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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.

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.

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.

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%).

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.

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.

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.