The CKC Challenge: Exploring Tools for Collaborative Knowledge Construction

The great success of Web 2.0 is mainly fuelled by an infrastructure that allows web users to create, share, tag, and connect content and knowledge easily. The tools for developing structured knowledge in this manner have started to appear as well. However, there are few, if any, user studies that are aimed at understanding what users expect from such tools, what works and what doesn't. We organized the Collaborative Knowledge Construction (CKC) Challenge to assess the state of the art for the tools that support collaborative processes for creation of various forms of structured knowledge. The goal of the Challenge was to get users to try out different tools and to learn what users expect from such tools /features that users need, features that they like or dislike. The Challenge task was to construct structured knowledge for a portal that would provide information about research. The Challenge design contained several incentives for users to participate. Forty-nine users registered for the Challenge; thirty three of them participated actively by using the tools. We collected extensive feedback from the users where they discussed their thoughts on all the tools that they tried. In this paper, we present the results of the Challenge, discuss the features that users expect from tools for collaborative knowledge constructions, the features on which Challenge participants disagreed, and the lessons that we learned

How orthogonal are the OBO Foundry ontologies?

<p>Abstract</p> <p>Background</p> <p>Ontologies in biomedicine facilitate information integration, data exchange, search and query of biomedical data, and other critical knowledge-intensive tasks. The OBO Foundry is a collaborative effort to establish a set of principles for ontology development with the eventual goal of creating a set of interoperable reference ontologies in the domain of biomedicine. One of the key requirements to achieve this goal is to ensure that ontology developers reuse term definitions that others have already created rather than create their own definitions, thereby making the ontologies orthogonal.</p> <p>Methods</p> <p>We used a simple lexical algorithm to analyze the extent to which the set of OBO Foundry candidate ontologies identified from September 2009 to September 2010 conforms to this vision. Specifically, we analyzed (1) the level of explicit term reuse in this set of ontologies, (2) the level of overlap, where two ontologies define similar terms independently, and (3) how the levels of reuse and overlap changed during the course of this year.</p> <p>Results</p> <p>We found that 30% of the ontologies reuse terms from other Foundry candidates and 96% of the candidate ontologies contain terms that overlap with terms from the other ontologies. We found that while term reuse increased among the ontologies between September 2009 and September 2010, the level of overlap among the ontologies remained relatively constant. Additionally, we analyzed the six ontologies announced as OBO Foundry members on March 5, 2010, and identified that the level of overlap was extremely low, but, notably, so was the level of term reuse.</p> <p>Conclusions</p> <p>We have created a prototype web application that allows OBO Foundry ontology developers to see which classes from their ontologies overlap with classes from other ontologies in the OBO Foundry (<url>http://obomap.bioontology.org</url>). From our analysis, we conclude that while the OBO Foundry has made significant progress toward orthogonality during the period of this study through increased adoption of explicit term reuse, a large amount of overlap remains among these ontologies. Furthermore, the characteristics of the identified overlap, such as the terms it comprises and its distribution among the ontologies, indicate that the achieving orthogonality will be exceptionally difficult, if not impossible.</p

Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains

Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases (ICD) as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the ICD, which is currently under active development by the WHO contains nearly 50,000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding how these stakeholders collaborate will enable us to improve editing environments that support such collaborations. We uncover how large ontology-engineering projects, such as the ICD in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users subsequently change) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology-engineering projects and tools in the biomedical domain.Comment: Published in the Journal of Biomedical Informatic

Context-Specific Ontology Integration: A Bayesian Approach

We introduce a principled computational framework and methodology for automated discovery of context-specific functional links between ontologies. Our model leverages over disparate free-text literature resources to score the model of dependency linking two terms under a context against their model of independence. We identify linked terms as those having a significant bayes factor (p < 0.01). To scale our algorithm over massive ontologies, we propose a heuristic pruning technique as an efficient algorithm for inferring such links. We have applied this method to translationalize Gene Ontology to all other ontologies available at National Center of Biomedical Ontology (NCBO) BioPortal under the context of Human Disease ontology. Our results show that in addition to broadening the scope of hypothesis for researchers, our work can potentially be used to explore continuum of relationships among ontologies to guide various biological experiments

Bioportal: Ontologies and integrated data resources at the click of the mouse

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content

Protégé: A Tool for Managing and Using Terminology in Radiology Applications

The development of standard terminologies such as RadLex is becoming important in radiology applications, such as structured reporting, teaching file authoring, report indexing, and text mining. The development and maintenance of these terminologies are challenging, however, because there are few specialized tools to help developers to browse, visualize, and edit large taxonomies. Protégé (http://protege.stanford.edu) is an open-source tool that allows developers to create and to manage terminologies and ontologies. It is more than a terminology-editing tool, as it also provides a platform for developers to use the terminologies in end-user applications. There are more than 70,000 registered users of Protégé who are using the system to manage terminologies and ontologies in many different domains. The RadLex project has recently adopted Protégé for managing its radiology terminology. Protégé provides several features particularly useful to managing radiology terminologies: an intuitive graphical user interface for navigating large taxonomies, visualization components for viewing complex term relationships, and a programming interface so developers can create terminology-driven radiology applications. In addition, Protégé has an extensible plug-in architecture, and its large user community has contributed a rich library of components and extensions that provide much additional useful functionalities. In this report, we describe Protégé’s features and its particular advantages in the radiology domain in the creation, maintenance, and use of radiology terminology

The universal ontology: A vision for conceptual modeling and the semantic web

This paper puts forward a vision of a universal ontology (UO) aiming at solving, or at least greatly alleviating, the semantic integration problem in the field of conceptual modeling and the understandability problem in the field of the semantic web. So far it has been assumed that the UO is not feasible in practice, but we think that it is time to revisit that assumption in the light of the current state-of-the-art. This paper aims to be a step in this direction. We try to make an initial proposal of a feasible UO. We present the scope of the UO, the kinds of its concepts, and the elements that could comprise the specification of each concept. We propose a modular structure for the UO consisting of four levels. We argue that the UO needs a complete set of concept composition operators, and we sketch three of them. We also tackle a few issues related to the feasibility of the UO, which we think that they could be surmountable. Finally, we discuss the desirability of the UO, and we explain why we conjecture that there are already organizations that have the knowledge and resources needed to develop it, and that might have an interest in its development in the near future.Peer ReviewedPostprint (author's final draft