My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development
Tóm tắt
Embryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physically based modeling are used to assist the visualization and the simulation of virtual humans for numerous domains such as surgical simulation and learning. On the other side, the ontology-based approach applied to knowledge representation is more and more successfully adopted in the life-science domains to formalize biological entities and phenomena, thanks to a declarative approach for expressing and reasoning over symbolic information. 3D models and ontologies are two complementary ways to describe biological entities that remain largely separated. Indeed, while many ontologies providing a unified formalization of anatomy and embryology exist, they remain only descriptive and make the access to anatomical content of complex 3D embryology models and simulations difficult. In this work, we present a novel ontology describing the development of the human embryology deforming 3D models. Beyond describing how organs and structures are composed, our ontology integrates a procedural description of their 3D representations, temporal deformation and relations with respect to their developments. We also created inferences rules to express complex connections between entities. It results in a unified description of both the knowledge of the organs deformation and their 3D representations enabling to visualize dynamically the embryo deformation during the Carnegie stages. Through a simplified ontology, containing representative entities which are linked to spatial position and temporal process information, we illustrate the added-value of such a declarative approach for interactive simulation and visualization of 3D embryos. Combining ontologies and 3D models enables a declarative description of different embryological models that capture the complexity of human developmental anatomy. Visualizing embryos with 3D geometric models and their animated deformations perhaps paves the way towards some kind of hypothesis-driven application. These can also be used to assist the learning process of this complex knowledge.
http://www.mycorporisfabrica.org/
Tài liệu tham khảo
Gruber TR. A translation approach to portable ontology specifications. Knowl Acquis. 1993;5:199–220.
The Open Biological and Biomedical Ontologies: http://www.obofoundry.org/. Accessed 20 June 2015.
NCBO BioPortal: http://bioportal.bioontology.org/. Accessed 20 June 2015.
Rosse C, Mejino JLV. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform. 2003;36(6):478–500.
Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA. Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012;13(1):R5.
The Gene Ontology Consortium. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010;38:D331–5.
Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. The Drosophila anatomy ontology. J Biomed Semant. 2013;4:32.
Kaufman MH. The atlas of mouse development. Academic press San Diego, California 92101-4495, USA; 1992
Davidson D, Bard J, Brune R, Burger A, Dubreuil C, Hill W, et al. The mouse atlas and graphical gene-expression database. Seminars in cell & developmental biology. Elsevier; 1997 Academic Press
Bard JBL, Baldock RA, Kaufman M, Davidson D. Graphical gene-expression database for mouse development. Eur J Morphol. 1997;35(1):32–4.
Baldock R, Bard J, Kaufman M, Davidson D. A real mouse for your computer. BioEssays News Rev Mol Cell Dev Biol. 1992;14(7):501–2.
Ringwald M, Baldock R, Bard J, Kaufman M, Eppig JT, Richardson JE, et al. A database for mouse development. Science. 1994;265(5181):2033–4.
Brune RM, Bard JB, Dubreuil C, Guest E, Hill W, Kaufman M, et al. A three-dimensional model of the mouse at embryonic day 9. Dev Biol. 1999;216(2):457–68.
Milyaev N, Osumi-Sutherland D, Reeve S, Burton N, Baldock RA, Armstrong JD. The Virtual Fly Brain browser and query interface. Bioinformatics. 2012;28(3):411–5.
Jones AR, Overly CC, Sunkin SM. The Allen Brain Atlas: 5 years and beyond. Nat Rev Neurosci. 2009;10:821–8.
Burger A, Davidson D, Baldock R. Formalization of mouse embryo anatomy. Bioinforma Oxf Engl. 2004;20(2):259–67.
Hayamizu TF, Wicks MN, Davidson D, Burger A, Ringwald M, Baldock RA. EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update. J Biomed Semant. 2013;4:15.
EMAPA : http://wiki.obofoundry.org/wiki/index.php/EMAPA:Main_Page. Accessed 20 June 2015.
Hunter A, Kaufman MH, McKay A, Baldock R, Simmen MW, Bard JBL. An ontology of human developmental anatomy. J Anat. 2003;203(4):347–55.
Bard J. A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1–20). J Anat. 2012;221(5):406–16.
Palombi O, Ulliana F, Favier V, Léon J-C, Rousset M-C. My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models. J Biomed Semant. 2014;5:20.
My Corporis Fabrica (MyCF): http://mycorporisfabrica.org/mycf/. Accessed 20 June 2015.
Dicko A, Gilles B, Faure F, Palombi O. From Generic to Specific Musculoskeletal Simulations Using an Ontology-Based Modeling Pipeline. Springer Berlin Heidelberg. Intelligent Computer Graphics 2012. Berlin, Heidelberg: 2013. p. 227–42
Rubin DL, Dameron O, Bashir Y, Grossman D, Dev P, Musen MA. Using ontologies linked with geometric models to reason about penetrating injuries. Artif Intell Med. juill 2006;37(3):167‑76.
Kerwin J, Yang Y, Merchan P, Sarma S, Thompson J, Wang X, et al. The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain. J Anat. 2010;217(4):289–99.
Human Developmental Studies Network (HUDSEN) : http://hudsen.org/. Accessed 20 June 2015.
Gasser RF, Cork RJ, Stillwell BJ, McWilliams DT. Rebirth of Human Embryology. Dev Dyn Off Publ Am Assoc Anat. 2014;243(5):621–8.
The Virtual Human Embryo: http://www.ehd.org/virtual-human-embryo/. Accessed 20 June 2015.
Sirin E, Parsia B, Grau BC, Kalyanpur A, Katz Y. Pellet: A practical OWL-DL reasoner. Journal of Web Semantics. 2007;5(2):51–3.
Racerpro: http://www.racer-systems.com/. Accessed 20 June 2015.
Datalog rules: http://docs.racket-lang.org/datalog/. Accessed 20 June 2015.
F. Baader, D. Calvanese, D. McGuinness, D. Nardi, and P. F. Patel-Schneider, editors. The Description Logic Handbook: Theory, Implementation, and Applications. Cambridge University Press CB2 2RU, UK, 2003
D. Allemang and J. Hendler. Semantic Web for the Working Ontologist: Effective Modeling in RDFS and OWL. Morgan-Kaufman, Burlington MA 01803, 2008
Linked Data: http://linkeddata.org/. Accessed 20 June 2015.
Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, et al. The Drosophila phenotype ontology. J Biomed Semant. 2013;4(1):30.
Schriml LM, Arze C, Nadendla S, Chang Y-WW, Mazaitis M, Felix V, et al. Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res. 2012;40(D1):D940–6.
Ju T, Schaefer S, Warren J. Mean Value Coordinates for Closed Triangular Meshes. ACM SIGGRAPH 2005. New York, NY, USA: ACM; 2005. p. 561–6.
Joshi P, Meyer M, DeRose T, Green B, Sanocki T. Harmonic coordinates for character articulation. ACM Trans Graph. 2007;26(99):71.
Lipman Y, Levin D, Cohen-Or D. Green Coordinates. ACM SIGGRAPH 2008. New York, NY, USA: ACM; 2008. p. 78:1–78:10.
Top Braid Composer: http://www.topquadrant.com/. Accessed 20 June 2015.
RDF - Semantic Web Standards: http://www.w3.org/RDF/
SPARQL Query Language for RDF: http://www.w3.org/TR/rdf-sparql-query/
Blender: http://www.blender.org/
Python: https://www.python.org/. Accessed 20 June 2015.