KC-Viz: a novel approach to visualizing and nNavigating ontologies

There is empirical evidence that the user interaction metaphors used in ontology engineering toolkits are largely inadequate and that novel interactive frameworks for human ontology interaction are needed. Here we present a novel tool for visualizing and navigating ontologies, called KC Viz, which exploits an innovative ontology summarization method to support a ’middleout ontology browsing’ approach, where it becomes possible to navigate ontologies starting from the most information-rich nodes (i.e., key concepts). This approach is similar to map-based visualization and navigation in Geographical Information Systems, where, e.g., major cities are displayed more prominently than others, depending on the current level of granularity

Specification and implementation of mapping rule visualization and editing : MapVOWL and the RMLEditor

Visual tools are implemented to help users in defining how to generate Linked Data from raw data. This is possible thanks to mapping languages which enable detaching mapping rules from the implementation that executes them. However, no thorough research has been conducted so far on how to visualize such mapping rules, especially if they become large and require considering multiple heterogeneous raw data sources and transformed data values. In the past, we proposed the RMLEditor, a visual graph-based user interface, which allows users to easily create mapping rules for generating Linked Data from raw data. In this paper, we build on top of our existing work: we (i) specify a visual notation for graph visualizations used to represent mapping rules, (ii) introduce an approach for manipulating rules when large visualizations emerge, and (iii) propose an approach to uniformly visualize data fraction of raw data sources combined with an interactive interface for uniform data fraction transformations. We perform two additional comparative user studies. The first one compares the use of the visual notation to present mapping rules to the use of a mapping language directly, which reveals that the visual notation is preferred. The second one compares the use of the graph-based RMLEditor for creating mapping rules to the form-based RMLx Visual Editor, which reveals that graph-based visualizations are preferred to create mapping rules through the use of our proposed visual notation and uniform representation of heterogeneous data sources and data values. (C) 2018 Elsevier B.V. All rights reserved

National Center for Biomedical Ontology: Advancing biomedicine through structured organization of scientific knowledge

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease

Visual support for ontology learning: an experience report

Ontology learning methods aim to automate ontology construction. They are complex methods involving several elements such as documents, terms and concepts. During the development of an ontology learning method, as well as during its deployment, several situations occur where understanding the relations between these elements is crucial. Our hypothesis is that visual techniques can be used to aid this understanding. To support this claim, we present a set of such complex situations and describe the visual solutions that we developed to support them

Investigating the use of background knowledge for assessing the relevance of statements to an ontology in ontology evolution

The tasks of learning and enriching ontologies with new concepts and relations have attracted a lot of attention in the research community, leading to a number of tools facilitating the process of building and updating ontologies. These tools often discover new elements of information to be included in the considered ontology from external data sources such as text documents or databases, transforming these elements into ontology compatible statements or axioms. While some techniques are used to make sure that statements to be added are compatible with the ontology (e.g. through conflict detection), such tools generally pay little attention to the relevance of the statement in question. It is either assumed that any statement extracted from a data source is relevant, or that the user will assess whether a statement adds value to the ontology. In this paper, we investigate the use of background knowledge about the context where statements appear to assess their relevance. We devise a methodology to extract such a context from ontologies available online, to map it to the considered ontology and to visualize this mapping in a way that allows to study the intersection and complementarity of the two sources of knowledge. By applying this methodology on several examples, we identified an initial set of patterns giving strong indications concerning the relevance of a statement, as well as interesting issues to be considered when applying such techniques

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.

VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community

Automated UML-based ontology generation in OSLO²

In 2015, Flanders Information started the OSLO2 project, aimed at easing the exchange of data and increasing the interoperability of Belgian government services. RDF ontologies were developed to break apart the government data silos and stimulate data reuse. However, ontology design still encounters a number of difficulties. Since domain experts are generally unfamiliar with RDF, a design process is needed that allows these experts to efficiently contribute to intermediate ontology prototypes. We designed the OSLO2 ontologies using UML, a modeling language well known within the government, as a single source specification. From this source, the ontology and other relevant documents are generated. This paper describes the conversion tooling and the pragmatic approaches that were taken into account in its design. While this tooling is somewhat focused on the design principles used in the OSLO2 project, it can serve as the basis for a generic conversion tool. All source code and documentation are available online