On the formalization and reuse of scientific research

The reuse of scientific knowledge obtained from one investigation in another investigation is basic to the advance of science. Scientific investigations should therefore be recorded in ways that promote the reuse of the knowledge they generate. The use of logical formalisms to describe scientific knowledge has potential advantages in facilitating such reuse. Here, we propose a formal framework for using logical formalisms to promote reuse. We demonstrate the utility of this framework by using it in a worked example from biology: demonstrating cycles of investigation formalization [F] and reuse [R] to generate new knowledge. We first used logic to formally describe a Robot scientist investigation into yeast (Saccharomyces cerevisiae) functional genomics [f₁]. With Robot scientists, unlike human scientists, the production of comprehensive metadata about their investigations is a natural by-product of the way they work. We then demonstrated how this formalism enabled the reuse of the research in investigating yeast phenotypes [r₁ = R(f₁)]. This investigation found that the removal of non-essential enzymes generally resulted in enhanced growth. The phenotype investigation was then formally described using the same logical formalism as the functional genomics investigation [f₂ = F(r₁)]. We then demonstrated how this formalism enabled the reuse of the phenotype investigation to investigate yeast systems-biology modelling [r₂ = R(f₂)]. This investigation found that yeast flux-balance analysis models fail to predict the observed changes in growth. Finally, the systems biology investigation was formalized for reuse in future investigations [f₃ = F(r₂)]. These cycles of reuse are a model for the general reuse of scientific knowledge.     

蛋白质功能预测方法研究进展

蛋白质功能预测是后基因组时代生物信息学的研究热点之一。利用计算方法预测蛋白质的功能,可以弥补传统生物实验方法周期长、效率低和成本高等方面不足。首先介绍蛋白质功能预测的研究背景,并从计算角度定义蛋白质功能预测问题;然后,对蛋白质功能预测方法的研究现状进行分析与总结,最后指出已有方法中存在的不足及未来的研究方向。     

基于环境变迁的构件组合模型

Internet为分布构件的重用提供了平台，准确、高效的构件组合是新型软件生产的重要环节．针对新一代的软件模型．网构软件，本文首先建立了构件的环境本体，并提出将变迁图作为刻画环境本体的模型；其次提出了基于环境及其状态变迁的构件描述框架；然后针对网构软件的特征，提出了基于环境变迁的构件组合算法，最后用具体的案例展示了算法的可行性．     

基于本体的防汛信息系统设计

近年来,伴随着水利信息化的不断推进,系统开发者和系统用户之间沟通困难的问题开始涌现,严重阻碍了系统开发的进程。本文回顾了国外本体研究的进展,分析了国内基于本体的信息系统开发的实践,通过使用本体能力问题帮助系统开发者获取用户需求,并研究了本体在数据库中的存储设计。     

基于语义网的供需网知识协同研究

为满足应用程序基于知识的互操作,支持供需网协同工作,针对现有供需网协同缺乏语义支持的问题,提出了一个基于语义网的供需网知识协同框架和层次体系结构,设计了一个供需网本体转换模型,并对模型中本体实例生成算法的局部本体映射和多种相似度度量方法计算语义相似度、小波网络修正权值的全局本体映射进行了重点讨论.     

用本体论来解决协同编著中的一致性问题

协同编著是一个群体认知和创造的过程。不同背景的人对同一个主题的理解产生的自然差异会导致主题的偏移。目前,国内外协同编著研发还没有很好地解决协同编著过程发散而又要求主题一致性收敛的问题。利用本体论中的领域本体,为实现人人交互提供一种共享的语义基础,从而为解决协同编著中的主题一致性问题提供一种研究思路。另外,可以用协议本体解决系统之间的通信问题并提出了基于本体论的协同编著模型的构想。     

基于本体的高校知识分析和推理

以高校知识为研究和应用背景,研究基于本体理论的高校知识本体结构化表示和描述,并采用protege 4.0建立了高校知识本体。同时从高校知识中提取出基本公理、类内公理和类间公理,建立公理库,并采用protege的PAL推理引擎对高校知识进行一致性分析和推理。解决了高校知识语义层次上的信息共享和交互的问题,为高校知识的管理提供语义支撑。     

面向企业间业务协作的异构系统集成方法

为实现企业间无缝的业务协作,提出了一种基于本体的实现企业间业务协作的方法,研究了该方法所涉及的关键技术——本体的建立、本体间的映射、异构系统基于语义的互操作等。文章使用XML文档来描述企业间的业务协作信息,屏蔽了企业间数据源在语法和结构上的异构;构建了业务协作企业局部本体,屏蔽了企业间数据源在语义层的异构;为实现企业间的基于语义的互操作,基于相似度计算建立了本体间的映射机制。根据该方案,开发了1个原型系统,为企业间业务协作的异构系统集成提供了1套全面的解决方案。图4表2参9     

Transcriptome and Gene Ontology (GO) Enrichment Analysis Reveals Genes Involved in Biotin Metabolism That Affect l-Lysine Production in Corynebacterium glutamicum

Corynebacterium glutamicum is widely used for amino acid production. In the present study, 543 genes showed a significant change in their mRNA expression levels in l-lysine-producing C. glutamicum ATCC21300 than that in the wild-type C. glutamicum ATCC13032. Among these 543 differentially expressed genes (DEGs), 28 genes were up- or downregulated. In addition, 454 DEGs were functionally enriched and categorized based on BLAST sequence homologies and gene ontology (GO) annotations using the Blast2GO software. Interestingly, NCgl0071 (bioB, encoding biotin synthase) was expressed at levels ~20-fold higher in the l-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain. Five other genes involved in biotin metabolism or transport—NCgl2515 (bioA, encoding adenosylmethionine-8-amino-7-oxononanoate aminotransferase), NCgl2516 (bioD, encoding dithiobiotin synthetase), NCgl1883, NCgl1884, and NCgl1885—were also expressed at significantly higher levels in the l-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain, which we determined using both next-generation RNA sequencing and quantitative real-time PCR analysis. When we disrupted the bioB gene in C. glutamicum ATCC21300, l-lysine production decreased by approximately 76%, and the three genes involved in biotin transport (NCgl1883, NCgl1884, and NCgl1885) were significantly downregulated. These results will be helpful to improve our understanding of C. glutamicum for industrial amino acid production.     

Identification and Functional Analysis of MicroRNAs in Mice following Focal Cerebral Ischemia Injury

Numerous studies have demonstrated that genes, RNAs, and proteins are involved in the occurrence and development of stroke. In addition, previous studies concluded that microRNAs (miRNAs or miRs) are closely related to the pathological process of ischemic and hypoxic disease. Therefore, the aims of this study were to quantify the altered expression levels of miRNAs in the infarct region 6 h after middle cerebral artery occlusion (MCAO)-induced focal cerebral ischemia in mice using a large-scale miRNAs microarray. Firstly, MCAO-induced cerebral ischemic injuries were investigated by observing the changes of neurological deficits, infarct volume and edema ratio. One hundred and eighteen differentially expressed miRNAs were identified in the infarct region of mice following the MCAOs compared with sham group (p < 0.05 was considered as significant). Among these 118 significantly expressed microRNAs, we found that 12 miRNAs were up-regulated with fold changes lager than two, and 18 miRNAs were down-regulated with fold changes less than 0.5 in the infarct region of mice following the 6 h MCAOs, compared with the sham group. Then, these 30 miRNAs with expression in fold change larger than two or less than 0.5 was predicted, and the functions of the target genes of 30 miRNAs were analyzed using a bioinformatics method. Finally, the miRNA-gene network was established and the functional miRNA-mRNA pairs were identified, which provided insight into the roles of the specific miRNAs that regulated specified genes in the ischemic injuries. The miRNAs identified in this study may represent effective therapeutic targets for stroke, and further study of the role of these targets may increase our understanding of the mechanisms underlying ischemic injuries.