Reflect: augmented browsing for the life scientist

Pafilis, Evangelos; O’Donoghue, Seán I.; Jensen, Lars Juhl; Horn, Heiko; Kuhn, Michael; Brown, Nigel P.; Schneider, Reinhard

doi:10.1038/nbt0609-508

Cited by 83 publications

(65 citation statements)

References 11 publications

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“…Most work so far has focused on augmenting existing papers with annotations or linkages to other resources on the web (c.f. Ceol et al 2008;Pafilis et al 2009) and some even embed support for visual analysis tools (Attwood et al 2010). Still, Lackes et al (2009) argue that existing websites of research database and communication do not support the full bidirectionalflow of information between the author(s) and the reader(s).…”

Section: The Research Paper Goes 'Live'mentioning

confidence: 99%

Making journal articles ‘live’: turning academic writing into scientific dialog

et al. 2011

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Web 2.0 services and social networking offer possibilities to transform academic publishing to facilitate scientific dialogue. We present 'The Live Paper' in this editorial as a concept to consider how to leverage existing web technologies to produce rich, omnidirectional, and interactive narratives on research. Following the format of a traditional research report we describe and discuss how to enrich research reports utilizing various types of analytical tools, data, and web services in a published paper embedded in evolving scientific discourse. We also consider how the live papers would influence the practice, culture, and economy of academic research. We conclude that geospatial researchers have an opportunity to lead this development towards richer and more open ways of communicating our findings. The technology and infrastructure to do so exist today, but several barriers remain.

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Section: The Research Paper Goes 'Live'mentioning

confidence: 99%

Making journal articles ‘live’: turning academic writing into scientific dialog

et al. 2011

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“…Formality is required if computers are to be harnessed to do the tedious work for us; seamlessness is essential if the work of humans is to be made easy and burden free. Although we are some way away from 9 Notwithstanding these pioneering endeavours, it is clear that we are barely keeping up with the demand for intelligent mechanisms to manage our interactions with the scholarly record, and are failing to maintain sensible control over our expanding library of knowledge. The Web, as one might expect, is buzzing with opinions on the source of the problem.…”

Section: Mining Data Tombsmentioning

confidence: 99%

Ceci n'est pas un hamburger: modelling and representing the scholarly article

et al. 2011

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Current approaches to publishing scholarly work are falling behind the growing demands of modern readers, who need easy access to the underlying data, as well as the ability to consume content on an ever‐growing variety of electronic devices. The pros and cons of the various formats for representing the scholarly article are hotly contested, but as yet these debates have had little tangible impact on the publishing world where, in spite of its apparent limitations, the PDF remains the dominant form of distribution. We discuss fundamental philosophical differences between a scholarly work and its representation, and describe Utopia Documents, which realizes those differences in software, aiming to resolve many of the current issues in this area.

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“…Reflect [18] is a web application and service that annotates biochemical entities (in particular genes, proteins and small molecules) in web pages and allows the user to further explore an identified entity. By clicking the annotated term, a small popup window showing summary information is displayed, which gives a concise summary of the most important features of the selected entity (e.g.…”

Section: Annotation Tools For the Life Science Domainmentioning

confidence: 99%