“i” at the end of data version denotes the part_of tree used for aggregative representation of larger concepts are modified by adding “inferred relations" to the original FMA.
This change substantially increased the number of concepts represented by 3D images.
According to the extent of change in the trees, the naming for the tree may be altered in the future.
CAUTION For map URL users:
Improving obj files and part_of tree is performed constantly which improves the coverage and qualities of image representation of concepts specified in the map URL.
We recommend users to configure your anatomography "without denoting data version", because they will be interpreted and rendered by the latest combinations of obj files.
Whats new
ontology aggregating obj files into larger segments was updated from fma3.0 to 3.2.1. (Jan, 2016)
To fma3.2.1, whole/part relations among ipsilateral copies of bilateral entities were supplemented by 6078 inference (amounts 4498 parallel (R to R)+1580 conversing (R to uni, L to uni) relations) (Jan,2016) [2]
The new concept relations were applied retrospectively and all concept icons were regenerated accordingly (4.3i).
The number of concepts are 3899 (4.3i)
Downloading custom 3D map in obj files is supported (Dec, 2015)
New data release: Now (April 15, 2014), peripheral nerves and cranial vessels are under inspection and concept mapping. They will be released in a month as version 5.0.
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）
For new visitors
What is this site about? (Map editor)
What you can do with BodyParts3D/Anatomography [4]
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.
This ELEMENTAL DATA() is mapped to the corresponding , or the closest concept chosen from FMA.
Form the side of concept mapping concept to contour is called representation.
Those mapped ELEMENTALS are re-used in generating logical aggregation of contour data for higher order concepts .
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)
Accordingly, the same concept may be represented by different COMPOUND DATA () depending on the choice of the logic.
For example, big organ have only COMPOUND contour in part-of logic but no is-a contor because it dose dot have categorical subordinates.
Representation have two types; ELEMENTAL/DIRECT representation and COMPOUND/SECONDARYrepresentation.
COMPOUND representation may be complete() in some cases such as "left hand+right hand-->hands".
But in most cases, only a subset of subordinate concept have "ELEMENTAL DATA.
In such cases, representation has a feature called representation density.
The ration of represented subordinate concepts and all subordinate concepts in COMPOUND is density shown by red/white Pie.
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
Stats in concept number
In the present version, relations of logic and contour representation s are as follows. [12]
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
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 Jose L.V. Mejino, Jr, MD, Augusto V. Agoncillo, MD, Kurt L. Rickard, PhD, and Cornelius Rosse, MD, DSc [14]
Terms in FMA
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
Lung -has regional part- Lobe of lung;Lobe of lung -has constitutional part- Visceral pleura, Lung parenchyma etc.;
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.
Accordingly, the following are valid assertions:
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). [15]
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.[16]
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. [17]
Concept have FMAID (mostly), and contour data (=3D polygon files = obj files). They are different entities.
A relation of concept/FMA1234 and contour data/FJ3456.obj is called Representation.
Since representation may change time to time, we put representation ID "BP1234" for these paired ID.
Representation have two types; ELEMENTAL/DIRECT representation and COMPOUND/SECONDARY representation.
A contour data file made by artist is referred to as: ELEMENTAL DATAdenoted by red target in icon (image here)
Concept manually mapped with one ELEMENTAL DATAfor its sufficient representation is: ELEMENTAL/DIRECTLY represented concept
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)
The ratio of existing part and missing part in COMPOUND is shown by red/white Pie.
About representation, concept,
More infromation sources
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.
Presentations BMB2009| BMB2008| BMB2007
Seminars (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
"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 Andre Barros Sales. "Definicao de criterios para avaliar bonecos anatomicos 3D na web para ensino na area da saude ou aplicacoes medicas." Extensio: Revista Eletronica de Extensao 9.14 (2013): 44-54.
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 [21]
Imaging-genetics in dyslexia: Connecting risk genetic variants to brain neuroimaging and ultimately to reading impairmentsJohn D. Eichera, Jeffrey R. Gruena, b, c, <img alt="Corresponding author contact information" src="">, [22]
) is mapped to the corresponding , or the closest concept chosen from FMA.
) depending on the choice of the logic.
) in some cases such as "left hand+right hand-->hands".
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