View source for Biology:Anatomography

{{Infobox website
| name           = Anatomography
| alexa          = 
| logo           = [[File:BodyParts3D Anatomography.png|250px|Anatomography logo.]][[File:Screenshot Anatomography en.png|250px|Anatomography screenshot]]
| caption        = 
| url            = [http://lifesciencedb.jp/bp3d/?lng=en lifesciencedb.jp/bp3d]
| commercial     = No
| type           = 
| language       = English or [[Social:Japanese language|Japanese]]
| registration   = 
| owner          = Database Center for Life Science
| author         = Kousaku Okubo
| launch date    = 2009-02-09<ref name="LAUNCH"/>
| content_license = [[File:CC-BY-SA icon.svg]]<br />CC-BY-SA 2.1-ja<ref name="CREDIT">[http://lifesciencedb.jp/bp3d/info/userGuide/faq/credit.html FAQs - credit.] (in Japanese) DBCLS. Retrieved 2012-10-12.</ref>
| current status = Active
| slogan         = 
| revenue        = 
}}
[[File:Introduction to BodyParts3D Anatomography.webm|thumb|Clip gives an overview of the functionality of the Anatomography server.]]
'''Anatomography''' is an interactive website which supports generating anatomical diagrams and animations of the [[Medicine:Human body|human body]]. The Anatomography website is maintained by the DBCLS (Database Center for Life Science) non-profit research institute located at the University of Tokyo. Anatomical diagrams generated by Anatomography, and 3D polygon data used on the website (called BodyParts3D), are freely available under the [[Creative Commons license|Creative Commons Attribution-ShareAlike license]].<ref name="CREDIT"/>

==Description==
Anatomography was launched on Feb. 9, 2009<ref name="LAUNCH">[http://lifesciencedb.jp/bp3d/info/userGuide/releaseNotes/index.html Release notes] (in Japanese).  DBCLS. Retrieved 2012-10-12.</ref> by founder and chief director Kousaku Okubo (大久保 公策), professor of the [[Biology:DNA Data Bank of Japan|DNA Data Bank of Japan]] at the [[Organization:National Institute of Genetics|National Institute of Genetics]].

Human body polygon data used in the site are called "'''BodyParts3D'''".<ref name="PMID18835852">{{Cite journal|pmid=18835852|pmc=2686534|year=2009|last1=Mitsuhashi|first1=N|last2=Fujieda|first2=K|last3=Tamura|first3=T|last4=Kawamoto|first4=S|last5=Takagi|first5=T|last6=Okubo|first6=K|title=BodyParts3D: 3D structure database for anatomical concepts|volume=37|issue=Database issue|pages=D782–5|doi=10.1093/nar/gkn613|journal=Nucleic Acids Research}}{{Open access}}</ref> BodyParts3D polygon data are extracted from full-body MRI images. The MRI image set that BodyParts3D is based on is called "TARO". Taro is a common given name for males in Japanese, as John is in English. TARO is a 2mm * 2mm * 2mm [[Voxel|voxel]] dataset of the human male created by the [[Organization:National Institute of Information and Communications Technology|National Institute of Information and Communications Technology]].<ref>{{Cite journal|pmid=14971769|year=2004|last1=Nagaoka|first1=T|last2=Watanabe|first2=S|last3=Sakurai|first3=K|last4=Kunieda|first4=E|last5=Watanabe|first5=S|last6=Taki|first6=M|last7=Yamanaka|first7=Y|title=Development of realistic high-resolution whole-body voxel models of Japanese adult males and females of average height and weight, and application of models to radio-frequency electromagnetic-field dosimetry|volume=49|issue=1|pages=1–15|journal=Physics in Medicine and Biology|doi=10.1088/0031-9155/49/1/001}}</ref> TARO was published freely on November, 2004.<ref>[http://www.itmedia.co.jp/news/articles/0411/10/news106.html 日本人の数値人体モデルDB「TARO」と「HANAKO」公開 2004/11/10] (in Japanese). ITMedia. Retrieved 2012-10-12.</ref><ref>[http://www2.nict.go.jp/pub/whatsnew/press/h16/041110-2/041110-2.html 報道発表:日本人平均成人男女の数値人体モデルデータベース公開のお知らせ 2004-11-10] (in Japanese). National Institute of Information and Communications Technology. Retrieved 2012-10-12.</ref>

The construction process of BodyParts3D is as follows.<ref name="PMID18835852"/>
*Phase 1: Additional anatomical segmentations were introduced in the original TARO data. 
*Phase 2: Then, missing details were supplemented and blurred contours were clarified using a 3D editing program by referring to textbooks, atlases,<ref name="RELEASE3.0">[ftp://ftp.biosciencedbc.jp/archive/bodyparts3d/LATEST/release_3.0_e.html BodyParts3D Release Note (Release 3.0, 2011/6/20)] DBCLS. Retrieved 2012-10-15.</ref> and mock-up models by medical illustrators. 
*Phase 3: Further segmentation and data modification will continue in collaboration with clinical researchers until sufficient concept coverage is achieved.

BodyParts3D polygon data are distributed in the [[Wavefront .obj file|OBJ]] file format. The entire data file's size is 127 [[Megabyte|MB]] (polygon reduced) and 521 MB (high quality) as of version 3.0.<ref>[http://dbarchive.biosciencedbc.jp/en/bodyparts3d/download.html Download - BodyParts3D] DBCLS. Retrieved 2012-10-15.</ref> The number of body parts (organs) registered in BodyParts3D is 1,523 as of version 3.0.<ref name="RELEASE3.0"/>

==License==
Images generated by Anatomography and the polygon data included in BodyParts3D are licensed under the [[Creative Commons license]],<ref name="CREDIT"/> in hope of widening usage and democratizing medical knowledge.<ref name="Mitsuhashi2010"/>

==Funding==
The BodyParts3D/Anatomography project was funded by MEXT (Japanese Ministry of Education, Culture, Sports, Science and Technology) from [[Physics:Fiscal year|FY]]2007 to FY2010.<ref>[http://dbarchive.biosciencedbc.jp/en/bodyparts3d/desc.html BodyParts3D Database Description] Life Science Database Archive. Retrieved 2012-10-19.</ref><ref name="DBCLS_FAQ">[http://dbcls.rois.ac.jp/en/faq FAQ - About the Database Center for Life Science (DBCLS)] {{Webarchive|url=https://web.archive.org/web/20130130014120/http://dbcls.rois.ac.jp/en/faq |date=2013-01-30 }} DBCLS. Retrieved 2012-10-19.</ref> As of FY2011, the project has been funded by the JST (Japan Science and Technology Agency).<ref name="DBCLS_FAQ"/>

==Reception==
Diagrams from Anatomography are used, for example, in Canadian science TV show Le code Chastenay,<ref>[http://lecodechastenay.telequebec.tv/emission.aspx?id=54 「LE CODE CHASTENAY」Emission 48], 2010-01-19 aired</ref> Internet encyclopedia  Wikipedia, as lecture material in universities, and elsewhere to share knowledge.<ref name="Mitsuhashi2010">三橋 信孝、藤枝 香、今井 紫緒、武藤 勇、田村 卓郎、川本 祥子、高木 利久、大久保 公策 [https://symposium.lifesciencedb.jp/godo/wp-content/themes/zenlite/documents/19.pdf 「BodyParts3DとAnatomography: 医学での情報共有を「動機付ける」素材」{{ja icon}}]{{dead link|date=October 2016 |bot=InternetArchiveBot |fix-attempted=yes }} シンポジウム「ライフサイエンスの未来へ～10年先のデータベースを考える～」/ Nobutaka Mitsuhashi, Kaori Fujieda, Shio Imai, Isamu Muto, Takuro Tamura, Shoko Kawamoto, Toshihisa Takagi and  Kousaku Okubo  "BodyParts3D and Anatomography: Materials motivating sharing information in medicine" Poster presentation at "Symposium: Toward the Future of Life Science - Thinking Databases of 10 Years Later" held in the University of Tokyo at 2010-10-05. Retrieved 2012-10-12.</ref> About usage of Anatomography on websites like Wikipedia and Wikimedia Commons, developers say "spreading of usages by anonymous users on like Wikipedia and Wikimedia Commons is what we had expected."<ref name="Mitsuhashi2010"/>

==Technical features==
BodyParts3D/Anatomography project uses the [[Organization:Foundational Model of Anatomy|Foundational Model of Anatomy]] (FMA). The FMA is an open-source anatomical [[Ontology (information science)|ontology]] developed and maintained by the Structural Informatics Group at the [[Organization:University of Washington|University of Washington]]. In BodyParts3D, each body-part is managed by an FMA identifier (FMAID) defined by the FMA. For example, the [[Biology:Vertebral column|vertebral column]] is registered as ''[https://archive.is/20130218184836/http://lifesciencedb.jp/bp3d/ag_annotation.cgi?i=FMA13478&lng=en&t=Conventional&position=rotate FMA13478]'', the [[Biology:Temporal lobe|temporal lobe]] is registered as ''[https://web.archive.org/web/20160304100116/http://lifesciencedb.jp/bp3d/ag_annotation.cgi?i=FMA61825&lng=en&t=Conventional&position=rotate FMA61825]'', and so on.

==Version history==
*Version 1.0 (Feb. 9, 2009) <ref name="LAUNCH"/>
*Version 2.0 (Apr. 28, 2010)<ref>[http://dbcls.rois.ac.jp/en/archives/163 "BodyParts3D/Anatomography" Updates] {{webarchive |url=https://web.archive.org/web/20100605012516/http://dbcls.rois.ac.jp/en/archives/163 |date=June 5, 2010 }} Posted on April 28, 2010. DBCLS. Retrieved 2012-10-16.</ref> Total number of body parts is 1,324.<ref>[ftp://ftp.biosciencedbc.jp/archive/bodyparts3d/20100816/release_2.0_e.html BodyParts3D Release Note (Release 2.0, 2010/4/28)] DBCLS. Retrieved 2012-10-15.</ref>
*Version 3.0 (Jun. 20, 2011) Total number of body parts is 1,523.<ref name="RELEASE3.0"/>
* Version 4.0 (May 16, 2013)<ref>[ftp://ftp.biosciencedbc.jp/archive/bodyparts3d/LATEST/release_4.0_e.html "BodyParts3D Release Notes, v4.0"]. Retrieved 2015-11-18.</ref>

==Similar services==
*Zygote Body - Free web service provided by the [[Software:Zygote Media Group|Zygote Media Group]] located in American Fork, Utah, US. Zygote Body was launched as '''Google Body''' on December 15, 2010. The polygon data used on the website is a commercial product. As of October, 2012, the price of its full-body polygon data is $13,995.<ref>[http://www.3dscience.com/3D_Models/Human_Anatomy/Collections/Male_Collection.php Male Anatomy Collection 5.0] 3Dscience.com. (Zygote Media Group, Inc.). Retrieved 2012-10-19.</ref>
*[https://www.biodigitalhuman.com BioDigital Human] - Free web service and commercial product provided by [[Company:BioDigital|BioDigital]], Inc. located in New York, New York, US.  The BioDigital Human was published in 2011.  The web site won a SXSW Interactive Award in 2013.

==Others==
A few tutorial videos on using Anatomography are available on [[Company:YouTube|YouTube]],<ref>{{Cite journal|pmid=21803786|pmc=3294242|year=2012|last1=Kawano|first1=S|last2=Ono|first2=H|last3=Takagi|first3=T|last4=Bono|first4=H|title=Tutorial videos of bioinformatics resources: Online distribution trial in Japan named TogoTV|volume=13|issue=2|pages=258–68|doi=10.1093/bib/bbr039|journal=Briefings in bioinformatics}}{{Open access}}</ref> see external links.

==Additional images==
<gallery>
BodyParts3D ver.2.0.jpg|Bones and muscles.
Anatomography rib cage and heart.png|[[Biology:Heart|Heart]] and its [[Biology:Blood vessel|blood vessel]]s.
Anatomography skull and eyeball.png|[[Biology:Skull|Skull]] and eyeballs.
Frontal lobe animation.gif|Brain and [[Biology:Frontal lobe|frontal lobe]].
Human right foot bones 3D print.jpg|[[3D printing|3D printing]] of BodyParts3D foot bone data.
Cervical vertebrae from BodyParts3D on MeshLab.png| Painting colors on cervical vertebrae polygon data, included in BodyParts3D data, using [[Software:MeshLab|MeshLab]].
BodyParts3D Blender.png|Downloaded BodyParts3D polygon data, edited with [[Software:Blender|Blender]].
Dr ohkubo.png|Chief director Kousaku Okubo at University of Tokyo conference.<ref>Conference "Balancing IP Protection and Data Sharing in Science" held at the University of Tokyo, 2009-10-05. [http://symposium.lifesciencedb.jp/IPDS/okubo Okubo's presentation in Japanese] {{webarchive |url=https://web.archive.org/web/20130610053855/http://symposium.lifesciencedb.jp/IPDS/okubo |date=June 10, 2013 }}, just before [[Biography:Lawrence Lessig|Lawrence Lessig]]'s lecture. Entire videos of each lecture are available on the [http://symposium.lifesciencedb.jp/IPDS/program conference website's program schedule page (partly Japanese, partly English)] {{webarchive |url=https://web.archive.org/web/20130204103647/http://symposium.lifesciencedb.jp/IPDS/program |date=February 4, 2013 }}.</ref>
</gallery>

==See also==
*Human anatomy
*[[Open science]]
*[[Open data]]
*[[Organization:Science Commons|Science Commons]]
*[[Philosophy:Democratization of knowledge|Democratization of knowledge]]

==References==
{{Reflist}}

==External links==
*[http://lifesciencedb.jp/bp3d/?lng=en Anatomography]
*[http://dbarchive.biosciencedbc.jp/en/bodyparts3d/download.html BodyParts3D polygon data] 
*[http://dbcls.rois.ac.jp/en/ Database Center for Life Science]

[[Category:Human anatomy]]
[[Category:Medical websites]]
[[Category:Anatomical simulation]]
[[Category:Open science]]
[[Category:Open data]]

{{Sourceattribution|Anatomography|1}}