1,720,988 research outputs found
A Unified Medical Language System (UMLS) based system for Literature-Based Discovery in medicine.
No full textLiterature-Based Discovery (LBD) is a technique that can be used in translational research to connect the very sparse and huge information available in scientific publications in order to extract new knowledge. This paper presents an LBD system based on the open discovery paradigm exploiting NLP techniques and UMLS medical concepts mapping, to provide a set of tools useful to discover unknown relationships. The system has been evaluated on the problem of discovering new candidate genes potentially related to dilated cardiomyopathies (DCM), and can be used in any medical context to connect different type of concepts. The validation of the system involves reproducing the discovery of genes currently associated to DCM. Validation showed that the system is able to discover many gene-disease associations by using the literature available before their first publication in a scientific article
Methods in biomedical informatics
No full textSeeking to cross the bridge among overview, theory, and practice, this book incorporates both methodological approaches and their potential application in the domains associated with biomedical informatics.The multi-contributor book is useful for (1) those coming from a domain seeking biomedical informatics approaches for addressing specific needs; and, (2) current biomedical informaticians seeking a foundational background for methods that might be utilized in practical scenarios germane to their ongoing research.A unique characteristic of the text is its balance between foundational coverage of core topics in biomedical informatics with practical "in-the-trenches" scenarios. Contributors represent leading experts from the biomedical informatics field: individuals who have demonstrated effective use of methodology in real-world, high-quality data applications. Contains appendices that function as primers on: (1) Unix; (2) Ruby; (3) Databases; and (4) Web Services.-
Towards Literature-Based Biomarker Discovery: an Analysis of Pubmed Abstracts on Diabetic Retinopathy
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Text Mining approaches for automated literature knowledge extraction and representation.
No full textDue to the overwhelming volume of published scientific papers, information tools for automated literature analysis are essential to support current biomedical research. We have developed a knowledge extraction tool to help researcher in discovering useful information which can support their reasoning process. The tool is composed of a search engine based on Text Mining and Natural Language Processing techniques, and an analysis module which process the search results in order to build annotation similarity networks. We tested our approach on the available knowledge about the genetic mechanism of cardiac diseases, where the target is to find both known and possible hypothetical relations between specific candidate genes and the trait of interest. We show that the system i) is able to effectively retrieve medical concepts and genes and ii) plays a relevant role assisting researchers in the formulation and evaluation of novel literature-based hypotheses
A Semantic Collaborative System for the Management of Translational Research Projects
No full textTranslational research projects aim at combining -omics, structural and functional studies with clinical investigation results to translate basic knowledge of genetic diseases into routine clinical practice. Biomedical informatics can fruitfully support this kind of research by implementing information technology solutions to support the multidisciplinary project team in the different phases of its investigation.
In this paper we present a semantic wiki-based system purposely implemented for supporting the consortium members of the EU project Inheritance in sharing and disseminating data and knowledge about genetic dilated cardiomyopathies (DCM) [Ahamad et al., 2005]. It consists of a collaborative system that is used to track project activities, share ideas and data, foster exchange of information between the investigators to support several activities of the INHERITANCE translational research project. Moreover, it can be used to easily manage the scientific research products by adding semantic tags on the basis of the underlying knowledge model. A Natural Language Processing (NLP) based module has been developed to this aim; it extracts the relevant molecular and medical concepts from the scientific material shared by the project team and store them as RDF form by enabling the semantic querying of data
Extracting Diagnoses and Drug-Abuse Patterns from Italian Clinical Reports of Patients with Headache Disorders
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