Applications of ontologies in requirements engineering: a systematic review of the literature

There is an increase use of ontology-driven approaches to support requirements engineering (RE) activities, such as elicitation, analysis, specification, validation and management of requirements. However, the RE community still lacks a comprehensive understanding of how ontologies are used in RE process. Thus, the main objective of this work is to investigate and better understand how ontologies support RE as well as identify to what extent they have been applied to this field. In order to meet our goal, we conducted a systematic literature review (SLR) to identify the primary studies on the use of ontologies in RE, following a predefined review protocol. We then identified the main RE phases addressed, the requirements modelling styles that have been used in conjunction with ontologies, the types of requirements that have been supported by the use of ontologies and the ontology languages that have been adopted. We also examined the types of contributions reported and looked for evidences of the benefits of ontology-driven RE. In summary, the main findings of this work are: (1) there are empirical evidences of the benefits of using ontologies in RE activities both in industry and academy, specially for reducing ambiguity, inconsistency and incompleteness of requirements; (2) the majority of studies only partially address the RE process; (3) there is a great diversity of RE modelling styles supported by ontologies; (4) most studies addressed only functional requirements; (5) several studies describe the use/development of tools to support different types of ontology-driven RE approaches; (6) about half of the studies followed W3C recommendations on ontology-related languages; and (7) a great variety of RE ontologies were identified; nevertheless, none of them has been broadly adopted by the community. Finally, we conclude this work by showing several promising research opportunities that are quite important and interesting but underexplored in current research and practice.     

An adaptive learning approach for 3-D surface reconstruction from point clouds.

In this paper, we propose a multiresolution approach for surface reconstruction from clouds of unorganized points representing an object surface in 3-D space. The proposed method uses a set of mesh operators and simple rules for selective mesh refinement, with a strategy based on Kohonen's self-organizing map (SOM). Basically, a self-adaptive scheme is used for iteratively moving vertices of an initial simple mesh in the direction of the set of points, ideally the object boundary. Successive refinement and motion of vertices are applied leading to a more detailed surface, in a multiresolution, iterative scheme. Reconstruction was experimented on with several point sets, including different shapes and sizes. Results show generated meshes very close to object final shapes. We include measures of performance and discuss robustness.     

A Secure Grid Medical Data Manager Interfaced to the gLite Middleware

The medical community is producing and manipulating a tremendous volume of digital data for which computerized archiving, processing and analysis is needed. Grid infrastructures are promising for dealing with challenges arising in computerized medicine but the manipulation of medical data on such infrastructures faces both the problem of interconnecting medical information systems to Grid middlewares and of preserving patients’ privacy in a wide and distributed multi-user system. These constraints are often limiting the use of Grids for manipulating sensitive medical data. This paper describes our design of a medical data management system taking advantage of the advanced gLite data management services, developed in the context of the EGEE project, to fulfill the stringent needs of the medical community. It ensures medical data protection through strict data access control, anonymization and encryption. The multi-level access control provides the flexibility needed for implementing complex medical use-cases. Data anonymization prevents the exposure of most sensitive data to unauthorized users, and data encryption guarantees data protection even when it is stored at remote sites. Moreover, the developed prototype provides a Grid storage resource manager (SRM) interface to standard medical DICOM servers thereby enabling transparent access to medical data without interfering with medical practice.     

Interval + Image = Wavelet: For Image Processing under Interval Uncertainty,Wavelets Are Optimal

In computer and electronic manufacturing, it is very important to be able to automatically check whether the surface mounted devices (SMD) are correctly placed on the printed circuit boards. The inspection of these boards has to be done on a shop floor, where statistical characteristics of the noise vary so much that, in essence, we only have interval estimates for this noise.We show that under this interval uncertainty, the optimal image processing technique consists of using Haar wavelets. Wavelets indeed lead to much better results than previously used Fourier transform techniques.On a more fundamental level, our result is a step towards solving an important problem related to wavelets: that wavelet transforms often empirically work much better than other methods, but there are very few theoretical explanations of this efficiency. Our results shows that, probably, such a theoretical explanation can be obtained if we take interval uncertainty into consideration.     

A theoretical evaluation of the effect of water on the electronic properties of low density amorphous carbon nanoparticles

Monte Carlo simulations combined with first-principles calculations were carried out to investigate the structure and electronic properties of amorphous carbon nanoparticles containing between 287 and 467 atoms, isolated and in an aqueous environment. Carbon interactions were described in terms of the semiemperical Tersoff potential and the interactions of the nanoparticles with water were described by an all-atom Lennard–Jones potential. The nanostructures were generated from low mass density amorphous carbon phases simulated under ambient conditions. Our study has indicated that the formation energy of these nanomaterials is slightly affected by the initial configuration of the amorphous phase. The large number of dangling bonds present in the nanostructures leads to huge magnetic moments, in a 31–42 μ_B range, calculated for the amorphous nanostructures containing distinct sp²/sp³ ratios. Also, these nanoparticles exhibit strong interaction energies with the aqueous environment, which are in agreement with the high reactivity expected for these amorphous systems. Most importantly, the calculated magnetism appears to be reduced between 1% and 14% in the presence of water, depending on both the nanoparticle density and surface.     

Genomic studies of milk-related traits in water buffalo (Bubalus bubalis) based on single-step genomic best linear unbiased prediction and random regression models

Genomic selection has been widely implemented in many livestock breeding programs, but it remains incipient in buffalo. Therefore, this study aimed to (1) estimate variance components incorporating genomic information in Murrah buffalo; (2) evaluate the performance of genomic prediction for milk-related traits using single- and multitrait random regression models (RRM) and the single-step genomic best linear unbiased prediction approach; and (3) estimate longitudinal SNP effects and candidate genes potentially associated with time-dependent variation in milk, fat, and protein yields, as well as somatic cell score (SCS) in multiple parities. The data used to estimate the genetic parameters consisted of a total of 323,140 test-day records. The average daily heritability estimates were moderate (0.35 ± 0.02 for milk yield, 0.22 ± 0.03 for fat yield, 0.42 ± 0.03 for protein yield, and 0.16 ± 0.03 for SCS). The highest heritability estimates, considering all traits studied, were observed between 20 and 280 d in milk (DIM). The genetic correlation estimates at different DIM among the evaluated traits ranged from ?0.10 (156 to 185 DIM for SCS) to 0.61 (36 to 65 DIM for fat yield). In general, direct selection for any of the traits evaluated is expected to result in indirect genetic gains for milk yield, fat yield, and protein yield but also increase SCS at certain lactation stages, which is undesirable. The predicted RRM coefficients were used to derive the genomic estimated breeding values (GEBV) for each time point (from 5 to 305 DIM). In general, the tuning parameters evaluated when constructing the hybrid genomic relationship matrices had a small effect on the GEBV accuracy and a greater effect on the bias estimates. The SNP solutions were back-solved from the GEBV predicted from the Legendre random regression coefficients, which were then used to estimate the longitudinal SNP effects (from 5 to 305 DIM). The daily SNP effect for 3 different lactation stages were performed considering 3 different lactation stages for each trait and parity: from 5 to 70, from 71 to 150, and from 151 to 305 DIM. Important genomic regions related to the analyzed traits and parities that explain more than 0.50% of the total additive genetic variance were selected for further analyses of candidate genes. In general, similar potential candidate genes were found between traits, but our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the traits across parities. These results contribute to a better understanding of the genetic architecture of milk production traits in dairy buffalo and reinforce the relevance of incorporating genomic information to genetically evaluate longitudinal traits in dairy buffalo. Furthermore, the candidate genes identified can be used as target genes in future functional genomics studies.     

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