Site information

=Information = http://lifesciencedb.jp/bp3d/API/animation.cgi?shorten=W95vWfPnKH1Lb4HXrafqO99b&.gif 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| http://lifesciencedb.jp/bp3d/API/animation.cgi?av=09051901&iw=200&ih=200&bcl=FFFFFF&cf=0&hf=0&model=bp3d&bv=4.0&tn=isa&dt=20130717165714&cx=0&cy=-963.715&cz=1569.54&tx=0&ty=-75.659&tz=1569.54&ux=0&uy=0&uz=1&zm=4&cm=N&oid001=FMA223151&ocl001=f0d2a0&osz001=S&oop001=0.3&orp001=S&odcp001=0&oid002=FMA50081&ocl002=f0d2a0&osz002=S&oop002=1.0&orp002=S&odcp002=0&oid003=FMA72830&ocl003=FF0000&osz003=S&oop003=1&orp003=S&odcp003=0&dpl=0&dpod=1&dpol=0&crd=bp3d&pno001=1&px001=-38.8246&py001=-69.5065&pz001=1560.5617&pax001=2.4161&pay001=-1.9003&paz001=0.8424&pux001=0&puy001=0&puz001=1&ps001=PM&pcl001=FF3333&poi001=FMA50489&pon001=Right%20posterior%20parietal%20artery&pd001=&pcd001=bp3d&pno002=2&px002=-60.0093&py002=-28.6194&pz002=1560.719&pax002=1.427&pay002=-2.2553&paz002=1.7423&pux002=0&puy002=0&puz002=1&ps002=PM&pcl002=009900&poi002=FMA50473&pon002=Temporo-occipital%20branch%20of%20right%20middle%20cerebral%20artery&pd002=&pcd002=bp3d&pno003=3&px003=-63.7296&py003=-82.4656&pz003=1565.4883&pax003=-1.6225&pay003=-2.2919&paz003=-1.5077&pux003=0&puy003=0&puz003=1&ps003=PM&pcl003=FFFF00&poi003=FMA50467&pon003=Middle%20temporal%20branch%20of%20right%20middle%20cerebral%20artery&pd003=&pcd003=bp3d&pno004=4&px004=-57.823&py004=-109.4351&pz004=1557.3696&pax004=0.0722&pay004=-2.7021&paz004=1.6888&pux004=0&puy004=0&puz004=1&ps004=PM&pcl004=FF8000&poi004=FMA50383&pon004=Right%20anterior%20temporal%20artery&pd004=&pcd004=bp3d.gif
 * Welcome to BodyParts3D/Anatomography.
 * BodyParts3D is an anatomical dictionary where terms are defined by 3D morphology of referents.
 * We plan to define all anatomical concepts listed in Terminologia Anatomica, started from those with volumes.
 * Anatomography is a web tool with which you can author your own model with BodyParts entry and publish as " embeddable interactive 3D image".


 * 

=For repeaters =

Notice
IMPORTANT MESSAGE TO USERS


 * There are still many concepts not represented in the data.
 * There could be many ERRORS to be used as ANATOMICAL EDUCATION.
 * Some parts were made from scratch by artists or distorted to fit into the environment.
 * Segmentation into finer pieces may cause confusion in assignment of concepts.
 * Authors may publish your models at your own risk of inclusion of such errors.
 * For notion and improvement, please feed back and share the PROBLEMS YOU FIND in the data.
 * Started from the provided TWITTER function in the BodyParts CARD (right side window) The SUBJECT of the comment ( parts form or its concept label) will be recorded automatically and properly distributed.
 * Your cooperation will be truly appreciated. -- BodyParts3D team

Whats new
2012/06/21: BodyParts3D rel 4.0 downloadable as a whole from LSDB archive. 2013/05/16: BodyParts3D rel 4.0 from Editor site. major update for map editor site 2011/06/20: BodyParts3D 3.0 published from editor site release note to rel. 3.0   2010/08/16: data download service at LSDB archive: all Rel.2.0 obj files 2010/07/21: BodyParts3D release 2.0 modeling note 2010/04/28: BodyParts3D release 2.0 with new editor site. release note to rel. 2.0(概要）
 * New data release
 * Old news and Notices

=For new visitors =

What is this site about? (Map editor)
http://www.youtube.com/watch?v=CJLH1PqH_hg 
 * What you can do with BodyParts3D/Anatomography
 * How to use : tutorial ftg on youtube


 * Bodyparts3D map editor site UI details
 * Step by step, how to use

API behind

 * Anatomography Web API specifications
 * Anatomography Web API sample code
 * Anatomography Web API (V1.0 service is no longer available） Web API implemented with SOAP for Java is no longer available. WSDL

Data download

 * A set of 4.0 contour data in OBJ format is downloadable from here. http://dbarchive.biosciencedbc.jp/en/bodyparts3d/download.html
 * BodyParts3D Release Note (Release 4.0, 2013/5)
 * Link to NBDC
 * http://dbarchive.biosciencedbc.jp/en/bodyparts3d/download.html

License
sample html source here ..
 * Users can copy modify and disseminate both contour data and rendered image under the license CC-BY SA 2.1JP

http://dbarchive.biosciencedbc.jp/en/bodyparts3d/lic.html

Introducing team and Project (Who are we)

 * Personel:
 * Funding Source:
 * Institutional background:
 * Out sourcing:

=For those who care (How dose this work)=

About Anatomography (mechanism of authoring site)

 * Whole Diagram
 * For those who cares very much (designed and depicted by Isamu Muto, Bits c.c.)
 * Data management:Representation and contour file, Versions, Search, Menu
 * About API mechanism

Processes for modelling

 * How do we made contour data
 * Modelling note
 * Contour concept mapping HOW DO I MAP OBJ DATA TO FMA CONCEPT
 * Mapping results (Obj vs FMA)
 * Data types (Compound and elementary)

Data types

 * 1) Artists make 3D contour of body parts from scratch or modification of clinical 3D images, scanned plastic models, with reference to anatomical textbooks, atlases and other image sources.
 * 2) This ELEMENTAL DATA(2jyuumaru) is mapped to the corresponding, or the closest concept chosen from FMA.
 * 3) Form the side of concept mapping concept to contour is called representation.
 * 4) Those mapped ELEMENTALS are re-used in generating logical aggregation of contour data for higher order concepts.
 * 5) For this purpose ontological relations of concepts provided from out-side of the project, at this moment FMA, is used. (build-up contour; build-up concept)
 * 6) Accordingly, the same concept may be represented by different COMPOUND DATA (paigurafu) depending on the choice of the logic.
 * 7) For example, big organ have only COMPOUND contour in part-of logic but no is-a contor because it dose dot have categorical subordinates.
 * 8) Representation have two types; ELEMENTAL/DIRECT representation and COMPOUND/SECONDARYrepresentation.
 * 9) COMPOUND representation may be complete in some cases such as "left hand+right hand-->hands".
 * 10) But in most cases, only a subset of subordinate concept have "ELEMENTAL DATA'''.
 * 11) In such cases, representation has a feature called representation density.
 * 12) The ration of represented subordinate concepts and all subordinate concepts in COMPOUND is density shown by red/white Pie.


 * 1) Build-up Representation of mandibula with FMA:Part-OF logic. IN bp3.0 data, with fma3.0 part-of logic, build-up representation density for FMA7485:Mandibura, is 3/7.

Data stats & Release Hx
In the present version, relations of logic and contour representation s are as follows.  bp3d_v2.0	FMA concepts	ELEMENTAL COMPOUND is-a tree	80457	843	643 part-of tree	35597	408	326 in both tree	30068	406	0 all unique FMA	80457	845	969 bp3d_v3.0	FMA concepts	ELEMENTAL COMPOUND is-a tree	80457	912	700 part-of tree	35597	436	353 in both tree	30068	433	0 all unique FMA	80457	915	1053 bp3d_v4.0	FMA concepts	ELEMENTAL 	COMPOUND is-a tree	80457	1651	1254 part-of tree	35597	765	603 in both tree	30068	764	3 all unique FMA	80457	1652	1854 TA	FMA Material Anatomical Entity	460y1	4600 Inmaterial Anatomical Entity	2238	2306 ※obj有無に関係無くTA-FMA対応がある数 Material Anatomical Entity TA：4601 IS-A			PART-OF V2	V3	V4	V2	V3	V4 element	       96	99	211	63	73	137 compound	299	334	514	66	74	161 Material Anatomical Entity	IS-A			PART-OF FMA：4600	V2	V3	V4	V2	V3	V4 element	93	98	207	63	72	133 compound	293	325	499	63	71	160 Inmaterial Anatomical Entity TA:2238 IS-A			PART-OF V2	V3	V4	V2	V3	V4 element	     12	17	22	0	0	0 compound     10	12	14	5	5	5 Inmaterial Anatomical Entity FMA:2306 IS-A			PART-OF V2	V3	V4	V2	V3	V4 element	     12	17	21	0	0	0 compound	8	10	12	5	5	5
 * Stats in concept number


 * Release 4.0 (2013/5) Release Note (2013/5)
 * Release 3.0 (2011/6/20)
 * Release Note (2011/6/20)
 * Release Note (2010/4/28)
 * Modeling Note (PDF)(2010/7/21)
 * BodyParts3D Origin and insertion of skeletal muscles (Excel)(2010/8/30)
 * Release 1.0 (2009/2/9)

FMA Foundation model of Anatomy of Wahington-U

 * Rosse C, Mejino JL, Modayur BR, Jakobovits R, Hinshaw KP, Brinkley JF. Motivation and organizational principles for anatomical knowledge representation: the Digital Anatomist Symbolic Knowledge Base. J Am Med Inform Assoc. 1998;5:17–40.
 * Extraction from AMIA Annu Symp Proc. 2003; 2003: 450–454.PMCID: PMC1480337 Representing Complexity in Part-Whole Relationships within the Foundational Model of Anatomy by José L.V. Mejino, Jr, MD, Augusto V. Agoncillo, MD, Kurt L. Rickard, PhD, and Cornelius Rosse, MD, DSc

Terms in FMA
examples:
 * Constitutional part is a primary partition of an anatomical structure into its compositionally distinct anatomical elements.
 * In the context of the whole, an element is any relatively simple component of which a larger, more complex anatomical structure is compounded; i.e., the partition is compositional rather than spatial.
 * Regional part is a primary partition that spatially subdivides an anatomical structure into sets of diverse constitutional parts that share a given location within the whole; i.e., the partition is spatial rather than compositional.
 * Entities in all subclasses of Anatomical structure have both constitutional and regional parts, as illustrated by the following
 * Neuron -has constitutional part-Plasma membrane, Protoplasm;
 * Neuron-has regional part-Cell body, Axon, Dendrite;
 * Lung -has constitutional part- Visceral pleura, Lung parenchyma, Intrapulmonary airway, Vasculature, Neural network;
 * Lung -has regional part- Lobe of lung;Lobe of lung -has constitutional part- Visceral pleura, Lung parenchyma etc.;

Accordingly, the following are valid assertions:
 * Part-whole relationships are valid only for entities of the same dimension;
 * boundary relationships are valid for entities that differ by one in their dimensionality.
 * Right ventricle -has part- Wall of right ventricle, Cavity of right ventricle (3D anatomical entities);
 * Surface of heart -has part- Diaphragmatic surface of heart (2D entities); and
 * Surface of heart -bounds- Heart (2D and 3D entities, respectively).

Terminologia Anatomica
"Terminologia Anatomica (TA) is the international standard on human anatomic terminology. It was developed by the Federative Committee on Anatomical Terminology (FCAT) and the International Federation of Associations of Anatomists (IFAA) and was released in 1998.[1] It supersedes the previous standard, Nomina Anatomica.[2] Terminologia Anatomica contains terminology for about 7500 human gross (macroscopic) anatomical structures.[3] In April 2011, Terminologia Anatomica was published online by the Federative International Programme on Anatomical Terminologies (FIPAT), the successor of FCAT." http://en.wikipedia.org/wiki/Terminologia_anatomica
 * Short introduction and link
 * TA contains terminology for about 7500 human gross (macroscopic) anatomical structures, while TH contains terminology for cellular structures, tissue and organs at the microscopic level.

Funato's Japanses translation digital text @ Keiko Univ. Med.Schl.
http://www.anatomy.med.keio.ac.jp/funatoka/TA.html

Image templates and reference

 * Taro
 * Stanford
 * MAI
 * Talairach
 * Reference books heavily used
 * FENEIS
 * FUNATO's site
 * RauberKopsch
 * Reference 3D data and sites
 * Visible
 * BodyBrowser
 * Lung CD

Terminology

 * 1) Concept have FMAID (mostly), and contour data (=3D polygon files = obj files). They are different entities.
 * 2) A relation of concept/FMA1234 and contour data/FJ3456.obj is called Representation.
 * 3) Since representation may change time to time, we put representation ID "BP1234" for these paired ID.
 * 4) Representation have two types; ELEMENTAL/DIRECT representation and COMPOUND/SECONDARY representation.
 * 5) A contour data file made by artist is referred to as: ELEMENTAL DATAdenoted by red target in icon (image here)
 * 6) Concept manually mapped with one ELEMENTAL DATAfor its sufficient representation is: ELEMENTAL/DIRECTLY represented concept
 * 7) Contour file made operationally by joining one or more ELEMENTAL DATA according to the provided tree of concepts are: COMPOUND/SECONDARY represented DATA; COMPOUNDS. denoted by red/white pie (image here)
 * 8) The ratio of existing part and missing part in COMPOUND is shown by red/white Pie.
 * About representation, concept,

More infromation sources

 * 発表論文 Nobutaka Mitsuhashi, Kaori Fujieda, Takuro Tamura, Shoko Kawamoto, Toshihisa Takagi, and Kousaku Okubo BodyParts3D: 3D structure database for anatomical concepts Nucleic Acids Research, 2009, Vol. 37, Database issue D782-D785, DOI 10.1093/nar/gkn613.
 * プレゼン資料 日本分子生物学会 BMB2009| BMB2008| BMB2007
 * 統合データベース講習会(AJACS) 2010年度: AJACSみちのく(2010/8)| AJACS and DDBJing in 東京(2010/6)| AJACS湘南２(2010/6) 2009年度: AJACSりんくう(2009/11)| AJACS近江２(2009/10)| AJACS三河(2009/7) 2008年度: AJACS長津田(2009/1)| AJACS近江| AJACS博多| AJACS本郷１
 * 統合データベースプロジェクト主催シンポジウム 「データベースが拓くこれからのライフサイエンス」(2009/6/21)

=Dissemination status=
 * Wikipedia article on "Creative commons licence" http://en.wikipedia.org/wiki/Creative_Commons_license
 * wikimedia commons : Thanks to many, especially to "WAS A BEE" : https://commons.wikimedia.org/wiki/Category:Animations_from_Anatomography
 * TV programs: France, UK, US
 * research projects : 工学部中村研、　（株）久保田、　（株）テルモ、東京大学大学院 学際情報学府國吉・原田研究室 修士課程1年藤井 敬子
 * anonymous ftp: 60 countries in 5month (2012,Jan-May). downloads from several mirror sites are uncountable.
 * iPhone app　by Third party:
 * https://itunes.apple.com/jp/app/anatomy-cardiovascular-system/id560434744?mt=8
 * https://itunes.apple.com/jp/app/skeletal-anatomy./id547000107?mt=8
 * https://itunes.apple.com/jp/app/digestive-pro/id548187116?mt=8
 * https://itunes.apple.com/jp/app/brain-3d-for-iphone/id545703549?mt=8
 * http://www.cndp.fr/entrepot/themadoc/vivre-sa-sexualite-les-bases-neurobiologiques-du-comportement-sexuel/en-pratique/premiere-s.html

Scholarly journals

 * "Among the assessed manikins, the Human BioDigital and Anatomography were the ones with the best scores overall, 16 points or 80%. In the big picture, the manikins had a mean score of 2.78 points or 55.56% with a standard deviation of 1.56." says Mata, Thiago Henrique, and André Barros Sales. "Definição de critérios para avaliar bonecos anatômicos 3D na web para ensino na área da saúde ou aplicações médicas." Extensio: Revista Eletrônica de Extensão 9.14 (2013): 44-54.
 * Imaging genetics in dyslexia by John D. Eichera, Jeffrey R. Gruena, http://www.sciencedirect.com/science/article/pii/S1096719213002266
 * Cell Volume 144, Issue 4, 18 February 2011, Pages 459, 461
 * A computer model based on real anatomy for electrophysiology study
 * The Benefit of Non Contrast-Enhanced Magnetic Resonance Angiography for Predicting Vascular Access Surgery Outcome: A Computer Model Perspective http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0053615
 * Affordable Ultrasound Training Simulator
 * Automated differentiation of pre-diagnosis Huntington's disease from healthy control individuals based on quadratic discriminant analysis of the basal ganglia: The IMAGE-HD study                       http://www.sciencedirect.com/science/article/pii/S0969996112003294
 * Darwin y su Contribución a las Humanidades y a la Sociedad                       http://pmrb.net/home/sites/default/files/darwin_humanidades1.pdf
 * Automated differentiation of pre-diagnosis Huntington's disease from healthy control individuals based on quadratic discriminant analysis of the basal ganglia: The IMAGE-HD study
 * A computer model based on real anatomy for electrophysiological study: http://www.sciencedirect.com/science/article/pii/S0965997811000536
 * Identification and functional characterization of microRNAs in medulloblastoma:http://archiv.ub.uni-heidelberg.de/volltextserver/12648/
 * Estimation of sex from the human hyoid bone in a contemproary white European population http://library2.smu.ca/handle/01/24904#.UZ5KFbX0FqU
 * 日本整形外科学会調査2009:http://www.joa.or.jp/jp/media/comment/pdf/investigation_2009.pdf
 * Modélisation des processus émotionnels dans la prise de décision http://tel.archives-ouvertes.fr/docs/00/69/66/75/PDF/manuscript.pdf
 * De patiënt in de Nederlandse gezondheidszorg (book) http://books.google.co.jp/books?hl=ja&lr=&id=kheAOHEikv8C&oi=fnd&pg=PT94&dq=%22anatomography%22&ots=_P5b6kQCzZ&sig=hJ_zr3oU4XEwhpD11S5LhEzgFzU
 * Practical Aspects of Some Bio-magnetic Inverse Problems http://www.sigmath.es.osaka-u.ac.jp/suzuki/pdf/biomag.pdf
 * Toward Integration of Biological and Physiological Functions at Multiple Levels http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059937/
 * Imaging-genetics in dyslexia: Connecting risk genetic variants to brain neuroimaging and ultimately to reading impairmentsJohn D. Eichera, Jeffrey R. Gruena, b, c, ,

BLOGS
http://gfxhome.ws/uploads/posts/2012-08/thumbs/1344680655_ihnwy.jpg
 * WIKIMEDIA foundation global blog:https://blog.wikimedia.org/2013/09/11/wikiskills-teachers-more-lessons-learned/
 * CAN ACN http://can-acn.org/no-room-for-inaccuracy-in-the-brain
 * PLOSABLE http://askabiologist.asu.edu/plosable/give-your-brain-break
 * Neuroscience Prize http://www.kavlifoundation.org/2012-neuroscience-prize-explanatory-notes
 * A&P report http://theapstudent.blogspot.jp/2009_11_09_archive.html
 * Science update http://www.scienceupdate.com/2013/06/bomb/>
 * SiLog http://www.scilogs.com/scientific_and_medical_libraries/open-data-tools-turning-data-into-actionable-intelligence/
 * Science inclusive http://scienceinclusive.com/2011/10/do-our-brains-determine-our-facebook-friend-count/
 * Francesco Giorlando's blog: http://f.giorlando.org/life-sciences-data-base
 * http://www.scilogs.com/next_regeneration/inflamm-aging-inflammatory-signals-in-the-brain-regulate-the-lifespan/
 * Blog article explaining how data can be reused in CAD software: http://craig.bonsignore.com/2012/10/07/open-3d-human-anatomy/
 * Blog article with embed http://teslabar.blogspot.jp/2011/12/bodyparts3d.html
 * NEDO Thorax surgery aid project; report http://www.nedo.go.jp/content/100502220.pdf
 * NEDO endoscopic surgery project : 資料5-1 - 新エネルギー・産業技術総合開発機構　http://www.nedo.go.jp/content/100519719.pdf　　2012/09/13
 * ICT convention : https://www.facebook.com/media/set/?set=a.10151393356163204.1073741829.44244463203&type=3
 * BodyParts in matlab: http://wspr.wordpress.com/2013/05/
 * Download mirrors
 * http://torrentmedia.org/bodyparts3d++use+multiple+obj+files.html
 * http://img33.imageshack.us/img33/659/ihnwy.jpg|200px
 * http://u26019801.letitbit.net/download/06236.0a9a6c89e706edf54a97f94a9734/BodyParts3D_3.0_obj.rar.html
 * http://www.vincedoyle.com/?do=searchcloud&subaction=search&story=BodyParts3D%203.0%20obj

3rd party delivations
http://preview.turbosquid.com/Preview/2013/05/21__09_32_43/skeletoncover01.bmp0c0eb295-1e0f-4a4f-81f6-cad046f86efaLarge.jpg
 * Remix video: by drbruno http://vimeo.com/56883598
 * By Artist: scyrus