Database reverse engineering: From requirements to CARE tools

This paper analyzes the requirements that CASE tools should meet for effective database reverse engineering (DBRE), and proposes a general architecture for data-centered applications reverse engineering CASE environments. First, the paper describes a generic DBMS-independent DBRE methodology, then it analyzes the main characteristics of DBRE activities in order to collect a set of desirable requirements. Finally, it describes DB-MAIN, an operational CASE tool developed according to these requirements. The main features of this tool that are described in this paper are its unique generic specification model, its repository, its transformation toolkit, its user interface, the text processors, the assistants, the methodological control and its functional extensibility. Finally, the paper describes five real-world projects in which the methodology and the CASE tool were applied. This is a heavily revised and extended version of “Requirements for Information System Reverse Engineering Support” by J.-L. Hainaut, V. Englebert, J. Henrard, J.-M. Hick, D. Roland, which first appeared in the Proceedings of the Second Working Conference on Reverse Engineering, IEEE Computer Society Press, pp. 136–145, July 1995. This paper presents some results of the DB-MAIN project. This project is partially supported by the Région Wallonne, the European Union, and by a consortium comprising ACEC-OSI (Be), ARIANE-II (Be), Banque UCL (Lux), BBL (Be), Centre de recherche public H. Tudor (Lux), CGER (Be), Cockerill-Sambre (Be), CONCIS (Fr), D'Ieteren (Be), DIGITAL, EDF (Fr), EPFL (CH), Groupe S (Be), IBM, OBLOG Software (Port), ORIGIN (Be), Ville de Namur (Be), Winterthur (Be), 3 Suisses (Be). The DB-Process subproject is supported by the Communauté Fran?aise de Belgique.     

物理量单位的智能导出算法及其应用

推导物理量的单位是物理作业中不可缺少的重要环节。提出一种物理量单位的智能导出算法,即计算机根据物理量的运算式自动推导出待求物理量的单位。实验结果表明,物理量单位导出及换算算法的结果正确,对算术运算式中的物理量单位导出及换算的正确率为100%,且物理量数值的运算正确。     

红外光电立靶数据库的设计与应用

为了解决靶场测试中数据丢失现象的问题,建立了红外光电立靶系统数据库。通过对红外光电立靶数据库的总体设计进行了研究,定义了数据库的结构,并对数据库的建立方法进行了约定,实现了对数据的存储、查询和管理,数据查询方便、快捷。分析和应用结果表明红外光电立靶数据库为软件测试系统提供了可靠的数据支持,便于对测试结果进行统计分析,提高红外光电立靶测试系统的质量与水平。     

Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors

We present a computational protocol which uses the known three-dimensional structure of a target enzyme to identify possible ligands from databases of compounds with low molecular weight. This is accomplished by first mapping the essential interactions in the binding site with the program GRID. The resulting regions of favorable interaction between target and ligand are translated into a database query, and with UNITY a flexible 3D database search is performed. The feasibility of this approach is calibrated with thrombin as the target. Our results show that the resulting hit lists are enriched with thrombin inhibitors compared to the total database.     

Chemical Kinetics Database and Predictive Schemes for Humid Air Plasma Chemistry. Part I: Positive Ion–Molecule Reactions

Reliable kinetic and thermodynamic data are required to model the evolution of electric discharge or electron-beam decomposition chemistry of gases in humid air streams. In this first segment of a continuing series, we provide a core database describing the initially dominant ion-neutral molecule reactions in humid air plasmas. Recommended reaction rate data and extrapolation tools are presented in a manner to facilitate prediction of reactivities and reaction channels as a function of temperature, pressure, and applied electric field.     

基于串级质谱信息进行蛋白质数据库搜索的结果可靠性分析

SEQUEST与Mascot为目前蛋白组学分析研究中使用最为广泛的蛋白质库搜索工具.尝试将Mascot与SEQUEST搜索结果进行比较,进而采用不同多变量判别方法对二者的搜索结果进行判别分析,以降低其结果的假阳性率.通过对Mascot与SEQUEST搜索结果进行比较,发现所得结果差异很大;利用多变量判别分析方法对Mascot及SEQUEST搜索结果进行判别分析,可有效提高SEQUEST结果中假阳性结果与正确结果之间的区分能力.对于Mascot搜索结果,采用多变量判别分析方法仍无法显著降低其假阳性结果,利用Decoy库搜索结果进行估计时亦存在导致错误估计的风险.     

基于遗传编程方法的微孔磷酸铝的定向合成研究

根据微孔磷酸铝合成数据的特点,针对合成数据库中合成参数过多和交叉描述等问题,利用改进的遗传编程算法对具有(6,8)元环的微孔磷酸铝合成参数进行特征提取,优化出新的复合特征来更好地描述磷酸铝合成中溶剂和模板剂的特征,并通过参数进化过程的研究,考察了模板剂和溶剂对产物生成的具体影响,从而指导具有特定结构磷酸铝的定向合成.     

High resolution mass spectrometry based profiling of diet-related deoxyribonucleic acid adducts

Exposure of DNA to endo- and exogenous DNA binding chemicals can result in the formation of DNA adducts and is believed to be the first step in chemically induced carcinogenesis. DNA adductomics is a relatively new field of research which studies the formation of known and unknown DNA adducts in DNA due to exposure to genotoxic chemicals. In this study, a new UHPLC-HRMS(/MS)-based DNA adduct detection method was developed and validated. Four targeted DNA adducts, which all have been linked to dietary genotoxicity, were included in the described method; O⁶-methylguanine (O⁶-MeG), O⁶-carboxymethylguanine (O⁶-CMG), pyrimidopurinone (M1G) and methylhydroxypropanoguanine (CroG). As a supplementary tool for DNA adductomics, a DNA adduct database, which currently contains 123 different diet-related DNA adducts, was constructed. By means of the newly developed method and database, all 4 targeted DNA adducts and 32 untargeted DNA adducts could be detected in different DNA samples. The obtained results clearly demonstrate the merit of the described method for both targeted and untargeted DNA adduct detection in vitro and in vivo, whilst the diet-related DNA adduct database can distinctly facilitate data interpretation.     

Crystal structures of four δ‐keto esters and a Cambridge Structural Database analysis of cyano–halogen interactions

The revived interest in halogen bonding as a tool in pharmaceutical cocrystals and drug design has indicated that cyano–halogen interactions could play an important role. The crystal structures of four closely related δ‐keto esters, which differ only in the substitution at a single C atom (by H, OMe, Cl and Br), are compared, namely ethyl 2‐cyano‐5‐oxo‐5‐phenyl‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₁₉H₂₂N₂O₃, (1), ethyl 2‐cyano‐5‐(4‐methoxyphenyl)‐5‐oxo‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₂₀H₂₄N₂O₄, (2), ethyl 5‐(4‐chlorophenyl)‐2‐cyano‐5‐oxo‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₁₉H₂₁ClN₂O₃, (3), and the previously published ethyl 5‐(4‐bromophenyl)‐2‐cyano‐5‐oxo‐3‐(piperidin‐1‐yl)pent‐2‐enoate, C₁₉H₂₁BrN₂O₃, (4) [Maurya, Vasudev & Gupta (2013). RSC Adv. 3 , 12955–12962]. The molecular conformations are very similar, while there are differences in the molecular assemblies. Intermolecular C—H...O hydrogen bonds are found to be the primary interactions in the crystal packing and are present in all four structures. The halogenated derivatives have additional aromatic–aromatic interactions and cyano–halogen interactions, further stabilizing the molecular packing. A database analysis of cyano–halogen interactions using the Cambridge Structural Database [CSD; Groom & Allen (2014). Angew. Chem. Int. Ed. 53 , 662–671] revealed that about 13% of the organic molecular crystals containing both cyano and halogen groups have cyano–halogen interactions in their packing. Three geometric parameters for the C—X...N[triple‐bond]C interaction (X = F, Cl, Br or I), viz. the N...X distance and the C—X...N and C—N...X angles, were analysed. The results indicate that all the short cyano–halogen contacts in the CSD can be classified as halogen bonds, which are directional noncovalent interactions.