共查询到20条相似文献,搜索用时 15 毫秒
1.
Thierry Lombardot Renzo Kottmann Gregory Giuliani Andrea de Bono Nans Addor Frank Oliver Glöckner 《BMC bioinformatics》2007,8(1):406
Background
Marine ecological genomics can be defined as the application of genomic sciences to understand the structure and function of marine ecosystems. In this field of research, the analysis of genomes and metagenomes of environmental relevance must take into account the corresponding habitat (contextual) data, e.g. water depth, physical and chemical parameters. The creation of specialised software tools and databases is requisite to allow this new kind of integrated analysis. 相似文献2.
Background
Biomedical ontologies are critical for integration of data from diverse sources and for use by knowledge-based biomedical applications, especially natural language processing as well as associated mining and reasoning systems. The effectiveness of these systems is heavily dependent on the quality of the ontological terms and their classifications. To assist in developing and maintaining the ontologies objectively, we propose automatic approaches to classify and/or validate their semantic categories. In previous work, we developed an approach using contextual syntactic features obtained from a large domain corpus to reclassify and validate concepts of the Unified Medical Language System (UMLS), a comprehensive resource of biomedical terminology. In this paper, we introduce another classification approach based on words of the concept strings and compare it to the contextual syntactic approach. 相似文献3.
Background
Providing for long-term and consistent public access to scientific data is a growing concern in biomedical research. One aspect of this problem can be demonstrated by evaluating the persistence of supplementary data associated with published biomedical papers. 相似文献4.
Background
With the growing amount of biomedical data available in public databases it has become increasingly important to annotate data in a consistent way in order to allow easy access to this rich source of information. Annotating the data using controlled vocabulary terms and ontologies makes it much easier to compare and analyze data from different sources. However, finding the correct controlled vocabulary terms can sometimes be a difficult task for the end user annotating these data. 相似文献5.
Catherine C Beauheim Farrell Wymore Michael Nitzberg Zachariah K Zachariah Heng Jin JH Pate Skene Catherine A Ball Gavin Sherlock 《BMC bioinformatics》2007,8(1):338
Background
Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. 相似文献6.
Background
The ferlin gene family possesses a rare and identifying feature consisting of multiple tandem C2 domains and a C-terminal transmembrane domain. Much currently remains unknown about the fundamental function of this gene family, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease. The availability of genome sequences from a wide range of species makes it possible to explore the evolution of the ferlin family, providing contextual insight into characteristic features that define the ferlin gene family in its present form in humans. 相似文献7.
Romain Bourqui Ludovic Cottret Vincent Lacroix David Auber Patrick Mary Marie-France Sagot Fabien Jourdan 《BMC systems biology》2007,1(1):29-19
Background
The tools that are available to draw and to manipulate the representations of metabolism are usually restricted to metabolic pathways. This limitation becomes problematic when studying processes that span several pathways. The various attempts that have been made to draw genome-scale metabolic networks are confronted with two shortcomings: 1- they do not use contextual information which leads to dense, hard to interpret drawings, 2- they impose to fit to very constrained standards, which implies, in particular, duplicating nodes making topological analysis considerably more difficult. 相似文献8.
9.
Background
Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. 相似文献10.
Background
Protein subcellular localization is an important determinant of protein function and hence, reliable methods for prediction of localization are needed. A number of prediction algorithms have been developed based on amino acid compositions or on the N-terminal characteristics (signal peptides) of proteins. However, such approaches lead to a loss of contextual information. Moreover, where information about the physicochemical properties of amino acids has been used, the methods employed to exploit that information are less than optimal and could use the information more effectively. 相似文献11.
12.
The provenance and biochemical roles of eukaryotic MORC proteins have remained poorly understood since the discovery of their prototype MORC1, which is required for meiotic nuclear division in animals. The MORC family contains a combination of a gyrase, histidine kinase, and MutL (GHKL) and S5 domains that together constitute a catalytically active ATPase module. We identify the prokaryotic MORCs and establish that the MORC family belongs to a larger radiation of several families of GHKL proteins (paraMORCs) in prokaryotes. Using contextual information from conserved gene neighborhoods we show that these proteins primarily function in restriction-modification systems, in conjunction with diverse superfamily II DNA helicases and endonucleases. The common ancestor of these GHKL proteins, MutL and topoisomerase ATPase modules appears to have catalyzed structural reorganization of protein complexes and concomitant DNA-superstructure manipulations along with fused or standalone nuclease domains. Furthermore, contextual associations of the prokaryotic MORCs and their relatives suggest that their eukaryotic counterparts are likely to carry out chromatin remodeling by DNA superstructure manipulation in response to epigenetic signals such as histone and DNA methylation. 相似文献
13.
Martijn P. G. Broen Vera A. M. Marsman Mark L. Kuijf Robert J. Van Oostenbrugge Jim van Os Albert F. G. Leentjens 《PloS one》2016,11(3)
Background
In Parkinson''s disease (PD), the complex relationship between motor symptoms, affective states, and contextual factors remains to be elucidated. The Experience Sampling Method provides (ESM) a novel approach to this issue. Using a mobile device with a special purpose application (app), motor symptoms, affective states and contextual factors are assessed repeatedly at random moments in the flow of daily life, yielding an intensive time series of symptoms and experience. The aim of this study was to study the feasibility of this method.Method
We studied the feasibility of a five-day period of ESM in PD and its ability to objectify diurnal fluctuations in motor symptom severity and their relation with affect and contextual factors in five PD patients with motor fluctuations.Results
Participants achieved a high compliance, with 84% of assessment moments completed without disturbance of daily activities. The utility of the device was rated 8 on a 10-point scale. We were able to capture extensive diurnal fluctuations that were not revealed by routine clinical assessment. In addition, we were able to detect clinically relevant associations between motor symptoms, emotional fluctuations and contextual factors at an intra-individual level.Conclusions
ESM represents a viable and novel approach to elucidate relationships between motor symptoms, affective states and contextual factors at the level of individual subjects. ESM holds promise for clinical practice and scientific research. 相似文献14.
An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development 总被引:1,自引:0,他引:1
Background
Accuracy in quantitative real-time RT-PCR is dependent on high quality RNA, consistent cDNA synthesis, and validated stable reference genes for data normalization. Reference genes used for normalization impact the results generated from expression studies and, hence, should be evaluated prior to use across samples and treatments. Few statistically validated reference genes have been reported in grapevine. Moreover, success in isolating high quality RNA from grapevine tissues is typically limiting due to low pH, and high polyphenolic and polysaccharide contents. 相似文献15.
Background
A central goal of Systems Biology is to model and analyze biological signaling pathways that interact with one another to form complex networks. Here we introduce Qualitative networks, an extension of Boolean networks. With this framework, we use formal verification methods to check whether a model is consistent with the laboratory experimental observations on which it is based. If the model does not conform to the data, we suggest a revised model and the new hypotheses are tested in-silico. 相似文献16.
Background
With the vast amounts of biomedical data being generated by high-throughput analysis methods, controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform controlled vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries. 相似文献17.
Background
Mass spectrometry has become a standard method by which the proteomic profile of cell or tissue samples is characterized. To fully take advantage of tandem mass spectrometry (MS/MS) techniques in large scale protein characterization studies robust and consistent data analysis procedures are crucial. In this work we present a machine learning based protocol for the identification of correct peptide-spectrum matches from Sequest database search results, improving on previously published protocols. 相似文献18.
19.
Background
Normalization of gene expression data refers to the comparison of expression values using reference standards that are consistent across all conditions of an experiment. In PCR studies, genes designated as "housekeeping genes" have been used as internal reference genes under the assumption that their expression is stable and independent of experimental conditions. However, verification of this assumption is rarely performed. Here we assess the use of gene microarray analysis to facilitate selection of internal reference sequences with higher expression stability across experimental conditions than can be expected using traditional selection methods. 相似文献20.
Cheryl B Stetler Judith A Ritchie Jo Rycroft-Malone Alyce A Schultz Martin P Charns 《Implementation science : IS》2009,4(1):1-19