The Genomic HyperBrowser: inferential genomics at the sequence level

The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical analysis of sequence-level genomic information. We provide a growing collection of generic biological investigations that query pairwise relations between tracks, represented as mathematical objects, along the genome. The Genomic HyperBrowser implements the approach and is available at http://hyperbrowser.uio.no

Extracting corpus specific knowledge bases from Wikipedia

Thesauri are useful knowledge structures for assisting information retrieval. Yet their production is labor-intensive, and few domains have comprehensive thesauri that cover domain-specific concepts and contemporary usage. One approach, which has been attempted without much success for decades, is to seek statistical natural language processing algorithms that work on free text. Instead, we propose to replace costly professional indexers with thousands of dedicated amateur volunteers--namely, those that are producing Wikipedia. This vast, open encyclopedia represents a rich tapestry of topics and semantics and a huge investment of human effort and judgment. We show how this can be directly exploited to provide WikiSauri: manually-defined yet inexpensive thesaurus structures that are specifically tailored to expose the topics, terminology and semantics of individual document collections. We also offer concrete evidence of the effectiveness of WikiSauri for assisting information retrieval

From Artifacts to Aggregations: Modeling Scientific Life Cycles on the Semantic Web

In the process of scientific research, many information objects are generated, all of which may remain valuable indefinitely. However, artifacts such as instrument data and associated calibration information may have little value in isolation; their meaning is derived from their relationships to each other. Individual artifacts are best represented as components of a life cycle that is specific to a scientific research domain or project. Current cataloging practices do not describe objects at a sufficient level of granularity nor do they offer the globally persistent identifiers necessary to discover and manage scholarly products with World Wide Web standards. The Open Archives Initiative's Object Reuse and Exchange data model (OAI-ORE) meets these requirements. We demonstrate a conceptual implementation of OAI-ORE to represent the scientific life cycles of embedded networked sensor applications in seismology and environmental sciences. By establishing relationships between publications, data, and contextual research information, we illustrate how to obtain a richer and more realistic view of scientific practices. That view can facilitate new forms of scientific research and learning. Our analysis is framed by studies of scientific practices in a large, multi-disciplinary, multi-university science and engineering research center, the Center for Embedded Networked Sensing (CENS).Comment: 28 pages. To appear in the Journal of the American Society for Information Science and Technology (JASIST

Producing space, producing China : a critical intervention

The concepts of the production and representation of space and place are receiving an increasing amount of attention in both the humanities and the social sciences. This paper will use the theoretical knowledge that has and continues to be produced on the subject to come to a better understanding of the spatial origins that constitute the place that is Chinese nation state. The analysis of spatial practises should shed light on the question what China is and wherefrom it receives the legitimacy for its social-spatial integrity. It will be argued that the arrival of modernity and its universal measurement of time and space were essential components in the gradual transformation from ethnocentric place to a territorially defined nation state. The political production and organisation of space employed for the formation of the nation state is argued to be the consequence of the same (globalising) logic that is now said to question and undermine its territorial integrity. Modernity and globalisation are in this paper, in other words, considered to be similar, if not identical, spatial-temporal concepts that both help to create and destruct places. This is arguably best visible in the constant production and reproduction of the most sophisticated of spatial organisations: our cities. I will argue that despite the changing face of cities, of which the disputed contemporary "globalisation" is but one of many, the spatial reality that is the modern nation state remains the same. This is not to return to an orthodox realist interpretation but to understand the very "stuff" that space and place are made of

Constructing commons in the cultural environment

This Article sets out a framework for investigating sharing and resource-pooling arrangements for information- and knowledge-based works. We argue that adapting the approach pioneered by Elinor Ostrom and her collaborators to commons arrangements in the natural environment provides a template for examining the construction of commons in the cultural environment. The approach promises to lead to a better understanding of how participants in commons and pooling arrangements structure their interactions in relation to the environments in which they are embedded, in relation to information and knowledge resources that they produce and use, and in relation to one another