MOTIVATION: A major component in increasing our understanding of the biology of an organism is the mapping of its genotypic potential into its phenotypic expression profiles. This mapping is executed by the machinery of gene regulation, which is esse...
Database : the journal of biological databases and curation
Jan 1, 2019
Knowledge of the molecular interactions of biological and chemical entities and their involvement in biological processes or clinical phenotypes is important for data interpretation. Unfortunately, this knowledge is mostly embedded in the literature ...
After years of development, the RadLex terminology contains a large set of controlled terms for the radiology domain, but gaps still exist. We developed a data-driven approach to discover new terms for RadLex by mining a large corpus of radiology rep...
Journal of the American Medical Informatics Association : JAMIA
Jul 1, 2018
OBJECTIVE: The goal of this work is to map Unified Medical Language System (UMLS) concepts to DBpedia resources using widely accepted ontology relations from the Simple Knowledge Organization System (skos:exactMatch, skos:closeMatch) and from the Res...
Journal of the American Medical Informatics Association : JAMIA
Jun 1, 2018
OBJECTIVE: Distributional semantics algorithms, which learn vector space representations of words and phrases from large corpora, identify related terms based on contextual usage patterns. We hypothesize that distributional semantics can speed up lex...
Studies in health technology and informatics
Jan 1, 2018
Current medical systems need to be able to communicate complex and detailed medical data securely and efficiently. However, the quantity of available healthcare data is rising rapidly, far exceeding the capacity to deliver personal or public health b...
MOTIVATION: The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with ea...
Studies in health technology and informatics
Jan 1, 2017
We developed an easy-to-use tool for non-technical biomedical researchers to conduct Named-Entity Recognition (NER) on biomedical text, in a familiar spreadsheet environment. The system is a simple, offline, easy to install, end-user front-end to the...
Studies in health technology and informatics
Jan 1, 2017
Concept mapping is important in natural language processing (NLP) for bioinformatics. The UMLS Metathesaurus provides a rich synonym thesaurus and is a popular resource for concept mapping. Query expansion using synonyms for subterm substitutions is ...
Studies in health technology and informatics
Jan 1, 2017
The SNIK project converts textbooks about information management in hospitals to a domain ontology that provides a shared vocabulary for institutions to model and integrate processes, data and infrastructure. To accommodate user groups with different...
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