Dependence relationships between Gene Ontology terms based on TIGR gene product annotations

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use statistical methods and formal ontological principles as a first step towards finding answers to this question

Using the Pattern-of-Life in Networks to Improve the Effectiveness of Intrusion Detection Systems

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.As the complexity of cyber-attacks keeps increasing, new and more robust detection mechanisms need to be developed. The next generation of Intrusion Detection Systems (IDSs) should be able to adapt their detection characteristics based not only on the measureable network traffic, but also on the available high- level information related to the protected network to improve their detection results. We make use of the Pattern-of-Life (PoL) of a network as the main source of high-level information, which is correlated with the time of the day and the usage of the network resources. We propose the use of a Fuzzy Cognitive Map (FCM) to incorporate the PoL into the detection process. The main aim of this work is to evidence the improved the detection performance of an IDS using an FCM to leverage on network related contextual information. The results that we present verify that the proposed method improves the effectiveness of our IDS by reducing the total number of false alarms; providing an improvement of 9.68% when all the considered metrics are combined and a peak improvement of up to 35.64%, depending on particular metric combination

Semantic Description, Publication and Discovery of Workflows in myGrid

The bioinformatics scientific process relies on in silico experiments, which are experiments executed in full in a computational environment. Scientists wish to encode the designs of these experiments as workflows because they provide minimal, declarative descriptions of the designs, overcoming many barriers to the sharing and re-use of these designs between scientists and enable the use of the most appropriate services available at any one time. We anticipate that the number of workflows will increase quickly as more scientists begin to make use of existing workflow construction tools to express their experiment designs. Discovery then becomes an increasingly hard problem, as it becomes more difficult for a scientist to identify the workflows relevant to their particular research goals amongst all those on offer. While many approaches exist for the publishing and discovery of services, there have been few attempts to address where and how authors of experimental designs should advertise the availability of their work or how relevant workflows can be discovered with minimal effort from the user. As the users designing and adapting experiments will not necessarily have a computer science background, we also have to consider how publishing and discovery can be achieved in such a way that they are not required to have detailed technical knowledge of workflow scripting languages. Furthermore, we believe they should be able to make use of others' expert knowledge (the semantics) of the given scientific domain. In this paper, we define the issues related to the semantic description, publishing and discovery of workflows, and demonstrate how the architecture created by the myGrid project aids scientists in this process. We give a walk-through of how users can construct, publish, annotate, discover and enact workflows via the user interfaces of the myGrid architecture; we then describe novel middleware protocols, making use of the Semantic Web technologies RDF and OWL to support workflow publishing and discovery

A Framework for Reference Management in the Semantic Web

Much of the semantic web relies upon open and unhindered interoperability between diverse systems. The successful convergence of multiple ontologies and referencing schemes is key. This is hampered by a lack of any means for managing and communicating co-references. We have therefore developed an ontology and framework for the exploration and resolution of potential co-references, in the semantic web at large, that allow the user to a) discover and record uniquely identifying attributes b) interface candidates with and create pipelines of other systems for reference management c) record identified duplicates in a usable and retrievable manner, and d) provide a consistent reference service for accessing them. This paper describes this ontology and a framework of web services designed to support and utilise it

Knowledge Rich Natural Language Queries over Structured Biological Databases

Increasingly, keyword, natural language and NoSQL queries are being used for information retrieval from traditional as well as non-traditional databases such as web, document, image, GIS, legal, and health databases. While their popularity are undeniable for obvious reasons, their engineering is far from simple. In most part, semantics and intent preserving mapping of a well understood natural language query expressed over a structured database schema to a structured query language is still a difficult task, and research to tame the complexity is intense. In this paper, we propose a multi-level knowledge-based middleware to facilitate such mappings that separate the conceptual level from the physical level. We augment these multi-level abstractions with a concept reasoner and a query strategy engine to dynamically link arbitrary natural language querying to well defined structured queries. We demonstrate the feasibility of our approach by presenting a Datalog based prototype system, called BioSmart, that can compute responses to arbitrary natural language queries over arbitrary databases once a syntactic classification of the natural language query is made

Toward an efficient ontology-based event correlation in SIEM

Cooperative intrusion detection use several intrusion detection systems (IDS) and analyzers in order to build a reliable overview of the monitored system trough a central security information and event management system (SIEM). In such environment, the definition of a shared vocabulary describing the exchanged information between tools is prominent. Since these pieces of information are structured, we propose in this paper to use an ontological representation based on Description Logics (DLs) which is a powerful tool for knowledge representation. Moreover, DLs are able to ensure a decidable reasoning. An alert correlation prototype is presented using this ontology, and an illustrative attack scenario is carried out to show the usefulness of the proposed ontolog