Search results for: biological ontology

Authors: Chia-Ta Tsai, Wen-Lin Huang, Shinn-Jang Ho, Li-Sun Shu, Shinn-Ying Ho

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Prediction of bacterial virulent protein sequences can give assistance to identification and characterization of novel virulence-associated factors and discover drug/vaccine targets against proteins indispensable to pathogenicity. Gene Ontology (GO) annotation which describes functions of genes and gene products as a controlled vocabulary of terms has been shown effectively for a variety of tasks such as gene expression study, GO annotation prediction, protein subcellular localization, etc. In this study, we propose a sequence-based method Virulent-GO by mining informative GO terms as features for predicting bacterial virulent proteins. Each protein in the datasets used by the existing method VirulentPred is annotated by using BLAST to obtain its homologies with known accession numbers for retrieving GO terms. After investigating various popular classifiers using the same five-fold cross-validation scheme, Virulent-GO using the single kind of GO term features with an accuracy of 82.5% is slightly better than VirulentPred with 81.8% using five kinds of sequence-based features. For the evaluation of independent test, Virulent-GO also yields better results (82.0%) than VirulentPred (80.7%). When evaluating single kind of feature with SVM, the GO term feature performs much well, compared with each of the five kinds of features.

Keywords: Bacterial virulence factors, GO terms, prediction, protein sequence.

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Authors: Fernando Alonso, Rafael Fernandez, Sonia Frutos, Javier Soriano

Abstract:

CIM is the standard formalism for modeling management information developed by the Distributed Management Task Force (DMTF) in the context of its WBEM proposal, designed to provide a conceptual view of the managed environment. In this paper, we propose the inclusion of formal knowledge representation techniques, based on Description Logics (DLs) and the Web Ontology Language (OWL), in CIM-based conceptual modeling, and then we examine the benefits of such a decision. The proposal is specified as a CIM metamodel level mapping to a highly expressive subset of DLs capable of capturing all the semantics of the models. The paper shows how the proposed mapping can be used for automatic reasoning about the management information models, as a design aid, by means of new-generation CASE tools, thanks to the use of state-of-the-art automatic reasoning systems that support the proposed logic and use algorithms that are sound and complete with respect to the semantics. Such a CASE tool framework has been developed by the authors and its architecture is also introduced. The proposed formalization is not only useful at design time, but also at run time through the use of rational autonomous agents, in response to a need recently recognized by the DMTF.

Keywords: CIM, Knowledge-based Information Models, Ontology Languages, OWL, Description Logics, Integrated Network Management, Intelligent Agents, Automatic Reasoning Techniques.

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Authors: Mohamed Ali AlShaari, Khalid M. ElFitori

Abstract:

In the field of Quran Studies known as GHAREEB AL QURAN (The study of the meanings of strange words and structures in Holy Quran), it is difficult to distinguish some pragmatic meanings from conceptual meanings. One who wants to study this subject may need to look for a common usage between any two words or more; to understand general meaning, and sometimes may need to look for common differences between them, even if there are synonyms (word sisters).

Some of the distinguished scholars of Arabic linguistics believe that there are no synonym words, they believe in varieties of meaning and multi-context usage. Based on this viewpoint, our method was designedto look for synonyms of a word, then the differences that distinct the word and their synonyms.

There are many available books that use such a method e.g. synonyms books, dictionaries, glossaries, and some books on the interpretations of strange vocabulary of the Holy Quran, but it is difficult to look up words in these written works.

For that reason, we proposed a logical entity, which we called Differences Matrix (DM).

DM groups the synonyms words to extract the relations between them and to know the general meaning, which defines the skeleton of all word synonyms; this meaning is expressed by a word of its sisters.

In Differences Matrix, we used  the sisters(words) as titles for rows and columns, and in the obtained  cells we tried to define the row title (word) by using column title (her sister), so the relations between sisters appear, the expected result is well defined groups of sisters for each word. We represented the obtained results formally, and used the defined groups as a base for building the ontology of the Holy Quran synonyms.

Keywords: Quran, synonyms, Differences Matrix, ontology

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Authors: Jung-Hyun Kim, Kew-Cheol Shim, Shin-Cheol Song, Kyoungho Kim, Nam-Il Kim, Jinho Bae, Keum-Hyun So

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The purpose of present paper was to investigate perceptions of Korean secondary school students about social issues related to biological sciences. Twenty issues were selected based on topics of articles in the newspaper from 2005 to 2010. The issues were categorized into biotechnology, health-disease and environment domains. Subjects were 541 high school students (male 253 and female 288). On the survey, students were asked to answer on 5-point Lickert scales how they thought of the effect of biological phenomena or events related to biological issues on the individual life and the society. They perceived that the biological issues would be more effectible on the society than on the individual life. Female students had a little more perceptions than males.

Keywords: biological issue, biological sciences, perception, secondary school

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Authors: Xin Bai, Han Yu, Yongchang Ji, Dan C. Marinescu

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We discuss the application of matching in the area of resource discovery and resource allocation in grid computing. We present a formal definition of matchmaking, overview algorithms to evaluate different matchmaking expressions, and develop a matchmaking service for an intelligent grid environment.

Keywords: Grid, Matchmaking, Ontology

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Authors: Mohammad Yasrebi, Somayeh Khosravi

Abstract:

Machine-understandable data when strongly interlinked constitutes the basis for the SemanticWeb. Annotating web documents is one of the major techniques for creating metadata on the Web. Annotating websitexs defines the containing data in a form which is suitable for interpretation by machines. In this paper, we present a better and improved approach than previous [1] to annotate the texts of the websites depends on the knowledge base.

Keywords: Knowledge base, ontology, semantic annotation, XML.

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Authors: S. H. Mirhossaini, H. Godini, A. Jafari

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Biological Ammonia removal (nitrification), the oxidation of ammonia to nitrate catalyzed by bacteria, is a key part of global nitrogen cycling. In the first step of nitrification, chemolithoautotrophic ammonia oxidizer transform ammonia to nitrite, this subsequently oxidized to nitrate by nitrite oxidizing bacteria. This process can be affected by several factors. In this study the effect of influent COD on biological ammonia removal in a bench-scale biological reactor was investigated. Experiments were carried out using synthetic wastewater. The initial ammonium concentration was 25mgNH4 +-N L-1. The effect of COD between 247.55±1.8 and 601.08±3.24mgL-1 on biological ammonia removal was investigated by varying the COD loading supplied to reactor. From the results obtained in this study it could be concluded in the range of 247.55±1.8 to 351.35±2.05mgL-1, there is a direct relationship between amount of COD and ammonia removal. However more than 351.35±2.05 up to 601.08±3.24mgL-1 were found an indirect relationship between them.

Keywords: Ammonia biological removal, Nitrification, InfluentCOD.

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Authors: K. Nirmala Devi, V. Murali Bhaskaran

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Traditional document representation for classification follows Bag of Words (BoW) approach to represent the term weights. The conventional method uses the Vector Space Model (VSM) to exploit the statistical information of terms in the documents and they fail to address the semantic information as well as order of the terms present in the documents. Although, the phrase based approach follows the order of the terms present in the documents rather than semantics behind the word. Therefore, a semantic concept based approach is used in this paper for enhancing the semantics by incorporating the ontology information. In this paper a novel method is proposed to forecast the intraday stock market price directional movement based on the sentiments from Twitter and money control news articles. The stock market forecasting is a very difficult and highly complicated task because it is affected by many factors such as economic conditions, political events and investor’s sentiment etc. The stock market series are generally dynamic, nonparametric, noisy and chaotic by nature. The sentiment analysis along with wisdom of crowds can automatically compute the collective intelligence of future performance in many areas like stock market, box office sales and election outcomes. The proposed method utilizes collective sentiments for stock market to predict the stock price directional movements. The collective sentiments in the above social media have powerful prediction on the stock price directional movements as up/down by using Granger Causality test.

Keywords: Bag of Words, Collective Sentiments, Ontology, Semantic relations, Sentiments, Social media, Stock Prediction, Twitter, Vector Space Model and wisdom of crowds.

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Authors: Kasim Terzic, Bernd Neumann

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Scene interpretation systems need to match (often ambiguous) low-level input data to concepts from a high-level ontology. In many domains, these decisions are uncertain and benefit greatly from proper context. This paper demonstrates the use of decision trees for estimating class probabilities for regions described by feature vectors, and shows how context can be introduced in order to improve the matching performance.

Keywords: Classification, Decision Trees, Interpretation, Vision

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Authors: Batel Noureddine, Mehenni Mohamed, Kouadik Smain

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In a transcutanious inductive coupling of a biomedical implant, a new formula is given for the study of the Radio Frequency power attenuation by the biological tissue. The loss of the signal power is related to its interaction with the biological tissue and the composition of this one. A confrontation with the practical measurements done with a synthetic muscle into a Faraday cage, allowed a checking of the obtained theoretical results. The supply/data transfer systems used in the case of biomedical implants, can be well dimensioned by taking in account this type of power attenuation.

Keywords: Biological tissue, coupled coils, implanted device, power attenuation.

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Authors: Jamal Bakkas, Mohamed Bahaj, Abdellatif Soklabi

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The intense use of the web has made it a very changing environment, its content is in permanent evolution to adapt to the demands. The standards have accompanied this evolution by passing from standards that regroup data with their presentations without any structuring such as HTML, to standards that separate both and give more importance to the structural aspect of the content such as XML standard and its derivatives. Currently, with the appearance of the Semantic Web, ontologies become increasingly present on the web and standards that allow their representations as OWL and RDF/RDFS begin to gain momentum. This paper provided an automatic method that converts XML schema document to ontologies represented in OWL.

Keywords: XML Schema, OWL, RDB, Mapping, Ontology.

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Authors: Noura Meshaan Al-Otaibi, Amin Yousef Noaman

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Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. This research suggests the use of Service Oriented Architecture (SOA) to integrate biological data from different data sources. This work shows SOA will solve the problems that facing integration process and if the biologist scientists can access the biological data in easier way. There are several methods to implement SOA but web service is the most popular method. The Microsoft .Net Framework used to implement proposed architecture.

Keywords: Bioinformatics, Biological data, Data Integration, SOA and Web Services.

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Authors: Haytham Al-Feel, M.A.Koutb, Hoda Suoror

Abstract:

There are many problems associated with the World Wide Web: getting lost in the hyperspace; the web content is still accessible only to humans and difficulties of web administration. The solution to these problems is the Semantic Web which is considered to be the extension for the current web presents information in both human readable and machine processable form. The aim of this study is to reach new generic foundation architecture for the Semantic Web because there is no clear architecture for it, there are four versions, but still up to now there is no agreement for one of these versions nor is there a clear picture for the relation between different layers and technologies inside this architecture. This can be done depending on the idea of previous versions as well as Gerber-s evaluation method as a step toward an agreement for one Semantic Web architecture.

Keywords: Semantic Web Architecture, XML, RDF and Ontology.

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Authors: Supriyo Goswami, Debabrata Mazumder

Abstract:

Chrome tannery wastewater causes serious environmental hazard due to its high pollution potential. As a result, rigorous treatment is necessary for abatement of pollution from this type of wastewater. There are many research studies on chrome tannery wastewater treatment in the field of physical, chemical, and biological methods. In general, biological treatment process is found ineffective for direct application because of adverse effects by toxic chromium, sulphide, chloride etc. However, biological methods were employed mainly for a few sub processes generating significant amount of organic matter and without chromium, chlorides etc. In this context the present paper reviews the characteristics feature and pollution potential of wastewater generated from chrome tannery units and treatment of the same. The different biological processes used earlier and their chronological development for treatment of the chrome tannery wastewater are thoroughly reviewed in this paper. In this regard, the scope of hybrid bioreactor - an advanced technology option has also been explored, as this kind of treatment is well suited for the wastewater having inhibitory substances. 

Keywords: Composite tannery wastewater, biological treatment, Hybrid bioreactor, Organic removal

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Authors: Victoria Konidari, Yvan Abernot

Abstract:

This paper seeks to explore the actual classroom setting, to examine its role for students- learning, and attitude in the class. It presents a theoretical approach of the classroom as system to be explored and examines the concrete reality of Greek secondary education students, under the light of the above approach. Based on the findings of a quantitative and qualitative research, authors propose a rather ontological approach of the classroom and underline what the key-elements for such approach should be. The paper explores extensively the theoretical dimensions for the change of paradigm required and addresses the new issues to be considered.

Keywords: Group, class, collective subject, field, temporality, ontology.

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Authors: Helyane B. Borges, Julio Cesar Nievola

Abstract:

Hierarchical classification is a problem with applications in many areas as protein function prediction where the dates are hierarchically structured. Therefore, it is necessary the development of algorithms able to induce hierarchical classification models. This paper presents experimenters using the algorithm for hierarchical classification called Multi-label Hierarchical Classification using a Competitive Neural Network (MHC-CNN). It was tested in ten datasets the Gene Ontology (GO) Cellular Component Domain. The results are compared with the Clus-HMC and Clus-HSC using the hF-Measure.

Keywords: Hierarchical Classification, Competitive Neural Network, Global Classifier.

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Authors: Hossein Shabanali Fami, Omid Sharifi, Javad Ghasemi, Mahtab Pouratashi, Mona Sadat Moghadasian

Abstract:

The main purpose of this study was to investigate perception of greenhouse vegetable growers regarding use of biological control practices during the growing season. The statistical population of the study included greenhouse vegetable growers in Jiroft county (N=1862). A sample of 137 vegetable growers was selected, using random sampling method. Data were collected via a questionnaire. The validity of the instrument was obtained by the faculty members of the Department of Agricultural Development and Management in the University of Tehran. Cronbach’s alpha was applied to estimate the reliability which showed a high reliability for the instrument. Data was analyzed using SPSS/Windows 13.5. The results revealed that greenhouse vegetable growers had moderate level of perception regarding biological control practices. Levels of vegetable growers’ perceptions regarding biological control practices were different on the basis of their academic qualifications as well as educational level and job. In addition, the results indicated that about 54.1% of variations in vegetable growers’ perceptions could be explained by variables such as awareness of biological control practices, knowledge on pests, annual production and age.

Keywords: Greenhouse, biological control, biological agents, perception, vegetable grower.

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Authors: Chathurika D. Abeyrathne, Malka N. Halgamuge, Peter M. Farrell

Abstract:

There is an ongoing controversy in the literature related to the biological effects of weak, low frequency electromagnetic fields. The physical arguments and interpretation of the experimental evidence are inconsistent, where some physical arguments and experimental demonstrations tend to reject the likelihood of any effect of the fields at extremely low level. The problem arises of explaining, how the low-energy influences of weak magnetic fields can compete with the thermal and electrical noise of cells at normal temperature using the theoretical studies. The magnetoreception in animals involve radical pair mechanism. The same mechanism has been shown to be involved in the circadian rhythm synchronization in mammals. These reactions can be influenced by the weak magnetic fields. Hence, it is postulated the biological clock can be affected by weak magnetic fields and these disruptions to the rhythm can cause adverse biological effects. In this paper, likelihood of altering the biological clock via the radical pair mechanism is analyzed to simplify these studies of controversy.

Keywords: Bio-effect, biological clock, magnetoreception, radical pair mechanism, weak magnetic field.

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Authors: M. Mojaddam, M. Araei, T. Saki Nejad, M. Soltani Howyzeh

Abstract:

In order to study the effect of different levels of triple super phosphate chemical fertilizer and biological phosphate fertilizer (fertile 2) on some morphological traits of corn this research was carried out in Ahvaz in 2002 as a factorial experiment in randomized complete block design with 4 replications). The experiment included two factors: first, biological phosphate fertilizer (fertile 2) at three levels of 0, 100, 200 g/ha; second, triple super phosphate chemical fertilizer at three levels of 0, 60, 90 kg/ha of pure phosphorus (P2O5). The obtained results indicated that fertilizer treatments had a significant effect on some morphological traits at 1% probability level. In this regard, P2B2 treatment (100 g/ha biological phosphate fertilizer (fertile 2) and 60 kg/ha triple super phosphate fertilizer) had the greatest plant height, stem diameter, number of leaves and ear length. It seems that in Ahvaz weather conditions, decrease of consumption of triple superphosphate chemical fertilizer to less than a half along with the consumption of biological phosphate fertilizer (fertile 2) is highly important in order to achieve optimal results. Therefore, it can be concluded that biological fertilizers can be used as a suitable substitute for some of the chemical fertilizers in sustainable agricultural systems.

Keywords: Biological phosphate fertilizer, corn (SC704), morphological, triple super phosphate.

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Authors: Mohammad Yasrebi, Mehran Mohsenzadeh, Mashalla Abbasi-Dezfuli

Abstract:

Machine-understandable data when strongly interlinked constitutes the basis for the SemanticWeb. Annotating web documents is one of the major techniques for creating metadata on the Web. Annotating websites defines the containing data in a form which is suitable for interpretation by machines. In this paper, we present a new approach to annotate websites and documents by promoting the abstraction level of the annotation process to a conceptual level. By this means, we hope to solve some of the problems of the current annotation solutions.

Keywords: Knowledge base, ontology, semantic annotation, semantic web.

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Authors: Ali Akbar Jamali

Abstract:

This paper discusses site selection process for biological soil conservation planning. It was supported by a valuefocused approach and spatial multi-criteria evaluation techniques. A first set of spatial criteria was used to design a number of potential sites. Next, a new set of spatial and non-spatial criteria was employed, including the natural factors and the financial costs, together with the degree of suitability for the Bonkuh watershed to biological soil conservation planning and to recommend the most acceptable program. The whole process was facilitated by a new software tool that supports spatial multiple criteria evaluation, or SMCE in GIS software (ILWIS). The application of this tool, combined with a continual feedback by the public attentions, has provided an effective methodology to solve complex decisional problem in biological soil conservation planning.

Keywords: GIS, Biological soil conservation planning, Spatial multi-criteria evaluation, Iran

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Authors: Mohammad Yasrebi, Mehran Mohsenzadeh

Abstract:

The third phase of web means semantic web requires many web pages which are annotated with metadata. Thus, a crucial question is where to acquire these metadata. In this paper we propose our approach, a semi-automatic method to annotate the texts of documents and web pages and employs with a quite comprehensive knowledge base to categorize instances with regard to ontology. The approach is evaluated against the manual annotations and one of the most popular annotation tools which works the same as our tool. The approach is implemented in .net framework and uses the WordNet for knowledge base, an annotation tool for the Semantic Web.

Keywords: Semantic Annotation, Metadata, Information Extraction, Semantic Web, knowledge base.

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Authors: Adama Sow, Abdoulaye Guiss´e, Oumar Niang

Abstract:

To assist medical diagnosis, we propose a federation of several existing and open medical ontologies and terminologies. The goal is to merge the strengths of all these resources to provide clinicians the access to a variety of shared knowledges that can facilitate identification and association of human diseases and all of their available characteristic signs such as symptoms and clinical signs. This work results to an integration model loaded from target known ontologies of the bioportal platform such as DOID, MESH, and SNOMED for diseases selection, SYMP, and CSSO for all existing signs.

Keywords: Medical decision, medical ontologies, ontologies integration, linked data, knowledge ingeneering, e-health system.

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Authors: Erin Lynne Plettenberg, Jeremy Vickery

Abstract:

In an access-control situation, the role of a user determines whether a data request is appropriate. This paper combines vetted web mining and logic modeling to build a lightweight system for determining the role of a health care provider based only on their prior authorized requests. The model identifies provider roles with 100% recall from very little data. This shows the value of vetted web mining in AI systems, and suggests the impact of the ICD classification on medical practice.

Keywords: Ontology, logic modeling, electronic medical records, information extraction, vetted web mining.

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Authors: Rita Kumar, Alka Sharma, Purnima Dhall, Niha M. Kulshreshtha, Anil Kumar

Abstract:

The efficient operation of any biological treatment process requires pre-treatment of incompatible pollutants such as acids, bases, oil, toxic substances, etc. which hamper the treatment of other major components which are otherwise degradable. The pre-treatment of alkaline waste-waters, generated from various industries like textile, paper & pulp, potato-processing industries, etc., having a pH of 10 or higher, is essential. The pre-treatment, i.e., neutralization of such alkaline waste-waters can be achieved by chemical as well as biological means. However, the biological pretreatment offers better package over the chemical means by being safe and economical. The biological pre-treatment can be accomplished by using a blend of microorganisms able to withstand such harsh alkaline conditions. In the present study, for the proper pre-treatment of alkaline waste-waters, a package of alkalophilic bacteria is formulated to neutralise the alkaline pH of the industrial waste-waters. The developed microbial package is cost-effective as well as environmental friendly.

Keywords: alkaline, alkalophilic bacteria, biological, pollutants, textile.

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Authors: Hadi Khosravi Farsani, Mohammadali Nematbakhsh

Abstract:

To overcome the product overload of Internet shoppers, we introduce a semantic recommendation procedure which is more efficient when applied to Internet shopping malls. The suggested procedure recommends the semantic products to the customers and is originally based on Web usage mining, product classification, association rule mining, and frequently purchasing. We applied the procedure to the data set of MovieLens Company for performance evaluation, and some experimental results are provided. The experimental results have shown superior performance in terms of coverage and precision.

Keywords: Personalization, Recommendation, OWL Ontology, Electronic Catalogs, Classification.

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Authors: B.A.Gobin, R.K.Subramanian

Abstract:

This paper gives an overview of the mapping mechanism of SEAM-a methodology for the automatic generation of knowledge models and its mapping onto Java codes. It discusses the rules that will be used to map the different components in the knowledge model automatically onto Java classes, properties and methods. The aim of developing this mechanism is to help in the creation of a prototype which will be used to validate the knowledge model which has been generated automatically. It will also help to link the modeling phase with the implementation phase as existing knowledge engineering methodologies do not provide for proper guidelines for the transition from the knowledge modeling phase to development phase. This will decrease the development overheads associated to the development of Knowledge Based Systems.

Keywords: KBS, OWL, ontology, knowledge models

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Authors: Mohamed Kholif, Suaad Awad Mohamed

Abstract:

In this paper we present semantic assistant agent (SAA), an open source digital library agent which takes user query for finding information in the digital library and takes resources- metadata and stores it semantically. SAA uses Semantic Web to improve browsing and searching for resources in digital library. All metadata stored in the library are available in RDF format for querying and processing by SemanSreach which is a part of SAA architecture. The architecture includes a generic RDF-based model that represents relationships among objects and their components. Queries against these relationships are supported by an RDF triple store.

Keywords: Digital Library, Dublin Core, Ontology, Semantic web.

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Authors: Miquel Colobran, Josep M. Basart

Abstract:

One of the most ancient humankind concerns is knowledge formalization i.e. what a concept is. Concept Analysis, a branch of analytical philosophy, relies on the purpose of decompose the elements, relations and meanings of a concept. This paper aims at presenting a method to make a concept analysis obtaining a knowledge representation suitable to be processed by a computer system using either object-oriented or ontology technologies. Security notion is, usually, known as a set of different concepts related to “some kind of protection". Our method concludes that a more general framework for the concept, despite it is dynamic, is possible and any particular definition (instantiation) depends on the elements used by its construction instead of the concept itself.

Keywords: Concept analysis, Knowledge representation, Security, UML.

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Authors: Efendi Zaenudin, Chien-Hung Huang, Ka-Lok Ng

Abstract:

Essential genes play an important role in the survival of an organism. It has been shown that cancer-associated essential genes are genes necessary for cancer cell proliferation, where these genes are potential therapeutic targets. Also, it was demonstrated that mutations of the cancer-associated essential genes give rise to the resistance of immunotherapy for patients with tumors. In the present study, we focus on studying the biological effects of the essential genes from a network perspective. We hypothesize that one can analyze a biological molecular network by decomposing it into both three-node and four-node digraphs (subgraphs). These network subgraphs encode the regulatory interaction information among the network’s genetic elements. In this study, the frequency of occurrence of the subgraph-associated essential genes in a molecular network was quantified by using the statistical parameter, odds ratio. Biological effects of subgraph-associated essential genes are discussed. In summary, the subgraph approach provides a systematic method for analyzing molecular networks and it can capture useful biological information for biomedical research.

Keywords: Biological molecular networks, essential genes, graph theory, network subgraphs.

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