Giovani Rubert Librelotto

TM-Builder: An Ontology Builder based on XML Topic Maps

Everyday a huge number of new information resources are linked to the web. This way the web is growing very fast, making search tasks more and more difficult with worse results. To solve the problem several initiatives were undertaken and a new area of research and development emerged: the one called Semantic Web. When we refer to the semantic web we are thinking about a network of concepts. Each concept has a group of related resources and can be related to other concepts; we can then use this concept network to navigate among web resources or simply among information resources. From the undertaken initiatives one became an ISO standard: Topic Maps ISO 13250. The aim of this paper is to introduce a Topic Map (TM) Builder , that is a processor that extracts topics and relations from instances of a family of XML documents. A TM-Builder is strongly dependent on the resources structure. So, to extract a topic map for different collections of information resources (sets of documents with different structures) we have to implement several TM-Builders, one for each collection. This is not very easy! To overcome this inconvenient we have created an XML abstraction layer for TM-Buildersthat enables us to specify the topic map we want to build from a concrete family of resources, in order to generate automatically the intended extractor. To describe that process, i.e. the extraction of knowledge from XML documents to produce a TM, we present a language to specify topic maps for a class of XML documents, that we call XSTM (XML Specification for Topic Maps). We also discuss a XSL processor that automatically generates the Extractor from its formal specification written in XSTM, the XSTM-P.

Topic maps constraint languages: understanding and comparing

Topic map constraint language (TMCL) provides a means to express constraints on topic maps conforming to ISO/IEC 13250. In this article, we will use a test suite and show, step-by-step, the way we handled several kinds of topic maps constraints in many different instances in order to answer questions like: Do they do the same job? Are there some kinds of topic maps constraints that are easier to specify with one of them? Do you need different background to use the tools? Is it possible to use them in similar situations (the same topic maps instances)? May we use them to produce an equal result? How do AsTMa!, OSL, Toma and XTche relate to TMCL? What kind of constraints each one of these three cannot specify? We will conclude this paper with a summary of the comparisons accomplished between those topic maps constraint languages over the use case proposed.

Metamorphosis : a topic maps based environment to handle heterogeneous information resources

Nowadays, data handled by an institution or company is spread out by more than one database and lots of documents of different types. To extract the information implicit in that data, it is necessary to pick parts from those various archives. To obtain a general overview, those information slices should be integrated. Different approaches can be followed to achieve that integration, ranging from the merge of resources till the fusion of the extracted parts. In this paper, we introduce Metamorphosis – a Topic Maps oriented environment that enables a conceptual navigation among heterogenous information systems – and we argue that Metamorphosis can be used to achieve, via Topic Maps, the referred semantic integration.

Induced genome maintenance pathways in pre-cancer tissues describe an anti-cancer barrier in tumor development

A recent model proposing that a barrier is raised against tumor evolution in pre-cancer tissues is investigated. For that we quantify expression alterations in genome maintenance pathways: DNA damage response, death pathways and cell cycle and also differentially expressed genes in transcriptomes of pre-cancerous and cancerous lesions deposited in the GEO database. We find that the main alterations in pre-cancer samples comprising the barrier are: (1) DNA double strand-breaks signaling and repair pathways induction, (2) upregulation of cyclin-dependent kinases, (3) p53 dependent (and independent) repair and apoptosis pathways induction and (4) replicative senescence induction early in tissue transformation. In the cancer samples we find that the induced pathways in pre-cancer are systematically inhibited and the only remaining induced pathway is p53, whereas the retinoblastoma pathway arises induced in most samples. The results give support to the model, furthermore they reveal the involvement of additional mechanisms in pre-cancer, including the early induction of replicative senescence and of p53 independent apoptosis.

Applying Pervasive Computing in an Architecture for Homecare Environments

Every year the queues in publics and privates hospitals grows due to, among others, the increasing of the world population and the delay in the patients attendance. This is a serious problem faced by administrators of hospitals whose believe that it is increasingly difficult to offer quality service to those who search for it. One of the ways to decrease these queues is through the development of homecare systems that ensure the patient to receive the clinic treatment directly in his house. These kind of systems would help to decrease the queues and consequently, would improve the attendance of those who goes to the hospitals looking for assistance. Considering this, we present in this paper the modelling of an architecture for pervasive systems to be applied in homecare environments. The pervasive systems developed from this modelling aim to improve the services provided by healthcare professionals in the treatment of patients that are located in their houses. The architecture uses concepts of pervasive computing to provide access to information anytime and wherever the user is, once a homecare environment has a high level of dynamicity of the involved. The knowledge representation of the environment needed in the modelling of the architecture is made through ontologies due to the possibility of reuse of the information stored, as well as the interoperability of information among different computational devices.

A framework to specify, extract and manage topic maps driven by ontology

The ability to extract and merge data that from documents (or databases) of different types, in order to acquire knowledge from a vast repository of information, is of unquestionable value. However that desirable integration is not an easy task. Different approaches can be followed to achieve it, ranging from the merge of resources (implying their conversion to a common format) till the fusion of the extracted parts. The idea is to interoperate those resources keeping them independent, without changes or transformations, creating over them an integration layer that gives us a general overview, as the information slices were gathered. This is possible creating a semantic network, or a conceptual map, over the resources, which relates data items among them mapping each one to its different occurrences in the repository; formally speaking, that conceptual map corresponds to the ontology that describes the knowledge we want to acquire. In this paper, we introduce Metamorphosis, a Topic Maps oriented environment to extract data from heterogeneous information repositories and to generate a browser and conceptual navigator for the extracted knowledge.

Middleware for management of end-user programming of clinical activities in a pervasive environment

Currently, Pervasive Computing has focused on the development of programmable and interactive environments, which are intended to help the user in daily activities. The health system of the future envisages the use of Pervasive Computing as a way of optimizing and automating clinical activities. Under such perspective, the present study has tried to adapt a middleware for pervasive environment management to support and manage the accomplishment of clinical tasks (pervasive applications that help physicians perform their activities), fulfilling some requirements of activities-oriented computing, and creating a tool that will help physicians in their daily tasks.

XCSL : XML constraint specification language

After being able to mark-up text and validate its structure according to a document type specication, we may start thinking it would be natural to be able to validate some nonstructural issues in the documents. This paper is to formally discuss semantic-related aspects. In that context, we introduce a domain specic language developed for such a purpose: XCSL. XCSL is not just a language, it is also a processing model. Furthermore, we discuss the general philosophy underlying the proposed approach, presenting the architecture of our semantic validation system, and we detail the respective processor. To illustrate the use of XCSL language and the subsequent processing, we present two case-studies. Nowadays, we can nd some other languages to restrict XML documents to those semantically valid | namely Schematron and XML-Schema. So, before concluding the paper, we compare XCSL to those approaches.

A Reduced CRM-Compatible Form Ontology for the Virtual Emigration Museum

In this paper we discuss the construction of a Reduced CRM-compatible form ontology for the virtual Emigration Museum based in the international standard for museum ontologies, CIDOC-CRM. To extract knowledge from the information of the virtual Emigration Museum when navigating through it, abstract data models should be used to conceptualize, the emigration documents stored in a relational database. In that way, resorting to an ontology (as abstract layer), the information contained in those documents can be accessed by the end-users (the museum visitors) to learn about the emigration phenomena. We also describe how we instantiate the ontology through a parser that automatically translates a plain text description of emigration data into RDF. Finally, we also discuss the choice of a triple storage system to save the RDF triples in order to enable the use of SPARQL to query the RDF data.

Formal Description and Automatic Generation of Learning Spaces Based on Ontologies

A good virtual Learning Space (LS) should convey pertinent learning information to the visitors at the most adequate time and locations to favor their knowledge acquisition.Considering the consolidation of the internet and the improvement of the interaction, searching, and learning mechanisms, we propose a generic architecture, called CaVa, to create virtual Learning Spaces building up on cultural institution documents. More precisely, our proposal is to automatically create ontology-based virtual learning environments.Thus, to impart relevant learning materials to the virtual LS, we propose the use of ontologies to represent the key concepts and semantic relations in an user- and machine-understandable format. These concepts together with the data (extracted from the real documents) stored in a digital storage format (XML datasets, relational databases, etc.) are displayed in an ontology-based learning space that enables the visitors to use the available features and tools to learn about a specific domain.According to the approach here discussed, each desired virtual LS must be specified rigorously through a domain specific language (DSL) that was designed and implemented.To validate the proposed architecture, three case studies will be used as instances of CaVa architecture.