Natasha Noy

The Semantic Web - ISWC 2011 - 10th International Semantic Web Conference, Bonn, Germany, October 23-27, 2011, Proceedings, Part I

The Semantic Web - ISWC 2011 - 10th International Semantic Web Conference, Bonn, Germany, October 23-27, 2011, Proceedings, Part I

OMEN: a probabilistic ontology mapping tool

Most existing ontology mapping tools are inexact. Inexact ontology mapping rules, if not rectified, result in imprecision in the applications that use them. We describe a framework to probabilistically improve existing ontology mappings using a Bayesian Network. Omen, an Ontology Mapping ENhancer, is based on a set of meta-rules that captures the influence of the ontology structure and the existing matches to match nodes that are neighbours to matched nodes in the two ontologies. We have implemented a protype ontology matcher that can either map concepts across two input ontologies or enhance existing matches between ontology concepts. Preliminary experiments demonstrate that Omen enhances existing ontology mappings in our test cases.

The Semantic Web - ISWC 2013

As collaborative, or network science spreads into more science, engineering and medical fields, both the participants and their funders have expressed a very strong desire for highly functional data and information capabilities that are a) easy to use, b) integrated in a variety of ways, c) leverage prior investments and keep pace with rapid technical change, and d) are not expensive or timeconsuming to build or maintain. In response, and based on our accummulated experience over the last decade and a maturing of several key semantic web approaches, we have adapted, extended, and integrated several open source applications and frameworks that handle major portions of functionality for these platforms. At minimum, these functions include: an object-type repository, collaboration tools, an ability to identify and manage all key entities in the platform, and an integrated portal to manage diverse content and applications, with varied access levels and privacy options. At the same time, there is increasing attention to how researchers present and explain results based on interpretation of increasingly diverse and heterogeneous data and information sources. With the renewed emphasis on good data practices, informatics practitioners have responded to this challenge with maturing informatics-based approaches. These approaches include, but are not limited to, use case development; information modeling and architectures; elaborating vocabularies; mediating interfaces to data and related services on the Web; and traceable provenance. The current era of data-intensive research presents numerous challenges to both individuals and research teams. In environmental science especially, sub-fields that were data-poor are becoming data-rich (volume, type and mode), while some that were largely model/ simulation driven are now dramatically shifting to data-driven or least to data-model assimilation approaches. These paradigm shifts make it very hard for researchers used to one mode to shift to another, let alone produce products of their work that are usable or understandable by non-specialists. However, it is exactly at these frontiers where much of the exciting environmental science needs to be performed and appreciated.

Jambalaya: an interactive environment for exploring ontologies

This demonstration presents a visualization environment for exploring ontologies. An ontology defines a common vocabulary and structure of an information space for researchers and domain experts to exchange and share knowledge. A domain expert defines classes to represent concepts in a domain of discourse, with slots representing properties and relationships between the concepts. A class may be subclassed to represent more specific concepts. An ontology, together with a set of instances, constitutes a knowledge base. The Protégé tool [1] supports the modeling of ontologies to guide acquisition of content knowledge from subject-matter experts. In this demonstration, we present Jambalaya: the integration of a visualization tool called SHriMP [2] with Protégé.

The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research

The biomedical research community relies on a diverse set of resources, both within their own institutions and at other research centers. In addition, an increasing number of shared electronic resources have been developed. Without effective means to locate and query these resources, it is challenging, if not impossible, for investigators to be aware of the myriad resources available, or to effectively perform resource discovery when the need arises. In this paper, we describe the development and use of the Biomedical Resource Ontology (BRO) to enable semantic annotation and discovery of biomedical resources. We also describe the Resource Discovery System (RDS) which is a federated, inter-institutional pilot project that uses the BRO to facilitate resource discovery on the Internet. Through the RDS framework and its associated Biositemaps infrastructure, the BRO facilitates semantic search and discovery of biomedical resources, breaking down barriers and streamlining scientific research that will improve human health.

Using annotations from controlled vocabularies to find meaningful associations

This paper presents the LSLink (or Life Science Link) methodology that provides users with a set of tools to explore the rich Web of interconnected and annotated objects in multiple repositories, and to identify meaningful associations. Consider a physical link between objects in two repositories, where each of the objects is annotated with controlled vocabulary (CV) terms from two ontologies. Using a set of LSLink instances generated from a background dataset of knowledge we identify associations between pairs of CV terms that are potentially significant and may lead to new knowledge. We develop an approach based on the logarithm of the odds (LOD) to determine a confidence and support in the associations between pairs of CV terms. Using a case study of Entrez Gene objects annotated with GO terms linked to PubMed objects annotated with MeSH terms, we describe a user validation and analysis task to explore potentially significant associations.

The Semantic Web - ISWC 2014 - 13th International Semantic Web Conference, Riva del Garda, Italy, October 19-23, 2014. Proceedings, Part II

Linked data, its quality, link discovery and application in the life sciences.- Data integration.- Search and query answering.- SPARQL.- Ontology based data access and query rewriting and reasoning Natural language processing and information extraction.- User interaction and personalization, and social media Ontology alignment and modularization.- Sensors and streams.- Biomedicine and drug discovery.- Smart cities.- Sensor streams.- Multimedia.- Visualization.- Link generation.- Ontology development.- Linked stream data.- Federated query processing.- Tag recommendation.- Entity summarization.- Mobile semantic web.

Crowdsourcing and the Semantic Web (Dagstuhl Seminar 14282).

Semantic technologies provide flexible and scalable solutions to master and make sense of an increasingly vast and complex data landscape. However, while this potential has been acknowledged for various application scenarios and domains, and a number of success stories exist, it is equally clear that the development and deployment of semantic technologies will always remain reliant of human input and intervention. This is due to the very nature of some of the tasks associated with the semantic data management life cycle, which are famous for their knowledge-intensive and/or context-specific character; examples range from conceptual modeling in almost any flavor, to labeling resources (in different languages), describing their content in terms of ontological terms, or recognizing similar concepts and entities. For this reason, the Semantic Web community has always looked into applying the latest theories, methods and tools from CSCW (Computer Supported Cooperative Work), participatory design, Web 2.0, social computing, and, more recently crowdsourcing to find ways to engage with users and encourage their involvement in the execution of technical tasks. Existing approaches include the usage of wikis as semantic content authoring environments, leveraging folksonomies to create formal ontologies, but also human computation approaches such as games with a purpose or micro-tasks. This document provides a summary of the Dagstuhl Seminar 14282: Crowdsourcing and the Semantic Web, which in July 2014 brought together researchers of the emerging scientific community at the intersection of crowdsourcing and Semantic Web technologies. We collect the position statements written by the participants of seminar, which played a central role in the discussions about the evolution of our research field.

The Semantic Web – ISWC 2014

We present the Dutch Ships and Sailors Linked Data Cloud. This heterogeneous dataset brings together four curated datasets on Dutch Maritime history as five-star linked data. The individual datasets use separate datamodels, designed in close collaboration with maritime historical researchers. The individual models are mapped to a common interoperability layer, allowing for analysis of the data on the general level. We present the datasets, modeling decisions, internal links and links to external data sources. We show ways of accessing the data and present a number of examples of how the dataset can be used for historical research. The Dutch Ships and Sailors Linked Data Cloud is a potential hub dataset for digital history research and a prime example of the benefits of Linked Data for this field.