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Open Access Highly Accessed Software

Userscripts for the Life Sciences

Egon L Willighagen1*, Noel M O'Boyle2, Harini Gopalakrishnan3, Dazhi Jiao3, Rajarshi Guha3, Christoph Steinbeck4 and David J Wild3

Author Affiliations

1 Cologne University Bioinformatics Center, Cologne University, Cologne, Germany

2 Cambridge Crystallographic Data Centre, Cambridge, UK

3 School of Informatics, Indiana University, Bloomington, USA

4 Wilhelm-Schickard-Institut, Center for Bioinformatics, University of Tübingen, Tübingen, Germany

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BMC Bioinformatics 2007, 8:487  doi:10.1186/1471-2105-8-487

Published: 21 December 2007

Abstract

Background

The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources.

Results

Several userscripts are presented that enrich biology and chemistry related web resources by incorporating or linking to other computational or data sources on the web. The scripts make use of Greasemonkey-like plugins for web browsers and are written in JavaScript. Information from third-party resources are extracted using open Application Programming Interfaces, while common Universal Resource Locator schemes are used to make deep links to related information in that external resource. The userscripts presented here use a variety of techniques and resources, and show the potential of such scripts.

Conclusion

This paper discusses a number of userscripts that aggregate information from two or more web resources. Examples are shown that enrich web pages with information from other resources, and show how information from web pages can be used to link to, search, and process information in other resources. Due to the nature of userscripts, scientists are able to select those scripts they find useful on a daily basis, as the scripts run directly in their own web browser rather than on the web server. This flexibility allows the scientists to tune the features of web resources to optimise their productivity.