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Published literature in molecular genetics may collectively provide much information on gene regulation networks. Dedicated computational approaches are required to sip through large volumes of text and infer gene interactions. We propose a novel sieve-based relation extraction system that uses linear-chain conditional random fields and rules. Also, we(More)
BACKGROUND Interleukin (IL)-15 is an important mediator in chronic inflammatory diseases. Recently, we have described the association of IL-15 haplotypes with bronchial asthma. Asthma genetics is highly complex - about every second candidate gene is not confirmed in consecutive studies. We were interested in whether association of asthma with IL-15 holds in(More)
The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the availability of a large, manually annotated text corpus is desirable. Furthermore, large corpora permit the robust evaluation and comparison of(More)
Received (received date) Revised (revised date) Accepted (day month year) Communicated by (xxxxxxxxxx) Large software projects are among most sophisticated human-made systems consisting of a network of interdependent parts. Past studies of software systems from the perspective of complex networks have already led to notable discoveries with different(More)
The basic indicators of a researcher's productivity and impact are still the number of publications and their citation counts. These metrics are clear, straightforward, and easy to obtain. When a ranking of scholars is needed, for instance in grant, award, or promotion procedures, their use is the fastest and cheapest way of prioritizing some scientists(More)
Traditional information extraction (IE) tasks roughly consist of named-entity recognition, relation extraction and coreference resolution. Much work in this area focuses primarily on separate subtasks where best performance can be achieved only on specialized domains. In this paper we present a collective IE approach combining all three tasks by employing(More)
The amount of chemical information is rapidly growing in the scientific literature and all other sorts of free text documents. We here propose a novel system that uses different types of linear-chain conditional random fields models and combines their results using a support vector machine classifier. We introduce the constituent-based models, which are in(More)
Coreference resolution tries to identify all expressions (called mentions) in observed text that refer to the same entity. Beside entity extraction and relation extraction, it represents one of the three complementary tasks in Information Extraction. In this paper we describe a novel coreference resolution system SkipCor that reformulates the problem as a(More)
Due to numerous public information sources and services, many methods to combine heterogeneous data were proposed recently. However, general end-to-end solutions are still rare, especially systems taking into account different context dimensions. Therefore, the techniques often prove insufficient or are limited to a certain domain. In this paper we briefly(More)
Relational database to ontology mapping and ontology matching techniques are mostly addressed separately, even though it is known that the real power of semantic data lies in data interconnection. The latter is especially important when designing a new ontology, which often includes at least some of the concepts that already exist in the linked open data(More)