BodyParts3D
2011/08/25WebSite: http://lifesciencedb.jp/bp3d/?lng=en
FTP Site: ftp://ftp.biosciencedbc.jp/archive/bodyparts3d/
BodyParts3D is a dictionary-type database for anatomy in which shapes and positions of body parts are represented by 3D human models. This directory contains the models labeled with anatomical terms in BodyParts3D.
README Content
1. Database Component
- README
- Release note (Rel. 2.0)
- Table of 3D organ model IDs and organ names
- Data describing the conventional inclusion relations between two organs
- Data describing the definition of compound organs
- Organ ID-specific polygon mesh data 1 (Polygon reduction rate = 95%)
- Organ ID-specific polygon mesh data 2 (Polygon reduction rate = 99%)
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "BodyParts3D" data. |
| File | README_e.html (English) |
2.2 Release Note
| Data name | Release note (Rel. 2.0) |
| Description of data contents | HTML file that describes main update points since the previous release (Rel. 1.0, 2009/2/9) |
| File | release_2.0_e.html (English) |
2.3 Table of 3D organ model IDs and organ names
| Data name | Table of 3D organ model IDs and organ names |
| Description of data contents |
List of downloadable 3D organ models in a tab-delimited text file format, describing the correspondence between 3D organ model IDs and organ names |
| File | parts_list_e.txt (69KB) |
Each column is delimited by a tab character in the file.
Data items are the following:
| Data item | Description |
|---|---|
| id | ID of the corresponding FMA (Foundational Model of Anatomy), starting with "FMA". If a corresponding concept is not found in the FMA, a BodyParts3D's original ID that begins with "BP" is assigned. |
| en | English name. Basically, a preferred name of FMA is assigned. |
| phase_number | The stage of data generation, i.e. the quality of data, which consists of three phases from phase1 to phase3. |
| organ_system | Organ system to which the organ belongs (e.g. nervous system or circulatory system) |
2.4 Data describing the inclusion (part-of) relations between two organs
| Data name | Data describing the inclusion (part-of) relations between two organs |
| Description of data contents |
File of data describing the inclusion (part-of) relations between two organs of the downloadable 3D organ models. This is the conventional type hierarchy shown at the "Tree" tab of "BP3D Viewer" (http://lifesciencedb.jp/bp3d). |
| File | conventional_part_of.txt (106KB) |
Each column is delimited by a tab character in the file.
Data items are the following:
| Data item | Description |
|---|---|
| id | Organ ID |
| name | English name of the organ in the first column |
| part id | ID of an organ that is part of the organ in the first and second columns |
| part name | English name of the organ in the third column (part id) |
2.5 Data describing the definition of compound organs
| Data name | Data describing the definition of compound organs |
| Description of data contents |
In BodyParts3D, only atomic organs are constructed as polygon meshes. Compound organs defined as a sum of atomic ones are not provided in the form of the meshes. This file describes which atomic body parts consistute each compound organ according to the "conventional" inclusion relations described above. |
| File | compound_parts.txt (256KB) |
Each column is delimited by a tab character in the file.
Data items are the following:
| Data item | Description |
|---|---|
| compound id | Compound organID |
| compound name | English name of the organ in the first column |
| primitive id | ID of an atomic organ that constitutes the organ in the first and second columns |
| primitive name | English name of the organ in the third column (primitive id) |
2.6 Organ ID-specific polygon mesh data
2.6.1 Polygon reduction rate = 95.0%
| Data name | Organ ID-specific polygon mesh data 1 (Polygon reduction rate = 95.0%) |
| Description of data contents |
BodyParts3D phase-2 or 3 3D organ model data with the polygon reduction rate of 95%. The zip-compressed download files contain multiple files of organ ID-specific polygon data in Wavefront OBJ format. The polygon data file is named as "organ ID" of the 3D organ models followed by the extension ".obj". |
| File | BodyParts3D_2.0_obj_95.zip (500MB) |
2.7 Organ ID-specific polygon mesh data 2 (Polygon reduction rate = 99.0%)
| Data name | Organ ID-specific polygon mesh data 2 (Polygon reduction rate = 99.0%) |
| Description of data contents |
BodyParts3D phase-2 or 3 3D organ model data with the polygon reduction rate of 99%. The zip-compressed download files contain multiple files of organ ID-specific polygon data in Wavefront OBJ format. The polygon data file is named as "organ ID" of the 3D organ models followed by the extension ".obj". |
| File | BodyParts3D_2.0_obj_99.zip (121MB) |
About polygon data
A polygon mesh with the reduction rate of 95% is more precise than that with 99% because 95% has five times more polygons (triangles) than 99%.
<Reference>
- Description of a wavefont obj format (from Wikipedia)
- Description of polygon(from Wikipedia)
3. License
You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The license for this database is specified in the Creative Commons Attribution-Share Alike 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "BodyParts3D, © The Database Center for Life Science licensed under CC Attribution-Share Alike 2.1 Japan".
The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- freely create and distribute database and other derivative works based on part or whole of the data from this database,
- You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any derivative work.
- You must distribute any derivative work based on part or whole of the data from this database under the license.
- You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.
Database Center for Life Science
Research Organization of Information and Systems
E-mail : info [at] dbcls [dot] rois [dot] ac [dot] jp
4. Update History
| Date | Update contents |
| 2011/08/25 | "License" is updated. |
| 2010/08/16 | 3D data (rel. 2.0) is updated. |
| 2010/03/29 | BodyParts3D English archive site is opened. |
| 2009/02/09 | 3D data (rel. 1.0) is updated. |
| 2008/08 | BodyPart3D(http://lifesciencedb.jp/bp3d/?lng=en) is released. |
5. Literature
Mitsuhashi N, Fujieda K, Tamura T, Kawamoto S, Takagi T, Okubo K.BodyParts3D: 3D structure database for anatomical concepts.
Nucleic Acids Res. 2009 Jan;37(Database issue):D782-5. Epub 2008 Oct 3.
PMID: 18835852
6. Contact address
When you have any question about "BodyPart3D", contact the following:
Database Center for Life Science
Research Organization of Information and Systems
E-mail : info [at] dbcls [dot] rois [dot] ac [dot] jp