Search results for: Gene Ontology

Authors: Souâad Boudebza, Omar Nouali, Faiçal Azouaou

Abstract:

Social networks have recently gained a growing interest on the web. Traditional formalisms for representing social networks are static and suffer from the lack of semantics. In this paper, we will show how semantic web technologies can be used to model social data. The SemTemp ontology aligns and extends existing ontologies such as FOAF, SIOC, SKOS and OWL-Time to provide a temporal and semantically rich description of social data. We also present a modeling scenario to illustrate how our ontology can be used to model social networks.

Keywords: Ontology, semantic web, social network, temporal modeling.

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Authors: A. R. Vazifedoost, M. Rahgozar, F. Oroumchian

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Knowledge discovery from text and ontology learning are relatively new fields. However their usage is extended in many fields like Information Retrieval (IR) and its related domains. Human Plausible Reasoning based (HPR) IR systems for example need a knowledge base as their underlying system which is currently made by hand. In this paper we propose an architecture based on ontology learning methods to automatically generate the needed HPR knowledge base.

Keywords: Ontology Learning, Human Plausible Reasoning, knowledge extraction, knowledge representation.

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Authors: Katrin Zaiß, Tim Schlüter, Stefan Conrad

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Ontology Matching is a task needed in various applica-tions, for example for comparison or merging purposes. In literature,many algorithms solving the matching problem can be found, butmost of them do not consider instances at all. Mappings are deter-mined by calculating the string-similarity of labels, by recognizinglinguistic word relations (synonyms, subsumptions etc.) or by ana-lyzing the (graph) structure. Due to the facts that instances are oftenmodeled within the ontology and that the set of instances describesthe meaning of the concepts better than their meta information,instances should definitely be incorporated into the matching process.In this paper several novel instance-based matching algorithms arepresented which enhance the quality of matching results obtainedwith common concept-based methods. Different kinds of formalismsare use to classify concepts on account of their instances and finallyto compare the concepts directly.KeywordsInstances, Ontology Matching, Semantic Web

Keywords: Instances, Ontology Matching, Semantic Web

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Authors: Jin Si, Yanzhong Wang

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The essence of the 21st century is knowledge economy. Knowledge has become the key resource of economic growth and social development. Construction industry is no exception. Because of the characteristic of complexity, project manager can't depend only on information management. The only way to improve the level of construction project management is to set up a kind of effective knowledge accumulation mechanism. This paper first introduced the IFC standard and the concept of ontology. Then put forward the construction method of the architectural engineering domain ontology based on IFC. And finally build up the concepts, properties and the relationship between the concepts of the ontology. The deficiency of this paper is also pointed out.

Keywords: Construction Engineering, IFC, Ontology

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Authors: Liming Chen, Baoxin Xiu, Zhaoyun Ding, Bin Liu, Xianqiang Zhu

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In the era of big data, public investors are faced with more complicated information related to investment decisions than ever before. To survive in the fierce competition, it has become increasingly urgent for investors to combine multi-source knowledge and evaluate the companies’ true value efficiently. For this, a rule-based ontology reasoning method is proposed to support steel companies’ value assessment. Considering the delay in financial disclosure and based on cost-benefit analysis, this paper introduces the supply chain enterprises financial analysis and constructs the ontology model used to value the value of steel company. In addition, domain knowledge is formally expressed with the help of Web Ontology Language (OWL) language and SWRL (Semantic Web Rule Language) rules. Finally, a case study on a steel company in China proved the effectiveness of the method we proposed.

Keywords: Financial ontology, steel company, supply chain, ontology reasoning.

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Authors: Frederike Ohrem, Lukas Sikorski, Bastian Haarmann

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Often the users of a semantic search application are facing the problem that they do not find appropriate terms for their search. This holds especially if the data to be searched is from a technical field in which the user does not have expertise. In order to support the user finding the results he seeks, we developed a domain-specific ontology and implemented it into a search application. The ontology serves as a knowledge base, suggesting technical terms to the user which he can add to his query. In this paper, we present the search application and the underlying ontology as well as the project EnArgus in which the application was developed.

Keywords: Information system, knowledge representation, ontology, semantic search.

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Authors: Sunitha Abburu, Golla Suresh Babu

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The issues that limit application interoperability is lack of common vocabulary, common structure, application domain knowledge ontology based semantic technology provides solutions that resolves application interoperability issues. Ontology is broadly used in diverse applications such as artificial intelligence, bioinformatics, biomedical, information integration, etc. Ontology can be used to interpret the knowledge of various domains. To reuse, enrich the available ontologies and reduce the duplication of ontologies of the same domain, there is a strong need to integrate the ontologies of the particular domain. The integrated ontology gives complete knowledge about the domain by sharing this comprehensive domain ontology among the groups. As per the literature survey there is no well-defined methodology to represent knowledge of a whole domain. The current research addresses a systematic methodology for knowledge representation using multiple sub-ontologies at different levels that addresses application interoperability and enables semantic information retrieval. The current method represents complete knowledge of a domain by importing concepts from multiple sub ontologies of same and relative domains that reduces ontology duplication, rework, implementation cost through ontology reusability.

Keywords: Knowledge acquisition, knowledge representation, knowledge transfer, ontologies, semantics.

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Authors: Norazah Yusof, Andi Besse Firdausiah Mansur

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Social learning network analysis has drawn attention for most researcher on e-learning research domain. This is due to the fact that it has the capability to identify the behavior of student during their social interaction inside e-learning. Normally, the social network analysis (SNA) is treating the students' interaction merely as node and edge with less meaning. This paper focuses on providing an ontology structure of e-learning Moodle that can enrich the relationships among students, as well as between the students and the teacher. This ontology structure brings great benefit to the future development of e-learning system.

Keywords: Ontology, e-learning, © Learning Network, Moodle.

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Authors: S. Banerjee

Abstract:

The paper describes design of an ontology in the financial domain for mutual funds. The design of this ontology consists of four steps, namely, specification, knowledge acquisition, implementation and semantic query. Specification includes a description of the taxonomy and different types mutual funds and their scope. Knowledge acquisition involves the information extraction from heterogeneous resources. Implementation describes the conceptualization and encoding of this data. Finally, semantic query permits complex queries to integrated data, mapping of these database entities to ontological concepts.

Keywords: Ontology, Semantic Web, Mutual Funds.

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Authors: Lan Yang, Kathryn Cormican, Ming Yu

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ISO/IEC/IEEE 15288: 2015, Systems and Software Engineering - System Life Cycle Processes is an international standard that provides generic top-level process descriptions to support systems engineering (SE). However, the processes defined in the standard needs improvement to lift integrity and consistency. The goal of this research is to explore the way by building an ontology model for the SE standard to manage the knowledge of SE. The ontology model gives a whole picture of the SE knowledge domain by building connections between SE concepts. Moreover, it creates a hierarchical classification of the concepts to fulfil different requirements of displaying and analysing SE knowledge.

Keywords: Knowledge management, model-based systems engineering, ontology modelling, systems engineering ontology.

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Authors: Ahmad Luthfi

Abstract:

One of the main goals of a computer forensic analyst is to determine the cause and effect of the acquisition of a digital evidence in order to obtain relevant information on the case is being handled. In order to get fast and accurate results, this paper will discuss the approach known as Ontology Framework. This model uses a structured hierarchy of layers that create connectivity between the variant and searching investigation of activity that a computer forensic analysis activities can be carried out automatically. There are two main layers are used, namely Analysis Tools and Operating System. By using the concept of Ontology, the second layer is automatically designed to help investigator to perform the acquisition of digital evidence. The methodology of automation approach of this research is by utilizing Forward Chaining where the system will perform a search against investigative steps and atomically structured in accordance with the rules of the Ontology.

Keywords: Ontology, Framework, Automation, Forensics.

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Authors: Rossitza M. Setchi, Qiao Tang

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Nowadays, ontologies are the only widely accepted paradigm for the management of sharable and reusable knowledge in a way that allows its automatic interpretation. They are collaboratively created across the Web and used to index, search and annotate documents. The vast majority of the ontology based approaches, however, focus on indexing texts at document level. Recently, with the advances in ontological engineering, it became clear that information indexing can largely benefit from the use of general purpose ontologies which aid the indexing of documents at word level. This paper presents a concept indexing algorithm, which adds ontology information to words and phrases and allows full text to be searched, browsed and analyzed at different levels of abstraction. This algorithm uses a general purpose ontology, OntoRo, and an ontologically tagged corpus, OntoCorp, both developed for the purpose of this research. OntoRo and OntoCorp are used in a two-stage supervised machine learning process aimed at generating ontology tagging rules. The first experimental tests show a tagging accuracy of 78.91% which is encouraging in terms of the further improvement of the algorithm.

Keywords: Concepts, indexing, machine learning, ontology, tagging.

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Authors: Jawad Makki, Anne-Marie Alquier, Violaine Prince

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In this paper we propose an NLP-based method for Ontology Population from texts and apply it to semi automatic instantiate a Generic Knowledge Base (Generic Domain Ontology) in the risk management domain. The approach is semi-automatic and uses a domain expert intervention for validation. The proposed approach relies on a set of Instances Recognition Rules based on syntactic structures, and on the predicative power of verbs in the instantiation process. It is not domain dependent since it heavily relies on linguistic knowledge. A description of an experiment performed on a part of the ontology of the PRIMA1 project (supported by the European community) is given. A first validation of the method is done by populating this ontology with Chemical Fact Sheets from Environmental Protection Agency2. The results of this experiment complete the paper and support the hypothesis that relying on the predicative power of verbs in the instantiation process improves the performance.

Keywords: Information Extraction, Instance Recognition Rules, Ontology Population, Risk Management, Semantic analysis.

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Authors: Waralak Vongdoiwang Siricharoen

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One of object oriented software developing problem is the difficulty of searching the appropriate and suitable objects for starting the system. In this work, ontologies appear in the part of supporting the object discovering in the initial of object oriented software developing. There are many researches try to demonstrate that there is a great potential between object model and ontologies. Constructing ontology from object model is called ontology engineering can be done; On the other hand, this research is aiming to support the idea of building object model from ontology is also promising and practical. Ontology classes are available online in any specific areas, which can be searched by semantic search engine. There are also many helping tools to do so; one of them which are used in this research is Protégé ontology editor and Visual Paradigm. To put them together give a great outcome. This research will be shown how it works efficiently with the real case study by using ontology classes in travel/tourism domain area. It needs to combine classes, properties, and relationships from more than two ontologies in order to generate the object model. In this paper presents a simple methodology framework which explains the process of discovering objects. The results show that this framework has great value while there is possible for expansion. Reusing of existing ontologies offers a much cheaper alternative than building new ones from scratch. More ontologies are becoming available on the web, and online ontologies libraries for storing and indexing ontologies are increasing in number and demand. Semantic and Ontologies search engines have also started to appear, to facilitate search and retrieval of online ontologies.

Keywords: Software Developing, Ontology, Ontology Library, Artificial Intelligent, Protégé, Object Model.

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Authors: Sihem Mostefai, Abdelaziz Bouras, Mohamed Batouche

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To achieve competitive advantage nowadays, most of the industrial companies are considering that success is sustained to great product development. That is to manage the product throughout its entire lifetime ranging from design, manufacture, operation and destruction. Achieving this goal requires a tight collaboration between partners from a wide variety of domains, resulting in various product data types and formats, as well as different software tools. So far, the lack of a meaningful unified representation for product data semantics has slowed down efficient product development. This paper proposes an ontology based approach to enable such semantic interoperability. Generic and extendible product ontology is described, gathering main concepts pertaining to the mechanical field and the relations that hold among them. The ontology is not exhaustive; nevertheless, it shows that such a unified representation is possible and easily exploitable. This is illustrated thru a case study with an example product and some semantic requests to which the ontology responds quite easily. The study proves the efficiency of ontologies as a support to product data exchange and information sharing, especially in product development environments where collaboration is not just a choice but a mandatory prerequisite.

Keywords: Information exchange, product lifecyclemanagement, product ontology, semantic interoperability.

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Authors: Eun-Jung Ko, Hyung-Jik Lee, Jeun-Woo Lee

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In ubiqutious healthcare environment, user's health data are transfered to the remote healthcare server by the user's wearable system or mobile phone. These collected user's health data should be managed and analyzed in the healthcare server, so that care giver or user can monitor user's physiological state. In this paper, we designed and developed the intelligent Healthcare Server to manage the user's health data using CDSS and ontology. Our system can analyze user's health data semantically using CDSS and ontology, and report the result of user's physiological raw data to the user and care giver.

Keywords: u-healthcare, CDSS, healthcare server, health data, ontology.

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Authors: Visit Hirankitti, Vuong Tran Xuan

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Meta-reasoning is essential for multi-agent communication. In this paper we propose a framework of multi-agent communication in which agents employ meta-reasoning to reason with agent and ontology locations in order to communicate semantic information with other agents on the semantic web and also reason with multiple distributed ontologies. We shall argue that multi-agent communication of Semantic Web information cannot be realized without the need to reason with agent and ontology locations. This is because for an agent to be able to communicate with another agent, it must know where and how to send a message to that agent. Similarly, for an agent to be able to reason with an external semantic web ontology, it must know where and how to access to that ontology. The agent framework and its communication mechanism are formulated entirely in meta-logic.

Keywords: Semantic Web, agent communication, ontologies.

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Authors: Masao Okabe

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Nowadays, in Japan, variety of students get into a university and one of the main roles of introductory courses for freshmen is to make such students well prepared for subsequent intermediate courses. For that purpose, the flipped-mastery model is not enough because videos usually used in a flipped classroom is not adaptive and does not fit all freshmen with different academic performances. This paper proposes an ontology-navigated tutoring system called EduGraph. Using EduGraph, students can prepare for and review a class, in a more flexibly personalizable way than by videos. Structuralizing learning materials by its ontology, EduGraph also helps students integrate what they learn as knowledge, and makes learning materials sharable. EduGraph was used for an introductory course for freshmen. This application suggests that EduGraph is effective.

Keywords: Adaptive e-learning, flipped classroom, mastery learning, ontology.

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Authors: Hei-Chia Wang, Che-Tsung Yang

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While the explosive increase in information published on the Web, researchers have to filter information when searching for conference related information. To make it easier for users to search related information, this paper uses Topic Maps and social information to implement ontology since ontology can provide the formalisms and knowledge structuring for comprehensive and transportable machine understanding that digital information requires. Besides enhancing information in Topic Maps, this paper proposes a method of constructing research Topic Maps considering social information. First, extract conference data from the web. Then extract conference topics and the relationships between them through the proposed method. Finally visualize it for users to search and browse. This paper uses ontology, containing abundant of knowledge hierarchy structure, to facilitate researchers getting useful search results. However, most previous ontology construction methods didn-t take “people" into account. So this paper also analyzes the social information which helps researchers find the possibilities of cooperation/combination as well as associations between research topics, and tries to offer better results.

Keywords: Ontology, topic maps, social information, co-authorship.

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Authors: Hassan Noureddine, Maria Sokhn, Iman Jarkass, Elena Mugellini, Omar Abou Khaled

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From the importance of the conference and its constructive role in the studies discussion, there must be a strong organization that allows the exploitation of the discussions in opening new horizons. The vast amount of information scattered across the web, make it difficult to find experts, who can play a prominent role in organizing conferences. In this paper we proposed a new approach of extracting researchers- information from various Web resources and correlating them in order to confirm their correctness. As a validator of this approach, we propose a service that will be useful to set up a conference. Its main objective is to find appropriate experts, as well as the social events for a conference. For this application we us Semantic Web technologies like RDF and ontology to represent the confirmed information, which are linked to another ontology (skills ontology) that are used to present and compute the expertise.

Keywords: Expert finding, Information extraction, Ontologies, Semantic web, Social events.

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Authors: Salvador Mandujano

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This paper describes the design and results of FROID, an outbound intrusion detection system built with agent technology and supported by an attacker-centric ontology. The prototype features a misuse-based detection mechanism that identifies remote attack tools in execution. Misuse signatures composed of attributes selected through entropy analysis of outgoing traffic streams and process runtime data are derived from execution variants of attack programs. The core of the architecture is a mesh of self-contained detection cells organized non-hierarchically that group agents in a functional fashion. The experiments show performance gains when the ontology is enabled as well as an increase in accuracy achieved when correlation cells combine detection evidence received from independent detection cells.

Keywords: Outbound intrusion detection, knowledge management, multiagent systems, ontology.

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Authors: Kazuki Sonoda, Masahiro Hori

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When designing information systems that deal with large amount of domain knowledge, system designers need to consider ambiguities of labeling termsin domain vocabulary for navigating users in the information space. The goal of this study is to develop a methodology for system designers to label navigation items, taking account of ambiguities stems from synonyms or polysemes of labeling terms. In this paper, we propose a method for concept labeling based on mappings between domain ontology andthesaurus, and report results of an empirical evaluation.

Keywords: Concept Labeling, Ontology, Thesaurus, VocabularyProblem

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Authors: Masaki Yamaguchi, Akira Ito, Noriaki Okamoto, Yoshinori Kawabe, Masamichi Kamihira

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Heat-inducible gene expression vectors are useful for hyperthermia-induced cancer gene therapy, because the combination of hyperthermia and gene therapy can considerably improve the therapeutic effects. In the present study, we developed an enhanced heat-inducible transgene expression system in which a heat-shock protein (HSP) promoter and tetracycline-responsive transactivator were combined. When the transactivator plasmid containing the tetracycline-responsive transactivator gene was co-transfected with the reporter gene expression plasmid, a high level of heat-induced gene expression was observed compared with that using the HSP promoter without the transactivator. In vitro evaluation of the therapeutic effect using HeLa cells showed that heat-induced therapeutic gene expression caused cell death in a high percentage of these cells, indicating that this strategy is promising for cancer gene therapy.

Keywords: Inducible gene expression, Gene therapy, Hyperthermia, Heat shock protein, Tetracycline transactivator.

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Authors: Ilkka Niskanen, Jarmo Kalaoja, Julia Kantorovitch, Toni Piirainen

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Ontologies are broadly used in the context of networked home environments. With ontologies it is possible to define and store context information, as well as to model different kinds of physical environments. Ontologies are central to networked home environments as they carry the meaning. However, ontologies and the OWL language is complex. Several ontology visualization approaches have been developed to enhance the understanding of ontologies. The domain of networked home environments sets some special requirements for the ontology visualization approach. The visualization tool presented here, visualizes ontologies in a domain-specific way. It represents effectively the physical structures and spatial relationships of networked home environments. In addition, it provides extensive interaction possibilities for editing and manipulating the visualization. The tool shortens the gap from beginner to intermediate OWL ontology reader by visualizing instances in their actual locations and making OWL ontologies more interesting and concrete, and above all easier to comprehend.

Keywords: Ontologies, visualization, interaction.

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Authors: Marc Sango, Olimpia Hoinaru, Christophe Gransart, Laurence Duchien

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Ontologies offer a means for representing and sharing information in many domains, particularly in complex domains. For example, it can be used for representing and sharing information of System Requirement Specification (SRS) of complex systems like the SRS of ERTMS/ETCS written in natural language. Since this system is a real-time and critical system, generic ontologies, such as OWL and generic ERTMS ontologies provide minimal support for modeling temporal information omnipresent in these SRS documents. To support the modeling of temporal information, one of the challenges is to enable representation of dynamic features evolving in time within a generic ontology with a minimal redesign of it. The separation of temporal information from other information can help to predict system runtime operation and to properly design and implement them. In addition, it is helpful to provide a reasoning and querying techniques to reason and query temporal information represented in the ontology in order to detect potential temporal inconsistencies. To address this challenge, we propose a lightweight 3-layer temporal Quality of Service (QoS) ontology for representing, reasoning and querying over temporal and non-temporal information in a complex domain ontology. Representing QoS entities in separated layers can clarify the distinction between the non QoS entities and the QoS entities in an ontology. The upper generic layer of the proposed ontology provides an intuitive knowledge of domain components, specially ERTMS/ETCS components. The separation of the intermediate QoS layer from the lower QoS layer allows us to focus on specific QoS Characteristics, such as temporal or integrity characteristics. In this paper, we focus on temporal information that can be used to predict system runtime operation. To evaluate our approach, an example of the proposed domain ontology for handover operation, as well as a reasoning rule over temporal relations in this domain-specific ontology, are presented.

Keywords: System Requirement Specification, ERTMS/ETCS, Temporal Ontologies, Domain Ontologies.

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Authors: Dalanya Asaad Mohammed, Dara Abdul Razaq

Abstract:

A total of twenty tensile biopsies were collected from children undergoing tonsillectomy from teaching hospital ENT department and Kurdistan private hospital in sulaimani city. All biopsies were homogenized and cultured; the obtained bacterial isolates were purified and identified by biochemical tests and VITEK 2 compact system. Among the twenty studied samples, only one Pseudomonas putida with probability of 99% was isolated. Antimicrobial susceptibility was carried out by disk diffusion method, Pseudomonas putida showed resistance to all antibiotics used except vancomycin. The isolate further subjected to PCR and DNA sequence analysis of blaVIM gene using different set of primers for different regions of VIM gene. The results were found to be PCR positive for the blaVIM gene. To determine the sequence of blaVIM gene, DNA sequencing performed. Sequence alignment of blaVIM gene with previously recorded blaVIM gene in NCBI- database showed that P. putida isolate have different blaVIM gene.

Keywords: Clinical isolates, Putida, Sulaimani, Vim gene.

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Authors: Ankit Agrawal, Ankush Mittal

Abstract:

A gene network gives the knowledge of the regulatory relationships among the genes. Each gene has its activators and inhibitors that regulate its expression positively and negatively respectively. Genes themselves are believed to act as activators and inhibitors of other genes. They can even activate one set of genes and inhibit another set. Identifying gene networks is one of the most crucial and challenging problems in Bioinformatics. Most work done so far either assumes that there is no time delay in gene regulation or there is a constant time delay. We here propose a Dynamic Time- Lagged Correlation Based Method (DTCBM) to learn the gene networks, which uses time-lagged correlation to find the potential gene interactions, and then uses a post-processing stage to remove false gene interactions to common parents, and finally uses dynamic correlation thresholds for each gene to construct the gene network. DTCBM finds correlation between gene expression signals shifted in time, and therefore takes into consideration the multi time delay relationships among the genes. The implementation of our method is done in MATLAB and experimental results on Saccharomyces cerevisiae gene expression data and comparison with other methods indicate that it has a better performance.

Keywords: Activators, correlation, dynamic time-lagged correlation based method, inhibitors, multi-time delay gene network.

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Authors: Meltem Serhatli, Ferda N. Alpaslan

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Processing the data by computers and performing reasoning tasks is an important aim in Computer Science. Semantic Web is one step towards it. The use of ontologies to enhance the information by semantically is the current trend. Huge amount of domain specific, unstructured on-line data needs to be expressed in machine understandable and semantically searchable format. Currently users are often forced to search manually in the results returned by the keyword-based search services. They also want to use their native languages to express what they search. In this paper, an ontology-based automated question answering system on software test documents domain is presented. The system allows users to enter a question about the domain by means of natural language and returns exact answer of the questions. Conversion of the natural language question into the ontology based query is the challenging part of the system. To be able to achieve this, a new algorithm regarding free text to ontology based search engine query conversion is proposed. The algorithm is based on investigation of suitable question type and parsing the words of the question sentence.

Keywords: Description Logics, ontology, question answering, reasoning.

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Authors: Khlopova N.S., Glazko V.I., Glazko T.T.

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Using DNA microarrays the comparative analysis of a gene expression profiles is carried out in a liver and kidneys of pigs. The hypothesis of a cross hybridization of one probe with different cDNA sites of the same gene or different genes is checked up, and it is shown, that cross hybridization can be a source of essential errors at revealing of a key genes in organ-specific transcriptome. It is reveald that distinctions in profiles of a gene expression are well coordinated with function, morphology, biochemistry and histology of these organs.

Keywords: Microarray, gene expression profiles, key genes.

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Authors: Wararat Rungworawut, Twittie Senivongse

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Business process model describes process flow of a business and can be seen as the requirement for developing a software application. This paper discusses a BPM2CD guideline which complements the Model Driven Architecture concept by suggesting how to create a platform-independent software model in the form of a UML class diagram from a business process model. An important step is the identification of UML classes from the business process model. A technique for object-oriented analysis called domain analysis is borrowed and key concepts in the business process model will be discovered and proposed as candidate classes for the class diagram. The paper enhances this step by using ontology search to help identify important classes for the business domain. As ontology is a source of knowledge for a particular domain which itself can link to ontologies of related domains, the search can give a refined set of candidate classes for the resulting class diagram.

Keywords: Business Process Model, Model DrivenArchitecture, Ontology, UML Class Diagram.

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