BodyParts3D
2025/02/27Web Site: http://lifesciencedb.jp/bp3d/
The dictionary-type database for anatomy in which anatomical concepts are represented by 3D structure data that specify corresponding segments of a three-dimensional whole-body model for an adult human male.
README Content
1. Database Component
- README
- Table of 3D organ model IDs and organ names (IS-A Tree)
- Table of 3D organ model IDs and organ names (PART-OF Tree)
- Data describing the inclusion relationships between two organs (IS-A Tree)
- Data describing the inclusion relationships between two organs (PART-OF Tree)
- Data describing the definition of compound organs (IS-A Tree)
- Data describing the definition of compound organs (PART-OF Tree)
- Polygon mesh data (Polygon reduction rate = 99% IS-A Tree)
- Polygon mesh data (Polygon reduction rate = 99% PART-OF Tree)
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 Table of 3D organ model IDs and organ names (IS-A Tree)
| Data name | Table of 3D organ model IDs and organ names (IS-A Tree) |
|---|---|
| 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 available in IS-A Tree. |
| File | isa_parts_list_e.txt (IS-A Tree) (126 KB) |
Data items are the following:
Each column is delimited by a tab character in the file.
| Data item | Description |
|---|---|
| concept id | ID of the corresponding FMA (Foundational Model of Anatomy). |
| representation id | ID of the corresponding 3D representation. |
| en | English name. Basically, a preferred name of FMA is assigned. |
2.3 Table of 3D organ model IDs and organ names (PART-OF Tree)
| Data name | Table of 3D organ model IDs and organ names (PART-OF Tree) |
|---|---|
| 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 available in PART-OF Tree. |
| File | partof_parts_list_e.txt (PART-OF Tree) (58 KB) |
Data items are the following:
Each column is delimited by a tab character in the file.
| Data item | Description |
|---|---|
| concept id | ID of the corresponding FMA (Foundational Model of Anatomy). |
| representation id | ID of the corresponding 3D representation. |
| en | English name. Basically, a preferred name of FMA is assigned. |
2.4 Data describing the inclusion relationships between two organs (IS-A Tree)
| Data name | Data describing the inclusion relationships between two organs (IS-A Tree) |
|---|---|
| Description of data contents | File of data describing the inclusion relationships between two organs of the downloadable 3D organ models. |
| File | isa_inclusion_relation_list.txt (203 KB) |
Data items are the following:
Each column is delimited by a tab character in the file.
| Data item | Description |
|---|---|
| parent id | Concept ID of parent organ |
| parent name | English name of parent organ |
| child id | Concept ID of an organ that is included in the parent organ |
| child name | English name of an organ that included in the parent organ |
2.5 Data describing the inclusion relationships between two organs (PART-OF Tree)
| Data name | Data describing the inclusion relationships between two organs (PART-OF Tree) |
|---|---|
| Description of data contents | File of data describing the inclusion relationships between two organs of the downloadable 3D organ models. |
| File | partof_inclusion_relation_list.txt (90 KB) |
Data items are the following:
Each column is delimited by a tab character in the file.
| Data item | Description |
|---|---|
| parent id | Concept ID of parent organ |
| parent name | English name of parent organ |
| child id | Concept ID of an organ that is included in the parent organ |
| child name | English name of an organ that included in the parent organ |
2.6 Data describing the definition of compound organs (IS-A Tree)
| Data name | Data describing the definition of compound organs (IS-A Tree) |
|---|---|
| Description of data contents | In BodyParts3D, only atomic organs (ELEMENT) are constructed as polygon meshes. Compound organs (COMPOUND) defined as a sum of atomic ones are not provided in the form of the meshes. This file describes which ELEMENT parts consistute each COMPOUND organ. |
| File | isa_element_parts.txt (1.1 MB) |
Data items are the following:
Each column is delimited by a tab character in the file.
| Data item | Description |
|---|---|
| concept id | Concept ID of COMPOUND organ |
| name | Name of COMPOUND organ |
| element file id | Polygon mesh file ID of ELEMENT constituting the COMPOUND organ |
2.7 Data describing the definition of compound organs (PART-OF Tree)
| Data name | Data describing the definition of compound organs (PART-OF Tree) |
|---|---|
| Description of data contents | In BodyParts3D, only atomic organs (ELEMENT) are constructed as polygon meshes. Compound organs (COMPOUND) defined as a sum of atomic ones are not provided in the form of the meshes. This file describes which ELEMENT parts consistute each COMPOUND organ. |
| File | partof_element_parts.txt (654 KB) |
Data items are the following:
Each column is delimited by a tab character in the file.
| Data item | Description |
|---|---|
| concept id | Concept ID of COMPOUND organ |
| name | Name of COMPOUND organ |
| element file id | Polygon mesh file ID of ELEMENT constituting the COMPOUND organ |
2.8 Polygon mesh data (Polygon reduction rate = 99% IS-A Tree)
| Data name | Polygon mesh data (Polygon reduction rate = 99% IS-A Tree) |
|---|---|
| Description of data contents | BodyParts3D organ model data with the polygon reduction rate of 99%. The zip-compressed download files contain multiple files of ELEMENT file ID-specific polygon data in Wavefront OBJ format. |
| File | isa_BP3D_4.0_obj_99.zip (136 MB) |
Data items are the following:
About polygon data
- Description of a wavefont obj format
(from Wikipedia) - Description of Polygon (from Wikipedia)
2.9 Polygon mesh data (Polygon reduction rate = 99% PART-OF Tree)
| Data name | Polygon mesh data (Polygon reduction rate = 99% PART-OF Tree) |
|---|---|
| Description of data contents | BodyParts3D organ model data with the polygon reduction rate of 99%. The zip-compressed download files contain multiple files of ELEMENT file ID-specific polygon data in Wavefront OBJ format. |
| File | partof_BP3D_4.0_obj_99.zip (62 MB) |
Data items are the following:
About polygon data
- 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 4.0 International.
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 4.0 International".
The summary of the Creative Commons Attribution 4.0 International 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 adapted material.
- 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 : 
4. Update History
| Date | Update contents |
|---|---|
| 2025/02/27 | "License" is updated. |
| 2013/06/19 | 3D data (Release 4.0) is updated. |
| 2013/04/11 | Changed the email address in the contact information. |
| 2013/01/17 | Added simple search URLs for the following data.
|
| 2011/09/15 | 3D data (Release 3.0) is updated. |
| 2011/08/25 | "License" is updated. |
| 2010/08/16 | 3D data (Release 2.0) is updated. |
| 2010/03/29 | BodyParts3D English archive site is opened. |
| 2009/02/09 | 3D data (Release 1.0) is updated. |
| 2008/08/12 | 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. 2008 Oct 3.
PMID: 18835852
6. Contact address
When you have any question about "BodyParts3D", contact the following:Database Center for Life Science
Research Organization of Information and Systems
E-mail :