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Regarding ontology editors, it is observed that there are several gaps left by the main tools available on the web for editing and viewing ontologies. The proposal for this work is to provide more efficient and effective editing interfaces, providing a practical tool that improves the visualizing OWL graphs.

A linguagem XML (Exlensibk\' Markup Language) vem sendo muito utilizada em diversas aplicações e já é reconhecida como uma linguagem padrão para representação de documentos tanto no meio acadêmico quanto no comercial. Porém, a disponibilidade de uma grande quantidade de dados apresenta vários problemas práticos que o padrão XML, por si só, não pode resolver. O objetivo deste trabalho é desenvolver um servidor XML capaz de realizar diversas operações (como adicionar, consultar, apagar e transformar) sobre um repositório de documentos XML e XSL (Exiensihk\' Stylesheei Language). Esses documentos são representados na forma de objetos Java que obedecem ao modelo de interfaces DOM (Documeni Ob/ect Model), um modelo padrão usado em várias aplicações da Internet. Para o armazenamento é utilizado o serviço JavaSpaces, que pode ser usado como um repositório persistente para esses objetos DOM-Java. O servidor XML utiliza a linguagem XQL (XML Query Language) na realização de consultas. Além disso, ele permite, através da linguagem XSL, a conversão de documentos XML para outras linguagens. The Extensible Markup Language (XML) has heen used in several applications and it is being already recognized as a standard language for document representation in the academic and business wor!ds. However, great amounts of data present several practical problems that the XML standard itself does not address. The goal of this project was to develop a XML server capable of doing many kinds of operations (such as adding, querying, deleting and transforming) over a repostory of XML and XSL (Extensible Stylesheet Language) documents. These docurnents are represented using Java objccts conforming to the DOM (Document Object Model) interface model, a standard model used in many Internet applications. For object storage, the JavaSpaces service is used as a persistent repository for the DOM-Java objects. The XML server uses the XQL (XML Query Language) as query language. It a!so aliows the conversion of XML documents into other !anguages using the XSL language.

Currently, Linked Open Data (LOD) have enabled integrated data sharing across disciplines over the Web. However, for LOD users, in areas such as biodiversity (which massively use the Web to disseminate data), the task of transforming data file contents in CSV (Comma Separated Value) to RDF (Resource Description Framework) is not trivial. We have developed a new approach to map data files in CSV to RDF format based on a domain-specific language (DSL) called BioDSL. Using it, biodiversity data users can write compact programs to map their data to RDF and link them to the LOD. Biodiversity vocabularies and ontologies, such as Darwin Core and OntoBio, can be used with BioDSL to enrich user data. Existing tools are exclusively focused on mapping (CSV to RDF), offering little or no support for linking data to the LOD (interconnecting user entities to LOD entities). They also are more complex to use than BioDSL.

A second opinion about cancer stage is crucial when clinicians assess patient treatment progress. Staging is a process that takes into account description, location, characteristics, and possible metastasis of tumors in a patient. It should follow standards, such as the TNM Classification of Malignant Tumors. However, in clinical practice, the implementation of this process can be tedious and error prone. In order to alleviate these problems, we intend to assist radiologists by providing a second opinion in the evaluation of cancer stage. For doing this, we developed a TNM classifier based on semantic annotations, made by radiologists, using the ePAD tool. It transforms the annotations (stored using the AIM format), using axioms and rules, into AIM4-O ontology instances. From then, it automatically calculates the liver TNM cancer stage. The AIM4-O ontology was developed, as part of this work, to represent annotations in the Web Ontology Language (OWL). A dataset of 51 liver radiology reports with staging data, from NCI’s Genomic Data Commons (GDC), were used to evaluate our classifier. When compared with the stages attributed by physicians, the classifier stages had a precision of 85.7% and recall of 81.0%. In addition, 3 radiologists from 2 different institutions manually reviewed a random sample of 4 of the 51 records and agreed with the tool staging. AIM4-O was also evaluated with good results. Our classifier can be integrated into AIM aware imaging tools, such as ePAD, to offer a second opinion about staging as part of the cancer treatment workflow.

The concept of agricultural sustainability could be summarized as the ability of agricultural systems to maintain their production in the long term without depleting the available resources for future uses. This study proposes a decision support system for assessing the sustainability of the agricultural production and industrial processing of sugarcane in south-central Brazil by providing information structured according to criteria and indicators in the environmental, economic, and social dimensions. The information is organized using three tools: i) spreadsheets for evaluating technological efficiency, production efficiency and costs (Sugarcane Agro-industrial System Efficiency Index); ii) spreadsheet for evaluating sustainability indicators and generating the Sustainability Index; and iii) a combination of both indexes to construct the Sustainability Matrix and Semaphore, and to provide recommendations for sustainability management. The proposed decision support system contains a software (version 1.0, wherein all the information is available in electronic format, which helps to maximize assessment accuracy). Therefore, strategies such as the SustenAgro system, which helps to manage and to guide public policies, can improve the sector and enable suppliers and mills to ensure sustainable growth.

Nowadays, the Web has become one of the main sources of biodiversity information. An increasing number of biodiversity research institutions add new specimens and their related information to their biological collections and make this information available on the Web. However, mechanisms which are currently available provide insufficient provenance of biodiversity information. In this paper, we propose a new biodiversity provenance model extending the W3C PROV Data Model. Biodiversity data is mapped to terms from relevant ontologies, such as Dublin Core and GeoSPARQL, stored in triple stores and queried using SPARQL endpoints. Additionally, we provide a use case using our provenance model to enrich collection data.

This paper is about the use of natural language to communicate with computers. Most researches that have pursued this goal consider only requests expressed in English. A way to facilitate the use of several languages in natural language systems is by using an interlingua. An interlingua is an intermediary representation for natural language information that can be processed by machines. We propose to convert natural language requests into an interlingua [universal networking language (UNL)] and to execute these requests using software components. In order to achieve this goal, we propose OntoMap, an ontology-based architecture to perform the semantic mapping between UNL sentences and software components. OntoMap also performs component search and retrieval based on semantic information formalized in ontologies and rules.

Current implementations of gazetteers, geographic directories that associate place names to geographic coordinates, cannot use semantics to answer complex queries (most gazetteers are just thesauri of place names), use domain ontologies for place name disambiguation, make their data sets available in the Semantic Web or support the use of Volunteered Geographic Information (VGI). A new generation of gazetteers has to tackle these problems. In this paper, we present a new architecture for gazetteers that uses VGI and Semantic Web tools, such as ontologies and Linked Open Data to overcome these limitations. We also present a gazetteer, the Semantic Web Interactive Gazetteer (SWI), implemented using this architecture, and show that it can be used to add absent geographic coordinates to biodiversity records. In our tests, we use this gazetteer to correct geographic data from a big sample (around 142,000 occurrence records of Amazonian specimens) from SpeciesLink, a big repository of biodiversity collection records from Brazil. The tests showed that the SWI Gazetteer was able to add geographic coordinates to around 30,000 records, increasing the records with coordinates from 30.29% to 57.5% of the total number of records in the sample (representing an increase of 90%).

Biodiversity is essential to life on Earth and motivates many efforts to collect data about species. These data are collected in different places and published in different formats. Researchers use it to extract new knowledge about living things, but it is difficult to retrieve, combine and integrate data sources from different places. This work will investigate how to integrate biodiversity information from heterogeneous sources using Semantic Web technologies. Its main objective is to propose an architecture to link biodiversity data using mainly their spatiotemporal dimension, effectively search these linked data sets and test them using real use cases, defined with the help of biodiversity experts. It is also an important objective to propose a suitable provenance model that captures not only data origin but also temporal information. This architecture will be tested on a set of representative data from important Brazilian institutions that are involved in studies of biodiversity.

Information about cancer stage in a patient is crucial when clinicians assess treatment progress. Determining cancer stage is a process that takes into account the description, location, characteristics and possible metastasis of cancerous tumors in a patient. It should follow classification standards, such as TNM Classification of Malignant Tumors. However, in clinical practice, the implementation of this process can be tedious and error-prone and create uncertainty. In order to alleviate these problems, we intend to assist radiologists by providing a second opinion in the evaluation of cancer stage in patients. For doing this, Semantic Web technologies, such as ontologies and reasoning, will be used to automatically classify cancer stages. This classification will use semantic annotations, made by radiologists (using the ePAD tool) and stored in the AIM format, and rules of an ontology representing the TNM standard. The whole process will be validated through a proof of concept with users from the Radiology Dept. of the Stanford University.

Quantitative and semantic information about medical images are vital parts of a radiological report. However, current image viewing systems do not record it in a format that permits machine interpretation. The ePAD tool can generate machine-computable image annotations on 2D images as part of a radiologist's routine workflow. The tool has been evaluated in image studies with good results. Since ePAD currently only provides 2D visualization and annotation of images, we developed a plugin to ePAD for the visualization of volumetric image datasets, using the three planes: axial, frontal and sagittal. A study with 6 radiologists was carried out to determine the best interface for also marking 3D ROIs. Video prototypes were created for 3 options: join pixels based on intensity similarity, detect borders around image features, and paint ROIs using a spheric 3D cursor. The 3D cursor was the preferred option. We present these results and also show the final 3D cursor implementation.

Architecture descriptions have been the focus of several studies in which they contribute for the design, evaluation, and evolution of software systems. In parallel, ontologies have been proposed for sharing and disseminating knowledge on a particular domain. In this scenario, the ontology proposed in the ISO/IEC/IEEE 42010 standard for architecture descriptions represents an important effort towards improving architecture descriptions as it establishes a common vocabulary. Nonetheless, a formal ontology for this standard could also support automatic conformance validation and enhance architectural descriptions reuse. However, a formal ontology for this standard is not available yet. Therefore, the main contribution of this paper is the proposal of OntolAD, a formal ontology expressed in OWL 2 for the ISO/IEC/IEEE 42010 standard. We demonstrate the feasibility of our formal ontology by applying it for describing the service-oriented architecture style (SOA). We conclude this study with interesting perspectives of using this ontology in future work.

A method of peer review for student groups is proposed. In this method, groups of students publish their assignments results over the Internet. A fellow student group reviews their work and publishes their findings (on the Internet). Finally, the two groups debate their points of view in front of the class. The debate and healthy competition among groups give the students a chance to learn how to give and receive criticism in a constructive way. This should increase the students' ability to interact and work in groups, an important skill for computer science professionals.

The design of collaborative learning (CL) scenarios that increase both students' learning and motivation is a challenge that the Computer-Supported Collaborative Learning (CSCL) community has been addressing in the past few years. On one hand, CSCL design (i.e. scripts) has shown to be an effective approach to support meaningful interactions and better learning. On the other hand, scripted collaboration sometimes decrease motivation of students to participate in the CL process, which makes more difficult the use of group activities over time. To deal with the problem of motivation, researchers and educators are now looking at Gamification techniques to engage students. Gamification in education is a complex task that requires, from instructional designers, knowledge about game elements (such as leaderboards and point systems), game design (how to combine game elements) and their impact on motivation and learning. To help the adequate use of gamification in collaborative learning activities we have applied ontological engineering techniques to develop an Ontology called OntoGaCLeS in order to formalize the representation of gamification concepts and explain how they affect motivation in CL situations. This paper will present the ontological structure to represent gamified CL scenarios and show the utility of our approach to define personalized conceptual models to gamify CL scenario based on students' needs and individual characteristics.

The Semantic Web uses ontologies to associate meaning to Web content so machines can process it. One inherent problem to this approach is that, as its popularity increases, there is an ever growing number of ontologies available to be used, leading to difficulties in choosing appropriate ones. With that in mind, we created a system that allows users to evaluate ontologies/rules. It is composed by the Metadata description For Ontologies/Rules (MetaFOR), an ontology in OWL, and a tool to convert any OWL ontology to MetaFOR. With the MetaFOR version of an ontology, it is possible to use SWRL rules to identify anomalies in it. These can be problems already documented in the literature or user defined ones. SWRL is familiar to users, so it is easier to define new project specific anomalies. We present a case study where the system detects 9 problems, from the literature, and two user defined ones.

Due to the increased amount of available biodiversity data, many biodiversity research institutions are now making their databases openly available on the web. Researchers in the field use this databases to extract new knowledge and also share their own discoveries. However, when these researchers need to find relevant information in the data, they still rely on the traditional search approach, based on text matching, that is not appropriate to be used in these large amounts of heterogeneous biodiversity's data, leading to search results with low precision and recall. We present a new architecture that tackle this problem using a semantic search system for biodiversity data. Semantic search aims to improve search accuracy by using ontologies to understand user objectives and the contextual meaning of terms used in the search to generate more relevant results. Biodiversity data is mapped to terms from relevant ontologies, such as Darwin Core, DBpedia, Ontobio and Catalogue of Life, stored using semantic web formats and queried using semantic web tools (such as triple stores). A prototype semantic search tool was successfully implemented and evaluated by users from the National Research Institute for the Amazon (INPA). Our results show that the semantic search approach has a better precision (28% improvement) and recall (25% improvement) when compared to keyword based search, when used in a big set of representative biodiversity data (206,000 records) from INPA and the Emilio Gueldi Museum in Para (MPEG). We also show that, because the biodiversity data is now in semantic web format and mapped to ontology terms, it is easy to enhance it with information from other sources, an example using deforestation data (from the National Institute of Space Research - INPE) to enrich collection data is shown.

The design of collaborative learning (CL) scenarios that increase both students’ learning and motivation is a challenge that the CSCL community has been addressing in the past few years. On one hand, CSCL design (i.e. scripts) has been shown to be effective to support meaningful interactions and better learning. On the other hand, scripted collaboration often does not motivate students to participate in the CL process, which makes more difficult the use of group activities over time. To deal with the problem of motivation, researchers and educators are now looking at gamification techniques to engage students. Gamification is an interesting concept that deals with the introduction and use of game design elements in a proper way to satisfy individual motivational needs. The use of gamification in educational settings is a complex task that requires, from instructional designers, knowledge about game elements (such as leaderboards and point systems), game design (e.g. how to combine game elements) and their impact on motivation and learning. Today, to the best of our knowledge, there are no approaches for the formal systematization of the instructional design knowledge about gamification and its application in CL scenarios. Thus, to address this issue, we have applied ontological engineering techniques to develop an Ontology called OntoGaCLeS. In this paper, we present the main concepts and ontological structure used to represent gamified CL scenarios. In this ontology, we formalize the representation of gamification concepts and explain how they affect motivation in the context of collaborative learning. Particularly, we will focus on the definition of player roles and gameplay strategies. Furthermore, to show the utility of our approach, we illustrate how to use our ontology to define a personalized gamification model that is used to gamify a CL scenario based on motivational needs and individual traits of learners in a group.

There are two key challenges hindering effective use of quantitative assessment of imaging in cancer response assessment: 1) Radiologists usually describe the cancer lesions in imaging studies subjectively and sometimes ambiguously, and 2) it is difficult to repurpose imaging data, because lesion measurements are not recorded in a format that permits machine interpretation and interoperability. We have developed a freely available software platform on the basis of open standards, the electronic Physician Annotation Device (ePAD), to tackle these challenges in two ways. First, ePAD facilitates the radiologist in carrying out cancer lesion measurements as part of routine clinical trial image interpretation workflow. Second, ePAD records all image measurements and annotations in a data format that permits repurposing image data for analyses of alternative imaging biomarkers of treatment response. To determine the impact of ePAD on radiologist efficiency in quantitative assessment of imaging studies, a radiologist evaluated computed tomography (CT) imaging studies from 20 subjects having one baseline and three consecutive follow-up imaging studies with and without ePAD. The radiologist made measurements of target lesions in each imaging study using Response Evaluation Criteria in Solid Tumors 1.1 criteria, initially with the aid of ePAD, and then after a 30-day washout period, the exams were reread without ePAD. The mean total time required to review the images and summarize measurements of target lesions was 15% (P < .039) shorter using ePAD than without using this tool. In addition, it was possible to rapidly reanalyze the images to explore lesion cross-sectional area as an alternative imaging biomarker to linear measure.We conclude that ePAD appears promising to potentially improve reader efficiency for quantitative assessment of CT examinations, and it may enable discovery of future novel image-based biomarkers of cancer treatment response.

Medical imaging plays an important role in the diagnosis, prognosis and treatment of cancer. Quantitative and qualitative data about medical images are vital components of a radiological report and are very important to the oncologist that requests the radiological exams. However, traditional methods to register these data are inefficient and error prone. The use of unstructured free text in radiology reports makes it impossible to perform even simple calculations, such as changes in lesion dimensions. It also makes the aggregated analysis of many reports difficult. Free text reports lack a reference to the image regions of the finds they refer to and are not machine-computable. This paper proposes a method to provide support for collaborative work among radiologists and oncologists (providing care or taking part in clinical trials) using an imaging web tool, ePAD, to generate structured radiology reports that can be machine-computable. It also shows how ePAD uses Rad Lex ontology terms and the Annotation and Image Markup (AIM) language (and templates) to generate the reports.

BACKGROUND:Ontologies are commonly used in biomedicine to organize concepts to describe domains such as anatomies, environments, experiment, taxonomies etc. NCBO BioPortal currently hosts about 180 different biomedical ontologies. These ontologies have been mainly expressed in either the Open Biomedical Ontology (OBO) format or the Web Ontology Language (OWL). OBO emerged from the Gene Ontology, and supports most of the biomedical ontology content. In comparison, OWL is a Semantic Web language, and is supported by the World Wide Web consortium together with integral query languages, rule languages and distributed infrastructure for information interchange. These features are highly desirable for the OBO content as well. A convenient method for leveraging these features for OBO ontologies is by transforming OBO ontologies to OWL.RESULTS:We have developed a methodology for translating OBO ontologies to OWL using the organization of the Semantic Web itself to guide the work. The approach reveals that the constructs of OBO can be grouped together to form a similar layer cake. Thus we were able to decompose the problem into two parts. Most OBO constructs have easy and obvious equivalence to a construct in OWL. A small subset of OBO constructs requires deeper consideration. We have defined transformations for all constructs in an effort to foster a standard common mapping between OBO and OWL. Our mapping produces OWL-DL, a Description Logics based subset of OWL with desirable computational properties for efficiency and correctness. Our Java implementation of the mapping is part of the official Gene Ontology project source.CONCLUSIONS:Our transformation system provides a lossless roundtrip mapping for OBO ontologies, i.e. an OBO ontology may be translated to OWL and back without loss of knowledge. In addition, it provides a roadmap for bridging the gap between the two ontology languages in order to enable the use of ontology content in a language independent manner.

O ensino de logica de programacao se constitui num desafio para os cursos de computacao. Neste sentido, esforcos tem sido empregados para o desenvolvimento de estrategias e ferramentas que auxiliem o ensino e contribuam para o aprendizado de disciplinas a fins. Desta forma, e proposta uma abordagem colaborativa, baseada em desafios, que visa complementar e apoiar o aprendizado e ensino de logica de programacao. Essa abordagem visa criar um ambiente atraente e motivador, sob a perspectiva do aluno, com ferramentas que permitam ao professor acompanhar a evolucao dos alunos. Tambem e apresentada uma ferramenta que implementa essa abordagem e testes realizados na mesma.

In the last few years, education has been going through an important change: the introduction of information technology in the educational process. Many efforts have been conducted to realize the benefits of such technologies, such as the MIT-Media Lab One Laptop per Child initiative (MIT, 2007) in education. As a result of these efforts, there are many tools available today to produce multimedia educational material for the Web such as WebCT (WebCT, 2004). However, teachers are not sure how to use these tools to create effective models for teaching over the Internet. After a teacher puts classroom slides, schedules, and other static information on Web pages, what more can this technology offer? A possible response to this question is to use Internet technologies to promote collaborative learning. Collaborative learning (CL) is an educational strategy based on social theories in which students, joined in small groups, are responsible for the learning experience of each other (Gokhale, 1995; Panitz, 2002). In CL, the main goal of the teacher is to organize collective activities that can stimulate the development of skills such as creativity, oral expression, and critical thinking, among others. When supported by computers and Internet technologies, collaborative learning is referenced as computer supported collaborative learning (CSCL). The main goal of CSCL is to use software and hardware to support and increase group work and learning. The peer review method, known by almost everyone in the academic world, when applied as an educational tool, can be considered a kind of collaborative learning activity. This article describes an educational method that uses peer review and the Internet to promote interaction among students. This method, which has been used and refined since 1997 (by the first author), has been used in different computer science courses at the ICMC-USP. Software tools, such as the WebCoM—Web Course Manager tool (Silva & Moreira, 2003)—are used to support the peer review method and to improve interaction among students. The main advantages of the peer review method and the WebCoM tool over other works in this context are that they: • Allow debate between groups (workers and reviewers) to improve interaction and social abilities among students; • Focus on the interaction among students and their social skills; • Also offer support for group activities (such as reports and assignments) without peer review. Results generated by the experience of managing classes with the WebCoM tool are also presented.

The Open Biomedical Ontologies (OBO) format from the GO consortium is a very successful format for biomedical ontologies, including the Gene Ontology. But it lacks formal computational definitions for its constructs and tools, like DL reasoners, to facilitate ontology development/maintenance. We describe the OBO Converter, a Java tool to convert files from OBO format to Web Ontology Language (OWL) (and vice versa) that can also be used as a Protégé Tab plug-in. It uses the OBO to OWL mapping provided by the National Center for Biomedical Ontologies (NCBO) (a joint effort of OBO developers and OWL experts) and offers options to ease the task of saving/reading files in both formats. Availability: bioontology.org/tools/oboinowl/obo_converter.html Contact: dilvan@stanford.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Although there are many Internet-based educational applications available today, they usually do not allow functionality extensions, change or reuse. In this context, this paper presents a framework - the WebMODE, based on the J2EE component architecture, for helping the development of more customizable educational applications. This framework merges important features from popular content management systems (such as pluggable modules) to the model view controller architecture, found in popular frameworks for Web development.

In the last few years, education has gone through an important change—the introduction of information technology in the educational process. Many efforts have been conducted to realize the benefits of technologies like the Internet in education. As a result of these efforts, there are many tools available today to produce multimedia educational material for the Web, such as WebCT (WebCT, 2004). However, teachers are not sure how to use these tools to create effective models for teaching over the Internet. After a teacher puts classroom slides, schedules, and other static information in his or her Web pages, what more can this technology offer? A possible response to this question is to use Internet technologies to promote collaborative learning.

Although there are many Internet-based educational applications available today, they usually do not allow functionality extensions, change or reuse. In this context, this paper presents a framework, based on the J2EE component architecture, for helping the development of more customizable educational applications. In order to reach its goal, it merges significant features from popular CMS (such as pluggable modules) to the MVC architecture, found in most popular frameworks for Web development.

Agents are defined as software components that communicate with their peers by exchanging messages in a communication language. They are used in the placer server of the Agents system, a distributed, client-server system that generates mask level layout of full custom VLSI leaf cells. The system is formed from four server programs: the Placer, Router, Database and Broker. This paper describes the placer server which uses groups of these small software agents and the genetic algorithm to place optimally the components of a leaf cell.

A program for the design of leaf cells for silicon compilers of digital VLSI circuits, is being developed. It uses rule based modules to put together basic circuits, check design rules, check designs constraints and to control each of these constituent tasks. An optimization algorithm, in this case a genetic algorithm, optimizes the layout, under the control of the rule system. The program is divided into modules that can run together using a client-server model. >

Publisher Summary Software agents are characterized by their ability to communicate and cooperate with each other. This key characteristic is exploited in the layout generation domain by the Agents system to generate flexible very large scale integration (VLSI) mask level layouts. At a high level, the system is subdivided into four large agents (macroagents) distributed over a network of computers: the Placer, the Router, the Database, and the Broker. The Placer places components in a cell, the Router wires the circuits sent to it, the Database keeps all the information that is dependent upon the fabrication process, and the Broker manages the services of the other agents. At a lower level, inside the Router and Placer agents, small relatively simple agents (microagents) work together to accomplish complex tasks. These microagents are responsible for all reasoning carried out by the Router and the Placer because they hold the basic inference routines and the knowledge needed by the agents. The key concept is that competence emerges out of the collective behavior of a large number of relatively simple agents.

A program for the design of leaf cells for silicon compilers of digital VLSI (Very Large Scale Integrated) circuits, is being developed. This program uses rule based reasoning and genetic algorithmic search techniques, whenever each is appropriate. Leaf cells are subcircuits of a complexity comparable with SSI (Small Scale Integration) components such as one-bit adders, flip-flops or multiplexers. They typically contain between 10 to 100 transistors. Silicon compilers can use libraries of ready designed leaf cells or each leaf cell can be automatically generated [1] by synthesis tools such as the program we are developing. The main advantage of the synthesis approach is that circuit performance will not be sacrificed since a new, optimal layout will be produced whatever the complexity of the circuit and whenever the fabrication process is upgraded.