Improving Ontology Recommendation and Reuse in WebCORE by Collaborative Assessments

In this work, we present an extension of CORE [8], a tool for Collaborative Ontology Reuse and Evaluation. The system receives an informal description of a specific semantic domain and determines which ontologies from a repository are the most appropriate to describe the given domain. For this task, the environment is divided into three modules. The first component receives the problem description as a set of terms, and allows the user to refine and enlarge it using WordNet. The second module applies multiple automatic criteria to evaluate the ontologies of the repository, and determines which ones fit best the problem description. A ranked list of ontologies is returned for each criterion, and the lists are combined by means of rank fusion techniques. Finally, the third component uses manual user evaluations in order to incorporate a human, collaborative assessment of the ontologies. The new version of the system incorporates several novelties, such as its implementation as a web application; the incorporation of a NLP module to manage the problem definitions; modifications on the automatic ontology retrieval strategies; and a collaborative framework to find potential relevant terms according to previous user queries. Finally, we present some early experiments on ontology retrieval and evaluation, showing the benefits of our system

A community based approach for managing ontology alignments

The Semantic Web is rapidly becoming a defacto distributed repository for semantically represented data, thus leveraging on the added on value of the network effect. Various ontology mapping techniques and tools have been devised to facilitate the bridging and integration of distributed data repositories. Nevertheless, ontology mapping can benefitfrom human supervision to increase accuracy of results. The spread of Web 2.0 approaches demonstrate the possibility of using collaborative techniques for reaching consensus. While a number of prototypes for collaborative ontology construction are being developed, collaborative ontology mapping is not yet well investigated. In this paper, we describe a prototype that combines off-the-shelf ontology mapping tools with social software techniques to enable users to collaborate on mapping ontologies

Towards Exascale Scientific Metadata Management

Advances in technology and computing hardware are enabling scientists from all areas of science to produce massive amounts of data using large-scale simulations or observational facilities. In this era of data deluge, effective coordination between the data production and the analysis phases hinges on the availability of metadata that describe the scientific datasets. Existing workflow engines have been capturing a limited form of metadata to provide provenance information about the identity and lineage of the data. However, much of the data produced by simulations, experiments, and analyses still need to be annotated manually in an ad hoc manner by domain scientists. Systematic and transparent acquisition of rich metadata becomes a crucial prerequisite to sustain and accelerate the pace of scientific innovation. Yet, ubiquitous and domain-agnostic metadata management infrastructure that can meet the demands of extreme-scale science is notable by its absence. To address this gap in scientific data management research and practice, we present our vision for an integrated approach that (1) automatically captures and manipulates information-rich metadata while the data is being produced or analyzed and (2) stores metadata within each dataset to permeate metadata-oblivious processes and to query metadata through established and standardized data access interfaces. We motivate the need for the proposed integrated approach using applications from plasma physics, climate modeling and neuroscience, and then discuss research challenges and possible solutions

Developing Knowledge Models of Social Media: A Case Study on LinkedIn

User Generated Content (UGC) exchanged via large Social Network is considered a very important knowledge source about all aspects of the social engagements (e.g. interests, events, personal information, personal preferences, social experience, skills etc.). However this data is inherently unstructured or semi-structured. In this paper, we describe the results of a case study on LinkedIn Ireland public profiles. The study investigated how the available knowledge could be harvested from LinkedIn in a novel way by developing and applying a reusable knowledge model using linked open data vocabularies and semantic web. In addition, the paper discusses the crawling and data normalisation strategies that we developed, so that high quality metadata could be extracted from the LinkedIn public profiles. Apart from the search engine in LinkedIn.com itself, there are no well known publicly available endpoints that allow users to query knowledge concerning the interests of individuals on LinkedIn. In particular, we present a system that extracts and converts information from raw web pages of LinkedIn public profiles into a machine-readable, interoperable format using data mining and Semantic Web technologies. The outcomes of our research can be summarized as follows: (1) A reusable knowledge model which can represent LinkedIn public users and company profiles using linked data vocabularies and structured data, (2) a public SPARQL endpoint to access structured data about Irish industry and public profiles, (3) a scalable data crawling strategy and mashup based data normalisation approach. The proposed data mining and knowledge representation proposed in this paper are evaluated in four ways: (1) We evaluate metadata quality using automated techniques, such as data completeness and data linkage. (2) Data accuracy is evaluated via user studies. In particular, accuracy is evaluated by comparison of manually entered metadata fields and the metadata which was automatically extracted. (3) User perceived metadata quality is measured by asking users to rate the automatically extracted metadata in user studies. (4) Finally, the paper discusses how the extracted metadata suits for a user interface design. Overall, the evaluations show that the extracted metadata is of high quality and meets the requirements of a data visualisation user interface

Design and implementation of a filter engine for semantic web documents

This report describes our project that addresses the challenge of changes in the semantic web. Some studies have already been done for the so-called adaptive semantic web, such as applying inferring rules. In this study, we apply the technology of Event Notification System (ENS). Treating changes as events, we developed a notification system for such events

DRIVER Technology Watch Report

This report is part of the Discovery Workpackage (WP4) and is the third report out of four deliverables. The objective of this report is to give an overview of the latest technical developments in the world of digital repositories, digital libraries and beyond, in order to serve as theoretical and practical input for the technical DRIVER developments, especially those focused on enhanced publications. This report consists of two main parts, one part focuses on interoperability standards for enhanced publications, the other part consists of three subchapters, which give a landscape picture of current and surfacing technologies and communities crucial to DRIVER. These three subchapters contain the GRID, CRIS and LTP communities and technologies. Every chapter contains a theoretical explanation, followed by case studies and the outcomes and opportunities for DRIVER in this field

Validation and Evaluation

In this technical report, we present prototypical implementations of innovative tools and methods for personalized and contextualized (multimedia) search, collaborative ontology evolution, ontology evaluation and cost models, and dynamic access and trends in distributed (semantic) knowledge, developed according to the working plan outlined in Technical Report TR-B-12-04. The prototypes complete the next milestone on the path to an integral Corporate Semantic Web architecture based on the three pillars Corporate Ontology Engineering, Corporate Semantic Collaboration, and Corporate Semantic Search, as envisioned in TR-B-08-09

Developing Predictive Molecular Maps of Human Disease through Community-based Modeling

The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics

A rapid prototyping/artificial intelligence approach to space station-era information management and access

Applications of rapid prototyping and Artificial Intelligence techniques to problems associated with Space Station-era information management systems are described. In particular, the work is centered on issues related to: (1) intelligent man-machine interfaces applied to scientific data user support, and (2) the requirement that intelligent information management systems (IIMS) be able to efficiently process metadata updates concerning types of data handled. The advanced IIMS represents functional capabilities driven almost entirely by the needs of potential users. Space Station-era scientific data projected to be generated is likely to be significantly greater than data currently processed and analyzed. Information about scientific data must be presented clearly, concisely, and with support features to allow users at all levels of expertise efficient and cost-effective data access. Additionally, mechanisms for allowing more efficient IIMS metadata update processes must be addressed. The work reported covers the following IIMS design aspects: IIMS data and metadata modeling, including the automatic updating of IIMS-contained metadata, IIMS user-system interface considerations, including significant problems associated with remote access, user profiles, and on-line tutorial capabilities, and development of an IIMS query and browse facility, including the capability to deal with spatial information. A working prototype has been developed and is being enhanced

BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing (HPC) techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems (SWfMS) and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process