Multi-View Ontology Explorer (MOE): Interactive Visual Exploration of Ontologies

An ontology is an explicit specification of a conceptualization. This specification consists of a common vocabulary and information structure of a domain. Ontologies have applications in many fields to semantically link information in a standardized manner. In these fields, it is often crucial for both expert and non-expert users to quickly grasp the contents of an ontology; and to achieve this, many ontology tools implement visualization components. There are many past works on ontology visualization, and most of these tools are adapted from tree and graph based visualization techniques (e.g. treemaps, node-link graphs, and 3D interfaces). However, due to the enormous size of ontologies, these existing tools have their own shortcomings when dealing information overload, usually resulting in clutter and occlusion on the screen. In this thesis, we propose a set of novel visualizations and interactions to visualize very large ontologies. We design 5 dynamically linked visualizations that focus on a different level of abstraction individually. These different levels of abstraction start from a high-level overview down to a low-level entity. In addition, these visualizations collectively visualize landmarks, routes, and survey knowledge to support the formation of mental models. Search and save features are implemented to support on-demand and guided exploration. Finally, we implement our design as a web application

Imaging Informatics and the Human Brain Project: the Role of Structure, Review

(no abstract

III: Small: Information Integration and Human Interaction for Indoor and Outdoor Spaces

The goal of this research project is to provide a framework model that integrates existing models of indoor and outdoor space, and to use this model to develop an interactive platform for navigation in mixed indoor and outdoor spaces. The user should feel the transition between inside and outside to be seamless, in terms of the navigational support provided. The approach consists of integration of indoors and outdoors on several levels: conceptual models (ontologies), formal system designs, data models, and human interaction. At the conceptual level, the project draws on existing ontologies as well as examining the affordances that the space provides. For example, an outside pedestrian walkway affords the same function as an inside corridor. Formal models of place and connection are also used to precisely specify the design of the navigational support system. Behavioral experiments with human participants assess the validity of our framework for supporting human spatial learning and navigation in integrated indoor and outdoor environments. These experiments also enable the identification and extraction of the salient features of indoor and outdoor spaces for incorporation into the framework. Findings from the human studies will help validate the efficacy of our formal framework for supporting human spatial learning and navigation in such integrated environments. Results will be distributed using the project Web site (www.spatial.maine.edu/IOspace) and will be incorporated into graduate level courses on human interaction with mobile devices, shared with public school teachers participating in the University of Maine\u27s NSF-funded RET (Research Experiences for Teachers). The research teams are working with two companies and one research center on technology transfer for building indoor-outdoor navigation tools with a wide range of applications, including those for the persons with disabilities

III: Small: Information Integration and Human Interaction for Indoor and Outdoor Spaces

The goal of this research project is to provide a framework model that integrates existing models of indoor and outdoor space, and to use this model to develop an interactive platform for navigation in mixed indoor and outdoor spaces. The user should feel the transition between inside and outside to be seamless, in terms of the navigational support provided. The approach consists of integration of indoors and outdoors on several levels: conceptual models (ontologies), formal system designs, data models, and human interaction. At the conceptual level, the project draws on existing ontologies as well as examining the affordances that the space provides. For example, an outside pedestrian walkway affords the same function as an inside corridor. Formal models of place and connection are also used to precisely specify the design of the navigational support system. Behavioral experiments with human participants assess the validity of our framework for supporting human spatial learning and navigation in integrated indoor and outdoor environments. These experiments also enable the identification and extraction of the salient features of indoor and outdoor spaces for incorporation into the framework. Findings from the human studies will help validate the efficacy of our formal framework for supporting human spatial learning and navigation in such integrated environments. Results will be distributed using the project Web site (www.spatial.maine.edu/IOspace) and will be incorporated into graduate level courses on human interaction with mobile devices, shared with public school teachers participating in the University of Maine\u27s NSF-funded RET (Research Experiences for Teachers). The research teams are working with two companies and one research center on technology transfer for building indoor-outdoor navigation tools with a wide range of applications, including those for the persons with disabilities

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.

Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for achieving
the goals. This report builds on the 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems (Boline et al., 2007, _Nature Preceedings_, doi:10.1038/npre.2007.1046.1) and includes a more detailed analysis of both the current state and desired state of digital atlasing along with specific recommendations for achieving these goals

Social Navigation for Semantic Web Applications Using Space Maps

In this paper we deal with personalized navigation in an open information space. Our aim is to support effective orientation in increasing amount of information accessible through the Web. We present a method for personalized navigation based on social navigation where the information space is represented by an ontology. Navigational information is obtained by following user footsteps. It is attached to information fragment mapped to the user goal and to description of this goal using an ontology. This information is used later to show the way to similar goals. We use ontology representation of the information space that supports the effective navigation and the navigational ability to deal with frequent changes of information content in open environments. We demonstrate the proposed method in the context of developed software tool PENA for personalized navigation support in labor supply domain

Visual analysis of anatomy ontologies and related genomic information

Challenges in scientific research include the difficulty in obtaining overviews of the large amount of data required for analysis, and in resolving the differences in terminology used to store and interpret information in multiple, independently created data sets. Ontologies provide one solution for analysis involving multiple data sources, improving cross-referencing and data integration. This thesis looks at harnessing advanced human perception to reduce the cognitive load in the analysis of the multiple, complex data sets the bioinformatics user group studied use in research, taking advantage also of users’ domain knowledge, to build mental models of data that map to its underlying structure. Guided by a user-centred approach, prototypes were developed to provide a visual method for exploring users’ information requirements and to identify solutions for these requirements. 2D and 3D node-link graphs were built to visualise the hierarchically structured ontology data, to improve analysis of individual and comparison of multiple data sets, by providing overviews of the data, followed by techniques for detailed analysis of regions of interest. Iterative, heuristic and structured user evaluations were used to assess and refine the options developed for the presentation and analysis of the ontology data. The evaluation results confirmed the advantages that visualisation provides over text-based analysis, and also highlighted the advantages of each of 2D and 3D for visual data analysis.Overseas Research Students Awards SchemeJames Watt Scholarshi

Visualization methods for analysis of 3D multi-scale medical data

[no abstract

Application of Neuroanatomical Ontologies for Neuroimaging Data Annotation

The annotation of functional neuroimaging results for data sharing and re-use is particularly challenging, due to the diversity of terminologies of neuroanatomical structures and cortical parcellation schemes. To address this challenge, we extended the Foundational Model of Anatomy Ontology (FMA) to include cytoarchitectural, Brodmann area labels, and a morphological cortical labeling scheme (e.g., the part of Brodmann area 6 in the left precentral gyrus). This representation was also used to augment the neuroanatomical axis of RadLex, the ontology for clinical imaging. The resulting neuroanatomical ontology contains explicit relationships indicating which brain regions are “part of” which other regions, across cytoarchitectural and morphological labeling schemas. We annotated a large functional neuroimaging dataset with terms from the ontology and applied a reasoning engine to analyze this dataset in conjunction with the ontology, and achieved successful inferences from the most specific level (e.g., how many subjects showed activation in a subpart of the middle frontal gyrus) to more general (how many activations were found in areas connected via a known white matter tract?). In summary, we have produced a neuroanatomical ontology that harmonizes several different terminologies of neuroanatomical structures and cortical parcellation schemes. This neuroanatomical ontology is publicly available as a view of FMA at the Bioportal website1. The ontological encoding of anatomic knowledge can be exploited by computer reasoning engines to make inferences about neuroanatomical relationships described in imaging datasets using different terminologies. This approach could ultimately enable knowledge discovery from large, distributed fMRI studies or medical record mining