Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data

Abstract

The advances made in recent years in the field of structural biology significantly increased the throughput and complexity of data that scientists have to deal with. Combining and analyzing such heterogeneous amounts of data became a crucial time consumer in the daily tasks of scientists. However, only few efforts have been made to offer scientists an alternative to the standard compartmentalized tools they use to explore their data and that involve a regular back and forth between them. We propose here an integrated pipeline especially designed for immersive environments, promoting direct interactions on semantically linked 2D and 3D heterogeneous data, displayed in a common working space. The creation of a semantic definition describing the content and the context of a molecular scene leads to the creation of an intelligent system where data are (1) combined through pre-existing or inferred links present in our hierarchical definition of the concepts, (2) enriched with suitable and adaptive analyses proposed to the user with respect to the current task and (3) interactively presented in a unique working environment to be explored.

Creating explorable extended reality environments with semantic annotations

“…The semantic web is one of the predominant approaches to knowledge representation in different domains and one of the main trends in the evolution of the web [4]. It gains increasing attention in the context of graphical systems and XR, e.g., for photogrammetry [3], molecular visualization [46,47], content description and retrieval [43,44], design of industrial spaces [38], archaeology [13] as well as feature-based data exchange between heterogeneous CAD systems [53,60]. Due to the use of the semantic web in our method, XR behavior can be represented with general or domain knowledge, thus being intelligible to average users and domain experts who are not IT-specialists.…”

X3D Ontology for Querying 3D Models on the Semantic Web

“…These standards permit design of ontologies, which are specifi- (Bille, W., et al, 2004)- [Bille et al 2004]; (AIM@SHAPE), (Spagnuolo, et al, M., 2008(Spagnuolo, et al, M., )-[aim 2017Spagnuolo and Falcidieno 2008]; (Gutierrez, et al, M., 2007)- [Gutiérrez et al 2007]; (Kalogerakis, E., et al, 2006)- [Kalogerakis et al 2006]; (Pittarello, F., et al, 2006)- [Pittarello and De Faveri 2006]; (Attene, M., et al, 2007)- [Attene et al 2007]; (Floriani, L., et al, 2007)- [De Floriani et al 2007]; (Chu, Y., et al, 2012)- [Chu and Li 2012]; (Kapahnke, P., et al, 2010)- [Kapahnke et al 2010]; (Vasilakis, G., et al, 2010)- [Vasilakis et al 2010]; (Albrecht, S., et al, 2011)-[Albrecht et al 2011; (Wiebusch, D., et al, 2012)- [Wiebusch and Latoschik 2012]; (Flotyński, J., et al, 2013)- [Flotyński and Walczak 2013;Flotyński and Walczak 2013b]; (Flotyński, J., et al, 2014(Flotyński, J., et al, , 2016 (Drap, P., et al 2017)- [Drap et al 2017]; (Trellet, M., et al, 2018)- [Trellet et al 2018]; (Kontakis, K., et al, 2017)- [Kontakis et al 2014]; (Radics, P.J., et al, 2015)-[Radics et al 2015; (Flotyński, J., et al, 2017)- Flotyński and Walczak 2014;Flotyński and Walczak 2017a] (1) They are not integrated with 3D formats. It hinders t...…”

Inference-based creation of synthetic 3D content with ontologies

“…In [46,47], an approach to semantic representation of 3D molecular models has been proposed. The approach combines different input (e.g., interaction using different haptic and motion tracking devices) and output (e.g., presentation in 2D and 3D) modalities to enable presentation and interaction suitable for particular types of content and tasks to be done.…”

“…Moreover, two basic shapes (mp:Box and mp:Cylinder) are created (24)(25)(26)(27)(28)(29)(30)(31)(32) and assembled into the do:Stand PO class (34)(35)(36)(37)(38)(39)(40)(41)(42). Every mp:Box and mp:Cylinder included in a do:Stand has dimensions and position (44)(45)(46)(47)(48)(49)(50)(51)(52)(53)(54)(55)(56). The do:incorporates RL is an equivalent to the co:includes (58-59), while the do:standsOn RL determines the x, y and z coordinates of an individual by semantic rules (61-77).…”

“…This can lead to much better methods of creating, indexing, searching, querying and analyzing of content. The use of the semantic web for describing 3D content recently gains increasing attention of the research community in different applications such as 3D content retrieval [45], design of industrial spaces [43], archaeology [19] and molecular visualization [46,47].…”