On BioScience and Life and Such

The Elsevier Grand Challenge: Entry # 2

In Uncategorized on August 13, 2008 at 1:03 pm

Please find below, my rejected submission to “The Elsevier Grand Challenge“. I humbly admit defeat to some terrific-looking projects, – best of luck to:
Sean O’Donoghue and Lars Jensen
Reflect: Automated Annotation of Scientific Terms
Timothy Baldwin, Lawrence Cavedon, Sarvnaz Karimi, David Martinez, David Newman, Falk Scholer and Justin Zobel
Effective Search, Classification, and Visualisation of Information from Large Collections of Biomedical Literature
Vit Novacek, Siegfried Handschuh and Tudor Groza
Teaching Machines to Teach Us: A Truly Knowledge-Based Publication Management
Amr Ahmed, Andrew Arnold, Luis Pedro Coelho, Saboor Sheikh, Eric Xing, William Cohen and Robert F. Murphy
Information Retrieval and Topic Discovery using both Figures and Captions in Biological Literature
Stephen Wan, Robert Dale and Cecile Paris
In-Context Summaries of Cited Documents: A Research Prototype for Academic and Scholarly Literature
Roderic Page
Towards realising Darwin’s dream: setting the trees free
Jose Gonzalez-Brenes, Aabid Shariff, Sourish Chaudhuri and Carolyn Rose
Automating the Generation of Life Science Protocols
Glenn Ford, Sameer Antani, Dina Demner Fushman and George Thoma
Tools to build and use Interactive Publications
Michael Greenacre and Trevor Hastie
Guided Tours in N-Dimensional Space:  Dynamic Visualization of Multivariate Data
Alexander Garcia and Alberto Labarga
A tale of two cities in the land of serendipity: The semantic web and the social web heading towards a living document in life sciences.
Whoever wins it is my hope that Elsevier publication turns open access, and to survive I think they will have to, in one way or another.

SciPhu Project Description:

SciPhu.com (http://sciphu.com/) is a blog where anyone is invited to publish scientific content, and anyone is likewise, invited to review (comment on) these publications (blog posts). All posts and all comments are freely and publicly available to everyone. SciPhu= Science + Phusis (Phusis – An Ancient Greek word often translated as birth or nature – Wikipedia).

  1. Project Goals, Purpose, and Outcomes.
    SciPhu.com is a blog based, open access and unrestricted publishing model. A hybrid in the spirit of Wikipedia and JustScience.The idea behind SciPhu-publishing is to be able to publish and peer-review scientific information more efficiently than standard peer-reviewing.The SciPhu vision of the future of science publishing:

    a) Improve the process/methods/results of creating, reviewing and editing scientific content: We wanted the reviewing process while retaining its scientific credibility, to be faster and less rigid. One answer, we found, was blogger-reviewing (which in this setting is just a fancy name for commenting on blog posts).

    b) Interpret, visualize or connect the knowledge more effectively:
    Blogging is a good starting point since there are so many knowledgeable scientific bloggers on the internet scene.

    c) Provide tools/ideas for measuring the impact of these improvements. SciPhu.com is already launched and statistics on visitors, rating of posts (scientific articles), and comments are and will be, continously available for evaluation.

  2. Detailed Project Description: Content and Functionalities
    The end goal of SciPhu is to be able to quality control scientific information from any source, so that the twisted scientific reality that sometimes ends up in the popular press (and ultimately in public opinion) can be promptly countered with proper scientific information. To achieve this goal, a solid referee-base with scientific authority and credibility needs to be affiliated with the site. Building such a referee community is a major milestone and challenge. As a starting point towards this goal, the SciPhu.com blog provides a novel/preliminary blog/internet-publishing channel for the scientific community. Sciphu.com is already a way of publishing that is completely free of (any kind of) charge, less rigid, more efficient and more interactive than many existing publishing models. SciPhu publishing is unlimited open-access and has the potential to reach a broad audience and aims be a pivotal tool to keep scientific authority intact, free and unpolitical.
  3. Project Background
    Sciphu.com is run by molecular biologists currently working in diagnostics. Our professional and educational backgrounds are university PhD degrees and small business life-sciences research activities within, biochemistry, genetics, cancer (and cell) biology and molecular biology. We are enthusiasts of web development and experienced users of many computer applications, but have little formal training in programming and web-design/develoment. Running a blog and possibly a future wiki however, requires only minimum skills to achieve adequate functionality.
  4. Methods
    While SciPhu today is a blog, future plans involve developing the site into a proper web-portal of some sort within the next 4-7 years. A wiki-based model is planned as the next developing step within the next 2 years. Such a wiki would have enhanced interaction with publishers and revieweres and the posssibilities for building a referee-community will improve over the blog-model. The blog model requires very little programming as most of the necessary tools are already provided gratis by hosting companies (Blogger/google, WordPress etc.) or by blogging community members. A wiki-based web-site requires more programming and web-design, but still at a level manageable by enthusisasts rather than requiring professionals. However, the goal is to involve web-developers to reach the maximum potential of this publishing model. A requirement will always be free of charge, open access, without restrictions, both for reading and publishing. A possible future business model is to offer peer-review expertise to commercial publishers or other commercial entities in need of scientific content quality control.

This publishing solution is not very high tech (but, it may evolve to be), it does not enjoy the recognition that many of the high ranked science journals do (but with active commenting, it can).

As with so many other things in professional life, the potential lies in the numbers. Only if many scientists are willing to use publishing channels like these, will it become a success.

Also at minimum two other issues need to be resolved to make the model into a proper publishing channel: 1) DOI numbers and 2) Proper backup and safe long term data storage. To solve the DOI-number issue, the use of the researchblogging (http://researchblogging.org/) icon and tracking is used, but this solution must be improved upon, presumably in cooperation with an exisiting publishing entity.

This is the age of the web and no-limit communication accessible to all. Our recommendation is: Say goodbye to the stale publishing standards of yesterday and come participate in the interactive self-justice of web-publishing.

More on the SciPhu model:

1. http://sciphu.com/

2. https://sciphu.wordpress.com/2008/04/07/launching-sciphucom/

3. https://sciphu.wordpress.com/2008/05/19/new-post-on-sciphucom-the-advantages-of-blog-publishing/


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