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We present BITOLA, an interactive literature-based biomedical discovery support system. The goal of this system is to discover new, potentially meaningful relations between a given starting concept of interest and other concepts, by mining the bibliographic database MEDLINE. To make the system more suitable for disease candidate gene discovery and to(More)
OBJECTIVES Terminology and knowledge resources are essential components of interoperability among disparate systems. This paper evaluates whether names and relationships needed in biomedical informatics are present in the UMLS. METHODS Terms for five broad categories of concepts were extracted from LocusLink and mapped to the UMLS Metathesausus.(More)
One of the most important objects in bioinformatics is a gene product (protein or RNA). For many gene products, functional information is summarized in a set of Gene Ontology (GO) annotations. For these genes, it is reasonable to include similarity measures based on the terms found in the GO or other taxonomy. In this paper, we introduce several novel(More)
OBJECTIVES While several sources of biomedical knowledge are available, these resources are often highly specialized and usually not suitable for a lay audience. This paper evaluates whether concepts needed for molecular biology and genetic diseases are present in WordNet, the electronic lexical database. METHODS Terms for four broad categories of(More)
The authors have developed the Genetics Home Reference, a consumer resource that addresses the health implications of the Human Genome Project. The research results made possible by the Human Genome Project are being made available increasingly in scientific databases on the Internet, but, because of the often highly technical nature of these databases,(More)
The surge of information generated by the Human Genome Project has left many health professionals and their patients struggling to understand the role of genetics in health and disease. To aid the lay public and health professionals, the US National Library of Medicine developed an online resource called 'Genetics Home Reference' (GHR), located at(More)
We present an initial analysis of the National Library of Medicine's (NLM) Gene Indexing initiative. Gene Indexing occurs at the time of indexing for all 4600 journals and over 500,000 articles added to PubMed/MEDLINE each year. Gene Indexing links articles about the basic biology of a gene or protein within eight model organisms to a specific record in the(More)
We present an interactive literature based biomedical discovery support system (BITOLA). The goal of the system is to discover new, potentially meaningful relations between a given starting concept of interest and other concepts, by mining the bibliographic database Medline. To make the system more suitable for disease candidate gene discovery and to(More)
We present the BioMediator (www.biomediator.org) system and the process of executing queries on it. The system was designed as a tool for posing queries across semantically and syntactically heterogeneous data particularly in the biological arena. We use examples from researchers at the University of Washington, and the University of Missouri-Columbia, to(More)
BACKGROUND Selecting patient cohorts is a critical, iterative, and often time-consuming aspect of studies involving human subjects; informatics tools for helping streamline the process have been identified as important infrastructure components for enabling clinical and translational research. We describe the evaluation of a free and open source cohort(More)