An information retrieval approach to ontology mapping

In this paper, we present a heuristic mapping method and a prototype mapping system that support the process of semi-automatic ontology mapping for the purpose of improving semantic interoperability in heterogeneous systems. The approach is based on the idea of semantic enrichment, i.e., using instance information of the ontology to enrich the original ontology and calculate similarities between concepts in two ontologies. The functional settings for the mapping system are discussed and the evaluation of the prototype implementation of the approach is reported. \ud \u

FAIRE-seq data analysis of Chlamydomonas reinhardtii under carbon deprivation

For the genome-wide identification of nucleosome depleted regions under carbon deprivation, we analyze an available set of data from an assay of formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq). Mapping to the sequenced nuclear genome of C.reinhardtii, followed by the identification of the enrichment-sequenced fragments was performed. We examined the location of these fragments relative to annotated genes. The related genes were associated to the corresponding Gene-Ontology (GO), for an evaluation of over-representate GO categories. Some genes, link with functions or locations, that have been previous described, indicating the success of the method finding carbon-metabolism related fragments

Evaluating the semantic web: a task-based approach

The increased availability of online knowledge has led to the design of several algorithms that solve a variety of tasks by harvesting the Semantic Web, i.e. by dynamically selecting and exploring a multitude of online ontologies. Our hypothesis is that the performance of such novel algorithms implicity provides an insight into the quality of the used ontologies and thus opens the way to a task-based evaluation of the Semantic Web. We have investigated this hypothesis by studying the lessons learnt about online ontologies when used to solve three tasks: ontology matching, folksonomy enrichment, and word sense disambiguation. Our analysis leads to a suit of conclusions about the status of the Semantic Web, which highlight a number of strengths and weaknesses of the semantic information available online and complement the findings of other analysis of the Semantic Web landscape

Collaborative recommendations with content-based filters for cultural activities via a scalable event distribution platform

Nowadays, most people have limited leisure time and the offer of (cultural) activities to spend this time is enormous. Consequently, picking the most appropriate events becomes increasingly difficult for end-users. This complexity of choice reinforces the necessity of filtering systems that assist users in finding and selecting relevant events. Whereas traditional filtering tools enable e.g. the use of keyword-based or filtered searches, innovative recommender systems draw on user ratings, preferences, and metadata describing the events. Existing collaborative recommendation techniques, developed for suggesting web-shop products or audio-visual content, have difficulties with sparse rating data and can not cope at all with event-specific restrictions like availability, time, and location. Moreover, aggregating, enriching, and distributing these events are additional requisites for an optimal communication channel. In this paper, we propose a highly-scalable event recommendation platform which considers event-specific characteristics. Personal suggestions are generated by an advanced collaborative filtering algorithm, which is more robust on sparse data by extending user profiles with presumable future consumptions. The events, which are described using an RDF/OWL representation of the EventsML-G2 standard, are categorized and enriched via smart indexing and open linked data sets. This metadata model enables additional content-based filters, which consider event-specific characteristics, on the recommendation list. The integration of these different functionalities is realized by a scalable and extendable bus architecture. Finally, focus group conversations were organized with external experts, cultural mediators, and potential end-users to evaluate the event distribution platform and investigate the possible added value of recommendations for cultural participation

Using association rule mining to enrich semantic concepts for video retrieval

In order to achieve true content-based information retrieval on video we should analyse and index video with high-level semantic concepts in addition to using user-generated tags and structured metadata like title, date, etc. However the range of such high-level semantic concepts, detected either manually or automatically, usually limited compared to the richness of information content in video and the potential vocabulary of available concepts for indexing. Even though there is work to improve the performance of individual concept classifiers, we should strive to make the best use of whatever partial sets of semantic concept occurrences are available to us. We describe in this paper our method for using association rule mining to automatically enrich the representation of video content through a set of semantic concepts based on concept co-occurrence patterns. We describe our experiments on the TRECVid 2005 video corpus annotated with the 449 concepts of the LSCOM ontology. The evaluation of our results shows the usefulness of our approach

Ontology Enrichment from Free-text Clinical Documents: A Comparison of Alternative Approaches

While the biomedical informatics community widely acknowledges the utility of domain ontologies, there remain many barriers to their effective use. One important requirement of domain ontologies is that they achieve a high degree of coverage of the domain concepts and concept relationships. However, the development of these ontologies is typically a manual, time-consuming, and often error-prone process. Limited resources result in missing concepts and relationships, as well as difficulty in updating the ontology as domain knowledge changes. Methodologies developed in the fields of Natural Language Processing (NLP), Information Extraction (IE), Information Retrieval (IR), and Machine Learning (ML) provide techniques for automating the enrichment of ontology from free-text documents. In this dissertation, I extended these methodologies into biomedical ontology development. First, I reviewed existing methodologies and systems developed in the fields of NLP, IR, and IE, and discussed how existing methods can benefit the development of biomedical ontologies. This previously unconducted review was published in the Journal of Biomedical Informatics. Second, I compared the effectiveness of three methods from two different approaches, the symbolic (the Hearst method) and the statistical (the Church and Lin methods), using clinical free-text documents. Third, I developed a methodological framework for Ontology Learning (OL) evaluation and comparison. This framework permits evaluation of the two types of OL approaches that include three OL methods. The significance of this work is as follows: 1) The results from the comparative study showed the potential of these methods for biomedical ontology enrichment. For the two targeted domains (NCIT and RadLex), the Hearst method revealed an average of 21% and 11% new concept acceptance rates, respectively. The Lin method produced a 74% acceptance rate for NCIT; the Church method, 53%. As a result of this study (published in the Journal of Methods of Information in Medicine), many suggested candidates have been incorporated into the NCIT; 2) The evaluation framework is flexible and general enough that it can analyze the performance of ontology enrichment methods for many domains, thus expediting the process of automation and minimizing the likelihood that key concepts and relationships would be missed as domain knowledge evolves

Expanding sensor networks to automate knowledge acquisition

The availability of accurate, low-cost sensors to scientists has resulted in widespread deployment in a variety of sporting and health environments. The sensor data output is often in a raw, proprietary or unstructured format. As a result, it is often difficult to query multiple sensors for complex properties or actions. In our research, we deploy a heterogeneous sensor network to detect the various biological and physiological properties in athletes during training activities. The goal for exercise physiologists is to quickly identify key intervals in exercise such as moments of stress or fatigue. This is not currently possible because of low level sensors and a lack of query language support. Thus, our motivation is to expand the sensor network with a contextual layer that enriches raw sensor data, so that it can be exploited by a high level query language. To achieve this, the domain expert specifies events in a tradiational event-condition-action format to deliver the required contextual enrichment