open Biomedical Ontologies:

Figure 7: Subclasses of the Subdivision of http://obo.sourceforge.net/
pathological skeletal system class
[5] Rosse C, Mejino JLV Jr.: A reference ontology
for biomedical informatics: the Foundational Model
of Anatomy, J Biomed Inform, 2003 Dec;
36(6):478-500.

[6] Smith B, Khler J, Kumar A.: On the

application of formal principles to life science data:
A case study in the Gene Ontology, DILS 2004:
Data Integration in the Life Sciences. 2004; 124-
Figure 8: Subclasses of the Subdivision of 139.
pathological axial skeletal system class
[7] Zhang S, Bodenreider O.: Law and order:
Ultimately, in the Fig. 9 all subclasses of the Assessing and enforcing compliance with
Pathological vertebral column class are illustrated. ontological modelling principles, Computers in
Biology and Medicine 2005: in press.

[8] Cook DL, Mejino JLV, Rosse C.: Evolution of a

Foundational Model of Physiology: Symbolic
representation for functional bioinformatics,
Medinfo 2004; 2004:336-340.

[9] Jose L.V. Mejino Jr, Daniel L. Rubin, and

James F. Brinkley: FMA-RadLex: An Application
Ontology of Radiological Anatomy derived from
Figure 9: Subclasses of the Subdivision of the Foundational Model of Anatomy Reference
pathological vertebral column class Ontology, Proceedings AMIA Symposium 2008:
Page 465-469.
ACKNOWLEDGEMENT
[10] Rosse C, Mejino JLV 2007: The Foundational
By vertical integration of the FMA reference Model of Anatomy Ontology, in: Burger A,
ontology with the BFO top-level ontology the Davidson D, Baldock R. (eds.), Anatomy
process of horizontal integration of the two
reference ontologies: PRO and PathRO is
supported, forming accordingly the new reference 1
ontology OBR, which range over the domains of Ontological modeling in bioengineering, Project
anatomy, physiology and pathology. This ontology funded by national Ministry of science, Faculty of
can be successfully applied in development of the mechanical engineering, University of Kragujevac,
Serbia (2008-2010)

UbiCC Journal - Volume 4 No. 3 668

Special Issue on ICIT 2009 Conference - Bioinformatics and Image

Ontologies for Bioinformatics: Principles and [13] Rubin DL 2007: Creating and curating a
Practice, pp 59-117, New York: Springer. terminology for Radiology: Ontology Modeling and
Analysis, J Digit Imaging.
[11] Online vailable at:
http://www.rsna.org/radlex. [14] Marwede D, Fielding M and Kahn T. 2007
RadiO: A Prototype Application Ontology for
[12] Langlotz CP: RadLex 2006. a new method for Radiology Reporting Tasks, Proc AMIA 2007,
indexing online educational materials, Chicago. IL, pp 513-517.
Radiographics 26:15951597.
[15] FMA Online vailable at:
http://fma.biostr.washington.edu.

UbiCC Journal - Volume 4 No. 3 669