RESUMO
SUMMARY: Progress in high-throughput genomic technologies has led to the development of a variety of resources that link genes to functional information contained in the biomedical literature. However, tools attempting to link small molecules to normal and diseased physiology and published data relevant to biologists and clinical investigators, are still lacking. With metabolomics rapidly emerging as a new omics field, the task of annotating small molecule metabolites becomes highly relevant. Our tool Metab2MeSH uses a statistical approach to reliably and automatically annotate compounds with concepts defined in Medical Subject Headings, and the National Library of Medicine's controlled vocabulary for biomedical concepts. These annotations provide links from compounds to biomedical literature and complement existing resources such as PubChem and the Human Metabolome Database.
Assuntos
Medical Subject Headings , Metabolômica , Bases de Dados de Compostos Químicos , Bases de Dados Genéticas , Humanos , Neoplasias/metabolismo , Vocabulário ControladoRESUMO
The biomedical research community relies on a diverse set of resources, both within their own institutions and at other research centers. In addition, an increasing number of shared electronic resources have been developed. Without effective means to locate and query these resources, it is challenging, if not impossible, for investigators to be aware of the myriad resources available, or to effectively perform resource discovery when the need arises. In this paper, we describe the development and use of the Biomedical Resource Ontology (BRO) to enable semantic annotation and discovery of biomedical resources. We also describe the Resource Discovery System (RDS) which is a federated, inter-institutional pilot project that uses the BRO to facilitate resource discovery on the Internet. Through the RDS framework and its associated Biositemaps infrastructure, the BRO facilitates semantic search and discovery of biomedical resources, breaking down barriers and streamlining scientific research that will improve human health.
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Pesquisa Biomédica , Sistemas de Gerenciamento de Base de Dados , Documentação , Informática Médica , Pesquisa Translacional Biomédica , Animais , Biologia Computacional , Humanos , Internet , Semântica , Interface Usuário-ComputadorRESUMO
The synthesis of cyclic alkenyl boronic half acids from vinyl and propenyl boronic esters and homoallylic alcohols by ring-closing metathesis is reported. The method is compatible with both conventional and microwave heating and comparable yields are obtained under both conditions. The cyclic alkenyl boronic acids participate in Suzuki-Miyaura coupling reactions in good yields.
Assuntos
Álcoois/química , Álcoois/síntese química , Ácidos Borônicos/química , Ácidos Borônicos/síntese química , Ésteres/química , Ciclização , Micro-Ondas , Estrutura Molecular , EstereoisomerismoRESUMO
Molecular interaction data exists in a number of repositories, each with its own data format, molecule identifier and information coverage. Michigan molecular interactions (MiMI) assists scientists searching through this profusion of molecular interaction data. The original release of MiMI gathered data from well-known protein interaction databases, and deep merged this information while keeping track of provenance. Based on the feedback received from users, MiMI has been completely redesigned. This article describes the resulting MiMI Release 2 (MiMIr2). New functionality includes extension from proteins to genes and to pathways; identification of highlighted sentences in source publications; seamless two-way linkage with Cytoscape; query facilities based on MeSH/GO terms and other concepts; approximate graph matching to find relevant pathways; support for querying in bulk; and a user focus-group driven interface design. MiMI is part of the NIH's; National Center for Integrative Biomedical Informatics (NCIBI) and is publicly available at: http://mimi.ncibi.org.