Profile Ontology Research Articles

Ontology-based multi-agents for intelligent healthcare applications

A healthy diet and lifestyle are the most effective approaches to prevent disease. Good eating habits are central to a healthy lifestyle. When a person eats too much or too little on a continual basis, the risk of disease will increase. Therefore, developing healthy and balanced eating habits is essential to disease prevention. This paper proposes an ontology-based multi-agents (OMAS), including a personal knowledge agent, a fuzzy inference agent, and a semantic generation agent, for evaluating the health of diets. Using the proposed approach, domain experts can create nutritional facts for common Taiwanese foods. Next, the users are requested to input foods eaten. Finally, the food ontology and personal profile ontology are constructed by domain experts. Fuzzy markup language (FML) is used to describe the knowledge base and rule base of the OMAS. Additionally, web ontology language (OWL) is employed to describe the food ontology and personal profile ontology. Finally, the OMAS semantically analyzes dietary status for users based on the pre-constructed ontology and fuzzy inference results. Using the generated semantic analysis, people can obtain health information about what they eat, which can lead to a healthy lifestyle and healthy diet. Experimental results show that the proposed approach works effectively and diet health status can be provided as a reference to promote healthy living.

Natural variation for seed dormancy in Arabidopsis is regulated by additive genetic and molecular pathways.

Timing of germination is presumably under strong natural selection as it determines the environmental conditions in which a plant germinates and initiates its postembryonic life cycle. To investigate how seed dormancy is controlled, quantitative trait loci (QTL) analyses has been performed in six Arabidopsis thaliana recombinant inbred line populations by analyzing them simultaneously using a mixed model QTL approach. The recombinant inbred line populations were derived from crosses between the reference accession Landsberg erecta (Ler) and accessions from different world regions. In total, 11 delay of germination (DOG) QTL have been identified, and nine of them have been confirmed by near isogenic lines (NILs). The absence of strong epistatic interactions between the different DOG loci suggests that they affect dormancy mainly by distinct genetic pathways. This was confirmed by analyzing the transcriptome of freshly harvested dry seeds of five different DOG NILs. All five DOG NILs showed discernible and different expression patterns compared with the expression of their genetic background Ler. The genes identified in the different DOG NILs represent largely different gene ontology profiles. It is proposed that natural variation for seed dormancy in Arabidopsis is mainly controlled by different additive genetic and molecular pathways rather than epistatic interactions, indicating the involvement of several independent pathways.

Structural and Role-Oriented Web Service Discovery with Taxonomies in OWL-S

In this paper, we describe and evaluate a Web service discovery framework using OWL-S advertisements, combined with the distinction between service and Web service of the WSMO discovery framework. More specifically, we follow the Web service discovery model, which is based on abstract and lightweight semantic Web service descriptions, using the service profile ontology of OWL-S. Our goal is to determine fast an initial set of candidate Web services for a specific request. This set can then be used in more fine-grained discovery approaches, based on richer Web service descriptions. Our Web service matchmaking algorithm extends object-based matching techniques used in structural case-based reasoning, allowing 1) the retrieval of Web services not only based on subsumption relationships, but exploiting also the structural information of OWL ontologies and 2) the exploitation of Web services classification in profile taxonomies, performing domain-dependent discovery. Furthermore, we describe how the typical paradigm of profile input/output annotation with ontology concepts can be extended, allowing ontology roles to be considered as well. We have implemented our framework in the OWLS-SLR system, which we extensively evaluate and compare to the OWLS-MX matchmaker.

A Type-2 Fuzzy Ontology and its Application to Personal Diabetic Diet Recommendation

It has been widely pointed out that classical ontology is not sufficient to deal with imprecise and vague knowledge for some real-world applications like personal diabetic-diet recommendation. On the other hand, fuzzy ontology can effectively help to handle and process uncertain data and knowledge. This paper proposes a novel ontology model, which is based on interval type-2 fuzzy sets (T2FSs), called type-2 fuzzy ontology (T2FO), with applications to knowledge representation in the field of personal diabetic-diet recommendation. The T2FO is composed of 1) a type-2 fuzzy personal profile ontology ( type-2 FPPO); 2) a type-2 fuzzy food ontology ( type-2 FFO); and 3) a type-2 fuzzy-personal food ontology (type-2 FPFO). In addition, the paper also presents a T2FS-based intelligent diet-recommendation agent ( IDRA), including 1) T2FS construction; 2) a T2FS-based personal ontology filter; 3) a T2FS-based fuzzy inference mechanism; 4) a T2FS-based diet-planning mechanism; 5) a T2FS-based menu-recommendation mechanism; and 6) a T2FS-based semantic-description mechanism. In the proposed approach, first, the domain experts plan the diet goal for the involved diabetes and create the nutrition facts of common Taiwanese food. Second, the involved diabetics are requested to routinely input eaten items. Third, the ontology-creating mechanism constructs a T2FO, including a type-2 FPPO, a type-2 FFO, and a set of type-2 FPFOs. Finally, the T2FS-based IDRA retrieves the built T2FO to recommend a personal diabetic meal plan. The experimental results show that the proposed approach can work effectively and that the menu can be provided as a reference for the involved diabetes after diet validation by domain experts.

Integration of microRNA changes in vivo identifies novel molecular features of muscle insulin resistance in type 2 diabetes

BackgroundSkeletal muscle insulin resistance (IR) is considered a critical component of type II diabetes, yet to date IR has evaded characterization at the global gene expression level in humans. MicroRNAs (miRNAs) are considered fine-scale rheostats of protein-coding gene product abundance. The relative importance and mode of action of miRNAs in human complex diseases remains to be fully elucidated. We produce a global map of coding and non-coding RNAs in human muscle IR with the aim of identifying novel disease biomarkers.MethodsWe profiled >47,000 mRNA sequences and >500 human miRNAs using gene-chips and 118 subjects (n = 71 patients versus n = 47 controls). A tissue-specific gene-ranking system was developed to stratify thousands of miRNA target-genes, removing false positives, yielding a weighted inhibitor score, which integrated the net impact of both up- and down-regulated miRNAs. Both informatic and protein detection validation was used to verify the predictions of in vivo changes.ResultsThe muscle mRNA transcriptome is invariant with respect to insulin or glucose homeostasis. In contrast, a third of miRNAs detected in muscle were altered in disease (n = 62), many changing prior to the onset of clinical diabetes. The novel ranking metric identified six canonical pathways with proven links to metabolic disease while the control data demonstrated no enrichment. The Benjamini-Hochberg adjusted Gene Ontology profile of the highest ranked targets was metabolic (P < 7.4 × 10-8), post-translational modification (P < 9.7 × 10-5) and developmental (P < 1.3 × 10-6) processes. Protein profiling of six development-related genes validated the predictions. Brain-derived neurotrophic factor protein was detectable only in muscle satellite cells and was increased in diabetes patients compared with controls, consistent with the observation that global miRNA changes were opposite from those found during myogenic differentiation.ConclusionsWe provide evidence that IR in humans may be related to coordinated changes in multiple microRNAs, which act to target relevant signaling pathways. It would appear that miRNAs can produce marked changes in target protein abundance in vivo by working in a combinatorial manner. Thus, miRNA detection represents a new molecular biomarker strategy for insulin resistance, where micrograms of patient material is needed to monitor efficacy during drug or life-style interventions.

The differential transcriptome and ontology profiles of floating and cumulus granulosa cells in stimulated human antral follicles

Communication between various ovarian cell types is a prerequisite for folliculogenesis and ovulation. In antral follicles granulosa cells divide into two distinct populations of mural and cumulus granulosa cells (CGC), enveloping the antrum and surrounding the oocyte, respectively. Both cell types, with the mural compartment in excess, contribute to the floating granulosa cell (FGC) population in the follicular fluid. The aim of this study was to compare the transcriptomes of FGC and CGC in stimulated antral follicles obtained from 19 women undergoing IVF-ICSI procedure. FGC were obtained from follicular fluid during the follicle puncture procedure and CGC were acquired after oocyte denudation for micromanipulation. Gene expression analysis was conducted using the genome-wide Affymetrix transcriptome array. The expression profile of the two granulosa cell populations varied significantly. Out of 28 869 analysed transcripts 4480 were differentially expressed (q-value < 10(-4)) and 489 showed > or =2-fold difference in the expression level with 222 genes up-regulated in FGC and 267 in CGC. The transcriptome of FGC showed higher expression of genes involved in immune response, hematological system function and organismal injury, although CGC had genes involved in protein degradation and nervous system function up-regulated. Cell-to-cell signalling and interaction pathways were noted in both cell populations. Furthermore, numerous novel transcripts that have not been previously described in follicular physiology were identified. In conclusion, our results provide a solid basis for future studies in follicular biology that will help to identify molecular markers for oocyte and embryo viability in IVF.

Combining ontological profiles with context in information retrieval

An ontology is a formal conceptualization of a domain, specifying the concepts of the domain and the relations between them. It is however not a straight forward task to use this knowledge for information retrieval purposes. In this paper we describe the concept of an ontological profile, which is a semantic extension of an ontology where each ontology concept is given a description in terms of a vector of weighted keywords. An experiment has been conducted with a prototype search engine using ontological profiles for query expansion. The evaluation shows encouraging results compared to standard keyword based search. Furthermore, we describe the notion of context in an information retrieval setting and address how we can combine semantics and context in search based on query expansion.

Global brain gene expression analysis links glutamatergic and GABAergic alterations to suicide and major depression.

BackgroundMost studies investigating the neurobiology of depression and suicide have focused on the serotonergic system. While it seems clear that serotonergic alterations play a role in the pathogenesis of these major public health problems, dysfunction in additional neurotransmitter systems and other molecular alterations may also be implicated. Microarray expression studies are excellent screening tools to generate hypotheses about additional molecular processes that may be at play. In this study we investigated brain regions that are known to be implicated in the neurobiology of suicide and major depression are likely to represent valid global molecular alterations.Methodology/Principal FindingsWe performed gene expression analysis using the HG-U133AB chipset in 17 cortical and subcortical brain regions from suicides with and without major depression and controls. Total mRNA for microarray analysis was obtained from 663 brain samples isolated from 39 male subjects, including 26 suicide cases and 13 controls diagnosed by means of psychological autopsies. Independent brain samples from 34 subjects and animal studies were used to control for the potential confounding effects of comorbidity with alcohol. Using a Gene Ontology analysis as our starting point, we identified molecular pathways that may be involved in depression and suicide, and performed follow-up analyses on these possible targets. Methodology included gene expression measures from microarrays, Gene Score Resampling for global ontological profiling, and semi-quantitative RT-PCR. We observed the highest number of suicide specific alterations in prefrontal cortical areas and hippocampus. Our results revealed alterations of synaptic neurotransmission and intracellular signaling. Among these, Glutamatergic (GLU) and GABAergic related genes were globally altered. Semi-quantitative RT-PCR results investigating expression of GLU and GABA receptor subunit genes were consistent with microarray data.Conclusions/SignificanceThe observed results represent the first overview of global expression changes in brains of suicide victims with and without major depression and suggest a global brain alteration of GLU and GABA receptor subunit genes in these conditions.

Notice of Violation of IEEE Publication Principles Ontology-based semantic recommendation system in home network environment

Notice of Violation of IEEE Publication Principles<br>"Ontology-based Semantic Recommendation System in Home Network Environment"<br> by Jinhyung Kim, Dongwon Jeong and Doo-kwon Baik<br> in the IEEE Transactions on Consumer Electronics, Vol 55, No. 3, August 2009, pp. 1178-1184<br><br> After careful and considered review of the content and authorship of this paper by a duly constituted expert committee, this paper has been found to be in violation of IEEE's Publication Principles. <br><br> This paper contains text and figures that have been copied from the paper cited below. The original text was copied without attribution (including appropriate references to the original author(s) and/or paper title) and without permission. <br><br> Due to the nature of this violation, reasonable effort should be made to remove all past references to this paper, and future references should be made to the following article: <br><br> "Applying User Profile Ontology for Mining Web site Adaptation Recommendations"<br> by Tarmo Robal and Ahto Kalja<br> in the Proceedings of the 11th East-European Conference on Advances in Databases and Information Systems (ADBIS 2007), pp. 126-135<br><br> <br/> Home network is one of the predominant applications in ubiquitous computing. In home network environment, we need semantic recommendation system for exact and abundant information recommendation to users. For semantic recommendation system, we construct ontology for user profiles and home network services firstly in this paper. In addition to, we suggest recommendation method for ontology-based semantic recommendation. By using the suggested system, we can support more precise and richer information recommendation.

The role of ontologies in supporting distributed medical systems

Introduction: The K4, Care European Project proposes a standard model for home-care (HC) assistance of elderly chronic patients (ECP), coordinating all professionals and institutions involved in HC for proper assistance. The model is supported by a distributed multi agent platform (MAP), a metaphor of the HC itself. Every person involved is represented by an intelligent agent interacting with other agents, representing other colleagues. Warnings are sent to the corresponding agent when required by other agents for some action to complete a medical service. Correct transferring of the HC knowledge to the MAP is a key issue. Methods: The actor profile ontology (APO) was build to determine the behaviour of MAP: the services to be provided have been specified by combinations of simpler actions; liabilities, responsibilities and access rights of every kind of professional involved in HC is specified, as well as interaction between different professionals. Agents are created according to APO definitions. Results: A prototype is implemented where physicians, nurses, social workers, carers... coordinate through their personal agents for HC of ECP, according to APO. The platform is currently being tested with real patients in Pollenza (It). Conclusion: Ontologies allow knowledge transmission to a computer application. APO provides high flexibility to mid and log-term evolution of HC, as changing it automatically changes the system behaviour. The basic structure of an ontology to support distributed medical complex systems is identified and this structure is easily exportable to other kind of medical systems, like hospital management or provision of dependency services.

Search in Social Tagging Systems Using Ontological User Profiles

In this paper we present a modified hierarchical agglomerative clustering algorithm for building tag ontologies for social tagging systems. The modified algorithm first uses a clustering algorithm called Domain Similarity Clustering By Committee (DSCBC) (Tomuro et al. 2007) to derive a set of tag committees. We apply DSCBC to the tags entered by the users of social tagging systems and derive (un-ambiguous) committees of tags. Using the committees, a tag ontology is constructed in which an ambiguous tag is separated into multiple, disambiguated tags/nodes. Then a tag profile of a given user is matched against the ontology, and an ontological profile of the user is created. Finally a preference vector is fed into the (modified) FolkRank algorithm (Hotho et al. 2006a), and the web resources ordered based on the user's preferences are returned. We run our system on the data from two social tagging systems and compare the results with other algorithms. The results showed our algorithm achieved marked improvements over other algorithms.

Towards a study opportunities recommender system in ontological principles-based on semantic web environment

A professional career selection is a complicated process for university student candidates and often little technical tolls are available for who aim to enter to superior education since it is necessary to consider incidence of a multiplicity of variables to obtain a satisfactory answer that comes near to idea that they have preconceived. These variables build up a complex relations map that requires formulation of an exhaustive and rigorous conceptual scheme. In this research a domain ontological model is presented as support to student's decision making for opportunities of University studies level of Venezuelan education For declaration of domain ontological model developed, information provided by two organisms (OPSU & CNU) is used. Both are responsible to design policies and strategies for superior education in Venezuela. The ontology is designed and created using Methontology approach, since this methodology offers possibility of improving progressive creation or captures and knowledge articulation, its elements and relations. In order to represent ontology Protege 3.1.1 tool is used, based on ontological language for Web: OWL (Web Ontology Language) and; finally, to accede and to visualize ontology, an application based on Semantic Web is developed. In field of computation, computer science and systems, concept of profiles or users models has many meanings and connotations, its first and greater diffusion arise with development and use of on-line increasing systems; however, they have gain great preponderance recently, not only to refer and/or to respond to passive user who approaches the system, but for possibility of taking care of a user stimulated and attracted by the system. In that sense, possibility of this personalized attention and/or recommendations from the system will be obviously conditioned by user context. Centered on possibility of giving that customized attention from which they must select an option between many, it is tried in future to construct a meta-ontology that integrates domain ontology with a user profile ontology, thus aiming towards to a Semantic Recommendation System under Multiagent approach in future, that could be useful to support students decision making process for career selection over different study opportunities in Higher Education level in Venezuela.

“The Unity of the Generative Power”: Modern Taxonomy and the Problem of Animal Generation

Much recent scholarly treatment of the theoretical and practical underpinnings of biological taxonomy from the 16th to the 18th centuries has failed to adequately consider the importance of the mode of generation of some living entity in the determination of its species membership, as well as in the determination of the ontological profile of the species itself. In this article, I show how a unique set of considerations was brought to bear in the classification of creatures whose species membership was thought to be entirely determined by descent from parents of the same kind, in contrast with creatures whose generation could proceed spontaneously or through budding. Concretely, the relevance of mode of generation to the practice of taxonomy means that we must rethink the role of the early modern botanists in the development of a universal science of applied taxonomy. I argue that the task of classifying ‘higher’ biological kinds—those united, in Kant's language, through their generative power—is one with...

Knowledge extraction and representation of collaborative activity through ontology-based and Social Network Analysis technologies

This paper describes an approach for extracting and representing the knowledge generated from collaborative interaction of small learning teams that work together in distance to carry out a software project or a case study. Our approach is based on ontology, Social Network Analysis (SNA) and fuzzy classification, which has been initially developed as a mechanism to analyse and understand behavioural patterns from collaboration performed in different scenarios. Through the SNA we are able to define an ontological profile that provides a deep knowledge about the participants' roles, intentions and effects; hence a fuzzy model can perform inferences over individual indicators.

Increase in mitochondrial biogenesis, oxidative stress, and glycolysis in murine lymphomas

Lymphomas adapt to their environment by undergoing a complex series of biochemical changes that are currently not well understood. To better define these changes, we examined the gene expression and gene ontology profiles of thymic lymphomas from a commonly used model of carcinogenesis, the p53 −/− mouse. These tumors show a highly significant upregulation of mitochondrial biogenesis, mitochondrial protein translation, mtDNA copy number, reactive oxygen species, antioxidant defenses, proton transport, ATP synthesis, hypoxia response, and glycolysis, indicating a fundamental change in the bioenergetic profile of the transformed T cell. Our results suggest that T cell tumorigenesis involves a simultaneous upregulation of mitochondrial biogenesis, mitochondrial respiration, and glycolytic activity. These processes would allow cells to adapt to the stressful tumor environment by facilitating energy production and thereby promote tumor growth. Understanding these adaptations is likely to result in improved therapeutic strategies for this tumor type.

Stage- and Gender-Specific Proteomic Analysis of Brugia malayi Excretory-Secretory Products

IntroductionWhile we lack a complete understanding of the molecular mechanisms by which parasites establish and achieve protection from host immune responses, it is accepted that many of these processes are mediated by products, primarily proteins, released from the parasite. Parasitic nematodes occur in different life stages and anatomical compartments within the host. Little is known about the composition and variability of products released at different developmental stages and their contribution to parasite survival and progression of the infection.Methodology/Principal FindingsTo gain a deeper understanding on these aspects, we collected and analyzed through 1D-SDS PAGE and LC-MS/MS the Excretory-Secretory Products (ESP) of adult female, adult male and microfilariae of the filarial nematode Brugia malayi, one of the etiological agents of human lymphatic filariasis. This proteomic analysis led to the identification of 228 proteins. The list includes 76 proteins with unknown function as well as also proteins with potential immunoregulatory properties, such as protease inhibitors, cytokine homologues and carbohydrate-binding proteins. Larval and adult ESP differed in composition. Only 32 proteins were shared between all three stages/genders. Consistent with this observation, different gene ontology profiles were associated with the different ESP.Conclusions/SignificanceA comparative analysis of the proteins released in vitro by different forms of a parasitic nematode dwelling in the same host is presented. The catalog of secreted proteins reflects different stage- and gender-specific related processes and different strategies of immune evasion, providing valuable insights on the contribution of each form of the parasite for establishing the host–parasite interaction.

Gene expression in a canine basilar artery vasospasm model: a genome-wide network-based analysis

To investigate the changes of gene expression on the cerebral vasospasm after subarachnoid hemorrhage, we used genome-wide microarray for a canine double-hemorrhage model and analyzed the data by using a network-based analysis. Six dogs were assigned to two groups of three animals: control and hemorrhage. The effects were assessed by the changes in gene expressions in the artery 7 days after the first blood injection. Among 23,914 genes, 447 and 66 genes were up-regulated more than two- and fivefold, respectively, and 332 and 25 genes were down-regulated more than two- and fivefold, respectively. According to gene ontology, genes related to cell communication (P = 5.28E-10), host–pathogen interaction (7.65E-8), and defense–immunity protein activity (0.000183) were significantly overrepresented. The top high-level function for the merged network derived from the network-based analysis was cell signaling, revealing that the subgroup that regulates the quantity of Ca2+ to have the strongest association significance (P = 4.75E-16). Canine microarray analysis followed by gene ontology profiling and connectivity analysis identified several functional groups and individual genes responding to cerebral vasospasm. Ca2+ regulation may play a key role in these gene expression changes and may be involved in the pathogenesis of cerebral vasospasm.

K4care: a new intelligent system for home care

The K4CARE project (FP6-IST-4 IST-2004- 026968) is a EC project about the development, integration and use of several Information and Communication Technologies (ICT) and intelligent Computer Science (CS) technologies in the framework of Home Care (HC). The main objective of the K4CARE project is to improve the capabilities of the new EU society to manage and respond to the needs of the increasing number of senior population requiring a personalized HC assistance. K4CARE will develop: a model for HC service which can be shared by the EU countries; an Electronic Home Care Record; a telematic and knowledge-based CS platform; a multi-agent system; Actor Profile Ontologies for representing the profiles of the subjects involved in the K4CARE model; Case Profile Ontologies for representing symptoms, diseases, syndromes; Formal Intervention Plans. The K4CARE project is developed by thirteen EU partners: eight centres with geriatric, medical and healthcare competencies and five ICT and CS centres

Developing a knowledge management platform for automotive build-to-order production network

Modern global companies have to build a supply chain network strategy that provides maximum flexibility and can optimally respond to changes in their environment. The emergence of automotive build-to-order production networks is one of the consequences of these changes in the automotive industry. Production networks can be seen as a step beyond the linear supply chain topography. However, when dealing with multiple organizations and multiple processes within a complicated production network, identifying and locating a member that has responsibility and/or competence in a particular part of the network can be a laborious, time-consuming process. Developing and maintaining a competence directory of all the relevant parties associated with troubleshooting and potential problem solving can significantly reduce the production lead time. Moreover, linking this directory to key decision points and frequent problems can further enhance its effectiveness. Consequently, the problem of semantic interoperability between members of such organizations is of major importance. This paper proposes an approach to developing a knowledge management platform for a build-to-order production network to solve the above problem. The approach is based on application of such technologies as ontology management, context management and profiling.

Transcriptional Changes in the Hookworm, Ancylostoma caninum, during the Transition from a Free-Living to a Parasitic Larva

BackgroundThird-stage larvae (L3) of the canine hookworm, Ancylostoma caninum, undergo arrested development preceding transmission to a host. Many of the mRNAs up-regulated at this stage are likely to encode proteins that facilitate the transition from a free-living to a parasitic larva. The initial phase of mammalian host invasion by A. caninum L3 (herein termed “activation”) can be mimicked in vitro by culturing L3 in serum-containing medium.Methodology/Principal FindingsThe mRNAs differentially transcribed between activated and non-activated L3 were identified by suppression subtractive hybridisation (SSH). The analysis of these mRNAs on a custom oligonucleotide microarray printed with the SSH expressed sequence tags (ESTs) and publicly available A. caninum ESTs (non-subtracted) yielded 602 differentially expressed mRNAs, of which the most highly represented sequences encoded members of the pathogenesis-related protein (PRP) superfamily and proteases. Comparison of these A. caninum mRNAs with those of Caenorhabditis elegans larvae exiting from developmental (dauer) arrest demonstrated unexpectedly large differences in gene ontology profiles. C. elegans dauer exiting L3 up-regulated expression of mostly intracellular molecules involved in growth and development. Such mRNAs are virtually absent from activated hookworm larvae, and instead are over-represented by mRNAs encoding extracellular proteins with putative roles in host-parasite interactions.Conclusions/SignificanceAlthough this should not invalidate C. elegans dauer exit as a model for hookworm activation, it highlights the limitations of this free-living nematode as a model organism for the transition of nematode larvae from a free-living to a parasitic state.