Machine-assisted Cyber Threat Analysis using Conceptual Knowledge Discovery

Over the last years, computer networks have evolved into highly dynamic and interconnected environments, involving multiple heterogeneous devices and providing a myriad of services on top of them. This complex landscape has made it extremely difficult for security administrators to keep accurate and be effective in protecting their systems against cyber threats. In this paper, we describe our vision and scientific posture on how artificial intelligence techniques and a smart use of security knowledge may assist system administrators in better defending their networks. To that end, we put forward a research roadmap involving three complimentary axes, namely, (I) the use of FCA-based mechanisms for managing configuration vulnerabilities, (II) the exploitation of knowledge representation techniques for automated security reasoning, and (III) the design of a cyber threat intelligence mechanism as a CKDD process. Then, we describe a machine-assisted process for cyber threat analysis which provides a holistic perspective of how these three research axes are integrated together

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists’ toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. Results We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy’s capability for enriching, modifying and querying biomedical ontologies. Conclusions Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses

Research Objects: Towards Exchange and Reuse of Digital Knowledge

What will researchers be publishing in the future? Whilst there is little question that the Web will be the publication platform, as scholars move away from paper towards digital content, there is a need for mechanisms that support the production of self-contained units of knowledge and facilitate the publication, sharing and reuse of such entities.

 In this paper we discuss the notion of _research objects_, semantically rich aggregations of resources, that can possess some scientific intent or support some research objective. We present a number of principles that we expect such objects and their associated services to follow

Assessing and refining mappings to RDF to improve dataset quality

RDF dataset quality assessment is currently performed primarily after data is published. However, there is neither a systematic way to incorporate its results into the dataset nor the assessment into the publishing workflow. Adjustments are manually -but rarely- applied. Nevertheless, the root of the violations which often derive from the mappings that specify how the RDF dataset will be generated, is not identified. We suggest an incremental, iterative and uniform validation workflow for RDF datasets stemming originally from (semi-) structured data (e.g., CSV, XML, JSON). In this work, we focus on assessing and improving their mappings. We incorporate (i) a test-driven approach for assessing the mappings instead of the RDF dataset itself, as mappings reflect how the dataset will be formed when generated; and (ii) perform semi-automatic mapping refinements based on the results of the quality assessment. The proposed workflow is applied to diverse cases, e.g., large, crowdsourced datasets such as DBpedia, or newly generated, such as iLastic. Our evaluation indicates the efficiency of our workflow, as it significantly improves the overall quality of an RDF dataset in the observed cases

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: NL

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: N

Ontology-based knowledge representation of experiment metadata in biological data mining

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes

Research Objects: Towards Exchange and Reuse of Digital Knowledge

What will researchers be publishing in the future? Whilst there is little question that the Web will be the publication platform, as scholars move away from paper towards digital content, there is a need for mechanisms that support the production of self-contained units of knowledge and facilitate the publication, sharing and reuse of such entities. In this paper we discuss the notion of research objects, semantically rich aggregations of resources, that possess some scientifi?c intent or support some research objective. We present a number of principles that we expect such objects and their associated services to follow

AGROVOC: The linked data concept hub for food and agriculture

Newly acquired, aggregated and shared data are essential for innovation in food and agriculture to improve the discoverability of research. Since the early 1980′s, the Food and Agriculture Organization of the United Nations (FAO) has coordinated AGROVOC, a valuable tool for data to be classified homogeneously, facilitating interoperability and reuse. AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its highest impact is through facilitating the access and visibility of data across domains and languages. This chapter has the aim of describing the current status of one of the most popular thesaurus in all FAO’s areas of interest, and how it has become the Linked Data Concept Hub for food and agriculture, through new procedures put in plac