InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

peer-reviewedInnateDB (http://www.innatedb.com) is an integrated analysis platform that has been specifically designed to facilitate systems-level analyses of mammalian innate immunity networks, pathways and genes. In this article, we provide details of recent updates and improvements to the database. InnateDB now contains >196 000 human, mouse and bovine experimentally validated molecular interactions and 3000 pathway annotations of relevance to all mammalian cellular systems (i.e. not just immune relevant pathways and interactions). In addition, the InnateDB team has, to date, manually curated in excess of 18 000 molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks, pathways and their component molecules. More recently, InnateDB has also initiated the curation of allergy- and asthma-related interactions. Furthermore, we report a range of improvements to our integrated bioinformatics solutions including web service access to InnateDB interaction data using Proteomics Standards Initiative Common Query Interface, enhanced Gene Ontology analysis for innate immunity, and the availability of new network visualizations tools. Finally, the recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism.This work was supported by Genome BC through the Pathogenomics of Innate Immunity (PI2) project and by the Foundation for the National Institutes of Health and the Canadian Institutes of Health Research under the Grand Challenges in Global Health Research Initiative [Grand Challenges ID: 419]. Further funding was also provided by AllerGen grants 12ASI1 and 12B&B2. D.J.L. was funded in part during this project by a postdoctoral trainee award from the Michael Smith Foundation for Health Research (MSFHR). F.S.L.B. is a MSFHR Senior Scholar and R.E.W.H. holds a Canada Research Chair (CRC). Funding to enable bovine systems biology in InnateDB is provided by Teagasc [RMIS6018] and the Teagasc Walsh Fellowship scheme. IMEx is funded by the European Commission under the PSIMEx project [contract number FP7-HEALTH-2007-223411]. Funding for open access charge: Teagasc [RMIS6018]

The IR has Two Faces: Positioning Institutional Repositories for Success

This article will describe ongoing efforts at University of Nevada, Las Vegas (UNLV) Libraries to evolve the role of the institutional repository (IR) and to effectively position it within the context of the Libraries’ collections, research support, and scholarly communication services. A major component of this process is re-examining the fundamental aims of the IR and aligning it to the Libraries and the campus strategic goals. The authors situate UNLV Libraries’ experience within the context of the current literature to provide background and reasoning for our decision to pursue two, at times conflicting, aims for the IR: one for scholarly communication and another for research administration

Data curation standards and social science occupational information resources

Occupational information resources - data about the characteristics of different occupational positions - are widely used in the social sciences, across a range of disciplines and international contexts. They are available in many formats, most often constituting small electronic files that are made freely downloadable from academic web-pages. However there are several challenges associated with how occupational information resources are distributed to, and exploited by, social researchers. In this paper we describe features of occupational information resources, and indicate the role digital curation can play in exploiting them. We report upon the strategies used in the GEODE research project (Grid Enabled Occupational Data Environment, http://www.geode.stir.ac.uk). This project attempts to develop long-term standards for the distribution of occupational information resources, by providing a standardized framework-based electronic depository for occupational information resources, and by providing a data indexing service, based on e-Science middleware, which collates occupational information resources and makes them readily accessible to non-specialist social scientists

Extracting, Transforming and Archiving Scientific Data

It is becoming common to archive research datasets that are not only large but also numerous. In addition, their corresponding metadata and the software required to analyse or display them need to be archived. Yet the manual curation of research data can be difficult and expensive, particularly in very large digital repositories, hence the importance of models and tools for automating digital curation tasks. The automation of these tasks faces three major challenges: (1) research data and data sources are highly heterogeneous, (2) future research needs are difficult to anticipate, (3) data is hard to index. To address these problems, we propose the Extract, Transform and Archive (ETA) model for managing and mechanizing the curation of research data. Specifically, we propose a scalable strategy for addressing the research-data problem, ranging from the extraction of legacy data to its long-term storage. We review some existing solutions and propose novel avenues of research.Comment: 8 pages, Fourth Workshop on Very Large Digital Libraries, 201

Enhanced Search for Educational Resources - A Perspective and a Prototype from ccLearn

Users of search tools who seek educational materials on the Internet are typically presented with either a web-scale search (e.g., Google or Yahoo) or a specialized, site-specific tool. The specialized search tools often rely upon custom data fields, such as user-entered ratings, to provide additional value. As currently designed, these systems are generally too labor intensive to manage and scale up beyond a single site or set of resources.However, custom (or structured) data of some form is necessary if search outcomes foreducational materials are to be improved. For example, design criteria and evaluative metrics are crucial attributes for educational resources, and these currently require human labeling and verification. Thus, one challenge is to design a search tool that capitalizes on available structured data (also called metadata) but is not crippled if the data are missing. This information should be amenable to repurposing by anyone, which means that it must be archived in a manner that can be discovered and leveraged easily.In this paper, we describe the extent to which DiscoverEd, a prototype developed by ccLearn, meets the design challenge of a scalable, enhanced search platform for educational resources. We then explore some of the key challenges regarding enhanced search for topic-specific Internet resources generally. We conclude by illustrating some possible future developments and third-party enhancements to the DiscoverEd prototype

1st INCF Workshop on Sustainability of Neuroscience Databases

The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability

Handmade films and artist-run labs. The chemical sites of film’s counterculture

This article addresses handmade films and especially artist-run labs as sites of hands-on film culture that reactivate moments and materials from media history. Drawing on existing research, discourses and discussions with contemporary experimental filmmakers affiliated with labs or practicing their work in relation to film lab infrastructure, we focus on these sites of creation, preservation and circulation of technical knowledge about analog film. But instead of reinforcing the binary of analog vs. digital, we argue that the various material practices from self-made apparatuses to photochemistry and film emulsions are ways of understanding the multiple materials and layered histories that define post-digital culture of film. This focus links our discussion with some themes in media archaeology (experimental media archaeology as a practice) and to current discussions about labs as arts and humanities infrastructure for collective project and practice-based methods