共查询到20条相似文献,搜索用时 15 毫秒
1.
Background
As protein interactions mediate most cellular mechanisms, protein-protein interaction networks are essential in the study of cellular processes. Consequently, several large-scale interactome mapping projects have been undertaken, and protein-protein interactions are being distilled into databases through literature curation; yet protein-protein interaction data are still far from comprehensive, even in the model organism Saccharomyces cerevisiae. Estimating the interactome size is important for evaluating the completeness of current datasets, in order to measure the remaining efforts that are required. 相似文献2.
Kimberly Van Auken Joshua Jaffery Juancarlos Chan Hans-Michael Müller Paul W Sternberg 《BMC bioinformatics》2009,10(1):228
Background
Manual curation of experimental data from the biomedical literature is an expensive and time-consuming endeavor. Nevertheless, most biological knowledge bases still rely heavily on manual curation for data extraction and entry. Text mining software that can semi- or fully automate information retrieval from the literature would thus provide a significant boost to manual curation efforts. 相似文献3.
Background
Brucellaspecies are Gram-negative, facultative intracellular bacteria that cause brucellosis in humans and animals. Sequences of fourBrucellagenomes have been published, and variousBrucellagene and genome data and analysis resources exist. A web gateway to integrate these resources will greatly facilitateBrucellaresearch.Brucellagenome data in current databases is largely derived from computational analysis without experimental validation typically found in peer-reviewed publications. It is partially due to the lack of a literature mining and curation system able to efficiently incorporate the large amount of literature data into genome annotation. It is further hypothesized that literature-basedBrucellagene annotation would increase understanding of complicatedBrucellapathogenesis mechanisms. 相似文献4.
Background
The architectural structure of cellular networks provides a framework for innovations as well as constraints for protein evolution. This issue has previously been studied extensively by analyzing protein interaction networks. However, it is unclear how signaling networks influence and constrain protein evolution and conversely, how protein evolution modifies and shapes the functional consequences of signaling networks. In this study, we constructed a human signaling network containing more than 1,600 nodes and 5,000 links through manual curation of signaling pathways, and analyzed the d N/d S values of human-mouse orthologues on the network. 相似文献5.
Ganesh A Viswanathan German Nudelman Sonali Patil Stuart C Sealfon 《BMC bioinformatics》2007,8(1):168
Background
Cellular processes depend on the function of intracellular molecular networks. The curation of the literature relevant to specific biological pathways is important for many theoretical and experimental research teams and communities. No current tool supports web publication or hosting of user-developed large scale annotated pathway diagrams. Sharing via web publication is needed to allow real-time access to the current literature pathway knowledgebase, both privately within a research team or publicly among the outside research community. Web publication also facilitates team and/or community input into the curation process while allowing centralized control of the curation and validation process. We have developed new tool to address these needs. Biological Pathway Publisher (BioPP) is a software suite for converting CellDesigner Systems Biology Markup Language (CD-SBML) formatted pathways into a web viewable format. The BioPP suite is available for private use and for depositing knowledgebases into a newly created public repository. 相似文献6.
Background
The construction of interaction networks between proteins is central to understanding the underlying biological processes. However, since many useful relations are excluded in databases and remain hidden in raw text, a study on automatic interaction extraction from text is important in bioinformatics field. 相似文献7.
8.
Background
The elucidation of whole-cell regulatory, metabolic, interaction and other biological networks generates the need for a meaningful ranking of network elements. Centrality analysis ranks network elements according to their importance within the network structure and different centrality measures focus on different importance concepts. Central elements of biological networks have been found to be, for example, essential for viability. 相似文献9.
Cyrille Lepoivre Aurélie Bergon Fabrice Lopez Narayanan B Perumal Catherine Nguyen Jean Imbert Denis Puthier 《BMC bioinformatics》2012,13(1):19
Background
Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph. 相似文献10.
11.
Background
Experimentally verified protein-protein interactions (PPIs) cannot be easily retrieved by researchers unless they are stored in PPI databases. The curation of such databases can be facilitated by employing text-mining systems to identify genes which play the interactor role in PPIs and to map these genes to unique database identifiers (interactor normalization task or INT) and then to return a list of interaction pairs for each article (interaction pair task or IPT). These two tasks are evaluated in terms of the area under curve of the interpolated precision/recall (AUC iP/R) score because the order of identifiers in the output list is important for ease of curation. 相似文献12.
Background
Bifurcation analysis has proven to be a powerful method for understanding the qualitative behavior of gene regulatory networks. In addition to the more traditional forward problem of determining the mapping from parameter space to the space of model behavior, the inverse problem of determining model parameters to result in certain desired properties of the bifurcation diagram provides an attractive methodology for addressing important biological problems. These include understanding how the robustness of qualitative behavior arises from system design as well as providing a way to engineer biological networks with qualitative properties. 相似文献13.
Background
Several protein-protein interaction studies have been performed for the yeast Saccharomyces cerevisiae using different high-throughput experimental techniques. All these results are collected in the BioGRID database and the SGD database provide detailed annotation of the different proteins. Despite the value of BioGRID for studying protein-protein interactions, there is a need for manual curation of these interactions in order to remove false positives. 相似文献14.
Andreas Hoppe Sabrina Hoffmann Andreas Gerasch Christoph Gille Hermann-Georg Holzhütter 《BMC bioinformatics》2011,12(1):28
Background
Flux-balance analysis based on linear optimization is widely used to compute metabolic fluxes in large metabolic networks and gains increasingly importance in network curation and structural analysis. Thus, a computational tool flexible enough to realize a wide variety of FBA algorithms and able to handle batch series of flux-balance optimizations is of great benefit. 相似文献15.
16.
Background
Despite several recent advances in the automated generation of draft metabolic reconstructions, the manual curation of these networks to produce high quality genome-scale metabolic models remains a labour-intensive and challenging task.Results
We present PathwayBooster, an open-source software tool to support the manual comparison and curation of metabolic models. It combines gene annotations from GenBank files and other sources with information retrieved from the metabolic databases BRENDA and KEGG to produce a set of pathway diagrams and reports summarising the evidence for the presence of a reaction in a given organism’s metabolic network. By comparing multiple sources of evidence within a common framework, PathwayBooster assists the curator in the identification of likely false positive (misannotated enzyme) and false negative (pathway hole) reactions. Reaction evidence may be taken from alternative annotations of the same genome and/or a set of closely related organisms.Conclusions
By integrating and visualising evidence from multiple sources, PathwayBooster reduces the manual effort required in the curation of a metabolic model. The software is available online at http://www.theosysbio.bio.ic.ac.uk/resources/pathwaybooster/.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0447-2) contains supplementary material, which is available to authorized users. 相似文献17.
Background
Substantial amounts of data on cell signaling, metabolic, gene regulatory and other biological pathways have been accumulated in literature and electronic databases. Conventionally, this information is stored in the form of pathway diagrams and can be characterized as highly "compartmental" (i.e. individual pathways are not connected into more general networks). Current approaches for representing pathways are limited in their capacity to model molecular interactions in their spatial and temporal context. Moreover, the critical knowledge of cause-effect relationships among signaling events is not reflected by most conventional approaches for manipulating pathways. 相似文献18.
Richard A Notebaart Frank HJ van Enckevort Christof Francke Roland J Siezen Bas Teusink 《BMC bioinformatics》2006,7(1):296
Background
The genomic information of a species allows for the genome-scale reconstruction of its metabolic capacity. Such a metabolic reconstruction gives support to metabolic engineering, but also to integrative bioinformatics and visualization. Sequence-based automatic reconstructions require extensive manual curation, which can be very time-consuming. Therefore, we present a method to accelerate the time-consuming process of network reconstruction for a query species. The method exploits the availability of well-curated metabolic networks and uses high-resolution predictions of gene equivalency between species, allowing the transfer of gene-reaction associations from curated networks. 相似文献19.
Background
Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. 相似文献20.
Chatr-aryamontri A Kerrien S Khadake J Orchard S Ceol A Licata L Castagnoli L Costa S Derow C Huntley R Aranda B Leroy C Thorneycroft D Apweiler R Cesareni G Hermjakob H 《Genome biology》2008,9(Z2):S5