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Measures of semantic similarity between concepts are widely used in Natural Language Processing. In this article, we show how six existing domain-independent measures can be adapted to the biomedical domain. These measures were originally based on WordNet, an English lexical database of concepts and relations. In this research, we adapt these measures to(More)
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF,(More)
We aim to build and evaluate an open-source natural language processing system for information extraction from electronic medical record clinical free-text. We describe and evaluate our system, the clinical Text Analysis and Knowledge Extraction System (cTAKES), released open-source at http://www.ohnlp.org. The cTAKES builds on existing open-source(More)
OBJECTIVE To define the characteristics of serum prostate-specific antigen (PSA) in a population of healthy men without clinically evident prostate cancer, but who are at risk for developing the malignancy. The influence of patient age and prostatic size on the serum PSA concentration was assessed in order to use PSA more appropriately to detect clinically(More)
BACKGROUND The strong correlation between national consumption of fat and national rate of mortality from prostate cancer has raised the hypothesis that dietary fat increases the risk of this malignancy. Case-control and cohort studies have not consistently supported this hypothesis. PURPOSE We examined prospectively the relationship between prostate(More)
A unified model for text categorization and text retrieval is introduced. We use a training set of manually categorized documents to learn word-category associations, and use these associations to predict the categories of arbitrary documents. Similarly, we use a training set of queries and their related documents to obtain empirical associations between(More)
A total of 10 SULT genes are presently known to be expressed in human tissues. We performed a comprehensive genome-wide search for novel SULT genes using two different but complementary approaches, and developed a novel graphical display to aid in the annotation of the hits. Seven novel human SULT genes were identified, five of which were predicted to be(More)
Semantic interoperability among terminologies, data elements, and information models is fundamental and critical for sharing information from the scientific bench to the clinical bedside and back among systems. To meet this need, the vision for CDISC is to build a global, accessible electronic library, which enables precise and standardized data element(More)
To establish the age-specific prevalence of urinary symptoms among a community-based cohort of men, a randomly selected sample of men were screened and invited to participate in a longitudinal survey of urinary symptoms. The population of Olmsted County, Minnesota, as enumerated by the Rochester Epidemiology Project, formed the sampling base for this study.(More)
Recent epidemiologic evidence indicates an association between fat distribution and many diseases. To assess the validity of circumference measurements obtained by self-report, the authors analyzed data from 123 men aged 40-75 years and 140 women aged 41-65 years, drawn from two large ongoing prospective studies. On mailed questionnaires, subjects were(More)