Bridging the gap between social tagging and semantic annotation: E.D. the Entity Describer

Semantic annotation enables the development of efficient computational methods for analyzing and interacting with information, thus maximizing its value. With the already substantial and constantly expanding data generation capacity of the life sciences as well as the concomitant increase in the knowledge distributed in scientific articles, new ways to produce semantic annotations of this information are crucial. While automated techniques certainly facilitate the process, manual annotation remains the gold standard in most domains. In this manuscript, we describe a prototype mass-collaborative semantic annotation system that, by distributing the annotation workload across the broad community of biomedical researchers, may help to produce the volume of meaningful annotations needed by modern biomedical science. We present E.D., the Entity Describer, a mashup of the Connotea social tagging system, an index of semantic web-accessible controlled vocabularies, and a new public RDF database for storing social semantic annotations

From open content to open thinking

So far Open Educational Resources (OER) research has focused on the objective to 'open' education by making accessible free educational resources to the world. In the latest years the movement has matured, and a growing amount of OER have been made available by universities, researchers and scholars through several portals. Nonetheless, the level of adoption of OERs into common teaching practices remains quite low. In this paper we suggest that one of the main barriers to OER's adoption is the lack of 'opening up' to people's thinking around OERs and we propose Cohere, a tool which aims at making this thinking visible and exportable in ways that support the emergence of 'collective intelligence' around OERs research. Accessing Collective Intelligence (CI) around OERs is presented as a medium to know and understand what people think, how people design and use OERs thus increasing the easy of re-use of OER in learning and research practices

Reason Maintenance - Conceptual Framework

This paper describes the conceptual framework for reason maintenance developed as part of WP2

Just an Update on PMING Distance for Web-based Semantic Similarity in Artificial Intelligence and Data Mining

One of the main problems that emerges in the classic approach to semantics is the difficulty in acquisition and maintenance of ontologies and semantic annotations. On the other hand, the Internet explosion and the massive diffusion of mobile smart devices lead to the creation of a worldwide system, which information is daily checked and fueled by the contribution of millions of users who interacts in a collaborative way. Search engines, continually exploring the Web, are a natural source of information on which to base a modern approach to semantic annotation. A promising idea is that it is possible to generalize the semantic similarity, under the assumption that semantically similar terms behave similarly, and define collaborative proximity measures based on the indexing information returned by search engines. The PMING Distance is a proximity measure used in data mining and information retrieval, which collaborative information express the degree of relationship between two terms, using only the number of documents returned as result for a query on a search engine. In this work, the PMINIG Distance is updated, providing a novel formal algebraic definition, which corrects previous works. The novel point of view underlines the features of the PMING to be a locally normalized linear combination of the Pointwise Mutual Information and Normalized Google Distance. The analyzed measure dynamically reflects the collaborative change made on the web resources

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecular interactions containing detailed description of various cell mechanisms. It is difficult to explore these large maps, to comment their content and to maintain them. Though there exist several tools addressing these problems individually, the scientific community still lacks an environment that combines these three capabilities together. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. NaviCell combines three features: (1) efficient map browsing based on Google Maps engine; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting the community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of their interest in the context of signaling pathways and cross-talks between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive fashion due to an imbedded blogging system. NaviCell provides an easy way to explore large-scale maps of molecular interactions, thanks to the Google Maps and WordPress interfaces, already familiar to many users. Semantic zooming used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization meaningful to the user. In addition, NaviCell provides a framework for community-based map curation.Comment: 20 pages, 5 figures, submitte

Accurator: Nichesourcing for Cultural Heritage

With more and more cultural heritage data being published online, their usefulness in this open context depends on the quality and diversity of descriptive metadata for collection objects. In many cases, existing metadata is not adequate for a variety of retrieval and research tasks and more specific annotations are necessary. However, eliciting such annotations is a challenge since it often requires domain-specific knowledge. Where crowdsourcing can be successfully used for eliciting simple annotations, identifying people with the required expertise might prove troublesome for tasks requiring more complex or domain-specific knowledge. Nichesourcing addresses this problem, by tapping into the expert knowledge available in niche communities. This paper presents Accurator, a methodology for conducting nichesourcing campaigns for cultural heritage institutions, by addressing communities, organizing events and tailoring a web-based annotation tool to a domain of choice. The contribution of this paper is threefold: 1) a nichesourcing methodology, 2) an annotation tool for experts and 3) validation of the methodology and tool in three case studies. The three domains of the case studies are birds on art, bible prints and fashion images. We compare the quality and quantity of obtained annotations in the three case studies, showing that the nichesourcing methodology in combination with the image annotation tool can be used to collect high quality annotations in a variety of domains and annotation tasks. A user evaluation indicates the tool is suited and usable for domain specific annotation tasks

Do peers see more in a paper than its authors?

Recent years have shown a gradual shift in the content of biomedical publications that is freely accessible, from titles and abstracts to full text. This has enabled new forms of automatic text analysis and has given rise to some interesting questions: How informative is the abstract compared to the full-text? What important information in the full-text is not present in the abstract? What should a good summary contain that is not already in the abstract? Do authors and peers see an article differently? We answer these questions by comparing the information content of the abstract to that in citances-sentences containing citations to that article. We contrast the important points of an article as judged by its authors versus as seen by peers. Focusing on the area of molecular interactions, we perform manual and automatic analysis, and we find that the set of all citances to a target article not only covers most information (entities, functions, experimental methods, and other biological concepts) found in its abstract, but also contains 20% more concepts. We further present a detailed summary of the differences across information types, and we examine the effects other citations and time have on the content of citances