BodyParts3D - 3D structure database for anatomical concepts

As of August 2008, 382 anatomical concepts, sufficient for explaining specimens in most molecular biology experiments, have been specified as 3D objects. Addition of concepts and refinement of data will be continued in collaboration with clinical researchers, until sufficient resolution and accuracy for most clinical application is achieved. BodyParts3D data is made available to the public expecting prosperity of downstream applications by the third parties for bioinformatics and medical communication.

Why BodyParts3D is needed

For explicit representation of anatomical knowledge, a tree-like connection of terms by spatial, functional, or developmental relationships has often been employed. However, extensive declaration of relationships, especially spatial ones, such as connection, vicinity, perforation, encapsulation, usually impairs consistency or conciseness of the entire representation. To obtain a both rich and comprehensible representation of spatial information, we started BodyParts3D construction. Although laborious, specifying terms by segmentation of a whole body model is straightforward because all spatial relationships among segments are originally represented in the whole-body model per se. If desired, any specific relationship can be extracted in the form of a tree-like structure by computation afterwards. Conversely, BodyParts3D and tree type functional ontologies, such as GALEN and FMA, complement each other.

Construction process of BodyParts3D

BodyParts3D is constructed on the framework of voxel-human model for electromagnetic dosimetry, “TARO Model” [1], which was created from a whole body set of 2mm-interval MRI images of a male volunteer. Anatomical segmentations were made on the original data (phase 1). Then, missing details were supplemented and contours were clarified referring to textbooks, atlases and mock-up models by medical illustrators using a 3D editor program (phase2). Further segmentation and data modification will continue until sufficient vocabulary is achieved in collaboration with clinical researchers (phase 3).

Use of BodyParts3D

In addition to be used as anatomy ontology, BodyParts3D has some unique usages. Firstly, any given region of a human body can be illustrated for various communication purposes by combining body parts data using rendering software by humans and even by programs. Secondly, it can be used as a blank map of the human body. Using open parameters, such as surface color or transparency for body parts, numerical or qualitative attributes for body parts obtained from molecular biological or medical studies can be represented on the human body. Such unique usages will be facilitated if a rendering service with BodyPart3D data is provided.

References

[1] Nagaoka T, Watanabe S, Sakurai K, Kuneida E, Watanabe S, Taki M, Yamanka Y. (2004) Development of realistic high resolution whole-body voxel models of Japanese adult male and female of average height and weight, and application of models to radio-frequency electromagnetic-field dosimetry. Phys Med Biol 49:1–15.