Halil Kilicoglu

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An experiment was performed at the National Library of Medicine((R)) (NLM((R))) in word sense disambiguation (WSD) using the Journal Descriptor Indexing (JDI) methodology. The motivation is the need to solve the ambiguity problem confronting NLM's MetaMap system, which maps free text to terms corresponding to concepts in NLM's Unified Medical Language(More)
We explore a rule-based methodology for the BioNLP’09 Shared Task on Event Extraction, using dependency parsing as the underlying principle for extracting and characterizing events. We approach the speculation and negation detection task with the same principle. Evaluation results demonstrate the utility of this syntax-based approach and point out some(More)
Due to the nature of scientific methodology, research articles are rich in speculative and tentative statements, also known as hedges. We explore a linguistically motivated approach to the problem of recognizing such language in biomedical research articles. Our approach draws on prior linguistic work as well as existing lexical resources to create a(More)
SUMMARY Effective access to the vast biomedical knowledge present in the scientific literature is challenging. Semantic relations are increasingly used in knowledge management applications supporting biomedical research to help address this challenge. We describe SemMedDB, a repository of semantic predications (subject-predicate-object triples) extracted(More)
The second BioNLP Shared Task on Event Extraction (BioNLP-ST’11) follows up the previous shared task competition with a focus on generalization with respect to text types, event types and subject domains. In this spirit, we re-engineered and extended our event extraction system, emphasizing linguistic generalizations and avoiding domain-, event typeor text(More)
To support more effective biomedical information management, Semantic MEDLINE integrates document retrieval, advanced natural language processing, automatic summarization and visualization into a single Web portal. The application is intended to help manage the results of PubMed searches by condensing core semantic content in the citations retrieved. Output(More)
Considerable research is being directed at extracting molecular biology information from text. Particularly challenging in this regard is to identify relations between entities, such as protein-protein interactions or molecular pathways. In this paper we present a natural language processing method for extracting causal relations between genetic phenomena(More)
The growing numbers of topically relevant biomedical publications readily available due to advances in document retrieval methods pose a challenge to clinicians practicing evidence-based medicine. It is increasingly time consuming to acquire and critically appraise the available evidence. This problem could be addressed in part if methods were available to(More)
Drug therapies are often used effectively without their underlying mechanism being completely understood. We exploit the literature-based discovery paradigm to investigate these mechanisms and propose a discovery pattern that draws on semantic predications extracted from MEDLINE citations. The use of semantic predications and the discovery pattern provides(More)