Nucleic Acids Research Advance Access originally published online on October 3, 2008
Nucleic Acids Research 2009 37(Database issue):D782-D785; doi:10.1093/nar/gkn613
Nucleic Acids Research, 2009, Vol. 37, Database issue D782-D785
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
BodyParts3D: 3D structure database for anatomical concepts
Nobutaka Mitsuhashi1,
Kaori Fujieda1,
Takuro Tamura2,
Shoko Kawamoto1,
Toshihisa Takagi1 and
Kousaku Okubo1,3,*
1Database Center for Life Science, Research Organization of Information and Systems, Faculty of Engineering Bldg.12, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, 2Bits Co., Ltd., 20-3-A402 Shimotogari, Shizuoka 411-0943 and 3Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
*To whom correspondence should be addressed. Tel: +81 55 981 5836; Fax: +81 55 981 5837; Email: kokubo{at}genes.nig.ac.jp
Received August 15, 2008. Revised September 8, 2008. Accepted September 9, 2008.
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ABSTRACT
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BodyParts3D is a dictionary-type database for anatomy in which
anatomical concepts are represented by 3D structure data that
specify corresponding segments of a 3D whole-body model for
an adult human male. It encompasses morphological and geometrical
knowledge in anatomy and complements ontological representation.
Moreover, BodyParts3D introduces a universal coordinate system
in human anatomy, which may facilitate management of samples
and data in biomedical research and clinical practice. As of
today, 382 anatomical concepts, sufficient for mapping materials
in most molecular medicine experiments, have been specified.
Expansion of the dictionary by adding further segments and details
to the whole-body model will continue in collaboration with
clinical researchers until sufficient resolution and accuracy
for most clinical application are achieved. BodyParts3D is accessible
at:
http://lifesciencedb.jp/ag/bp3d/.
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WHY BodyParts3D IS NEEDED
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Anatomical knowledge is an essential reference for communicating
and reasoning about objects and events in the human body. Accordingly,
explicit representation of this knowledge allows computational
manipulation of data, literature and clinical records and benefits
biomedical research and practice in many ways. Anatomy ontology,
symbolic representation of concepts and relationships, is a
widely accepted approach for this goal. An obvious drawback
in symbolic representation is its limited power in representing
physical specification of the body, i.e. morphology of body
parts and topological and geometrical relationships among the
parts, although such physical specification comprises a substantial
amount of human anatomical knowledge (
1,
2). To obtain both computable
and comprehensible representation of a physical specification
of a ‘standard human body’, we started constructing
an anatomical dictionary by specifying body parts through segmentation
of a 3D model of a male human body (
Figure 1). Although laborious,
dictionary construction was straightforward because all spatial
relationships among segments are originally represented in the
whole-body model. If desired, any specific relationship can
be extracted by computation afterwards (
Table 1). Conversely,
ontological representation of categorical, taxonomical and developmental
knowledge about human body parts in a symbolic structure functions
complementary to BodyParts3D.
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Figure 1. Representations of the mitral valve in (A) representative anatomy ontology, the Foundation Model of Anatomy (FMA) (1) and (B) BodyParts3D. FMA data were obtained from Open Biomedical Ontologies (OBO) (http://www.obofoundry.org/cgi-bin/detail.cgi?id=fma_lite). In (B), mitral valve (red) is shown with left posterior papillary muscle (deep blue) on the background of left ventricle (light blue), and left atrium (green) in the blow up image. Behind this, heart (yellow) is shown on the background of mediastinum (pink).
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Table 1. Examples of topological relationships in BodyParts3D for deriving relationships between entity A and B defined in FMA
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CONSTRUCTION PROCESS OF BodyParts3D
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BodyParts3D was constructed on the framework of a voxel human
model for electromagnetic dosimetry, ‘TARO’ (
4),
which was created from a whole-body set of 2 mm interval MRI
images of a male volunteer. Additional anatomical segmentations
were introduced in the original data (phase 1). Then, missing
details were supplemented and blurred contours were clarified
using a 3D editing program by referring to textbooks, atlases
and mock-up models by medical illustrators (phase 2). Further
segmentation and data modification will continue in collaboration
with clinical researchers until sufficient concept coverage
is achieved (phase 3). Consistent inclusion of non-material
entities such as surfaces, holes, notches, edges and points
and also discrimination of
bona fide boundaries and conceptual
boundaries will be the challenge in expanding the dictionary.
The number of concepts specified as of today is shown for each
anatomical system and construction phase in
Figure 2.
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USE OF BodyParts3D
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Besides being a computable and comprehensible anatomy dictionary,
BodyParts3D introduces a coordinate system to the human body
structure. A relevant body position in medical research and
practice, such as the origin of biopsy specimen or tumor location,
can be indexed correctly, with respect to the relative spatial
relation to surrounding anatomical markers, in this coordinate
system for management, sharing and visualization of data. A
rendering server that allows users to specify a relevant position
in the context of graphical images of the desired body region
with the desired body parts, as shown in
Figures 1 and
2, will
facilitate such indexing as well as visualization.
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RELATED WORKS
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There are several high-resolution 3D atlases based on a set
of photographic images of serial sections of a male cadaver,
published from the National Library of Medicine's ‘Visible
Human Project’ (
http://www.nlm.nih.gov/research/visible/visible_human.html).
One prominent example is ‘Voxel-Man’ (
5,
6), in which
a 3D model was extensively segmented and mapped to structured
vocabulary. Interestingly, in these works, realistic details,
such as small vasculature and texture of tissues, were pursued
at the expense of handy data size. Consequently, down stream
applications required a computer dedicated for graphics in a
local environment and are limited to educational settings or
surgical simulations rather than for the prosper of bioinformatics
and information sharing. In addition, it is reported that there
are several independent nonpublic projects that constructed
detailed 3D human models for various purposes (
7).
The Edinburgh Mouse Atlas Project (EMAP) (8) is a project in mouse genomics that elegantly uses a combination of ontology and a 3D modeling. In EMAP, the segmentation of the 3D model was limited to early embryonic stages because the primary aim of the modeling was to introduce visible and sharable demarcation to embryonic body parts that have no morphologically clear borders.
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DATA ACCESS AND AVAILABILITY
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In BodyParts3D, 3D data files are labeled with corresponding
Foundation Model of Anatomy (FMA) concept IDs and indexed with
their English synonyms as well as their Japanese equivalents
for searching (
Figure 2). Each 3D data file in BodyParts3D whose
phase is two or higher is downloadable in VTK or STL formats
at:
http://lifesciencedb.jp/ag/bp3d/download/.
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CONCLUSIONS
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Universally, our bodies are composed of the same set of anatomically
discriminable body parts that amounts as many as independent
anatomical concepts, being arranged in the same geometrical
positions. In this sense, the person-to-person difference in
our body structure is not much larger than item-to-item difference
in the structure of manufactured products of the same model.
In manufacturing, engineering drawings, often called as blueprints, are central in sharing information among designers, manufactures and repairing mechanics. BodyParts3D is designed to serve as such blueprints in information sharing among basic and applied medical researchers and clinicians. BodyParts3D can be accessed at: http://lifesciencedb.jp/ag/bp3d/.
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FUNDING
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Funding for open access charge: The Integrated Database Project,
Ministry of Education, Culture, Sports, Science and Technology
of Japan.
Conflict of interest statement. None declared.
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ACKNOWLEDGEMENTS
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We thank ‘TARO’ development team for generously
providing their data. ‘TARO’ is a voxel model phantom
for radio-frequency electromagnetic-field dosimetry developed
by the National Institute of Information and Communications
Technology (NICT), Kitasato University, Keio University and
Tokyo Metropolitan Univ.
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REFERENCES
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- Höhne KH, Pflesser B, Pommert A, Riemer M, Schiemann T, Schubert R, Tiede U. A new representation of knowledge concerning human anatomy and function. Nat. Med. (1995) 1:506–511.[CrossRef][Web of Science][Medline]
- Höhne KH, Pflesser B, Pommert A, Priesmeyer K, Riemer M, Schiemann T, Schubert R, Tiede U, Frederking H, Gehrmann S, et al, VOXEL-MAN 3D navigator: inner organs. Regional, Systemic and Radiological Anatomy (2003) Heidelberg: Springer-Verlag Electronic Media.
- Turinsky AL, Fanea E, Trinh Q, Wat S, Hallgrímsson B, Dong X, Shu X, Stromer JN, Hill JW, Edwards C, et al. CAVEman: standardized anatomical context for biomedical data mapping. J. Anat. Sci. Educ. (2007) 1:10–18.
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WHY BodyParts3D IS NEEDED