Information Sciences Focus Paper about a Knowledge Organization (WebProtégé)
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Information Sciences Focus Paper about a Knowledge Organization (WebProtégé)
Introduction
The high adoption of Web 2.0 platforms, semantic web technologies, and ontologies in the real world has enhanced the development of ontology tools that are well suited for new interaction, construction, and knowledge consumption. Today, users do not know how crucial online collaboration and web-based content creation are to the current world. One ontology tool that fits the present world is WebProtégé, which is an ontology editor and a tool for knowledge acquisition that is popular for its lightweight and effectiveness in web activities. It is responsible for developing the ontology process while integrating these features (Tudorache, Nyulas, Noy, & Musen, 2013).
WebProtégé supports the ontology services by using Google Web Toolkit (GWT) to create the protégé and user interface (UI). It is also a web application that edits OWL 2ontologies, providing rich and complex information about things requested by users. The tool also offers various features to its users that help in collaboration. Apart from that, WebProtégé is characterized by a simple UI that allows users to edit descriptions and annotations prevalent in ontologies of various fields, such as biomedical and education. The latest version of WebProtégé supports the OWL 2 language and allows editing of lightweight ontology since its UI is customizable and has been primarily configured for the role (Horridge et al., 2014).
Architecture of WebProtégé
WebProtégé’s architecture creates a platform whereby users interact with client applications like collaborative protégé and WebProtégé on a desktop and web browser, respectively. It connects to a servlet engine that has server logic for the application. As a result, all clients connect to the same collaborative framework with features such as access control, storage of information, and change tracking, among many others.
| Servlet Container | ||
| Remote Services Interface | ||
| Protégé 3.x implementation | OWL-API implementation | Other implementation |
| Web Side Applications |
| Client Side Applications
|
| WebProtégé (JavaScript) |
| Other Web Applications |
RPC
WebProtégé’s REST services
| Collaborative framework | ||||||
| Notes and discussions | Change tracking | Access Control | Workflow | |||
| Ontology access (API) | ||||||
| RDF | OWL | DB | Frames | |||
| Java API |
| RMI |
| Collaborative Protégé (Java) |
RMI
| Other rich client applications applications |
RMI
Java API
Case Study: Importance of WebProtégé in Biomedicine
Most public mature ontologies are present in many domains, including biomedicine. (Tudorache, Nyulas, Noy, & Musen, 2013). Ontologies are essential artifacts in life sciences and the field of bioinformatics. It refers to what is entailed in parts of a subject and how they are connected. It is important in every academic discipline or field and is usually established to organize data into information and knowledge categories and bound complexity. Most biomedical ontologies are developed by experts working together and who consider the end-users for additional input. Additionally, most biomedical ontologies are hosted on platforms such as the OntoBee, OBOLibrary, and BioPortal, where they are usually published and exchanged as OWL 2 ontology files.
WebProtégé is important in the biomedical field as it provides support for a section of the language ideal for seizing biomedical knowledge. It is catered for by tools such as OBOEdit that allows the efficient sharing of information between people. WebProtégé distributes the (UI) views that are specialized for editing OBO metadata and definitions related to biomedical ontologies. These UI views tailored by OBO and collaborative development functionality enhance the importance of WebProtégé by making it attractive for developing biomedical ontologies in the community.
Further, it is based on a project notion that includes custom UI configuration settings, a collection of OWL ontologies, and collaboration settings. These projects can either be initialized with existing ontologies or created from scratch and imported or uploaded. A vital feature of WebProtégé is that it supports the development of ontology by multiple users in a collaborative way and in real-time. It allows users to share their completed projects with collaborators by adding them as editors, viewers, or commenters. It provides several features to help enhance collaboration (Horridge et al., 2014).
Reflection
The introduction and use of WebProtégé to improve teaching capabilities in the education sector focuses on developing the educational processes of institutions and information space. For instance, in our school, the use of this tool in information science courses was helpful as it enabled us to organize our learning process and created a platform whereby we were able to work actively as a team. It also increased our enthusiasm while studying as a team and individually as we improved our results by studying and analyzing our work. When used alongside the traditional teaching methods, this tool increased our collaborative skills as the learning process was transformed to be more mobile, interactive, individual, and strictly mobile. This is because the tool’s features allowed us to exchange live messages amongst ourselves, discuss issues, change tracking by revising, and change notifications. The tool is also efficient as it is easy to use, and as students, it quickly and efficiently responded to our requests and actions. It enhanced our technological skills during research, making it easy for us to access online information effectively.
Moreover, WebProtégé was also important to our lectures as it made it easier for them to analyze and assess our skills as students. It also encouraged them to look for better and innovative teaching methods. By having a wide range of features, this tool helped them organize their work, reducing the time used to teach and allowing them to create more time to do other things. Using this method, it was easier for them to teach us how to collaborate, interact, share, and reflect on various issues.
Discussion and conclusions
WebProtégé is not only a lightweight ontology web editor but also a tool that supports collaboration. It is used across a wide range of domains, including the biomedical and education fields. In the biomedical field, WebProtégé makes it easy to detect information in texts despite having a technical and scientific nature. Therefore, it is important to develop ontologies, enhancing concept description and relationships, information search, data integration, and reasoning in the biomedical field. In education, WebProtégé encourages collaboration among students and is vital to the work of lecturers. To students, the tool is essential as it supports group work and collaborative success. It connects them to a common collaboration framework where they can talk about issues, offer opinions, comment, edits, and contribute to the other users’ work. While supporting the collaborative working method, this tool also allows students to work individually to assess their capabilities, skills, and knowledge. However, this tool also possesses various limitations as it is restricted and optimized for lightweight ontology development, which is OWL 2 ontology. These limitations inhibit the tool from developing other web ontology languages.
Those who have used the tool have discovered that, in addition to being easy to operate, it is also useful in providing information through ontology development. The tool has also been implemented in domains with mature ontologies to obtain accurate and simplified information that everyone can easily understand. That could be hard to obtain using the other web ontology development tools. It is an essential tool that has helped various organizations solve issues and obtain web-based information while also storing user data. Although it only supports the OWL 2 ontology language, WebProtégé creates a highly configurable user interface that creates a comfortable environment for beginners and experts. The tool also has a wide range of collaboration features available to support the importation and exportation of ontology documents. These features include emails and watches’ notifications, sharing and permissions, discussions and threaded notes, OWL, OBO, among many other formats that can be uploaded and downloaded. Information science researchers should, therefore, look for solutions to eliminate WebProtégé limitations to increase its use in web processes.
Limitations and recommendations
The current version of WebProtégé is, however, limited to OWL 2 ontology language as its architecture is not flexible to accommodate other ontology languages. This can be corrected by enhancing its architecture to create a platform that will manage ontology changes and provide a more feasible way to solve conflicts during the editing process. Additionally, this tool has a narrow range of collaboration features that can be extended to support a wider range by revealing the UI’s change tracking information. This solution would support various collaborative workflow types and also enforce editing and browsing ontologies’ access policies. Also, the tool has poor scalability when it comes to developing large ontologies as it is limited in the use of JavaScript. This can be changed by developing widgets incorporated with pagination support to handle large ontologies.
References
Horridge, M., Tudorache, T., Nuylas, C., Vendetti, J., Noy, N. F., & Musen, M. A. (2014). WebProtégé: A collaborative Web-based platform for editing biomedical ontologies. Bioinformatics, 30(16), 2384-2385. doi:10.1093/bioinformatics/btu256
Tudorache, T., Nyulas, C., Noy, N. F., & Musen, M. A. (2013). WebProtégé: A collaborative ontology editor and knowledge acquisition tool for the Web. Semantic Web, 4(1), 89-99. doi:10.3233/sw-2012-0057