A Hub System for Cloud-Computing Based Business-Collaboration: Automating Ontology-Enabled Electronic Business-Service Discovery

The management and coordination of business-process collaboration experiences changes because of globalization, specialization, and innovation. Service-oriented computing (SOC) is a means towards businessprocess automation and recently, many industry standards emerged to become part of the service-oriented architecture (SOA) stack. In a globalized world, organizations face new challenges for setting up and carrying out collaborations in semi-automating ecosystems for business services. For being efficient and effective, many companies express their services electronically in what we term business-process as a service (BPaaS). Companies then source BPaaS on the fly from third parties if they are not able to create all service-value inhouse because of reasons such as lack of reasoures, lack of know-how, cost- and time-reduction needs. Thus, a need emerges for BPaaS-HUBs that not only store service offers and requests together with information about their issuing organizations and assigned owners, but that also allow an evaluation of trust and reputation in an anonymized electronic service marketplace. In this paper, we analyze the requirements, design architecture and system behavior of such a BPaaS-HUB to enable a fast setup and enactment of business-process collaboration. Moving into a cloud-computing setting, the results of this paper allow system designers to quickly evaluate which services they need for instantiationg the BPaaS-HUB architecture. Furthermore, the results also show what the protocol of a backbone service bus is that allows a communication between services that implement the BPaaS-HUB. Finally, the paper analyzes where an instantiation must assign additional computing resources vor the avoidance of performance bottlenecks.

Unified Taxonomy for Reference Ontology of Shape Features in Product Model

This paper presents a unified taxonomy of shape features. Such taxonomy is required to construct ontologies to address heterogeneity in product/shape models. Literature provides separate classifications for volumetric, deformation and free-form surface features. The unified taxonomy proposed allows classification, representation and extraction of shape features in a product model. The novelty of the taxonomy is that the classification is based purely on shape entities and therefore it is possible to automatically extract the features from any shape model. This enables the use of this taxonomy to build reference ontology.

Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions

Background: The number of genome-wide association studies (GWAS) has increased rapidly in the past couple of years, resulting in the identification of genes associated with different diseases. The next step in translating these findings into biomedically useful information is to find out the mechanism of the action of these genes. However, GWAS studies often implicate genes whose functions are currently unknown; for example, MYEOV, ANKLE1, TMEM45B and ORAOV1 are found to be associated with breast cancer, but their molecular function is unknown. Results: We carried out Bayesian inference of Gene Ontology (GO) term annotations of genes by employing the directed acyclic graph structure of GO and the network of protein-protein interactions (PPIs). The approach is designed based on the fact that two proteins that interact biophysically would be in physical proximity of each other, would possess complementary molecular function, and play role in related biological processes. Predicted GO terms were ranked according to their relative association scores and the approach was evaluated quantitatively by plotting the precision versus recall values and F-scores (the harmonic mean of precision and recall) versus varying thresholds. Precisions of similar to 58% and similar to 40% for localization and functions respectively of proteins were determined at a threshold of similar to 30 (top 30 GO terms in the ranked list). Comparison with function prediction based on semantic similarity among nodes in an ontology and incorporation of those similarities in a k nearest neighbor classifier confirmed that our results compared favorably. Conclusions: This approach was applied to predict the cellular component and molecular function GO terms of all human proteins that have interacting partners possessing at least one known GO annotation. The list of predictions is available at http://severus.dbmi.pitt.edu/engo/GOPRED.html. We present the algorithm, evaluations and the results of the computational predictions, especially for genes identified in GWAS studies to be associated with diseases, which are of translational interest.

MAS Ontology: uma ontologia de métodos orientados a agentes

A modelagem orientada a agentes surge como paradigma no desenvolvimento de software, haja vista a quantidade de iniciativas e estudos que remetem à utilização de agentes de software como solução para tratar de problemas mais complexos. Apesar da popularidade de utilização de agentes, especialistas esbarram na falta de universalidade de uma metodologia para construção dos Sistemas Multiagentes (MAS), pois estas acabam pecando pelo excesso ou falta de soluções para modelar o problema. Esta dissertação propõe o uso de uma Ontologia sobre Metodologias Multiagentes, seguindo os princípios da Engenharia de Métodos Situacionais que se propõe a usar fragmentos de métodos para construção de metodologias baseados na especificidade do projeto em desenvolvimento. O objetivo do estudo é sedimentar o conhecimento na área de Metodologias Multiagentes, auxiliando o engenheiro de software a escolher a melhor metodologia ou o melhor fragmento de metodologia capaz de modelar um Sistema Multiagentes.

An ontology for a Robot Scientist

Soldatova, L., Clare, A., Sparkes, A. and King, R. D. (2006) An ontology for a robot scientist. Bioinformatics 2006 22: 464-471

ART: An ontology based tool for the translation of papers into Semantic Web format

To be presented at SIG/ISMB07 ontology workshop: http://bio-ontologies.org.uk/index.php To be published in BMC Bioinformatics. Sponsorship: JISC

A unified anatomy ontology of the vertebrate skeletal system.

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.

BACKGROUND: A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on synonyms and common names, and monophyletic supraspecific taxa that reflect our current understanding of phylogenetic relationships. DESCRIPTION: As a step towards development of such a resource, and to enable large-scale integration of phenotypic data across vertebrates, we created the Vertebrate Taxonomy Ontology (VTO), a semantically defined taxonomic resource derived from the integration of existing taxonomic compilations, and freely distributed under a Creative Commons Zero (CC0) public domain waiver. The VTO includes both extant and extinct vertebrates and currently contains 106,947 taxonomic terms, 22 taxonomic ranks, 104,736 synonyms, and 162,400 cross-references to other taxonomic resources. Key challenges in constructing the VTO included (1) extracting and merging names, synonyms, and identifiers from heterogeneous sources; (2) structuring hierarchies of terms based on evolutionary relationships and the principle of monophyly; and (3) automating this process as much as possible to accommodate updates in source taxonomies. CONCLUSIONS: The VTO is the primary source of taxonomic information used by the Phenoscape Knowledgebase (http://phenoscape.org/), which integrates genetic and evolutionary phenotype data across both model and non-model vertebrates. The VTO is useful for inferring phenotypic changes on the vertebrate tree of life, which enables queries for candidate genes for various episodes in vertebrate evolution.

The Ontology of Thisness

The paper seeks to give an account of what it is for an individual to instantiate thisness, and how an individual and its thisness are related (where the thisness of an individual x is the property of being identical to x). Such an account is completely lacking in the literature, even among those who defend and make use of thisness. My approach is to seek out a model for the instantiation of thisness by canvassing realist accounts of the substance/attribute relation , and then make appropriate modifications to the most likely candidate in order to accommodate an individual's instantiation of thisness (the accounts cannot be strictly identical for reasons that I explain). I go on to suggest that the model can be appropriately applied in the case of other individuals which might instantiate thisness: for example, persons and events (where these are conceived as fundamental categories of ontology distinct from material substances).

Demos and Denomination::flags, fealty, and the political ontology of protests in Northern Ireland

This paper will examine some of the ways in which processes of denomination
have shaped Northern Irish politics before and after the ‘Belfast’, or ‘Good Friday
Agreement’ of 1998. We concentrate on the formation of the ‘Unionist’ or ‘Loyalist
community’, principally because the flag protests of 2012-2013 have brought the
issue of this community identity to the fore again. The flag is part of a whole
machinery of what we, in this paper, will call ‘denomination’ in Northern Irish
politics and elsewhere. The religious overtones of the term are neither accidental
nor incidental. Acts of denomination posit (assertively, authoritatively) a
collective identity, conceived and constituted ontologically, as an existent entity,
and stake a claim to a whole territory.

Behavioral Model Generation from Use Cases Based on Ontology Mapping and GRASP Patterns

This paper contributes a new approach for developing UML software designs from Natural Language (NL), making use of a meta-domain oriented ontology, well established software design principles and Natural Language Processing (NLP) tools. In the approach described here, banks of grammatical rules are used to assign event flows from essential use cases. A domain specific ontology is also constructed, permitting semantic mapping between the NL input and the modeled domain. Rules based on the widely-used General Responsibility Assignment Software Principles (GRASP) are then applied to derive behavioral models.

Georg Lukács as a Communications Scholar: Cultural and Digital Labour in the Context of Lukács’ Ontology of Social Being

The task of this work is to apply thoughts from Georg Lukács’ final book, the Ontology of Social Being, for the theoretical analysis of cultural and digital labour. It discusses Lukács’ concepts of work and communication and relates them to the analysis of cultural and digital work. It also analyses his conception of the relation of labour and ideology and points out how we can make use of it for critically understanding social media ideologies. Lukács opposes the dualist separation of the realms of work and ideas. He introduces in this context the notion of teleological positing that allows us to better understand cultural and digital labour as well as associated ideologies, such as the engaging/connecting/sharing-ideology, today. The analysis shows that Lukács’ Ontology is in the age of Facebook, YouTube, and Twitter still a very relevant book, although it has thus far not received the attention that it deserves. This article also introduces the Ontology’s main ideas on work and culture, which is important because large parts of the book have not been translated from the German original into English. Lukács’ notion of teleological positing is crucial for understanding the common features of the economy and culture.

Withdrawing from Atmosphere: An Ontology of Air partitioning and Affective Engineering

The main objective of this text is to warn against atmospherics. However comfortable it might appear, an atmosphere is politically suspicious because it numbs a body into an affective embrace of stability and permanence. It becomes doubly suspicious because a body desires to be part of the atmosphere. For this reason, I rethink both affect and atmosphere ontologically rather than phenomenologically. I argue that an atmosphere is engineered by subsuming individual affects to what I call, following Sloterdijk, an atmospheric glasshouse. I suggest that this happens in four steps: a distinction between inside and outside through partitioning; inclusion of the outside inside; illusion of synthesis; and dissimulation. In order to do this, I begin with air as the elemental paradox of ontological continuum and rupture. I carry on with the passage from air to atmosphere while retaining the discourse around continuum and rupture. Finally, I indicate a way of rupturing the atmospheric continuum through the ontological movement of withdrawal from the atmosphere. The ultimate goal of the article is to sketch a problematic of atmospherics that puts together without synthesising an elemental ontology of continuum and rupture.

Withdrawing from atmosphere: An ontology of air partitioning and affective engineering

The main objective of this text is to warn against atmospherics. However comfortable it might appear, an atmosphere is politically suspicious because it numbs a body into an affective embrace of stability and permanence. It becomes doubly suspicious because a body desires to be part of the atmosphere. For this reason, I rethink both affect and atmosphere ontologically rather than phenomenologically. I argue that an atmosphere is engineered by subsuming individual affects to what I call, following Sloterdijk, an atmospheric glasshouse. I suggest that this happens in four steps: a distinction between inside and outside through partitioning; inclusion of the outside inside; illusion of synthesis; and dissimulation. In order to do this, I begin with air as the elemental paradox of ontological continuum and rupture. I carry on with the passage from air to atmosphere while retaining the discourse around continuum and rupture. Finally, I indicate a way of rupturing the atmospheric continuum through the ontological movement of withdrawal from the atmosphere. The ultimate goal of the article is to sketch a problematic of atmospherics that puts together without synthesising an elemental ontology of continuum and rupture.

Enhancing Agent Mediated Electronic Markets with Ontology Matching Services and Social Network Support

Os Mercados Eletrónicos atingiram uma complexidade e nível de sofisticação tão elevados, que tornaram inadequados os modelos de software convencionais. Estes mercados são caracterizados por serem abertos, dinâmicos e competitivos, e constituídos por várias entidades independentes e heterogéneas. Tais entidades desempenham os seus papéis de forma autónoma, seguindo os seus objetivos, reagindo às ocorrências do ambiente em que se inserem e interagindo umas com as outras. Esta realidade levou a que existisse por parte da comunidade científica um especial interesse no estudo da negociação automática executada por agentes de software [Zhang et al., 2011]. No entanto, a diversidade dos atores envolvidos pode levar à existência de diferentes conceptualizações das suas necessidades e capacidades dando origem a incompatibilidades semânticas, que podem prejudicar a negociação e impedir a ocorrência de transações que satisfaçam as partes envolvidas. Os novos mercados devem, assim, possuir mecanismos que lhes permitam exibir novas capacidades, nomeadamente a capacidade de auxiliar na comunicação entre os diferentes agentes. Pelo que, é defendido neste trabalho que os mercados devem oferecer serviços de ontologias que permitam facilitar a interoperabilidade entre os agentes. No entanto, os humanos tendem a ser relutantes em aceitar a conceptualização de outros, a não ser que sejam convencidos de que poderão conseguir um bom negócio. Neste contexto, a aplicação e exploração de relações capturadas em redes sociais pode resultar no estabelecimento de relações de confiança entre vendedores e consumidores, e ao mesmo tempo, conduzir a um aumento da eficiência da negociação e consequentemente na satisfação das partes envolvidas. O sistema AEMOS é uma plataforma de comércio eletrónico baseada em agentes que inclui serviços de ontologias, mais especificamente, serviços de alinhamento de ontologias, incluindo a recomendação de possíveis alinhamentos entre as ontologias dos parceiros de negociação. Este sistema inclui também uma componente baseada numa rede social, que é construída aplicando técnicas de análise de redes socias sobre informação recolhida pelo mercado, e que permite melhorar a recomendação de alinhamentos e auxiliar os agentes na sua escolha. Neste trabalho são apresentados o desenvolvimento e implementação do sistema AEMOS, mais concretamente: • É proposto um novo modelo para comércio eletrónico baseado em agentes que disponibiliza serviços de ontologias; • Adicionalmente propõem-se o uso de redes sociais emergentes para captar e explorar informação sobre relações entre os diferentes parceiros de negócio; • É definida e implementada uma componente de serviços de ontologias que é capaz de: • o Sugerir alinhamentos entre ontologias para pares de agentes; • o Traduzir mensagens escritas de acordo com uma ontologia em mensagens escritas de acordo com outra, utilizando alinhamentos previamente aprovados; • o Melhorar os seus próprios serviços recorrendo às funcionalidades disponibilizadas pela componente de redes sociais; • É definida e implementada uma componente de redes sociais que: • o É capaz de construir e gerir um grafo de relações de proximidade entre agentes, e de relações de adequação de alinhamentos a agentes, tendo em conta os perfis, comportamento e interação dos agentes, bem como a cobertura e utilização dos alinhamentos; • o Explora e adapta técnicas e algoritmos de análise de redes sociais às várias fases dos processos do mercado eletrónico. A implementação e experimentação do modelo proposto demonstra como a colaboração entre os diferentes agentes pode ser vantajosa na melhoria do desempenho do sistema e como a inclusão e combinação de serviços de ontologias e redes sociais se reflete na eficiência da negociação de transações e na dinâmica do mercado como um todo.