Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases

BACKGROUND: Complex biological database systems have become key computational tools used daily by scientists and researchers. Many of these systems must be capable of executing on multiple different hardware and software configurations and are also often made available to users via the Internet. We have used the Java Data Object (JDO) persistence technology to develop the database layer of such a system known as the SigPath information management system. SigPath is an example of a complex biological database that needs to store various types of information connected by many relationships. RESULTS: Using this system as an example, we perform a critical evaluation of current JDO technology; discuss the suitability of the JDO standard to achieve portability, scalability and performance. We show that JDO supports portability of the SigPath system from a relational database backend to an object database backend and achieves acceptable scalability. To answer the performance question, we have created the SigPath JDO application benchmark that we distribute under the Gnu General Public License. This benchmark can be used as an example of using JDO technology to create a complex biological database and makes it possible for vendors and users of the technology to evaluate the performance of other JDO implementations for similar applications. CONCLUSIONS: The SigPath JDO benchmark and our discussion of JDO technology in the context of biological databases will be useful to bioinformaticians who design new complex biological databases and aim to create systems that can be ported easily to a variety of database backends

Information management applied to bioinformatics

Bioinformatics, the discipline concerned with biological information management is essential in the post-genome era, where the complexity of data processing allows for contemporaneous multi level research including that at the genome level, transcriptome level, proteome level, the metabolome level, and the integration of these -omic studies towards gaining an understanding of biology at the systems level. This research is also having a major impact on disease research and drug discovery, particularly through pharmacogenomics studies. In this study innovative resources have been generated via the use of two case studies. One was of the Research & Development Genetics (RDG) department at AstraZeneca, Alderley Park and the other was of the Pharmacogenomics Group at the Sanger Institute in Cambridge UK. In the AstraZeneca case study senior scientists were interviewed using semi-structured interviews to determine information behaviour through the study scientific workflows. Document analysis was used to generate an understanding of the underpinning concepts and fonned one of the sources of context-dependent information on which the interview questions were based. The objectives of the Sanger Institute case study were slightly different as interviews were carried out with eight scientists together with the use of participation observation, to collect data to develop a database standard for one process of their Pharmacogenomics workflow. The results indicated that AstraZeneca would benefit through upgrading their data management solutions in the laboratory and by development of resources for the storage of data from larger scale projects such as whole genome scans. These studies will also generate very large amounts of data and the analysis of these will require more sophisticated statistical methods. At the Sanger Institute a minimum information standard was reported for the manual design of primers and included in a decision making tree developed for Polymerase Chain Reactions (PCRs). This tree also illustrates problems that can be encountered when designing primers along with procedures that can be taken to address such issues.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Constraints to Automating Public Sector Service Deliveries in Ghana: The Example of Permit Acquisition and Detection of Unauthorized Building Processes in Metropolitan Assemblies

Automated public services have brought enormous benefits to many countries; yet developing countries have not fully exploited its benefits owing to certain barriers and Ghana is no exception to this. This research explores the factors militating against automating permit acquisition and detection of unauthorized building processes in Metropolitan Assemblies in Ghana, using the Sekondi-Takoradi Metropolitan Assembly as a case study, and come out with measures to curb them. This survey used questionnaires to collect data from 75 respondents; data was analyzed using Relative Importance Analysis. The survey revealed that barriers to automating permit acquisition and detection of unauthorized building processes in the Metropolis were Political, Educational, Cultural, Social, Administrative, Economical, Legislative and Technological barriers; with political barriers contributing most to the phenomena whiles technological barriers were relatively the least contributing barrier.This paper will help local authorities in policy formulation to curb barriers to automating public services. Keywords: Automating, Unauthorized Buildings, Permit, Barriers and Questionnaire

A framework for identifying genotypic information from clinical records: exploiting integrated ontology structures to transfer annotations between ICD codes and Gene Ontologies

Although some methods are proposed for automatic ontology generation, none of them address the issue of integrating large-scale heterogeneous biomedical ontologies. We propose a novel approach for integrating various types of ontologies efficiently and apply it to integrate International Classification of Diseases, Ninth Revision, Clinical Modification (ICD9CM) and Gene Ontologies (GO). This approach is one of the early attempts to quantify the associations among clinical terms (e.g. ICD9 codes) based on their corresponding genomic relationships. We reconstructed a merged tree for a partial set of GO and ICD9 codes and measured the performance of this tree in terms of associations’ relevance by comparing them with two well-known disease-gene datasets (i.e. MalaCards and Disease Ontology). Furthermore, we compared the genomic-based ICD9 associations to temporal relationships between them from electronic health records. Our analysis shows promising associations supported by both comparisons suggesting a high reliability. We also manually analyzed several significant associations and found promising support from literature

An Automated Methodology For A Comprehensive Definition Of The Supply Chain Using Generic Ontological Components

Today, worldwide business communities are in the era of the Supply Chains. A Supply Chain is a collection of several independent enterprises that partner together to achieve specific goals. These enterprises may plan, source, produce, deliver, or transport materials to satisfy an immediate or projected market demand, and may provide the after sales support, warranty services, and returns. Each enterprise in the Supply Chain has roles and elements. The roles include supplier, customer, or carrier and the elements include functional units, processes, information, information resources, materials, objects, decisions, practices, and performance measures. Each enterprise, individually, manages these elements in addition to their flows, their interdependencies, and their complex interactions. Since a Supply Chain brings several enterprises together to complement each other to achieve a unified goal, the elements in each enterprise have to complement each other and have to be managed together as one unit to achieve the unified goal efficiently. Moreover, since there are a large number of elements to be defined and managed in a single enterprise, then the number of elements to be defined and managed when considering the whole Supply Chain is massive. The supply chain community is using the Supply Chain Operations Reference model (SCOR model) to define their supply chains. However, the SCOR model methodology is limited in defining the supply chain. The SCOR model defines the supply chain in terms of processes, performance metrics, and best practices. In fact, the supply chain community, SCOR users in particular, exerts massive effort to render an adequate supply chain definition that includes the other elements besides the elements covered in the SCOR model. Also, the SCOR model is delivered to the user in a document, which puts a tremendous burden on the user to use the model and makes it difficult to share the definition within the enterprise or across the supply chain. This research is directed towards overcoming the limitations and shortcomings of the current supply chain definition methodology. This research proposes a methodology and a tool that will enable an automated and comprehensive definition of the Supply Chain at any level of details. The proposed comprehensive definition methodology captures all the constituent parts of the Supply Chain at four different levels which are, the supply chain level, the enterprise level, the elements level, and the interaction level. At the Supply Chain level, the various enterprises that constitute the supply chain are defined. At the enterprise level, the enterprise elements are identified. At the enterprises\u27 elements level, each element in the enterprise is explicitly defined. At the interaction level, the flows, interdependence, and interactions that exist between and within the other three levels are identified and defined. The methodology utilized several modeling techniques to generate generic explicit views and models that represents the four levels. The developed views and models were transformed to a series of questions and answers, where the questions correspond to what a view provides and the answers are the knowledge captured and generated from the view. The questions and answers were integrated to render a generic multi-view of the supply chain. The methodology and the multi-view were implemented in an ontology-based tool. The ontology includes sets of generic supply chain ontological components that represent the supply chain elements and a set of automated procedures that can be utilized to define a specific supply chain. A specific supply chain can be defined by re-using the generic components and customizing them to the supply chain specifics. The ontology-based tool was developed to function in the supply chain dynamic, information intensive, geographically dispersed, and heterogeneous environment. To that end, the tool was developed to be generic, sharable, automated, customizable, extensible, and scalable

Ontological approach for database integration

Database integration is one of the research areas that have gained a lot of attention from researcher. It has the goal of representing the data from different database sources in one unified form. To reach database integration we have to face two obstacles. The first one is the distribution of data, and the second is the heterogeneity. The Web ensures addressing the distribution problem, and for the case of heterogeneity there are many approaches that can be used to solve the database integration problem, such as data warehouse and federated databases. The problem in these two approaches is the lack of semantics. Therefore, our approach exploits the Semantic Web methodology. The hybrid ontology method can be facilitated in solving the database integration problem. In this method two elements are available; the source (database) and the domain ontology, however, the local ontology is missing. In fact, to ensure the success of this method the local ontologies should be produced. Our approach obtains the semantics from the logical model of database to generate local ontology. Then, the validation and the enhancement can be acquired from the semantics obtained from the conceptual model of the database. Now, our approach can be applied in the generation phase and the validation-enrichment phase. In the generation phase in our approach, we utilise the reverse engineering techniques in order to catch the semantics hidden in the SQL language. Then, the approach reproduces the logical model of the database. Finally, our transformation system will be applied to generate an ontology. In our transformation system, all the concepts of classes, relationships and axioms will be generated. Firstly, the process of class creation contains many rules participating together to produce classes. Our unique rules succeeded in solving problems such as fragmentation and hierarchy. Also, our rules eliminate the superfluous classes of multi-valued attribute relation as well as taking care of neglected cases such as: relationships with additional attributes. The final class creation rule is for generic relation cases. The rules of the relationship between concepts are generated with eliminating the relationships between integrated concepts. Finally, there are many rules that consider the relationship and the attributes constraints which should be transformed to axioms in the ontological model. The formal rules of our approach are domain independent; also, it produces a generic ontology that is not restricted to a specific ontology language. The rules consider the gap between the database model and the ontological model. Therefore, some database constructs would not have an equivalent in the ontological model. The second phase consists of the validation and the enrichment processes. The best way to validate the transformation result is to facilitate the semantics obtained from the conceptual model of the database. In the validation phase, the domain expert captures the missing or the superfluous concepts (classes or relationships). In the enrichment phase, the generalisation method can be applied to classes that share common attributes. Also, the concepts of complex or composite attributes can be represented as classes. We implement the transformation system by a tool called SQL2OWL in order to show the correctness and the functionally of our approach. The evaluation of our system showed the success of our proposed approach. The evaluation goes through many techniques. Firstly, a comparative study is held between the results produced by our approach and the similar approaches. The second evaluation technique is the weighting score system which specify the criteria that affect the transformation system. The final evaluation technique is the score scheme. We consider the quality of the transformation system by applying the compliance measure in order to show the strength of our approach compared to the existing approaches. Finally the measures of success that our approach considered are the system scalability and the completeness

Building web service ontologies

Harmelen, F.A.H. van [Promotor]Stuckenschmidt, H. [Copromotor

Framework for collaborative knowledge management in organizations

Nowadays organizations have been pushed to speed up the rate of industrial transformation to high value products and services. The capability to agilely respond to new market demands became a strategic pillar for innovation, and knowledge management could support organizations to achieve that goal. However, current knowledge management approaches tend to be over complex or too academic, with interfaces difficult to manage, even more if cooperative handling is required. Nevertheless, in an ideal framework, both tacit and explicit knowledge management should be addressed to achieve knowledge handling with precise and semantically meaningful definitions. Moreover, with the increase of Internet usage, the amount of available information explodes. It leads to the observed progress in the creation of mechanisms to retrieve useful knowledge from the huge existent amount of information sources. However, a same knowledge representation of a thing could mean differently to different people and applications. Contributing towards this direction, this thesis proposes a framework capable of gathering the knowledge held by domain experts and domain sources through a knowledge management system and transform it into explicit ontologies. This enables to build tools with advanced reasoning capacities with the aim to support enterprises decision-making processes. The author also intends to address the problem of knowledge transference within an among organizations. This will be done through a module (part of the proposed framework) for domain’s lexicon establishment which purpose is to represent and unify the understanding of the domain’s used semantic

Coalition based approach for shop floor agility – a multiagent approach

Dissertation submitted for a PhD degree in Electrical Engineering, speciality of Robotics and Integrated Manufacturing from the Universidade Nova de Lisboa, Faculdade de Ciências e TecnologiaThis thesis addresses the problem of shop floor agility. In order to cope with the disturbances and uncertainties that characterise the current business scenarios faced by manufacturing companies, the capability of their shop floors needs to be improved quickly, such that these shop floors may be adapted, changed or become easily modifiable (shop floor reengineering). One of the critical elements in any shop floor reengineering process is the way the control/supervision architecture is changed or modified to accommodate for the new processes and equipment. This thesis, therefore, proposes an architecture to support the fast adaptation or changes in the control/supervision architecture. This architecture postulates that manufacturing systems are no more than compositions of modularised manufacturing components whose interactions when aggregated are governed by contractual mechanisms that favour configuration over reprogramming. A multiagent based reference architecture called Coalition Based Approach for Shop floor Agility – CoBASA, was created to support fast adaptation and changes of shop floor control architectures with minimal effort. The coalitions are composed of agentified manufacturing components (modules), whose relationships within the coalitions are governed by contracts that are configured whenever a coalition is established. Creating and changing a coalition do not involve programming effort because it only requires changes to the contract that regulates it