Wikis semânticos: da Web para a Web Semântica

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Classificação de workflows baseados em web services

Over the last decades changes have occurred in communication within and between enterprises, made easier by technologies suchas E-commerce, Internet, ERP systems and remote meetings and there was a rapid progress in network technology, which has changed the way business is done. A standardized way to offer services over the internet is using web services. Web services are a kind of remote procedure call and are generally used to integrate systems, independent of language, both client and server. It is common to use several web services run in sequence to perform a business process. To this type of process, gives the name of workflow. Thus, Web services are the primary components of workflows. A tool that provides a way of visualizing the behavior of a workflow can assist the administrator and is required. The present work presents the development of a tool that allows the administrator to classify visually services components and evaluate their importance in the final performance of a workflow. As proof of concept we used several virtual servers and computers where each computer has received a set of web services. A proxy was added between each call of workflows collecting relevant information and storing them in a database for later analysis. The analysis was based on Quality of Service parameters

Ambiente web de suporte à transcrição fonética automática de lemas em verbetes de dicionários do português do Brasil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Ontologias no processo de indexação automática de documentos textuais

Pós-graduação em Ciência da Informação - FFC

Ontologias no processo de indexação automática de documentos textuais

Pós-graduação em Ciência da Informação - FFC

A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation

The Neotropical evaniid genus Evaniscus Szepligeti currently includes six species. Two new species are described, Evaniscus lansdownei Mullins, sp. n. from Colombia and Brazil and E. rafaeli Kawada, sp. n. from Brazil. Evaniscus sulcigenis Roman, syn. n., is synonymized under E. rufithorax Enderlein. An identification key to species of Evaniscus is provided. Thirty-five parsimony informative morphological characters are analyzed for six ingroup and four outgroup taxa. A topology resulting in a monophyletic Evaniscus is presented with E. tibialis and E. rafaeli as sister to the remaining Evaniscus species. The Hymenoptera Anatomy Ontology and other relevant biomedical ontologies are employed to create semantic phenotype statements in Entity-Quality (EQ) format for species descriptions. This approach is an early effort to formalize species descriptions and to make descriptive data available to other domains.

A UML profile for the OBO relation ontology

Background: Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain. Results: We have studied the OBO Relation Ontology, the UML metamodel and the UML profiling mechanism. Based on these studies, we have proposed an extension to the UML metamodel in conformance with the OBO Relation Ontology and we have defined a profile that implements the extended metamodel. Finally, we have applied the proposed UML profile in the development of a number of fragments from different ontologies. Particularly, we have considered the Gene Ontology (GO), the PRotein Ontology (PRO) and the Xenopus Anatomy and Development Ontology (XAO). Conclusions: The use of an established and well-known graphical language in the development of biomedical ontologies provides a more intuitive form of capturing and representing knowledge than using only text-based notations. The use of the profile requires the domain expert to reason about the underlying semantics of the concepts and relationships being modeled, which helps preventing the introduction of inconsistencies in an ontology under development and facilitates the identification and correction of errors in an already defined ontology.

BayGO: Bayesian analysis of ontology term enrichment in microarray data

Abstract Background The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. Results BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at http://blasto.iq.usp.br/~tkoide/BayGO in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. Conclusion The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one to measure the statistical association between generic ontology terms and differential expression, instead of working only with the common significance analysis.

A Fuzzy Ontology-Driven Approach to Semantic Interoperability in e-Government Big Data

With the increasing production of information from e-government initiatives, there is also the need to transform a large volume of unstructured data into useful information for society. All this information should be easily accessible and made available in a meaningful and effective way in order to achieve semantic interoperability in electronic government services, which is a challenge to be pursued by governments round the world. Our aim is to discuss the context of e-Government Big Data and to present a framework to promote semantic interoperability through automatic generation of ontologies from unstructured information found in the Internet. We propose the use of fuzzy mechanisms to deal with natural language terms and present some related works found in this area. The results achieved in this study are based on the architectural definition and major components and requirements in order to compose the proposed framework. With this, it is possible to take advantage of the large volume of information generated from e-Government initiatives and use it to benefit society.

A holistic approach to model-based testing of Web service compositions

The behavior of composed Web services depends on the results of the invoked services; unexpected behavior of one of the invoked services can threat the correct execution of an entire composition. This paper proposes an event-based approach to black-box testing of Web service compositions based on event sequence graphs, which are extended by facilities to deal not only with service behavior under regular circumstances (i.e., where cooperating services are working as expected) but also with their behavior in undesirable situations (i.e., where cooperating services are not working as expected). Furthermore, the approach can be used independently of artifacts (e.g., Business Process Execution Language) or type of composition (orchestration/choreography). A large case study, based on a commercial Web application, demonstrates the feasibility of the approach and analyzes its characteristics. Test generation and execution are supported by dedicated tools. Especially, the use of an enterprise service bus for test execution is noteworthy and differs from other approaches. The results of the case study encourage to suggest that the new approach has the power to detect faults systematically, performing properly even with complex and large compositions. Copyright © 2012 John Wiley & Sons, Ltd.

Data and behavioral contracts for web services

The recent trend in Web services is fostering a computing scenario where loosely coupled parties interact in a distributed and dynamic environment. Such interactions are sequences of xml messages and in order to assemble parties – either statically or dynamically – it is important to verify that the “contracts” of the parties are “compatible”. The Web Service Description Language (wsdl) is a standard used for describing one-way (asynchronous) and request/response (synchronous) interactions. Web Service Conversation Language extends wscl contracts by allowing the description of arbitrary, possibly cyclic sequences of exchanged messages between communicating parties. Unfortunately, neither wsdl nor wscl can effectively define a notion of compatibility, for the very simple reason that they do not provide any formal characterization of their contract languages. We define two contract languages for Web services. The first one is a data contract language and allow us to describe a Web service in terms of messages (xml documents) that can be sent or received. The second one is a behavioral contract language and allow us to give an abstract definition of the Web service conversation protocol. Both these languages are equipped with a sort of “sub-typing” relation and, therefore, they are suitable to be used for querying Web services repositories. In particular a query for a service compatible with a given contract may safely return services with “greater” contract.

An ontology-based approach to define and manage B2B interoperability

Electronic business surely represents the new development perspective for world-wide trade. Together with the idea of ebusiness, and the exigency to exchange business messages between trading partners, the concept of business-to-business (B2B) integration arouse. B2B integration is becoming necessary to allow partners to communicate and exchange business documents, like catalogues, purchase orders, reports and invoices, overcoming architectural, applicative, and semantic differences, according to the business processes implemented by each enterprise. Business relationships can be very heterogeneous, and consequently there are variousways to integrate enterprises with each other. Moreover nowadays not only large enterprises, but also the small- and medium- enterprises are moving towards ebusiness: more than two-thirds of Small and Medium Enterprises (SMEs) use the Internet as a business tool. One of the business areas which is actively facing the interoperability problem is that related with the supply chain management. In order to really allow the SMEs to improve their business and to fully exploit ICT technologies in their business transactions, there are three main players that must be considered and joined: the new emerging ICT technologies, the scenario and the requirements of the enterprises and the world of standards and standardisation bodies. This thesis presents the definition and the development of an interoperability framework (and the bounded standardisation intiatives) to provide the Textile/Clothing sectorwith a shared set of business documents and protocols for electronic transactions. Considering also some limitations, the thesis proposes a ontology-based approach to improve the functionalities of the developed framework and, exploiting the technologies of the semantic web, to improve the standardisation life-cycle, intended as the development, dissemination and adoption of B2B protocols for specific business domain. The use of ontologies allows the semantic modellisation of knowledge domains, upon which it is possible to develop a set of components for a better management of B2B protocols, and to ease their comprehension and adoption for the target users.

A communication infrastructure to support knowledge level agents on the web

Agent Communication Languages (ACLs) have been developed to provide a way for agents to communicate with each other supporting cooperation in Multi-Agent Systems. In the past few years many ACLs have been proposed for Multi-Agent Systems, such as KQML and FIPA-ACL. The goal of these languages is to support high-level, human like communication among agents, exploiting Knowledge Level features rather than symbol level ones. Adopting these ACLs, and mainly the FIPA-ACL specifications, many agent platforms and prototypes have been developed. Despite these efforts, an important issue in the research on ACLs is still open and concerns how these languages should deal (at the Knowledge Level) with possible failures of agents. Indeed, the notion of Knowledge Level cannot be straightforwardly extended to a distributed framework such as MASs, because problems concerning communication and concurrency may arise when several Knowledge Level agents interact (for example deadlock or starvation). The main contribution of this Thesis is the design and the implementation of NOWHERE, a platform to support Knowledge Level Agents on the Web. NOWHERE exploits an advanced Agent Communication Language, FT-ACL, which provides high-level fault-tolerant communication primitives and satisfies a set of well defined Knowledge Level programming requirements. NOWHERE is well integrated with current technologies, for example providing full integration for Web services. Supporting different middleware used to send messages, it can be adapted to various scenarios. In this Thesis we present the design and the implementation of the architecture, together with a discussion of the most interesting details and a comparison with other emerging agent platforms. We also present several case studies where we discuss the benefits of programming agents using the NOWHERE architecture, comparing the results with other solutions. Finally, the complete source code of the basic examples can be found in appendix.

Frame-driven Extraction of Linked Data and Ontologies from Text

Ontology design and population -core aspects of semantic technologies- re- cently have become fields of great interest due to the increasing need of domain-specific knowledge bases that can boost the use of Semantic Web. For building such knowledge resources, the state of the art tools for ontology design require a lot of human work. Producing meaningful schemas and populating them with domain-specific data is in fact a very difficult and time-consuming task. Even more if the task consists in modelling knowledge at a web scale. The primary aim of this work is to investigate a novel and flexible method- ology for automatically learning ontology from textual data, lightening the human workload required for conceptualizing domain-specific knowledge and populating an extracted schema with real data, speeding up the whole ontology production process. Here computational linguistics plays a fundamental role, from automati- cally identifying facts from natural language and extracting frame of relations among recognized entities, to producing linked data with which extending existing knowledge bases or creating new ones. In the state of the art, automatic ontology learning systems are mainly based on plain-pipelined linguistics classifiers performing tasks such as Named Entity recognition, Entity resolution, Taxonomy and Relation extraction [11]. These approaches present some weaknesses, specially in capturing struc- tures through which the meaning of complex concepts is expressed [24]. Humans, in fact, tend to organize knowledge in well-defined patterns, which include participant entities and meaningful relations linking entities with each other. In literature, these structures have been called Semantic Frames by Fill- 6 Introduction more [20], or more recently as Knowledge Patterns [23]. Some NLP studies has recently shown the possibility of performing more accurate deep parsing with the ability of logically understanding the structure of discourse [7]. In this work, some of these technologies have been investigated and em- ployed to produce accurate ontology schemas. The long-term goal is to collect large amounts of semantically structured information from the web of crowds, through an automated process, in order to identify and investigate the cognitive patterns used by human to organize their knowledge.

Ontologie per il Web Semantico: un'analisi comparativa

Il lavoro svolto in questa tesi è stato quello di analizzare il Web Semantico e i suoi linguaggi di rappresentazione delle informazioni. Inoltre sono state introdotte le ontologie evidenziando il loro ruolo all’interno del Web Semantico. Infine è stato fatto uno studio riguardo le ontologie attualmente sviluppate, allo scopo di portare a termine un’analisi comparativa delle stesse.