@article {2018|2089,
	title = {Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data.},
	journal = {J Integr Bioinform},
	volume = {15},
	year = {2018},
	month = {2018 Jul 09},
	abstract = {<p>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.</p>
},
	keywords = {Computer Graphics, Humans, Imaging, Three-Dimensional, Models, Structural, Semantics, Software, Statistics as Topic, User-Computer Interface},
	issn = {1613-4516},
	doi = {10.1515/jib-2018-0004},
	author = {Trellet, Mikael and Nicolas F{\'e}rey and Floty{\'n}ski, Jakub and Marc Baaden and Bourdot, Patrick}
}
@conference {2016|1415,
	title = {Interactive visual analytics of molecular data in immersive environments via a semantic definition of the content and the context},
	booktitle = {2016 Workshop on Immersive Analytics (IA)},
	year = {2016},
	month = {March},
	abstract = {<p>Bringing together, in a unique immersive environment, visualization and analysis of scientific and complex data requires a thorough approach in order to fulfill scientists\&$\#$39; specific expectations. Such an approach needs to consider the highly heterogeneous nature of data, the dynamic interactions between experts and data, and the large amount of data involved in scientific studies. Whereas small and static scientific datasets can quickly be deciphered thanks to standard immersive tools such as 3D visualization software packages, bigger and dynamic datasets exceed the analytical capacity of these tools, requiring an efficient platform for their manipulation. Through the example of the structural biology field we discuss the need for an approach based on a high-level definition of the content (scientific data) and the context (immersive environments and interfaces). Our design is illustrated by a platform for dynamic and intelligent representation of data to the user. The data hierarchical classification will provide new ways to interact with the data via intelligent and direct relationships between them. This approach is based on the semantic definition of all the concepts manipulated in the virtual environment, either abstract or concrete, which allows for an adaptive and interactive experience of both visualization and analysis.</p>
},
	keywords = {Computer Graphics [I.3.7]: Three-Dimensional Graphics and Realism-Virtual Reality, content high-level definition, content management, content semantic definition, Context, context high-level definition, context semantic definition, data analysis, data dynamic representation, data intelligent representation, data visualisation, Data visualization, molecular data interactive visual analysis, Ontologies, Resource description framework, Semantics, static scientific datasets, structural biology field, Three-dimensional displays, Tools, virtual environment, Virtual Reality},
	doi = {10.1109/IMMERSIVE.2016.7932383},
	author = {M. Trellet and Nicolas F{\'e}rey and Marc Baaden and P. Bourdot}
}
